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Sample records for highly diverse denitrifying

  1. Relationships Between Denitrifier Abundance, Denitrifier Diversity and Denitrification in Gulf of Mexico Hypoxic Zone Sediments.

    Science.gov (United States)

    Proctor, L. M.; Childs, C.; MacAuley, S.

    2002-12-01

    The largest zone of anthropogenic bottom water hypoxia in the Western Hemisphere occurs seasonally in the northern Gulf of Mexico. This hypoxic zone reaches its greatest extent in the summer months and is a consequence of seasonal stratification of the water column combined with the decomposition of organic matter derived from accelerated rates of primary production. The enhanced primary production is driven by inorganic nitrogen input from the Mississippi River and these conditions would seem ideal for supporting high levels of denitrification. Yet sediment denitrification exhibited a wide range, even at the height of the seasonal hypoxia. Therefore, we compared benthic denitrifier abundances and denitrifier diversity at several stations over two seasons exhibiting extremes in denitrification to evaluate the relationship between abundances, diversity and denitrification levels. Sediment denitrification ranged from 20 to 100 umol m-2 h-1, with rates in July, 2000 approximately half that observed in July, 2001. The highest rates were generally observed at stations with bottom water DO concentrations between 1 and 3 mg l-1. Relative denitrifier abundances, using nirS and nirK as proxies for denitrifiers, suggested a direct relationship between abundances and denitrification while denitrifier diversity, measured by T-RFLPs of nirS and nirK, suggested an inverse relationship between diversity and denitrification. These results suggest that several factors are important in understanding what controls denitrification in Gulf of Mexico hypoxic zone sediments.

  2. Diversity and activity of denitrifiers of Chilean arid soil ecosystems

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    Julieta eOrlando

    2012-04-01

    Full Text Available The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study, we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of

  3. Diversity and activity of denitrifiers of chilean arid soil ecosystems.

    Science.gov (United States)

    Orlando, Julieta; Carú, Margarita; Pommerenke, Bianca; Braker, Gesche

    2012-01-01

    The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility, and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS) genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of denitrifiers in particular.

  4. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  5. Denitrifying sulfide removal process on high-salinity wastewaters.

    Science.gov (United States)

    Liu, Chunshuang; Zhao, Chaocheng; Wang, Aijie; Guo, Yadong; Lee, Duu-Jong

    2015-08-01

    Denitrifying sulfide removal (DSR) process comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide, and acetate into nitrogen gas, elemental sulfur (S(0)), and carbon dioxide, respectively. Sulfide- and nitrate-laden wastewaters at 2-35 g/L NaCl were treated by DSR process. A C/N ratio of 3:1 was proposed to maintain high S(0) conversion rate. The granular sludge with a compact structure and smooth outer surface was formed. The microbial communities of DSR consortium via high-throughput sequencing method suggested that salinity shifts the predominating heterotrophic denitrifiers at 10 g/L NaCl.

  6. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

    NARCIS (Netherlands)

    Lipsewers, Y.A.; Hopmans, E.C.; Meysman, F.J.R.; Sinninghe Damsté, J.S.; Villanueva, L.

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox,

  7. Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake grevelingen

    NARCIS (Netherlands)

    Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J.R.; Sinninghe Damsté, Jaap S.|info:eu-repo/dai/nl/07401370X; Villanueva, Laura

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox,

  8. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

    Science.gov (United States)

    Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J. R.; Sinninghe Damsté, Jaap S.; Villanueva, Laura

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments. PMID:27812355

  9. Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline Lake Grevelingen

    Directory of Open Access Journals (Sweden)

    Yvonne A. Lipsewers

    2016-10-01

    Full Text Available Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution at three different locations before (March and during summer hypoxia (August. The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen- and sulfur cycling in Lake Grevelingen sediments.

  10. Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Jayakumar, D.A.; Francis, C.A.; Naqvi, S.W.A.; Ward, B.B.

    Denitrification often occurs in the water column, underlying zones of intense productivity and decomposition in upwelling regions. In the denitrifying zone off the southwest coast of India, high concentrations of nitrite (greater than 15 mu M...

  11. Diversity of Nitrate-Reducing and Denitrifying Bacteria in a Marine Aquaculture Biofilter and their Response to Sulfide

    DEFF Research Database (Denmark)

    Krieger, Bärbel; Schwermer, Carsten U.; Rezakhani, Nastaran

    2006-01-01

    with Alphaproteobacteria but also including Beta- and Gammaproteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The diversity of the isolates was compared to the cultivation-independent diversity of nitrate-reducing and denitrifying bacteria based on narG and nosZ as functional marker genes. Growth experiments...

  12. Denitrification and Biodiversity of Denitrifiers in a High-Mountain Mediterranean Lake

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    Antonio Castellano-Hinojosa

    2017-10-01

    Full Text Available Wet deposition of reactive nitrogen (Nr species is considered a main factor contributing to N inputs, of which nitrate (NO3− is usually the major component in high-mountain lakes. The microbial group of denitrifiers are largely responsible for reduction of nitrate to molecular dinitrogen (N2 in terrestrial and aquatic ecosystems, but the role of denitrification in removal of contaminant nitrates in high-mountain lakes is not well understood. We have used the oligotrophic, high-altitude La Caldera lake in the Sierra Nevada range (Spain as a model to study the role of denitrification in nitrate removal. Dissolved inorganic Nr concentration in the water column of la Caldera, mainly nitrate, decreased over the ice-free season which was not associated with growth of microbial plankton or variations in the ultraviolet radiation. Denitrification activity, estimated as nitrous oxide (N2O production, was measured in the water column and in sediments of the lake, and had maximal values in the month of August. Relative abundance of denitrifying bacteria in sediments was studied by quantitative polymerase chain reaction of the 16S rRNA and the two phylogenetically distinct clades nosZI and nosZII genes encoding nitrous oxide reductases. Diversity of denitrifiers in sediments was assessed using a culture-dependent approach and after the construction of clone libraries employing the nosZI gene as a molecular marker. In addition to genera Polymorphum, Paracoccus, Azospirillum, Pseudomonas, Hyphomicrobium, Thauera, and Methylophaga, which were present in the clone libraries, Arthrobacter, Burkholderia, and Rhizobium were also detected in culture media that were not found in the clone libraries. Analysis of biological activities involved in the C, N, P, and S cycles from sediments revealed that nitrate was not a limiting nutrient in the lake, allowed N2O production and determined denitrifiers’ community structure. All these results indicate that

  13. Denitrification and Biodiversity of Denitrifiers in a High-Mountain Mediterranean Lake

    Science.gov (United States)

    Castellano-Hinojosa, Antonio; Correa-Galeote, David; Carrillo, Presentación; Bedmar, Eulogio J.; Medina-Sánchez, Juan M.

    2017-01-01

    Wet deposition of reactive nitrogen (Nr) species is considered a main factor contributing to N inputs, of which nitrate (NO3−) is usually the major component in high-mountain lakes. The microbial group of denitrifiers are largely responsible for reduction of nitrate to molecular dinitrogen (N2) in terrestrial and aquatic ecosystems, but the role of denitrification in removal of contaminant nitrates in high-mountain lakes is not well understood. We have used the oligotrophic, high-altitude La Caldera lake in the Sierra Nevada range (Spain) as a model to study the role of denitrification in nitrate removal. Dissolved inorganic Nr concentration in the water column of la Caldera, mainly nitrate, decreased over the ice-free season which was not associated with growth of microbial plankton or variations in the ultraviolet radiation. Denitrification activity, estimated as nitrous oxide (N2O) production, was measured in the water column and in sediments of the lake, and had maximal values in the month of August. Relative abundance of denitrifying bacteria in sediments was studied by quantitative polymerase chain reaction of the 16S rRNA and the two phylogenetically distinct clades nosZI and nosZII genes encoding nitrous oxide reductases. Diversity of denitrifiers in sediments was assessed using a culture-dependent approach and after the construction of clone libraries employing the nosZI gene as a molecular marker. In addition to genera Polymorphum, Paracoccus, Azospirillum, Pseudomonas, Hyphomicrobium, Thauera, and Methylophaga, which were present in the clone libraries, Arthrobacter, Burkholderia, and Rhizobium were also detected in culture media that were not found in the clone libraries. Analysis of biological activities involved in the C, N, P, and S cycles from sediments revealed that nitrate was not a limiting nutrient in the lake, allowed N2O production and determined denitrifiers’ community structure. All these results indicate that denitrification could be a

  14. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China.

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    Fan, Zhou; Han, Rui-Ming; Ma, Jie; Wang, Guo-Xiang

    2016-07-01

    nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.

  15. Denitrifying sulfide removal process on high-salinity wastewaters in the presence of Halomonas sp.

    Science.gov (United States)

    Liu, Chunshuang; Zhao, Dongfeng; Ma, Wenjuan; Guo, Yadong; Wang, Aijie; Wang, Qilin; Lee, Duu-Jong

    2016-02-01

    Biological conversion of sulfide, acetate, and nitrate to, respectively, elemental sulfur (S(0)), carbon dioxide, and nitrogen-containing gas (such as N2) at NaCl concentration of 35-70 g/L was achieved in an expanded granular sludge bed (EGSB) reactor. A C/N ratio of 1:1 was noted to achieve high sulfide removal and S(0) conversion rate at high salinity. The extracellular polymeric substance (EPS) quantities were increased with NaCl concentration, being 11.4-mg/g volatile-suspended solids at 70 mg/L NaCl. The denitrifying sulfide removal (DSR) consortium incorporated Thauera sp. and Halomonas sp. as the heterotrophs and Azoarcus sp. being the autotrophs at high salinity condition. Halomonas sp. correlates with the enhanced DSR performance at high salinity.

  16. Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands.

    Directory of Open Access Journals (Sweden)

    Xavier Le Roux

    Full Text Available Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively, the abundance of nitrifiers (bacterial and archaeal amoA gene number and denitrifiers (nirK, nirS and nosZ gene number, and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species, though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification

  17. Biopotentiality of High Efficient Aerobic Denitrifier Bacillus megaterium S379 for Intensive Aquaculture Water Quality Management.

    Science.gov (United States)

    Gao, Junqian; Gao, Dan; Liu, Hao; Cai, Jiajai; Zhang, Junqi; Qi, Zhengliang

    2018-05-24

    Excessive nitrite accumulation is a very tough issue for intensive aquaculture. A high efficient aerobic denitrifier Bacillus megaterium S379 with 91.71±0.17% of NO 2 - -N (65 mg L -1 ) removal was successfully isolated for solving the problem. Denitrification of S379 showed excellent environment adaptation that it kept high nitrite removal ratio (more than 85%) when temperature ranged from 25°C to 40°C and pH varied between 7.0 and 9.0, and could endure as high as 560 mg L -1 of NO 2 - -N. Immobilization of S379 could enhance denitrification even when NO 2 - -N adding amount got to 340 mg L -1 . Immobilized cells also showed well pollutants removal performance in aquaculture wastewater treatment. Moreover, S379 possessed positive hydrolase activities for starch, casein, cellulose and fat and bore more than 60 ppt of salinity. Totally, all the results revealed significant potentiality of immobilized S379 applied in aquaculture water quality management. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

    Energy Technology Data Exchange (ETDEWEB)

    Green, Stefan [Florida State University; Prakash, Om [Florida State University; Jasrotia, Puja [Florida State University; Overholt, Will [Florida State University; Cardenas, Erick [Michigan State University, East Lansing; Hubbard, Daniela [Florida State University; Tiedje, James M. [Michigan State University, East Lansing; Watson, David B [ORNL; Schadt, Christopher Warren [ORNL; Brooks, Scott C [ORNL; Kostka, Joel [Florida State University

    2011-01-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of ribosomal RNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure, and denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as concentration of nitrogen species, oxygen and sampling season did not appear to strongly influence the distribution of Rhodanobacter. Results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  19. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

    Science.gov (United States)

    Green, Stefan J; Prakash, Om; Jasrotia, Puja; Overholt, Will A; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M; Watson, David B; Schadt, Christopher W; Brooks, Scott C; Kostka, Joel E

    2012-02-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  20. Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination

    International Nuclear Information System (INIS)

    Green, Stefan; Prakash, Om; Gihring, Thomas; Akob, Denise M.; Jasrotia, Puja; Jardine, Philip M.; Watson, David B.; Brown, Steven David; Palumbo, Anthony Vito; Kostka, Joel

    2010-01-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available with which to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria) and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were confirmed as complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. Ribosomal RNA gene analyses reveal that bacteria from the genus Rhodanobacter comprise a diverse population of circumneutral to moderately acidophilic denitrifiers at the ORIFRC site, with a high relative abundance in areas of the acidic source zone. Rhodanobacter species do not contain a periplasmic nitrite reductase and have not been previously detected in functional gene surveys of denitrifying bacteria at the OR-IFRC site. Sequences of nitrite and nitrous oxide reductase genes were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation, genomic and metagenomic data are essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifying microorganisms. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

  1. Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.

    Science.gov (United States)

    Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq; Caicedo, Luis Miguel; Guo, Hanwen; Fu, Xindi; Wang, Hongtao

    2017-11-01

    Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.

  2. Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

    Science.gov (United States)

    Jha, Neha; Saggar, Surinder; Giltrap, Donna; Tillman, Russ; Deslippe, Julie

    2017-09-01

    Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O

  3. Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics

    DEFF Research Database (Denmark)

    Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq

    2017-01-01

    Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures......, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion...

  4. Experimental investigation of activities and tolerance of denitrifying bacteria under alkaline and reducing condition

    International Nuclear Information System (INIS)

    Mine, Tatsuya; Mihara, Morihiro; Ooi, Takao

    2000-07-01

    In the geological disposal system of TRU wastes, nitrogen generation by denitrifying bacteria could provide significant impact on the assessment of this system, because nitrate contained in process concentrated liquid waste might be electron acceptor for denitrifying bacteria. In this study, the activities and tolerance of denitrifying under disposal condition were investigated. Pseudomonas denitrificans as denitrifying bacteria was used. The results showed that Pseudomonas denitrificans had activity under reducing condition, but under high pH condition (pH>9.5), the activity of Pseudomonas denitrificans was not detected. It is possible that the activity of Pseudomonas denitrificans would be low under disposal condition. (author)

  5. [Identification and function test of an alkali-tolerant denitrifying bacterium].

    Science.gov (United States)

    Wang, Ru; Zheng, Ping; Li, Wei; Chen, Hui; Chen, Tingting; Ghulam, Abbas

    2013-04-04

    We obtained an alkali-tolerant denitrifying bacterium, and determined its denitrifying activity and alkali-tolerance. An alkali-tolerant denitrifying bacterial strain was obtained by isolation and purification. We identified the bacterial strain by morphological observation, physiological test and 16S rRNA analysis. We determined the denitrifying activity and alkali-tolerance by effects of initial nitrate concentration and initial pH on denitrification. An alkali-tolerant denitrifier strain R9 was isolated from the lab-scale high-rate denitrifying reactor, and it was identified as Diaphorobater nitroreducens. The strain R9 grew heterotrophically with methanol as the electron donor and nitrate as the electron acceptor. The nitrate conversion was 93.25% when strain R9 was cultivated for 288 h with initial nitrate concentration 50 mg/L and initial pH 9.0. The denitrification activity could be inhibited at high nitrate concentration with a half inhibition constant of 202.73 mg N/L. Strain R9 showed a good alkali tolerance with the nitrate removal rate at pH 11.0 remained 86% of that at pH 9.0. Strain R9 was identified as Diaphorobater nitroreducens, and it was an alkali-tolerant denitrifying bacterium with optimum pH value of 9.0.

  6. Denitrifying Bioreactors Resist Disturbance from Fluctuating Water Levels

    Directory of Open Access Journals (Sweden)

    Sarah K. Hathaway

    2017-06-01

    Full Text Available Nitrate can be removed from wastewater streams, including subsurface agricultural drainage systems, using woodchip bioreactors to promote microbial denitrification. However, the variations in water flow in these systems could make reliable performance from this microbially-mediated process a challenge. In the current work, the effects of fluctuating water levels on nitrate removal, denitrifying activity, and microbial community composition in laboratory-scale bioreactors were investigated. The performance was sensitive to changing water level. An average of 31% nitrate was removed at high water level and 59% at low water level, despite flow adjustments to maintain a constant theoretical hydraulic retention time. The potential activity, as assessed through denitrifying enzyme assays, averaged 0.0008 mg N2O-N/h/dry g woodchip and did not show statistically significant differences between reactors, sampling depths, or operational conditions. In the denitrifying enzyme assays, nitrate removal consistently exceeded nitrous oxide production. The denitrifying bacterial communities were not significantly different from each other, regardless of water level, meaning that the denitrifying bacterial community did not change in response to disturbance. The overall bacterial communities, however, became more distinct between the two reactors when one reactor was operated with periodic disturbances of changing water height, and showed a stronger effect at the most severely disturbed location. The communities were not distinguishable, though, when comparing the same location under high and low water levels, indicating that the communities in the disturbed reactor were adapted to fluctuating conditions rather than to high or low water level. Overall, these results describe a biological treatment process and microbial community that is resistant to disturbance via water level fluctuations.

  7. Enhanced performance of denitrifying sulfide removal process under micro-aerobic condition.

    Science.gov (United States)

    Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

    2010-07-15

    The denitrifying sulfide removal (DSR) process with bio-granules comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide and acetate into di-nitrogen gas, elementary sulfur and carbon dioxide, respectively, at high loading rates. This study determines the reaction rate of sulfide oxidized into sulfur, as well as the reduction of nitrate to nitrite, would be enhanced under a micro-aerobic condition. The presence of limited oxygen mitigated the inhibition effects of sulfide on denitrifier activities, and enhanced the performance of DSR granules. The advantages and disadvantages of applying the micro-aerobic condition to the DSR process are discussed. 2010 Elsevier B.V. All rights reserved.

  8. Enhanced performance of denitrifying sulfide removal process under micro-aerobic condition

    International Nuclear Information System (INIS)

    Chen Chuan; Ren Nanqi; Wang Aijie; Liu Lihong; Lee, Duu-Jong

    2010-01-01

    The denitrifying sulfide removal (DSR) process with bio-granules comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide and acetate into di-nitrogen gas, elementary sulfur and carbon dioxide, respectively, at high loading rates. This study determines the reaction rate of sulfide oxidized into sulfur, as well as the reduction of nitrate to nitrite, would be enhanced under a micro-aerobic condition. The presence of limited oxygen mitigated the inhibition effects of sulfide on denitrifier activities, and enhanced the performance of DSR granules. The advantages and disadvantages of applying the micro-aerobic condition to the DSR process are discussed.

  9. Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems

    DEFF Research Database (Denmark)

    Mcllroy, Simon; Starnawska, Anna; Starnawski, Piotr

    2015-01-01

    Denitrification is essential to the removal of nitrogen from wastewater during treatment, yet an understanding of the diversity of the active denitrifying bacteria responsible in full-scale wastewater treatment plants (WWTPs) is lacking. In this study, stable-isotope probing (SIP) was applied......-labelled complex substrate was used for SIP incubations, under nitrite-reducing conditions, in order to maximize the capture of the potentially metabolically diverse denitrifiers likely present. Members of the Rhodoferax, Dechloromonas, Sulfuritalea, Haliangium and Thermomonas were represented in the 16S rRNA gene...

  10. Identification of the autotrophic denitrifying community in nitrate removal reactors by DNA-stable isotope probing.

    Science.gov (United States)

    Xing, Wei; Li, Jinlong; Cong, Yuan; Gao, Wei; Jia, Zhongjun; Li, Desheng

    2017-04-01

    Autotrophic denitrification has attracted increasing attention for wastewater with insufficient organic carbon sources. Nevertheless, in situ identification of autotrophic denitrifying communities in reactors remains challenging. Here, a process combining micro-electrolysis and autotrophic denitrification with high nitrate removal efficiency was presented. Two batch reactors were fed organic-free nitrate influent, with H 13 CO 3 - and H 12 CO 3 - as inorganic carbon sources. DNA-based stable-isotope probing (DNA-SIP) was used to obtain molecular evidence for autotrophic denitrifying communities. The results showed that the nirS gene was strongly labeled by H 13 CO 3 - , demonstrating that the inorganic carbon source was assimilated by autotrophic denitrifiers. High-throughput sequencing and clone library analysis identified Thiobacillus-like bacteria as the most dominant autotrophic denitrifiers. However, 88% of nirS genes cloned from the 13 C-labeled "heavy" DNA fraction showed low similarity with all culturable denitrifiers. These findings provided functional and taxonomical identification of autotrophic denitrifying communities, facilitating application of autotrophic denitrification process for wastewater treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Reduction of produced elementary sulfur in denitrifying sulfide removal process.

    Science.gov (United States)

    Zhou, Xu; Liu, Lihong; Chen, Chuan; Ren, Nanqi; Wang, Aijie; Lee, Duu-Jong

    2011-05-01

    Denitrifying sulfide removal (DSR) processes simultaneously convert sulfide, nitrate, and chemical oxygen demand from industrial wastewater into elemental sulfur, dinitrogen gas, and carbon dioxide, respectively. The failure of a DSR process is signaled by high concentrations of sulfide in reactor effluent. Conventionally, DSR reactor failure is blamed for overcompetition for heterotroph to autotroph communities. This study indicates that the elementary sulfur produced by oxidizing sulfide that is a recoverable resource from sulfide-laden wastewaters can be reduced back to sulfide by sulfur-reducing Methanobacterium sp. The Methanobacterium sp. was stimulated with excess organic carbon (acetate) when nitrite was completely consumed by heterotrophic denitrifiers. Adjusting hydraulic retention time of a DSR reactor when nitrite is completely consumed provides an additional control variable for maximizing DSR performance.

  12. New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches.

    Science.gov (United States)

    Xu, Sai; Lu, Wenjing; Muhammad, Farooq Mustafa; Liu, Yanting; Guo, Hanwen; Meng, Ruihong; Wang, Hongtao

    2018-03-01

    The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (pbacteria. Copyright © 2017. Published by Elsevier B.V.

  13. Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities.

    Science.gov (United States)

    Florio, Alessandro; Pommier, Thomas; Gervaix, Jonathan; Bérard, Annette; Le Roux, Xavier

    2017-08-21

    Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms. We quantified (de)nitrifiers abundance and activity in the rhizosphere of inoculated and non-inoculated maize on 4 sites over 2 years, and ancillary soil variables. Inoculation effects on nitrification and nitrifiers (AOA, AOB) were not consistent between the three sampling dates. Inoculation influenced denitrifiers abundance (nirK, nirS) differently among sites. In sites with high C limitation for denitrifiers (i.e. limitation of denitrification by C > 66%), inoculation increased nirS-denitrifier abundance (up to 56%) and gross N 2 O production (up to 84%), likely due to increased root C exudation. Conversely, in sites with low C limitation (<47%), inoculation decreased nirS-denitrifier abundance (down to -23%) and gross N 2 O production (down to -18%) likely due to an increased roots-denitrifiers competition for nitrate.

  14. Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.

    Science.gov (United States)

    Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M Dolors; Colprim, Jesús; Bañeras, Lluís

    2013-01-01

    The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A · m(-3) NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A · m(-3) NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.

  15. Nitrogen fixation in denitrified marine waters.

    Directory of Open Access Journals (Sweden)

    Camila Fernandez

    Full Text Available Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria, whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria. Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP, a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ. Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m(-2 d(-1. Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m(-2 d(-1 than the oxic euphotic layer (48±68 µmol m(-2 d(-1. Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions.

  16. Nitrogen Fixation in Denitrified Marine Waters

    Science.gov (United States)

    Fernandez, Camila; Farías, Laura; Ulloa, Osvaldo

    2011-01-01

    Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m−2 d−1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m−2 d−1) than the oxic euphotic layer (48±68 µmol m−2 d−1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions. PMID:21687726

  17. Warming-induced changes in denitrifier community structure modulate the ability of phototrophic river biofilms to denitrify

    Energy Technology Data Exchange (ETDEWEB)

    Boulêtreau, Stéphanie, E-mail: stephanie.bouletreau@univ-tlse3.fr [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Lyautey, Emilie [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Dubois, Sophie [Université de Bordeaux, EPOC - OASU, UMR 5805, Station Marine d' Arcachon, 2 rue du Professeur Jolyet, 33120 Arcachon (France); Compin, Arthur [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Delattre, Cécile; Touron-Bodilis, Aurélie [EDF Recherche et Développement, LNHE (Laboratoire National d' Hydraulique et Environnement), 6 quai Watier, F-78401 Chatou (France); Mastrorillo, Sylvain [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Garabetian, Frédéric [Université de Bordeaux, EPOC - OASU, UMR 5805, Station Marine d' Arcachon, 2 rue du Professeur Jolyet, 33120 Arcachon (France)

    2014-01-01

    Microbial denitrification is the main nitrogen removing process in freshwater ecosystems. The aim of this study was to show whether and how water warming (+ 2.5 °C) drives bacterial diversity and structuring and how bacterial diversity affects denitrification enzymatic activity in phototrophic river biofilms (PRB). We used water warming associated to the immediate thermal release of a nuclear power plant cooling circuit to produce natural PRB assemblages on glass slides while testing 2 temperatures (mean temperature of 17 °C versus 19.5 °C). PRB were sampled at 2 sampling times during PRB accretion (6 and 21 days) in both temperatures. Bacterial community composition was assessed using ARISA. Denitrifier community abundance and denitrification gene mRNA levels were estimated by q-PCR and qRT-PCR, respectively, of 5 genes encoding catalytic subunits of the denitrification key enzymes. Denitrification enzyme activity (DEA) was measured by the acetylene-block assay at 20 °C. A mean water warming of 2.5 °C was sufficient to produce contrasted total bacterial and denitrifier communities and, therefore, to affect DEA. Indirect temperature effect on DEA may have varied between sampling time, increasing by up to 10 the denitrification rate of 6-day-old PRB and decreasing by up to 5 the denitrification rate of 21-day-old PRB. The present results suggest that indirect effects of warming through changes in bacterial community composition, coupled to the strong direct effect of temperature on DEA already demonstrated in PRB, could modulate dissolved nitrogen removal by denitrification in rivers and streams. - Highlights: •We produced river biofilms in 2 mean temperature conditions: 17 vs 19.5 °C. •We compared their denitrifiers' structuring and functioning in 6d- and 21d-old biofilms. •A difference of 2.5 °C produced contrasted denitrifier communities. •The indirect temperature effect on denitrification activity shifted between biofilm age.

  18. Optimizing BTEX biodegradation under denitrifying conditions

    International Nuclear Information System (INIS)

    Hutchins, S.R.

    1991-01-01

    Leaking underground storage tanks are a major source of ground water contamination by petroleum hydrocarbons. Gasoline and other fuels contain benzene, toluene, ethylbenzene, and xylenes (collectively known as BTEX), which are hazardous compounds, regulated by the U.S. Environmental Protection Agency (EPA). Laboratory tests were conducted to determine optimum conditions for benzene, toluene, ethylbenzene, and xylene (collectively known as BTEX) biodegradation by aquifer microorganisms under denitrifying conditions. Microcosms, constructed with aquifer samples from Traverse City, Michigan, were amended with selected concentrations of nutrients and one or more hydrocarbons. Toluene, ethylbenzene, m-xylene, and p-xylene, were degraded to below 5 micrograms/L when present as sole source substrates; stoichiometric calculations indicated that nitrate removal was sufficient to account for 70 to 80% of the compounds being mineralized. o-Xylene was recalcitrant when present as a sole source substrate, but was slowly degraded in the presence of the other hydrocarbons. Benzene was not degraded within one year, regardless of whether it was available as a sole source substrate or in combination with toluene, phenol, or catechol. Pre-exposure to low levels of BTEX and nutrients had variable effects, as did the addition of different concentrations of ammonia and phosphate. Nitrate concentrations as high as 500 mg/L NO3-N were slightly inhibitory. These data indicate that nitrate-mediated biodegradation of BTEX at Traverse City can occur under a variety of environmental conditions with rates relatively independent of nutrient concentrations. However, the data reaffirm that benzene is recalcitrant under strictly anaerobic conditions in these samples

  19. Functional consortium for denitrifying sulfide removal process.

    Science.gov (United States)

    Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

    2010-03-01

    Denitrifying sulfide removal (DSR) process simultaneously converts sulfide, nitrate, and chemical oxygen demand from industrial wastewaters to elemental sulfur, nitrogen gas, and carbon dioxide, respectively. This investigation utilizes a dilution-to-extinction approach at 10(-2) to 10(-6) dilutions to elucidate the correlation between the composition of the microbial community and the DSR performance. In the original suspension and in 10(-2) dilution, the strains Stenotrophomonas sp., Thauera sp., and Azoarcus sp. are the heterotrophic denitrifiers and the strains Paracoccus sp. and Pseudomonas sp. are the sulfide-oxidizing denitrifers. The 10(-4) dilution is identified as the functional consortium for the present DSR system, which comprises two functional strains, Stenotrophomonas sp. strain Paracoccus sp. At 10(-6) dilution, all DSR performance was lost. The functions of the constituent cells in the DSR granules were discussed based on data obtained using the dilution-to-extinction approach.

  20. Coexistence of nitrifying, anammox and denitrifying bacteria in a sequencing batch reactor

    Directory of Open Access Journals (Sweden)

    Michela eLangone

    2014-02-01

    Full Text Available Elevated nitrogen removal efficiencies from ammonium-rich wastewaters have been demonstrated by several applications, that combine nitritation and anammox processes. Denitrification will occur simultaneously when organic carbon is also present. In this study, the activity of aerobic ammonia oxidizing, anammox and denitrifying bacteria in a full scale Sequencing Batch Reactor, treating digester supernatants, was studied by means of batch-assays. AOB and anammox activities were maximum at pH of 8.0 and 7.8-8.0, rispectively. Short term effect of nitrite on anammox activity was studied, showing nitrite up to 42 mg/L did not result in inhibition. Both denitrification via nitrate and nitrite were measured. To reduce nitrite-oxidizing activity, high of NH3 – N (1.9-10 mg N-NH3/L and low nitrite (3-8 mg TNN/L are required conditions during the whole SBR cycle.Molecular analysis showed the nitritation-anammox sludge harbored a high microbial diversity, where each microorganism has a specific role. Using ammonia monooxygenase α –subunit (amoA gene as a marker, our analyses suggested different macro- and micro-environments in the reactor strongly affect the AOB community, allowing the development of different AOB species, such as N. europaea/eutropha and N. oligotropha groups, which improve the stability of nitritation process. A specific PCR primer set, used to target the 16S rRNA gene of anammox bacteria, confirmed the presence of the Ca. Brocadia fulgida type, able to grow in precence of organic matter and to tolerate high nitrite concentrations. The diversity of denitrifiers was assessed by using dissimilatory nitrite reductase (nirS gene-based analyses, who showed denitifiers were related to different betaproteobacterial genera, such as Thauera, Pseudomonas, Dechloromonas and Aromatoleum, able to assist in forming microbial aggregates. Concerning possible secondary processes, no n-damo bacteria were found while NOB from the genus of Nitrobacter

  1. Site-specific variability in BTEX biodegradation under denitrifying conditions

    International Nuclear Information System (INIS)

    Kao, C.M.; Borden, R.C.

    1997-01-01

    Laboratory microcosm experiments were conducted to evaluate the feasibility of benzene, toluene, ethylbenzene, m-xylene, and o-xylene (BTEX) biodegradation under denitrifying conditions. Nine different sources of inocula, including contaminated and uncontaminated soil cores from four different sites and activated sludge, were used to establish microcosms. BTEX was not degraded under denitrifying conditions in microcosms inoculated with aquifer material from Rocky Point and Traverse City. However, rapid depletion of glucose under denitrifying conditions was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing aquifer material from Fort Bragg and Sleeping Bear Dunes and sewage sludge. Benzene was recalcitrant in all microcosms tested. The degradation of o-xylene ceased after toluene, ethylbenzene, and m-xylene were depleted in the Fort Bragg and sludge microcosms, but o-xylene continued to degrade in microcosms with contaminated Sleeping Bear Dunes soil. The most probable number (MPN) of denitrifiers in these nine different inocula were measured using a microtiter technique. There was no correlation between the MPN of denitrifiers and the TEX degradation rate under denitrifying conditions. Experimental results indicate that the degradation sequence and TEX degradation rate under denitrifying conditions may differ among sites. Results also indicate that denitrification alone may not be a suitable bioremediation technology for gasoline-contaminated aquifers because of the inability of denitrifiers to degrade benzene

  2. Highly task-related diversity vs. less task-related diversity among university staff

    DEFF Research Database (Denmark)

    Lauring, Jakob; Selmer, Jan

    2013-01-01

    from 489 university staff members showed that age diversity and cultural diversity, representing highly task-related diversity, were positively associated with most of the variables depicting group cohesiveness. On the other hand, gender diversity, illustrating less task-related diversity, seemed......As only very few large-scale studies have investigated multi-cultural university staff and as none of these studies have dealt with diversity and group processes, this survey was directed toward staffs in 16 science departments from three large universities in Denmark. Results based on the response...

  3. Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge.

    Science.gov (United States)

    Morgan-Sagastume, Fernando; Nielsen, Jeppe Lund; Nielsen, Per Halkjaer

    2008-11-01

    The denitrification capacity of different phylogenetic bacterial groups was investigated on addition of different substrates in activated sludge from two nutrient-removal plants. Nitrate/nitrite consumption rates (CRs) were calculated from nitrate and nitrite biosensor, in situ measurements. The nitrate/nitrite CRs depended on the substrate added, and acetate alone or combined with other substrates yielded the highest rates (3-6 mg N gVSS(-1) h(-1)). The nitrate CRs were similar to the nitrite CRs for most substrates tested. The structure of the active denitrifying population was investigated using heterotrophic CO2 microautoradiography (HetCO2-MAR) and FISH. Probe-defined denitrifiers appeared as specialized substrate utilizers despite acetate being preferentially used by most of them. Azoarcus and Accumulibacter abundance in the two different sludges was related to differences in their substrate-specific nitrate/nitrite CRs. Aquaspirillum-related bacteria were the most abundant potential denitrifiers (c. 20% of biovolume); however, Accumulibacter (3-7%) and Azoarcus (2-13%) may have primarily driven denitrification by utilizing pyruvate, ethanol, and acetate. Activated sludge denitrification was potentially conducted by a diverse, versatile population including not only Betaproteobacteria (Aquaspirillum, Thauera, Accumulibacter, and Azoarcus) but also some Alphaproteobacteria and Gammaproteobacteria, as indicated by the assimilation of 14CO2 by these probe-defined groups with a complex substrate mixture as an electron donor and nitrite as an electron acceptor in HetCO2-MAR-FISH tests.

  4. Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir

    Directory of Open Access Journals (Sweden)

    Tamara N. Nazina

    2017-04-01

    Full Text Available The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively. The DNA-derived clone libraries were found to contain bacterial and archaeal 16S rRNA genes and the alkB genes encoding alkane monooxygenases similar to those encoded by alkB-geo1 and alkB-geo6 of geobacilli. The 16S rRNA genes of methanogens (Methanomethylovorans, Methanoculleus, Methanolinea, Methanothrix, and Methanocalculus were predominant in the DNA-derived library of Archaea cloned sequences; among the bacterial sequences, the 16S rRNA genes of members of the genus Geobacillus were the most numerous. The RNA-derived library contained only bacterial cDNA of the 16S rRNA sequences belonging to metabolically active aerobic organotrophic bacteria (Tepidimonas, Pseudomonas, Acinetobacter, as well as of denitrifying (Azoarcus, Tepidiphilus, Calditerrivibrio, fermenting (Bellilinea, iron-reducing (Geobacter, and sulfate- and sulfur-reducing bacteria (Desulfomicrobium, Desulfuromonas. The presence of the microorganisms of the main functional groups revealed by molecular techniques was confirmed by the results of cultural, radioisotope, and geochemical research. Functioning of the mesophilic and thermophilic branches was shown for the microbial food chain of the near-bottom zone of the injection well, which included the microorganisms of the carbon, sulfur, iron, and nitrogen cycles.

  5. Diverse microbial species survive high ammonia concentrations

    Science.gov (United States)

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  6. IDENTIFICATION AND ECOPHYSIOLOGY OF ACTIVE DENITRIFIERS IN ACTIVATED SLUDGE

    DEFF Research Database (Denmark)

    Hansen, Aviaja Anna; Le-Quy, Vang; Nielsen, Kåre Lehmann

    reactor studies. To obtain better identification of active denitrifying communities in full-scale wastewater treatment plants (WWTPs) we applied DNA-SIP with 13C-labelled substrates, and RT-PCR of expressed denitrification genes (nirS, nirK and nosZ) upon various substrate-inductions. To come around...... were determined with quantitative FISH, while their active metabolic pathways were investigated directly in activated sludge with a tag-based metatranscriptomic approach under acetate-utilizing and denitrifying conditions. The different methods revealed a majority of denitrifiers in all WWTPs belonging...

  7. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

    DEFF Research Database (Denmark)

    Priemé, Anders; Wolsing, Martin

    2004-01-01

    Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...

  8. In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition

    DEFF Research Database (Denmark)

    Kofoed, Michael Vedel; Stief, Peter; Poulsen, Morten

    can be designed to target a broader range of denitrifying bacteria; however, they require two-pass CARD-FISH, which may result in (too) high background fluorescence. In a first application example, habitat-specific polynucleotide probes were used to quantify bacteria expressing narG and nos...... reduction of nitrate to dinitrogen gas, is essential for the removal of fixed nitrogen from natural and engineered ecosystems. However, community structure and activity dynamics of denitrifying bacteria in most systems are poorly understood, partially due to difficulties in identifying and quantifying...... and catalyzed fluorescent reporter deposition (CARD-FISH). The general feasibility of the approach was first tested with pure cultures of Pseudomonas stutzeri and various denitrifying and nitrate-reducing isolates. Detailed studies of probe specificity and hybridization conditions using Clone-FISH of nar...

  9. Perceptions of Diversity Training Needs in High Tech Business.

    Science.gov (United States)

    Lieberman, Devorah A.; Gurtov, Ellene

    A study questioned 12 human resource personnel, corporation managers, and diversity trainers about their perceptions of diversity training needs in Pacific Northwest high tech organizations. The overarching research questions for the study were as follows: (1) What are the most frequently reported diversity training needs among human resource…

  10. Insight into the short- and long-term effects of Cu(II) on denitrifying biogranules

    International Nuclear Information System (INIS)

    Chen, Hui; Chen, Qian-Qian; Jiang, Xiao-Yan; Hu, Hai-Yan; Shi, Man-Ling; Jin, Ren-Cun

    2016-01-01

    Highlights: • It is the first time to evaluate the effect of Cu"2"+ on denitrifying biogranules. • A high level of Cu(II) was investigated during batch assays and continuous tests. • Mechanisms of the effects of Cu"2"+ on denitrifying biogranules were discussed. • Effects of pre-exposure to Cu"2"+ and starvation treatments were investigated. - Abstract: This study aimed to investigate the short- and long-term effects of Cu"2"+ on the activity and performance of denitrifying bacteria. The short-term effects of various concentrations of Cu"2"+ on the denitrifying bacteria were evaluated using batch assays. The specific denitrifying activity (SDA) decreased from 14.3 ± 2.2 (without Cu"2"+) to 6.1 ± 0.1 mg N h"−"1 g"−"1 VSS (100 mgCu"2"+ L"−"1) when Cu"2"+ increased from 0 to 100 mg L"−"1 with an increment of 10 mgCu"2"+ L"−"1. A non-competitive inhibition model was used to calculate the 50% inhibition concentration (IC_5_0) of Cu"2"+ on denitrifying sludge (30.6 ± 2.5 mg L"−"1). Monod and Luong models were applied to investigate the influence of the initial substrate concentration, and the results suggested that the maximum substrate removal rate would be reduced with Cu"2"+ supplementation. Pre-exposure to Cu"2"+ could lead to an 18.2–46.2% decrease in the SDA and decreasing percentage of the SDA increased with both exposure time and concentration. In the continuous-flow test, Cu"2"+ concentration varied from 1 to 75 mg L"−"1; however, no clear deterioration was observed in the reactor, and the reactor was kept stable, with the total nitrogen removal efficiency and total organic carbon efficiency greater than 89.0 and 85.0%, respectively. The results demonstrated the short-term inhibition of Cu"2"+ upon denitrification, and no notable adversity was observed during the continuous-flow test after long-term acclimation.

  11. Simultaneous removal of sulfide, nitrate and acetate under denitrifying sulfide removal condition: Modeling and experimental validation

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xijun; Chen, Chuan; Wang, Aijie; Guo, Wanqian; Zhou, Xu [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Lee, Duu-Jong, E-mail: djlee@ntu.edu.tw [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan (China); Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Ren, Nanqi, E-mail: rnq@hit.edu.cn [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Chang, Jo-Shu [Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan (China)

    2014-01-15

    Graphical abstract: Model evaluation applied to case study 1: (A-G) S{sup 2−}, NO{sub 3}{sup −}-N, NO{sub 2}{sup −}-N, and Ac{sup −}-C profiles under initial sulfide concentrations of 156.2 (A), 539 (B), 964 (C), 1490 (D), 342.7 (E), 718 (F), and 1140.7 (G) mg L{sup −1}. The solid line represents simulated result and scatter represents experimental result. -- Highlights: • This work developed a mathematical model for DSR process. • Kinetics of sulfur–nitrogen–carbon and interactions between denitrifiers were studied. • Kinetic parameters of the model were estimated via data fitting. • The model described kinetic behaviors of DSR processes over wide parametric range. -- Abstract: Simultaneous removal of sulfide (S{sup 2−}), nitrate (NO{sub 3}{sup −}) and acetate (Ac{sup −}) under denitrifying sulfide removal process (DSR) is a novel biological wastewater treatment process. This work developed a mathematical model to describe the kinetic behavior of sulfur–nitrogen–carbon and interactions between autotrophic denitrifiers and heterotrophic denitrifiers. The kinetic parameters of the model were estimated via data fitting considering the effects of initial S{sup 2−} concentration, S{sup 2−}/NO{sub 3}{sup −}-N ratio and Ac{sup −}-C/NO{sub 3}{sup −}-N ratio. Simulation supported that the heterotrophic denitratation step (NO{sub 3}{sup −} reduction to NO{sub 2}{sup −}) was inhibited by S{sup 2−} compared with the denitritation step (NO{sub 2}{sup −} reduction to N{sub 2}). Also, the S{sup 2−} oxidation by autotrophic denitrifiers was shown two times lower in rate with NO{sub 2}{sup −} as electron acceptor than that with NO{sub 3}{sup −} as electron acceptor. NO{sub 3}{sup −} reduction by autotrophic denitrifiers occurs 3–10 times slower when S{sup 0} participates as final electron donor compared to the S{sup 2−}-driven pathway. Model simulation on continuous-flow DSR reactor suggested that the adjustment of

  12. Mapping spatial patterns of denitrifiers at large scales (Invited)

    Science.gov (United States)

    Philippot, L.; Ramette, A.; Saby, N.; Bru, D.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.

    2010-12-01

    Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distribution were analyzed by canonical variation partitioning. Our results indicate that 43% to 85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of denitrifiers at the landscape scale. Studying the distribution of the denitrifiers at large scale can help closing the artificial gap between the investigation of microbial processes and microbial community ecology, therefore facilitating our understanding of the relationships between the ecology of denitrifiers and N-fluxes by denitrification.

  13. Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots.

    Science.gov (United States)

    Flores-Mireles, Ana L; Winans, Stephen C; Holguin, Gina

    2007-11-01

    An analysis of the molecular diversity of N(2) fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N(2) fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.

  14. Molecular Characterization of Diazotrophic and Denitrifying Bacteria Associated with Mangrove Roots▿

    Science.gov (United States)

    Flores-Mireles, Ana L.; Winans, Stephen C.; Holguin, Gina

    2007-01-01

    An analysis of the molecular diversity of N2 fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N2 fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments. PMID:17827324

  15. Denitrifying woodchip bioreactor and phosphorus filter pairing to minimize pollution swapping

    Science.gov (United States)

    Christianson, Laura E.; Lepine, Christine; Sibrell, Philip; Penn, Chad J.; Summerfelt, Steven T.

    2017-01-01

    Pairing denitrifying woodchip bioreactors and phosphorus-sorbing filters provides a unique, engineered approach for dual nutrient removal from waters impaired with both nitrogen (N) and phosphorus (P). This column study aimed to test placement of two P-filter media (acid mine drainage treatment residuals and steel slag) relative to a denitrifying system to maximize N and P removal and minimize pollution swapping under varying flow conditions (i.e., woodchip column hydraulic retention times (HRTs) of 7.2, 18, and 51 h; P-filter HRTs of 7.6–59 min). Woodchip denitrification columns were placed either upstream or downstream of P-filters filled with either medium. The configuration with woodchip denitrifying systems placed upstream of the P-filters generally provided optimized dissolved P removal efficiencies and removal rates. The P-filters placed upstream of the woodchip columns exhibited better P removal than downstream-placed P-filters only under overly long (i.e., N-limited) retention times when highly reduced effluent exited the woodchip bioreactors. The paired configurations using mine drainage residuals provided significantly greater P removal than the steel slag P-filters (e.g., 25–133 versus 8.8–48 g P removed m−3 filter media d−1, respectively), but there were no significant differences in N removal between treatments (removal rates: 8.0–18 g N removed m−3 woodchips d−1; N removal efficiencies: 18–95% across all HRTs). The range of HRTs tested here resulted in various undesirable pollution swapping by-products from the denitrifying bioreactors: nitrite production when nitrate removal was not complete and sulfate reduction, chemical oxygen demand production and decreased pH during overly long retention times. The downstream P-filter placement provided a polishing step for removal of chemical oxygen demand and nitrite.

  16. Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community.

    Science.gov (United States)

    Zaghmouri, Imen; Michotey, Valerie D; Armougom, Fabrice; Guasco, Sophie; Bonin, Patricia C

    2018-05-01

    The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

    Science.gov (United States)

    Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

  18. Algal MIPs, high diversity and conserved motifs.

    Science.gov (United States)

    Anderberg, Hanna I; Danielson, Jonas Å H; Johanson, Urban

    2011-04-21

    Major intrinsic proteins (MIPs) also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in terrestrial plants but little is known about their evolutionary history. In an attempt to investigate the origin of the plant MIP subfamilies, genomes of chlorophyte algae, the sister group of charophyte algae and land plants, were searched for MIP encoding genes. A total of 22 MIPs were identified in the nine analysed genomes and phylogenetic analyses classified them into seven subfamilies. Two of these, Plasma membrane Intrinsic Proteins (PIPs) and GlpF-like Intrinsic Proteins (GIPs), are also present in land plants and divergence dating support a common origin of these algal and land plant MIPs, predating the evolution of terrestrial plants. The subfamilies unique to algae were named MIPA to MIPE to facilitate the use of a common nomenclature for plant MIPs reflecting phylogenetically stable groups. All of the investigated genomes contained at least one MIP gene but only a few species encoded MIPs belonging to more than one subfamily. Our results suggest that at least two of the seven subfamilies found in land plants were present already in an algal ancestor. The total variation of MIPs and the number of different subfamilies in chlorophyte algae is likely to be even higher than that found in land plants. Our analyses indicate that genetic exchanges between several of the algal subfamilies have occurred. The PIP1 and PIP2 groups and the Ca2+ gating appear to be specific to land plants whereas the pH gating is a more ancient characteristic shared by all PIPs. Further studies are needed to discern the function of the algal specific subfamilies MIPA-E and to fully understand the evolutionary relationship of algal and terrestrial plant MIPs.

  19. Algal MIPs, high diversity and conserved motifs

    Directory of Open Access Journals (Sweden)

    Johanson Urban

    2011-04-01

    Full Text Available Abstract Background Major intrinsic proteins (MIPs also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in terrestrial plants but little is known about their evolutionary history. In an attempt to investigate the origin of the plant MIP subfamilies, genomes of chlorophyte algae, the sister group of charophyte algae and land plants, were searched for MIP encoding genes. Results A total of 22 MIPs were identified in the nine analysed genomes and phylogenetic analyses classified them into seven subfamilies. Two of these, Plasma membrane Intrinsic Proteins (PIPs and GlpF-like Intrinsic Proteins (GIPs, are also present in land plants and divergence dating support a common origin of these algal and land plant MIPs, predating the evolution of terrestrial plants. The subfamilies unique to algae were named MIPA to MIPE to facilitate the use of a common nomenclature for plant MIPs reflecting phylogenetically stable groups. All of the investigated genomes contained at least one MIP gene but only a few species encoded MIPs belonging to more than one subfamily. Conclusions Our results suggest that at least two of the seven subfamilies found in land plants were present already in an algal ancestor. The total variation of MIPs and the number of different subfamilies in chlorophyte algae is likely to be even higher than that found in land plants. Our analyses indicate that genetic exchanges between several of the algal subfamilies have occurred. The PIP1 and PIP2 groups and the Ca2+ gating appear to be specific to land plants whereas the pH gating is a more ancient characteristic shared by all PIPs. Further studies are needed to discern the function of the algal specific subfamilies MIPA-E and to fully understand the evolutionary relationship of algal and terrestrial plant MIPs.

