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

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.

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.

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.

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)

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

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.

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...

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

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

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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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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...

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.

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.

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.

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.

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.)

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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

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.

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.

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...

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...

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

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 ...

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.)

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

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.

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

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.

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.

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%.

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...

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.

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

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.

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

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

Directory of Open Access Journals (Sweden)

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.

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.

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

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

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.

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...

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

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...

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.

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

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.

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...

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.

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.

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.

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.

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.

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.

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

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...

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

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

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.

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.

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...

[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

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...

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.

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

[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.

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

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...

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

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.

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. ...

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.

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.

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

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

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

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.

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.

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.

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.

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.

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...

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.

Structure of nitrogen-converting communities induced by hydraulic retention time and COD/N ratio in constantly aerated granular sludge reactors treating digester supernatant.

Science.gov (United States)

Cydzik-Kwiatkowska, Agnieszka; Rusanowska, Paulina; Zielińska, Magdalena; Bernat, Katarzyna; Wojnowska-Baryła, Irena

2014-02-01

This study investigated how hydraulic retention time (HRT) and COD/N ratio affect nitrogen-converting consortia in constantly aerated granules treating high-ammonium digester supernatant. Three HRTs (10, 13, 19 h) were tested at COD/N ratios of 4.5 and 2.3. Denaturing gradient gel electrophoresis and relative real-time PCR were used to characterize the microbial communities. When changes in HRT and COD/N increased nitrogen loading, the ratio of the relative abundance of aerobic to anaerobic ammonium-oxidizers decreased. The COD/N ratio determined the species composition of the denitrifiers; however, Thiobacillus denitrificans, Pseudomonas denitrificans and Azoarcus sp. showed a high tolerance to the environmental conditions and occurred in the granules from all reactors. Denitrifier genera that support granule formation were identified, such as Pseudomonas, Shinella, and Flavobacterium. In aerated granules, nirK-possessing bacteria were more diverse than nirS-possessing bacteria. At a low COD/N ratio, N2O-reducer diversity increased because of the presence of bacteria known as aerobic denitrifiers. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

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.

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.

Structure of hydrocarbonoclastic nitrate-reducing bacterial communities in bioturbated coastal marine sediments.

Science.gov (United States)

Stauffert, Magalie; Cravo-Laureau, Cristiana; Duran, Robert

2014-09-01

The organisation of denitrifying microorganisms in oil-polluted bioturbated sediments was investigated in mesocosms under conditions as closer as possible to that observed in the environment. Molecular and culture-dependent approaches revealed that denitrifying Gammaproteobacteria were abundant in oil-polluted and bioturbated sediments suggesting that they may play a key role in hydrocarbon degradation in the environment. T-RFLP and gene libraries analyses targeting nirS gene showed that denitrifying microbial communities structure was slightly affected by either the addition of Hediste diversicolor or crude oil revealing the metabolic versatility of denitrifying microorganisms. From oil-polluted sediments, distinct denitrifying hydrocarbonoclastic bacterial consortia were obtained by enrichment cultures on high molecular weight polyaromatic hydrocarbons (PAHs) (dibenzothiophene, fluoranthene, pyrene and chrysene) under nitrate-reducing conditions. Interestingly, molecular characterisation of the consortia showed that the denitrifying communities obtained from oiled microcosms with addition of H. diversicolor were different to that observed without H. diversicolor addition, especially with fluoranthene and chrysene revealing the bacterial diversity involved in the degradation of these PAHs. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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.

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.

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

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.

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 .

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.

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

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

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...

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.

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

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…

Nitrite survival and nitrous oxide production of denitrifying phosphorus removal sludges in long-term nitrite/nitrate-fed sequencing batch reactors.

Science.gov (United States)