  20. Nitrate Removal Rates in Denitrifying Bioreactors During Storm Flows

    Science.gov (United States)

    Pluer, W.; Walter, T.

    2017-12-01

    Field denitrifying bioreactors are designed to reduce excess nitrate (NO3-) pollution in runoff from agricultural fields. Field bioreactors saturate organic matter to create conditions that facilitate microbial denitrification. Prior studies using steady flow in lab-scale bioreactors showed that a hydraulic retention time (HRT) between 4 and 10 hours was optimal for reducing NO3- loads. However, during storm-induced events, flow rate and actual HRT fluctuate. These fluctuations have the potential to disrupt the system in significant ways that are not captured by the idealized steady-flow HRT models. The goal of this study was to investigate removal rate during dynamic storm flows of variable rates and durations. Our results indicate that storm peak flow and duration were not significant controlling variables. Instead, we found high correlations (p=0.004) in average removal rates between bioreactors displaying a predominantly uniform flow pattern compared with bioreactors that exhibited preferential flow (24.4 and 21.4 g N m-3 d-1, respectively). This suggests that the internal flow patterns are a more significant driver of removal rate than external factors of the storm hydrograph. Designing for flow patterns in addition to theoretical HRT will facilitate complete mixing within the bioreactors. This will help maximize excess NO3- removal during large storm-induced runoff events.

  1. Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, C. [Miami Univ., Oxford, OH (United States). Dept. of Microbiology; Wu, W.M. [Stanford Univ., CA (United States). Dept. of Civil and Environmental Engineering; Gentry, T.J. [Oak Ridge National Lab., TN (US). Environmental Sciences Div.] (and others)

    2006-08-15

    High levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the Y-12 National Security Complex in Oak Ridge, TN. A field-scale denitrifying fluidized bed reactor (FBR) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. After inoculation, biofilms developed on the granular activated carbon particles. Changes in the bacterial community of the FBR were evaluated with clone libraries (n=500 partial sequences) of the small-subunit rRNA gene for samples taken over a 4-month start-up period. Early phases of start-up operation were characterized by a period of selection, followed by low diversity and predominance by Azoarcus-like sequences. Possible explanations were high pH and nutrient limitations. After amelioration of these conditions, diversification increased rapidly, with the appearance of Dechloromonas, Pseudomonas, and Hydrogenophaga sequences. Changes in NO{sub 3}, SO{sub 4}, and pH also likely contributed to shifts in community composition. The detection of sulfate-reducing-bacteria-like sequences closely related to Desulfovibrio and Desulfuromonas in the FBR have important implications for downstream applications at the field site. (orig.)

  2. Maintaining High Challenge and High Support for Diverse Learners

    Science.gov (United States)

    Athanases, Steven

    2012-01-01

    As teachers, schools and school leaders work to better prepare California's culturally and linguistically diverse students, methods for doing so vary widely. One approach prioritizes safe spaces, welcoming environments, well-structured routines--school and classroom culture features essential for students' well-being. A second key priority, often…

  3. Microsatellite markers suggest high genetic diversity in an urban ...

    Indian Academy of Sciences (India)

    FRANCISCO MORINHA

    diversity in an urban population of Cooper's hawks (Accipiter cooperii). J. Genet. 95, e19–e24. ... high quality habitat for this species (Boggie and Mannan. 2014) and the rapid ... The high densities of birds in urban populations can result in the ..... comparing urban and rural Cooper's hawk populations are mandatory to ...

  4. Diversity

    Science.gov (United States)

    Portraits In Courage Vol. VIII Portraits In Courage Vol. IX Portraits In Courage Vol. X AF Sites Social -Wide Initiative to Promote Diversity and Inclusion in the Federal Workforce Executive Order 13548 : Virtual Diversity Conference Air Force Diversity & Inclusion Air Force Diversity Graphic There is no

  5. Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples

    OpenAIRE

    Kester, R.A.; Boer, W. de; Laanbroek, H.J.

    1996-01-01

    The contribution of nitrifiers and denitrifiers to the nitrous oxide production in slurries of calcareous silt loam and river bank sediment at different oxygen concentrations was determined using acetylene as nitrification inhibitor. The addition of 10 Pa acetylene resulted in inhibition of nitrous oxide production at oxic conditions, but strongly enhanced the nitrous oxide production at oxygen-poor and anoxic conditions. Inhibition of nitrification by short exposure (1 to 24 h) to high conce...

  6. Denitrifying woodchip bioreactor and phosphorus filter pairing to minimize pollution swapping.

    Science.gov (United States)

    Christianson, Laura E; Lepine, Christine; Sibrell, Philip L; Penn, Chad; Summerfelt, Steven T

    2017-09-15

    Pairing denitrifying woodchip bioreactors and phosphorus-sorbing filters provides a unique, engineered approach for dual nutrient removal from waters impaired with both nitrogen (N) and phosphorus (P). This column study aimed to test placement of two P-filter media (acid mine drainage treatment residuals and steel slag) relative to a denitrifying system to maximize N and P removal and minimize pollution swapping under varying flow conditions (i.e., woodchip column hydraulic retention times (HRTs) of 7.2, 18, and 51 h; P-filter HRTs of 7.6-59 min). Woodchip denitrification columns were placed either upstream or downstream of P-filters filled with either medium. The configuration with woodchip denitrifying systems placed upstream of the P-filters generally provided optimized dissolved P removal efficiencies and removal rates. The P-filters placed upstream of the woodchip columns exhibited better P removal than downstream-placed P-filters only under overly long (i.e., N-limited) retention times when highly reduced effluent exited the woodchip bioreactors. The paired configurations using mine drainage residuals provided significantly greater P removal than the steel slag P-filters (e.g., 25-133 versus 8.8-48 g P removed m -3 filter media d -1 , respectively), but there were no significant differences in N removal between treatments (removal rates: 8.0-18 g N removed m -3 woodchips d -1 ; N removal efficiencies: 18-95% across all HRTs). The range of HRTs tested here resulted in various undesirable pollution swapping by-products from the denitrifying bioreactors: nitrite production when nitrate removal was not complete and sulfate reduction, chemical oxygen demand production and decreased pH during overly long retention times. The downstream P-filter placement provided a polishing step for removal of chemical oxygen demand and nitrite. Copyright © 2017 The Conservation Fund. Published by Elsevier Ltd.. All rights reserved.

  7. Limnology and cyanobacterial diversity of high altitude lakes of ...

    Indian Academy of Sciences (India)

    Limnological data of four high altitude lakes from the cold desert region of Himachal Pradesh, India, has been correlated with cyanobacterial diversity. Physico-chemical characteristics and nutrient contents of the studied lakes revealed that Sissu Lake is mesotrophic while Chandra Tal, Suraj Tal and Deepak Tal are ...

  8. Inhibitory Effect of Gamma-Irradiated Chitosan on the Growth of Denitrifiers

    Directory of Open Access Journals (Sweden)

    Javier Vilcáez

    2009-01-01

    Full Text Available In order to find an environmentally benign substitute to hazardous inhibitory agents, the inhibitory effect of -irradiated chitosans against a mixed culture of denitrifying bacteria was experimentally evaluated. Unlike other studies using pure aerobic cultures, the observed effect was not a complete inhibition but a transient inhibition reflected by prolonged lag phases and reduced growth rates. Raw chitosan under acid conditions (pH 6.3 exerted the strongest inhibition followed by the 100 kGy and 500 kGy irradiated chitosans, respectively. Therefore, because the molecular weight of chitosan decreases with the degree of -irradiation, the inhibitory properties of chitosan due to its high molecular weight were more relevant than the inhibitory properties gained due to the modification of the surface charge and/or chemical structure by -irradiation. High dosage of -irradiated appeared to increase the growth of mixed denitrifying bacteria in acid pH media. However, in neutral pH media, high dosage of -irradiation appeared to enhance the inhibitory effect of chitosan.

  9. Oxygen regulation of nitrate uptake in denitrifying Pseudomonas aeruginosa.

    OpenAIRE

    Hernandez, D; Rowe, J J

    1987-01-01

    Oxygen had an immediate and reversible inhibitory effect on nitrate respiration by denitrifying cultures of Pseudomonas aeruginosa. Inhibition of nitrate utilization by oxygen appeared to be at the level of nitrate uptake, since nitrate reduction to nitrite in cell extracts was not affected by oxygen. The degree of oxygen inhibition was dependent on the concentration of oxygen, and increasing nitrate concentrations could not overcome the inhibition. The inhibitory effect of oxygen was maximal...

  10. High genetic diversity of Jatropha curcas assessed by ISSR.

    Science.gov (United States)

    Díaz, B G; Argollo, D M; Franco, M C; Nucci, S M; Siqueira, W J; de Laat, D M; Colombo, C A

    2017-05-31

    Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.

  11. Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

    Science.gov (United States)

    Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

    2016-10-01

    Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3-64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7-25.4%), Firmicutes (3.0-20.1%), Acidobacteria (2.7-15.7%), Actinobacteria (2.2-8.7%), Bacteroidetes (0.5-9.7%), and Verrucomicrobia (2.4-5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

  12. [Agrobacterium rubi strains from blueberry plants are highly diverse].

    Science.gov (United States)

    Abrahamovich, Eliana; López, Ana C; Alippi, Adriana M

    2014-01-01

    The diversity of a collection of Agrobacterium rubi strains isolated from blueberries from different regions of Argentina was studied by conventional microbiological tests and molecular techniques. Results from biochemical and physiological reactions, as well as from rep-PCR and RFLP analysis of PCR-amplified 23S rDNA showed high phenotypic and genotypic intraspecific variation. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

  13. DRIVERS OF THE DYNAMICS OF DIAZOTROPHS AND DENITRIFIERS IN NORTH SEA BOTTOM WATERS AND SEDIMENTS

    Directory of Open Access Journals (Sweden)

    Lucas eStal

    2015-07-01

    Full Text Available The fixation of dinitrogen (N2 and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L-1 d-1 and from undetectable to 8.2 nmol N g-1 d-1 in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 µmol m-2 d-1 and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and

  14. Determination of a Screening Metric for High Diversity DNA Libraries.

    Science.gov (United States)

    Guido, Nicholas J; Handerson, Steven; Joseph, Elaine M; Leake, Devin; Kung, Li A

    2016-01-01

    The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

  15. Determination of a Screening Metric for High Diversity DNA Libraries.

    Directory of Open Access Journals (Sweden)

    Nicholas J Guido

    Full Text Available The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

  16. Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

    Science.gov (United States)

    Braker, Gesche; Ayala-del-Río, Héctor L.; Devol, Allan H.; Fesefeldt, Andreas; Tiedje, James M.

    2001-01-01

    Steep vertical gradients of oxidants (O2 and NO3−) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities. PMID:11282647

  17. Rare species support vulnerable functions in high-diversity ecosystems.

    Science.gov (United States)

    Mouillot, David; Bellwood, David R; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C E Timothy; Renaud, Julien; Thuiller, Wilfried

    2013-01-01

    Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

  18. Rare species support vulnerable functions in high-diversity ecosystems.

    Directory of Open Access Journals (Sweden)

    David Mouillot

    Full Text Available Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees, we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by

  19. De novo assembly of highly diverse viral populations

    Directory of Open Access Journals (Sweden)

    Yang Xiao

    2012-09-01

    Full Text Available Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

  20. Understanding Students' Precollege Experiences with Racial Diversity: The High School as Microsystem

    Science.gov (United States)

    Park, Julie J.; Chang, Stephanie H.

    2015-01-01

    Few qualitative studies consider how high school experiences affect readiness for diversity engagement in college. Using data from an ethnographic case study, three central trends (student experiences within homogeneous high schools, racial divisions within diverse high schools, and students who attended diverse high schools but had little…

  1. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  2. Removal of pharmaceutical and personal care products (PPCPs) under nitrifying and denitrifying conditions.

    Science.gov (United States)

    Suarez, Sonia; Lema, Juan M; Omil, Francisco

    2010-05-01

    The contribution of volatilization, sorption and transformation to the removal of 16 Pharmaceutical and Personal Care Products (PPCPs) in two lab-scale conventional activated sludge reactors, working under nitrifying (aerobic) and denitrifying (anoxic) conditions for more than 1.5 years, have been assessed. Pseudo-first order biological degradation rate constants (k(biol)) were calculated for the selected compounds in both reactors. Faster degradation kinetics were measured in the nitrifying reactor compared to the denitrifying system for the majority of PPCPs. Compounds could be classified according to their k(biol) into very highly (k(biol)>5Lg(SS)(-1)d(-1)), highly (1fragrances (HHCB, AHTN and ADBI) were transformed to a large extent under aerobic (>75%) and anoxic (>65%) conditions, whereas naproxen (NPX), ethinylestradiol (EE2), roxithromycin (ROX) and erythromycin (ERY) were only significantly transformed in the aerobic reactor (>80%). The anti-depressant citalopram (CTL) was moderately biotransformed under both, aerobic and anoxic conditions (>60% and >40%, respectively). Some compounds, as carbamazepine (CBZ), diazepam (DZP), sulfamethoxazole (SMX) and trimethoprim (TMP), manifested high resistance to biological transformation. Solids Retention Time (SRT(aerobic) >50d and 20d and <20d) had a slightly positive effect on the removal of FLX, NPX, CTL, EE2 and natural estrogens (increase in removal efficiencies <10%). Removal of diclofenac (DCF) in the aerobic reactor was positively affected by the development of nitrifying biomass and increased from 0% up to 74%. Similarly, efficient anoxic transformation of ibuprofen (75%) was observed after an adaptation period of 340d. Temperature (16-26 degrees C) only had a slight effect on the removal of CTL which increased in 4%.

  3. Heterotrophic ammonium removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Providencia rettgeri YL

    Institute of Scientific and Technical Information of China (English)

    TAYLOR Shauna M; HE Yiliang; ZHAO Bin; HUANG Jue

    2009-01-01

    Bacterium Providencia rettgeri YL was found to exhibit an unusual ability to heterotrophically nitrify and aerobically denitrify various concentrations of ammonium (NH4+-N). In order to further analyze its removal ability, several experiments were conducted to identify the growth and ammonium removal response in different carbon to nitrogen (C/N) mass ratios, shaking speeds, temperatures, ammonium concentrations and to qualitatively verify the production of nitrogen gas using gas chromatography techniques. Results showed that under optimum conditions (C/N 10, 30℃, 120 r/min), YL can significantly remove low and high concentrations of ammonium within 12 to 48 h of growth. The nitrification products hydroxylamine (NH2OH), nitrite (NO2-) and nitrate (NO3-) as well as the denitrification product, nitrogen gas (N2), were detected under completely aerobic conditions.

  4. Effects of Selected Root Exudate Components on Nitrogen Removal and Development of Denitrifying Bacteria in Constructed Wetlands

    Directory of Open Access Journals (Sweden)

    Hailu Wu

    2017-06-01

    Full Text Available Root exudates, particularly low molecular weight carbon (LMWC substrates, are major drivers of bacterial diversity and activity in the rhizosphere environment. However, it is not well understood how specific LMWC compounds—such as organic acids, soluble sugars, and amino acids—influence the community structures of denitrifying bacteria or if there are specific functions of LMWC substrates that preferentially respond to nitrogen (N removal in constructed wetlands (CWs. To address these knowledge gaps, we added mixtures of artificial exudates to CW microcosms containing N pollutant. N removal efficiency was observed over a 48-h experimental period, and at the end of the experiment, DNA was extracted from microbial samples for assessment of the bacterial community. The removal efficiencies of TN for the exudates treatments were higher than for control groups by 47.1–58.67%. Organic acid and soluble sugar treatments increased N removal, while amino acids were negative to N removal. The microbial community was changed when artificial exudates were added, but there were no significant relationships between LMWC compounds and bacterial community composition. These results indicate that although the responses of community structures of denitrifying bacteria to LMWC additions are still uncertain, there is evidence for N removal in response to exudate additions across LMWC types.

  5. Mathematical Modeling of Nitrous Oxide Production during Denitrifying Phosphorus Removal Process.

    Science.gov (United States)

    Liu, Yiwen; Peng, Lai; Chen, Xueming; Ni, Bing-Jie

    2015-07-21

    A denitrifying phosphorus removal process undergoes frequent alternating anaerobic/anoxic conditions to achieve phosphate release and uptake, during which microbial internal storage polymers (e.g., Polyhydroxyalkanoate (PHA)) could be produced and consumed dynamically. The PHA turnovers play important roles in nitrous oxide (N2O) accumulation during the denitrifying phosphorus removal process. In this work, a mathematical model is developed to describe N2O dynamics and the key role of PHA consumption on N2O accumulation during the denitrifying phosphorus removal process for the first time. In this model, the four-step anoxic storage of polyphosphate and four-step anoxic growth on PHA using nitrate, nitrite, nitric oxide (NO), and N2O consecutively by denitrifying polyphosphate accumulating organisms (DPAOs) are taken into account for describing all potential N2O accumulation steps in the denitrifying phosphorus removal process. The developed model is successfully applied to reproduce experimental data on N2O production obtained from four independent denitrifying phosphorus removal study reports with different experimental conditions. The model satisfactorily describes the N2O accumulation, nitrogen reduction, phosphate release and uptake, and PHA dynamics for all systems, suggesting the validity and applicability of the model. The results indicated a substantial role of PHA consumption in N2O accumulation due to the relatively low N2O reduction rate by using PHA during denitrifying phosphorus removal.

  6. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

  7. High diversity at PRDM9 in chimpanzees and bonobos.

    Directory of Open Access Journals (Sweden)

    Linn Fenna Groeneveld

    Full Text Available BACKGROUND: The PRDM9 locus in mammals has increasingly attracted research attention due to its role in mediating chromosomal recombination and possible involvement in hybrid sterility and hence speciation processes. The aim of this study was to characterize sequence variation at the PRDM9 locus in a sample of our closest living relatives, the chimpanzees and bonobos. METHODOLOGY/PRINCIPAL FINDINGS: PRDM9 contains a highly variable and repetitive zinc finger array. We amplified this domain using long-range PCR and determined the DNA sequences using conventional Sanger sequencing. From 17 chimpanzees representing three subspecies and five bonobos we obtained a total of 12 alleles differing at the nucleotide level. Based on a data set consisting of our data and recently published Pan PRDM9 sequences, we found that at the subspecies level, diversity levels did not differ among chimpanzee subspecies or between chimpanzee subspecies and bonobos. In contrast, the sample of chimpanzees harbors significantly more diversity at PRDM9 than samples of humans. Pan PRDM9 shows signs of rapid evolution including no alleles or ZnFs in common with humans as well as signals of positive selection in the residues responsible for DNA binding. CONCLUSIONS AND SIGNIFICANCE: The high number of alleles specific to the genus Pan, signs of positive selection in the DNA binding residues, and reported lack of conservation of recombination hotspots between chimpanzees and humans suggest that PRDM9 could be active in hotspot recruitment in the genus Pan. Chimpanzees and bonobos are considered separate species and do not have overlapping ranges in the wild, making the presence of shared alleles at the amino acid level between the chimpanzee and bonobo species interesting in view of the hypothesis that PRDM9 plays a universal role in interspecific hybrid sterility.

  8. High diversity of genogroup I picobirnaviruses in mammals

    Directory of Open Access Journals (Sweden)

    Patrick CY Woo

    2016-11-01

    Full Text Available In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs were positive by RT-PCR targeting the partial RdRp gene in specimens from 5 cattle, 6 monkeys, 17 horses, 9 pigs, 1 rabbit, 1 dog and 12 California sea lions, with 11, 9, 23, 17, 1, 1 and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4 to 89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segments 1 (viral loads 1.7×104 to 5.9×106/ml and 15 segments 2 (viral loads 4.1×103 to 1.3×106/ml of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1 to C4. In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1 to R9. In four sea lions, PBVs were detected in two different years, with the same segment 1 clade (C3 present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.

  9. Performance of denitrifying microbial fuel cell with biocathode over nitrite

    Directory of Open Access Journals (Sweden)

    Zhao eHuimin

    2016-03-01

    Full Text Available Microbial fuel cell (MFC with nitrite as an electron acceptor in cathode provided a new technology for nitrogen removal and electricity production simultaneously. The influences of influent nitrite concentration and external resistance on the performance of denitrifying MFC were investigated. The optimal effectiveness were obtained with the maximum total nitrogen (TN removal rate of 54.80±0.01 g m-3 d-1. It would be rather desirable for the TN removal than electricity generation at lower external resistance. Denaturing gradient gel electrophoresis suggested that Proteobacteria was the predominant phylum, accounting for 35.72%. Thiobacillus and Afipia might benefit to nitrite removal. The presence of nitrifying Devosia indicated that nitrite was oxidized to nitrate via a biochemical mechanism in the cathode. Ignavibacterium and Anaerolineaceae was found in the cathode as a heterotrophic bacterium with sodium acetate as substrate, which illustrated that sodium acetate in anode was likely permeated through proton exchange membrane to the cathode .

  10. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.

    Directory of Open Access Journals (Sweden)

    Yuan Liu

    Full Text Available While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg-1. Copy numbers of amoA (AOA and AOB genes were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.

  11. A preliminary study of anaerobic thiosulfate-oxidising bacteria as denitrifiers in the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    LokaBharathi, P.A.; Chandramohan, D.; Nair, S.

    Bacteria which oxidize thiosulfate and reduce nitrate (TONRB) and bacteria which oxidize thiosulfate and denitrify (TODB) sampled at 5-, 100-, 200-and 300-m depths were enumerated in agar shake cultures by colony counting and by applying MPN...

  12. Complete Nutrient Removal Coupled to Nitrous Oxide Production as a Bioenergy Source by Denitrifying Polyphosphate-Accumulating Organisms.

    Science.gov (United States)

    Gao, Han; Liu, Miaomiao; Griffin, James S; Xu, Longcheng; Xiang, Da; Scherson, Yaniv D; Liu, Wen-Tso; Wells, George F

    2017-04-18

    Coupled aerobic-anoxic nitrous decomposition operation (CANDO) is a promising emerging bioprocess for wastewater treatment that enables direct energy recovery from nitrogen (N) in three steps: (1) ammonium oxidation to nitrite; (2) denitrification of nitrite to nitrous oxide (N 2 O); and (3) N 2 O conversion to N 2 with energy generation. However, CANDO does not currently target phosphorus (P) removal. Here, we demonstrate that denitrifying polyphosphate-accumulating organism (PAO) enrichment cultures are capable of catalyzing simultaneous biological N and P removal coupled to N 2 O generation in a second generation CANDO process, CANDO+P. Over 7 months (>300 cycles) of operation of a prototype lab-scale CANDO+P sequencing batch reactor treating synthetic municipal wastewater, we observed stable and near-complete N removal accompanied by sustained high-rate, high-yield N 2 O production with partial P removal. A substantial increase in abundance of the PAO Candidatus Accumulibacter phosphatis was observed, increasing from 5% of the total bacterial community in the inoculum to over 50% after 4 months. PAO enrichment was accompanied by a strong shift in the dominant Accumulibacter population from clade IIC to clade IA, based on qPCR monitoring of polyphosphate kinase 1 (ppk1) gene variants. Our work demonstrates the feasibility of combining high-rate, high-yield N 2 O production for bioenergy production with combined N and P removal from wastewater, and it further suggests a putative denitrifying PAO niche for Accumulibacter clade IA.

  13. Isolation and characteristic of an aerobic denitrifier with high ...

    African Journals Online (AJOL)

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    2011-09-12

    Sep 12, 2011 ... involve in synthetic biology directly. Although, some carbon sources could enhance the denitrification efficiency, the C/N ratio must be properly controlled. In sufficient carbon source conditions, the aerobic denitrification efficiency of. DL-23 was not raised with the increase of C/N ratio. Within C/N ratio of 10 ...

  14. High genetic diversity among Mycobacterium tuberculosis strains in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    Taher Azimi

    2018-05-01

    Full Text Available Introduction: Tuberculosis (TB still remains an important public health problem in Iran. The genotyping of Mycobacterium tuberculosis isolates is expected to lead to a better understanding of M. tuberculosis transmission in Tehran, the most populated city of Iran. Materials and Methods: A total of 2300 clinical specimens were obtained from TB suspected patients who were referred to a TB center in Tehran from Jan 2014 to Dec 2016. Identification was performed using both conventional and molecular methods. The presence of resistance to rifampicin was examined by the GeneXpert MTB/RIF. The standard 15-locus mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR typing method was applied to genotype of clinical isolates. Results: Of 2300 specimens, 80 isolates were identified as M. tuberculosis by using biochemical and molecular tests. Of 80 M. tuberculosis isolates, 76 (95% had unique genotypic profiles and 4 (5% shared a profile with one or more other strains. Based on single loci variation (SLV 4 clonal complexes were observed. NEW-1 was found to be the most predominant lineage (22.5% followed by West African (1.25%, Central Asian (CAS/Delhi (1.25%, Bovis (1.25%, H37Rv (1.25% and multiple matches (1.25%. Loci MIRU10, MIRU26, MTUB21 and QUB26 were found as highly discriminative. No mutation was detected in the hotspot region of rifampicin by using GeneXpert MTB/RIF. Conclusions: Our study findings show that there was considerable genotypic diversity among M. tuberculosis isolates in Tehran. The 15-locus MIRU-VNTR showed high HGDI and could be used as a first-line genotyping method for epidemiological studies. Keywords: Mycobacterium tuberculosis, Genotyping, MIRU-VNTR, Tehran, Iran

  15. High bacterial diversity in epilithic biofilms of oligotrophic mountain lakes.

    Science.gov (United States)

    Bartrons, Mireia; Catalan, Jordi; Casamayor, Emilio O

    2012-11-01

    Benthic microbial biofilms attached to rocks (epilithic) are major sites of carbon cycling and can dominate ecosystem primary production in oligotrophic lakes. We studied the bacterial community composition of littoral epilithic biofilms in five connected oligotrophic high mountain lakes located at different altitudes by genetic fingerprinting and clone libraries of the 16S rRNA gene. Different intra-lake samples were analyzed, and consistent changes in community structure (chlorophyll a and organic matter contents, and bacterial community composition) were observed along the altitudinal gradient, particularly related with the location of the lake above or below the treeline. Epilithic biofilm genetic fingerprints were both more diverse among lakes than within lakes and significantly different between montane (below the tree line) and alpine lakes (above the tree line). The genetic richness in the epilithic biofilm was much higher than in the plankton of the same lacustrine area studied in previous works, with significantly idiosyncratic phylogenetic composition (specifically distinct from lake plankton or mountain soils). Data suggest the coexistence of aerobic, anaerobic, phototrophic, and chemotrophic microorganisms in the biofilm, Bacteroidetes and Cyanobacteria being the most important bacterial taxa, followed by Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Chlorobi, Planctomycetes, and Verrucomicrobia. The degree of novelty was especially high for epilithic Bacteroidetes, and up to 50 % of the sequences formed monophyletic clusters distantly related to any previously reported sequence. More than 35 % of the total sequences matched at <95 % identity to any previously reported 16S rRNA gene, indicating that alpine epilithic biofilms are unexplored habitats that contain a substantial degree of novelty within a short geographical distance. Further research is needed to determine whether these communities are involved in more biogeochemical pathways than

  16. Mapping the distribution of the denitrifier community at large scales (Invited)

    Science.gov (United States)

    Philippot, L.; Bru, D.; Ramette, A.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.

    2010-12-01

    Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distribution were analyzed by canonical variation partitioning. Our results indicate that 43% to 85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 740 km and used geostatistical modelling to generate predictive maps of the distribution of denitrifiers at the landscape scale. Studying the distribution of the denitrifiers at large scale can help closing the artificial gap between the investigation of microbial processes and microbial community ecology, therefore facilitating our understanding of the relationships between the ecology of denitrifiers and N-fluxes by denitrification.

  17. Analysis of denitrifier community in a bioaugmented sequencing batch reactor for the treatment of coking wastewater containing pyridine and quinoline

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Yaohui; Xing, Rui; Wen, Donghui; Tang, Xiaoyan [Peking Univ., Beijing (CN). Key Lab. of Water and Sediment Sciences (Ministry of Education); Sun, Qinghua [Peking Univ., Beijing (CN). Key Lab. of Water and Sediment Sciences (Ministry of Education); Chinese Center for Disease Control and Prevention, Beijing (China). Inst. of Environmental Health and Related Product Safety

    2011-05-15

    The denitrifier community and associated nitrate and nitrite reduction in the bioaugmented and general sequencing batch reactors (SBRs) during the treatment of coking wastewater containing pyridine and quinoline were investigated. The efficiency and stability of nitrate and nitrite reduction in SBR was considerably improved after inoculation with four pyridine- or quinoline-degrading bacterial strains (including three denitrifying strains). Terminal restriction fragment length polymorphism (T-RFLP) based on the nosZ gene revealed that the structures of the denitrifier communities in bioaugmented and non-bioaugmented reactors were distinct and varied during the course of the experiment. Bioaugmentation protected indigenous denitrifiers from disruptions caused by pyridine and quinoline. Clone library analysis showed that one of the added denitrifiers comprised approximately 6% of the denitrifier population in the bioaugmented sludge. (orig.)

  18. Sample-size dependence of diversity indices and the determination of sufficient sample size in a high-diversity deep-sea environment

    OpenAIRE

    Soetaert, K.; Heip, C.H.R.

    1990-01-01

    Diversity indices, although designed for comparative purposes, often cannot be used as such, due to their sample-size dependence. It is argued here that this dependence is more pronounced in high diversity than in low diversity assemblages and that indices more sensitive to rarer species require larger sample sizes to estimate diversity with reasonable precision than indices which put more weight on commoner species. This was tested for Hill's diversity number N sub(0) to N sub( proportional ...

  19. Microbial diversity of a high salinity oil field

    International Nuclear Information System (INIS)

    Neria, I.; Gales, G.; Alazard, D.; Ollivier, B.; Borgomano, J.; Joulian, C.

    2009-01-01

    This work is a preliminary study to investigate the microbial diversity of an onshore oil field. It aim to compare results obtained from molecular methods, physicochemical analyses and cultivation. A core of 1150 m depth sediments ( in situ T=45 degree centigrade) was collected and immediately frozen with liquid nitrogen prior to further investigation. Macroscopic and Scanning Electron Microscopy analyses were performed. (Author)

  20. Microsatellite genotyping reveals high genetic diversity but low ...

    African Journals Online (AJOL)

    JMwacharos

    2016-03-16

    Mar 16, 2016 ... diversity and (2) Investigate population structure and extent of admixture .... to estimate and partition genetic variation within and ... K between 1 and 40 and inferred its most optimal value ... populations of 0.84 ± 0.021 with the lowest mean in ..... on population stratification and the distribution of genetic.

  1. Effect of pH on the denitrifying enzyme activity in pasture soils in relation to the intrinsic differences in denitrifier communities

    Czech Academy of Sciences Publication Activity Database

    Čuhel, Jiří; Šimek, Miloslav

    2011-01-01

    Roč. 56, č. 3 (2011), s. 230-235 ISSN 0015-5632 R&D Projects: GA MŠk LC06066; GA AV ČR IAA600660605 Institutional research plan: CEZ:AV0Z60660521 Keywords : pH * denitrifying enzyme activity * pasture soils Subject RIV: EH - Ecology, Behaviour Impact factor: 0.677, year: 2011

  2. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    OpenAIRE

    Henrique Machado; Henrique Machado; Lone Gram

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

  3. Genes associated to lactose metabolism illustrate the high diversity of Carnobacterium maltaromaticum

    DEFF Research Database (Denmark)

    Iskandar, Christelle F.; Cailliez-Grimal, Catherine; Rahman, Abdur

    2016-01-01

    The dairy population of Carnobacterium maltaromaticum is characterized by a high diversity suggesting a high diversity of the genetic traits linked to the dairy process. As lactose is the main carbon source in milk, the genetics of lactose metabolism was investigated in this LAB. Comparative...

  4. Mechanisms of nitrous oxide (N2 O) formation and reduction in denitrifying biofilms.

    Science.gov (United States)

    Sabba, Fabrizio; Picioreanu, Cristian; Nerenberg, Robert

    2017-12-01

    Nitrous oxide (N 2 O) is a potent greenhouse gas that can be formed in wastewater treatment processes by ammonium oxidizing and denitrifying microorganisms. While N 2 O emissions from suspended growth systems have been extensively studied, and some recent studies have addressed emissions from nitrifying biofilms, much less is known about N 2 O emissions from denitrifying biofilm processes. This research used modeling to evaluate the mechanisms of N 2 O formation and reduction in denitrifying biofilms. The kinetic model included formation and consumption of key denitrification species, including nitrate (NO3-), nitrite (NO2-), nitric oxide (NO), and N 2 O. The model showed that, in presence of excess of electron donor, denitrifying biofilms have two distinct layers of activity: an outer layer where there is net production of N 2 O and an inner layer where there is net consumption. The presence of oxygen (O 2 ) had an important effect on N 2 O emission from suspended growth systems, but a smaller effect on biofilm systems. The effects of NO3- and O 2 differed significantly based on the biofilm thickness. Overall, the effects of biofilm thickness and bulk substrate concentrations on N 2 O emissions are complex and not always intuitive. A key mechanism for denitrifying biofilms is the diffusion of N 2 O and other intermediates from one zone of the biofilm to another. This leads to zones of N 2 O formation or consumption transformations that would not exist in suspended growth systems. © 2017 Wiley Periodicals, Inc.

  5. Benzene and ethylbenzene removal by denitrifying culture in a horizontal fixed bed anaerobic reactor

    Energy Technology Data Exchange (ETDEWEB)

    Gusmao, V.R.; Chinalia, F.A.; Sakamoto, I.K.; Varesche [Univ. de Sao Paulo (Brazil). Dept. de Hidraulica e Saneamento; Thiemann, O.H. [Univ. de Sao Paulo (Brazil). Inst. de Fisica de Sao Carlos

    2004-07-01

    Benzene, ethylbenzene, toluene, and xylene are toxic and are important constituents of gasoline and other petroleum fuels. These compounds are potential health hazards because of their high solubility and hence their ability to contaminate groundwater. Anaerobic immobilized biomass is a way of treating wastewater contaminated with the above compounds. The performance of a specially adapted biofilm is critical in the viability of this idea. In this investigation, an especially adapted biofilm was obtained using a denitrifying bacterial strain isolated from a slaughterhouse wastewater treatment plant. The strain was cultured in a liquid medium with added ethanol, nitrate, ethylbenzene, and benzene. To assess the viability of the strain for the purposes of degradation of ethylbenzene, and benzene two separate horizontal reactors were prepared with polyurethane foam in order to immobilize the biomass. Various concentrations of the two compounds were admitted. At high concentrations chemical oxygen demand decreased dramatically and benzene and ethylbenzene removal almost 100 per cent. DNA sequencing of the biofilm showed that Paracoccus versutus was the dominant species in the ethylbenzene reactor. 7 refs., 6 figs.

  6. Local endemicity and high diversity characterise high-latitude coral- Symbiodinium partnerships

    Science.gov (United States)

    Wicks, L. C.; Sampayo, E.; Gardner, J. P. A.; Davy, S. K.

    2010-12-01

    Obligate symbiotic dinoflagellates ( Symbiodinium) residing within the tissues of most reef invertebrates are important in determining the tolerance range of their host. Coral communities living at high latitudes experience wide fluctuations in environmental conditions and thus provide an ideal system to gain insights into the range within which the symbiotic relationship can be sustained. Further, understanding whether and how symbiont communities associated with high-latitude coral reefs are different from their tropical counterparts will provide clues to the potential of corals to cope with marginal or changing conditions. However, little is known of the host and symbiont partnerships at high latitudes. Symbiodinium diversity and specificity of high-latitude coral communities were explored using denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA at Lord Howe Island (31°S; Australia), and the Kermadec Islands (29°S; New Zealand). All but one host associated with clade C Symbiodinium, the exception being a soft coral ( Capnella sp.) that contained Symbiodinium B1. Besides ‘host-generalist’ Symbiodinium types C1 and C3, approximately 72% of the Symbiodinium identified were novel C types, and zonation of symbionts in relation to environmental parameters such as depth and turbidity was evident in certain host species. The high-latitude Symbiodinium communities showed little overlap and relatively high diversity compared with communities sampled on the tropical Great Barrier Reef. Although host specificity was maintained in certain species, others shared symbionts and this potential reduction of fidelity at high-latitude locations may be the result of locally challenging and highly variable environmental conditions.

  7. Use of vegetable oil in a pilot-scale denitrifying barrier

    Science.gov (United States)

    Hunter, William J.

    2001-12-01

    Nitrate in drinking water is a hazard to both humans and animals. Contaminated water can cause methemoglobinemia and may pose a cancer risk. Permeable barriers containing innocuous oils, which stimulate denitrification, can remove nitrate from flowing groundwater. For this study, a sand tank (1.1×2.0×0.085 m in size) containing sand was used as a one-dimensional open-top scale model of an aquifer. A meter-long area near the center of the tank contained sand coated with soybean oil. This region served as a permeable denitrifying barrier. Water containing 20 mg l -1 nitrate-N was pumped through the barrier at a high flow rate, 1112 l week -1, for 30 weeks. During the 30-week study, the barrier removed 39% of the total nitrate-N present in the water. The barrier was most efficient during the first 10 weeks of the study when almost all of the nitrate and nitrogen was removed. Efficiency declined with time so that by week 30 almost no nitrate was removed by the system. Nitrite levels in the effluent water remained low throughout the study. Barriers could be used to protect groundwater from nitrate contamination or for the in situ treatment of contaminated water. At the low flow rates that exist in most aquifers, such barriers should be effective at removing nitrate from groundwater for a much longer period of time.

  8. High diversity of fungi in air particulate matter.

    Science.gov (United States)

    Fröhlich-Nowoisky, Janine; Pickersgill, Daniel A; Després, Viviane R; Pöschl, Ulrich

    2009-08-04

    Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 microm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.

  9. High local genetic diversity of canine parvovirus from Ecuador.

    Science.gov (United States)

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers.

    Science.gov (United States)

    Tao, Rui; Wakelin, Steven A; Liang, Yongchao; Hu, Baowei; Chu, Guixin

    2018-01-15

    The effects of consecutive application of chemical fertilizer with or without organic fertilizer on soil N 2 O emissions and denitrifying community structure in a drip-irrigated field were determined. The four fertilizer treatments were (i) unfertilized, (ii) chemical fertilizer, (iii) 60% chemical fertilizer plus cattle manure, and (iv) 60% chemical fertilizer plus biofertilizer. The treatments with organic amendments (i.e. cattle manure and biofertilizer) reduced cumulative N 2 O emissions by 4.9-9.9%, reduced the N 2 O emission factor by 1.3-42%, and increased denitrifying enzyme activities by 14.3-56.2%. The nirK gene copy numbers were greatest in soil which received only chemical fertilizer. In contrast, nirS- and nosZ-copy numbers were greatest in soil amended with chemical fertilizer plus biofertilizer. Chemical fertilizer application with or without organic fertilizer significantly changed the community structure of nirK-type denitrifiers relative to the unfertilized soil. In comparison, the nirS- and nosZ-type denitrifier genotypes varied in treatments receiving organic fertilizer but not chemical fertilizer alone. The changes in the denitrifier communities were closely associated with soil organic carbon (SOC), NO 3 - , NH 4 + , water holding capacity, and soil pH. Modeling indicated that N 2 O emissions in this soil were primarily associated with the abundance of nirS type denitrifying bacteria, SOC, and NO 3 - . Overall, our findings indicate that (i) the organic fertilizers increased denitrifying enzyme activity, increased denitrifying-bacteria gene copy numbers, but reduced N 2 O emissions, and (ii) nirS- and nosZ-type denitrifiers were more sensitive than nirK-type denitrifiers to the organic fertilizers. Copyright © 2017. Published by Elsevier B.V.

  11. High recombination frequency creates genotypic diversity in colonies of the leaf-cutting ant Acromyrmex echinatior

    DEFF Research Database (Denmark)

    Sirviö, A.; Gadau, J.; Rueppell, O.

    2006-01-01

    Honeybees are known to have genetically diverse colonies because queens mate with many males and the recombination rate is extremely high. Genetic diversity among social insect workers has been hypothesized to improve general performance of large and complex colonies, but this idea has not been t...

  12. Gay Youth in American Public High Schools: Invisible Diversity.

    Science.gov (United States)

    Reed, Donald B.

    Gay youth enter high school with the knowledge that they are different and with the belief that heterosexuality is normal and that homosexuality is not normal. Also, gay youth enter high school with the belief that honesty and integrity are important personal values. Additionally, the gay youth enter high school without family knowledge of their…

  13. Relative Contribution of nirK- and nirS- Bacterial Denitrifiers as Well as Fungal Denitrifiers to Nitrous Oxide Production from Dairy Manure Compost.

    Science.gov (United States)

    Maeda, Koki; Toyoda, Sakae; Philippot, Laurent; Hattori, Shohei; Nakajima, Keiichi; Ito, Yumi; Yoshida, Naohiro

    2017-12-19

    The relative contribution of fungi, bacteria, and nirS and nirK denirifiers to nitrous oxide (N 2 O) emission with unknown isotopic signature from dairy manure compost was examined by selective inhibition techniques. Chloramphenicol (CHP), cycloheximide (CYH), and diethyl dithiocarbamate (DDTC) were used to suppress the activity of bacteria, fungi, and nirK-possessing denitrifiers, respectively. Produced N 2 O were surveyed to isotopocule analysis, and its 15 N site preference (SP) and δ 18 O values were compared. Bacteria, fungi, nirS, and nirK gene abundances were compared by qPCR. The results showed that N 2 O production was strongly inhibited by CHP addition in surface pile samples (82.2%) as well as in nitrite-amended core samples (98.4%), while CYH addition did not inhibit the N 2 O production. N 2 O with unknown isotopic signature (SP = 15.3-16.2‰), accompanied by δ 18 O (19.0-26.8‰) values which were close to bacterial denitrification, was also suppressed by CHP and DDTC addition (95.3%) indicating that nirK denitrifiers were responsible for this N 2 O production despite being less abundant than nirS denitrifiers. Altogether, our results suggest that bacteria are important for N 2 O production with different SP values both from compost surface and pile core. However, further work is required to decipher whether N 2 O with unknown isotopic signature is mostly due to nirK denitrifiers that are taxonomically different from the SP-characterized strains and therefore have different SP values rather than also being interwoven with the contribution of the NO-detoxifying pathway and/or of co-denitrification.

  14. Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition.

    Science.gov (United States)

    Lee, Jessica A; Francis, Christopher A

    2017-12-01

    Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd 1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Denitrification of groundwater using a sulfur-oxidizing autotrophic denitrifying anaerobic fluidized-bed MBR: performance and bacterial community structure.

    Science.gov (United States)

    Zhang, Lili; Zhang, Chao; Hu, Chengzhi; Liu, Huijuan; Qu, Jiuhui

    2015-03-01

    This paper investigates a novel sulfur-oxidizing autotrophic denitrifying anaerobic fluidized bed membrane bioreactor (AnFB-MBR) that has the potential to overcome the limitations of conventional sulfur-oxidizing autotrophic denitrification systems. The AnFB-MBR produced consistent high-quality product water when fed by a synthetic groundwater with NO3 (-)-N ranging 25-80 mg/L and operated at hydraulic retention times of 0.5-5.0 h. A nitrate removal rate of up to 4.0 g NO3 (-)-N/Lreactord was attained by the bioreactor, which exceeded any reported removal capacity. The flux of AnFB-MBR was maintained in the range of 1.5-15 L m(-2) h(-1). Successful membrane cleaning was practiced with cleaning cycles of 35-81 days, which had no obvious effect on the AnFB-MBR performance. The (15) N-tracer analyses elucidated that nitrogen was converted into (15) N2-N and (15) N-biomass accounting for 88.1-93.1 % and 6.4-11.6 % of the total nitrogen produced, respectively. Only 0.3-0.5 % of removed nitrogen was in form of (15)N2O-N in sulfur-oxidizing autotrophic denitrification process, reducing potential risks of a significant amount of N2O emissions. The sulfur-oxidizing autotrophic denitrifying bacterial consortium was composed mainly of bacteria from Proteobacteria, Chlorobi, and Chloroflexi phyla, with genera Thiobacillus, Sulfurimonas, and Ignavibacteriales dominating the consortium. The pyrosequencing assays also suggested that the stable microbial communities corresponded to the elevated performance of the AnFB-MBR. Overall, this research described relatively high nitrate removal, acceptable flux, indicating future potential for the technology in practice.

  16. Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1.

    Science.gov (United States)

    Putonti, Catherine; Polley, Nathaniel; Castignetti, Domenic

    2018-02-08

    Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant heterotrophic nitrifier-denitrifier capable of synthesizing nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC content of 64.8%. This draft assembly consists of 38 scaffolds. Copyright © 2018 Putonti et al.

  17. Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1

    OpenAIRE

    Putonti, Catherine; Polley, Nathaniel; Castignetti, Domenic

    2018-01-01

    ABSTRACT Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant heterotrophic nitrifier-denitrifier capable of synthesizing nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC content of 64.8%. This draft assembly consists of 38 scaffolds.

  18. nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary.

    Science.gov (United States)

    Lisa, Jessica A; Jayakumar, Amal; Ward, Bess B; Song, Bongkeun

    2017-12-01

    Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe 2+ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H 2 S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Distribution of baroduric, psychrotrophic and culturable nitrifying and denitrifying bacteria in the Central Indian Basin

    Digital Repository Service at National Institute of Oceanography (India)

    LokaBharathi, P.A.; PradeepRam, A.S.; Nair, S.; Nath, B.N.; Chandramohan, D.

    The abundance of baroduric, culturable nitrifying and denitrifying bacteria in the deep-sea cores of Central Indian Basin (CIB) at ca 5000 m depth was investigated. Analysis of 8 cores, sampled between 10 degrees 00 minutes S and 75 degrees 55...

  20. Microbial characterization of toluene-degrading denitrifying consortia obtained from terrestrial and marine ecosystems.

    Science.gov (United States)

    An, Y-J; Joo, Y-H; Hong, I-Y; Ryu, H-W; Cho, K-S

    2004-10-01

    The degradation characteristics of toluene coupled to nitrate reduction were investigated in enrichment culture and the microbial communities of toluene-degrading denitrifying consortia were characterized by denaturing gradient gel electrophoresis (DGGE) technique. Anaerobic nitrate-reducing bacteria were enriched from oil-contaminated soil samples collected from terrestrial (rice field) and marine (tidal flat) ecosystems. Enriched consortia degraded toluene in the presence of nitrate as a terminal electron acceptor. The degradation rate of toluene was affected by the initial substrate concentration and co-existence of other hydrocarbons. The types of toluene-degrading denitrifying consortia depended on the type of ecosystem. The clone RS-7 obtained from the enriched consortium of the rice field was most closely related to a toluene-degrading and denitrifying bacterium, Azoarcus denitrificians (A. tolulyticus sp. nov.). The clone TS-11 detected in the tidal flat enriched consortium was affiliated to Thauera sp. strain S2 (T. aminoaromatica sp. nov.) that was able to degrade toluene under denitrifying conditions. This indicates that environmental factors greatly influence microbial communities obtained from terrestrial (rice field) and marine (tidal flat) ecosystems.

  1. Plastic carrier polishing chamber reduces pollution swapping from denitrifying woodchip bioreactors

    Science.gov (United States)

    Denitrifying bioreactors with solid organic carbon sources (i.e., “woodchip bioreactors”) have proven to be relatively simple and cost effective treatment systems for nitrate-laden agricultural and aquacultural waters and wastewaters. However, because this technology is still relatively new, design ...

  2. Plastic biofilm carrier after corn cobs reduces nitrate loading in laboratory denitrifying bioreactors

    Science.gov (United States)

    Nitrate-nitrogen removal rates can be increased substantially in denitrifying bioreactors with a corn cob bed medium compared to woodchips; however, additional organic carbon (C) is released into the effluent. This laboratory column experiment was conducted to test the performance of a post-bed cha...

  3. Anaerobic degradation of long-chain alkylamines by a denitrifying Pseudomonas stutzeri

    NARCIS (Netherlands)

    Nguyen, P.D.; Ginkel, van C.G.; Plugge, C.M.