Wang, Yayi; Zhou, Shuai; Ye, Liu; Wang, Hong; Stephenson, Tom; Jiang, Xuxin

2014-12-15

Nitrite-based phosphorus (P) removal could be useful for innovative biological P removal systems where energy and carbon savings are a priority. However, using nitrite for denitrification may cause nitrous oxide (N2O) accumulation and emissions. A denitrifying nitrite-fed P removal system [Formula: see text] was successfully set up in a sequencing batch reactor (SBR) and was run for 210 days. The maximum pulse addition of nitrite to [Formula: see text] was 11 mg NO2(-)-N/L in the bulk, and a total of 34 mg NO2(-)-N/L of nitrite was added over three additions. Fluorescent in situ hybridization results indicated that the P-accumulating organisms (PAOs) abundance was 75 ± 1.1% in [Formula: see text] , approximately 13.6% higher than that in a parallel P removal SBR using nitrate [Formula: see text] . Type II Accumulibacter (PAOII) (unable to use nitrate as an electron acceptor) was the main PAOs species in [Formula: see text] , contributing 72% to total PAOs. Compared with [Formula: see text] , [Formula: see text] biomass had enhanced nitrite/free nitrous acid (FNA) endurance, as demonstrated by its higher nitrite denitrification and P uptake rates. N2O accumulated temporarily in [Formula: see text] after each pulse of nitrite. Peak N2O concentrations in the bulk for [Formula: see text] were generally 6-11 times higher than that in [Formula: see text] ; these accumulations were rapidly denitrified to nitrogen gases. N2O concentration increased rapidly in nitrate-cultivated biomass when 5 or 10 mg NO2(-)-N/L per pulse was added. Whereas, N2O accumulation did not occur in nitrite-cultivated biomass until up to 30 mg NO2(-)-N/L per pulse was added. Long-term acclimation to nitrite and pulse addition of nitrite in [Formula: see text] reduced the risk of nitrite accumulation, and mitigated N2O accumulation and emissions from denitrifying P removal by nitrite. Copyright © 2014 Elsevier Ltd. All rights reserved.

[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.

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.

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

Directory of Open Access Journals (Sweden)

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

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…

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

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.

iDynoMiCS: next‐generation individual‐based modelling of biofilms

DEFF Research Database (Denmark)

Lardon, Laurent; Merkey, Brian; Martins, Sónia

2011-01-01

how environmentally fluctuating oxygen availability affects the diversity and composition of a community of denitrifying bacteria that induce the denitrification pathway under anoxic or low oxygen conditions. We tested the hypothesis that the existence of these diverse strategies of denitrification...... and higher at intermediate frequency of change. The highly modular nature of the new computational model made this case study straightforward to implement, and reflects the sort of novel studies that can easily be executed with the new model....

Insight into the effects of biochar on manure composting: evidence supporting the relationship between N2O emission and denitrifying community.

Science.gov (United States)

Wang, Cheng; Lu, Haohao; Dong, Da; Deng, Hui; Strong, P J; Wang, Hailong; Wu, Weixiang

2013-07-02

Although nitrous oxide (N2O) emissions from composting contribute to the accelerated greenhouse effect, it is difficult to implement practical methods to mitigate these emissions. In this study, the effects of biochar amendment during pig manure composting were investigated to evaluate the inter-relationships between N2O emission and the abundance of denitrifying bacteria. Analytical results from two pilot composting treatments with (PWSB, pig manure + wood chips + sawdust + biochar) or without (PWS, pig manure + wood chips + sawdust) biochar (3% w/w) demonstrated that biochar amendment not only lowered NO2(-)-N concentrations but also lowered the total N2O emissions from pig manure composting, especially during the later stages. Quantification of functional genes involved in denitrification and Spearman rank correlations matrix revealed that the N2O emission rates correlated with the abundance of nosZ, nirK, and nirS genes. Biochar-amended pig manure had a higher pH and a lower moisture content. Biochar amendment altered the abundance of denitrifying bacteria significantly; less N2O-producing and more N2O-consuming bacteria were present in the PWSB, and this significantly lowered N2O emissions in the maturation phase. Together, the results demonstrate that biochar amendment could be a novel greenhouse gas mitigation strategy during pig manure composting.

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.

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 ...

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.

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...

Insights into the effect of soil pH on N.sub.2./sub.O and N.sub.2./sub. emissions and denitrifier community size and activity

Czech Academy of Sciences Publication Activity Database

Čuhel, Jiří; Šimek, Miloslav; Laughlin, R.J.; Bru, D.; Chéneby, D.; Watson, C.J.; Philippot, L.

2010-01-01

Roč. 76, č. 6 (2010), s. 1870-1878 ISSN 0099-2240 R&D Projects: GA MŠk MEB020726; GA MŠk LC06066; GA AV ČR IAA600660605 Institutional research plan: CEZ:AV0Z60660521 Keywords : soil pH * N 2 O and N 2 emissions * denitrifier community Subject RIV: EH - Ecology, Behaviour Impact factor: 3.778, year: 2010

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

Summary report on the aerobic degradation of diesel fuel and the degradation of toluene under aerobic, denitrifying and sulfate reducing conditions

International Nuclear Information System (INIS)

Coyne, P.; Smith, G.

1995-01-01

This report contains a number of studies that were performed to better understand the technology of the biodegradation of petroleum hydrocarbons. Topics of investigation include the following: diesel fuel degradation by Rhodococcus erythropolis; BTEX degradation by soil isolates; aerobic degradation of diesel fuel-respirometry; aerobic degradation of diesel fuel-shake culture; aerobic toluene degradation by A3; effect of HEPES, B1, and myo-inositol addition on the growth of A3; aerobic and anaerobic toluene degradation by contaminated soils; denitrifying bacteria MPNs; sulfate-reducing bacteria MPNs; and aerobic, DNB and SRB enrichments

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.

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....

Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms.