    2008-01-01

    The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. Strain ZN6 was isolated from a mixture of soil and active sludge and was identified as representing Pseudomonas stutzeri, based on partial 16S rRNA gene sequence

  4. Post-cold-storage conditioning time affects soil denitrifying enzyme activity

    DEFF Research Database (Denmark)

    Chirinda, Ngonidzashe; Olesen, Jørgen Eivind; Porter, John Roy

    2011-01-01

    Soil denitrifying enzyme activity (DEA) is often assessed after cold storage. Previous studies using the short-term acetylene inhibition method have not considered conditioning time (post-cold-storage warm-up time prior to soil analysis) as a factor influencing results. We observed fluctuations...

  5. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

    Science.gov (United States)

    Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

    2018-01-01

    Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms

  6. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances

    Directory of Open Access Journals (Sweden)

    Xingang Zhou

    2018-04-01

    Full Text Available Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA, nirS, and nirK genes. Results showed that 1–2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity (P < 0.05. Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile (P < 0.001. At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria, Planctomycetes, and Cyanobacteria, the first cropping of JA with Actinobacteria, the second cropping of JA with Acidobacteria, Armatimonadetes, Gemmatimonadetes, and Proteobacteria. At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO

  7. Transverse colon conduit urinary diversion in patients treated with very high dose pelvic irradiation

    International Nuclear Information System (INIS)

    Ravi, R.; Dewan, A.K.; Pandey, K.K.

    1994-01-01

    Urinary diversion may be required in patients receiving pelvic irradiation for gynaecological or genitourinary cancers either as part of a planned or salvage surgical procedure or for urological complications of irradiation. Records were reviewed for 30 such patients who underwent transverse colon conduit as a primary form of urinary diversion. Most of the conduits were constructed using refluxing ureterocolic anastomoses with stents. The results showed no operative mortality. Although the procedure was associated with a complication rate of 37% and a re-operation rate of 20%, there were no bowel or urinary anastomotic leaks. The operation could be safely performed on patients with renal failure, with 83% of such patients showing normal or improved serum creatinine levels post operatively. The advantages of transverse colon conduit urinary diversion are the use of non-irradiated bowel and ureters for diversion. It is recommended as a primary form of urinary diversion in these high risk cases. (Author)

  8. Community structures and activity of denitrifying microbes in a forested catchment in central Japan: survey using nitrite reductase genes

    Science.gov (United States)

    Ohte, N.; Aoki, M.; Katsuyama, C.; Suwa, Y.; Tange, T.

    2012-12-01

    To elucidate the mechanisms of denitrification processes in the forested catchment, microbial ecological approaches have been applied in an experimental watershed that has previously investigated its hydrological processes. The study catchment is located in the Chiba prefecture in central Japan under the temperate Asian monsoon climate. Potential activities of denitrification of soil samples were measured by incubation experiments under anoxic condition associated with Na15NO3 addition. Existence and variety of microbes having nitrite reductase genes were investigated by PCR amplification, cloning and sequencings of nirK and nirS fragments after DNA extraction. Contrary to our early expectation that the potential denitrification activity was higher at deeper soil horizon with consistent groundwater residence than that in the surface soil, denitrification potential was higher in shallower soil horizons than deeper soils. This suggested that the deficiency of NO3- as a respiratory substrate for denitrifier occurred in deeper soils especially in the summer. However, high denitrification activity and presence of microbes having nirK and nirS in surface soils usually under aerobic condition was explainable by the fact that the majority of denitrifying bacteria have been recognized as a facultative anaerobic bacterium. This also suggests the possibility of that denitrification occurs even in the surface soils if the wet condition is provided by rainwater during and after a storm event. Community structures of microbes having nirK were different between near surface and deeper soil horizons, and ones having nirS was different between saturated zone (under groundwater table) and unsaturated soil horizons. These imply that microbial communities with nisK are sensitive to the concentration of soil organic matters and ones with nirS is sensitive to soil moisture contents.

  9. Soil denitrifier community size changes with land use change to perennial bioenergy cropping systems

    Science.gov (United States)

    Thompson, Karen A.; Deen, Bill; Dunfield, Kari E.

    2016-10-01

    Dedicated biomass crops are required for future bioenergy production. However, the effects of large-scale land use change (LUC) from traditional annual crops, such as corn-soybean rotations to the perennial grasses (PGs) switchgrass and miscanthus, on soil microbial community functioning is largely unknown. Specifically, ecologically significant denitrifying communities, which regulate N2O production and consumption in soils, may respond differently to LUC due to differences in carbon (C) and nitrogen (N) inputs between crop types and management systems. Our objective was to quantify bacterial denitrifying gene abundances as influenced by corn-soybean crop production compared to PG biomass production. A field trial was established in 2008 at the Elora Research Station in Ontario, Canada (n  =  30), with miscanthus and switchgrass grown alongside corn-soybean rotations at different N rates (0 and 160 kg N ha-1) and biomass harvest dates within PG plots. Soil was collected on four dates from 2011 to 2012 and quantitative PCR was used to enumerate the total bacterial community (16S rRNA) and communities of bacterial denitrifiers by targeting nitrite reductase (nirS) and N2O reductase (nosZ) genes. Miscanthus produced significantly larger yields and supported larger nosZ denitrifying communities than corn-soybean rotations regardless of management, indicating large-scale LUC from corn-soybean to miscanthus may be suitable in variable Ontario climatic conditions and under varied management, while potentially mitigating soil N2O emissions. Harvesting switchgrass in the spring decreased yields in N-fertilized plots, but did not affect gene abundances. Standing miscanthus overwinter resulted in higher 16S rRNA and nirS gene copies than in fall-harvested crops. However, the size of the total (16S rRNA) and denitrifying bacterial communities changed differently over time and in response to LUC, indicating varying controls on these communities.

  10. The high diversity of arsenolipids in herring fillet (Clupea harengus).

    Science.gov (United States)

    Lischka, S; Arroyo-Abad, U; Mattusch, J; Kühn, A; Piechotta, Ch

    2013-06-15

    Arsenolipids represent a relevant step in the biosynthesis of organoarsenicals from inorganic arsenic compounds. Their fate after human consumption is still uncertain. By means of a HPLC-ICP-MS/ESI-Q-TOF-MS method, 16 lipid soluble arsenic compounds, including seven formerly unknown organoarsenicals, have been identified in commercial herring fillet. The structural assignment was done by exact mass and high resolution MS/MS data. This is the first identification of arsenolipids in herring (Clupea harengus). They contribute with (3.6±0.2) mg kg(-1) arsenic to 62.3% of the total arsenic content of (5.7±0.3) mg of arsenic per kg dry mass. Current studies indicate that a metabolization by humans to cancerous dimethylarsinic acid is very likely. The presented results are highly relevant as herring is a very popular food fish species in Europe. Moreover, the screening of different fish species revealed that arsenolipids are more widespread than previously assumed. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. High Schools, Race, and America's Future: What Students Can Teach Us about Morality, Diversity, and Community

    Science.gov (United States)

    Blum, Lawrence

    2012-01-01

    In "High Schools, Race, and America's Future", Lawrence Blum offers a lively account of a rigorous high school course on race and racism. Set in a racially, ethnically, and economically diverse high school, the book chronicles students' engagement with one another, with a rich and challenging academic curriculum, and with questions that relate…

  12. Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

    Science.gov (United States)

    Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

    2010-06-01

    Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

  13. High bat (Chiroptera) diversity in the Early Eocene of India

    Science.gov (United States)

    Smith, Thierry; Rana, Rajendra S.; Missiaen, Pieter; Rose, Kenneth D.; Sahni, Ashok; Singh, Hukam; Singh, Lachham

    2007-12-01

    The geographic origin of bats is still unknown, and fossils of earliest bats are rare and poorly diversified, with, maybe, the exception of Europe. The earliest bats are recorded from the Early Eocene of North America, Europe, North Africa and Australia where they seem to appear suddenly and simultaneously. Until now, the oldest record in Asia was from the Middle Eocene. In this paper, we report the discovery of the oldest bat fauna of Asia dating from the Early Eocene of the Cambay Formation at Vastan Lignite Mine in Western India. The fossil taxa are described on the basis of well-preserved fragments of dentaries and lower teeth. The fauna is highly diversified and is represented by seven species belonging to seven genera and at least four families. Two genera and five species are new. Three species exhibit very primitive dental characters, whereas four others indicate more advanced states. Unexpectedly, this fauna presents strong affinities with the European faunas from the French Paris Basin and the German Messel locality. This could result from the limited fossil record of bats in Asia, but could also suggest new palaeobiogeographic scenarios involving the relative position of India during the Early Eocene.

  14. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages

    NARCIS (Netherlands)

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-01-01

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth

  15. Co-occurrence of linguistic and biological diversity in biodiversity hotspots and high biodiversity wilderness areas.

    Science.gov (United States)

    Gorenflo, L J; Romaine, Suzanne; Mittermeier, Russell A; Walker-Painemilla, Kristen

    2012-05-22

    As the world grows less biologically diverse, it is becoming less linguistically and culturally diverse as well. Biologists estimate annual loss of species at 1,000 times or more greater than historic rates, and linguists predict that 50-90% of the world's languages will disappear by the end of this century. Prior studies indicate similarities in the geographic arrangement of biological and linguistic diversity, although conclusions have often been constrained by use of data with limited spatial precision. Here we use greatly improved datasets to explore the co-occurrence of linguistic and biological diversity in regions containing many of the Earth's remaining species: biodiversity hotspots and high biodiversity wilderness areas. Results indicate that these regions often contain considerable linguistic diversity, accounting for 70% of all languages on Earth. Moreover, the languages involved are frequently unique (endemic) to particular regions, with many facing extinction. Likely reasons for co-occurrence of linguistic and biological diversity are complex and appear to vary among localities, although strong geographic concordance between biological and linguistic diversity in many areas argues for some form of functional connection. Languages in high biodiversity regions also often co-occur with one or more specific conservation priorities, here defined as endangered species and protected areas, marking particular localities important for maintaining both forms of diversity. The results reported in this article provide a starting point for focused research exploring the relationship between biological and linguistic-cultural diversity, and for developing integrated strategies designed to conserve species and languages in regions rich in both.

  16. Co-composting of municipal solid waste mixed with matured sewage sludge: The relationship between N2O emissions and denitrifying gene abundance.

    Science.gov (United States)

    Bian, Rongxing; Sun, Yingjie; Li, Weihua; Ma, Qiang; Chai, Xiaoli

    2017-12-01

    Aerobic composting is an alternative measure to the disposal of municipal solid waste (MSW). However, it produces nitrous oxide (N 2 O), a highly potent greenhouse via microbial nitrification and denitrification. In this study, the effects of matured sewage sludge (MSS) amendment on N 2 O emissions and the inter-relationships between N 2 O emissions and the abundance of denitrifying bacteria were investigated during aerobic composting of MSW. The results demonstrated that MSW composting with MSS amendments (C1, and C2, with a MSW to MSS ratio of 2:1 and 4:1, (v/v), respectively) significantly increased N 2 O emissions during the initial stage, yet contributed to the mitigation of N 2 O emissions during the cooling and maturation stage. MSS amended composting emitted a total of 18.4%-25.7% less N 2 O than the control treatment without MSS amendment (CK). Matured sewage sludge amendment also significantly altered the abundance of denitrifying bacteria. The quantification of denitrifying functional genes revealed that the N 2 O emission rate had a significant positive correlation with the abundance of the nirS, nirK genes in both treatments with MSS amendment. The nosZ/(nirS + nirK) ratio could be a good indicator for predicting N 2 O emissions. The higher N 2 O emission rate during the initial stage of composting mixed with MSS was characterized by lower nosZ/(nirS + nirK) ratios, compared to CK treatment. Higher ratios of nosZ/(nirS + nirK) were measured during the cooling and maturation stage in treatments with MSS which resulted in a reduction of the N 2 O emissions. These results demonstrated that MSS amendment could be a valid strategy for mitigating N 2 O emissions during MSW composting. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. High-technology exports of EEC countries: Persistence and diversity of specialization patterns

    International Nuclear Information System (INIS)

    Papagni, E.

    1992-01-01

    This analysis of the persistence and diversity of specialization patterns in EEC high technology exports is based on a package of products selected from the Eurostat database, COMEXT. High technology goods are considered as an innovative output indicator. A test of hypotheses of hysteresis and diversity of trade patterns at a national level is performed to verify some claims made by the 'evolutionary' theory of innovation and trade. The three-mode principal component analysis carried out confirms the persistence of specialization patterns of each EEC country in high technology exports, and highlights their sharp differences

  18. Microbial Species and Functional Diversity in Rice Rhizosphere of High-yield Special Ecological Areas

    Directory of Open Access Journals (Sweden)

    PAN Li-yuan

    2016-11-01

    Full Text Available Taoyuan, Yunnan Province is a special eco-site which keeps the highest yield records of rice cultivation in small planting areas. Soil microbial species and functional diversity were evaluated using cultivation method and BIOLOG ecoplates. The results showed that the microbial community of the high yield region was more abundant, and the total microbial population was 2 times of the control, furthermore, the areas belonged to the healthy "bacteria" soil, which was showed as bacteria > actinomycetes > fungi. Bacteria were the dominant populations in the rhizosphere of high yielding rice field, and the yield formation of rice was not correlated with the depth of soil layers. In order to obtain more species diversity information, Shannon diversity index H, Shannon evenness index E and Simpson index D were analyzed, and the results showed that microbial community diversity and evenness were not the main differences between the high and general yield areas. Then, the functional diversity of soil microbial community was investigated through the average well color development(AWCD and diversity index analyses. The results of AWCD analysis indicated that the metabolic activity of soil microbial community in high yield paddy soils were stronger than the control. Moreover, the difference range from large to small showed as tillering stage > harvest period > seedling period > rotation period, the stronger the rice growth, the greater the difference between the high yield region and the control. At tillering stage and harvest stage, due to the vigorous plant growth, the root exudates were rich, and the microbial communities of high yield paddy soils showed a strong metabolic activity and strong ability to use carbon sources. The results of Shannon, Simpson and McIntosh indices analysis indicated that common microbial species was not a key factor affecting the yield of rice. Tillering stage was a key period for the growth of high yield rice, and many

  19. Seasonal variations of nitrate reducing and denitrifying bacteria utilizing hexadecane in Mandovi estuary, Goa, West Coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Sousa, T.D.; Ingole, B.; Sousa, S.D.; Bhosle, S.

    > cfu/ml on minimal media containing hexadecane as the sole carbon source. Highest bacterial counts were obtained during the monsoons. 22% of bacteria capable of hexadecane utilization were nitrate reducing and 12% were denitrifying. 29...

  20. RELATIONSHIP BETWEEN THE CONCENTRATION OF DENITRIFIERS AND PSEUDOMONAS SPP. IN SOILS: IMPLICATIONS FOR BTX BIOREMEDIATION (R823420)

    Science.gov (United States)

    Aquifer microcosms were used to investigate the effect of stimulating denitrification on microbial population shifts and BTX degradation potential. Selective pressurefor facultative denitrifiers was applied to a treatment set by feeding acetate and nitrate, and cycling electr...

  1. Reactor staging influences microbial community composition and diversity of denitrifying MBBRs- Implications on pharmaceutical removal

    DEFF Research Database (Denmark)

    Torresi, Elena; Gülay, Arda; Polesel, Fabio

    2018-01-01

    The subdivision of biofilm reactor in two or more stages (i.e., reactor staging) represents an option for process optimisation of biological treatment. In our previous work, we showed that the gradient of influent organic substrate availability (induced by the staging) can influence the microbial...

  2. Awareness of Consequence of High School Students on Loss of Bio-Diversity

    Science.gov (United States)

    Kasot, Nazim; Özbas, Serap

    2015-01-01

    The aim of this study is to assess the egoistic, altruistic and biospheric awareness of the consequence of high school students regarding the loss of bio-diversity, then comparing the results on the basis of some independent variables (gender, class and family income). The research data were collected from 884 ninth and tenth grade high school…

  3. Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process.

    Science.gov (United States)

    Fu, Liang; Ding, Jing; Lu, Yong-Ze; Ding, Zhao-Wei; Zeng, Raymond J

    2017-05-01

    The co-culture system of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) has a potential application in wastewater treatment plant. This study explored the effects of permutation and combination of nitrate, nitrite, and ammonium on the culture enrichment from freshwater sediments. The co-existence of NO 3 - , NO 2 - , and NH 4 + shortened the enrichment time from 75 to 30 days and achieved a total nitrogen removal rate of 106.5 mg/L/day on day 132. Even though ammonium addition led to Anammox bacteria increase and a higher nitrogen removal rate, DAMO bacteria still dominated in different reactors with the highest proportion of 64.7% and the maximum abundance was 3.07 ± 0.25 × 10 8 copies/L (increased by five orders of magnitude) in the nitrite reactor. DAMO bacteria showed greater diversity in the nitrate reactor, and one was similar to M. oxyfera; DAMO bacteria in the nitrite reactor were relatively unified and similar to M. sinica. Interestingly, no DAMO archaea were found in the nitrate reactor. This study will improve the understanding of the impact of nitrogen source on DAMO and Anammox co-culture enrichment.

  4. Plathelminth abundance in North Sea salt marshes: environmental instability causes high diversity

    Science.gov (United States)

    Armonies, Werner

    1986-09-01

    Although supralittoral salt marshes are habitats of high environmental instability, the meiofauna is rich in species and abundance is high. The community structure of free-living Plathelminthes (Turbellaria) in these salt marshes is described. On an average, 104 individuals are found below an area of 10 cm2. The average species density in ungrazed salt marshes is 11.3 below 10 cm2 and 45.2 below 100 cm2, indicating strong small-scale heterogenity. The faunal similarity between sediment and the corresponding above-ground vegetation is higher than between adjacent sample sites. Species prefer distinct ranges of salinity. In the lower part of the supralittoral salt marshes, the annual fluctuations of salinity are strongest and highly unpredictable. This region is richest in plathelminth species and abundance; diversity is highest, and the faunal composition of parallel samples is quite similar. In the upper part of the supralittoral salt marshes, the annual variability of salinity is lower, plathelminths are poor in species diversity and abundance. Parallel samples often have no species in common. Thus, those salt marsh regions with the most unstable environment are inhabited by the most diverse species assemblage. Compared to other littoral zones of the North Sea, however, plathelminth diversity in salt marshes is low. The observed plathelminth diversity pattern can apparently be explained by the “dynamic equilibrium model” (Huston, 1979).

  5. Relative rates of nitric oxide and nitrous oxide production by nitrifiers, denitrifiers, and nitrate respirers

    Science.gov (United States)

    Anderson, I. C.; Levine, J. S.

    1986-01-01

    An account is given of the atmospheric chemical and photochemical effects of biogenic nitric and nitrous oxide emissions. The magnitude of the biogenic emission of NO is noted to remain uncertain. Possible soil sources of NO and N2O encompass nitrification by autotropic and heterotropic nitrifiers, denitrification by nitrifiers and denitrifiers, nitrate respiration by fermenters, and chemodenitrification. Oxygen availability is the primary determinant of these organisms' relative rates of activity. The characteristics of this major influence are presently investigated in light of the effect of oxygen partial pressure on NO and N2O production by a wide variety of common soil-nitrifying, denitrifying, and nitrate-respiring bacteria under laboratory conditions. The results obtained indicate that aerobic soils are primary sources only when there is sufficient moisture to furnish anaerobic microsites for denitrification.

  6. Diversity and social cohesion : the case of Jane-Finch, a highly diverse lower-income Toronto neighbourhood

    NARCIS (Netherlands)

    Ahmadi, D.

    2017-01-01

    Diversity has increasingly emerged as the core focus of many studies concerning factors impacting on social cohesion. Various scholars have concluded that diversity is detrimental to cohesion. Most of this research, however, draws generalisations based upon quantitative data and fails to account

  7. Highly enriched Betaproteobacteria growing anaerobically with p-xylene and nitrate

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Probian, Christina; Wilkes, Heinz

    2010-01-01

    The identity of the microorganisms capable of anaerobic p-xylene degradation under denitrifying conditions is hitherto unknown. Here, we report highly enriched cultures of freshwater denitrifying bacteria that grow anaerobically with p-xylene as the sole organic carbon source and electron donor. ...

  8. Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

    Science.gov (United States)

    Coelho, G R C; Brondani, C; Hoffmann, L V; Valdisser, P A M R; Borba, T C O; Mendonça, J A; Rodrigues, L A; de Menezes, I P P

    2017-09-21

    The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

  9. Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.

    Science.gov (United States)

    Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Menna, Pâmela; Bangel, Eliane Villamil; Hungria, Mariangela

    2012-04-01

    Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.

  10. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    Science.gov (United States)

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

  11. Anaerobic oxidation of 2-chloroethanol under denitrifying conditions by Pseudomonas stutzeri strain JJ.

    Science.gov (United States)

    Dijk, J A; Stams, A J M; Schraa, G; Ballerstedt, H; de Bont, J A M; Gerritse, J

    2003-11-01

    A bacterium that uses 2-chloroethanol as sole energy and carbon source coupled to denitrification was isolated from 1,2-dichloroethane-contaminated soil. Its 16 S rDNA sequence showed 98% similarity with the type strain of Pseudomonas stutzeri (DSM 5190) and the isolate was tentatively identified as Pseudomonas stutzeri strain JJ. Strain JJ oxidized 2-chloroethanol completely to CO(2) with NO(3)(- )or O(2) as electron acceptor, with a preference for O(2) if supplied in combination. Optimum growth on 2-chloroethanol with nitrate occurred at 30 degrees C with a mu(max) of 0.14 h(-1) and a yield of 4.4 g protein per mol 2-chloroethanol metabolized. Under aerobic conditions, the mu(max) was 0.31 h(-1). NO(2)(-) also served as electron acceptor, but reduction of Fe(OH)(3), MnO(2), SO(4)(2-), fumarate or ClO(3)(-) was not observed. Another chlorinated compound used as sole energy and carbon source under aerobic and denitrifying conditions was chloroacetate. Various different bacterial strains, including some closely related Pseudomonas stutzeri strains, were tested for their ability to grow on 2-chloroethanol as sole energy and carbon source under aerobic and denitrifying conditions, respectively. Only three strains, Pseudomonas stutzeri strain LMD 76.42, Pseudomonas putida US2 and Xanthobacter autotrophicus GJ10, grew aerobically on 2-chloroethanol. This is the first report of oxidation of 2-chloroethanol under denitrifying conditions by a pure bacterial culture.

  12. Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

    Science.gov (United States)

    Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

    2013-01-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  13. Bioavailability and biodegradation of weathered diesel fuel in aquifer material under denitrifying conditions

    International Nuclear Information System (INIS)

    Bregnard, T.P.A.; Hoehener, P.; Zeyer, J.

    1998-01-01

    During the in situ bioremediation of a diesel fuel-contaminated aquifer in Menziken, Switzerland, aquifer material containing weathered diesel fuel (WDF) and indigenous microorganisms was excavated. This material was used to identify factors limiting WDF biodegradation under denitrifying conditions. Incubations of this material for 360 to 390 d under denitrifying conditions resulted in degradation of 23% of the WDF with concomitant consumption of NO 3 - and production of inorganic carbon. The biodegradation of WDF and the rate of NO 3 - consumption was stimulated by agitation of the microcosms. Biodegradation was not stimulated by the addition of a biosurfactant (rhamnolipids) or a synthetic surfactant (Triton X-100) at concentrations above their critical micelle concentrations. The rhamnolipids were biodegraded preferentially to WDF, whereas Triton X-100 was not degraded. Both surfactants reduced the surface tension of the growth medium from 72 to <35 dynes/cm and enhanced the apparent aqueous solubility of the model hydrocarbon n-hexadecane by four orders of magnitude. Solvent-extracted WDF, added at a concentration equal to that already present in the aquifer material, was also biodegraded by the microcosms, but not at a higher rate than the WDF already present in the material. The results show that the denitrifying biodegradation of WDF is not necessarily limited by bioavailability but rather by the inherent recalcitrance of WDF

  14. Characterization of bacterial consortia capable of degrading 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions.

    Science.gov (United States)

    Song, Bongkeun; Kerkhof, Lee J; Häggblom, Max M

    2002-08-06

    4-Chlorobenzoate and 4-bromobenzoate were readily degraded in denitrifying enrichment cultures established with river sediment, estuarine sediment or agricultural soil as inoculum. Stable denitrifying consortia were obtained and maintained by serial dilution and repeated feeding of substrates. Microbial community analyses were performed to characterize the 4-chlorobenzoate and 4-bromobenzoate degrading consortia with terminal restriction fragment length polymorphism (T-RFLP) and cloning of 16S rRNA genes from the cultures. Interestingly, two major terminal restriction fragments (T-RFs) in the 4-chlorobenzoate degrading consortia and one T-RF in the 4-bromobenzoate utilizing consortium were observed from T-RFLP analysis regardless of their geographical and ecological origins. The two T-RFs (clones 4CB1 and 4CB2) in 4-chlorobenzoate degrading consortia were identified as members of the beta-subunit of the Proteobacteria on the basis of 16S rRNA sequencing analysis. Phylogenetic analysis of 16S rRNA genes showed that clone 4CB1 was closely related to Thauera aromatica while clone 4CB2 was distantly related to the genera Limnobacter and Ralstonia. The 4-bromobenzoate utilizing consortium mainly consisted of one T-RF, which was identical to clone 4CB2 in spite of different enrichment substrate. This suggests that degradation of 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions was mediated by bacteria belonging to the beta-subunit of the Proteobacteria.

  15. Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates.

    Science.gov (United States)

    Henry, S; Texier, S; Hallet, S; Bru, D; Dambreville, C; Chèneby, D; Bizouard, F; Germon, J C; Philippot, L

    2008-11-01

    To determine to which extent root-derived carbon contributes to the effects of plants on nitrate reducers and denitrifiers, four solutions containing different proportions of sugar, organic acids and amino acids mimicking maize root exudates were added daily to soil microcosms at a concentration of 150 microg C g(-1) of soil. Water-amended soils were used as controls. After 1 month, the size and structure of the nitrate reducer and denitrifier communities were analysed using the narG and napA, and the nirK, nirS and nosZ genes as molecular markers respectively. Addition of artificial root exudates (ARE) did not strongly affect the structure or the density of nitrate reducer and denitrifier communities whereas potential nitrate reductase and denitrification activities were stimulated by the addition of root exudates. An effect of ARE composition was also observed on N(2)O production with an N(2)O:(N(2)O + N(2)) ratio of 0.3 in microcosms amended with ARE containing 80% of sugar and of 1 in microcosms amended with ARE containing 40% of sugar. Our study indicated that ARE stimulated nitrate reduction or denitrification activity with increases in the range of those observed with the whole plant. Furthermore, we demonstrated that the composition of the ARE affected the nature of the end-product of denitrification and could thus have a putative impact on greenhouse gas emissions.

  16. High genetic diversity in the coat protein and 3' untranslated regions

    Indian Academy of Sciences (India)

    The 3′ terminal region consisting of the coat protein (CP) coding sequence and 3′ untranslated region (3′UTR) was cloned and sequenced from seven isolates. Sequence comparisons revealed considerable genetic diversity among the isolates in their CP and 3′UTR, making CdMV one of the highly variable members ...

  17. Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)

    Science.gov (United States)

    Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

  18. iPad Deployment in a Diverse Urban High School: A Formative Experiment

    Science.gov (United States)

    Frey, Nancy; Fisher, Douglas; Lapp, Diane

    2015-01-01

    We explore the use of iPads in a diverse urban high school and the ways in which teachers and students were supported to integrate these tools into their instruction. We provided 4 English teachers with 20 iPads with little or no professional development about how to integrate them into their instruction. Using a formative experiment design, we…

  19. Individuals and the variation needed for high species diversity in forest trees

    Science.gov (United States)

    James S. Clark

    2010-01-01

    In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for...

  20. Disclosure Experiences of Urban, Ethnically Diverse LGBT High School Students: Implications for School Personnel

    Science.gov (United States)

    Varjas, Kris; Kiperman, Sarah; Meyers, Joel

    2016-01-01

    Disclosure of sexual orientation and/or gender identity is a milestone event for lesbian, gay, bisexual, or transgender (LGBT) youth and can have both positive and negative mental health consequences. Twenty-nine urban, ethnically diverse LGBT high school students participated in face-to-face, in-depth interviews. Qualitative results revealed two…

  1. High-demand jobs: age-related diversity in work ability?

    NARCIS (Netherlands)

    Sluiter, Judith K.

    2006-01-01

    High-demand jobs include 'specific' job demands that are not preventable with state of the art ergonomics knowledge and may overburden the bodily capacities, safety or health of workers. An interesting question is whether the age of the worker is an important factor in explanations of diversity in

  2. Some like it high! Phylogenetic diversity of high-elevation cyanobacterial community from biological soil crusts of Western Himalaya.

    Czech Academy of Sciences Publication Activity Database

    Čapková, K.; Hauer, T.; Řeháková, Klára; Doležal, J.

    2016-01-01

    Roč. 71, č. 1 (2016), s. 113-123 ISSN 0095-3628 Institutional support: RVO:60077344 Keywords : soil crusts * cyanobacterial diversity * Western Himalayas * high-elevation * desert * phosphorus Subject RIV: EH - Ecology, Behaviour Impact factor: 3.630, year: 2016

  3. High and distinct range-edge genetic diversity despite local bottlenecks.

    Directory of Open Access Journals (Sweden)

    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  4. Plant diversity on high elevation islands – drivers of species richness and endemism

    Directory of Open Access Journals (Sweden)

    Severin D.H. Irl

    2016-10-01

    Full Text Available High elevation islands elicit fascination because of their large array of endemic species and strong environmental gradients. First, I define a high elevation island according to geographic and environmental characteristics. Then, within this high elevation island framework, I address local disturbance effects on plant distribution, drivers of diversity and endemism on the island scale, and global patterns of treeline elevation and climate change. Locally, introduced herbivores have strong negative effects on the summit scrub of my model island La Palma (Canary Islands, while roads have unexpected positive effects on endemics. On the island scale, topography and climate drive diversity and endemism. Hotspots of endemicity are found in summit regions – a general pattern on high elevation islands. The global pattern of treeline elevation behaves quite differently on islands than on the mainland. A thorough literature review and climate projections suggest that climate change will profoundly affect oceanic island floras.

  5. Composition and diversity of High Andean in the Fauna Production Reserve Chimborazo, Ecuador

    Directory of Open Access Journals (Sweden)

    Jorge Caranqui

    2016-03-01

    Full Text Available The present study inquire the floristic diversity of 9 sampling in four plots of 1 m² of high andean in several locations in the “Reserva de Producción de Fauna Chimborazo”. For the development of this study, we used an adaptation of the method of plots “Gloria”. With coverage (% in each of the plots, Further the diversity indices and similarity with respective analysis were obtained. The data obtained reflect a diversity that can range from medium to low, believe that this is due to anthropogenic activities that have taken place in these ecosistems. With the presence mostly Calamagrostis intermedia, it could establish that the type of vegetation is herbaceous in high andean is higher percentage; is the species that is almost always present in most types of vegetation of the RPF Chimborazo and high dominance that influences the results of low floristic diversity indices was found in the analysis. As a result the most abundant family Asteraceae is well Poaceae.

  6. High endemism and stem density distinguish New Caledonian from other high-diversity rainforests in the Southwest Pacific.

    Science.gov (United States)

    Ibanez, Thomas; Blanchard, E; Hequet, V; Keppel, G; Laidlaw, M; Pouteau, R; Vandrot, H; Birnbaum, P

    2018-01-25

    The biodiversity hotspot of New Caledonia is globally renowned for the diversity and endemism of its flora. New Caledonia's tropical rainforests have been reported to have higher stem densities, higher concentrations of relictual lineages and higher endemism than other rainforests. This study investigates whether these aspects differ in New Caledonian rainforests compared to other high-diversity rainforests in the Southwest Pacific. Plants (with a diameter at breast height ≥10 cm) were surveyed in nine 1-ha rainforest plots across the main island of New Caledonia and compared with 14 1-ha plots in high-diversity rainforests of the Southwest Pacific (in Australia, Fiji, Papua New Guinea and the Solomon Islands). This facilitated a comparison of stem densities, taxonomic composition and diversity, and species turnover among plots and countries. The study inventoried 11 280 stems belonging to 335 species (93 species ha-1 on average) in New Caledonia. In comparison with other rainforests in the Southwest Pacific, New Caledonian rainforests exhibited higher stem density (1253 stems ha-1 on average) including abundant palms and tree ferns, with the high abundance of the latter being unparalleled outside New Caledonia. In all plots, the density of relictual species was ≥10 % for both stems and species, with no discernible differences among countries. Species endemism, reaching 89 % on average, was significantly higher in New Caledonia. Overall, species turnover increased with geographical distance, but not among New Caledonian plots. High stem density, high endemism and a high abundance of tree ferns with stem diameters ≥10 cm are therefore unique characteristics of New Caledonian rainforests. High endemism and high spatial species turnover imply that the current system consisting of a few protected areas is inadequate, and that the spatial distribution of plant species needs to be considered to adequately protect the exceptional flora of New Caledonian rainforests

  7. Microbial Diversity and Characteristics in Anaerobic Environments in KURT Groundwater

    International Nuclear Information System (INIS)

    Roh, Yul; Oh, Jong Min; Rhee, Sung Keun; Yong, Jong Joong

    2008-03-01

    The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxide, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

  8. Microbial Diversity in KURT Groundwater and Biomineralization Characteristics

    International Nuclear Information System (INIS)

    Roh, Yul; Rhee, Sung Keun; Oh, Jong Min; Park, Byung Jun

    2009-03-01

    The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxides, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

  9. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  10. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    Directory of Open Access Journals (Sweden)

    Annika M E Noreen

    Full Text Available Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter, 193 saplings (>1 yr, and 1,822 seedlings (<1 yr of the canopy tree Koompassia malaccensis (Fabaceae. We tested hypotheses relevant to the genetic consequences of habitat loss: (1 that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2 K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854, high allelic richness (R = 16.7-19.5, low inbreeding co-efficients (FIS = 0.013-0.076, and a large proportion (30.1% of rare alleles (i.e. frequency <1%. However, spatial genetic structure (SGS analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961, calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  11. Genetic diversity of dispersed seeds is highly variable among leks of the long-wattled umbrellabird

    Science.gov (United States)

    Ottewell, Kym; Browne, Luke; Cabrera, Domingo; Olivo, Jorge; Karubian, Jordan

    2018-01-01

    Frugivorous animals frequently generate clumped distributions of seeds away from source trees, but genetic consequences of this phenomenon remain poorly resolved. Seed dispersal of the palm Oenocarpus bataua by long-wattled umbrellabirds Cephalopterus penduliger generates high seed densities in leks (i.e., multi-male display sites), providing a suitable venue to investigate how dispersal by this frugivore may influence seed source diversity and genetic structure at local and landscape levels. We found moderate levels of maternal seed source diversity in primary seed rain across five leks in northwest Ecuador (unweighted mean alpha diversity α = 9.52, weighted mean αr = 3.52), with considerable variation among leks (αr range: 1.81-24.55). Qualitatively similar findings were obtained for allelic diversity and heterozygosity. Higher densities of O. bataua adults around leks were associated with higher values of αr and heterozygosity (non-significant trends) and allelic diversity (significant correlation). Seed source overlap between different leks was not common but did occur at low frequency, providing evidence for long-distance seed dispersal by umbrellabirds into leks. Our findings are consistent with the idea that seed pool diversity within leks may be shaped by the interaction between density of local trees, which can vary considerably between leks, and umbrellabird foraging ecology, particularly a lack of territorial defense of fruiting trees. Taken as a whole, this work adds to our growing appreciation of the ways resource distribution and associated frugivore foraging behaviors mechanistically shape seed dispersal outcomes and the distribution of plant genotypes across the landscape.

  12. Unexpected high diversity of galling insects in the Amazonian upper canopy: the savanna out there.

    Science.gov (United States)

    Julião, Genimar R; Venticinque, Eduardo M; Fernandes, G Wilson; Price, Peter W

    2014-01-01

    A relatively large number of studies reassert the strong relationship between galling insect diversity and extreme hydric and thermal status in some habitats, and an overall pattern of a greater number of galling species in the understory of scleromorphic vegetation. We compared galling insect diversity in the forest canopy and its relationship with tree richness among upland terra firme, várzea, and igapó floodplains in Amazonia, Brazil. The soils of these forest types have highly different hydric and nutritional status. Overall, we examined the upper layer of 1,091 tree crowns. Galling species richness and abundance were higher in terra firme forests compared to várzea and igapó forests. GLM-ANCOVA models revealed that the number of tree species sampled in each forest type was determinant in the gall-forming insect diversity. The ratio between galling insect richness and number of tree species sampled (GIR/TSS ratio) was higher in the terra firme forest and in seasonally flooded igapó, while the várzea presented the lowest GIR/TSS ratio. In this study, we recorded unprecedented values of galling species diversity and abundance per sampling point. The GIR/TSS ratio from várzea was approximately 2.5 times higher than the highest value of this ratio ever reported in the literature. Based on this fact, we ascertained that várzea and igapó floodplain forests (with lower GIA and GIR), together with the speciose terra firme galling community emerge as the gall diversity apex landscape among all biogeographic regions already investigated. Contrary to expectation, our results also support the "harsh environment hypothesis", and unveil the Amazonian upper canopy as similar to Mediterranean vegetation habitats, hygrothermically stressed environments with leaf temperature at lethal limits and high levels of leaf sclerophylly.

  13. Unexpected high diversity of galling insects in the Amazonian upper canopy: the savanna out there.

    Directory of Open Access Journals (Sweden)

    Genimar R Julião

    Full Text Available A relatively large number of studies reassert the strong relationship between galling insect diversity and extreme hydric and thermal status in some habitats, and an overall pattern of a greater number of galling species in the understory of scleromorphic vegetation. We compared galling insect diversity in the forest canopy and its relationship with tree richness among upland terra firme, várzea, and igapó floodplains in Amazonia, Brazil. The soils of these forest types have highly different hydric and nutritional status. Overall, we examined the upper layer of 1,091 tree crowns. Galling species richness and abundance were higher in terra firme forests compared to várzea and igapó forests. GLM-ANCOVA models revealed that the number of tree species sampled in each forest type was determinant in the gall-forming insect diversity. The ratio between galling insect richness and number of tree species sampled (GIR/TSS ratio was higher in the terra firme forest and in seasonally flooded igapó, while the várzea presented the lowest GIR/TSS ratio. In this study, we recorded unprecedented values of galling species diversity and abundance per sampling point. The GIR/TSS ratio from várzea was approximately 2.5 times higher than the highest value of this ratio ever reported in the literature. Based on this fact, we ascertained that várzea and igapó floodplain forests (with lower GIA and GIR, together with the speciose terra firme galling community emerge as the gall diversity apex landscape among all biogeographic regions already investigated. Contrary to expectation, our results also support the "harsh environment hypothesis", and unveil the Amazonian upper canopy as similar to Mediterranean vegetation habitats, hygrothermically stressed environments with leaf temperature at lethal limits and high levels of leaf sclerophylly.

  14. Simultaneous enrichment of denitrifying anaerobic methane-oxidizing microorganisms and anammox bacteria in a hollow-fiber membrane biofilm reactor.

    Science.gov (United States)

    Ding, Zhao-Wei; Lu, Yong-Ze; Fu, Liang; Ding, Jing; Zeng, Raymond J

    2017-01-01

    In this study, the coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes and anaerobic ammonium oxidation (anammox) bacteria was successfully enriched in a hollow-fiber membrane biofilm reactor (HfMBR) using freshwater sediment as the inoculum. The maximal removal rates of nitrate and ammonium were 78 mg N/L/day (131 mg N/m 2 /day) and 26 mg N/L/day (43 mg N/m 2 /day), respectively. Due to the high rate of methane mass transfer in HfMBR, the activity of DAMO archaea continued to increase during the enrichment period, indicating that HfMBR could be a powerful tool to enrich DAMO microorganisms. Effects of partial methane pressure, temperature, and pH on the cocultures were obvious. However, the microbial activity in HfMBR could be recovered quickly after the shock change of environmental factors. Furthermore, the result also found that DAMO bacteria likely had a stronger competitive advantage than anammox bacteria under the operating conditions in this study. High-throughput sequencing 16S rRNA genes illustrated that the dominant microbes were NC10, Euryarchaeota, Proteobacteria, Planctomycetes, and Chlorobi with relative abundance of 38.8, 26.2, 13.78, 6.2, and 3.6 %, respectively.

  15. High shrew diversity on Alaska's Seward Peninsula: Community assembly and environmental change

    Science.gov (United States)

    Hope, Andrew G.

    2012-01-01

    In September 2010, 6 species of shrews (genus: Sorex) were collected at a single locality on the Seward Peninsula of Alaska. Such high sympatric diversity within a single mammalian genus is seldom realized. This phenomenon at high latitudes highlights complex Arctic community dynamics that reflect significant turnover through time as a consequence of environmental change. Each of these shrew species occupies a broad geographic distribution collectively spanning the entire Holarctic, although the study site lies within Eastern Beringia, near the periphery of all individual ranges. A review of published genetic evidence reflects a depauperate shrew community within ice-free Beringia through the last glaciation, and recent assembly of current diversity during the Holocene.

  16. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

    Science.gov (United States)

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

    2016-07-05

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

  17. Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas.

    Science.gov (United States)

    Li, Huan; Qu, Jiapeng; Li, Tongtong; Wirth, Stephan; Zhang, Yanming; Zhao, Xinquan; Li, Xiangzhen

    2018-06-03

    The gut microbiota in mammals plays a key role in host metabolism and adaptation. However, relatively little is known regarding to how the animals adapts to extreme environments through regulating gut microbial diversity and function. Here, we investigated the diet, gut microbiota, short-chain fatty acid (SCFA) profiles, and cellulolytic activity from two common pika (Ochotona spp.) species in China, including Plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau and Daurian pika (Ochotona daurica) from the Inner Mongolia Grassland. Despite a partial diet overlap, Plateau pikas harbored lower diet diversity than Daurian pikas. Some bacteria (e.g., Prevotella and Ruminococcus) associated with fiber degradation were enriched in Plateau pikas. They harbored higher gut microbial diversity, total SCFA concentration, and cellulolytic activity than Daurian pikas. Interestingly, cellulolytic activity was positively correlated with the gut microbial diversity and SCFAs. Gut microbial communities and SCFA profiles were segregated structurally between host species. PICRUSt metagenome predictions demonstrated that microbial genes involved in carbohydrate metabolism and energy metabolism were overrepresented in the gut microbiota of Plateau pikas. Our results demonstrate that Plateau pikas harbor a stronger fermenting ability for the plant-based diet than Daurian pikas via gut microbial fermentation. The enhanced ability for utilization of plant-based diets in Plateau pikas may be partly a kind of microbiota adaptation for more energy requirements in cold and hypoxic high-altitude environments.

  18. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

    International Nuclear Information System (INIS)

    Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

    2016-01-01

    Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

  19. Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

    Directory of Open Access Journals (Sweden)

    Walid Mottawea

    2018-05-01

    Full Text Available Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

  20. Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

    NARCIS (Netherlands)

    Besaury, L.; Marty, F.; Buquet, S.; Mesnage, V.; Muijzer, G.; Quillet, L.

    2013-01-01

    Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions,

  1. Are Isotopologue Signatures of N2O from Bacterial Denitrifiers Indicative of NOR Type?

    Science.gov (United States)

    Well, R.; Braker, G.; Giesemann, A.; Flessa, H.

    2010-12-01

    Nitrous oxide (N2O) fluxes from soils result from its production by nitrification and denitrification and reduction during denitrification. The structure of the denitrifying microbial community contributes to the control of net N2O fluxes. Although molecular techniques are promising for identifying the active community of N2O producers, there are few data until now because methods to explore gene expression of N2O production are laborious and disregard regulation of activity at the enzyme level. The isotopologue signatures of N2O including δ18O, average δ15N (δ15Nbulk) and 15N site preference (SP = difference in δ15N between the central and peripheral N positions of the asymmetric N2O molecule) have been used to estimate the contribution of partial processes to net N2O fluxes to the atmosphere. However, the use of this approach to study N2O dynamics in soils requires knowledge of isotopic signatures of N2O precursors and isotopologue fractionation factors (ɛ) of all processes of N2O production and consumption. In contrast to δ18O and δ15Nbulk, SP is independent of precursor signatures and hence is a promising parameter here. It is assumed that SP of produced N2O is almost exclusively controlled by the enzymatic isotope effects of NO reductases (NOR). These enzymes are known to be structurally different between certain classes of N2O producers with each class causing different isotope effects (Schmidt et al., 2004). The NH2OH-to-N2O step of nitrifiers and the NO3-to-N2O step of fungal denitrifiers are associated with large site-specific 15N effects with SP of 33 to 37 ‰ (Sutka et al., 2006, 2008) while the few tested species of gram-negative bacterial denitrifiers (cNOR group) exhibited low SP of -5 to 0‰ (Sutka et al., 2006; Toyoda et al., 2005). The aim of our study was to determine site-specific fractionation factors of the NO3-to-N2O step (ɛSP) for several species of denitrifiers representing each of the known NOR-types of bacteria, i.e. cNOR, q

  2. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

    Directory of Open Access Journals (Sweden)

    Mikihiko eKawai

    2014-03-01

    Full Text Available Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5 and 107.0 mbsf at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB, key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.

  3. Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis.

    Science.gov (United States)

    Sun, Yihua; De Vos, Paul; Heylen, Kim

    2016-01-19

    Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated. B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages. Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N2O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N2O

  4. [Phylogenetic analysis and nitrogen removal characteristics of a heterotrophic nitrifying-aerobic denitrifying bacteria strain from marine environment].

    Science.gov (United States)

    Sun, Xuemei; Li, Qiufen; Zhang, Yan; Liu, Huaide; Zhao, Jun; Qu, Keming

    2012-06-04

    We determined the phylogenetic position of a heterotrophic nitrifying-aerobic denitrifying bacterium X3, and detected its nitrogen removal characteristics for providing evidence to explain the principle of heterotrophic nitrification-aerobic denitrification and to improve the process in purification of marine-culture wastewater. The evolutionary position of the strain was determined based on its morphological, physiological, biochemical characteristics and 16SrRNA gene sequence. The nitrification-denitrification ability of this strain was detected by detecting its nitrogen removal efficiency and growth on different inorganic nitrogen source. Strain X3 was identified as Halomonas sp. It grew optimally at salinity 3%, pH 8.5, C:N 10:1 at 28 degrees C, and it could still survive at 15% salinity. The removal of NH4+ -N, NO2(-) -N and NO3(-) -N was 98.29%, 99.07%, 96.48% respectively within 24 h. When three inorganic nitrogen existed simultaneously, it always utilized ammonia firstly, and the total inorganic nitrogen removal was higher than with only one nitrogen, suggesting that strain X3 has the ability of simultaneous nitrification and denitrification and completing the whole nitrogen removing process. Strain X3 belonged to the genus of Halomonas. It had strong simultaneous nitrification and denitrification capability and could live in high-salinity environment.

  5. Multiplicity and diversity of Plasmodium vivax infections in a highly endemic region in Papua New Guinea.

    Directory of Open Access Journals (Sweden)

    Cristian Koepfli

    2011-12-01

    Full Text Available Plasmodium vivax is highly endemic in the lowlands of Papua New Guinea and accounts for a large proportion of the malaria cases in children less than 5 years of age. We collected 2117 blood samples at 2-monthly intervals from a cohort of 268 children aged 1 to 4.5 years and estimated the diversity and multiplicity of P. vivax infection. All P. vivax clones were genotyped using the merozoite surface protein 1 F3 fragment (msp1F3 and the microsatellite MS16 as molecular markers. High diversity was observed with msp1F3 (H(E = 88.1% and MS16 (H(E = 97.8%. Of the 1162 P. vivax positive samples, 74% harbored multi-clone infections with a mean multiplicity of 2.7 (IQR = 1-3. The multiplicity of P. vivax infection increased slightly with age (P = 0.02, with the strongest increase in very young children. Intensified efforts to control malaria can benefit from knowledge of the diversity and MOI both for assessing the endemic situation and monitoring the effects of interventions.

  6. The Effect of Mutual Coupling on a High Altitude Platform Diversity System Using Compact Antenna Arrays

    Directory of Open Access Journals (Sweden)

    Tommy Hult

    2010-01-01

    Full Text Available We analyze the destructive effects of mutual coupling and spatial correlation between the separate antenna elements on a combined diversity system consisting of multiple HAPs (High-Altitude Platforms employing various compact MIMO (Multiple-Input Multiple-Output antenna array configurations, in order to enhance the mutual information in HAP communication links. In addition, we assess the influence of the separation angle between HAPs on system performance, and determine the optimal separation angles that maximize the total mutual information of the system for various compact MIMO antennas. Simulation results show that although the mutual information is degraded by mutual coupling and spatial correlation, the proposed HAP diversity system still provides better performance compared to a nondiversity system for all tested scenarios.