Science.gov (United States)

Bagella, Simonetta; Filigheddu, Rossella; Caria, Maria Carmela; Girlanda, Mariangela; Roggero, Pier Paolo

2014-12-01

The aims of this paper were (i) to define how contrasting land uses affected plant biodiversity in Mediterranean agro-silvo-pastoral-systems across a gradient of disturbance regimes: cork oak forests, secondary grasslands, hay crops, grass covered vineyards, tilled vineyards; (ii) to determine whether these patterns mirrored those of below-ground microorganisms and whether the components of γ-diversity followed a similar model. The disturbance regimes affected plant assemblage composition. Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops. Plant assemblage composition patterns mirrored those of Basidiomycota and Ascomycota. Richness in Basidiomycota, denitrifying bacteria and microbial biomass showed the same trend as that observed for vascular plant richness. The Shannon index pattern of below-ground microorganisms was different from that of plants. The plant γ-diversity component model weakly mirrored those of Ascomycota. Patchy diversity patterns suggest that the maintenance of contrasting land uses associated with different productions typical of agro-silvo-pastoral-systems can guarantee the conservation of biodiversity. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

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.

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

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

[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.

High genetic diversity of Jatropha curcas assessed by ISSR.

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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.

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 ...

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

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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).

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

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

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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.

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

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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.

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

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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.

Performance of Denitrifying Bioreactors at Reducing  Agricultural Nitrogen Pollution in a Humid  Subtropical Coastal Plain Climate

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Timothy Rosen

2017-02-01

Full Text Available Denitrifying bioreactors are an agricultural best management practice developed in the  midwestern United States to treat agricultural drainage water enriched with nitrate‐nitrogen (NO3N. The practice is spreading rapidly to agricultural regions with poor water quality due to nutrient  enrichment. This makes it imperative to track bioreactor NO3‐N reduction efficiency as this practice  gets deployed to new regions. This study evaluated the application and performance of denitrifying  bioreactors in the humid subtropical coastal plain environment of the Chesapeake Bay catchment to  provide data about regionally specific NO3‐N reduction efficiencies. NO3‐N samples were taken  before  and  after  treatment  at  three  denitrifying  bioreactors,  in  addition  to  other  nutrients  (orthophosphate‐phosphorus,  PO4‐P;  ammonium‐nitrogen,  NH4‐N;  total  nitrogen,  TN;  total  phosphorus,  TP  and  water  quality  parameters  (dissolved  oxygen,  DO;  oxidation  reduction  potential,  ORP;  pH;  specific  conductance,  SPC.  Total  removal  ranged  drastically  between  bioreactors from 10 to 133 kg N, with removal efficiencies of 9.0% to 62% and N removal rates of  0.21 to 5.36 g N removed per m3 of bioreactor per day. As the first bioreactor study in the humid  subtropical coastal plain, this data provides positive proof of concept that denitrifying bioreactor is  another tool for reducing N loads in agricultural tile drainage in this region.

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 ...

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

Simultaneous removal of organic matter and salt ions from coal gasification wastewater RO concentrate and microorganisms succession in a MBR.

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Jia, Shengyong; Han, Yuxing; Zhuang, Haifeng; Han, Hongjun; Li, Kun

2017-10-01

A lab-scale membrane bioreactor (MBR) with intermittent aeration was operated to treat the reverse osmosis concentrate derived from coal gasification wastewater. Results showed intermittent aeration represented slight effect on organic matter reduction but significant effect on nitrite and nitrate reduction, with 6h aeration and 6h non-aeration, removal efficiencies of organic matter, chloride, sulfate, nitrite and nitrate reached 48.35%, 40.91%, 34.28%, -36.05% and 64.34%, respectively. High-throughput sequencing showed a microorganisms succession from inoculated activated sludge (S1) to activated sludge in MBR (S2) with high salinity. Richness and diversity of microorganisms in S2 was lower than S1 and the community structure of S1 exhibited more even than S2. The most relative abundance of genus in S1 and S2 were unclassified_Desulfarculaceae (9.39%) and Roseibaca (62.1%), respectively. High salinity and intermittent aeration represented different influence on the denitrifying genus, and non-aeration phase provided feasible dissolved oxygen condition for denitrifying genera realizing denitrification. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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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

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

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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.

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

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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

De novo assembly of highly diverse viral populations

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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.

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,

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.

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.

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

Performance of a sequencing-batch membrane bioreactor (SMBR) with an automatic control strategy treating high-strength swine wastewater.

Science.gov (United States)

Sui, Qianwen; Jiang, Chao; Yu, Dawei; Chen, Meixue; Zhang, Junya; Wang, Yawei; Wei, Yuansong

2018-01-15

Due to high-strength of organic matters, nutrients and pathogen, swine wastewater is a major source of pollution to rural environment and surface water. A sequencing-batch membrane bioreactor (SMBR) system with an automatic control strategy was developed for high-strength swine wastewater treatment. Short-cut nitrification and denitrification (SND) was achieved at nitrite accumulation rate of 83.6%, with removal rates of COD, NH 4 + -N and TN at 95%, 99% and 93%, respectively, at reduced HRT of 6.0 d and TN loading rate of 0.02kgN/(kgVSS d). With effective membrane separation, the reduction of total bacteria (TB) and putative pathogen were 2.77 logs and 1%, respectively. The shift of microbial community was well responded to controlling parameters. During the SND process, ammonia oxidizing bacteria (AOB) (Nitrosomonas, Nitrosospira) and nitrite oxidizing bacteria (NOB) (Nitrospira) were enriched by 52 times and reduced by 2 times, respectively. The denitrifiers (Thauera) were well enriched and the diversity was enhanced. Copyright © 2017. Published by Elsevier B.V.

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.

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.

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.

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.

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.

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.

The effect of poly-β-hydroxyalkanoates degradation rate on nitrous oxide production in a denitrifying phosphorus removal system.

Science.gov (United States)

Wei, Yan; Wang, Shuying; Ma, Bin; Li, Xiyao; Yuan, Zhiguo; He, Yuelan; Peng, Yongzhen

2014-10-01

Poly-β-hydroxyalkanoates (PHAs) and free nitrous acid (FNA) have been revealed as significant factors causing nitrous oxide (N2O) production in denitrifying phosphorus removal systems. In this study, the effect of PHA degradation rate on N2O production was studied at low FNA levels. N2O production always maintained at approximately 40% of the amount of nitrite reduced independent of the PHA degradation rate. The electrons distributed to nitrite reduction were 1.6 times that to N2O reduction. This indicated that electron competition between these two steps was not affected by the PHA degradation rate. Continuous feed of nitrate was proposed, and demonstrated to reduce N2O accumulation by 75%. While being kept low, a possible compounding effect of a low-level FNA could not be ruled out. The sludge used likely contained both polyphosphate- and glycogen-accumulating organisms, and the results could not be simply attributed to either group of organisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spatial Variability of Cyanobacteria and Heterotrophic Bacteria in Lake Taihu (China).

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Qian, Haifeng; Lu, Tao; Song, Hao; Lavoie, Michel; Xu, Jiahui; Fan, Xiaoji; Pan, Xiangliang

2017-09-01

Cyanobacterial blooms frequently occur in Lake Taihu (China), but the intertwined relationships between biotic and abiotic factors modulating the frequency and duration of the blooms remain enigmatic. To better understand the relationships between the key abiotic and biotic factors and cyanobacterial blooms, we measured the abundance and diversity of prokaryotic organisms by high-throughput sequencing, the abundance of key genes involved in microcystin production and nitrogen fixation or loss as well as several physicochemical parameters at several stations in Lake Taihu during a cyanobacterial bloom of Microcystis sp.. Measurements of the copy number of denitrification-related genes and 16S rRNA analyses show that denitrification potential and denitrifying bacteria abundance increased in concert with non-diazotrophic cyanobacteria (Microcystis sp.), suggesting limited competition between cyanobacteria and heterotrophic denitrifiers for nutrients, although potential bacteria-mediated N loss may hamper Microcystis growth. The present study provides insight into the importance of different abiotic and biotic factors in controlling cyanobacteria and heterotrophic bacteria spatial variability in Lake Taihu.

Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from salt marsh sediments

Science.gov (United States)

Kearns, Patrick J.; Angell, John H.; Feinman, Sarah G.; Bowen, Jennifer L.

2015-03-01

Enrichment of natural waters, soils, and sediments by inorganic nutrients, including nitrogen, is occurring at an increasing rate and has fundamentally altered global biogeochemical cycles. Salt marshes are critical for the removal of land-derived nitrogen before it enters coastal waters. This is accomplished via multiple microbially mediated pathways, including denitrification. Many of these pathways, however, are also a source of the greenhouse gas nitrous oxide (N2O). We used clone libraries and quantative PCR (qPCR) to examine the effect of fertilization on the diversity and abundance of two functional genes associated with denitrification and N2O production (norB and nosZ) in experimental plots at the Great Sippewissett Salt Marsh (Falmouth, MA, USA) that have been enriched with nutrients for over 40 years. Our data showed distinct nosZ and norB community structures at different nitrogen loads, especially at the highest level of fertilization. Furthermore, calculations of the Shannon Diversity Index and Chao1 Richness Estimator indicated that nosZ gene diversity and richness increased with increased nitrogen supply, however no such relationship existed with regard to richness and diversity of the norB gene. Results from qPCR demonstrated that nosZ gene abundance was an order of magnitude lower in the extra-highly fertilized plots compared to the other plots, but the abundance of norB was not affected by fertilization. The majority of sequences obtained from the marsh plots had no close cultured relatives and they were divergent from previously sequenced norB and nosZ fragments. Despite their divergence from any cultured representatives, most of the norB and nosZ sequences appeared to be from members of the Alpha- and Betaproteobacteria, suggesting that these classes are particularly important in salt marsh nitrogen cycling. Our results suggest that both norB and nosZ containing microbes are affected by fertilization and that the Great Sippewissett Marsh may

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.