  7. High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

    Science.gov (United States)

    Steven, Blaire; Lionard, Marie; Kuske, Cheryl R; Vincent, Warwick F

    2013-01-01

    In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.

  8. Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.

    Science.gov (United States)

    Gollner, Sabine; Stuckas, Heiko; Kihara, Terue C; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

    2016-01-01

    Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid

  9. Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts.

    Science.gov (United States)

    Haynes, Benjamin T; Marcus, Alan D; Higgins, Damien P; Gongora, Jaime; Gray, Rachael; Šlapeta, Jan

    2014-12-01

    The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h=0.986) and nucleotide diversity (π=0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST=0.007) and a high gene flow (Nm=35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. [Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

    Science.gov (United States)

    Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

    2015-07-01

    To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

  11. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Steeves Buckland

    Full Text Available Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko, is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA markers in 13 subpopulations to: (i assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii estimate effective population sizes and migration rates of subpopulations; and (iii examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable

  12. Classroom Management Strategies of Highly Effective Teachers in Diverse Middle Schools: Be Strict and Calm, Not Mean

    Science.gov (United States)

    McGregor, Katheryne L.

    2012-01-01

    This qualitative research study investigated and identified the classroom management strategies of 12 highly effective middle school teachers who served diverse student populations at two different school sites. In addition, this research explored the beliefs and experiences of 305 diverse middle school students regarding their experiences with…

  13. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

    Directory of Open Access Journals (Sweden)

    Ziye eHu

    2014-07-01

    Full Text Available Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA are much higher than that of ammonia oxidizing bacteria (AOB. The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.

  14. A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

    Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

  15. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  16. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  17. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    Science.gov (United States)

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  18. Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels.

    Science.gov (United States)

    Props, Ruben; Schmidt, Marian L; Heyse, Jasmine; Vanderploeg, Henry A; Boon, Nico; Denef, Vincent J

    2018-02-01

    Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake-specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

    Science.gov (United States)

    Mitra, Sneha; Biswas, Anushua; Narlikar, Leelavati

    2018-04-23

    Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries. For example, consider a ChIP experiment targeting protein X, which binds DNA at its cognate sites, but simultaneously interacts with four other proteins. Each of these proteins also binds to its own specific cognate sites along distant parts of the genome, a scenario consistent with the current view of transcriptional hubs and chromatin loops. Since ChIP will pull down all X-associated regions, the final reported data will be a union of five distinct sets of regions, each containing binding sites of one of the five proteins, respectively. Characterizing all five different motifs and the corresponding sets is important to interpret the ChIP experiment and ultimately, the role of X in regulation. We present diversity which attempts exactly this: it partitions the data so that each partition can be characterized with its own de novo motif. Diversity uses a Bayesian approach to identify the optimal number of motifs and the associated partitions, which together explain the entire dataset. This is in contrast to standard motif finders, which report motifs individually enriched in the data, but do not necessarily explain all reported regions. We show that the different motifs and associated regions identified by diversity give insights into the various complexes that may be forming along the chromatin, something that has so far not been attempted from ChIP data. Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https://github.com/NarlikarLab/DIVERSITY

  20. Effects of mechanical disintegration of activated sludge on the activity of nitrifying and denitrifying bacteria and phosphorus accumulating organisms.

    Science.gov (United States)

    Zubrowska-Sudol, Monika; Walczak, Justyna

    2014-09-15

    The purpose of the study was to analyse the impact of hydrodynamic disintegration of thickened excess activated sludge, performed at different levels of energy density (70, 140 and 210 kJ/L), on the activity of microorganisms involved in nutrient removal from wastewater, i.e. nitrifiers, denitrifiers and phosphorus accumulating organisms (PAOs). Ammonium and nitrogen utilisation rates and phosphorus release rates for raw and disintegrated sludge were determined using batch tests. The experiment also included: 1) analysis of organic and nutrient compound release from activated sludge flocs, 2) determination of the sludge disintegration degree (DD), and 3) evaluation of respiratory activity of the biomass by using the oxygen uptake rate (OUR) batch test. It was shown that the activity degree of the examined groups of microorganisms depended on energy density and related sludge disintegration degree, and that inactivation of individual groups of microorganisms occurred at different values of DD. Least resistant to the destruction of activated sludge flocs turned out to be phosphorus accumulating organisms, while the most resistant were denitrifiers. A decrease of 20-40% in PAO activity was noted already at DD equal to 3-5%. The threshold values of DD, after crossing which the inactivation of nitrifiers and denitrifiers occurred, were equal to 8% and 10%, respectively. At lesser DD values an increase in the activity of these groups of microorganisms was observed, averaging 20.2-41.7% for nitrifiers and 9.98-36.3% for denitrifiers. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Toxic effects exerted on methanogenic, nitrifying and denitrifying bacteria by chemicals used in a milk analysis laboratory

    NARCIS (Netherlands)

    Lopez-Fiuza, J.; Buys, B.; Mosquera-Corral, A.; Omil, F.; Mendez, R.

    2002-01-01

    The toxic effects caused by the chemicals contained in wastewaters generated by laboratories involved in raw milk analyses were assessed using batch assays. These assays were carried out separately with methanogenic, ammonium-oxidizing, nitrite-oxidizing and denitrifying bacteria. Since sodium azide

  2. Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples

    NARCIS (Netherlands)

    Kester, R.A.; Boer, W. de; Laanbroek, H.J.

    1996-01-01

    The contribution of nitrifiers and denitrifiers to the nitrous oxide production in slurries of calcareous silt loam and river bank sediment at different oxygen concentrations was determined using acetylene as nitrification inhibitor. The addition of 10 Pa acetylene resulted in inhibition of

  3. Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples

    NARCIS (Netherlands)

    Kester, R.A.; De Boer, W.; Laanbroek, H.J.

    1996-01-01

    The contribution of nitrifiers and denitrifiers to the nitrous oxide production in slurries of calcareous silt loam and river bank sediment at different oxygen concentrations was determined using acetylene as nitrification inhibitor. The addition of 10 Pa acetylene resulted in inhibition of nitrous

  4. Edaphic Conditions Regulate Denitrification Directly and Indirectly by Altering Denitrifier Abundance in Wetlands along the Han River, China.

    Science.gov (United States)

    Xiong, Ziqian; Guo, Laodong; Zhang, Quanfa; Liu, Guihua; Liu, Wenzhi

    2017-05-16

    Riparian wetlands play a critical role in retaining nitrogen (N) from upland runoff and improving river water quality, mainly through biological processes such as soil denitrification. However, the relative contribution of abiotic and biotic factors to riparian denitrification capacity remains elusive. Here we report the spatiotemporal dynamics of potential and unamended soil denitrification rates in 20 wetlands along the Han River, an important water source in central China. We also quantified the abundance of soil denitrifying microorganisms using nirK and nirS genes. Results showed that soil denitrification rates were significantly different between riparian and reservoir shoreline wetlands, but not between mountain and lowland wetlands. In addition, soil denitrification rates showed strong seasonality, with higher values in August (summer) and April (spring) but lower values in January (winter). The potential and unamended denitrification rates were positively correlated with edaphic conditions (moisture and carbon concentration), denitrifier abundance, and plant species richness. Path analysis further revealed that edaphic conditions could regulate denitrification rates both directly and indirectly through their effects on denitrifier abundance. Our findings highlight that not only environmental factors, but also biotic factors including denitrifying microorganisms and standing vegetation, play an important role in regulating denitrification rate and N removal capacity in riparian wetlands.

  5. The Control of Microcystis spp. Bloom by Combining Indigenous Denitrifying Bacteria From Sutami Reservoir with Fimbristylis globulosa and Vetiveria zizanoides

    Directory of Open Access Journals (Sweden)

    Bayu Agung Prahardika

    2013-04-01

    Full Text Available The purpose of this research is to know the ability of polyculture macrophyte (Fimbristylis globulosa and Vetiveria zizanoides and the combination of both with consortium of indigenous denitrifying bacteria from Sutami reservoir that was added by Microcystis spp. or not to reduce the concentration of nitrate, dissolved phosphate and the carrying capacity of Microcystis spp. The experiment was done in a medium filled up with Sutami reservoir water enriched with 16 ppm of nitrate and 0.4 ppm of phosphate. The denitrifying bacteria used in this research were DR-14, DU-27-1, DU-30-1, DU-30-2, TA-8 and DU-27-4 isolated from Sutami reservoir. The treatments were incubated within 15 days. Microcystis spp. abundance was calculated every day, but the measurement of the concentration of nitrate and dissolved phosphate was done every six days. The results showed that both treatment and the combination of both macrophytes with a consortium of denitrifying indigenous bacteria were added or not either Microcystis able to reduce nitrate at 99% and 93-99% orthophosphoric. The combination of macrophytes with denitrifying indigenous bacterial consortium from Sutami reservoir was able to inhibit the carrying capacity of Microcystis spp. highest up to 47.87%. They could also significantly reduce the abundance of Microcystis from 107 cells/mL in earlier days of the treatment into 0.35x104 cells/mL after fifteen days of incubation.

  6. Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.

    Science.gov (United States)

    Nielsen, Maja; Schreiber, Lars; Finster, Kai; Schramm, Andreas

    2015-01-01

    Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate denitrifier, which can also produce N2 by co-denitrification. Oxygen is consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and contains key genes for both denitrification and dissimilatory nitrate reduction to ammonium.

  7. Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria

    Directory of Open Access Journals (Sweden)

    Eveline M. van den Berg

    2017-09-01

    Full Text Available Denitrification and dissimilatory reduction to ammonium (DNRA are competing nitrate-reduction processes that entail important biogeochemical consequences for nitrogen retention/removal in natural and man-made ecosystems. The nature of the available carbon source and electron donor have been suggested to play an important role on the outcome of this microbial competition. In this study, the influence of lactate as fermentable carbon source on the competition for nitrate was investigated for varying ratios of lactate and nitrate in the influent (Lac/N ratio. The study was conducted in an open chemostat culture, enriched from activated sludge, under strict anoxia. The mechanistic explanation of the conversions observed was based on integration of results from specific batch tests with biomass from the chemostat, molecular analysis of the biomass enriched, and a computational model. At high Lac/N ratio (2.97 mol/mol both fermentative and respiratory nitrate reduction to ammonium occurred, coupled to partial oxidation of lactate to acetate, and to acetate oxidation respectively. Remaining lactate was fermented to propionate and acetate. At a decreased Lac/N ratio (1.15 mol/mol, the molar percentage of nitrate reduced to ammonium decreased to 58%, even though lactate was supplied in adequate amounts for full ammonification and nitrate remained the growth limiting compound. Data evaluation at this Lac/N ratio suggested conversions were comparable to the higher Lac/N ratio, except for lactate oxidation to acetate that was coupled to denitrification instead of ammonification. Respiratory DNRA on acetate was likely catalyzed by two Geobacter species related to G. luticola and G. lovleyi. Two Clostridiales members were likely responsible for lactate fermentation and partial lactate fermentation to acetate coupled to fermentative DNRA. An organism related to Propionivibrio militaris was identified as the organism likely responsible for denitrification. The

  8. A collective phase in resource competition in a highly diverse ecosystem

    Science.gov (United States)

    Tikhonov, Mikhail; Monasson, Remi

    Recent technological advances uncovered that most habitats, including the human body, harbor hundreds of coexisting microbial ``species''. The problem of understanding such complex communities is currently at the forefront of medical and environmental sciences. A particularly intriguing question is whether the high-diversity regime (large number of species N) gives rise to qualitatively novel phenomena that could not be intuited from analysis of low-dimensional models (with few species). However, few existing approaches allow studying this regime, except in simulations. Here, we use methods of statistical physics to show that the large- N limit of a classic ecological model of resource competition introduced by MacArthur in 1969 can be solved analytically. Our results provide a tractable model where the implications of large dimensionality of eco-evolutionary problems can be investigated. In particular, we show that at high diversity, the MacArthur model exhibits a phase transition into a curious regime where the environment constructed by the community becomes a collective property, insensitive to the external conditions such as the total resource influx supplied to the community. Supported by Harvard Center of Mathematical Sciences and Applications, and the Simons Foundation. This work was completed at the Aspen Center for Physics, supported by National Science Foundation Grant PHY-1066293.

  9. High levels of diversity characterize mandrill (Mandrillus sphinx) Mhc-DRB sequences.

    Science.gov (United States)

    Abbott, Kristin M; Wickings, E Jean; Knapp, Leslie A

    2006-08-01

    The major histocompatibility complex (MHC) is highly polymorphic in most primate species studied thus far. The rhesus macaque (Macaca mulatta) has been studied extensively and the Mhc-DRB region demonstrates variability similar to humans. The extent of MHC diversity is relatively unknown for other Old World monkeys (OWM), especially among genera other than Macaca. A molecular survey of the Mhc-DRB region in mandrills (Mandrillus sphinx) revealed extensive variability, suggesting that other OWMs may also possess high levels of Mhc-DRB polymorphism. In the present study, 33 Mhc-DRB loci were identified from only 13 animals. Eleven were wild-born and presumed to be unrelated and two were captive-born twins. Two to seven different sequences were identified for each individual, suggesting that some mandrills may have as many as four Mhc-DRB loci on a single haplotype. From these sequences, representatives of at least six Mhc-DRB loci or lineages were identified. As observed in other primates, some new lineages may have arisen through the process of gene conversion. These findings indicate that mandrills have Mhc-DRB diversity not unlike rhesus macaques and humans.

  10. Impact of highly saline wetland ecosystem on floral diversity of the Cholistan desert

    International Nuclear Information System (INIS)

    Gill, A.H.; Ahmad, K.S.; Habib, S.; Ahmad, S.A.; Nawaz, T.; Ahmad, F.

    2012-01-01

    The impact of highly saline wetland ecosystem created under Salinity Control and Reclamation Project (SCARP) on floral diversity was investigated in the arid environments of Cholistan Desert. Species richness, diversity indices and evenness indices were worked out to look at the distance at which the salt water has altered the native vegetation. Four sites including SCARP ponds of different ages (S1, S2, S3 and S4), and a reference site (SR) were selected for vegetation studies and data were recorded by 1 x 1 m quadrats, which were laid on permanent transect lines. Salt water showed great influence on ecological parameters of the native vegetation up to 40 m. Multivariate (cluster) analysis showed close clustering of highly salt tolerant species, Aeluropus lagopoides, Tamarix dioica and Suaeda fruticosa in one group, and relatively less tolerant Crotalaria burhia, Cyperus conglomeratus, Indigofera argentea, Haloxylon salicornicum, Haloxylon stocksii, Neurada procumbens and Salsola baryosma in second group. Moderately salt tolerant Aristida adscensionis, Lasiurus scindicus and Sporobolus iocladus were clustered in a separate group. (author)

  11. Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle.

    Science.gov (United States)

    Bragina, Anastasia; Berg, Christian; Cardinale, Massimiliano; Shcherbakov, Andrey; Chebotar, Vladimir; Berg, Gabriele

    2012-04-01

    Knowledge about Sphagnum-associated microbial communities, their structure and their origin is important to understand and maintain climate-relevant Sphagnum-dominated bog ecosystems. We studied bacterial communities of two cosmopolitan Sphagnum species, which are well adapted to different abiotic parameters (Sphagnum magellanicum, which are strongly acidic and ombrotrophic, and Sphagnum fallax, which are weakly acidic and mesotrophic), in three Alpine bogs in Austria by a multifaceted approach. Great differences between bacterial fingerprints of both Sphagna were found independently from the site. This remarkable specificity was confirmed by a cloning and a deep sequencing approach. Besides the common Alphaproteobacteria, we found a discriminative spectrum of bacteria; although Gammaproteobacteria dominated S. magellanicum, S. fallax was mainly colonised by Verrucomicrobia and Planctomycetes. Using this information for fluorescent in situ hybridisation analyses, corresponding colonisation patterns for Alphaproteobacteria and Planctomycetes were detected. Bacterial colonies were found in high abundances inside the dead big hyalocytes, but they were always connected with the living chlorocytes. Using multivariate statistical analysis, the abiotic factors nutrient richness and pH were identified to modulate the composition of Sphagnum-specific bacterial communities. Interestingly, we found that the immense bacterial diversity was transferred via the sporophyte to the gametophyte, which can explain the high specificity of Sphagnum-associated bacteria over long distances. In contrast to higher plants, which acquire their bacteria mainly from the environment, mosses as the phylogenetically oldest land plants maintain their bacterial diversity within the whole lifecycle.

  12. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

    KAUST Repository

    Pearman, John K.

    2015-11-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  13. Importance of riparian remnants for frog species diversity in a highly fragmented rainforest.

    Science.gov (United States)

    Rodríguez-Mendoza, Clara; Pineda, Eduardo

    2010-12-23

    Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.

  14. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Directory of Open Access Journals (Sweden)

    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  15. High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2

    Directory of Open Access Journals (Sweden)

    Hellberg Michael E

    2010-05-01

    Full Text Available Abstract Background Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching. Results In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus, a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella possess proteins structurally similar to tachylectin-2. Conclusions Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1 part of Oculina's innate immunity repertoire, and 2 evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change.

  16. Multivariate analysis and clustering reveal high morphological diversity in Tunisian autochthonous grapes (Vitis vinifera: insights into characterization, conservation and commercialization

    Directory of Open Access Journals (Sweden)

    Myriam Lamine

    2014-06-01

    Significance and impact of the study: In this investigation, we highlight the importance of importance of breeding programs, commercialization and evaluation of economically valuable characteristics of the highly diverse autochthonous grapevine cultivars from Tunisia.

  17. Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes.

    Science.gov (United States)

    Porter, Stephanie S; Faber-Hammond, Joshua J; Friesen, Maren L

    2018-01-01

    Exotic, invasive plants and animals can wreak havoc on ecosystems by displacing natives and altering environmental conditions. However, much less is known about the identities or evolutionary dynamics of the symbiotic microbes that accompany invasive species. Most leguminous plants rely upon symbiotic rhizobium bacteria to fix nitrogen and are incapable of colonizing areas devoid of compatible rhizobia. We compare the genomes of symbiotic rhizobia in a portion of the legume's invaded range with those of the rhizobium symbionts from across the legume's native range. We show that in an area of California the legume Medicago polymorpha has invaded, its Ensifer medicae symbionts: (i) exhibit genome-wide patterns of relatedness that together with historical evidence support host-symbiont co-invasion from Europe into California, (ii) exhibit population genomic patterns consistent with the introduction of the majority of deep diversity from the native range, rather than a genetic bottleneck during colonization of California and (iii) harbor a large set of accessory genes uniquely enriched in binding functions, which could play a role in habitat invasion. Examining microbial symbiont genome dynamics during biological invasions is critical for assessing host-symbiont co-invasions whereby microbial symbiont range expansion underlies plant and animal invasions. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    DEFF Research Database (Denmark)

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes...... confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted...... of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential...

  19. Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti.

    Science.gov (United States)

    Godreuil, S; Renaud, F; Choisy, M; Depina, J J; Garnotel, E; Morillon, M; Van de Perre, P; Bañuls, A L

    2010-07-01

    Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.

  20. High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

    Science.gov (United States)

    Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

    2013-01-01

    Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

  1. Inspiring science achievement: a mixed methods examination of the practices and characteristics of successful science programs in diverse high schools

    Science.gov (United States)

    Scogin, Stephen C.; Cavlazoglu, Baki; LeBlanc, Jennifer; Stuessy, Carol L.

    2017-08-01

    While the achievement gap in science exists in the US, research associated with our investigation reveals some high school science programs serving diverse student bodies are successfully closing the gap. Using a mixed methods approach, we identified and investigated ten high schools in a large Southwestern state that fit the definition of "highly successful, highly diverse". By conducting interviews with science liaisons associated with each school and reviewing the literature, we developed a rubric identifying specific characteristics associated with successful science programs. These characteristics and practices included setting high expectations for students, providing extensive teacher support for student learning, and utilizing student-centered pedagogy. We used the rubric to assess the successful high school science programs and compare them to other high school science programs in the state (i.e., less successful and less diverse high school science programs). Highly successful, highly diverse schools were very different in their approach to science education when compared to the other programs. The findings from this study will help schools with diverse students to strengthen hiring practices, enhance teacher support mechanisms, and develop student-focused strategies in the classroom that increase science achievement.

  2. Soil biota suppress positive plant diversity effects on productivity at high but not low soil fertility

    NARCIS (Netherlands)

    Luo, Shan; Deyn, De Gerlinde B.; Jiang, B.; Yu, Shixiao

    2017-01-01

    Plant community productivity commonly increases with increasing plant diversity, which is explained by complementarity among plant species in resource utilization (complementarity effect), or by selection of particularly productive plant species in diverse plant communities (selection effect).

  3. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

    DEFF Research Database (Denmark)

    Schou, Mads F.; Loeschcke, Volker; Bechsgaard, Jesper

    2017-01-01

    fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent...

  4. Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya.

    Science.gov (United States)

    Čapková, Kateřina; Hauer, Tomáš; Řeháková, Klára; Doležal, Jiří

    2016-01-01

    The environment of high-altitudinal cold deserts of Western Himalaya is characterized by extensive development of biological soil crusts, with cyanobacteria as dominant component. The knowledge of their taxonomic composition and dependency on soil chemistry and elevation is still fragmentary. We studied the abundance and the phylogenetic diversity of the culturable cyanobacteria and eukaryotic microalgae in soil crusts along altitudinal gradients (4600-5900 m) at two sites in the dry mountains of Ladakh (SW Tibetan Plateau and Eastern Karakoram), using both microscopic and molecular approaches. The effects of environmental factors (altitude, mountain range, and soil physico-chemical parameters) on the composition and biovolume of phototrophs were tested by multivariate redundancy analysis and variance partitioning. Both phylogenetic diversity and composition of morphotypes were similar between Karakorum and Tibetan Plateau. Phylogenetic analysis of 16S rRNA gene revealed strains belonging to at least five genera. Besides clusters of common soil genera, e.g., Microcoleus, Nodosilinea, or Nostoc, two distinct clades of simple trichal taxa were newly discovered. The most abundant cyanobacterial orders were Oscillatoriales and Nostacales, whose biovolume increased with increasing elevation, while that of Chroococales decreased. Cyanobacterial species richness was low in that only 15 morphotypes were detected. The environmental factors accounted for 52 % of the total variability in microbial data, 38.7 % of which was explained solely by soil chemical properties, 14.5 % by altitude, and 8.4 % by mountain range. The elevation, soil phosphate, and magnesium were the most important predictors of soil phototrophic communities in both mountain ranges despite their different bedrocks and origin. The present investigation represents a first record on phylogenetic diversity of the cyanobacterial community of biological soil crusts from Western Himalayas and first record

  5. Asymmetric reduction of ketones and β-keto esters by (S)-1-phenylethanol dehydrogenase from denitrifying bacterium Aromatoleum aromaticum.

    Science.gov (United States)

    Dudzik, A; Snoch, W; Borowiecki, P; Opalinska-Piskorz, J; Witko, M; Heider, J; Szaleniec, M

    2015-06-01

    Enzyme-catalyzed enantioselective reductions of ketones and keto esters have become popular for the production of homochiral building blocks which are valuable synthons for the preparation of biologically active compounds at industrial scale. Among many kinds of biocatalysts, dehydrogenases/reductases from various microorganisms have been used to prepare optically pure enantiomers from carbonyl compounds. (S)-1-phenylethanol dehydrogenase (PEDH) was found in the denitrifying bacterium Aromatoleum aromaticum (strain EbN1) and belongs to the short-chain dehydrogenase/reductase family. It catalyzes the stereospecific oxidation of (S)-1-phenylethanol to acetophenone during anaerobic ethylbenzene mineralization, but also the reverse reaction, i.e., NADH-dependent enantioselective reduction of acetophenone to (S)-1-phenylethanol. In this work, we present the application of PEDH for asymmetric reduction of 42 prochiral ketones and 11 β-keto esters to enantiopure secondary alcohols. The high enantioselectivity of the reaction is explained by docking experiments and analysis of the interaction and binding energies of the theoretical enzyme-substrate complexes leading to the respective (S)- or (R)-alcohols. The conversions were carried out in a batch reactor using Escherichia coli cells with heterologously produced PEDH as whole-cell catalysts and isopropanol as reaction solvent and cosubstrate for NADH recovery. Ketones were converted to the respective secondary alcohols with excellent enantiomeric excesses and high productivities. Moreover, the progress of product formation was studied for nine para-substituted acetophenone derivatives and described by neural network models, which allow to predict reactor behavior and provides insight on enzyme reactivity. Finally, equilibrium constants for conversion of these substrates were derived from the progress curves of the reactions. The obtained values matched very well with theoretical predictions.

  6. Functional diversity of soil invertebrates: a potential tool to explain N2O emission?

    Science.gov (United States)

    Lubbers, Ingrid; De Deyn, Gerlinde; Drake, Harold; Hunger, Sindy; Oppermann, Timo; van Groenigen, Jan Willem

    2017-04-01

    Soil biota play a crucial role in the mineralization of nutrients from organic material. However, they can thereby increase emissions of the potent greenhouse gas nitrous oxide (N2O). Our current lack of understanding of the factors controlling N2O production and emission is impeding the development of effective mitigation strategies. It is the challenge to control N2O emissions from production systems without reducing crop yield, and diversity of soil fauna may play a key role. A high functional diversity of soil invertebrates is known to stimulate nitrogen mineralization and thereby plant growth, however, it is unknown whether a high functional diversity of soil invertebrates can concurrently diminish N2O emissions. We hypothesized that increased functional diversity of soil invertebrates reduces faunal-induced N2O emissions by facilitating more complete denitrification through (i) stimulating the activity of denitrifying microbes, and (ii) affecting the distribution of micro and macro pores, creating more anaerobic reaction sites. Using state-of-the-art X-ray tomography and next-generation sequencing, we studied effects of functional diversity on soil structural properties and the diversity of the microbial community (16S rRNA genes and 16S rRNA), and linked these to soil N2O emissions. In a 120-day study we found that the functional composition of the soil invertebrate community determined N2O emissions: earthworm activity was key to faunal-induced N2O emissions (a 32-fold increase after 120 days, Pstructural properties (mean pore size, pore size distribution) were found to be radically altered by earthworm activity. We conclude that the presence of a few functional groups (ecosystem engineers) is more important than overall increased functional diversity in explaining faunal-affected N2O emissions.

  7. High throughput screening and profiling of high-value carotenoids from a wide diversity of bacteria in surface seawater.

    Science.gov (United States)

    Asker, Dalal

    2018-09-30

    Carotenoids are valuable natural colorants that exhibit numerous health promoting properties, and thus are widely used in food, feeds, pharmaceutical and nutraceuticals industries. In this study, we isolated and identified novel microbial sources that produced high-value carotenoids using high throughput screening (HTS). A total of 701 pigmented microbial strains library including marine bacteria and red yeast was constructed. Carotenoids profiling using HPLC-DAD-MS methods showed 88 marine bacterial strains with potential for the production of high-value carotenoids including astaxanthin (28 strains), zeaxanthin (21 strains), lutein (1 strains) and canthaxanthin (2 strains). A comprehensive 16S rRNA gene based phylogenetic analysis revealed that these strains can be classified into 30 species belonging to five bacterial classes (Flavobacteriia, α-Proteobacteria, γ-Proteobacteria, Actinobacteria and Bacilli). Importantly, we discovered novel producers of zeaxanthin and lutein, and a high diversity in both carotenoids and producing microbial strains, which are promising and highly selective biotechnological sources for high-value carotenoids. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

    Directory of Open Access Journals (Sweden)

    Hector Fernando Arocha-Garza

    2017-05-01

    shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

  9. High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

    Science.gov (United States)

    Arocha-Garza, Hector Fernando; Canales-Del Castillo, Ricardo; Eguiarte, Luis E.; Souza, Valeria

    2017-01-01

    isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies. PMID:28480140

  10. North-South differentiation and a region of high diversity in European wolves (Canis lupus.

    Directory of Open Access Journals (Sweden)

    Astrid V Stronen

    Full Text Available European wolves (Canis lupus show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part.

  11. Race and Academic Achievement in Racially Diverse High Schools: Opportunity and Stratification.

    Science.gov (United States)

    Muller, Chandra; Riegle-Crumb, Catherine; Schiller, Kathryn S; Wilkinson, Lindsey; Frank, Kenneth A

    2010-04-01

    BACKGROUND/CONTEXT: Brown v Board of Education fundamentally changed our nation's schools, yet we know surprisingly little about how and whether they provide equality of educational opportunity. Although substantial evidence suggests that African American and Latino students who attend these schools face fewer learning opportunities than their White counterparts, until now, it has been impossible to examine this using a representative sample because of lack of data. PURPOSE/OBJECTIVE/RESEARCH QUESTION/FOCUS OF STUDY: This study uses newly available data to investigate whether racially diverse high schools offer equality of educational opportunity to students from different racial and ethnic groups. This is examined by measuring the relative representation of minority students in advanced math classes at the beginning of high school and estimating whether and how this opportunity structure limits the level of achievement attained by African American and Latino students by the end of high school. SETTING: This study uses data from the Adolescent Health and Academic Achievement Study (AHAA) and its partner study, the National Longitudinal Study of Adolescent Health (Add Health), a stratified, nationally representative study of students in U.S. high schools first surveyed in 1994-1995. POPULATION/PARTICIPANTS/SUBJECTS: Two samples of racially diverse high schools were used in the analysis: one with African Americans, Whites, and Asians (26 schools with 3,149 students), and the other with Latinos, Whites, and Asians (22 schools with 2,775 students). RESEARCH DESIGN: Quantitative analyses first assess how high schools vary in the extent to which minority students are underrepresented in advanced sophomore math classes. Hierarchical multilevel modeling is then used to estimate whether racial-ethnic differences in representation in advanced math have an impact on African American and Latino students' achievement by the end of high school, relative to the Whites and Asians

  12. Effect of land use on the density of nitrifying and denitrifying bacteria in the Colombian Coffee Region

    Directory of Open Access Journals (Sweden)

    Vallejo Quintero Victoria Eugenia

    2011-12-01

    Full Text Available

    Soil microbial communities involved in the cycling of nitrogen (N are essential to maintaining and improving soil fertility, productivity and functionality of natural and agricultural ecosystems. However, some compounds generated during the metabolic processes performed by nitrifying (NB and denitrifying (DB bacteria are associated with the production of greenhouse gases, groundwater pollution and acidification. Therefore, the study of these bacteria is essential for economic and environmental sustainability. This study evaluated the effect of different land uses in two river basins (La Vieja and Otun on NB and DB densities. Two sampling events (SE were conducted by selecting the most representative land uses. Physicochemical (T °, pH, moisture and nitrate and microbiological properties (NB and DB densities were evaluated. In both SEs, significantly higher densities of NB and DB were observed in the land uses: pasture, guadua (DB only and unshaded coffee (La Vieja and onion (Otun. These land uses, excluding guadua, are dependent on nitrogen fertilizers, which together with the activities of grazing livestock on pastures may lead to greater availability of substrates for the NB. The use of agricultural machinery and overgrazing in pasture and onion uses generate compacted soil and other physical disturbances, encouraging the growth of DB. Forests had the lowest densities of NB and DB possibly due to a reduced availability of N and the releasing of allelopathic compounds from certain plants. Finally, the densities of ammonium-oxidizing bacteria had the greatest differences between the land uses evaluated, demonstrating its high sensitivity to agricultural management practices and livestock. We suggest that changes in the abundance of this community could

  13. Molecular evidence and high genetic diversity of shrew-borne Seewis virus in Slovenia.

    Science.gov (United States)

    Resman, Katarina; Korva, Miša; Fajs, Luka; Zidarič, Tanja; Trilar, Tomi; Zupanc, Tatjana Avšič

    2013-10-01

    Seewis virus, the shrew-borne hantavirus from Sorex araneus, has been molecularly detected in reservoir hosts in many different central European countries and Russia. Slovenia is a known endemic country for rodent-borne hantaviruses, therefore the aim of the study was to investigate the presence of shrew-borne hantaviruses in insectivores. Viral L, S and M segment have been recovered only from tissue samples of 7 S. araneus, despite several shrew species were tested. Phylogenetic analysis showed high genetic diversity of SWSV in Slovenia, ranging from 3 to 19.4% for different viral segments. The most divergent were M segment sequences, with 19.4% nucleotide divergence among Slovenian strains. Above that, different SWSV strains from Slovenia do not group into separate geographic clusters. While three separate genetic clades were determined, two of them were simultaneously present in one location at the same time. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Modeling of Cr(VI) Bioreduction Under Fermentative and Denitrifying Conditions

    Science.gov (United States)

    Molins, S.; Steefel, C.; Yang, L.; Beller, H. R.

    2011-12-01

    The mechanisms of bioreductive immobilization of Cr(VI) were investigated by reactive transport modeling of a set of flow-through column experiments performed using natural Hanford 100H aquifer sediment. The columns were continuously eluted with 5 μM Cr(VI), 5 mM lactate as the electron donor, and selected electron acceptors (tested individually). Here we focus on the two separate experimental conditions that showed the most removal of Cr(VI) from solution: fermentation and denitrification. In each case, a network of enzymatic and abiotic reaction pathways was considered to interpret the rate of chromate reduction. The model included biomass growth and decay, and thermodynamic limitations on reaction rates, and was constrained by effluent concentrations measured by IC and ICP-MS and additional information from bacterial isolates from column effluent. Under denitrifying conditions, Cr(VI) reduction was modeled as co-metabolic with nitrate reduction based on experimental observations and previous studies on a denitrifying bacterium derived from the Hanford 100H aquifer. The reactive transport model results supported this interpretation of the reaction mechanism and were used to quantify the efficiency of the process. The models results also suggest that biomass growth likely relied on a nitrogen source other than ammonium (e.g. nitrate). Under fermentative conditions and based on cell suspension studies performed on a bacterial isolate from the columns, the model assumes that Cr(VI) reduction is carried out directly by fermentative bacteria that convert lactate into acetate and propionate. The evolution to complete lactate fermentation and Cr(VI) reduction took place over a week's time and simulations were used to determine an estimate for a lower limit of the rate of chromate reduction by calibration with the flow-through column experimental results. In spite of sulfate being added to these columns, sulfate reduction proceeded at a slow rate and was not well

  15. Limnology and cyanobacterial diversity of high altitude lakes of Lahaul-Spiti in Himachal Pradesh, India.

    Science.gov (United States)

    Singh, Y; Khattar, Jis; Singh, D P; Rahi, P; Gulati, A

    2014-09-01

    Limnological data of four high altitude lakes from the cold desert region of Himachal Pradesh, India, has been correlated with cyanobacterial diversity. Physico-chemical characteristics and nutrient contents of the studied lakes revealed that Sissu Lake is mesotrophic while Chandra Tal, Suraj Tal and Deepak Tal are ultra-oligotrophic. Based on morphology and 16S rRNA gene sequence, a total of 20 cyanobacterial species belonging to 11 genera were identified. Canonical correspondence analysis distinguished three groups of species with respect to their occurrence and nutrient/physical environment demand. The first group, which included Nostoc linckia, N. punctiforme, Nodularia sphaerocarpa, Geitlerinema acutissimum, Limnothrix redekii, Planktothrix agardhii and Plank. clathrata, was characteristic of water with high nutrient content and high temperature. The second group, including Gloeocapsopsis pleurocapsoides, Leptolyngbya antarctica, L. frigida, Pseudanabaena frigida and N. spongiaeforme, occurred in oligotrophic water with high pH and low temperature. The distribution of third group of Cyanobium parvum, Synechocystis pevalekii, L. benthonica, L. foveolarum, L. lurida, L. valderiana, Phormidium autumnale and P. chalybeum could not be associated with a particular environmental condition because of their presence in all sampling sites.

  16. Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing

    Science.gov (United States)

    Egge, Elianne Sirnæs; Johannessen, Torill Vik; Andersen, Tom; Eikrem, Wenche; Bittner, Lucie; Larsen, Aud; Sandaa, Ruth-Anne; Edvardsen, Bente

    2015-01-01

    Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. PMID:25893259

  17. Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing.

    Science.gov (United States)

    Egge, Elianne Sirnaes; Johannessen, Torill Vik; Andersen, Tom; Eikrem, Wenche; Bittner, Lucie; Larsen, Aud; Sandaa, Ruth-Anne; Edvardsen, Bente

    2015-06-01

    Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  18. High-throughput genotyping for species identification and diversity assessment in germplasm collections.

    Science.gov (United States)

    Mason, Annaliese S; Zhang, Jing; Tollenaere, Reece; Vasquez Teuber, Paula; Dalton-Morgan, Jessica; Hu, Liyong; Yan, Guijun; Edwards, David; Redden, Robert; Batley, Jacqueline

    2015-09-01

    Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers. © 2015 John Wiley & Sons Ltd.

  19. Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

    Science.gov (United States)

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  20. Bat guilds, a concept to classify the highly diverse foraging and echolocation behaviors of microchiropteran bats

    Directory of Open Access Journals (Sweden)

    Annette eDenzinger

    2013-07-01

    Full Text Available Throughout evolution the foraging and echolocation behaviors as well as the motor systems of bats have been adapted to the tasks they have to perform while searching and acquiring food. When bats exploit the same class of environmental resources in a similar way, they perform comparable tasks and thus share similar adaptations independent of their phylogeny. Species with similar adaptations are assigned to guilds or functional groups. Habitat type and foraging mode mainly determine the foraging tasks and thus the adaptations of bats. Therefore we use habitat type and foraging mode to define seven guilds. The habitat types open, edge and narrow space are defined according to the bats’ echolocation behavior in relation to the distance between bat and background or food item and background. Bats foraging in the aerial, trawling, flutter detecting, or active gleaning mode use only echolocation to acquire their food. When foraging in the passive gleaning mode bats do not use echolocation but rely on sensory cues from the food item to find it. Bat communities often comprise large numbers of species with a high diversity in foraging areas, foraging modes, and diets. The assignment of species living under similar constraints into guilds identifies pattern of community structure and helps to understand the factors that underlie the organization of highly diverse bat communities. Bat species from different guilds do not compete for food as they differ in their foraging behavior and in the environmental resources they use. However, sympatric living species belonging to the same guild often exploit the same class of resources. To avoid competition they should differ in their niche dimensions. The fine grain structure of bat communities below the rather coarse classification into guilds is determined by mechanisms that result in niche partitioning.

  1. Molecular approaches to understand the regulation of N2O emission from denitrifying bacteria - model strains and soil communities (Invited)

    Science.gov (United States)

    Frostegard, A.; Bakken, L. R.

    2010-12-01

    Emissions of N2O from agricultural soils are largely caused by denitrifying bacteria. Field measurements of N2O fluxes show large variations and depend on several environmental factors, and possibly also on the composition of the denitrifying microbial community. The temporal and spatial variation of fluxes are not adequately captured by biogeochemical models, and few options for mitigations have been invented, which underscores the need to understand the mechanisms underlying the emissions of N2O. Analyses of denitrification genes and transcripts extracted from soils are important for describing the system, but may have limited value for prediction of N2O emissions. In contrast, phenotypic analyses are direct measures of the organisms’ responses to changing environmental conditions. Our approach is to combine phenotypic characterizations using high-resolution gas kinetics, with gene transcription analyses to study denitrification regulatory phenotypes (DRP) of bacterial strains or complex microbial communities. The rich data sets obtained provide a basis for refinement of biochemical and physiological research on this key process in the nitrogen cycle. The strength of this combined approach is illustrated by a series of experiments investigating effects of soil pH on denitrification. Soil pH emerges as a master variable determining the microbial community composition as well as its denitrification product ratio (N2O/N2), with higher ratio in acid than in alkaline soil. It is therefore likely that emissions of N2O from agro-ecosystems will increase in large parts of the world where soil pH is decreasing due to intensified management and increased use of chemical fertilizers. Considering its immense implications, surprisingly few attempts have been made to unravel the mechanisms involved in the pH-control of the product stoichiometry of denitrification. We investigated the kinetics of gas transformations (O2, NO, N2O and N2) and transcription of functional genes

  2. Pseudomonads Isolated from Pristine Background Groundwater Proliferate More Effectively in Co-culture than in Monoculture Under Denitrifying Conditions

    Science.gov (United States)

    Aaring, A. B.; Lancaster, A.; Novichkov, P.; Adams, M. W. W.; Deutschbauer, A. M.; Chakraborty, R.

    2016-12-01

    As part of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) consortium, we study the microbial community at the U.S. Department of Energy's Field Research Center (FRC) in Oak Ridge. The groundwater at this site contains plumes of nitrate with concentrations up to 14,000mg/L among other contaminants, though molybdenum concentrations are low. Because molybdenum is essential to nitrate reduction, this can be inhibitory to growth. Several strains of Pseudomonas were isolated from the same background groundwater sample. These isolates utilized diverse carbon sources ranging from acetate to glucose while growing under denitrifying conditions. The strains were also screened for nitrate tolerance and a couple of them were shown to be tolerant to 300-400 mM nitrate under anaerobic conditions. In the field site the bacteria live in consortia rather than in isolation, therefore we hypothesized that growth of these strains will be more robust in co-culture, as the denitrification pathway was segmented between the species. Three of the isolates (Pseudomonas fluorescens strains N1B4, N2E2, N2E3) were selected for in-depth analysis based on growth in pairwise co-cultures relative to monocultures, and the availability of the relevant genetic tools, such as transposon mutant libraries. Full genome sequencing showed that strain N2E3 has a truncated dentrification pathway: it lacks nitrous oxide reductase. Our results show strain N2E2 grow to maximum cell density an average of 45 hours more quickly when grown with strain N2E3 than in monoculture. Utilizing RB-TnSeq libraries of our strains, it was also found that some genes involved in nitrate reduction, sulfate permeability, molybdenum utilization, and anaerobic reduction are important for growth under these conditions. In addition, a few unexpected genes were also shown to be positively correlated to growth, such as genes homologous to genes for DNA proofreading or antibiotic production. These

  3. Highly Adaptive Solid-Liquid Interfacing Triboelectric Nanogenerator for Harvesting Diverse Water Wave Energy.

    Science.gov (United States)

    Zhao, Xue Jiao; Kuang, Shuang Yang; Wang, Zhong Lin; Zhu, Guang

    2018-05-22

    Harvesting water wave energy presents a significantly practical route to energy supply for self-powered wireless sensing networks. Here we report a networked integrated triboelectric nanogenerator (NI-TENG) as a highly adaptive means of harvesting energy from interfacing interactions with various types of water waves. Having an arrayed networking structure, the NI-TENG can accommodate diverse water wave motions and generate stable electric output regardless of how random the water wave is. Nanoscaled surface morphology consisting of dense nanowire arrays is the key for obtaining high electric output. A NI-TENG having an area of 100 × 70 mm 2 can produce a stable short-circuit current of 13.5 μA and corresponding electric power of 1.03 mW at a water wave height of 12 cm. This merit promises practical applications of the NI-TENG in real circumstances, where water waves are highly variable and unpredictable. After energy storage, the generated electric energy can drive wireless sensing by autonomously transmitting data at a period less than 1 min. This work proposes a viable solution for powering individual standalone nodes in a wireless sensor network. Potential applications include but are not limited to long-term environment monitoring, marine surveillance, and off-shore navigation.

  4. High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

    Science.gov (United States)

    Ng, Terry Fei Fan; Marine, Rachel; Wang, Chunlin; Simmonds, Peter; Kapusinszky, Beatrix; Bodhidatta, Ladaporn; Oderinde, Bamidele Soji; Wommack, K. Eric

    2012-01-01

    Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high-throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, 90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses. PMID:22933275

  5. Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil.

    Science.gov (United States)

    Bergkemper, Fabian; Kublik, Susanne; Lang, Friederike; Krüger, Jaane; Vestergaard, Gisle; Schloter, Michael; Schulz, Stefanie

    2016-06-01

    Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biota for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited both primers reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter

  6. Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

    Science.gov (United States)

    Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

    2017-01-01

    Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

  7. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

    Science.gov (United States)

    Schuenemann, Verena J; Avanzi, Charlotte; Krause-Kyora, Ben; Seitz, Alexander; Herbig, Alexander; Inskip, Sarah; Bonazzi, Marion; Reiter, Ella; Urban, Christian; Dangvard Pedersen, Dorthe; Taylor, G Michael; Singh, Pushpendra; Stewart, Graham R; Velemínský, Petr; Likovsky, Jakub; Marcsik, Antónia; Molnár, Erika; Pálfi, György; Mariotti, Valentina; Riga, Alessandro; Belcastro, M Giovanna; Boldsen, Jesper L; Nebel, Almut; Mays, Simon; Donoghue, Helen D; Zakrzewski, Sonia; Benjak, Andrej; Nieselt, Kay; Cole, Stewart T; Krause, Johannes

    2018-05-01

    Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  8. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

    Directory of Open Access Journals (Sweden)

    Verena J Schuenemann

    2018-05-01

    Full Text Available Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  9. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

    Science.gov (United States)

    Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

    2017-01-01

    Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata , Avicennia marina , and Ceriops tagal , was undertaken using high - throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

  10. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Yanying Zhang

    2017-10-01

    Full Text Available Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

  11. HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.

    Science.gov (United States)

    Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M

    2013-09-01

    HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.

  12. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

    Science.gov (United States)

    Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

    2015-01-01

    Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how

  13. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

    Directory of Open Access Journals (Sweden)

    Abhishek Mitra

    Full Text Available Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding. Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants. Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively

  14. Engaging Students in the Research Process: Comparing Approaches Used with Diverse Learners in Two Urban High School Classrooms

    Science.gov (United States)

    Lawrence, Salika A.; Jefferson, Tiffany; Osborn, Nancy

    2017-01-01

    This paper describes instructional choices used by two high school teachers to engage students in the research process. Working with diverse learners in large urban high schools, the teachers used different approaches to support students' through the research process. The teachers' intentional teaching helped to engage students through structured…

  15. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

    Science.gov (United States)

    Tu, Zong-cai; Wang, Xiao-lan

    2016-01-01

    Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food. PMID:27992473

  16. Endohedral Metallofullerene as Molecular High Spin Qubit: Diverse Rabi Cycles in Gd2@C79N.

    Science.gov (United States)

    Hu, Ziqi; Dong, Bo-Wei; Liu, Zheng; Liu, Jun-Jie; Su, Jie; Yu, Changcheng; Xiong, Jin; Shi, Di-Er; Wang, Yuanyuan; Wang, Bing-Wu; Ardavan, Arzhang; Shi, Zujin; Jiang, Shang-Da; Gao, Song

    2018-01-24

    An anisotropic high-spin qubit with long coherence time could scale the quantum system up. It has been proposed that Grover's algorithm can be implemented in such systems. Dimetallic aza[80]fullerenes M 2 @C 79 N (M = Y or Gd) possess an unpaired electron located between two metal ions, offering an opportunity to manipulate spin(s) protected in the cage for quantum information processing. Herein, we report the crystallographic determination of Gd 2 @C 79 N for the first time. This molecular magnet with a collective high-spin ground state (S = 15/2) generated by strong magnetic coupling (J Gd-Rad = 350 ± 20 cm -1 ) has been unambiguously validated by magnetic susceptibility experiments. Gd 2 @C 79 N has quantum coherence and diverse Rabi cycles, allowing arbitrary superposition state manipulation between each adjacent level. The phase memory time reaches 5 μs at 5 K by dynamic decoupling. This molecule fulfills the requirements of Grover's searching algorithm proposed by Leuenberger and Loss.

  17. High-throughput screening of a diversity collection using biodefense category A and B priority pathogens.

    Science.gov (United States)

    Barrow, Esther W; Clinkenbeard, Patricia A; Duncan-Decocq, Rebecca A; Perteet, Rachel F; Hill, Kimberly D; Bourne, Philip C; Valderas, Michelle W; Bourne, Christina R; Clarkson, Nicole L; Clinkenbeard, Kenneth D; Barrow, William W

    2012-08-01

    One of the objectives of the National Institutes of Allergy and Infectious Diseases (NIAID) Biodefense Program is to identify or develop broad-spectrum antimicrobials for use against bioterrorism pathogens and emerging infectious agents. As a part of that program, our institution has screened the 10 000-compound MyriaScreen Diversity Collection of high-purity druglike compounds against three NIAID category A and one category B priority pathogens in an effort to identify potential compound classes for further drug development. The effective use of a Clinical and Laboratory Standards Institute-based high-throughput screening (HTS) 96-well-based format allowed for the identification of 49 compounds that had in vitro activity against all four pathogens with minimum inhibitory concentration values of ≤16 µg/mL. Adaptation of the HTS process was necessary to conduct the work in higher-level containment, in this case, biosafety level 3. Examination of chemical scaffolds shared by some of the 49 compounds and assessment of available chemical databases indicates that several may represent broad-spectrum antimicrobials whose activity is based on novel mechanisms of action.

  18. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    Science.gov (United States)

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica; Nielsen, Jens; Nielsen, Kristian Fog; Workman, Mhairi; Frisvad, Jens Christian

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species. PMID:27739446

  19. Depth and breadth: Bridging the gap between scientific inquiry and high-stakes testing with diverse junior high school students

    Science.gov (United States)

    Kang, Jee Sun Emily

    This study explored how inquiry-based teaching and learning processes occurred in two teachers' diverse 8th grade Physical Science classrooms in a Program Improvement junior high school within the context of high-stakes standardized testing. Instructors for the courses examined included not only the two 8th grade science teachers, but also graduate fellows from a nearby university. Research was drawn from inquiry-based instruction in science education, the achievement gap, and the high stakes testing movement, as well as situated learning theory to understand how opportunities for inquiry were negotiated within the diverse classroom context. Transcripts of taped class sessions; student work samples; interviews of teachers and students; and scores from the California Standards Test in science were collected and analyzed. Findings indicated that the teachers provided structured inquiry in order to support their students in learning about forces and to prepare them for the standardized test. Teachers also supported students in generating evidence-based explanations, connecting inquiry-based investigations with content on forces, proficiently using science vocabulary, and connecting concepts about forces to their daily lives. Findings from classroom data revealed constraints to student learning: students' limited language proficiency, peer counter culture, and limited time. Supports were evidenced as well: graduate fellows' support during investigations, teachers' guided questioning, standardized test preparation, literacy support, and home-school connections. There was no statistical difference in achievement on the Forces Unit test or science standardized test between classes with graduate fellows and without fellows. There was also no statistical difference in student performance between the two teachers' classrooms, even though their teaching styles were very different. However, there was a strong correlation between students' achievement on the chapter test and

  20. Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus.

    Science.gov (United States)

    Wessels, Jocelyn M; Lajoie, Julie; Vitali, Danielle; Omollo, Kenneth; Kimani, Joshua; Oyugi, Julius; Cheruiyot, Juliana; Kimani, Makubo; Mungai, John N; Akolo, Maureen; Stearns, Jennifer C; Surette, Michael G; Fowke, Keith R; Kaushic, Charu

    2017-01-01

    To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied. A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region). Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota. High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour.

  1. Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus.

    Directory of Open Access Journals (Sweden)

    Jocelyn M Wessels

    Full Text Available To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV, are associated with increased prevalence of sexually transmitted infections (STIs and human immunodeficiency virus (HIV acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied.A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19 and women engaged in sex work (female sex workers, FSW, N = 48, using Illumina sequencing (16S rRNA, V3 region.Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002 and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001. Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota.High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour.

  2. Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus

    Science.gov (United States)

    Wessels, Jocelyn M.; Lajoie, Julie; Vitali, Danielle; Omollo, Kenneth; Kimani, Joshua; Oyugi, Julius; Cheruiyot, Juliana; Kimani, Makubo; Mungai, John N.; Akolo, Maureen; Stearns, Jennifer C.; Surette, Michael G.; Fowke, Keith R.

    2017-01-01

    Objective To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied. Methods A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region). Results Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota. Conclusions High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour. PMID:29095928

  3. [Effect of short-time drought process on denitrifying bacteria abundance and N2O emission in paddy soil].

    Science.gov (United States)

    Lu, Jing; Liu, Jin-Bo; Sheng, Rong; Liu, Yi; Chen, An-Lei; Wei, Wen-Xue

    2014-10-01

    In order to investigate the impact of drying process on greenhouse gas emissions and denitrifying microorganisms in paddy soil, wetting-drying process was simulated in laboratory conditions. N2O flux, redox potential (Eh) were monitored and narG- and nosZ-containing denitrifiers abundances were determined by real-time PCR. N2O emission was significantly increased only 4 h after drying process began, and it was more than 6 times of continuous flooding (CF) at 24 h. In addition, narG and nosZ gene abundances were increased rapidly with the drying process, and N2O emission flux was significantly correlated with narG gene abundance (P driving microorganisms which caused the N2O emission in the short-time drought process in paddy soil.

  4. Pyruvic Oxime Nitrification and Copper and Nickel Resistance by a Cupriavidus pauculus, an Active Heterotrophic Nitrifier-Denitrifier

    OpenAIRE

    Ramirez, Miguel; Obrzydowski, Jennifer; Ayers, Mary; Virparia, Sonia; Wang, Meijing; Stefan, Kurtis; Linchangco, Richard; Castignetti, Domenic

    2014-01-01

    Heterotrophic nitrifiers synthesize nitrogenous gasses when nitrifying ammonium ion. A Cupriavidus pauculus, previously thought an Alcaligenes sp. and noted as an active heterotrophic nitrifier-denitrifier, was examined for its ability to produce nitrogen gas (N2) and nitrous oxide (N2O) while heterotrophically nitrifying the organic substrate pyruvic oxime [CH3–C(NOH)–COOH]. Neither N2 nor N2O were produced. Nucleotide and phylogenetic analyses indicated that the organism is a member of a g...

  5. Lifestyle behaviors and ethnic identity among diverse women at high risk for type 2 diabetes.

    Science.gov (United States)

    Brown, Susan D; Ehrlich, Samantha F; Kubo, Ai; Tsai, Ai-Lin; Hedderson, Monique M; Quesenberry, Charles P; Ferrara, Assiamira

    2016-07-01

    Diet and physical activity lifestyle behaviors are modifiable risk factors for type 2 diabetes and are shaped by culture, potentially influencing diabetes health disparities. We examined whether ethnic identity-the strength of attachment to one's ethnic group, and a long-standing focus of psychological research-could help account for variations in lifestyle behaviors within a diverse population at high risk for chronic disease. Using data from the Gestational Diabetes' Effects on Moms trial, this US-based cross-sectional study included 1463 pregnant women (74% from minority ethnic/racial groups; 46% born outside the US) with gestational diabetes (GDM), a common pregnancy complication conferring high risk for type 2 diabetes after delivery. Mixed linear regression models examined whether ethnic identity is associated with lifestyle behaviors after adjusting for demographic, clinical, and acculturative characteristics (e.g., nativity and length of residence in the US). In the overall sample, a one-unit increase in ethnic identity score was significantly associated with 3% greater fiber intake, 4% greater fruit/vegetable intake, 11% greater total activity, and 11% greater walking (p values ethnic/racial groups, a one-unit increase in ethnic identity score was significantly associated with 17% greater fiber intake among Filipina women; 5% lower total caloric intake among non-Hispanic White women; and 40% greater total activity, 35% greater walking, and 8% greater total caloric intake among Latina women (p values ≤ 0.03). Results from this large study suggest that ethnic group attachment is associated with some lifestyle behaviors, independent of acculturation indicators, among young women with GDM who are at high risk for type 2 diabetes. Stronger ethnic identity may promote certain choices known to be associated with reduced risk of type 2 diabetes. Prospective research is needed to clarify the temporal nature of associations between ethnic identity and

  6. Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression

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    Picard Flora

    2012-10-01

    Full Text Available Abstract Background In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level regulation at the systemic level, the detailed translational status (translatome of all mRNAs was measured in the model bacterium Lactococcus lactis in exponential phase growth. Results Results demonstrated that only part of the entire population of each mRNA species was engaged in translation. For transcripts involved in translation, the polysome size reached a maximum of 18 ribosomes. The fraction of mRNA engaged in translation (ribosome occupancy and ribosome density were not constant for all genes. This high degree of variability was analyzed by bioinformatics and statistical modeling in order to identify general rules of translational regulation. For most of the genes, the ribosome density was lower than the maximum value revealing major control of translation by initiation. Gene function was a major translational regulatory determinant. Both ribosome occupancy and ribosome density were particularly high for transcriptional regulators, demonstrating the positive role of translational regulation in the coordination of transcriptional networks. mRNA stability was a negative regulatory factor of ribosome occupancy and ribosome density, suggesting antagonistic regulation of translation and mRNA stability. Furthermore, ribosome occupancy was identified as a key component of intracellular protein levels underlining the importance of translational regulation. Conclusions We have determined, for the first time in a bacterium, the detailed translational status for all mRNAs present in the cell. We have demonstrated experimentally the high diversity of translational states allowing individual gene differentiation and the importance of translation-level regulation in the complex process linking gene expression to protein

  7. Theropod Fauna from Southern Australia Indicates High Polar Diversity and Climate-Driven Dinosaur Provinciality

    Science.gov (United States)

    Benson, Roger B. J.; Rich, Thomas H.; Vickers-Rich, Patricia; Hall, Mike

    2012-01-01

    The Early Cretaceous fauna of Victoria, Australia, provides unique data on the composition of high latitude southern hemisphere dinosaurs. We describe and review theropod dinosaur postcranial remains from the Aptian–Albian Otway and Strzelecki groups, based on at least 37 isolated bones, and more than 90 teeth from the Flat Rocks locality. Several specimens of medium- and large-bodied individuals (estimated up to ∼8.5 metres long) represent allosauroids. Tyrannosauroids are represented by elements indicating medium body sizes (∼3 metres long), likely including the holotype femur of Timimus hermani, and a single cervical vertebra represents a juvenile spinosaurid. Single specimens representing medium- and small-bodied theropods may be referrable to Ceratosauria, Ornithomimosauria, a basal coelurosaur, and at least three taxa within Maniraptora. Thus, nine theropod taxa may have been present. Alternatively, four distinct dorsal vertebrae indicate a minimum of four taxa. However, because most taxa are known from single bones, it is likely that small-bodied theropod diversity remains underestimated. The high abundance of allosauroids and basal coelurosaurs (including tyrannosauroids and possibly ornithomimosaurs), and the relative rarity of ceratosaurs, is strikingly dissimilar to penecontemporaneous dinosaur faunas of Africa and South America, which represent an arid, lower-latitude biome. Similarities between dinosaur faunas of Victoria and the northern continents concern the proportional representatation of higher clades, and may result from the prevailing temperate–polar climate of Australia, especially at high latitudes in Victoria, which is similar to the predominant warm–temperate climate of Laurasia, but distinct from the arid climate zone that covered extensive areas of Gondwana. Most dinosaur groups probably attained a near-cosmopolitan distribution in the Jurassic, prior to fragmentation of the Pangaean supercontinent, and some aspects of the

  8. High occurrence and unusual serotype diversity of non-typhoidal Salmonella in non-clinical niches, Angola.

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    Antunes, P; Campos, J; Mourão, J; Ribeiro, T G; Novais, C; Peixe, L

    2017-04-01

    Non-typhoidal Salmonella is an important burden, particularly in developing countries of the African region. We report for the first time in Angola, a sub-Saharan African country with commercial/travel relationships with Europe, an unexpectedly high occurrence of Salmonella (n = 12/63, 19%) from a high diversity of sources, particularly farm and wild animals. The detection of diverse serotypes (n = 12), involving putative new S. enterica subsp. salamae serotypes, is also of note, reinforcing the need for a comprehensive surveillance in Angola critical to identify animal/food/environmental sources of salmonellosis with impact on animal health, local people, tourists and exported products.

  9. High Levels of Genetic Diversity of Plasmodium falciparum Populations in Papua New Guinea despite Variable Infection Prevalence

    Science.gov (United States)

    Barry, Alyssa E.; Schultz, Lee; Senn, Nicholas; Nale, Joe; Kiniboro, Benson; Siba, Peter M.; Mueller, Ivo; Reeder, John C.

    2013-01-01

    High levels of genetic diversity in Plasmodium falciparum populations are an obstacle to malaria control. Here, we investigate the relationship between local variation in malaria epidemiology and parasite genetic diversity in Papua New Guinea (PNG). Cross-sectional malaria surveys were performed in 14 villages spanning four distinct malaria-endemic areas on the north coast, including one area that was sampled during the dry season. High-resolution msp2 genotyping of 2,147 blood samples identified 761 P. falciparum infections containing a total of 1,392 clones whose genotypes were used to measure genetic diversity. Considerable variability in infection prevalence and mean multiplicity of infection was observed at all of the study sites, with the area sampled during the dry season showing particularly striking local variability. Genetic diversity was strongly associated with multiplicity of infection but not with infection prevalence. In highly endemic areas, differences in infection prevalence may not translate into a decrease in parasite population diversity. PMID:23400571

  10. Denitrifying capabilities of Tetrasphaera and their contribution towards nitrous oxide production in enhanced biological phosphorus removal processes.

    Science.gov (United States)

    Marques, Ricardo; Ribera-Guardia, Anna; Santos, Jorge; Carvalho, Gilda; Reis, Maria A M; Pijuan, Maite; Oehmen, Adrian

    2018-06-15

    Denitrifying enhanced biological phosphorus removal (EBPR) systems can be an efficient means of removing phosphate (P) and nitrate (NO 3 - ) with low carbon source and oxygen requirements. Tetrasphaera is one of the most abundant polyphosphate accumulating organisms present in EBPR systems, but their capacity to achieve denitrifying EBPR has not previously been determined. An enriched Tetrasphaera culture, comprising over 80% of the bacterial biovolume was obtained in this work. Despite the denitrification capacity of Tetrasphaera, this culture achieved only low levels of anoxic P-uptake. Batch tests with different combinations of NO 3 - , nitrite (NO 2 - ) and nitrous oxide (N 2 O) revealed lower N 2 O accumulation by Tetrasphaera as compared to Accumulibacter and Competibacter when multiple electron acceptors were added. Electron competition was observed during the addition of multiple nitrogen electron acceptors species, where P uptake appeared to be slightly favoured over glycogen production in these situations. This study increases our understanding of the role of Tetrasphaera-related organisms in denitrifying EBPR systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Simultaneous pollutant removal and electricity generation in denitrifying microbial fuel cell with boric acid-borate buffer solution.

    Science.gov (United States)

    Chen, Gang; Zhang, Shaohui; Li, Meng; Wei, Yan

    2015-01-01

    A double-chamber denitrifying microbial fuel cell (MFC), using boric acid-borate buffer solution as an alternative to phosphate buffer solution, was set up to investigate the influence of buffer solution concentration, temperature and external resistance on electricity generation and pollutant removal efficiency. The result revealed that the denitrifying MFC with boric acid-borate buffer solution was successfully started up in 51 days, with a stable cell voltage of 205.1 ± 1.96 mV at an external resistance of 50 Ω. Higher concentration of buffer solution favored nitrogen removal and electricity generation. The maximum power density of 8.27 W/m(3) net cathodic chamber was obtained at a buffer solution concentration of 100 mmol/L. An increase in temperature benefitted electricity generation and nitrogen removal. A suitable temperature for this denitrifying MFC was suggested to be 25 °C. Decreasing the external resistance favored nitrogen removal and organic matter consumption by exoelectrogens.

  12. Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor

    Science.gov (United States)

    Bin, Zhang; Bin, Xue; Zhigang, Qiu; Zhiqiang, Chen; Junwen, Li; Taishi, Gong; Wenci, Zou; Jingfeng, Wang

    2015-08-01

    Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3--N could be removed or reduced, some amount of NO2--N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy.

  13. Optimum O2:CH4 Ratio Promotes the Synergy between Aerobic Methanotrophs and Denitrifiers to Enhance Nitrogen Removal

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    Jing Zhu

    2017-06-01

    Full Text Available The O2:CH4 ratio significantly effects nitrogen removal in mixed cultures where aerobic methane oxidation is coupled with denitrification (AME-D. The goal of this study was to investigate nitrogen removal of the AME-D process at four different O2:CH4 ratios [0, 0.05, 0.25, and 1 (v/v]. In batch tests, the highest denitrifying activity was observed when the O2:CH4 ratio was 0.25. At this ratio, the methanotrophs produced sufficient carbon sources for denitrifiers and the oxygen level did not inhibit nitrite removal. The results indicated that the synergy between methanotrophs and denitrifiers was significantly improved, thereby achieving a greater capacity of nitrogen removal. Based on thermodynamic and chemical analyses, methanol, butyrate, and formaldehyde could be the main trophic links of AME-D process in our study. Our research provides valuable information for improving the practical application of the AME-D systems.

  14. Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1.

    Science.gov (United States)

    Mauffrey, Florian; Cucaita, Alexandra; Constant, Philippe; Villemur, Richard

    2017-01-01

    Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N 2 O) reductase, suggesting that NO and N 2 O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Series of oxic and anoxic cultures of strain JAM1 were performed with N 2 O, [Formula: see text] or sodium nitroprusside, and growth and N 2 O, [Formula: see text], [Formula: see text] and N 2 concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of N 2 O, [Formula: see text] and [Formula: see text]. Isotopic labeling of N 2 O was performed in 15 NH 4 + -amended cultures. Cultures with the JAM1Δ narG1narG2 double mutant were performed to assess the involvement of the Nar systems on N 2 O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc -type nitric oxide reductase ( cnorB1 and cnorB2 ) and nitrous oxide reductase ( nosZ ), and also nnrS and norR that encode NO-sensitive regulators. Strain JAM1 can reduce NO to N 2 O and N 2 O to N 2 and can sustain growth under anoxic conditions by reducing N 2 O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce N 2 O, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of c norB1 , cnorB2, nnrS and nor

  15. Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

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    Florian Mauffrey

    2017-11-01

    Full Text Available Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\\mathrm{NO}}_{2}^{-}$ NO 2 − . These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar. Strain JAM1 also contains gene clusters encoding two nitric oxide (NO reductases and one nitrous oxide (N2O reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\\mathrm{NH}}_{4}^{+}$ NH 4 + -free cultures were also tested to assess the dynamics of N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2 and nitrous oxide reductase (nosZ, and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N

  16. Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing

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    Xin Fang

    2016-09-01

    Full Text Available More and more evidences indicate that diseases of the central nervous system (CNS have been seriously affected by faecal microbes. However, little work is done to explore interaction between amyotrophic lateral sclerosis (ALS and faecal microbes. In the present study, high-throughput sequencing method was used to compare the intestinal microbial diversity of healthy people and ALS patients. The principal coordinate analysis (PCoA, Venn and unweighted pair-group method using arithmetic averages (UPGMA showed an obvious microbial changes between healthy people (group H and ALS patients (group A, and the average ratios of Bacteroides, Faecalibacterium, Anaerostipes, Prevotella, Escherichia and Lachnospira at genus level between ALS patients and healthy people were 0.78, 2.18, 3.41, 0.35, 0.79 and 13.07. Furthermore, the decreased Firmicutes/Bacteroidetes ratio at phylum level using LEfSE (LDA >4.0, together with the significant increased genus Dorea (harmful microorganisms and significant reduced genus Oscillibacter, Anaerostipes, Lachnospiraceae (beneficial microorganisms in ALS patients, indicated that the imbalance in intestinal microflora constitution had a strong association with the pathogenesis of ALS.

  17. Evaluation of the Microbial Diversity in Amyotrophic Lateral Sclerosis Using High-Throughput Sequencing.

    Science.gov (United States)

    Fang, Xin; Wang, Xin; Yang, Shaoguo; Meng, Fanjing; Wang, Xiaolei; Wei, Hua; Chen, Tingtao

    2016-01-01

    More and more evidences indicate that diseases of the central nervous system have been seriously affected by fecal microbes. However, little work is done to explore interaction between amyotrophic lateral sclerosis (ALS) and fecal microbes. In the present study, high-throughput sequencing method was used to compare the intestinal microbial diversity of healthy people and ALS patients. The principal coordinate analysis, Venn and unweighted pair-group method using arithmetic averages (UPGMA) showed an obvious microbial changes between healthy people (group H) and ALS patients (group A), and the average ratios of Bacteroides , Faecalibacterium , Anaerostipes , Prevotella , Escherichia , and Lachnospira at genus level between ALS patients and healthy people were 0.78, 2.18, 3.41, 0.35, 0.79, and 13.07. Furthermore, the decreased Firmicutes/Bacteroidetes ratio at phylum level using LEfSE (LDA > 4.0), together with the significant increased genus Dorea (harmful microorganisms) and significant reduced genus Oscillibacter , Anaerostipes , Lachnospiraceae (beneficial microorganisms) in ALS patients, indicated that the imbalance in intestinal microflora constitution had a strong association with the pathogenesis of ALS.

  18. Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages.

    Science.gov (United States)

    Evans, James S; Erwin, Patrick M; Shenkar, Noa; López-Legentil, Susanna

    2017-09-08

    Many ascidian species have experienced worldwide introductions, exhibiting remarkable success in crossing geographic borders and adapting to local environmental conditions. To investigate the potential role of microbial symbionts in these introductions, we examined the microbial communities of three ascidian species common in North Carolina harbors. Replicate samples of the globally introduced species Distaplia bermudensis, Polyandrocarpa anguinea, and P. zorritensis (n = 5), and ambient seawater (n = 4), were collected in Wrightsville Beach, NC. Microbial communities were characterized by next-generation (Illumina) sequencing of partial (V4) 16S rRNA gene sequences. Ascidians hosted diverse symbiont communities, consisting of 5,696 unique microbial OTUs (at 97% sequenced identity) from 47 bacterial and three archaeal phyla. Permutational multivariate analyses of variance revealed clear differentiation of ascidian symbionts compared to seawater bacterioplankton, and distinct microbial communities inhabiting each ascidian species. 103 universal core OTUs (present in all ascidian replicates) were identified, including taxa previously described in marine invertebrate microbiomes with possible links to ammonia-oxidization, denitrification, pathogenesis, and heavy-metal processing. These results suggest ascidian microbial symbionts exhibit a high degree of host-specificity, forming intimate associations that may contribute to host adaptation to new environments via expanded tolerance thresholds and enhanced holobiont function.

  19. Changes in microbial diversity of brined green asparagus upon treatment with high hydrostatic pressure.

    Science.gov (United States)

    Toledo Del Árbol, Julia; Pérez Pulido, Rubén; La Storia, Antonietta; Grande Burgos, Maria José; Lucas, Rosario; Ercolini, Danilo; Gálvez, Antonio

    2016-01-04

    The application of high hydrostatic pressure (HHP, 600MPa, 8 min) on brined green asparagus and the changes in bacterial diversity after treatments and during storage at 4 °C (30 days) or 22 °C (10 days) were studied. HHP treatments reduced viable cell counts by 3.6 log cycles. The residual surviving population did not increase during storage at 4 °C. However, bacterial counts significantly increased at 22 °C by day 3, leading to rapid spoilage. The microbiota of green asparagus was composed mainly by Proteobacteria (mainly Pantoea and Pseudomonas), followed by Firmicutes (mainly Lactococcus and Enterococcus) and to a less extent Bacteroidetes and Actinobacteria. During chill storage of untreated asparagus, the relative abundance of Proteobacteria as well as Enterococcus and Lactococcus decreased while Lactobacillus increased. During storage of untreated asparagus at 22 °C, the abundance of Bacteroidetes decreased while Proteobacteria increased during late storage. The HHP treatment determined a reduction of the Proteobacteria both early after treatment and during chill storage. In the HHP treated samples stored at 22 °C, the relative abundance of Pseudomonas rapidly decreased at day 1, with an increase of Bacteroidetes. This was followed by a marked increase in Enterobacteriaceae (Escherichia) simultaneously with increase in viable counts and spoilage. Results from the study indicate that the effect of HHP treatments on the viability ofmicrobial populations in foods also has an impact on the dynamics of microbial populations during the storage of the treated foods.

  20. High Prevalence and Genotypic Diversity of the Human Papillomavirus in Amazonian Women, Brazil

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    Danielle Albuquerque Pires Rocha

    2013-01-01

    Full Text Available The aim of this study was to determine the prevalence of human papillomavirus (HPV in a women population living within the state of Amazonas, Brazil, and to determine the viral genotypes found. The study included 361 sexually active women over 18 years of age. We performed the Pap test and the molecular diagnosis for HPV DNA using polymerase chain reaction (PCR. The amplicons obtained were sequenced in automatic sequencer for genotyping. The presence of HPV DNA was found in 29.1% (105 of the women. Only 321 women presented satisfactory slides for cytological diagnosis, 97.9% (314 had normal cytology (negative for cancer, and 2.1% (7 had abnormal cytology (4 ASCUS, 1 LSIL, and 2 HSIL. The types more frequently found were HPV 16 (58.1% and HPV 58 (20.0%. Additionally, we found more 13 types of HPV. Compared with previous studies in Brazil, our data confirmed a high prevalence and genotypic diversity of HPV in Brazilian women.

  1. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.

    Science.gov (United States)

    Chen, Eric C H; Morin, Emmanuelle; Beaudet, Denis; Noel, Jessica; Yildirir, Gokalp; Ndikumana, Steve; Charron, Philippe; St-Onge, Camille; Giorgi, John; Krüger, Manuela; Marton, Timea; Ropars, Jeanne; Grigoriev, Igor V; Hainaut, Matthieu; Henrissat, Bernard; Roux, Christophe; Martin, Francis; Corradi, Nicolas

    2018-01-22

    Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

  2. Mosquito Surveillance for 15 Years Reveals High Genetic Diversity Among West Nile Viruses in Israel.

    Science.gov (United States)

    Lustig, Yaniv; Hindiyeh, Musa; Orshan, Laor; Weiss, Leah; Koren, Ravit; Katz-Likvornik, Shiri; Zadka, Hila; Glatman-Freedman, Aharona; Mendelson, Ella; Shulman, Lester M

    2016-04-01

    West Nile Virus (WNV) is endemic in Israel and has been the cause of several outbreaks in recent years. In 2000, a countrywide mosquito survey was established to monitor WNV activity and characterize viral genotypes in Israel. We analyzed data from 7135 pools containing 277 186 mosquitoes collected over the past 15 years and, here, report partial sequences of WNV genomes obtained from 102 of the 336 positive mosquito pools. Phylogenetic analysis demonstrated that cluster 4 and the Mediterranean and Eastern European subtypes of cluster 2 within WNV lineage 1 circulated in Israel, as did WNV lineage 2, highlighting a high genetic diversity of WNV genotypes in our region. As a major crossroads for bird migration between Africa and Eurasia and with a long history of human infection, Israel serves as a resource hub for WNV in Africa and Eurasia and provides valuable information on WNV circulation in these regions. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  3. New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali.

    Science.gov (United States)

    Dara, Antoine; Drábek, Elliott F; Travassos, Mark A; Moser, Kara A; Delcher, Arthur L; Su, Qi; Hostelley, Timothy; Coulibaly, Drissa; Daou, Modibo; Dembele, Ahmadou; Diarra, Issa; Kone, Abdoulaye K; Kouriba, Bourema; Laurens, Matthew B; Niangaly, Amadou; Traore, Karim; Tolo, Youssouf; Fraser, Claire M; Thera, Mahamadou A; Djimde, Abdoulaye A; Doumbo, Ogobara K; Plowe, Christopher V; Silva, Joana C

    2017-03-28

    Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40-60 var gene complement for individual infections has been notoriously difficult, impeding molecular epidemiological studies and the assessment of particular var elements as subunit vaccine candidates. We developed and validated a novel algorithm, Exon-Targeted Hybrid Assembly (ETHA), to perform targeted assembly of var gene sequences, based on a combination of Pacific Biosciences and Illumina data. Using ETHA, we characterized the repertoire of var genes in 12 samples from uncomplicated malaria infections in children from a single Malian village and showed them to be as genetically diverse as vars from isolates from around the globe. The gene var2csa, a member of the var family associated with placental malaria pathogenesis, was present in each genome, as were vars previously associated with severe malaria. ETHA, a tool to discover novel var sequences from clinical samples, will aid the understanding of malaria pathogenesis and inform the design of malaria vaccines based on PfEMP1. ETHA is available at: https://sourceforge.net/projects/etha/ .

  4. Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity

    Science.gov (United States)

    Marietou, Angeliki

    2014-01-01

    Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure. PMID:25063663

  5. Effects of Bubble-Mediated Processes on Nitrous Oxide Dynamics in Denitrifying Bioreactors

    Science.gov (United States)

    McGuire, P. M.; Falk, L. M.; Reid, M. C.

    2017-12-01

    To mitigate groundwater and surface water impacts of reactive nitrogen (N), agricultural and stormwater management practices can employ denitrifying bioreactors (DNBs) as low-cost solutions for enhancing N removal. Due to the variable nature of hydrologic events, DNBs experience dynamic flows which can impact physical and biological processes within the reactors and affect performance. A particular concern is incomplete denitrification, which can release the potent greenhouse gas nitrous oxide (N2O) to the atmosphere. This study aims to provide insight into the effects of varying hydrologic conditions upon the operation of DNBs by disentangling abiotic and biotic controls on denitrification and N2O dynamics within a laboratory-scale bioreactor. We hypothesize that under transient hydrologic flows, rising water levels lead to air entrapment and bubble formation within the DNB porous media. Mass transfer of oxygen (O2) between trapped gas and liquid phases creates aerobic microenvironments that can inhibit N2O reductase (NosZ) enzymes and lead to N2O accumulation. These bubbles also retard N2O transport and make N2O unavailable for biological reduction, further enhancing atmospheric fluxes when water levels fall. The laboratory-scale DNB permits measurements of longitudinal and vertical profiles of dissolved constituents as well as trace gas concentrations in the reactor headspace. We describe a set of experiments quantifying denitrification pathway biokinetics under steady-state and transient hydrologic conditions and evaluate the role of bubble-mediated processes in enhancing N2O accumulation and fluxes. We use sulfur hexafluoride and helium as dissolved gas tracers to examine the impact of bubble entrapment upon retarded gas transport and enhanced trace gas fluxes. A planar optode sensor within the bioreactor provides near-continuous 2-D profiles of dissolved O2 within the bioreactor and allows for identification of aerobic microenvironments. We use qPCR to

  6. Life Cycle Assessment of a Highly Diverse Vegetable Multi-Cropping System in Fengqiu County, China

    Directory of Open Access Journals (Sweden)

    Li Li

    2018-03-01

    Full Text Available Agricultural biodiversity usually leads to greater sustainability in production practices. To understand the environmental implications of the development of village-level multi-cropping in rural China, we compared the environmental impact of a highly diverse vegetable multi-cropping system to a conventional wheat/maize rotation system based on the method of life cycle assessment (LCA. Using household level cultivation data, this study examined the gate-to-gate environmental impacts of on-site cultivation practices relating to the production of 10,000 nutrient equivalent units. Results show that vegetable multi-cropping resulted in decreased average land requirement, and diesel, water and electricity usage by 69.8%, 62.2%, 71.7%, and 63.4%, respectively, while average nitrogen (Total N, phosphorus (P2O5, and potassium (K2O usage in vegetable multi-cropping systems decreased by 16.3%, 42.1%, and 75.8%, respectively. Additional corresponding effects led to a decrease in the total global warming, eutrophication, and acidification potentials from external inputs by 21.6%, 16.7%, and 16.2% of the entire system, respectively. Moreover, the midpoint human toxicity potential from pesticide usage of the vegetable multi-cropping system was lower than that of the conventional system. However, the midpoint eco-toxicity potential from pesticide usage was higher due to certain highly toxic substances, and both human and eco-toxicity potentials from heavy metals were all higher by a few orders of magnitudes. Thus, to mitigate these detrimental consequences, some related measures are proposed for sustainable practices in the future implementation of multi-cropping systems.

  7. Enabling Diverse Software Stacks on Supercomputers using High Performance Virtual Clusters.

    Energy Technology Data Exchange (ETDEWEB)

    Younge, Andrew J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Pedretti, Kevin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Grant, Ryan [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Brightwell, Ron [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-05-01

    While large-scale simulations have been the hallmark of the High Performance Computing (HPC) community for decades, Large Scale Data Analytics (LSDA) workloads are gaining attention within the scientific community not only as a processing component to large HPC simulations, but also as standalone scientific tools for knowledge discovery. With the path towards Exascale, new HPC runtime systems are also emerging in a way that differs from classical distributed com- puting models. However, system software for such capabilities on the latest extreme-scale DOE supercomputing needs to be enhanced to more appropriately support these types of emerging soft- ware ecosystems. In this paper, we propose the use of Virtual Clusters on advanced supercomputing resources to enable systems to support not only HPC workloads, but also emerging big data stacks. Specifi- cally, we have deployed the KVM hypervisor within Cray's Compute Node Linux on a XC-series supercomputer testbed. We also use libvirt and QEMU to manage and provision VMs directly on compute nodes, leveraging Ethernet-over-Aries network emulation. To our knowledge, this is the first known use of KVM on a true MPP supercomputer. We investigate the overhead our solution using HPC benchmarks, both evaluating single-node performance as well as weak scaling of a 32-node virtual cluster. Overall, we find single node performance of our solution using KVM on a Cray is very efficient with near-native performance. However overhead increases by up to 20% as virtual cluster size increases, due to limitations of the Ethernet-over-Aries bridged network. Furthermore, we deploy Apache Spark with large data analysis workloads in a Virtual Cluster, ef- fectively demonstrating how diverse software ecosystems can be supported by High Performance Virtual Clusters.

  8. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    Directory of Open Access Journals (Sweden)

    Yan Zheng

    Full Text Available The oriental fruit moth Grapholita ( = Cydia molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.

  9. Diversity and Phenology of Wild Bees in a Highly Disturbed Tropical Dry Forest "Desierto de la Tatacoa", Huila-Colombia.

    Science.gov (United States)

    Poveda-Coronel, C A; Riaño-Jiménez, D; Cure, J R

    2018-01-12

    Colombian tropical dry forest is considered the most endangered tropical biome due to anthropic activities. Desierto de la Tatacoa (DsT) is an example of high disturbed tropical dry forest which still maintains a high biodiversity. The objective of the study was to record the diversity and phenology of wild bees in this place by monthly sampling between December 2014 and December 2016 in a 9-km 2 area. During the study, there was a prolonged El Niño-Southern Oscillation period. Bees were collected by entomological nets, malaise traps, eugenol scent trapping, and nest traps. Shannon index was calculated to estimate diversity and Simpson index to determine dominance of a species. The effect of environmental conditions (wet and dry season) in richness and abundance was analyzed by paired T tests. A total of 3004 bee specimens were collected, belonging to 80 species from Apidae, Megachilidae, Halictidae, and Colletidae. Apidae was the most diverse. Shannon index value was 2.973 (discarding Apis mellifera Linnaeus 1758 data); thus, DsT can be considered as a zone of high wild bee diversity. Dry and rainy season showed differences in diversity (p < 0.05). Rainy season showed larger blooming periods and higher bee diversity than dry season. In both seasons, social species were dominant (e.g., A. mellifera or Trigona fulviventris Guérin 1844). Although DsT is a highly disturbed ecosystem, this study found it has the second highest number of genera and the fourth highest number of species reported in Colombia.

  10. High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia.

    Science.gov (United States)

    Arias, Leonardo; Barbieri, Chiara; Barreto, Guillermo; Stoneking, Mark; Pakendorf, Brigitte

    2018-02-01

    Northwestern Amazonia (NWA) is a center of high linguistic and cultural diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns, with some groups being foragers and others agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners are taken from different language groups. In this study, we use high-resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural diversity on the genetic relationships and population structure of NWA groups. We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1,030×. The mtDNA data revealed that NWA populations have high genetic diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher genetic diversity, while the foraging Nukak have lower genetic diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Contrary to the view of NWA as a pristine area inhabited by small human populations living in isolation, our data support a view of high diversity and contact among different ethnolinguistic groups, with movement along rivers probably facilitating this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world. © 2017 Wiley Periodicals, Inc.

  11. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

    KAUST Repository

    Perdigã o, Joã o; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel

    2014-01-01

    Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

  12. Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

    Science.gov (United States)

    Zhang, Xiao-Yong; Wang, Guang-Hua; Xu, Xin-Ya; Nong, Xu-Hua; Wang, Jie; Amin, Muhammad; Qi, Shu-Hua

    2016-10-01

    The present study investigated the fungal diversity in four different deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS1). A total of 40,297 fungal ITS1 sequences clustered into 420 operational taxonomic units (OTUs) with 97% sequence similarity and 170 taxa were recovered from these sediments. Most ITS1 sequences (78%) belonged to the phylum Ascomycota, followed by Basidiomycota (17.3%), Zygomycota (1.5%) and Chytridiomycota (0.8%), and a small proportion (2.4%) belonged to unassigned fungal phyla. Compared with previous studies on fungal diversity of sediments from deep-sea environments by culture-dependent approach and clone library analysis, the present result suggested that Illumina sequencing had been dramatically accelerating the discovery of fungal community of deep-sea sediments. Furthermore, our results revealed that Sordariomycetes was the most diverse and abundant fungal class in this study, challenging the traditional view that the diversity of Sordariomycetes phylotypes was low in the deep-sea environments. In addition, more than 12 taxa accounted for 21.5% sequences were found to be rarely reported as deep-sea fungi, suggesting the deep-sea sediments from Okinawa Trough harbored a plethora of different fungal communities compared with other deep-sea environments. To our knowledge, this study is the first exploration of the fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing.

  13. Motivators of and Barriers to Health-Promoting Behaviors among Culturally Diverse Middle and High School Students

    Science.gov (United States)

    Wippold, Guillermo M.; Tucker, Carolyn M; Smith, Tasia M.; Rodriguez, Victoria A.; Hayes, Lynda F.; Folger, Austin C.

    2018-01-01

    Background: Youth obesity in the United States is a major health concern. Obesity can be reduced by increasing health-promoting behaviors. Purpose: The goals of the present study were to (1) identify the strongest motivators of and barriers to health-promoting behaviors among a culturally diverse group of middle and high school students and (2)…

  14. Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

    NARCIS (Netherlands)

    Geisen, S.; Laros, I.; Vizcaino, A.; Bonkowski, M.; Groot, de G.A.

    2015-01-01

    Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into

  15. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae uncovered by microsatellite loci.

    Directory of Open Access Journals (Sweden)

    Chris D Lowe

    2010-12-01

    Full Text Available Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST values indicated weak to moderate population sub-division (0.01-0.12, but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.

  16. Mitigation of nitrous oxide (N2O) emissions from denitrifying fluidized bed bioreactors (DFBBRs) using calcium.

    Science.gov (United States)

    Eldyasti, Ahmed; Nakhla, George; Zhu, Jesse

    2014-12-01

    Nitrous oxide (N2O) is a significant anthropogenic greenhouse gases (AnGHGs) emitted from biological nutrient removal (BNR) processes. In this study, N2O production from denitrifying fluidized bed bioreactors (DFBBR) was reduced using calcium (Ca2+) dosage. The DFBBRs were operated on a synthetic municipal wastewater at four different calcium concentrations ranging from the typical municipal wastewater Ca2+ concentration (60 mg Ca2+/L) to 240 mg Ca2+/L at two different COD/N ratios. N2O emission rates, extracellular polymeric substances (EPS), water quality parameters, and microscopic images were monitored regularly in both phases. Calcium concentrations played a significant role in biofilm morphology with the detachment rates for R120Ca, R180Ca, and R240Ca 75% lower than for R60Ca, respectively. The N2O conversion rate at the typical municipal wastewater Ca2+ concentration (R60Ca) was about 0.53% of the influent nitrogen loading as compared with 0.34%, 0.42%, and 0.41% for R120Ca, R180Ca, and R240Ca, respectively corresponding to 21-36% reduction. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Storage and growth of denitrifiers in aerobic granules: part I. model development.

    Science.gov (United States)

    Ni, Bing-Jie; Yu, Han-Qing

    2008-02-01

    A mathematical model, based on the Activated Sludge Model No.3 (ASM3), is developed to describe the storage and growth activities of denitrifiers in aerobic granules under anoxic conditions. In this model, mass transfer, hydrolysis, simultaneous anoxic storage and growth, anoxic maintenance, and endogenous decay are all taken into account. The model established is implemented in the well-established AQUASIM simulation software. A combination of completely mixed reactor and biofilm reactor compartments provided by AQUASIM is used to simulate the mass transport and conversion processes occurring in both bulk liquid and granules. The modeling results explicitly show that the external substrate is immediately utilized for storage and growth at feast phase. More external substrates are diverted to storage process than the primary biomass production process. The model simulation indicates that the nitrate utilization rate (NUR) of granules-based denitrification process includes four linear phases of nitrate reduction. Furthermore, the methodology for determining the most important parameter in this model, that is, anoxic reduction factor, is established. (c) 2007 Wiley Periodicals, Inc.

  18. The optimal ecological factors and the denitrification populationof a denitrifying process for sulfate reducing bacteriainhibition

    Science.gov (United States)

    Li, Chunying

    2018-02-01

    SRB have great negative impacts on the oil production in Daqing Oil field. A continuous-flow anaerobic baffled reactors (ABR) are applied to investigate the feasibility and optimal ecological factors for the inhibition of SRB by denitrifying bacteria (DNB). The results showed that the SO42- to NO3- concentration ratio (SO42-/NO3-) are the most important ecological factor. The input of NO3- and lower COD can enhance the inhibition of S2-production effectively. The effective time of sulfate reduction is 6 h. Complete inhibition of SRB is obtained when the influent COD concentration is 600 mg/L, the SO42-/NO3- is 1/1 (600 mg/L for each), N is added simultaneously in the 2# and the 5# ABR chambers. By extracting the total DNA of wastewater from the effective chamber, 16SrDNA clones of a bacterium had been constructed. It is showed that the Proteobacteria accounted for eighty- four percent of the total clones. The dominant species was the Neisseria. Sixteen percent of the total clones were the Bacilli of Frimicutes. It indicated that DNB was effective and feasible for SRB inhibition.

  19. Elementary sulfur in effluent from denitrifying sulfide removal process as adsorbent for zinc(II).

    Science.gov (United States)

    Chen, Chuan; Zhou, Xu; Wang, Aijie; Wu, Dong-hai; Liu, Li-hong; Ren, Nanqi; Lee, Duu-Jong

    2012-10-01

    The denitrifying sulfide removal (DSR) process can simultaneously convert sulfide, nitrate and organic compounds into elementary sulfur (S(0)), di-nitrogen gas and carbon dioxide, respectively. However, the S(0) formed in the DSR process are micro-sized colloids with negatively charged surface, making isolation of S(0) colloids from other biological cells and metabolites difficult. This study proposed the use of S(0) in DSR effluent as a novel adsorbent for zinc removal from wastewaters. Batch and continuous tests were conducted for efficient zinc removal with S(0)-containing DSR effluent. At pHremoval rates of zinc(II) were increased with increasing pH. The formed S(0) colloids carried negative charge onto which zinc(II) ions could be adsorbed via electrostatic interactions. The zinc(II) adsorbed S(0) colloids further enhanced coagulation-sedimentation efficiency of suspended solids in DSR effluents. The DSR effluent presents a promising coagulant for zinc(II) containing wastewaters. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Cacao Cultivation under Diverse Shade Tree Cover Allows High Carbon Storage and Sequestration without Yield Losses.

    Science.gov (United States)

    Abou Rajab, Yasmin; Leuschner, Christoph; Barus, Henry; Tjoa, Aiyen; Hertel, Dietrich

    2016-01-01

    One of the main drivers of tropical forest loss is their conversion to oil palm, soy or cacao plantations with low biodiversity and greatly reduced carbon storage. Southeast Asian cacao plantations are often established under shade tree cover, but are later converted to non-shaded monocultures to avoid resource competition. We compared three co-occurring cacao cultivation systems (3 replicate stands each) with different shade intensity (non-shaded monoculture, cacao with the legume Gliricidia sepium shade trees, and cacao with several shade tree species) in Sulawesi (Indonesia) with respect to above- and belowground biomass and productivity, and cacao bean yield. Total biomass C stocks (above- and belowground) increased fivefold from the monoculture to the multi-shade tree system (from 11 to 57 Mg ha-1), total net primary production rose twofold (from 9 to 18 Mg C ha-1 yr-1). This increase was associated with a 6fold increase in aboveground biomass, but only a 3.5fold increase in root biomass, indicating a clear shift in C allocation to aboveground tree organs with increasing shade for both cacao and shade trees. Despite a canopy cover increase from 50 to 93%, cacao bean yield remained invariant across the systems (variation: 1.1-1.2 Mg C ha-1 yr-1). The monocultures had a twice as rapid leaf turnover suggesting that shading reduces the exposure of cacao to atmospheric drought, probably resulting in greater leaf longevity. Thus, contrary to general belief, cacao bean yield does not necessarily decrease under shading which seems to reduce physical stress. If planned properly, cacao plantations under a shade tree cover allow combining high yield with benefits for carbon sequestration and storage, production system stability under stress, and higher levels of animal and plant diversity.

  1. Tiny worms from a mighty continent: high diversity and new phylogenetic lineages of African monogeneans.

    Science.gov (United States)

    Přikrylová, Iva; Vanhove, Maarten P M; Janssens, Steven B; Billeter, Paul A; Huyse, Tine

    2013-04-01

    The family Gyrodactylidae contains one of the most significant radiations of platyhelminth fish parasites. The so-called hyperviviparity is very rare in the animal kingdom, and the rapid generation time can lead to an explosive population growth, which can cause massive losses in farmed fish. Here we present the first molecular phylogeny including all-but-one African genera, inferred from ITS and 18S rDNA sequences. The validity of nominal genera is discussed in relation to the systematic value of morphological characters traditionally used for generic identification. New complete 18S rDNA sequences of 18 gyrodactylid species of eight genera together with ITS rDNA gene sequences of eight species representing seven genera were generated and complemented with GenBank sequences. The maximum likelihood and Bayesian analyses pointed to a paraphyletic nature of African Gyrodactylus species. They formed well-supported clades possibly indicating speciation within host taxa: (1) parasites of cichlids (Cichlidae); (2) parasites of catfishes (Siluriformes), consisting of a lineage infecting mochokids and one infecting clariids. Macrogyrodactylus spp. firmly clustered into a monophyletic group. We found that Swingleus and Fundulotrema are very closely related and clearly cluster within Gyrodactylus. This supports earlier claims as to the paraphyly of the nominal genus Gyrodactylus as it is currently defined, and necessitates a revision of Swingleus and Fundulotrema. Molecular dating estimates confirmed a relatively young, certainly post-Gondwanan, origin of gyrodactylid lineages. Building on the previously suggested South-American origin of viviparous gyrodactylids, the dataset suggests subsequent intercontinental dispersal to Africa and from there repeated colonisation of the Holarctic. Even though the African continent has been heavily under sampled, the present diversity is far greater than in the intensively studied European fauna, probably because of the high endemicity

  2. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

    KAUST Repository

    Perdigão, João

    2014-11-18

    Background Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades. Results In the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM). The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation. Conclusions Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

  3. The diverse evolutionary paths of simulated high-z massive, compact galaxies to z = 0

    Science.gov (United States)

    Wellons, Sarah; Torrey, Paul; Ma, Chung-Pei; Rodriguez-Gomez, Vicente; Pillepich, Annalisa; Nelson, Dylan; Genel, Shy; Vogelsberger, Mark; Hernquist, Lars

    2016-02-01

    Massive quiescent galaxies have much smaller physical sizes at high redshift than today. The strong evolution of galaxy size may be caused by progenitor bias, major and minor mergers, adiabatic expansion, and/or renewed star formation, but it is difficult to test these theories observationally. Herein, we select a sample of 35 massive, compact galaxies (M* = 1-3 × 1011 M⊙, M*/R1.5 > 1010.5 M⊙/kpc1.5) at z = 2 in the cosmological hydrodynamical simulation Illustris and trace them forwards to z = 0 to uncover their evolution and identify their descendants. By z = 0, the original factor of 3 difference in stellar mass spreads to a factor of 20. The dark matter halo masses similarly spread from a factor of 5 to 40. The galaxies' evolutionary paths are diverse: about half acquire an ex situ envelope and are the core of a more massive descendant, a third survive undisturbed and gain very little mass, 15 per cent are consumed in a merger with a more massive galaxy, and a small remainder are thoroughly mixed by major mergers. The galaxies grow in size as well as mass, and only ˜10 per cent remain compact by z = 0. The majority of the size growth is driven by the acquisition of ex situ mass. The most massive galaxies at z = 0 are the most likely to have compact progenitors, but this trend possesses significant dispersion which precludes a direct linkage to compact galaxies at z = 2. The compact galaxies' merger rates are influenced by their z = 2 environments, so that isolated or satellite compact galaxies (which are protected from mergers) are the most likely to survive to the present day.

  4. Broadband High Efficiency Fractal-Like and Diverse Geometry Silicon Nanowire Arrays for Photovoltaic Applications

    Science.gov (United States)

    AL-Zoubi, Omar H.