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.

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

[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.

Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria.

Science.gov (United States)

He, Zhanfei; Geng, Sha; Cai, Chaoyang; Liu, Shuai; Liu, Yan; Pan, Yawei; Lou, Liping; Zheng, Ping; Xu, Xinhua; Hu, Baolan

2015-08-15

Anaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA and pmoA gene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescence in situ hybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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.

Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.

Science.gov (United States)

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

2016-01-01

The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage.

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.

The interplay of diversity training and diversity beliefs on team creativity in nationality diverse teams.

Science.gov (United States)

Homan, Astrid C; Buengeler, Claudia; Eckhoff, Robert A; van Ginkel, Wendy P; Voelpel, Sven C

2015-09-01

Attaining value from nationality diversity requires active diversity management, which organizations often employ in the form of diversity training programs. Interestingly, however, the previously reported effects of diversity training are often weak and, sometimes, even negative. This situation calls for research on the conditions under which diversity training helps or harms teams. We propose that diversity training can increase team creativity, but only for teams with less positive pretraining diversity beliefs (i.e., teams with a greater need for such training) and that are sufficiently diverse in nationality. Comparing the creativity of teams that attended nationality diversity training versus control training, we found that for teams with less positive diversity beliefs, diversity training increased creative performance when the team's nationality diversity was high, but undermined creativity when the team's nationality diversity was low. Diversity training had less impact on teams with more positive diversity beliefs, and training effects were not contingent upon these teams' diversity. Speaking to the underlying process, we showed that these interactive effects were driven by the experienced team efficacy of the team members. We discuss theoretical and practical implications for nationality diversity management. (c) 2015 APA, all rights reserved).

Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

Institute of Scientific and Technical Information of China (English)

GAO Zheng; WANG Xin; Angelos K. HANNIDES; Francis J. SANSONE; WANG Guangyi

2011-01-01

Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry.Although biogeochemical redox stratification has been well documented in marine sediments,its impact on microbial communities remains largely unknown.In this study,we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm.A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm.They were members of nine phyla and three candidate divisions,including Proteobacteria (Alpha-,Beta-,Gamma-,Delta-,and Epsilonproteobacteria),Actinobacteria,Acidobacteria,Bacteroidetes,Chloroflexi,Cyanobacteria,Firmicutes,Verrucomicrobia,Spirochaetes,and the candidate divisions WS3,SO31 and AO19.The vast majority of these phylotypes are related to clone sequences from other marine sediments,but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments.Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences.Results from the 16S rRNA,gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments,with the highest diversity found in the anoxic layer (15-25 mm) and the least diversity in the suboxic layer (3-5 mm).Analysis of the nosZ,and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers,with their highest diversity being in the anoxic and oxic sediment layers,respectively.These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.

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...

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

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.

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…

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)

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.

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.

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.

Functional-Structural Analysis of Nitrogen-Cycle Bacteria in a Hypersaline Mat from the Omani Desert

DEFF Research Database (Denmark)

Abed, Raeid M M; de Beer, Dirk; Stief, Peter

2015-01-01

to sequences from the Rhizobiales group. Sequences of the nosZ gene were the most diverse and clustered with sequences from various genera. Our results demonstrate that the hypersaline mat from Oman harbors nitrifying and denitrifying bacteria with the potential to perform respective processes at detectable...

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 ...

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...

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.

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

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.

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.

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.

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

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

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

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

Science.gov (United States)

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.

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

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.

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…

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

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.

[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.

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.

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.

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…

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

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...

Pyruvic oxime nitrification and copper and nickel resistance by a Cupriavidus pauculus, an active heterotrophic nitrifier-denitrifier.

Science.gov (United States)

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 genus (Cupriavidus) known for its resistance to metals and its metabolism of xenobiotics. The microbe (a Cupriavidus pauculus designated as C. pauculus strain UM1) was examined for its ability to perform heterotrophic nitrification in the presence of Cu(2+) and Ni(2+) and to metabolize the xenobiotic phenol. The bacterium heterotrophically nitrified well when either 1 mM Cu(2+) or 0.5 mM Ni(2+) was present in either enriched or minimal medium. The organism also used phenol as a sole carbon source in either the presence or absence of 1 mM Cu(2+) or 0.5 mM Ni(2+). The ability of this isolate to perform a number of different metabolisms, its noteworthy resistance to copper and nickel, and its potential use as a bioremediation agent are discussed.