    Solar energy has many advantages over conventional sources of energy. It is abundant, clean and sustainable. One way to convert solar energy directly into electrical energy is by using the photovoltaic solar cells (PVSC). Despite PVSC are becoming economically competitive, they still have high cost and low light to electricity conversion efficiency. Therefore, increasing the efficiency and reducing the cost are key elements for producing economically more competitive PVSC that would have significant impact on energy market and saving environment. A significant percentage of the PVSC cost is due to the materials cost. For that, thin films PVSC have been proposed which offer the benefits of the low amount of material and fabrication costs. Regrettably, thin film PVSC show poor light to electricity conversion efficiency because of many factors especially the high optical losses. To enhance conversion efficiency, numerous techniques have been proposed to reduce the optical losses and to enhance the absorption of light in thin film PVSC. One promising technique is the nanowire (NW) arrays in general and the silicon nanowire (SiNW) arrays in particular. The purpose of this research is to introduce vertically aligned SiNW arrays with enhanced and broadband absorption covering the entire solar spectrum while simultaneously reducing the amount of material used. To this end, we apply new concept for designing SiNW arrays based on employing diversity of physical dimensions, especially radial diversity within certain lattice configurations. In order to study the interaction of light with SiNW arrays and compute their optical properties, electromagnetic numerical modeling is used. A commercial numerical electromagnetic solver software package, high frequency structure simulation (HFSS), is utilized to model the SiNW arrays and to study their optical properties. We studied different geometries factors that affect the optical properties of SiNW arrays. Based on this study, we

  5. Nursing and health sciences workforce diversity research using PhotoVoice: a college and high school student participatory project.

    Science.gov (United States)

    Benavides-Vaello, Sandra; Katz, Janet R; Peterson, Jeffery Chaichana; Allen, Carol B; Paul, Robbie; Charette-Bluff, Andrea Lelana; Morris, Phyllis

    2014-04-01

    This participatory study used PhotoVoice and qualitative description to (a) mentor baccalaureate nursing and college students in workforce diversity research; (b) explore barriers and facilitators encountered by rural American Indian, Hispanic, and other high school students when attending college and pursuing careers in nursing or the health sciences; and (c) model a process of social action to help existing and future students. Baccalaureate nursing and graduate students participated in all stages of research, including dissemination. Five themes emerged from analysis of PhotoVoice data: (a) being afraid; (b) believing; (c) taking small steps; (d) facing fears; and (e) using support systems. Findings underscore the importance of helping students participate in efforts to increase work-force diversity through research. Increasing nursing and health sciences workforce diversity may require strategies developed within and tailored to specific cultures and communities. Copyright 2014, SLACK Incorporated.

  6. High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States.

    Science.gov (United States)

    Holguin, Claudia M; Baeza, Juan A; Mueller, John D; Agudelo, Paula

    2015-07-01

    Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group.

  7. Nitrous Oxide Emission and Denitrifier Abundance in Two Agricultural Soils Amended with Crop Residues and Urea in the North China Plain.

    Directory of Open Access Journals (Sweden)

    Jianmin Gao

    Full Text Available The application of crop residues combined with Nitrogen (N fertilizer has been broadly adopted in China. Crop residue amendments can provide readily available C and N, as well as other nutrients to agricultural soils, but also intensify the N fixation, further affecting N2O emissions. N2O pulses are obviously driven by rainfall, irrigation and fertilization. Fertilization before rainfall or followed by flooding irrigation is a general management practice for a wheat-maize rotation in the North China Plain. Yet, little is known on the impacts of crop residues combined with N fertilizer application on N2O emission under high soil moisture content. A laboratory incubation experiment was conducted to investigate the effects of two crop residue amendments (maize and wheat, individually or in combination with N fertilizer, on N2O emissions and denitrifier abundance in two main agricultural soils (one is an alluvial soil, pH 8.55, belongs to Ochri-Aquic Cambosols, OAC, the other is a lime concretion black soil, pH 6.61, belongs to Hapli-Aquic Vertosols, HAV under 80% WFPS (the water filled pore space in the North China Plain. Each type soil contains seven treatments: a control with no N fertilizer application (CK, N0, 200 kg N ha-1 (N200, 250 kg N ha-1 (N250, maize residue plus N200 (MN200, maize residue plus N250 (MN250, wheat residue plus N200 (WN200 and wheat residue plus N250 (WN250. Results showed that, in the HAV soil, MN250 and WN250 increased the cumulative N2O emissions by 60% and 30% compared with N250 treatment, respectively, but MN200 and WN200 decreased the cumulative N2O emissions by 20% and 50% compared with N200. In the OAC soil, compared with N200 or N250, WN200 and WN250 increased the cumulative N2O emission by 40%-50%, but MN200 and MN250 decreased the cumulative N2O emission by 10%-20%. Compared with CK, addition of crop residue or N fertilizer resulted in significant increases in N2O emissions in both soils. The cumulative N2O

  8. High spatial variation in terrestrial arthropod species diversity and composition near the Greenland ice cap

    DEFF Research Database (Denmark)

    Hansen, Rikke Reisner; Hansen, Oskar Liset Pryds; Bowden, Joseph James

    2016-01-01

    Arthropods form a major part of the terrestrial species diversity in the Arctic, and are particularly sensitive to temporal changes in the abiotic environment. It is assumed that most Arctic arthropods are habitat generalists and that their diversity patterns exhibit low spatial variation....... The empirical basis for this assumption, however, is weak. We examine the degree of spatial variation in species diversity and assemblage structure among five habitat types at two sites of similar abiotic conditions and plant species composition in southwest Greenland, using standardized field collection...... methods for spiders, beetles and butterflies. We employed non-metric multidimensional scaling, species richness estimation, community dissimilarity and indicator species analysis to test for local (within site)- and regional (between site)-scale differences in arthropod communities. To identify specific...

  9. High diversity in cretaceous ichthyosaurs from Europe prior to their extinction.

    Directory of Open Access Journals (Sweden)

    Valentin Fischer

    Full Text Available BACKGROUND: Ichthyosaurs are reptiles that inhabited the marine realm during most of the Mesozoic. Their Cretaceous representatives have traditionally been considered as the last survivors of a group declining since the Jurassic. Recently, however, an unexpected diversity has been described in Upper Jurassic-Lower Cretaceous deposits, but is widely spread across time and space, giving small clues on the adaptive potential and ecosystem control of the last ichthyosaurs. The famous but little studied English Gault Formation and 'greensands' deposits (the Upper Greensand Formation and the Cambridge Greensand Member of the Lower Chalk Formation offer an unprecedented opportunity to investigate this topic, containing thousands of ichthyosaur remains spanning the Early-Late Cretaceous boundary. METHODOLOGY/PRINCIPAL FINDINGS: To assess the diversity of the ichthyosaur assemblage from these sedimentary bodies, we recognized morphotypes within each type of bones. We grouped these morphotypes together, when possible, by using articulated specimens from the same formations and from new localities in the Vocontian Basin (France; a revised taxonomic scheme is proposed. We recognize the following taxa in the 'greensands': the platypterygiines 'Platypterygius' sp. and Sisteronia seeleyi gen. et sp. nov., indeterminate ophthalmosaurines and the rare incertae sedis Cetarthrosaurus walkeri. The taxonomic diversity of late Albian ichthyosaurs now matches that of older, well-known intervals such as the Toarcian or the Tithonian. Contrasting tooth shapes and wear patterns suggest that these ichthyosaurs colonized three distinct feeding guilds, despite the presence of numerous plesiosaur taxa. CONCLUSION/SIGNIFICANCE: Western Europe was a diversity hot-spot for ichthyosaurs a few million years prior to their final extinction. By contrast, the low diversity in Australia and U.S.A. suggests strong geographical disparities in the diversity pattern of Albian

  10. [Bacterial diversity in sequencing batch biofilm reactor (SBBR) for landfill leachate treatment using PCR-DGGE].

    Science.gov (United States)

    Xiao, Yong; Yang, Zhao-hui; Zeng, Guang-ming; Ma, Yan-he; Liu, You-sheng; Wang, Rong-juan; Xu, Zheng-yong

    2007-05-01

    For studying the bacterial diversity and the mechanism of denitrification in sequencing bath biofilm reactor (SBBR) treating landfill leachate to provide microbial evidence for technique improvements, total microbial DNA was extracted from samples which were collected from natural landfill leachate and biofilm of a SBBR that could efficiently remove NH4+ -N and COD of high concentration. 16S rDNA fragments were amplified from the total DNA successfully using a pair of universal bacterial 16S rDNA primer, GC341F and 907R, and then were used for denaturing gradient gel electrophoresis (DGGE) analysis. The bands in the gel were analyzed by statistical methods and excided from the gel for sequencing, and the sequences were used for homology analysis and then two phylogenetic trees were constructed using DNAStar software. Results indicated that the bacterial diversity of the biofilm in SBBR and the landfill leachate was abundant, and no obvious change of community structure happened during running in the biofilm, in which most bacteria came from the landfill leachate. There may be three different modes of denitrification in the reactor because several different nitrifying bacteria, denitrifying bacteria and anaerobic ammonia oxidation bacteria coexisted in it. The results provided some valuable references for studying microbiological mechanism of denitrification in SBBR.

  11. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes

    DEFF Research Database (Denmark)

    Barnes, Christopher James; Maldonado Goyzueta, Carla Brenda; Frøslev, Tobias Guldberg

    2016-01-01

    in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography...... variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full...

  12. Characterization of the diversity of mycosporine-like amino acids in lichens from high altitude region of Himalaya.

    Science.gov (United States)

    Shukla, Vertika; Kumari, Rupender; Patel, Davendra K; Upreti, Dalip K

    2016-01-01

    Lichens are tolerant to a number of environmental variables including high-intensity solar radiations, which is mainly due to the presence of chemical substances in the thallus. Especially, cyanobacterial lichens synthesize a unique class of chemical substances known as mycosporine-like amino acids (MAAs) the primary characteristic of which is strong ultraviolet (UV) absorption between 300 and 360 nm. In view of its UV-protecting potential, the applicability of mass spectral fragmentation using electrospray ionization tandem mass spectrometric analysis for the characterization of MAAs in lichen samples was explored. MAA compounds were characterized in four cyanobacteria-containing lichen species belonging to genus Peltigera, Stereocaulon and Lobaria. Among them, Peltigera and Lobaria are true cyanobacteria containing lichens (cyanolichens) while Stereocaulon is a tripartite lichen, as it contains both green algae (in the thallus) and cyanobacteria (in the cephalodia), collected from higher altitudes of Himalaya (Tungnath-Chopta in Garhwal Himalaya, 3432 m) from an exposed locality experiencing high light intensity. Mass spectral data of distinctive fragmentation pattern revealed that all the four species have good diversity of MAA compounds, especially Lobaria retigera was found to be enriched with highest diversity of oxo and imino MAAs. Overall, different numbers of oxo and imino MAA compounds were detected in the remaining lichen species. Good diversity of imino MAAs has ecological significance which is required to be investigated further. Moreover, the impressive diversity characterized in each lichen species suggests that lichens should be thoroughly studied for their MAAs contents.

  13. Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists.

    Science.gov (United States)

    Lentendu, Guillaume; Mahé, Frédéric; Bass, David; Rueckert, Sonja; Stoeck, Thorsten; Dunthorn, Micah

    2018-05-30

    Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests. © 2018 John Wiley & Sons Ltd.

  14. The Pedagogical Practices of Québec High School Teachers Relative to Sexual Diversity

    Science.gov (United States)

    Richard, Gabrielle

    2015-01-01

    This article explores the ways in which teachers describe their pedagogical and intervention practices relative to sexual diversity in Québec (Canada). Three variables closely associated with teachers who report inclusive practices emerge: experiential training (based on the experience of a lesbian, gay, or bisexual [LGB] teacher), contact…

  15. High Hopes and Harsh Realities: The Real Challenges to Building a Diverse Workforce. Technical Appendix

    Science.gov (United States)

    Putman, Hannah; Hansen, Michael; Walsh, Kate; Quintero, Diana

    2016-01-01

    Public schools are suffering from a well-publicized diversity problem. Minority students make up nearly half of all public school students, yet minority teachers comprise just 18 percent of the teacher workforce. In an effort to address what Slate has described as "the one cause in education everyone supports," school districts across…

  16. High Hopes and Harsh Realities: The Real Challenges to Building a Diverse Workforce

    Science.gov (United States)

    Putman, Hannah; Hansen, Michael; Walsh, Kate; Quintero, Diana

    2016-01-01

    Public schools are suffering from a well-publicized diversity problem. Minority students make up nearly half of all public school students, yet minority teachers comprise just 18 percent of the teacher workforce. In an effort to address what Slate has described as "the one cause in education everyone supports," school districts across…

  17. Intrinsic Motivation, Learning Goals, Engagement, and Achievement in a Diverse High School

    Science.gov (United States)

    Froiland, John Mark; Worrell, Frank C.

    2016-01-01

    Using structural equation models, with gender, parent education, and prior grade point average (GPA) as control variables, we examined the relationships among intrinsic motivation to learn, learning goals, behavioral engagement at school, and academic performance (measured by GPA) in 1,575 students in an ethnically and racially diverse high…

  18. A novel high-throughput drip-flow system to grow autotrophic biofilms of contrasting diversities

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen

    The impact of community diversity on the functioning and assembly of microbial systems remains a central questions in microbial ecology. This question is often addressed by either combining a few cultures without necessarily a history of coexistence, or by using environmental communities, which a...

  19. Soil fungal community and fuctional diversity assessments of agroecosystems in the Southern High Plains

    Science.gov (United States)

    Soil fungi perform a variety of ecosystem functions that are crucial to maintaining agroecosystem sustainability including aggregate stability and soil carbon storage. The purpose of this study was to compare soil fungal communities and functional diversity in integrated crop and livestock (ICL) sy...

  20. High bee and wasp diversity in a heterogeneous tropical farming system compared to protected forest.

    Directory of Open Access Journals (Sweden)

    Christof Schüepp

    Full Text Available It is a globally important challenge to meet increasing demands for resources and, at the same time, protect biodiversity and ecosystem services. Farming is usually regarded as a major threat to biodiversity due to its expansion into natural areas. We compared biodiversity of bees and wasps between heterogeneous small-scale farming areas and protected forest in northern coastal Belize, Central America. Malaise traps operated for three months during the transition from wet to dry season. Farming areas consisted of a mosaic of mixed crop types, open habitat, secondary forest, and agroforestry. Mean species richness per site (alpha diversity, as well as spatial and temporal community variation (beta diversity of bees and wasps were equal or higher in farming areas compared to protected forest. The higher species richness and community variation in farmland was due to additional species that did not occur in the forest, whereas most species trapped in forest were also found in farming areas. The overall regional species richness (gamma diversity increased by 70% with the inclusion of farming areas. Our results suggest that small-scale farming systems adjacent to protected forest may not only conserve, but even favour, biodiversity of some taxonomic groups. We can, however, not exclude possible declines of bee and wasp diversity in more intensified farmland or in landscapes completely covered by heterogeneous farming systems.

  1. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography.

    Directory of Open Access Journals (Sweden)

    Ruth Hershberg

    2008-12-01

    Full Text Available Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC. However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

  2. Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique.

    Science.gov (United States)

    Purahong, Witoon; Pietsch, Katherina A; Lentendu, Guillaume; Schöps, Ricardo; Bruelheide, Helge; Wirth, Christian; Buscot, François; Wubet, Tesfaye

    2017-01-01

    The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics ( Schima superba and Pinus massoniana ) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima . The two deadwood species differed significantly in WIF OTU richness ( Pinus > Schima ) and community composition ( P < 0.001). Variations in WIF community composition of both tree species were significantly explained by wood pH and ecological factors (biotic: deadwood species, basal area and abiotic: soil pH), but the WIF communities derived from each tree species correlated differently with abiotic factors. Interestingly, we found that deadwood decomposition rate significantly correlated with WIF communities and negatively correlated with WIF OTU richness. We conclude that the

  3. Populus species from diverse habitats maintain high night-time conductance under drought.

    Science.gov (United States)

    Cirelli, Damián; Equiza, María Alejandra; Lieffers, Victor James; Tyree, Melvin Thomas

    2016-02-01

    We investigated the interspecific variability in nocturnal whole-plant stomatal conductance under well-watered and drought conditions in seedlings of four species of Populus from habitats characterized by abundant water supply (mesic and riparian) or from drier upland sites. The study was carried out to determine whether (i) nocturnal conductance varies across different species of Populus according to their natural habitat, (ii) nocturnal conductance is affected by water stress similarly to daytime conductance based on species habitat and (iii) differences in conductance among species could be explained partly by differences in stomatal traits. We measured whole-plant transpiration and conductance (G) of greenhouse-grown seedlings using an automated high-resolution gravimetric technique. No relationship was found between habitat preference and daytime G (GD), but night-time G (GN) was on average 1.5 times higher in riparian and mesic species (P. deltoides Bartr. ex Marsh. and P. trichocarpa Torr. & Gray) than in those from drier environments (P. tremuloides Michx. and P. × petrowskyana Schr.). GN was not significantly reduced under drought in riparian species. Upland species restricted GN significantly in response to drought, but it was still at least one order of magnitude greater that the cuticular conductance until leaf death was imminent. Under both well-watered and drought conditions, GN declined with increasing vapour pressure deficit (D). Also, a small increase in GN towards the end of the night period was observed in P. deltoides and P. × petrowskyana, suggesting the involvement of endogenous regulation. The anatomical analyses indicated a positive correlation between G and variable stomatal pore index among species and revealed that stomata are not likely to be leaky but instead seem capable of complete occlusion, which raises the question of the possible physiological role of the significant GN observed under drought. Further comparisons among

  4. Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method.

    Science.gov (United States)

    Prevost, B; Lucas, F S; Ambert-Balay, K; Pothier, P; Moulin, L; Wurtzer, S

    2015-10-01

    Although clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya

    Czech Academy of Sciences Publication Activity Database

    Čapková, Kateřina; Hauer, Tomáš; Řeháková, Klára; Doležal, Jiří

    2016-01-01

    Roč. 71, č. 1 (2016), s. 113-123 ISSN 0095-3628 R&D Projects: GA ČR GA13-13368S Institutional support: RVO:67985939 Keywords : Soil crusts * Cyanobacterial diversity * Western Himalayas Subject RIV: EH - Ecology , Behaviour Impact factor: 3.630, year: 2016

  6. High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt

    Directory of Open Access Journals (Sweden)

    Alfonsina Arriaga-Jiménez

    2018-02-01

    Full Text Available Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest–shrubland–pasture (FSP mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled. These discoveries may indicate that speciation rate is high among these volcanoes—a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity

  7. High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt.

    Science.gov (United States)

    Arriaga-Jiménez, Alfonsina; Rös, Matthias; Halffter, Gonzalo

    2018-01-01

    Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB) in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest-shrubland-pasture (FSP) mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS) displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled). These discoveries may indicate that speciation rate is high among these volcanoes-a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity and abundance patterns

  8. [Distribution Characteristics of Nitrifiers and Denitrifiers in the River Sediments of Tongling City].

    Science.gov (United States)

    Cheng, Jian-hua; Dou, Zhi-yong; Sun, Qing-ye

    2016-04-15

    Rivers in mining areas were influenced by contaminants such as nitrogen, phosphorus and organic matter due to domestic and agricultural wastewater discharge in addition to pollutants caused by mining activities. In this study, surface sediment samples of rivers in Tongling city were collected to address the effect of season and pollution type on the abundance of nitrifiers and denitrifiers using quantitative polymerase chain reaction (QPCR) technique targeting at the ammonia monooxygenase (amoA) and nitrite reductase (nir) genes. The results showed that the average ahundance of ammonia oxidizing archaea (AGA) (ranging from 1.74 x 10⁵ to 1.45 x 10⁸ copies · g⁻¹) was 4.39 times that of ammonia oxidizing hacteria (AGH) (ranging from 1.39 x 10⁵ to 3.39 x 10⁷ copies · g⁻¹); and the average abundance of nirK gene (ranging from 4.45 x 10⁶ to 1.51 x 10⁸ copies · g) was almost a thirtieth part of nirS gene (ranging from 1.69 x 10⁷ to 8.55 x 10⁹ copies · g⁻¹). The abundance of AOA was higher in spring and autumn, and lower in summer and winter. And sediment AOB abundance was higher in spring and winter than in summer and autumn. Meanwhile, the abundance of nir genes was in the order of spring (nirS )/autumn (nirK) > summer > winter > autumn (nirS )/spring (nirK). Moreover, the abundance of bacterial and archaeal arnoA and nirS genes in sediments influenced by mine pollution was generally higher than that in sediments influenced by agricultural non-point pollution, whereas the abundance of nirK gene showed an opposite trend.

  9. DECREASING OF SODIUM NITRITE CONTENT IN COOKED SAUSAGES USING DENITRIFYING MICROORGANISMS

    Directory of Open Access Journals (Sweden)

    Bal-Prylypko L. V.

    2015-08-01

    Full Text Available The purpose of this work was to study reduction of sodium nitrite in cooked sausages by adding of the optimized amount of denitrifying microorganisms to the bacterial preparation maintaining quality characteristics of the product. To develop biotechnology of boiled sausages «Naturel» we selected bacterial preparation based on nitrite-reducing strains of Staphylococcus carnosus and S. carnosus ssp.utilis. It was used generally accepted and special methods. The content of total pigments and nitrozopigments was determined by a method based on the extraction of meat pigments by aqueous acetone; color stability of final products was evaluated as the difference in optical density of nitroso pigment extracts before and after exposure (40 min of the sample under the light source; analytical processing of the experimental data was carried out using modern software; quantitative evaluation of color characteristics was performed in the RGB using a multifunctional device Epson Stylus TX400. Mathematical modeling was carried out on the basis of full factorial experiment such as 22, the optimization was performed by Box–Wilson. According to the study, using of the bacterial preparation based on nitrite-reducing strains of Staphylococcus carnosus and S. carnosus ssp. utilis in biotechnology of boiled sausages «Naturel» has a positive effect on the formation of the complex of required color characteristics of final products (for prototypes of sausages the index redness was 1. 61 times higher compared to the control. Degradation of sodium nitrite and formation of nitroso pigments were intensified that improved the stability of color during the storage (the index of color fastness of experimental cooked sausages was higher by 19%. The results of performed investigations illustrate the possibility of production of cooked sausages with a minimized content of synthetic food additives and ingredients.

  10. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    Energy Technology Data Exchange (ETDEWEB)

    Kampman, Christel, E-mail: christel.kampman@wur.nl [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Hendrickx, Tim L.G. [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M. [Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands)

    2012-08-15

    Highlights: Black-Right-Pointing-Pointer A new concept for low-temperature anaerobic sewage treatment is proposed. Black-Right-Pointing-Pointer In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. Black-Right-Pointing-Pointer The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. Black-Right-Pointing-Pointer The volumetric consumption rate has to be increased by an order of magnitude for practical application. Black-Right-Pointing-Pointer Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to 'Candidatus Methylomirabilis oxyfera' were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO{sub 2}{sup -}-N/L d (using synthetic medium) and 37.8 mg NO{sub 2}{sup -}-N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass

  11. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    International Nuclear Information System (INIS)

    Kampman, Christel; Hendrickx, Tim L.G.; Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M.; Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy

    2012-01-01

    Highlights: ► A new concept for low-temperature anaerobic sewage treatment is proposed. ► In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. ► The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. ► The volumetric consumption rate has to be increased by an order of magnitude for practical application. ► Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to ‘Candidatus Methylomirabilis oxyfera’ were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO 2 − -N/L d (using synthetic medium) and 37.8 mg NO 2 − -N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass retention.

  12. The role of paraffin oil on the interaction between denitrifying anaerobic methane oxidation and Anammox processes.

    Science.gov (United States)

    Fu, Liang; Ding, Zhao-Wei; Ding, Jing; Zhang, Fang; Zeng, Raymond J

    2015-10-01

    Methane is sparingly soluble in water, resulting in a slow reaction rate in the denitrifying anaerobic methane oxidation (DAMO) process. The slow rate limits the feasibility of research to examine the interaction between the DAMO and the anaerobic ammonium oxidation (Anammox) process. In this study, optimized 5 % (v/v) paraffin oil was added as a second liquid phase to improve methane solubility in a reactor containing DAMO and Anammox microbes. After just addition, methane solubility was found to increase by 25 % and DAMO activity was enhanced. After a 100-day cultivation, the paraffin reactor showed almost two times higher consumption rates of NO3 (-) (0.2268 mmol/day) and NH4 (+) (0.1403 mmol/day), compared to the control reactor without paraffin oil. The microbes tended to distribute in the oil-water interface. The quantitative (q) PCR result showed the abundance of gene copies of DAMO archaea, DAMO bacteria, and Anammox bacteria in the paraffin reactor were higher than those in the control reactor after 1 month. Fluorescence in situ hybridization revealed that the percentages of the three microbes were 55.5 and 77.6 % in the control and paraffin reactors after 100 days, respectively. A simple model of mass balance was developed to describe the interactions between DAMO and Anammox microbes and validate the activity results. A mechanism was proposed to describe the possible way that paraffin oil enhanced DAMO activity. It is quite clear that paraffin oil enhances not only DAMO activity but also Anammox activity via the interaction between them; both NO3 (-) and NH4 (+) consumption rates were about two times those of the control.

  13. Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era

    Directory of Open Access Journals (Sweden)

    Claudia Masini d’Avila-Levy

    2015-01-01

    Full Text Available The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmaniaand Trypanosoma.Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.

  14. Clonal diversity and fine-scale genetic structure in a high andean treeline population

    Czech Academy of Sciences Publication Activity Database

    Peng, Y.; Macek, P.; Macková, Jana; Romoleroux, K.; Hensen, I.

    2015-01-01

    Roč. 47, č. 1 (2015), s. 59-65 ISSN 0006-3606 Grant - others:GA AV ČR(CZ) IAA601110702; GA MŠk(CZ) LM2010009 Program:IA Institutional support: RVO:60077344 Keywords : AFLP * clonal diversity * clonal propagation * fine-scale genetic structure * Polylepis reticulata * treeline Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.944, year: 2015

  15. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Czech Academy of Sciences Publication Activity Database

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, Jana; Knudsen, R.; Kuhn, J. A.; Henriksen, E. H.; Siwertsson, A.; Shaw, J. C.; Kuris, A. M.; Amundsen, P.-A.; Scholz, Tomáš; Lafferty, K. D.; Kostadinova, Aneta

    2017-01-01

    Roč. 47, č. 6 (2017), s. 327-345 ISSN 0020-7519 R&D Projects: GA ČR GA15-14198S; GA ČR GAP505/10/1562 Institutional support: RVO:60077344 Keywords : Trematode diversity * intermediate hosts * phylogeny * mitochondrial DNA * nuclear DNA * Lake Takvatn * Norway * Sub-Arctic Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 3.730, year: 2016

  16. High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom.

    Science.gov (United States)

    Liberato, Tarcísio; Troncone, Lanfranco Ranieri Paolo; Yamashiro, Edson T; Serrano, Solange M T; Zelanis, André

    2016-03-01

    Here we present a proteomic characterization of Phoneutria nigriventer venom. A shotgun proteomic approach allowed the identification, for the first time, of O-glycosyl hydrolases (chitinases) in P. nigriventer venom. The electrophoretic profiles under nonreducing and reducing conditions, and protein identification by mass spectrometry, indicated the presence of oligomeric toxin structures in the venom. Complementary proteomic approaches allowed for a qualitative and semi-quantitative profiling of P. nigriventer venom complexity, expanding its known venom proteome diversity.

  17. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Science.gov (United States)

    Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

    2015-01-01

    The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

  18. On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats.

    Science.gov (United States)

    Pessi, Igor Stelmach; Maalouf, Pedro De Carvalho; Laughinghouse, Haywood Dail; Baurain, Denis; Wilmotte, Annick

    2016-06-01

    The study of Antarctic cyanobacterial diversity has been mostly limited to morphological identification and traditional molecular techniques. High-throughput sequencing (HTS) allows a much better understanding of microbial distribution in the environment, but its application is hampered by several methodological and analytical challenges. In this work, we explored the use of HTS as a tool for the study of cyanobacterial diversity in Antarctic aquatic mats. Our results highlight the importance of using artificial communities to validate the parameters of the bioinformatics procedure used to analyze natural communities, since pipeline-dependent biases had a strong effect on the observed community structures. Analysis of microbial mats from five Antarctic lakes and an aquatic biofilm from the Sub-Antarctic showed that HTS is a valuable tool for the assessment of cyanobacterial diversity. The majority of the operational taxonomic units retrieved were related to filamentous taxa such as Leptolyngbya and Phormidium, which are common genera in Antarctic lacustrine microbial mats. However, other phylotypes related to different taxa such as Geitlerinema, Pseudanabaena, Synechococcus, Chamaesiphon, Calothrix, and Coleodesmium were also found. Results revealed a much higher diversity than what had been reported using traditional methods and also highlighted remarkable differences between the cyanobacterial communities of the studied lakes. The aquatic biofilm from the Sub-Antarctic had a distinct cyanobacterial community from the Antarctic lakes, which in turn displayed a salinity-dependent community structure at the phylotype level. © 2016 Phycological Society of America.

  19. Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization.

    Science.gov (United States)

    Tiago, Igor; Veríssimo, António

    2013-06-01

    Microbial and functional diversity were assessed, from a serpentinization-driven subterrestrial alkaline aquifer - Cabeço de Vide Aquifer (CVA) in Portugal. DGGE analyses revealed the presence of a stable microbial community. By 16S rRNA gene libraries and pyrosequencing analyses, a diverse bacterial composition was determined, contrasting with low archaeal diversity. Within Bacteria the majority of the populations were related to organisms or sequences affiliated to class Clostridia, but members of classes Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Deinococci, Gammaproteobacteria and of the phyla Bacteroidetes, Chloroflexi and Nitrospira were also detected. Domain Archaea encompassed mainly sequences affiliated to Euryarchaeota. Only form I RuBisCO - cbbL was detected. Autotrophic carbon fixation via the rTCA, 3-HP and 3-HP/4H-B cycles could not be confirmed. The detected APS reductase alpha subunit - aprA sequences were phylogenetically related to sequences of sulfate-reducing bacteria belonging to Clostridia, and also to sequences of chemolithoautothrophic sulfur-oxidizing bacteria belonging to Betaproteobacteria. Sequences of methyl coenzyme M reductase - mcrA were phylogenetically affiliated to sequences belonging to Anaerobic Methanotroph group 1 (ANME-1). The populations found and the functional key markers detected in CVA suggest that metabolisms related to H2 , methane and/or sulfur may be the major driving forces in this environment. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  20. Highly diverse recombining populations of Vibrio cholerae and Vibrio parahaemolyticus in French Mediterranean coastal lagoons

    Directory of Open Access Journals (Sweden)

    Kevin eEsteves

    2015-07-01

    Full Text Available Vibrio parahaemolyticus and Vibrio cholerae are ubiquitous to estuarine and marine environments. These two species can induce infections in humans. Therefore understanding the structure and dynamics of non-pandemic environmental populations in temperate regions, such as Mediterranean coastal systems, is important if we are to evaluate the risks of infection to humans.Environmental isolates of V. cholerae (n=109 and V. parahaemolyticus (n=89 sampled at different dates, stations and water salinities were investigated for virulence genes and by a multilocus sequence-based analysis (MLSA. V. cholerae isolates were all ctxA negative and only one isolate of V. parahaemolyticus displayed trh2 gene. Most Sequence Types (ST corresponded to unique ST isolated at one date or one station. Frequent recombination events were detected among different pathogenic species, V. parahaemolyticus, V. cholerae, Vibrio mimicus and Vibrio metoecus. Recombination had a major impact on the diversification of lineages. The genetic diversity assessed by the number of ST/strain was higher in low salinity conditions for V. parahaemolyticus and V. cholerae whereas the frequency of recombination events in V. cholerae was lower in low salinity. Mediterranean coastal lagoon systems housed V. cholerae and V. parahaemolyticus with genetic diversities equivalent to the worldwide diversity described so far. The presence of STs found in human infections as well as the frequency of recombination events in environmental vibrios populations could predict a potential epidemiological risk.

  1. Co-effects of pyrene and nitrate on the activity and abundance of soil denitrifiers under anaerobic condition.

    Science.gov (United States)

    Zhou, Zhi-Feng; Yao, Yan-Hong; Wang, Ming-Xia; Zuo, Xiao-Hu

    2017-10-01

    It has previously been confirmed that polycyclic aromatic hydrocarbons (PAHs) could be degraded by soil microbes coupling with denitrification, but the relationships among soil denitrifiers, PAHs, and nitrate under obligate anaerobic condition are still unclear. Here, co-effects of pyrene and nitrate on the activity and abundance of soil denitrifiers were investigated through a 45-day incubation experiment. Two groups of soil treatments with (N 30 ) and without (N 0 ) nitrate (30 mg kg -1 dry soil) amendment were conducted, and each group contained three treatments with different pyrene concentrations (0, 30, and 60 mg kg -1 dry soil denoted as P 0 , P 30 , and P 60 , respectively). The pyrene content, abundances of denitrification concerning genes (narG, periplasmic nitrate reductase gene; nirS, cd 1 -nitrite reductase gene; nirK, copper-containing nitrite reductase gene), and productions of N 2 O and CO 2 were measured at day 3, 14, 28, and 45, and the bacterial community structures in four represented treatments (N 0 P 0 , N 0 P 60 , N 30 P 0 , and N 30 P 60 ) were analyzed at day 45. The results indicated that the treatments with higher pyrene concentration had higher final pyrene removal rates than the treatments with lower pyrene concentration. Additionally, intensive emission of N 2 O was detected in all treatments only at day 3, but a continuous production of CO 2 was measured in each treatment during the incubation. Nitrate amendment could enhance the activity of soil denitrifiers, and be helpful for soil microbes to sustain their activity. While pyrene seemed had no influence on the productions of N 2 O and CO 2 , and amendment with pyrene or nitrate both had no obvious effect on abundances of denitrification concerning genes. Furthermore, it was nitrate but not pyrene had an obvious influence on the community structure of soil bacteria. These results revealed that, under anaerobic condition, the activity and abundance of soil denitrifiers both were

  2. An ecological paradox: high species diversity and low position of the upper forest line in the Andean Depression.

    Science.gov (United States)

    Peters, Thorsten; Braeuning, Achim; Muenchow, Jannes; Richter, Michael

    2014-06-01

    Systematic investigations of the upper forest line (UFL) primarily concentrate on mid and high latitudes of the Northern Hemisphere, whereas studies of Neotropical UFLs are still fragmentary. This article outlines the extraordinary high tree diversity at the UFL within the Andean Depression and unravels the links between the comparatively low position of the local UFL, high tree-species diversity, and climate. On the basis of Gentry's rapid inventory methodology for the tropics, vegetation sampling was conducted at 12 UFL sites, and local climate (temperature, wind, precipitation, and soil moisture) was investigated at six sites. Monotypic forests dominated by Polylepis were only found at the higher located margins of the Andean Depression while the lower situated core areas were characterized by a species-rich forest, which lacked the elsewhere dominant tree-species Polylepis. In total, a remarkably high tree-species number of 255 tree species of 40 different plant families was found. Beta-diversity was also high with more than two complete species turnovers. A non-linear relationship between the floristic similarity of the investigated study sites and elevation was detected. Temperatures at the investigated study sites clearly exceeded 5.5°C, the postulated threshold value for the upper tree growth limit in the tropics. Instead, quasi-permanent trade winds, high precipitation amounts, and high soil water contents affect the local position of the UFL in a negative way. Interestingly, most of the above-mentioned factors are also contributing to the high species richness. The result is a combination of a clearly marked upper forest line depression combined with an extraordinary forest line complexity, which was an almost unknown paradox.

  3. Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments.

    Science.gov (United States)

    Besaury, Ludovic; Marty, Florence; Buquet, Sylvaine; Mesnage, Valérie; Muyzer, Gerard; Quillet, Laurent

    2013-02-01

    Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.

  4. Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).

    Science.gov (United States)

    Palop-Esteban, M; Segarra-Moragues, J G; González-Candelas, F

    2007-09-01

    Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed.

  5. Long-range high-speed visible light communication system over 100-m outdoor transmission utilizing receiver diversity technology

    Science.gov (United States)

    Wang, Yiguang; Huang, Xingxing; Shi, Jianyang; Wang, Yuan-quan; Chi, Nan

    2016-05-01

    Visible light communication (VLC) has no doubt become a promising candidate for future wireless communications due to the increasing trends in the usage of light-emitting diodes (LEDs). In addition to indoor high-speed wireless access and positioning applications, VLC usage in outdoor scenarios, such as vehicle networks and intelligent transportation systems, are also attracting significant interest. However, the complex outdoor environment and ambient noise are the key challenges for long-range high-speed VLC outdoor applications. To improve system performance and transmission distance, we propose to use receiver diversity technology in an outdoor VLC system. Maximal ratio combining-based receiver diversity technology is utilized in two receivers to achieve the maximal signal-to-noise ratio. A 400-Mb/s VLC transmission using a phosphor-based white LED and a 1-Gb/s wavelength division multiplexing VLC transmission using a red-green-blue LED are both successfully achieved over a 100-m outdoor distance with the bit error rate below the 7% forward error correction limit of 3.8×10-3. To the best of our knowledge, this is the highest data rate at 100-m outdoor VLC transmission ever achieved. The experimental results clearly prove the benefit and feasibility of receiver diversity technology for long-range high-speed outdoor VLC systems.

  6. Long-term followup of bilateral high (Sober) urinary diversion in patients with posterior urethral valves and its effect on bladder function

    NARCIS (Netherlands)

    Ghanem, MA; Nijman, RJM

    Purpose: Although valve ablation is the treatment of choice in patients with posterior urethral valves (PLTV), temporary high (ureterostomy) diversion remains controversial. In this study we evaluated the effect of bilateral Sober high urinary diversion on renal and bladder function. Materials and

  7. Teacher-librarian collaboration (TLC in a highly diverse branch: supporting information literacy of geography students

    Directory of Open Access Journals (Sweden)

    Anne Kakkonen

    2010-09-01

    Full Text Available The purpose of this paper is to present an example of teacher-librarian collaboration (TLC in a highly diverse branch of geography as a part of bachelor's seminar teaching. One can say that everything is geography if the phenomenon in question is delimited in a certain region, place or space. Thus every other discipline provides its methods, paradigms and information sources into the use of geography. This obviously presents a challenge to the librarian as he tries to support the geography students' information seeking. The topics can vary between cellular biology applications to sociological perception which also means a large variety in information needs. In our paper we aim to describe different approaches of collaboration this kind of variety requires based on the experiences and feedback gathered in a project, the aim of which was to integrate information literacy (IL into the academic curriculum. Collaborating with teachers with different backgrounds and from different scientific traditions can be challenging for the librarian. Not only the information sources, databases and methods are different but it is the whole approach to the science that is different. Thus it is fairly obvious that the competence of a single librarian or a teacher is not sufficient for an effective IL instruction. The key here is the collaboration when librarian's information literacy and teacher's academic subject competence complete each other. A successful TLC gives opportunity for both marketing the idea of information literacy and the competence of a library professional. It may also increase the efficiency of teaching and studies and even shorten the time for a student to graduate. Especially in the case of seminar teaching TLC seems to give a valuable opportunity to instruct the students' seminar thesis along the way. In 2008, Kumpula Campus Library launched a project to integrate the IL teaching into the academic curriculum and to enhance the collaboration

  8. Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef.

    Science.gov (United States)

    Marcelino, Vanessa Rossetto; Morrow, Kathleen M; van Oppen, Madeleine J H; Bourne, David G; Verbruggen, Heroen

    2017-10-01

    The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO 2 reef (avg. pCO 2 811 μatm) is not significantly different from corals inhabiting reference sites (avg. pCO 2 357 μatm), suggesting that these microbiomes are less disturbed by OA than previously thought. Possible explanations may be that the endolithic microhabitat is highly homeostatic or that the endolithic micro-organisms are well adapted to a wide pH range. Some of the microbial taxa identified include nitrogen-fixing bacteria (Rhizobiales and cyanobacteria), algicidal bacteria in the phylum Bacteroidetes, symbiotic bacteria in the family Endozoicomoniaceae, and endolithic green algae, considered the major microbial agent of reef bioerosion. Additionally, we test whether host species has an effect on the endolithic community structure. We show that the endolithic community of massive Porites spp. is substantially different and more diverse than that found in skeletons of the branching species Seriatopora hystrix and Pocillopora damicornis. This study reveals highly diverse and structured microbial communities in Porites spp. skeletons that are possibly resilient to OA. © 2017 John Wiley & Sons Ltd.

  9. High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

    Directory of Open Access Journals (Sweden)

    Weiguo Hou

    2018-05-01

    Full Text Available Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length encoding the cyanophage gp23 major capsid protein (MCP. Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92% belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

  10. Origin, diversity and maturation of human antiviral antibodies analyzed by high-throughput sequencing

    Directory of Open Access Journals (Sweden)

    Ponraj ePrabakaran

    2012-08-01

    Full Text Available Our understanding of how antibodies are generated and function could help develop effective vaccines and antibody-based therapeutics against viruses such as HIV-1, SARS Coronavirus (CoV, and Hendra and Nipah viruses (henipaviruses. Although broadly neutralizing antibodies (bnAbs against the HIV-1 were observed in patients, elicitation of such bnAbs remains a major challenge when compared to other viral targets. We previously hypothesized that HIV-1 could have evolved a strategy to evade the immune system due to absent or very weak binding of germline antibodies to the conserved epitopes that may not be sufficient to initiate and/or maintain an effective immune response. To further explore our hypothesis, we used the 454 sequence analysis of a large naïve library of human IgM antibodies which had been used for selecting antibodies against SARS Coronavirus (CoV receptor-binding domain (RBD, and soluble G proteins (sG of Hendra and Nipah viruses (henipaviruses. We found that the human IgM repertoires from the 454 sequencing have diverse germline usages, recombination patterns, junction diversity and a lower extent of somatic mutation. In this study, we identified germline intermediates of antibodies specific to HIV-1 and other viruses as observed in normal individuals, and compared their genetic diversity and somatic mutation level along with available structural and functional data. Further computational analysis will provide framework for understanding the underlying genetic and molecular determinants related to maturation pathways of antiviral bnAbs that could be useful for applying novel approaches to the design of effective vaccine immunogens and antibody-based therapeutics.

  11. High Diversity of Hepatozoon spp. in Geckos of the Genus Tarentola.

    Science.gov (United States)

    Tomé, Beatriz; Rato, Catarina; Harris, D James; Perera, Ana

    2016-08-01

    :   Hemogregarines are the most-commonly reported hemoparasites in reptiles. In this work we analyzed samples from 572 individuals of 6 species of the wall gecko genus Tarentola from European and African countries adjacent to the Mediterranean Sea as well as from the Macaronesian islands. Screening was done using hemogregarine-specific primers for the 18S rRNA gene. Positive amplifications were sequenced so that the diversity of the hemogregarines from these hosts could be assessed within a phylogenetic framework. The results from the phylogenetic analysis showed that within Tarentola, the detected parasites are comprised of at least 4 distinct main lineages of Hepatozoon spp. In clades A and B, the new sequences clustered closely together with the ones previously known from individuals of the genus Tarentola and other species of geckos but also with those from other vertebrate host groups including skinks, snakes, iguanids, and rodents. Clade C included a sample from Tarentola angustimentalis of the Canary Islands. This sequence is the first molecular characterization of these hemogregarines in this archipelago. Until now, this lineage had only been found in lacertids, skinks, and snakes, so this infection extends the host range for this clade. Lastly, in the newly detected clade D, the retrieved parasite sequences form a group currently identified as exclusive of geckos. Our results show that geckos of Tarentola spp. harbor a great diversity of hemogregarines but also that further sampling and other tools, including a multi-locus approach using faster-evolving genetic markers, and identification of definitive hosts are needed to better understand the biology, diversity, and distribution of these parasites.

  12. Diversity of gall-inducing insects in the high altitude wetland forests in Pernambuco, Northeastern Brazil

    Directory of Open Access Journals (Sweden)

    JC Santos

    Full Text Available We report on the richness of galling insects in the altitudinal wetland forests of Pernambuco State, Northeastern Brazil. We found 80 distinct types of insect galls on 49 species of host plants belonging to 28 families and 35 genera. Most of the galled plant species belong to Nyctaginaceae, Fabaceae, Meliaceae, Sapindaceae and Myrtaceae. The most common gall were spheroid and globoid; most galls were glabrous, predominantly green and with one chamber, and on the leaves. Most galls were induced by Cecidomyiidae (Diptera. The results of this study contribute to existing knowledge richness of galling insects and host-plant diversity in the altitudinal wetland forests of Northeastern Brazil.

  13. High genetic diversity among and within bitter manioc varieties cultivated in different soil types in Central Amazonia

    Directory of Open Access Journals (Sweden)

    Alessandro Alves-Pereira

    2017-04-01

    Full Text Available Abstract Although manioc is well adapted to nutrient-poor Oxisols of Amazonia, ethnobotanical observations show that bitter manioc is also frequently cultivated in the highly fertile soils of the floodplains and Amazonian dark earths (ADE along the middle Madeira River. Because different sets of varieties are grown in each soil type, and there are agronomic similarities between ADE and floodplain varieties, it was hypothesized that varieties grown in ADE and floodplain were more closely related to each other than either is to varieties grown in Oxisols. We tested this hypothesis evaluating the intra-varietal genetic diversity and the genetic relationships among manioc varieties commonly cultivated in Oxisols, ADE and floodplain soils. Genetic results did not agree with ethnobotanical expectation, since the relationships between varieties were variable and most individuals of varieties with the same vernacular name, but grown in ADE and floodplain, were distinct. Although the same vernacular name could not always be associated with genetic similarities, there is still a great amount of variation among the varieties. Many ecological and genetic processes may explain the high genetic diversity and differentiation found for bitter manioc varieties, but all contribute to the maintenance and amplification of genetic diversity within the manioc in Central Amazonia.

  14. Highly diverse, massive organic data as explored by a composite QSPR strategy: an advanced study of boiling point.

    Science.gov (United States)

    Ivanova, A A; Ivanov, A A; Oliferenko, A A; Palyulin, V A; Zefirov, N S

    2005-06-01

    An improved strategy of quantitative structure-property relationship (QSPR) studies of diverse and inhomogeneous organic datasets has been proposed. A molecular connectivity term was successively corrected for different structural features encoded in fragmental descriptors. The so-called solvation index 1chis (a weighted Randic index) was used as a "leading" variable and standardized molecular fragments were employed as "corrective" class-specific variables. Performance of the new approach was illustrated by modelling a dataset of experimental normal boiling points of 833 organic compounds belonging to 20 structural classes. Firstly, separate QSPR models were derived for each class and for eight groups of structurally similar classes. Finally, a general model formed by combining all the classes together was derived (r2=0.957, s=12.9degreesC). The strategy outlined can find application in QSPR analyses of massive, highly diverse databases of organic compounds.

  15. Networking for Successful Diversity Recruiting: Creating a Highly Diverse Research Experiences for Undergraduates Program by Networking with Mentors, Faculty, and Students.

    Science.gov (United States)

    Dalbotten, D. M.; Berthelote, A.; Watts, N. B.

    2017-12-01

    Successfully recruiting for diversity begins as you plan your program and make sure that all elements of the program support diverse participation. The REU on Sustainable Land and Water Resources continues to be one of the most diverse NSF-funded Research Experience for Undergraduate Programs in the geosciences. Every aspect of the program, from recruiting, the application process, selecting participants, and the methods developed to support participant success have been scrutinized and tailored towards broadening participation. While the focus of the research has been on collaboration with Native American reservations to create community-based participatory research projects and improving access for Native American students, the PIs strive for ethnic and cultural diversity of the participants. Emphasis on networking and building relationships with minority-serving institutions has led to increasing numbers of underrepresented students applying to the REU. In 2017, a full 30% of our applications were from underrepresented groups. The authors will discuss methods for improved diversity recruiting, as well as ways to make every aspect of your program support diversity in the geosciences.

  16. High diversity of picornaviruses in rats from different continents revealed by deep sequencing.

    Science.gov (United States)

    Hansen, Thomas Arn; Mollerup, Sarah; Nguyen, Nam-Phuong; White, Nicole E; Coghlan, Megan; Alquezar-Planas, David E; Joshi, Tejal; Jensen, Randi Holm; Fridholm, Helena; Kjartansdóttir, Kristín Rós; Mourier, Tobias; Warnow, Tandy; Belsham, Graham J; Bunce, Michael; Willerslev, Eske; Nielsen, Lars Peter; Vinner, Lasse; Hansen, Anders Johannes

    2016-08-17

    Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

  17. Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.