Diversity and Complexity in the Classroom: Valuing Racial and Cultural Diversity

Science.gov (United States)

du Plessis, Pierre; Bisschoff, Tom

2007-01-01

From a diversity perspective, all students should receive an education that continuously affirms human diversity--one that embraces the history and culture of all racial groups and that teaches people of colour to take change of their own destinies. With regards to teaching, a diversity perspective assumes that teachers will hold high expectations…

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…

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.

Regional Diversity and Diversification in Mammals.

Science.gov (United States)

Machac, Antonin; Graham, Catherine H

2017-01-01

The effects of regional diversity on diversification remain controversial. The classic hypothesis that diversification decelerates as regional diversity increases has been recently revived. Yet, there is little geographic evidence for slower diversification across regions of high diversity, and diversity is often thought to promote diversification through its effects on ecological divergence and speciation. Here, we use the newest phylogeny for mammals (4,990 species) and two different methods to test the effects of regional diversity on diversification. We find that regions of high diversity are dominated by expanding clades that are far from their estimated carrying capacities. Regions of low diversity host clades that are small and mostly saturated. These results were supported across mammals and their six largest orders. They were corroborated by the two methods when controlling for clade relatedness, clade nestedness, and clade size. Together, these results reject the hypothesis that high geographic concentration of mammals effectively suppresses their further diversification. Instead, highly diverse regions (especially the tropics) seem to act as the engine of mammalian richness.

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.

[Distribution Characteristics of Nitrifiers and Denitrifiers in the River Sediments of Tongling City].

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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.

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

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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.

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.

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

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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

High diversity at PRDM9 in chimpanzees and bonobos.

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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.

Microbial ecology of denitrification in biological wastewater treatment.

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Lu, Huijie; Chandran, Kartik; Stensel, David

2014-11-01

Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

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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.

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

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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.

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.

Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.

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Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2013-07-01

The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Science.gov (United States)

2012-01-01

Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems.

Science.gov (United States)

Rachid, Caio T C C; Piccolo, Marisa C; Leite, Deborah Catharine A; Balieiro, Fabiano C; Coutinho, Heitor Luiz C; van Elsas, Jan Dirk; Peixoto, Raquel S; Rosado, Alexandre S

2012-08-08

Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Directory of Open Access Journals (Sweden)

Rachid Caio TCC

2012-08-01

Full Text Available Abstract Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane, next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA and denitrifying (nirK genes, greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil

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

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.

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

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Miguel Ramirez

2014-01-01

Full Text Available 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 genus (Cupriavidus known for its resistance to metals and its metabolism of xenobiotics. The microbe (a Cupriavidus pauculus designated as C. pauculus strain UM1 was examined for its ability to perform heterotrophic nitrification in the presence of Cu2+ and Ni2+ and to metabolize the xenobiotic phenol. The bacterium heterotrophically nitrified well when either 1 mM Cu2+ or 0.5 mM Ni2+ was present in either enriched or minimal medium. The organism also used phenol as a sole carbon source in either the presence or absence of 1 mM Cu2+ or 0.5 mM Ni2+. The ability of this isolate to perform a number of different metabolisms, its noteworthy resistance to copper and nickel, and its potential use as a bioremediation agent are discussed.

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…

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.

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.

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

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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.

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)

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

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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

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.

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

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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

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

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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.

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.

Multicontext Diversity: The critical dimension of diversity that can attract students and help them thrive

Science.gov (United States)

Weissmann, G. S.; Ibarra, R.; Howland-Davis, M.

2017-12-01

Diversity programs on college campuses have expanded over the past several decades, bringing a broad range of students to academia; however, these programs have not resulted in diversification of faculty or PhD students. Current diversity programs generally focus on two dimensions of diversity: (1) structural diversity, which aims to bring in students from underrepresented groups to college campuses through scholarships, admissions policies, and targeted marketing; and (2) multicultural diversity, which uses programs designed to give students from underrepresented groups homes on campus and programs designed to study cultural aspects of different groups. Though these programs are important, something else must be controlling the lack of minority participation in STEM at advanced levels. We posit that a third dimension of diversity, context diversity, is lacking in university education, especially in STEM fields, and without accessing this form of diversity, programs will never benefit from the broader diversity of society. Context diversity results through application of Multicontext theory, which both explains and predicts the inclusion of exclusion of people within an institutional culture. It describes how different cultures approach understanding the world around them. This "cultural ways of knowing and doing" has been described using a binary system, consisting of "Low Context" and "High Context" cultures. Ibarra (2001) described how a spectrum exists between these end members, and thus individuals brought up in different cultures will understand the world from somewhere along this context diversity spectrum. Academic culture tends to fall on the low context side of the spectrum. Thus, students (and faculty) who come from cultures that tend toward the high context side of the spectrum often feel excluded from the academic setting, especially in STEM fields which tend to be strongly low context in nature. A high percentage of students from underrepresented

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.