    Directory of Open Access Journals (Sweden)

    Luka Ausec

    Full Text Available Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.

  18. Highly Diverse Endophytic and Soil Fusarium oxysporum Populations Associated with Field-Grown Tomato Plants

    Science.gov (United States)

    Demers, Jill E.; Gugino, Beth K.

    2014-01-01

    The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates. PMID:25304514

  19. Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

    Science.gov (United States)

    Chao, Yuanqing; Mao, Yanping; Wang, Zhiping; Zhang, Tong

    2015-06-01

    The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilms formed on plastics, indicating that the metallic materials facilitate the formation of higher diversity biofilms. Moreover, variations in several dominant genera were observed during biofilm formation. Based on PCA analysis, the global functions in the DW biofilms were similar to other DW metagenomes. Beyond the global functions, the occurrences and abundances of specific protective genes involved in the glutathione metabolism, the SoxRS system, the OxyR system, RpoS regulated genes, and the production/degradation of extracellular polymeric substances were also evaluated. A near-complete and low-contamination draft genome was constructed from the metagenome of the DW biofilm, based on the coverage and tetranucleotide frequencies, and identified as a Bradyrhizobiaceae-like bacterium according to a phylogenetic analysis. Our findings provide new insight into DW biofilms, especially in terms of their metabolic functions.

  20. The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome.

    Science.gov (United States)

    Lopez-Sanchez, Maria-José; Sauvage, Elisabeth; Da Cunha, Violette; Clermont, Dominique; Ratsima Hariniaina, Elisoa; Gonzalez-Zorn, Bruno; Poyart, Claire; Rosinski-Chupin, Isabelle; Glaser, Philippe

    2012-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) confer immunity against mobile genetic elements (MGEs) in prokaryotes. Streptococcus agalactiae, a leading cause of neonatal infections contains in its genome two CRISPR/Cas systems. We show that type 1-C CRISPR2 is present in few strains but type 2-A CRISPR1 is ubiquitous. Comparative sequence analysis of the CRISPR1 spacer content of 351 S. agalactiae strains revealed that it is extremely diverse due to the acquisition of new spacers, spacer duplications and spacer deletions that witness the dynamics of this system. The spacer content profile mirrors the S. agalactiae population structure. Transfer of a conjugative transposon targeted by CRISPR1 selected for spacer rearrangements, suggesting that deletions and duplications pre-exist in the population. The comparison of protospacers located within MGE or the core genome and protospacer-associated motif-shuffling demonstrated that the GG motif is sufficient to discriminate self and non-self and for spacer selection and integration. Strikingly more than 40% of the 949 different CRISPR1 spacers identified target MGEs found in S. agalactiae genomes. We thus propose that the S. agalactiae type II-A CRISPR1/Cas system modulates the cohabitation of the species with its mobilome, as such contributing to the diversity of MGEs in the population. © 2012 Blackwell Publishing Ltd.

  1. High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae.

    Science.gov (United States)

    Ploch, Sebastian; Rose, Laura E; Bass, David; Bonkowski, Michael

    2016-09-01

    The largest biological surface on earth is formed by plant leaves. These leaf surfaces are colonized by a specialized suite of leaf-inhabiting microorganisms, recently termed "phyllosphere microbiome". Microbial prey, however, attract microbial predators. Protists in particular have been shown to structure bacterial communities on plant surfaces, but virtually nothing is known about the community composition of protists on leaves. Using newly designed specific primers targeting the 18S rDNA gene of Cercozoa, we investigated the species richness of this common protist group on leaves of four Brassicaceae species from two different locations in a cloning-based approach. The generated sequences revealed a broad diversity of leaf-associated Cercozoa, mostly bacterial feeders, but also including known plant pathogens and a taxon of potential endophytes that were recently described as algal predators in freshwater systems. This initial study shows that protists must be regarded as an integral part of the microbial diversity in the phyllosphere of plants. © 2016 The Authors. The Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

  2. Effect of carbon dioxide and bicarbonate as inorganic carbon sources on growth and adaptation of autohydrogenotrophic denitrifying bacteria

    International Nuclear Information System (INIS)

    Ghafari, Shahin; Hasan, Masitah; Aroua, Mohamed Kheireddine

    2009-01-01

    Acclimation of autohydrogenotrophic denitrifying bacteria using inorganic carbon source (CO 2 and bicarbonate) and hydrogen gas as electron donor was performed in this study. In this regard, activated sludge was used as the seed source and sequencing batch reactor (SBR) technique was applied for accomplishing the acclimatization. Three distinct strategies in feeding of carbon sources were applied: (I) continuous sparging of CO 2 , (II) bicarbonate plus continuous sparging of CO 2 , and (III) only bicarbonate. The pH-reducing nature of CO 2 showed an unfavorable impact on denitrification rate; however bicarbonate resulted in a buffered environment in the mixed liquor and provided a suitable mean to maintain the pH in the desirable range of 7-8.2. As a result, bicarbonate as the only carbon source showed a faster adaptation, while carbon dioxide as the only carbon source as well as a complementary carbon source added to bicarbonate resulted in longer acclimation period. Adapted hydrogenotrophic denitrifying bacteria, using bicarbonate and hydrogen gas in the aforementioned pH range, caused denitrification at a rate of 13.33 mg NO 3 - -N/g MLVSS/h for degrading 20 and 30 mg NO 3 - -N/L and 9.09 mg NO 3 - -N/g MLVSS/h for degrading 50 mg NO 3 - -N/L

  3. Effect of carbon dioxide and bicarbonate as inorganic carbon sources on growth and adaptation of autohydrogenotrophic denitrifying bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Ghafari, Shahin; Hasan, Masitah [Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia); Aroua, Mohamed Kheireddine [Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia)], E-mail: mk_aroua@um.edu.my

    2009-03-15

    Acclimation of autohydrogenotrophic denitrifying bacteria using inorganic carbon source (CO{sub 2} and bicarbonate) and hydrogen gas as electron donor was performed in this study. In this regard, activated sludge was used as the seed source and sequencing batch reactor (SBR) technique was applied for accomplishing the acclimatization. Three distinct strategies in feeding of carbon sources were applied: (I) continuous sparging of CO{sub 2}, (II) bicarbonate plus continuous sparging of CO{sub 2}, and (III) only bicarbonate. The pH-reducing nature of CO{sub 2} showed an unfavorable impact on denitrification rate; however bicarbonate resulted in a buffered environment in the mixed liquor and provided a suitable mean to maintain the pH in the desirable range of 7-8.2. As a result, bicarbonate as the only carbon source showed a faster adaptation, while carbon dioxide as the only carbon source as well as a complementary carbon source added to bicarbonate resulted in longer acclimation period. Adapted hydrogenotrophic denitrifying bacteria, using bicarbonate and hydrogen gas in the aforementioned pH range, caused denitrification at a rate of 13.33 mg NO{sub 3}{sup -}-N/g MLVSS/h for degrading 20 and 30 mg NO{sub 3}{sup -}-N/L and 9.09 mg NO{sub 3}{sup -}-N/g MLVSS/h for degrading 50 mg NO{sub 3}{sup -}-N/L.

  4. Performance of denitrifying microbial fuel cell subjected to variation in pH, COD concentration and external resistance.

    Science.gov (United States)

    Li, Jin-Tao; Zhang, Shao-Hui; Hua, Yu-Mei

    2013-01-01

    The effects of pH, chemical oxygen demand (COD) concentration and external resistance on denitrifying microbial fuel cell were evaluated in terms of electricity generation characteristics and pollutant removal performance. The results showed that anodic influent with weakly alkaline or neutral pH and cathodic influent with weakly acidic pH favored pollutant removal and electricity generation. The suitable influent pH of the anode and cathode were found to be 7.5-8.0 and 6.0-6.5, respectively. In the presence of sufficient nitrate in the cathode, higher influent COD concentration led to more electricity generation and greater pollutant removal rates. With an anodic influent pH of 8.0 and a cathodic influent pH of 6.0, an influent COD concentration of 400 mg/L was deemed to be appropriate. Low external resistance favored nitrate and COD removal. The results suggest that operation of denitrifying microbial fuel cell at a lower external resistance would be desirable for pollutant removal but not electricity generation.

  5. DQ High genotypic diversity among methicillin-resistant Staphylococcus pseudintermedius isolated from canine infections in Denmark

    DEFF Research Database (Denmark)

    Damborg, Peter; Moodley, Arshnee; Aalbaek, Bent

    2016-01-01

    genotypic diversity and antimicrobial resistance of clinical MRSP isolates obtained from dogs, including dogs sampled on multiple occasions, in Denmark over a six-year period. For that purpose a total of 46 clinical MRSP isolates obtained from 36 dogs between 2009 and 2014 were subjected to antimicrobial...... susceptibility testing, multilocus-sequence typing (MLST) and SCCmec typing. Results: Twenty-three sequence types were identified with ST71, mostly associated with SCCmec II-III, as the most common occurring in 13 dogs. Among the remaining 33 isolates, 19 belonged to clonal complex (CC) 258 comprising ST258...... resistant and almost all CC258 isolates being susceptible. Sixteen of the 19 CC258 isolates had oxacillin MICs of 0.5 g/L, whereas MICs for CC71 isolates were consistently above 4 g/L. Four of five dogs representing multiple isolates had distinct STs on different sampling events. Conclusions: The overall...

  6. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics

    DEFF Research Database (Denmark)

    Quaiser, Achim; Ochsenreiter, Torsten; Lanz, Christa

    2003-01-01

    fragments differed between 2.3% and 19.9% and were placed into two different subgroups of Acidobacteria (groups III and V). Although partial co-linearity was found between genomic fragments, the gene content around the rRNA operons was generally not conserved. Phylogenetic reconstructions with orthologues......Acidobacteria have been established as a novel phylum of Bacteria that is consistently detected in many different habitats around the globe by 16S rDNA-based molecular surveys. The phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important...... palustris and Bradyrhizobium japonicum, including a conserved two-component system. Phylogenetic analysis of the putative response regulator confirmed that this similarity between Rhizobiales and Acidobacteria might be due to a horizontal gene transfer. In total, our data give first insight into the genome...

  7. High diversity of nitrogen-fixing bacteria in upper reaches of Heihe River, Northwestern China

    Science.gov (United States)

    Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.

    2013-03-01

    Vegetation plays a key role to water conservation in southern Qilian Mountains (Northwestern China), the upper reaches of Heihe River. Nitrogen-fixing bacteria are crucial for vegetation protection because they can supply plants with nitrogen source. Nevertheless, little is known about nitrogen-fixing bacteria in this region. In present study, nifH gene clone libraries were established for detecting the difference of nitrogen-fixing bacterial communities between Potentilla parvifolia shrub and Carex alrofusca meadow in the southern Qilian Mountains. All the identified nitrogen-fixing bacterial clones belonged to Proteobacteria. At the genus level, the Azospirillum sp. was only detected in shrub soil while Thiocapsa sp., Derxiasp., Ectothiorhodospira sp., Mesorhizobium sp., Klebsiella sp., Ensifer sp., Methylocella sp. and Peseudomonas sp. were just detected in meadow soil. Shannon-Wiener index of nifH gene ranged from 1.5 to 2.8 and was higher in meadow soil than shrub soil. Contrarily, the nifH gene copies and CFUs of cultured nitrogen-fixing bacteria ranged from 0.4 × 107 to 6.9 × 107 copies g-1 soil and 0.97 × 106 to 12.78 × 106 g-1 soil, respectively. Furthermore, both of them were lower in meadow soil than shrub soil. Statistical analysis revealed that diversity and copies of nifH gene mostly correlated with aboveground biomass in shrub soil. In meadow soil, nifH gene diversity was principally affected by altitude while copies did by soil available K.

  8. High plant species diversity indirectly mitigates CO 2- and N-induced effects on grasshopper growth

    Science.gov (United States)

    Strengbom, Joachim; Reich, Peter B.; Ritchie, Mark E.

    2008-09-01

    We examined how elevated atmospheric [CO 2] and higher rate of nitrogen (N) input may influence grasshopper growth by changing food plant quality and how such effects may be modified by species diversity of the plant community. We reared grasshopper nymphs ( Melanoplus femurrubrum) on Poa pratensis from field-grown monocultures or polycultures (16 species) that were subjected to either ambient or elevated levels of CO 2 and N. Grasshopper growth rate was higher on P. pratensis leaves grown in monocultures than in polycultures, higher on P. pratensis grown under elevated than under ambient [CO 2], and higher on P. pratensis grown under elevated than under ambient [N]. The higher growth rate observed on P. pratensis exposed to elevated [CO 2] was, however, less pronounced for polyculture- than monoculture-grown P. pratensis. Growth rate of the grasshoppers was positively correlated with leaf [N], [C], and concentration of soluble carbohydrates + lipids. Concentration of non-structural carbohydrates + lipids was higher in leaves grown under elevated than under ambient [CO 2], and the difference between P. pratensis grown under ambient and elevated [CO 2] was greater for monoculture- than polyculture-grown P. pratensis. In addition, leaf N concentration was higher in P. pratensis grown in monocultures than in polycultures, suggesting that plant species richness, indirectly, may influence insect performance by changed nutritional value of the plants. Because we found interactive effects between all factors included ([CO 2], [N], and plant species diversity), our results suggest that these parameters may influence plant-insect interactions in a complex way that is not predictable from the sum of single factor manipulations.

  9. Three gene phylogeny of the Thoreales (Rhodophyta) reveals high species diversity.

    Science.gov (United States)

    Johnston, Emily T; Dixon, Kyatt R; West, John A; Buhari, Nurliah; Vis, Morgan L

    2018-04-01

    The freshwater red algal order Thoreales has triphasic life history composed of a diminutive diploid "Chantransia" stage, a distinctive macroscopic gametophyte with multi-axial growth and carposporophytes that develop on the gametophyte thallus. This order is comprised of two genera, Thorea and Nemalionopsis. Thorea has been widely reported with numerous species, whereas Nemalionopsis has been more rarely observed with only a few species described. DNA sequences from three loci (rbcL, cox1, and LSU) were used to examine the phylogenetic affinity of specimens collected from geographically distant locations including North America, South America, Europe, Pacific Islands, Southeast Asia, China, and India. Sixteen species of Thorea and two species of Nemalionopsis were recognized. Morphological observations confirmed the distinctness of the two genera and also provided some characters to distinguish species. However, many of the collections were in "Chantransia" stage rather than gametophyte stage, meaning that key diagnostic morphological characters were unavailable. Three new species are proposed primarily based on the DNA sequence data generated in this study, Thorea kokosinga-pueschelii, T. mauitukitukii, and T. quisqueyana. In addition to these newly described species, one DNA sequence from GenBank was not closely associated with other Thorea clades and may represent further diversity in the genus. Two species in Nemalionopsis are recognized, N. shawii and N. parkeri nom. et stat. nov. Thorea harbors more diversity than had been recognized by morphological data alone. Distribution data indicated that Nemalionopsis is common in the Pacific region, whereas Thorea is more globally distributed. Most species of Thorea have a regional distribution, but Thorea hispida appears to be cosmopolitan. © 2018 Phycological Society of America.

  10. Genetic and chemical diversity of high mucilaginous plants of Sida complex by ISSR markers and chemical fingerprinting.

    Science.gov (United States)

    Thul, Sanjog T; Srivastava, Ankit K; Singh, Subhash C; Shanker, Karuna

    2011-09-01

    A method was developed based on multiple approaches wherein DNA and chemical analysis was carried out toward differentiation of important species of Sida complex that is being used for commercial preparation. Isolated DNA samples were successfully performed through PCR amplification using ISSR markers and degree of genetic diversity among the different species of Sida is compared with that of chemical diversity. For genetic fingerprint investigation, selected 10 ISSR primers generating reproducible banding patterns were used. Among the total of 63 amplicons, 62 were recorded as polymorphic, genetic similarity index deduced from ISSR profiles ranged from 12 to 51%. Based on similarity index, S. acuta and S. rhombifolia found to be most similar (51%). High number of species-specific bands played pivotal role to delineate species at genetic level. Investigation based on HPTLC fingerprints analysis revealed 23 bands representing to characteristic chemicals and similarity index ranged from 73 to 91%. Prominent distinguishable bands were observed only in S. acuta, while S. cordifolia and S. rhombifolia shared most bands making them difficult to identify on chemical fingerprint basis. This report summarizes the genotypic and chemotypic diversity and the use of profiles for authentication of species of Sida complex.

  11. The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

    Science.gov (United States)

    Kim, Hyeun Bum; Isaacson, Richard E

    2015-06-12

    The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing.

    Directory of Open Access Journals (Sweden)

    Qiang Li

    Full Text Available The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960-1219 A.D. and Qing dynasties (1636-1912 A.D. and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities' diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.

  13. Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing.

    Science.gov (United States)

    Li, Qiang; Zhang, Bingjian; He, Zhang; Yang, Xiaoru

    The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960-1219 A.D.) and Qing dynasties (1636-1912 A.D.) and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities' diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.

  14. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    Directory of Open Access Journals (Sweden)

    Sharat Kumar Pradhan

    Full Text Available Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  15. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    Science.gov (United States)

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  16. Impact of ecological diversity on genetic and phytochemical variation injuniperus excelsa from high elevation zones of quetta valley, pakistan

    International Nuclear Information System (INIS)

    Seed, S.; Barozai, M.Y.K.; Ahmed, A.; Tareen, R.B.

    2017-01-01

    Juniperusexcelsa (Cupressaceae) is an evergreen tree and the second most diverse group of the conifers distributed abundantly in high elevation zones of Balochistan. Genetic and phytochemical variations in three naturally occurring populations of J.excelsa were analysed. Genetic variability was assessed by different molecular markers (RAPD, ISSR and URP) with an objective to use genetic diversity as a key to conserve the taxon which is also known as living fossil as dominated in Mesozoic era. Genetic diversity was assessed by polymorphic bands to generate a dendrogram based on UPGMA. Using tested markers, 116 bands were amplified out of which 67 bands were polymorphic with an average value of 8.37 (57%) bands per primer. Based on data, a cluster dendrogram was prepared that exhibited the mean genetic similarity matrix as 0.57 and two major clusters diverge at 0.49. The genetic similarity coefficient among all accessions ranged from 0.35 to 0.90. In phytochemical analysis, total phenolic and flavonoid contents were estimated and compared among all accessions. Ecological characteristics of the study sites were measured to check their impact on genetic and chemical variation. Soil properties were analyzed for Principal Component Analysis. Chemical variation of J. excelsa of three sites revealed by dissimilarity matrix exhibiting genetic distance based on TPC and Flavonoids. Cluster analysis represent two major groups. Mean concentration of TPC and flavonoids were 56+-9.15 and 150+-27.9 mg/g respectively. PCA of soil considered three factors had Eigen values >1 and explain cumulatively 4.60 %, 26.02% and 10.36 % of the variance. First factor was positively correlated with second and fifth, but negatively correlated with other factors. In conclusion, molecular marker profiling together with phytochemical variation of total phenolic and flavonoid content in all accessions of Juniperusexcelsa and impact of ecological diversity on Genetic and chemical variation can be used

  17. Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota)

    Science.gov (United States)

    József Geml; Gary A. Laursen; Ian C. Herriott; Jack M. McFarland; Michael G. Booth; Niall Lennon; H. Chad Nusbaum; D. Lee Taylor

    2010-01-01

    Although critical for the functioning of ecosystems, fungi are poorly known in high-latitude regions. Here, we provide the first genetic diversity assessment of one of the most diverse and abundant ectomycorrhizal genera in Alaska: Russula. We analyzed internal transcribed spacer rDNA sequences from sporocarps and soil samples using phylogenetic...

  18. Production of NO and N(inf2)O by Pure Cultures of Nitrifying and Denitrifying Bacteria during Changes in Aeration

    NARCIS (Netherlands)

    Kester, R.A.; De Boer, W.; Laanbroek, H.J.

    1997-01-01

    Peak emissions of NO and N2O are often observed after wetting of soil, The reactions to sudden changes in the aeration of cultures of nitrifying and denitrifying bacteria with respect to NO and N2O emissions were compared to obtain more information about the microbiological aspects of peak

  19. Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents

    International Nuclear Information System (INIS)

    Xiao, Ke-Qing; Li, Li-Guan; Ma, Li-Ping; Zhang, Si-Yu; Bao, Peng; Zhang, Tong; Zhu, Yong-Guan

    2016-01-01

    Microbe-mediated arsenic (As) metabolism plays a critical role in global As cycle, and As metabolism involves different types of genes encoding proteins facilitating its biotransformation and transportation processes. Here, we used metagenomic analysis based on high-throughput sequencing and constructed As metabolism protein databases to analyze As metabolism genes in five paddy soils with low-As contents. The results showed that highly diverse As metabolism genes were present in these paddy soils, with varied abundances and distribution for different types and subtypes of these genes. Arsenate reduction genes (ars) dominated in all soil samples, and significant correlation existed between the abundance of arr (arsenate respiration), aio (arsenite oxidation), and arsM (arsenite methylation) genes, indicating the co-existence and close-relation of different As resistance systems of microbes in wetland environments similar to these paddy soils after long-term evolution. Among all soil parameters, pH was an important factor controlling the distribution of As metabolism gene in five paddy soils (p = 0.018). To the best of our knowledge, this is the first study using high-throughput sequencing and metagenomics approach in characterizing As metabolism genes in the five paddy soil, showing their great potential in As biotransformation, and therefore in mitigating arsenic risk to humans. - Highlights: • Use metagenomics to analyze As metabolism genes in paddy soils with low-As content. • These genes were ubiquitous, abundant, and associated with diverse microbes. • pH as an important factor controlling their distribution in paddy soil. • Imply combinational effect of evolution and selection on As metabolism genes. - Metagenomics was used to analyze As metabolism genes in paddy soils with low-As contents. These genes were ubiquitous, abundant, and associated with diverse microbes.

  20. Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids.

    Science.gov (United States)

    Tennant, Jonathan P; Mannion, Philip D

    2014-01-01

    Atoposaurid crocodyliforms represent an important faunal component of Late Jurassic to Early Cretaceous Laurasian semi-aquatic to terrestrial ecosystems, with numerous spatiotemporally contemporaneous atoposaurids known from western Europe. In particular, the Late Jurassic of France and Germany records evidence for high diversity and possible sympatric atoposaurid species belonging to Alligatorellus, Alligatorium and Atoposaurus. However, atoposaurid taxonomy has received little attention, and many species are in need of revision. As such, this potentially high European diversity within a narrow spatiotemporal range might be a taxonomic artefact. Here we provide a taxonomic and anatomical revision of the Late Jurassic atoposaurid Alligatorellus. Initially described as A. beaumonti from the Kimmeridgian of Cerin, eastern France, additional material from the Tithonian of Solnhofen, south-eastern Germany, was subsequently referred to this species, with the two occurrences differentiated as A. beaumonti beaumonti and A. beaumonti bavaricus, respectively. We provide a revised diagnosis for the genus Alligatorellus, and note a number of anatomical differences between the French and German specimens, including osteoderm morphology and the configuration and pattern of sculpting of cranial elements. Consequently, we restrict the name Alligatorellus beaumonti to include only the French remains, and raise the rank of the German material to a distinct species: Alligatorellus bavaricus. A new diagnosis is provided for both species, and we suggest that a recently referred specimen from a coeval German locality cannot be conclusively referred to Alligatorellus. Although it has previously been suggested that Alligatorellus, Alligatorium and Atoposaurus might represent a single growth series of one species, we find no conclusive evidence to support this proposal, and provide a number of morphological differences to distinguish these three taxa that appear to be independent of

  1. Molecular Characterization of Human Atypical Sorbitol-Fermenting Enteropathogenic Escherichia coli O157 Reveals High Diversity.

    Science.gov (United States)

    Kossow, Annelene; Zhang, Wenlan; Bielaszewska, Martina; Rhode, Sophie; Hansen, Kevin; Fruth, Angelika; Rüter, Christian; Karch, Helge; Mellmann, Alexander

    2016-05-01

    Alongside the well-characterized enterohemorrhagic Escherichia coli (EHEC) O157:H7, serogroup O157 comprises sorbitol-fermenting typical and atypical enteropathogenic E. coli (EPEC/aEPEC) strains that carry the intimin-encoding gene eae but not Shiga toxin-encoding genes (stx). Since little is known about these pathogens, we characterized 30 clinical isolates from patients with hemolytic uremic syndrome (HUS) or uncomplicated diarrhea with respect to their flagellin gene (fliC) type and multilocus sequence type (MLST). Moreover, we applied whole-genome sequencing (WGS) to determine the phylogenetic relationship with other eae-positive EHEC serotypes and the composition of the rfbO157 region. fliC typing resulted in five fliC types (H7, H16, H34, H39, and H45). Isolates of each fliC type shared a unique ST. In comparison to the 42 HUS-associated E. coli (HUSEC) strains, only the stx-negative isolates with fliCH7 shared their ST with EHEC O157:H7/H(-) strains. With the exception of one O157:H(-) fliCH16 isolate, HUS was exclusively associated with fliCH7. WGS corroborated the separation of the fliCH7 isolates, which were closely related to the EHEC O157:H7/H(-) isolates, and the diverse group of isolates exhibiting different fliC types, indicating independent evolution of the different serotypes. This was also supported by the heterogeneity within the rfbO157 region that exhibited extensive recombinations. The genotypic subtypes and distribution of clinical symptoms suggested that the stx-negative O157 strains with fliCH7 were originally EHEC strains that lost stx The remaining isolates form a distinct and diverse group of atypical EPEC isolates that do not possess the full spectrum of virulence genes, underlining the importance of identifying the H antigen for clinical risk assessment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  2. Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance

    Directory of Open Access Journals (Sweden)

    Nicolas eBerthod

    2015-10-01

    Full Text Available Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice (SRC willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec to determine their bioenergy potential in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood, suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50 % of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry

  3. Can the reproductive system of a rare and narrowly endemic plant species explain its high genetic diversity?

    Directory of Open Access Journals (Sweden)

    Daniele M. Rodrigues

    2018-01-01

    Full Text Available ABSTRACT The reproductive system of flowering plants can be highly variable, affecting their biology, gene flow and genetic variability among populations. Petunia secreta is a rare annual endemic species of Pedra do Segredo, located in the municipality of Caçapava do Sul, state of Rio Grande do Sul, Brazil. Although rare, the species possesses a high level of genetic variability. We investigated the reproductive system of P. secreta, including fruit production and seed germinability, in order to determine if its reproductive system can explain its genetic diversity. We sampled five populations and conducted five greenhouse hand-pollination treatments: 1 autonomous apomixis; 2 self-pollination; 3 hand self-pollination; 4 geitonogamy; and 5 cross-pollination. We analysed a total of 40 plants, 468 flowers, and 6,500 seeds. Only autonomous apomixis and self-pollination did not produce fruit. No differences in fruit weight were observed among pollination treatments (P > 0.05. Seeds of two colours were produced, with no differences in germinability. Considering all plants, populations, and treatments, the average germinability was 73 % (range 9 % to 100 %. These results, along with other previous studies, indicate that the reproductive systems of P. secreta, and its large effective population size, can explain its high genetic diversity.

  4. CVD growth of large-area and high-quality HfS2 nanoforest on diverse substrates

    Science.gov (United States)

    Zheng, Binjie; Wang, Zegao; Qi, Fei; Wang, Xinqiang; Yu, Bo; Zhang, Wanli; Chen, Yuanfu

    2018-03-01

    Two-dimensional layered transition metal dichalcogenides (TMDs) have attracted burgeoning attention due to their various properties and wide potential applications. As a new TMD, hafnium disulfide (HfS2) is theoretically predicted to have better electrical performance than widely studied MoS2. The experimental researches also confirmed the extraordinary feature in electronics and optoelectronics. However, the maximal device performance may not be achieved due to its own limitation of planar structure and challenge of transfer without contamination. Here, through the chemical vapor deposition (CVD) technique, inch-size HfS2 nanoforest has been directly grown on diverse objective substrates covering insulating, semiconducting and conducting substrates. This direct CVD growth without conventional transfer process avoids contamination and degradation in quality, suggesting its promising and wide applications in high-quality and multifarious devices. It is noted that all the HfS2 nanoforests grown on diverse substrates are constructed with vertically aligned few-layered HfS2 nanosheets with high crystalline quality and edge orientation. Moreover, due to its unique structure, the HfS2 nanoforest owns abundant exposed edge sites and large active surface area, which is essential to apply in high-performance catalyst, sensor, and energy storage or field emitter.

  5. High genetic diversity and absence of founder effects in a worldwide aquatic invader.

    Science.gov (United States)

    Lejeusne, Christophe; Saunier, Alice; Petit, Nicolas; Béguer, Mélanie; Otani, Michio; Carlton, James T; Rico, Ciro; Green, Andy J

    2014-07-24

    The introduced oriental shrimp Palaemon macrodactylus has recently become widespread in temperate estuaries worldwide. However, this recent worldwide spread outside of its native range arises after a previous introduction to the US Pacific coast, where it was restricted for more than 30 years. Using a phylogeographic approach, the present work investigates the genetic history of the invasion of this decapod worldwide. Japan acted as the main native source area for worldwide introduced populations, but other native areas (likely South Korea and China) may act as source populations as well. The recently introduced European and NW Atlantic populations result from colonization from both Japan and an unknown area of the native range, although colonization from the NE Pacific could not be ruled out. Most introduced populations had higher haplotypic diversity than most native populations. P. macrodactylus has a strong potential to become one of the most widespread introduced species and may become the dominant estuarine shrimp in Europe. The ecological and economic consequences of this invasion remain to be thoroughly evaluated.

  6. Does the globally invasive marine angiosperm, Halophila stipulacea, have high genetic diversity or unique mutations?

    Science.gov (United States)

    Chiquillo, K.; Campese, L.; Barber, P. H.; Willette, D. A.

    2016-02-01

    Seagrasses are important primary producers in many marine ecosystems, and support a wide diversity of marine life. However, invasive seagrasses like Halophila stipulacea can have pronounced negative impacts on an ecosystem by displacing native seagrasses and changing the community composition of the reef. Endemic to the Red Sea, Persian Gulf and Indian Ocean, Halophila stipulacea has become invasive in the Mediterranean and Caribbean Seas, presumably as a result of the opening of the Suez Canal and international ship traffic. However, it is unclear why this marine angiosperm has become invasive in parts of its range and not others. It is hypothesized that invasive forms may have evolved rapidly in response to natural selection in new and novel environments. Alternatively, genetic variation of introduced populations may be uniquely suited to thrive in regions where it is invasive. In this study, we use RAD next-generation sequencing to screen thousands of SNPs to investigate the genetic basis of adaptation in both native and invasive populations. We test whether genes under selection in the native range are the same as in the invasive range, or whether new genes have arisen with the invasion of each marine basin. The comparison of SNP frequencies unique among basins and environmental variables will aid in predicting new areas of invasion, assisting in improved management strategies to combat this invasive seagrass.

  7. The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis.

    Science.gov (United States)

    Zhao, Liang; Song, Yulong; Li, Lin; Gan, Nanqin; Brand, Jerry J; Song, Lirong

    2018-05-01

    The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98. A large number of methylation motifs and R-M genes were identified in these strains, which differ substantially among different strains. Of the 35 motifs identified, eighteen had not previously been reported. Strain NIES-843 contains a larger number of total putative methyltransferase genes than have been reported previously from any bacterial genome. Genomic comparisons reveal that methyltransferases (some partial) may have been acquired from the environment through horizontal gene transfer. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. High-speed stimulated Raman scattering microscopy for studying the metabolic diversity of motile Euglena gracilis

    Science.gov (United States)

    Suzuki, Y.; Wakisaka, Y.; Iwata, O.; Nakashima, A.; Ito, T.; Hirose, M.; Domon, R.; Sugawara, M.; Tsumura, N.; Watarai, H.; Shimobaba, T.; Suzuki, K.; Goda, K.; Ozeki, Y.

    2017-02-01

    Microalgae have been receiving great attention for their ability to produce biomaterials that are applicable for food supplements, drugs, biodegradable plastics, and biofuels. Among such microalgae, Euglena gracilis has become a popular species by virtue of its capability of accumulating useful metabolites including paramylon and lipids. In order to maximize the production of desired metabolites, it is essential to find ideal culturing conditions and to develop efficient methods for genetic transformation. To achieve this, understanding and controlling cell-to-cell variations in response to external stress is essential, with chemically specific analysis of microalgal cells including E. gracilis. However, conventional analytical tools such as fluorescence microscopy and spontaneous Raman scattering are not suitable for evaluation of diverse populations of motile microalgae, being restricted either by the requirement for fluorescent labels or a limited imaging speed, respectively. Here we demonstrate video-rate label-free metabolite imaging of live E. gracilis using stimulated Raman scattering (SRS) - an optical spectroscopic method for probing the vibrational signatures of molecules with orders of magnitude higher sensitivity than spontaneous Raman scattering. Our SRS's highspeed image acquisition (27 metabolite images per second) allows for population analysis of live E. gracilis cells cultured under nitrogen-deficiency - a technique for promoting the accumulation of paramylon and lipids within the cell body. Thus, our SRS system's fast imaging capability enables quantification and analysis of previously unresolvable cell-to-cell variations in the metabolite accumulation of large motile E. gracilis cell populations.

  9. Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation.

    Science.gov (United States)

    Muller, Mischa F; Barnes, Irene; Kunene, Ncobile T; Crampton, Bridget G; Bluhm, Burton H; Phillips, Sonia M; Olivier, Nicholas A; Berger, Dave K

    2016-10-01

    South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The

  10. Teachers' Awareness of Cultural Diversity and Academic Achievement in Ninth Grade Academies and Senior High Schools

    Science.gov (United States)

    Whipps-Johnson, Jamellah Renee

    2016-01-01

    High school graduation rates are higher than they have ever been in 40 years, but disparities continue to exist for students of color and students from poverty when compared to their counterparts. High school reform efforts like creating small learning communities are promising, but small schools alone do not improve student outcomes.…

  11. Antifungal Bacteria on Woodland Salamander Skin Exhibit High Taxonomic Diversity and Geographic Variability.

    Science.gov (United States)

    Muletz-Wolz, Carly R; DiRenzo, Graziella V; Yarwood, Stephanie A; Campbell Grant, Evan H; Fleischer, Robert C; Lips, Karen R

    2017-05-01

    Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis Yet there has been no systematic survey of anti- B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti- B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus , 15 P. glutinosus , 9 P. cylindraceus ) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti- B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti- B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti- B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti- B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti- B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis Anti- B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a

  12. Denitrifiers in the surface zone are primarily responsible for the nitrous oxide emission of dairy manure compost

    Energy Technology Data Exchange (ETDEWEB)

    Maeda, Koki, E-mail: k_maeda@affrc.go.jp [Dairy Research Division, National Agricultural Research Center for Hokkaido Region, National Agricultural and Food Research Organization, 1 Hitsujigaoka, Sapporo 062-8555 (Japan); Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502 (Japan); Toyoda, Sakae [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502 (Japan); Hanajima, Dai [Dairy Research Division, National Agricultural Research Center for Hokkaido Region, National Agricultural and Food Research Organization, 1 Hitsujigaoka, Sapporo 062-8555 (Japan); Yoshida, Naohiro [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502 (Japan)

    2013-03-15

    Highlights: ► Nitrous oxide (N{sub 2}O) productions of each compost zones were compared. ► The pile surface emitted significant fluxes of N{sub 2}O. ► The isotopic signature of N{sub 2}O from surface and NO{sub 2}{sup −} amended core were different. ► The denitrifying gene abundance was significantly higher in pile surface than the pile core. -- Abstract: During the dairy manure composting process, significant nitrous oxide (N{sub 2}O) emissions occur just after the pile turnings. To understand the characteristics of this N{sub 2}O emission, samples were taken from the compost surface and core independently, and the N{sub 2}O production was monitored in laboratory incubation experiments. Equal amounts of surface and core samples were mixed to simulate the turning, and the {sup 15}N isotope ratios within the molecules of produced N{sub 2}O were analyzed by isotopomer analysis. The results showed that the surface samples emitted significant levels of N{sub 2}O, and these emissions were correlated with NO{sub x}{sup −}-N accumulation. Moreover, the surface samples and surface-core mixed samples incubated at 30 °C produced N{sub 2}O with a low site preference (SP) value (−0.9 to 7.0‰) that was close to bacteria denitrification (0‰), indicating that denitrifiers in the surface samples are responsible for this N{sub 2}O production. On the other hand, N{sub 2}O produced by NO{sub 2}{sup −}-amended core samples and surface samples incubated at 60 °C showed unrecognized isotopic signatures (SP = 11.4–20.3‰). From these results, it was revealed that the N{sub 2}O production occurring just after the turnings was mainly derived from bacterial denitrification (including nitrifier denitrification) of NO{sub x}{sup −}-N under mesophilic conditions, and surface denitrifying bacteria appeared to be the main contributor to this process.

  13. Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

    Science.gov (United States)

    Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

    2016-01-01

    Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area.

  14. Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

    Science.gov (United States)

    Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

    2016-01-01

    Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

  15. Genetic and oceanographic tools reveal high population connectivity and diversity in the endangered pen shell Pinna nobilis

    KAUST Repository

    Wesselmann, Marlene; Gonzá lez-Wangü emert, Mercedes; Serrã o, Ester A.; Engelen, Aschwin H.; Renault, Lionel; Garcí a-March, José R.; Duarte, Carlos M.; Hendriks, Iris E.

    2018-01-01

    For marine meta-populations with source-sink dynamics knowledge about genetic connectivity is important to conserve biodiversity and design marine protected areas (MPAs). We evaluate connectivity of a Mediterranean sessile species, Pinna nobilis. To address a large geographical scale, partial sequences of cytochrome oxidase I (COI, 590 bp) were used to evaluate phylogeographical patterns in the Western Mediterranean, and in the whole basin using overlapping sequences from the literature (243 bp). Additionally, we combined (1) larval trajectories based on oceanographic currents and early life-history traits and (2) 10 highly polymorphic microsatellite loci collected in the Western Mediterranean. COI results provided evidence for high diversity and low inter-population differentiation. Microsatellite genotypes showed increasing genetic differentiation with oceanographic transport time (isolation by oceanographic distance (IBD) set by marine currents). Genetic differentiation was detected between Banyuls and Murcia and between Murcia and Mallorca. However, no genetic break was detected between the Balearic populations and the mainland. Migration rates together with numerical Lagrangian simulations showed that (i) the Ebro Delta is a larval source for the Balearic populations (ii) Alicante is a sink population, accumulating allelic diversity from nearby populations. The inferred connectivity can be applied in the development of MPA networks in the Western Mediterranean.

  16. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.

    Science.gov (United States)

    Vasconcelos, Raquel; Montero-Mendieta, Santiago; Simó-Riudalbas, Marc; Sindaco, Roberto; Santos, Xavier; Fasola, Mauro; Llorente, Gustavo; Razzetti, Edoardo; Carranza, Salvador

    2016-01-01

    Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

  17. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.

    Directory of Open Access Journals (Sweden)

    Raquel Vasconcelos

    Full Text Available Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot and the conservation interest of its reptile fauna (94% endemics, we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs, cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

  18. Genetic and oceanographic tools reveal high population connectivity and diversity in the endangered pen shell Pinna nobilis

    KAUST Repository

    Wesselmann, Marlene

    2018-03-13

    For marine meta-populations with source-sink dynamics knowledge about genetic connectivity is important to conserve biodiversity and design marine protected areas (MPAs). We evaluate connectivity of a Mediterranean sessile species, Pinna nobilis. To address a large geographical scale, partial sequences of cytochrome oxidase I (COI, 590 bp) were used to evaluate phylogeographical patterns in the Western Mediterranean, and in the whole basin using overlapping sequences from the literature (243 bp). Additionally, we combined (1) larval trajectories based on oceanographic currents and early life-history traits and (2) 10 highly polymorphic microsatellite loci collected in the Western Mediterranean. COI results provided evidence for high diversity and low inter-population differentiation. Microsatellite genotypes showed increasing genetic differentiation with oceanographic transport time (isolation by oceanographic distance (IBD) set by marine currents). Genetic differentiation was detected between Banyuls and Murcia and between Murcia and Mallorca. However, no genetic break was detected between the Balearic populations and the mainland. Migration rates together with numerical Lagrangian simulations showed that (i) the Ebro Delta is a larval source for the Balearic populations (ii) Alicante is a sink population, accumulating allelic diversity from nearby populations. The inferred connectivity can be applied in the development of MPA networks in the Western Mediterranean.

  19. Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA).

    Science.gov (United States)

    Coveley, Suzanne; Elshahed, Mostafa S; Youssef, Noha H

    2015-01-01

    Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in Southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (28°, 30°, 32°, and 70 °C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature.

  20. Cellar-Associated Saccharomyces cerevisiae Population Structure Revealed High-Level Diversity and Perennial Persistence at Sauternes Wine Estates

    Science.gov (United States)

    Börlin, Marine; Venet, Pauline; Claisse, Olivier; Salin, Franck

    2016-01-01

    ABSTRACT Three wine estates (designated A, B, and C) were sampled in Sauternes, a typical appellation of the Bordeaux wine area producing sweet white wine. From those wine estates, 551 yeast strains were collected between 2012 and 2014, added to 102 older strains from 1992 to 2011 from wine estate C. All the strains were analyzed through 15 microsatellite markers, resulting in 503 unique Saccharomyces cerevisiae genotypes, revealing high genetic diversity and a low presence of commercial yeast starters. Population analysis performed using Fst genetic distance or ancestry profiles revealed that the two closest wine estates, B and C, which have juxtaposed vineyard plots and common seasonal staff, share more related isolates with each other than with wine estate A, indicating exchange between estates. The characterization of isolates collected 23 years ago at wine estate C in relation to recent isolates obtained at wine estate B revealed the long-term persistence of isolates. Last, during the 2014 harvest period, a temporal succession of ancestral subpopulations related to the different batches associated with the selective picking of noble rotted grapes was highlighted. IMPORTANCE High genetic diversity of S. cerevisiae isolates from spontaneous fermentation on wine estates in the Sauternes appellation of Bordeaux was revealed. Only 7% of all Sauternes strains were considered genetically related to specific commercial strains. The long-term persistence (over 20 years) of S. cerevisiae profiles on a given wine estate is highlighted. PMID:26969698

  1. Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.

    Science.gov (United States)

    Beesley, Nicola J; Williams, Diana J L; Paterson, Steve; Hodgkinson, Jane

    2017-01-01

    Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  2. Effect of Free Nitrous Acid on Nitrous Oxide Production and Denitrifying Phosphorus Removal by Polyphosphorus-Accumulating Organisms in Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    Zhijia Miao

    2018-01-01

    Full Text Available The inhibition of free nitrous acid (FNA on denitrifying phosphorus removal has been widely reported for enhanced biological phosphorus removal; however, few studies focus on the nitrous oxide (N2O production involved in this process. In this study, the effects of FNA on N2O production and anoxic phosphorus metabolism were investigated using phosphorus-accumulating organisms (PAOs culture highly enriched (91±4% in Candidatus Accumulibacter phosphatis. Results show that the FNA concentration notably inhibited anoxic phosphorus metabolism and phosphorus uptake. Poly-β-hydroxyalkanoate (PHA degradation was completely inhibited when the FNA concentration was approximately 0.0923 mgHNO2-N/L. Higher initial FNA concentrations (0.00035 to 0.0103 mgHNO2-N/L led to more PHA consumption/TN (0.444 to 0.916 mmol-C/(mmol-N·gVSS. Moreover, it was found that FNA, rather than nitrite and pH, was likely the true inhibitor of N2O production. The highest proportion of N2O to TN was 78.42% at 0.0031 mgHNO2-N/L (equivalent to 42.44 mgNO2-N/L at pH 7.5, due to the simultaneous effects of FNA on the subsequent conversion of NO2 into N2O and then into N2. The traditional nitrite knee point can only indicate the exhaustion of nitrite, instead of the complete removal of TN.

  3. Microbial diversity in a full-scale anaerobic reactor treating high ...

    African Journals Online (AJOL)

    Microbial characteristics in the up-flow anaerobic sludge blanket reactor (UASB) of a full-scale high concentration cassava alcohol wastewater plant capable of anaerobic hydrocarbon removal were analyzed using cultivation-independent molecular methods. Forty-five bacterial operational taxonomic units (OTUs) and 24 ...

  4. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2017-07-01

    Full Text Available Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD and extending the dry-season duration (ED but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08 was much lower than that of the net N transformation rate (0.55 ± 0.02 throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA and denitrifying genes (nirK, nirS, and nosZ, while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+ and dissolved organic carbon concentrations] during the experiment.

  5. Effects of classroom education on knowledge and attitudes regarding organ donation in ethnically diverse urban high schools

    Science.gov (United States)

    Cárdenas, Vicky; Thornton, John Daryl; Wong, Kristine A.; Spigner, Clarence; Allen, Margaret D.

    2010-01-01

    School-based health education is a promising approach for improving organ donation rates, but little is known about its efficacy among ethnically diverse youth. The impact of a classroom intervention was examined in a multicultural high school population where students’ ethnicities were 45% African American, 30% Asian American, and 33% Caucasian (allowing for multiracial choices). A baseline survey was administered to all health classes within 2 weeks prior to intervention. On the intervention day, classes randomly assigned to the intervention group received an educational session, followed by a second survey; in control classes, the second survey was taken before the educational session. At baseline, non-Caucasian ethnicity and male gender were each associated with lower levels of willingness to donate. Following the intervention, students in the intervention group demonstrated a significant increase in knowledge scores (p<0.001), as well as positive movement of opinion regarding willingness to donate (p<0.0001). Most importantly, the positive changes in opinion occurred independently of ethnicity and gender, in spite of these both being negative predictors of opinion at baseline. These results demonstrate that even a single classroom exposure can impact knowledge levels, correct misinformation, and effect opinion change on organ donation among an ethnically diverse adolescent population. PMID:20088915

  6. High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

    Science.gov (United States)

    Reddy, Umesh K; Nimmakayala, Padma; Levi, Amnon; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Tomason, Yan R; Vajja, Gopinath; Reddy, Rishi; Abburi, Lavanya; Wehner, Todd C; Ronin, Yefim; Karol, Abraham

    2014-09-15

    We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication. Copyright © 2014 Reddy et al.

  7. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments

    DEFF Research Database (Denmark)

    Klatt, Christian G.; Inskeep, William P.; Herrgard, Markus

    2013-01-01

    Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across...... the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average 53Mbp/site) were...

  8. High diversity, low disparity and small body size in plesiosaurs (Reptilia, Sauropterygia from the Triassic-Jurassic boundary.

    Directory of Open Access Journals (Sweden)

    Roger B J Benson

    Full Text Available Invasion of the open ocean by tetrapods represents a major evolutionary transition that occurred independently in cetaceans, mosasauroids, chelonioids (sea turtles, ichthyosaurs and plesiosaurs. Plesiosaurian reptiles invaded pelagic ocean environments immediately following the Late Triassic extinctions. This diversification is recorded by three intensively-sampled European fossil faunas, spanning 20 million years (Ma. These provide an unparalleled opportunity to document changes in key macroevolutionary parameters associated with secondary adaptation to pelagic life in tetrapods. A comprehensive assessment focuses on the oldest fauna, from the Blue Lias Formation of Street, and nearby localities, in Somerset, UK (Earliest Jurassic: 200 Ma, identifying three new species representing two small-bodied rhomaleosaurids (Stratesaurus taylori gen et sp. nov.; Avalonnectes arturi gen. et sp. nov and the most basal plesiosauroid, Eoplesiosaurus antiquior gen. et sp. nov. The initial radiation of plesiosaurs was characterised by high, but short-lived, diversity of an archaic clade, Rhomaleosauridae. Representatives of this initial radiation were replaced by derived, neoplesiosaurian plesiosaurs at small-medium body sizes during a more gradual accumulation of morphological disparity. This gradualistic modality suggests that adaptive radiations within tetrapod subclades are not always characterised by the initially high levels of disparity observed in the Paleozoic origins of major metazoan body plans, or in the origin of tetrapods. High rhomaleosaurid diversity immediately following the Triassic-Jurassic boundary supports the gradual model of Late Triassic extinctions, mostly predating the boundary itself. Increase in both maximum and minimum body length early in plesiosaurian history suggests a driven evolutionary trend. However, Maximum-likelihood models suggest only passive expansion into higher body size categories.

  9. [Analysis of diversity of Russian and Ukrainian bread wheat (Triticum aestivum L.) cultivars for high-molecular-weight glutenin subunits].