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.

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

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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.

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.

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.

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

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

Science.gov (United States)

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

KAUST Repository

Jessen, Christian

2013-04-22

Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

Science.gov (United States)

Jessen, Christian; Villa Lizcano, Javier Felipe; Bayer, Till; Roder, Cornelia; Aranda, Manuel; Wild, Christian; Voolstra, Christian R

2013-01-01

Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

Directory of Open Access Journals (Sweden)

Christian Jessen

Full Text Available Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion and/or herbivore exclusion (via caging in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

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.

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…

Diversity-Guided Evolutionary Algorithms

DEFF Research Database (Denmark)

Ursem, Rasmus Kjær

2002-01-01

Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

Diverse by Default

DEFF Research Database (Denmark)

Holck, Lotte

arguments that arise from migrants’ paradoxical situation. To improve their situation, the article discusses whether alternative conceptualization of talents, ‘high potentials’, and making the ambitions of diverse employees more prominent in strategic human resource management can be a relavant strategy......: Employing highlyskilled, career-minded migrants in low-skilled postions, migrants are simultaneously casted as a disposable, replicable and temporary resource, the ‘ideal worker’, AND as a ‘high potential’ for first line management. This extended business case of diversity draws on multifaceted business......This paper contributes to theoretical debates around migrant workers at the workplace, labour market inequality and the business case of diversity. Building on stories of overqualified migrant stuck in low-rank jobs due to their migration, this paper explores how migrant workers are simultaneous...

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)

Microbial characteristics of purple paddy soil in response to Pb pollution.

Science.gov (United States)

Jiang, Qiu-Ju; Zhang, Yue-Qiang; Zhang, La-Mei; Zhou, Xin-Bin; Shi, Xiao-Jun

2014-05-01

The study focused on the change of microbial characteristics affected by Plumbum pollution with purple paddy soil in an incubation experiment. The results showed that low concentration of Plumbum had little effect on most of microbial amounts, biological activity and enzymatic activity. However, denitrifying activity was inhibited severely, and inhibition rate was up to 98%. Medium and high concentration of Plumbum significantly reduced the amounts and activity of all microorganisms and enzymatic activity, which increased with incubation time. Negative correlations were found between Plumbum concentrations and microbial amounts, biological activity and enzymatic activities except fungi and actinomyces. Thus they can be used to indicate the Plumbum pollution levels to some extent. LD(50) of denitrifying bacteria (DB) and ED50 of denitrifying activity were 852mg/kg and 33.5mg/kg. Across all test soil microbes, denitrifying bacteria was most sensitive to Plumbum pollution in purple paddy soil. Value of early warning showed that anaerobic cellulose-decomposing bacteria (ACDB) and actinomyces were also sensitive to Plumbum pollution. We concluded that denitrifying activity, actinomyces, ACDB or DB can be chosen as predictor of Plumbum contamination in purple paddy soil.

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.

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.

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.

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.

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

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

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.

Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate.

Science.gov (United States)

Gabarró, J; Hernández-Del Amo, E; Gich, F; Ruscalleda, M; Balaguer, M D; Colprim, J

2013-12-01

This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

Discovering Diversity in Marketing Practice

OpenAIRE

Murray, John; O'Driscoll, Aidan; Torres, Ann

2002-01-01

Marketing practice varies among firms. However, the prescriptive literature emphasises a universal view of practice, a “one-size-fits-all” view. This paper addresses the issue of explaining diversity in competitive space and over time. Diversity in competitive space reflects the existence of different routes to high performance. Diversity over time reflects some combination of change in the individual firm and change in a population of firms. In the former case, diversity is shaped by organis...

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.

High abundance and diversity of consumers associated with eutrophic areas in a semi-desert macrotidal coastal ecosystem in Patagonia, Argentina

Science.gov (United States)

Martinetto, Paulina; Daleo, Pedro; Escapa, Mauricio; Alberti, Juan; Isacch, Juan Pablo; Fanjul, Eugenia; Botto, Florencia; Piriz, Maria Luz; Ponce, Gabriela; Casas, Graciela; Iribarne, Oscar

2010-07-01

Here we evaluated the response to eutrophication in terms of abundance and diversity of flora and fauna in a semi-desert macrotidal coastal system (San Antonio bay, Patagonia, Argentina, 40° 48' S) where signs of eutrophication (high nutrient concentration, seaweed blooms, high growth rate of macroalgae) have been reported. We compared abundances and species composition of macroalgae, small infaunal and epifaunal invertebrates, and birds associated with tidal channels of the San Antonio Bay subject to contrasting anthropogenic influence. Macroalgae were more abundant and diverse in the channel closer to human activity where nutrient concentrations were also higher. In contrast to what others have observed in eutrophic sites, small invertebrates and birds were also more abundant and diverse in the channel with macroalgal blooms and high nutrient concentration. The large water flushing during the tidal cycle could prevent anoxic or hypoxic events, making the environment suitable for consumers. Thus, this could be a case in which eutrophication supports high densities of consumers by increasing food availability, rather than negatively affecting the survival of organisms.