    Science.gov (United States)

    Dobrotvorskaia, T V; Martynov, S P

    2011-07-01

    The allelic diversity of high-moleculat-weght glutenin subunits (H WIGS) in Russian and Ukrainian bread wheat cultivars was analyzed. The diversity of spring wheat cultivars for alleles of the Glu-1 loci is characterized by medium values of the polymorphism index (polymorphism information content, PlC), and in winter wheats it varies from high at the Glu-A1 locus to low at the Glu-D1 locus. The spring and winter cultivars differ significantly in the frequencies of alleles of the glutenin loci. The combination of the Glu-A1b, Glu-B1c, and Glu-D1a alleles prevails among the spring cultivars, and the combination of the Glu-A1a, Glu-B1c, and Glu-D1d alleles prevails among the winter cultivars. The distribution of the Glu-1 alleles significantly depends on the moisture and heat supply in the region of origin of the cultivars. Drought resistance is associated with the Glu-D1a allele in the spring wheat and with the Glu-B1b allele in the winter wheat. The sources of the Glu-1 alleles were identified in the spring and wheat cultivars. The analysis of independence of the distribution of the spring and winter cultivars by the market classes and by the alleles of the HMWGS loci showed a highly significant association of the alleles of three Glu-1 loci with the market classes in foreign cultivars and independence or a weak association in the Russian and Ukrainian cultivars. This seems to be due to the absence of a statistically substantiated system of classification of the domestic cultivars on the basis of their quality.

  10. Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine.

    Directory of Open Access Journals (Sweden)

    Agota Fodor

    Full Text Available Nowadays, genome-wide association studies (GWAS and genomic selection (GS methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9 using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.

  11. Use of a high resolution melting (HRM assay to compare gag, pol, and env diversity in adults with different stages of HIV infection.

    Directory of Open Access Journals (Sweden)

    Matthew M Cousins

    Full Text Available Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual.HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative, 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14-540 days, and 67 with non-recent HIV infection (HIV infected >2 years. HRM scores were generated for two regions in gag, one region in pol, and three regions in env.Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection.The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined.

  12. Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection.

    Science.gov (United States)

    Cousins, Matthew M; Laeyendecker, Oliver; Beauchamp, Geetha; Brookmeyer, Ronald; Towler, William I; Hudelson, Sarah E; Khaki, Leila; Koblin, Beryl; Chesney, Margaret; Moore, Richard D; Kelen, Gabor D; Coates, Thomas; Celum, Connie; Buchbinder, Susan P; Seage, George R; Quinn, Thomas C; Donnell, Deborah; Eshleman, Susan H

    2011-01-01

    Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual. HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative), 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14-540 days), and 67 with non-recent HIV infection (HIV infected >2 years). HRM scores were generated for two regions in gag, one region in pol, and three regions in env. Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection. The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined.

  13. Abundance and diversity of methanogens: potential role in high arsenic groundwater in Hetao Plain of Inner Mongolia, China.

    Science.gov (United States)

    Wang, Y H; Li, P; Dai, X Y; Zhang, R; Jiang, Z; Jiang, D W; Wang, Y X

    2015-05-15

    To investigate the community diversity and abundance of methanogens and their potential role in high arsenic groundwater, 17 groundwater samples from Hetao Plain of Inner Mongolia were investigated with an integrated method including 16S rRNA gene clone library, quantitative polymerase chain reaction and geochemistry analyses. Total arsenic (AsTot) concentrations were 82.7-1088.7 μg/L and arsenite (AsIII) mostly dominated in these samples with percentages of 0.04-0.79. CH₄ concentrations ranged from 0.01 to 292 μg/L and distinctly elevated only when AsTot were relatively high and SO₄(2-) were distinctly low. Principal component analysis indicated that these samples were divided into three groups according to the variations of AsTot, CH₄ and SO₄(2-). AsTot concentrations were distinctly high in the group with high CH₄ and low SO₄(2-) comparing to the other two groups (one with high CH₄ and high SO₄(2-), the other with low CH₄ and SO₄(2-)). The mcrA gene (methyl coenzyme-M reductase gene) based phylogenetic analysis of methanogens population showed that methanogenic archaea was diverse but mainly composed of Methanomicrobiales, Methanosarcinales, Methanobacteria and unidentified groups, with Methanomicrobiales being distinctly dominant (50.6%). The mcrA gene abundance in high arsenic groundwater ranged from 3.01 × 10(3) to 3.80 × 10(6)copies/L and accounted for 0-30.2% of total archaeal 16S rRNA genes. The abundance of mcrA genes was positively correlated with the concentrations of AsTot (R=0.59), AsIII (R=0.57) and FeII (R=0.79), while it was negatively correlated with oxidation-reduction potential (R=-0.66) and SO₄(2-) concentration (R=-0.64). These results implied that methanogenic archaea might accelerate As release in groundwater aquifers in Hetao Plain. Copyright © 2015. Published by Elsevier B.V.

  14. Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing).

    Science.gov (United States)

    Vengerfeldt, Veiko; Špilka, Katerina; Saag, Mare; Preem, Jens-Konrad; Oopkaup, Kristjan; Truu, Jaak; Mändar, Reet

    2014-11-01

    Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patient's quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA). Samples were collected under strict aseptic conditions from 12 teeth (5 with primary CAP, 3 with secondary CAP, and 4 with a periapical abscess [PA]) and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products. Root canal specimens displayed highly polymicrobial communities in all 3 patient groups. One sample contained 5-8 (mean = 6.5) phyla of bacteria. The most numerous were Firmicutes and Bacteroidetes, but Actinobacteria, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Synergistetes were also present in most of the patients. One sample contained 30-70 different operational taxonomic units; the mean (± standard deviation) was lower in the primary CAP group (36 ± 4) than in the PA (45 ± 4) and secondary CAP (43 ± 13) groups (P < .05). The communities were individually different, but anaerobic bacteria predominated as the rule. Enterococcus faecalis was found only in patients with secondary CAP. One PA sample displayed a significantly high proportion (47%) of Proteobacteria, mainly at the expense of Janthinobacterium lividum. This study provided an in-depth characterization of the microbiota of periapical tissues, revealing highly polymicrobial communities and minor differences between the study groups. A full understanding of the etiology of periodontal disease will only be possible through further in-depth systems-level analyses of the host-microbiome interaction. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  15. A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities.

    Science.gov (United States)

    Price, Jacob R; Shieh, Wen K; Sales, Christopher M

    2015-12-25

    A novel reactor design, coined a high density bioreactor (HDBR), is presented for the cultivation and study of high density microbial communities. Past studies have evaluated the performance of the reactor for the removal of COD(1) and nitrogen species(2-4) by heterotrophic and chemoautotrophic bacteria, respectively. The HDBR design eliminates the requirement for external flocculation/sedimentation processes while still yielding effluent containing low suspended solids. In this study, the HDBR is applied as a photobioreactor (PBR) in order to characterize the nitrogen removal characteristics of an algae-based photosynthetic microbial community. As previously reported for this HDBR design, a stable biomass zone was established with a clear delineation between the biologically active portion of the reactor and the recycling reactor fluid, which resulted in a low suspended solid effluent. The algal community in the HDBR was observed to remove 18.4% of total nitrogen species in the influent. Varying NH4(+) and NO3(-) concentrations in the feed did not have an effect on NH4(+) removal (n=44, p=0.993 and n=44, p=0.610 respectively) while NH4(+) feed concentration was found to be negatively related with NO3(-) removal (n=44, p=0.000) and NO3(-) feed concentration was found to be positively correlated with NO3(-) removal (n=44, p=0.000). Consistent removal of NH4(+), combined with the accumulation of oxidized nitrogen species at high NH4(+) fluxes indicates the presence of ammonia- and nitrite-oxidizing bacteria within the microbial community.

  16. High Prevalence and Genotype Diversity of Anal HPV Infection among MSM in Northern Thailand.

    Directory of Open Access Journals (Sweden)

    Taweewat Supindham

    Full Text Available HPV infection is common and may cause cancer among men who have sex with men (MSM. Anal HPV infection (HPV+ was found in 85% of HIV-positive (HIV+ and 59% of HIV-negative (HIV- MSM in Bangkok, central Thailand. As little is known about HPV in this group in northern Thailand, we studied MSM subgroups comprised of gay men (GM, bisexual men (BM, and transgender women (TGW.From July 2012 through January 2013, 85 (42.5% of 200 GM, 30 (15% BM, and 85 (42.5% TGW who practiced receptive anal intercourse were recruited after informed consent, followed by self-assisted computer interview, HIV testing, and anal swabs for HPV genotyping.Of 197 adequate specimens, the overall prevalence of any HPV was 157 (80%. Prevalence was 89% (76/85 in GM, 48% (14/29 in BM, and 81% (67/83 in TGW. The most common high-risk types were HPV16 (27% of 197, HPV58 (23%, and HPV51 (18%. Prevalence of high-risk types was 74% in 85 GM, 35% in 29 BM, and 71% in 83 TGW. Prevalence of any HPV type, or high-risk type, was 100% and 94%, respectively, among 48 HIV+ MSM, 70% and 54% among 120 HIV- MSM. Of the 197 specimens, 36% (70 had HPV types 16 and/or 18 in the bivalent vaccine, compared to 48% (95 with ≥1 of types 16/18/06/11 in the quadrivalent, 56% (111 for 16/18/31/33/45/52/58 in the 7-valent, and 64% (126 for 16/18/31/33/45/52/58/06/11 in the 9-valent. HIV+, GM, and TGW were independently associated with HPV infection.We found higher rates of both any HPV and high-risk types than previous studies. Among the heretofore unstudied TGW, their equivalent HPV rates were comparable to GM. Current and investigational HPV vaccines could substantially protect GM, BM, and TGW from the serious consequences of HPV infection especially among HIV + MSM.

  17. [Influences of long-term application of organic and inorganic fertilizers on the composition and abundance of nirS-type denitrifiers in black soil].

    Science.gov (United States)

    Yin, Chang; Fan, Fen-Liang; Li, Zhao-Jun; Song, A-Lin; Zhu, Ping; Peng, Chang; Liang, Yong-Chao

    2012-11-01

    The objectives of this study were to explore the effects of long-term organic and inorganic fertilizations on the composition and abundance of nirS-type denitrifiers in black soil. Soil samples were collected from 4 treatments (i. e. no fertilizer treatment, CK; organic manure treatment, OM; chemical fertilizer treatment (NPK) and combination of organic and chemical fertilizers treatment (MNPK)) in Gongzhuling Long-term Fertilization Experiment Station. Composition and abundance of nirS-type denitrifiers were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR (Q-PCR), respectively. Denitrification enzyme activity (DEA) and soil properties were also measured. Application of organic fertilizers (OM and MNPK) significantly increased the DEAs of black soil, with the DEAs in OM and MNPK being 5.92 and 6.03 times higher than that in CK treatment, respectively, whereas there was no significant difference between NPK and CK. OM and MNPK treatments increased the abundances of nirS-type denitrifiers by 2.73 and 3.83 times relative to that of CK treatment, respectively. The abundance of nirS-type denitrifiers in NPK treatment was not significantly different from that of CK. The T-RFLP analysis of nirS genes showed significant differences in community composition between organic and inorganic treatments, with the emergence of a 79 bp T-RF, a significant decrease in relative abundance of the 84 bp T-RF and a loss of the 99 bp T-RF in all organic treatments. Phylogenetic analysis indicated that the airS-type denitrifiers in the black soil were mainly composed of alpha, beta and gamma-Proteobacteria. The 79 bp-type denitrifiers inhabiting exclusively in organic treatments (OM and MNPK) were affiliated to Pseudomonadaceae in gamma-Proteobacteria and Burkholderiales in beta-Proteobacteria. The 84 bp-types were related to Burkholderiales and Rhodocyclales. Correlation analysis indicated that pH, concentrations of total nitrogen

  18. High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors.

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    Daniela Janek

    2016-08-01

    Full Text Available The human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as Staphylococcus aureus. The potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied. Of 89 nasal Staphylococcus isolates, unexpectedly, the vast majority (84% was found to produce antimicrobial substances in particular under habitat-specific stress conditions, such as iron limitation or exposure to hydrogen peroxide. Activity spectra were generally narrow but highly variable with activities against certain nasal members of the Actinobacteria, Proteobacteria, Firmicutes, or several groups of bacteria. Staphylococcus species and many other Firmicutes were insusceptible to most of the compounds. A representative bacteriocin was identified as a nukacin-related peptide whose inactivation reduced the capacity of the producer Staphylococcus epidermidis IVK45 to limit growth of other nasal bacteria. Of note, the bacteriocin genes were found on mobile genetic elements exhibiting signs of extensive horizontal gene transfer and rearrangements. Thus, continuously evolving bacteriocins appear to govern bacterial competition in the human nose and specific bacteriocins may become important agents for eradication of notorious opportunistic pathogens from human microbiota.

  19. High diversity of the T-cell receptor repertoire of tumor-infiltrating lymphocytes in basal cell carcinoma

    DEFF Research Database (Denmark)

    Omland, Silje H; Hamrouni, Abdelbasset; Gniadecki, Robert

    2017-01-01

    to determine the clonality of TCR and degree of overlap in TCR repertoires between skin resident T-cells and TILs. We found high diversity of the TCR repertoire in BCC and control skin with random V-J gene usage and similar CDR3-length distribution. Lack of TCR repertoire restriction indicates absence of tumor......Whether specific T-cell clones are present in tumor infiltrating lymphocytes (TILs) in BCC is unknown. We employed deep sequencing of mRNA coding for the T-cell receptor (TCR) chains α- and β to characterize the repertoire of TILs in BCC. V and J gene-usage and CDR3 length were computed...

  20. Bacterial Glycosyltransferases: Challenges and opportunities of a highly diverse enzyme class toward tailoring natural products

    Directory of Open Access Journals (Sweden)

    Jochen eSchmid

    2016-02-01

    Full Text Available The enzyme subclass of glycosyltransferases (EC 2.4 currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition glycosyltransferases also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial glycosyltransferases show a higher sequence similarity in comparison to mammalian ones. Even when most glycosyltransferases are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial glycosyltransferases, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.

  1. A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

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    Myburg Alexander A

    2010-06-01

    Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees

  2. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.

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    Yehudit Hasin

    2008-11-01

    Full Text Available Olfactory receptors (ORs, which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction ( approximately 55% of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs, we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that approximately 50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used

  3. Atypical epidemiology of CTX-M-15 among Enterobacteriaceae from a high diversity of non-clinical niches in Angola.

    Science.gov (United States)

    Ribeiro, T G; Novais, Â; Peixe, L; Machado, E

    2016-05-01

    The objective of this study was to investigate the distribution and molecular epidemiology of ESBLs, acquired AmpCs and carbapenemases in Enterobacteriaceae from non-clinical niches in Angola, an under-researched sub-Saharan country. Eighty-one samples were recovered from healthy persons (n = 18), healthy animals (n = 33) and their environments (n = 10) or aquatic settings (n = 20) in south Angola (2013). Samples were plated onto CHROMagar™ Orientation with/without antibiotics. Standard methods were used for bacterial identification, characterization of bla genes, antibiotic susceptibility testing and conjugation assays. Clonal analysis (XbaI-PFGE, MLST and Escherichia coli phylogroups), location of bla and plasmid characterization (S1-PFGE, I-CeuI-PFGE, replicon typing and hybridization) were also performed. ESBLs (almost exclusively CTX-M-15, 98%) were detected in 21% (45/216) of the isolates, recovered from diverse non-clinical niches and belonging to different Enterobacteriaceae species (mainly E. coli). Acquired AmpCs or carbapenemases were not found. The pandemic B2-ST131 E. coli clone was not identified, but some widespread clonal complexes (CCs) from A (CC10 and CC168), B1 (CC156) or D (CC38) phylogroups were detected. blaCTX-M-15 was variably identified on typeable (29%; 100-335 kb; IncFII, IncFIIK6, IncHI2 and IncY) or non-typeable (16%; 70-330 kb) plasmids or on the chromosome (14%), while for 41% of the isolates its specific location was not determined. This study reports, for the first time in Angola, an unexpected high occurrence of CTX-M-15 in diverse non-clinical niches and Enterobacteriaceae species, and uncovers novel plasmid replicons in under-researched geographical regions. The diffusion of blaCTX-M-15 through such a high diversity of genetic backgrounds (clones, typeable/non-typeable plasmids and genetic environments) unveils an extraordinary ability for blaCTX-M-15 acquisition and mobilization favoured by unrecognized

  4. A High-Content Live-Cell Viability Assay and Its Validation on a Diverse 12K Compound Screen.

    Science.gov (United States)

    Chiaravalli, Jeanne; Glickman, J Fraser

    2017-08-01

    We have developed a new high-content cytotoxicity assay using live cells, called "ImageTOX." We used a high-throughput fluorescence microscope system, image segmentation software, and the combination of Hoechst 33342 and SYTO 17 to simultaneously score the relative size and the intensity of the nuclei, the nuclear membrane permeability, and the cell number in a 384-well microplate format. We then performed a screen of 12,668 diverse compounds and compared the results to a standard cytotoxicity assay. The ImageTOX assay identified similar sets of compounds to the standard cytotoxicity assay, while identifying more compounds having adverse effects on cell structure, earlier in treatment time. The ImageTOX assay uses inexpensive commercially available reagents and facilitates the use of live cells in toxicity screens. Furthermore, we show that we can measure the kinetic profile of compound toxicity in a high-content, high-throughput format, following the same set of cells over an extended period of time.

  5. Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa.

    Science.gov (United States)

    Geisen, S; Laros, I; Vizcaíno, A; Bonkowski, M; de Groot, G A

    2015-09-01

    Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of metazoan DNA using 454 HTS. We aimed at evaluating whether HTS quantitatively reveals true relative abundances of soil protists and at investigating whether the expected protist community structure is altered by the co-amplification of metazoan-associated protist taxa. Indeed, HTS revealed fundamentally different protist communities from those expected. Ciliate sequences were highly over-represented, while those of most amoebae and flagellates were under-represented or totally absent. These results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Furthermore, we detected a wide range of nonadded protist taxa probably introduced along with metazoan DNA, which altered the protist community structure. Among those, 20 taxa most closely resembled parasitic, often pathogenic taxa. Therewith, we provide the first HTS data in support of classical observational studies that showed that potential protist parasites are hosted by soil metazoa. Taken together, profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil metazoa obscure the true diversity of free-living soil protist communities. © 2015 John Wiley & Sons Ltd.

  6. A High Diversity of Eurasian Lineage Low Pathogenicity Avian Influenza A Viruses Circulate among Wild Birds Sampled in Egypt

    Science.gov (United States)

    Gerloff, Nancy A.; Jones, Joyce; Simpson, Natosha; Balish, Amanda; ElBadry, Maha Adel; Baghat, Verina; Rusev, Ivan; de Mattos, Cecilia C.; de Mattos, Carlos A.; Zonkle, Luay Elsayed Ahmed; Kis, Zoltan; Davis, C. Todd; Yingst, Sam; Cornelius, Claire; Soliman, Atef; Mohareb, Emad; Klimov, Alexander; Donis, Ruben O.

    2013-01-01

    Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian). The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring. PMID:23874653

  7. High Prevalence, Genetic Diversity and Intracellular Growth Ability of Legionella in Hot Spring Environments

    Science.gov (United States)

    Zhou, Haijian; Wang, Huanxin; Xu, Ying; Zhao, Mingqiang; Guan, Hong; Li, Machao; Shao, Zhujun

    2013-01-01

    Background Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. Methods Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. Results Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ≥0.2 mg/L, urea concentration of ≥0.05 mg/L, total microbial counts of ≥400 CFU/ml and total coliform of ≥3 MPN/L (pLegionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (pLegionella pneumophila was the most frequently isolated species (98.9%), and the isolated serogroups included serogroups 3 (25.3%), 6 (23.4%), 5 (19.2%), 1 (18.5%), 2 (10.2%), 8 (0.4%), 10 (0.8%), 9 (1.9%) and 12 (0.4%). Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. Conclusions Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control and prevention strategies are

  8. High prevalence, genetic diversity and intracellular growth ability of Legionella in hot spring environments.

    Directory of Open Access Journals (Sweden)

    Tian Qin

    Full Text Available BACKGROUND: Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. METHODS: Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE and sequence-based typing (SBT were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. RESULTS: Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ≥0.2 mg/L, urea concentration of ≥0.05 mg/L, total microbial counts of ≥400 CFU/ml and total coliform of ≥3 MPN/L (p<0.01. The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01. Legionella pneumophila was the most frequently isolated species (98.9%, and the isolated serogroups included serogroups 3 (25.3%, 6 (23.4%, 5 (19.2%, 1 (18.5%, 2 (10.2%, 8 (0.4%, 10 (0.8%, 9 (1.9% and 12 (0.4%. Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. CONCLUSIONS: Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control

  9. Recovery of diverse microbes in high turbidity surface water samples using dead-end ultrafiltration.

    Science.gov (United States)

    Mull, Bonnie; Hill, Vincent R

    2012-12-01

    Dead-end ultrafiltration (DEUF) has been reported to be a simple, field-deployable technique for recovering bacteria, viruses, and parasites from large-volume water samples for water quality testing and waterborne disease investigations. While DEUF has been reported for application to water samples having relatively low turbidity, little information is available regarding recovery efficiencies for this technique when applied to sampling turbid water samples such as those commonly found in lakes and rivers. This study evaluated the effectiveness of a DEUF technique for recovering MS2 bacteriophage, enterococci, Escherichia coli, Clostridium perfringens, and Cryptosporidium parvum oocysts in surface water samples having elevated turbidity. Average recovery efficiencies for each study microbe across all turbidity ranges were: MS2 (66%), C. parvum (49%), enterococci (85%), E. coli (81%), and C. perfringens (63%). The recovery efficiencies for MS2 and C. perfringens exhibited an inversely proportional relationship with turbidity, however no significant differences in recovery were observed for C. parvum, enterococci, or E. coli. Although ultrafilter clogging was observed, the DEUF method was able to process 100-L surface water samples at each turbidity level within 60 min. This study supports the use of the DEUF method for recovering a wide array of microbes in large-volume surface water samples having medium to high turbidity. Published by Elsevier B.V.

  10. Synthesis, characterization, and in vitro biological evaluation of highly stable diversely functionalized superparamagnetic iron oxide nanoparticles

    International Nuclear Information System (INIS)

    Bhattacharya, Dipsikha; Sahu, Sumanta K.; Banerjee, Indranil; Das, Manasmita; Mishra, Debashish; Maiti, Tapas K.; Pramanik, Panchanan

    2011-01-01

    In this article, we report the design and synthesis of a series of well-dispersed superparamagnetic iron oxide nanoparticles (SPIONs) using chitosan as a surface modifying agent to develop a potential T 2 contrast probe for magnetic resonance imaging (MRI). The amine, carboxyl, hydroxyl, and thiol functionalities were introduced on chitosan-coated magnetic probe via simple reactions with small reactive organic molecules to afford a series of biofunctionalized nanoparticles. Physico-chemical characterizations of these functionalized nanoparticles were performed by TEM, XRD, DLS, FTIR, and VSM. The colloidal stability of these functionalized iron oxide nanoparticles was investigated in presence of phosphate buffer saline, high salt concentrations and different cell media for 1 week. MRI analysis of human cervical carcinoma (HeLa) cell lines treated with nanoparticles elucidated that the amine-functionalized nanoparticles exhibited higher amount of signal darkening and lower T 2 relaxation in comparison to the others. The cellular internalization efficacy of these functionalized SPIONs was also investigated with HeLa cancer cell line by magnetically activated cell sorting (MACS) and fluorescence microscopy and results established selectively higher internalization efficacy of amine-functionalized nanoparticles to cancer cells. These positive attributes demonstrated that these nanoconjugates can be used as a promising platform for further in vitro and in vivo biological evaluations.

  11. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

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    Yandell Mark

    2010-07-01

    Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

  12. Community Structure and Function of High-temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

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    William P. Inskeep

    2013-06-01

    Full Text Available Six phototrophic microbial mat communities from different geothermal springs (YNP were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average~ 53 Mbp/site were subjected to multiple taxonomic, phylogenetic and functional analyses. All methods, including G+C content distribution, MEGAN analyses and oligonucleotide frequency-based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7 and Fischerella-like populations at White Creek (WC_6. Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp. were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae, and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria population from Bath Lake Vista Annex (BLVA_20. Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes; however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional

  13. Kinetic energy of throughfall in a highly diverse forest ecosystem in the humid subtropics

    Science.gov (United States)

    Geißler, Christian; Kühn, Peter; Scholten, Thomas

    2010-05-01

    conditions. Most of the energy is supposed to be absorbed by shrubs, herbs and the litter layer. For some species in the shrub and herb layer throughfall drops are crucial for seed dispersal (Nakanishi 2002). A higher kinetic energy of throughfall should be advantageous for seed dispersal and probably support biodiversity. Further, it is shown that the variability of kinetic energy in forests varies among the age of the forest stand which can be related to the forest structure. In our case there is a high variability in young forests (left out) and gaps in the tree layer. Old forests (> 80 years) also have a high variability in kinetic energy. There, external influences like snow and wind break result in a fragmentary tree layer which allows less erosive rainfall to reach the forest floor. Medium aged forests are more homogenous regarding canopy closure or tree heights. Generally, the variability of kinetic energy in forests is increasing with the amount of rainfall. Moreover, it is shown that the kinetic energy of throughfall is species specific. For the investigated tree species the values range between 24.41 J m-2 mm-1 (Daphniphyllum oldhamii) and 33.24 J m-2 mm-1 (Schima superba) while the concurrent rainfall in the open field has an average kinetic energy of 6.75 J m-2 mm-1. Leaf size and canopy architecture are supposed to be two of the controlling variables for specific species. These results give implications for afforestation measures and are important input variables for modeling of erosion processes. Chapman, G., 1948. Size of raindrops and their striking force at the soil surface in a Red Pine plantation. Transactions - American Geophysical Union, 29: 664-670. Ellison, W.D., 1947. Soil Erosion Studies - Part II. Agricultural Engineering, 28: 197-201. Geißler, C., Kühn, P., Böhnke, M., Bruelheide, H., Shi, X., Scholten, T., under review: Measuring splash erosion potential under vegetation using sand-filled splash cups. Hall, R.L., Calder, I.R., 1993. Drop size

  14. High diversity of vacA and cagA Helicobacter pylori genotypes in patients with and without gastric cancer.

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    Yolanda López-Vidal

    Full Text Available BACKGROUND: Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. The aim of this study was to assess the topographical distribution of H. pylori in the stomach as well as the vacA and cagA genotypes in patients with and without gastric cancer. METHODOLOGY/PRINCIPAL FINDINGS: Three gastric biopsies, from predetermined regions, were evaluated in 16 patients with gastric cancer and 14 patients with dyspeptic symptoms. From cancer patients, additional biopsy specimens were obtained from tumor centers and margins; among these samples, the presence of H. pylori vacA and cagA genotypes was evaluated. Positive H. pylori was 38% and 26% in biopsies obtained from the gastric cancer and non-cancer groups, respectively (p = 0.008, and 36% in tumor sites. In cancer patients, we found a preferential distribution of H. pylori in the fundus and corpus, whereas, in the non-cancer group, the distribution was uniform (p = 0.003. A majority of the biopsies were simultaneously cagA gene-positive and -negative. The fundus and corpus demonstrated a higher positivity rate for the cagA gene in the non-cancer group (p = 0.036. A mixture of cagA gene sizes was also significantly more frequent in this group (p = 0.003. Ninety-two percent of all the subjects showed more than one vacA gene genotype; s1b and m1 vacA genotypes were predominantly found in the gastric cancer group. The highest vacA-genotype signal-sequence diversity was found in the corpus and 5 cm from tumor margins. CONCLUSION/SIGNIFICANCE: High H. pylori colonization diversity, along with the cagA gene, was found predominantly in the fundus and corpus of patients with gastric cancer. The genotype diversity observed across systematic whole-organ and tumor sampling was remarkable. We find that there is insufficient evidence to support the association of one isolate with a specific disease, due to the multistrain nature of H. pylori infection shown in this work.

  15. Genetic History of Hepatitis C Virus in Venezuela: High Diversity and Long Time of Evolution of HCV Genotype 2

    Science.gov (United States)

    Sulbarán, Maria Z.; Di Lello, Federico A.; Sulbarán, Yoneira; Cosson, Clarisa; Loureiro, Carmen L.; Rangel, Héctor R.; Cantaloube, Jean F.; Campos, Rodolfo H.; Moratorio, Gonzalo; Cristina, Juan; Pujol, Flor H.

    2010-01-01

    Background The subtype diversity of the hepatitis C virus (HCV) genotypes is unknown in Venezuela. Methodology/Principal Findings Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1) was the most common genotype (63%), composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%), being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA) of G2j around 1785, before the introduction of G1b (1869) and G1a (1922). While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period. Conclusions/Significance Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies. PMID:21179440

  16. A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition.

    Science.gov (United States)

    Li, Wei; Wang, Mengmeng; Bian, Xiaomeng; Guo, Jiajia; Cai, Lei

    2016-01-01

    The intertidal region is one of the most dynamic environments in the biosphere, which potentially supports vast biodiversity. Fungi have been found to play important roles in marine ecosystems, e.g., as parasites or symbionts of plants and animals, and as decomposers of organic materials. The fungal diversity in intertidal region, however, remains poorly understood. In this study, sediment samples from various intertidal habitats of Chinese seas were collected and investigated for determination of fungal community and spatial distribution. Through ribosomal RNA internal transcribed spacer-2 (ITS2) metabarcoding, a high-level fungal diversity was revealed, as represented by 6,013 OTUs that spanned six phyla, 23 classes, 84 orders and 526 genera. The presence of typical decomposers (e.g., Corollospora in Ascomycota and Lepiota in Basidiomycota) and pathogens (e.g., Olpidium in Chytriomycota, Actinomucor in Zygomycota and unidentified Rozellomycota spp.), and even mycorrhizal fungi (e.g., Glomus in Glomeromycota) indicated a complicated origin of intertidal fungi. Interestingly, a small proportion of sequences were classified to obligate marine fungi (e.g., Corollospora, Lignincola, Remispora, Sigmoidea ). Our data also showed that the East China Sea significantly differed from other regions in terms of species richness and community composition, indicating a profound effect of the huge discharge of the Yangtze River. No significant difference in fungal communities was detected, however, among habitat types (i.e., aquaculture, dock, plant, river mouth and tourism). These observations raise further questions on adaptation of these members to environments and the ecological functions they probably perform.

  17. High-Precision and Low Latency RT-GNSS Processed Data for Diverse Geophysical and Natural Hazard Communities.

    Science.gov (United States)

    Mencin, David; Hodgkinson, Kathleen; Sievers, Charlie; David, Phillips; Charles, Meertens; Glen, Mattioli

    2017-04-01

    UNAVCO has been providing infrastructure and support for solid-earth sciences and earthquake natural hazards for the past two decades. Recent advances in GNSS technology and data processing are now providing position solutions with centimeter-level precision at high-rate (>1 Hz) and low latency (i.e. the time required for data to arrive for analysis, in this case less than 1 second). These data have the potential to improve our understanding in diverse areas of geophysics including properties of seismic, volcanic, magmatic and tsunami sources, and thus profoundly transform rapid event characterization and warning. Scientific and operational applications also include glacier and ice sheet motions; tropospheric modeling; and space weather. These areas of geophysics represent a spectrum of research fields, including geodesy, seismology, tropospheric weather, space weather and natural hazards. Processed Real-Time GNSS (RT-GNSS) data will require formats and standards that allow this broad and diverse community to use these data and associated meta-data in existing research infrastructure. These advances have critically highlighted the difficulties associated with merging data and metadata between scientific disciplines. Even seemingly very closely related fields such as geodesy and seismology, which both have rich histories of handling large volumes of data and metadata, do not go together well in any automated way. Community analysis strategies, or lack thereof, such as treatment of error prove difficult to address and are reflected in the data and metadata. In addition, these communities have differing security, accessibility and reliability requirements. We propose some solutions to the particular problem of making RT-GNSS processed solution data and metadata accessible to multiply scientific and natural hazard communities. Importantly, we discuss the roadblocks encounter and solved and those that remain to be addressed.

  18. Genetic history of hepatitis C virus in Venezuela: high diversity and long time of evolution of HCV genotype 2.

    Directory of Open Access Journals (Sweden)

    Maria Z Sulbarán

    Full Text Available BACKGROUND: The subtype diversity of the hepatitis C virus (HCV genotypes is unknown in Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1 was the most common genotype (63%, composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%, being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA of G2j around 1785, before the introduction of G1b (1869 and G1a (1922. While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period. CONCLUSIONS/SIGNIFICANCE: Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies.

  19. Chloroquine efficacy for Plasmodium vivax in Myanmar in populations with high genetic diversity and moderate parasite gene flow.

    Science.gov (United States)

    Htun, Myo Win; Mon, Nan Cho Nwe; Aye, Khin Myo; Hlaing, Chan Myae; Kyaw, Myat Phone; Handayuni, Irene; Trimarsanto, Hidayat; Bustos, Dorina; Ringwald, Pascal; Price, Ric N; Auburn, Sarah; Thriemer, Kamala

    2017-07-10

    Plasmodium vivax malaria remains a major public health burden in Myanmar. Resistance to chloroquine (CQ), the first-line treatment for P. vivax, has been reported in the country and has potential to undermine local control efforts. Patients over 6 years of age with uncomplicated P. vivax mono-infection were enrolled into clinical efficacy studies in Myawaddy in 2014 and Kawthoung in 2012. Study participants received a standard dose of CQ (25 mg/kg over 3 days) followed by weekly review until day 28. Pvmdr1 copy number (CN) and microsatellite diversity were assessed on samples from the patients enrolled in the clinical study and additional cross-sectional surveys undertaken in Myawaddy and Shwegyin in 2012. A total of 85 patients were enrolled in the CQ clinical studies, 25 in Myawaddy and 60 in Kawthoung. One patient in Myawaddy (1.2%) had an early treatment failure and two patients (2.3%) in Kawthoung presented with late treatment failures on day 28. The day 28 efficacy was 92.0% (95% CI 71.6-97.9) in Myawaddy and 98.3% (95% CI 88.7-99.8) in Kawthoung. By day 2, 92.2% (23/25) in Myawaddy and 85.0% (51/60) in Kawthoung were aparasitaemic. Genotyping and pvmdr1 CN assessment was undertaken on 43, 52 and 46 clinical isolates from Myawaddy, Kawthoung and Shwegyin respectively. Pvmdr1 amplification was observed in 3.2% (1/31) of isolates in Myawaddy, 0% (0/49) in Kawthoung and 2.5% (1/40) in Shwegyin. Diversity was high in all sites (H E 0.855-0.876), with low inter-population differentiation (F ST 0.016-0.026, P Myanmar, particularly given the potential connectivity between parasite population at different sites.

  20. Heat Production by the Denitrifying Bacterium Pseudomonas fluorescens and the Dissimilatory Ammonium-Producing Bacterium Pseudomonas putrefaciens during Anaerobic Growth with Nitrate as the Electron Acceptor

    OpenAIRE

    Samuelsson, M.-O.; Cadez, P.; Gustafsson, L.

    1988-01-01

    The heat production rate and the simultaneous nitrate consumption and production and consumption of nitrite and nitrous oxide were monitored during the anaerobic growth of two types of dissimilatory nitrate reducers. Pseudomonas fluorescens, a denitrifier, consumed nitrate and accumulated small amounts of nitrite or nitrous oxide. The heat production rate increased steadily during the course of nitrate consumption and decreased rapidly concomitant with the depletion of the electron acceptors....

  1. Effects of long-term elevated CO2 on N2-fixing, denitrifying and nitrifying enzyme activities in forest soils under Pinus sylvestriformis in Changbai Mountain

    Institute of Scientific and Technical Information of China (English)

    ZHENG Jun-Qiang; HAN Shi-Jie; REN Fei-Rong; ZHOU Yu-Mei; ZHANG Yan

    2008-01-01

    A study was conducted to determine the effects of elevated CO2 on soil N process at Changbai Mountain in Jilin Province,northeastern China (42o24'N,128o06'E,and 738 m elevation).A randomized complete block design of ambient and elevated CO2 was established in an open-top chamber facility in the spring of 1999.Changpai Scotch pine (Pinus sylvestris var.sylvestriformis seeds were sowed in May,1999 and CO2 fumigation treatments began after seeds germination.In each year,the exposure started at the end of April and stopped at the end of October.Soil samples were collected in June and August 2006 and in June 2007,and soil nitrifying,denitrifying and N2-fixing enzyme activities were measured.Results show that soil nitrifying enzyme activities (NEA) in the 5-10 cm soil layer were significantly increased at elevated CO2 by 30.3% in June 2006,by 30.9% in August 2006 and by 11.3% in June 2007.Soil denitrifying enzyme activities (DEA) were significantly decreased by elevated CO2 treatment in June 2006 (P < 0.012) and August 2006 (P < 0.005) samplings in our study; no significant difference was detected in June 2007,and no significant changes in N2-fixing enzyme activity were found.This study suggests that elevated CO2 can alter soil nitrifying enzyme and denitrifying enzyme activities.

  2. A doubling of microphytobenthos biomass coincides with a tenfold increase in denitrifier and total bacterial abundances in intertidal sediments of a temperate estuary.

    Directory of Open Access Journals (Sweden)

    Helen Decleyre

    Full Text Available Surface sediments are important systems for the removal of anthropogenically derived inorganic nitrogen in estuaries. They are often characterized by the presence of a microphytobenthos (MPB biofilm, which can impact bacterial communities in underlying sediments for example by secretion of extracellular polymeric substances (EPS and competition for nutrients (including nitrogen. Pyrosequencing and qPCR was performed on two intertidal surface sediments of the Westerschelde estuary characterized by a two-fold difference in MPB biomass but no difference in MPB composition. Doubling of MPB biomass was accompanied by a disproportionately (ten-fold increase in total bacterial abundances while, unexpectedly, no difference in general community structure was observed, despite significantly lower bacterial richness and distinct community membership, mostly for non-abundant taxa. Denitrifier abundances corresponded likewise while community structure, both for nirS and nirK denitrifiers, remained unchanged, suggesting that competition with diatoms for nitrate is negligible at concentrations in the investigated sediments (appr. 1 mg/l NO3-. This study indicates that MPB biomass increase has a general, significantly positive effect on total bacterial and denitrifier abundances, with stimulation or inhibition of specific bacterial groups that however do not result in a re-structured community.

  3. Communities of nirS-type denitrifiers in the water column of the oxygen minimum zone in the eastern South Pacific.

    Science.gov (United States)

    Castro-González, Maribeb; Braker, Gesche; Farías, Laura; Ulloa, Osvaldo

    2005-09-01

    The major sites of water column denitrification in the ocean are oxygen minimum zones (OMZ), such as one in the eastern South Pacific (ESP). To understand the structure of denitrifying communities in the OMZ off Chile, denitrifier communities at two sites in the Chilean OMZ (Antofagasta and Iquique) and at different water depths were explored by terminal restriction fragment length polymorphism analysis and cloning of polymerase chain reaction (PCR)-amplified nirS genes. NirS is a functional marker gene for denitrification encoding cytochrome cd1-containing nitrite reductase, which catalyses the reduction of nitrite to nitric oxide, the key step in denitrification. Major differences were found between communities from the two geographic locations. Shifts in community structure occurred along a biogeochemical gradient at Antofagasta. Canonical correspondence analysis indicated that O2, NO3-, NO2- and depth were important environmental factors governing these communities along the biogeochemical gradient in the water column. Phylogenetic analysis grouped the majority of clones from the ESP in distinct clusters of genes from presumably novel and yet uncultivated denitrifers. These nirS clusters were distantly related to those found in the water column of the Arabian Sea but the phylogenetic distance was even higher compared with environmental sequences from marine sediments or any other habitat. This finding suggests similar environmental conditions trigger the development of denitrifiers with related nirS genotypes despite large geographic distances.

  4. Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

    KAUST Repository

    Amer, Ranya A.

    2015-02-01

    Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

  5. High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China.

    Science.gov (United States)

    Wei, Yu-Jie; Wu, Yun; Yan, Yin-Zhuo; Zou, Wan; Xue, Jie; Ma, Wen-Rui; Wang, Wei; Tian, Ge; Wang, Li-Ye

    2018-01-01

    In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine.

  6. Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    Ranya A. Amer

    2015-01-01

    Full Text Available Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt. Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

  7. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.

    Science.gov (United States)

    Pagenkopp Lohan, K M; Fleischer, R C; Carney, K J; Holzer, K K; Ruiz, G M

    2016-04-01

    Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

  8. High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

    Science.gov (United States)

    Yan, Yin-zhuo; Zou, Wan; Ma, Wen-rui; Wang, Wei; Tian, Ge; Wang, Li-ye

    2018-01-01

    In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine. PMID:29565999

  9. Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

    Science.gov (United States)

    Amer, Ranya A.; El Gendi, Hamada M.; Goda, Doaa A.; Corsini, Anna; Cavalca, Lucia; Fusi, Marco; Daffonchio, Daniele; Abdel-Fattah, Yasser R.

    2015-01-01

    Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed. PMID:26273661

  10. Diversity management

    OpenAIRE

    Knákalová, Lucie

    2009-01-01

    The key topic of the work is diversity management, i.e. management of em-ployees" diversity within organization. Opening part of the work identifies the position of diversity within society and related phenomena such as stereotypes, biases and various forms of discrimination. Then the work discusses the role of diversity management in organizations, its principles and basic areas of focus. Attention is paid to certain social groups that the diversity management concept should especially deal ...

  11. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

    Science.gov (United States)

    Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  12. Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy

    Directory of Open Access Journals (Sweden)

    S Emil Ruff

    2016-03-01

    Full Text Available The anaerobic oxidation of methane (AOM is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME and sulfate-reducing bacteria (SRB, and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic-carbon depleted permeable sands off the Island of Elba (Italy. We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3 and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise

  13. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

    Science.gov (United States)

    Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  14. Beyond the Classroom: The Potential of After School Programs to Engage Diverse High School Students in the Geosciences

    Science.gov (United States)

    Pickering, J.; Briggs, D. E.; Alonzo, J.

    2011-12-01

    Over the last decade many influential reports on how to improve the state of STEM education in the United States have concluded that students need exciting science experiences that speak to their interests - beyond the classroom. High school students spend only about one third of their time in school. After school programs are an important opportunity to engage them in activities that enhance their understanding of complex scientific issues and allow them to explore their interests in more depth. For the last four years the Peabody Museum, in partnership with Yale faculty, other local universities and the New Haven Public Schools, has engaged a diverse group of New Haven teens in an after school program that provides them with multiple opportunities to explore the geosciences and related careers, together with access to the skills and support needed for college matriculation. The program exposes 100 students each year to the world of geoscience research; internships; the development of a Museum exhibition; field trips; opportunities for paid work interpreting geoscience exhibits; mentoring by successful college students; and an introduction to local higher education institutions. It is designed to address issues that particularly influence the college and career choices of students from communities traditionally underrepresented in STEM. Independent in-depth evaluation, using quantitative and qualitative methods, has shown that the program has enormous positive impact on the students. Results show that the program significantly improves students' knowledge and understanding of the geosciences and geoscience careers, together with college and college preparation. In the last two years 70% - 80% of respondents agreed that the program has changed the way they feel about science, and in 2010/11 over half of the students planned to pursue a science degree - a considerable increase from intentions voiced at the beginning of the program. The findings show that the

  15. The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

    Science.gov (United States)

    Lee, Seung-Hoon; Kang, Hojeong

    2016-02-01

    The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to

  16. Perspectives regarding disproportionate representation of culturally and linguistically diverse students in high-incidence special education programs in the United States

    Directory of Open Access Journals (Sweden)

    Jolanta Jonak

    2014-02-01

    Full Text Available Background The number of culturally and linguistically diverse students in the U.S. is growing, and research shows they are often underassessed, misdiagnosed, and placed into special education unnecessarily. This problem mainly concerns high-incidence, or judgmental, disabilities such as learning disability, emotional disturbance, or mental retardation. Participants and procedure In this study, the author examines how some educators perceive and address culturally and linguistically diverse students in the U.S. A survey developed by the author was used to examine how educators perceive culturally and linguistically diverse student populations and how one Midwestern school system in the United States dealt with culturally and linguistically diverse students’ needs versus expected ideal practices. Results Results indicated that most participants recognized that the issue of disproportionate representation is nationwide, but did not believe that their district shared that problem. Conclusions Participants indicated that best practices were not being followed maximally to reduce and avoid the problem of disproportionate representation of culturally and linguistically diverse students in special education programs. Difficulties in meeting students’ needs may be related to cultural differences that school personnel are unable to assess or address. Recommendations include suggestions for further studies and for applying the survey in other school systems to increase the understanding and improve their practice in working with culturally and linguistically diverse students.

  17. The high genetic variation of viruses of the genus Nairovirus reflects the diversity of their predominant tick hosts

    International Nuclear Information System (INIS)

    Honig, Jessica E.; Osborne, Jane C.; Nichol, Stuart T.

    2004-01-01

    The genus Nairovirus (family Bunyaviridae) contains seven serogroups consisting of 34 predominantly tick-borne viruses, including several associated with severe human and livestock diseases [e.g., Crimean Congo hemorrhagic fever (CCHF) and Nairobi sheep disease (NSD), respectively]. Before this report, no comparative genetic studies or molecular detection assays had been developed for this virus genus. To characterize at least one representative from each of the seven serogroups, reverse transcriptase-polymerase chain reaction (RT-PCR) primers targeting the L polymerase-encoding region of the RNA genome of these viruses were successfully designed based on conserved amino acid motifs present in the predicted catalytic core region. Sequence analysis showed the nairoviruses to be a highly diverse group, exhibiting up to 39.4% and 46.0% nucleotide and amino acid identity differences, respectively. Virus genetic relationships correlated well with serologic groupings and with tick host associations. Hosts of these viruses include both the hard (family Ixodidae) and soft (family Argasidae) ticks. Virus phylogenetic analysis reveals two major monophyletic groups: hard tick and soft tick-vectored viruses. In addition, viruses vectored by Ornithodoros, Carios, and Argas genera ticks also form three separate monophyletic lineages. The striking similarities between tick and nairovirus phylogenies are consistent with possible coevolution of the viruses and their tick hosts. Fossil and phylogenetic data placing the hard tick-soft tick divergence between 120 and 92 million years ago suggest an ancient origin for viruses of the genus Nairovirus

  18. High Genetic Diversity and Distinctiveness of Rear-Edge Climate Relicts Maintained by Ancient Tetraploidisation for Alnus glutinosa

    Science.gov (United States)

    Lepais, Olivier; Muller, Serge D.; Ben Saad-Limam, Samia; Benslama, Mohamed; Rhazi, Laila; Belouahem-Abed, Djamila; Daoud-Bouattour, Amina; Gammar, Amor Mokhtar; Ghrabi-Gammar, Zeineb; Bacles, Cécile Fanny Emilie

    2013-01-01

    Populations located at the rear-edge of a species’ distribution may have disproportionate ecological and evolutionary importance for biodiversity conservation in a changing global environment. Yet genetic studies of such populations remain rare. This study investigates the evolutionary history of North-African low latitude marginal populations of Alnus glutinosa Gaertn., a European tree species that plays a significant ecological role as a keystone of riparian ecosystems. We genotyped 551 adults from 19 populations located across North Africa at 12 microsatellite loci and applied a coalescent-based simulation approach to reconstruct the demographic and evolutionary history of these populations. Surprisingly, Moroccan trees were tetraploids demonstrating a strong distinctiveness of these populations within a species otherwise known as diploid. Best-fitting models of demographic reconstruction revealed the relict nature of Moroccan populations that were found to have withstood past climate change events and to be much older than Algerian and Tunisian populations. This study highlights the complex demographic history that can be encountered in rear-edge distribution margins that here consist of both old stable climate relict and more recent populations, distinctively diverse genetically both quantitatively and qualitatively. We emphasize the high evolutionary and conservation value of marginal rear-edge populations of a keystone riparian species in the context of on-going climate change in the Mediterranean region. PMID:24098677

  19. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  20. Classification of High-Mountain Vegetation Communities within a Diverse Giant Mountains Ecosystem Using Airborne APEX Hyperspectral Imagery

    Directory of Open Access Journals (Sweden)

    Adriana Marcinkowska-Ochtyra

    2018-04-01

    Full Text Available Mapping plant communities is a difficult and time consuming endeavor. Methods relying on field surveys deliver high quality data but are usually limited to relatively small areas. In this paper we apply airborne hyperspectral data to vegetation mapping in remote and hard to reach areas. We classified 22 vegetation communities in the Giant Mountains on 3.12-m Airborne Prism Experiment (APEX hyperspectral images, registered in 288 spectral bands (10 Septe