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.

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.

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.

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.

Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus.

Science.gov (United States)

Tay, Y C; Chng, M W P; Sew, W W G; Rheindt, F E; Tun, K P P; Meier, R

2016-08-01

The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.

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.

Creative work environments in sport organizations: the influence of sexual orientation diversity and commitment to diversity.

Science.gov (United States)

Cunningham, George B

2011-01-01

Drawing from creative capital theory, the purpose of this study was to examine the degree to which sexual orientation diversity and commitment to diversity were predictive of workplaces that fostered creativity. Data were collected from 653 senior level athletic administrators and aggregated to the athletic department level of analysis (n = 199). Moderated regression indicated that sexual orientation diversity did not influence the presence of a creative work environment. There was however, a significant sexual orientation diversity × commitment to diversity interaction. When commitment to diversity was high, there was a positive association between sexual orientation diversity and a creative work environment; on the other hand, when commitment to diversity was low, the aforementioned relationship was negative. Results provide support for the notion that all diversity forms can be a source of enrichment and understanding, thereby benefiting the workplace.

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.

Identity, Diversity and Diversity Management

DEFF Research Database (Denmark)

Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

2016-01-01

– The work can encourage policy makers, diversity and HR managers to question their own practices and assumptions leading to more theoretical informed diversity management practices. Originality/value – The theoretical connections between identity and diversity literature have so far not been reviewed......The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...... and limitations – is crucial for successful diversity management research and practice. Research limitations/implications – The authors argue for a better understanding of differences, overlaps and limits of different identity perspectives, and for a stronger engagement with practice. Practical implications...

Biological anoxic treatment of O2-free VOC emissions from the petrochemical industry: A proof of concept study

International Nuclear Information System (INIS)

Muñoz, Raúl; Souza, Theo S.O.; Glittmann, Lina; Pérez, Rebeca; Quijano, Guillermo

2013-01-01

Highlights: • The treatment of O 2 -free VOC emissions can be done by means of denitrifying processes. •Toluene vapors were successfully removed under anoxic denitrifying conditions. • A high bacterial diversity was observed. • Actinobacteria and Proteobacteria were the predominant phyla. • The nature and number of metabolites accumulated varied with the toluene load -- Abstract: An innovative biofiltration technology based on anoxic biodegradation was proposed in this work for the treatment of inert VOC-laden emissions from the petrochemical industry. Anoxic biofiltration does not require conventional O 2 supply to mineralize VOCs, which increases process safety and allows for the reuse of the residual gas for inertization purposes in plant. The potential of this technology was evaluated in a biotrickling filter using toluene as a model VOC at loads of 3, 5, 12 and 34 g m −3 h −1 (corresponding to empty bed residence times of 16, 8, 4 and 1.3 min) with a maximum elimination capacity of ∼3 g m −3 h −1 . However, significant differences in the nature and number of metabolites accumulated at each toluene load tested were observed, o- and p-cresol being detected only at 34 g m −3 h −1 , while benzyl alcohol, benzaldehyde and phenol were detected at lower loads. A complete toluene removal was maintained after increasing the inlet toluene concentration from 0.5 to 1 g m −3 (which entailed a loading rate increase from 3 to 6 g m −3 h −1 ), indicating that the system was limited by mass transfer rather than by biological activity. A high bacterial diversity was observed, the predominant phyla being Actinobacteria and Proteobacteria

Biological anoxic treatment of O{sub 2}-free VOC emissions from the petrochemical industry: A proof of concept study

Energy Technology Data Exchange (ETDEWEB)

Muñoz, Raúl; Souza, Theo S.O. [Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr Mergelina s/n, 47011 Valladolid (Spain); Glittmann, Lina [Ostfalia University of Applied Sciences, Department of Supply Engineering, Wolfenbüttel (Germany); Pérez, Rebeca [Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr Mergelina s/n, 47011 Valladolid (Spain); Quijano, Guillermo [Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr Mergelina s/n, 47011 Valladolid (Spain)

2013-09-15

Highlights: • The treatment of O{sub 2}-free VOC emissions can be done by means of denitrifying processes. •Toluene vapors were successfully removed under anoxic denitrifying conditions. • A high bacterial diversity was observed. • Actinobacteria and Proteobacteria were the predominant phyla. • The nature and number of metabolites accumulated varied with the toluene load -- Abstract: An innovative biofiltration technology based on anoxic biodegradation was proposed in this work for the treatment of inert VOC-laden emissions from the petrochemical industry. Anoxic biofiltration does not require conventional O{sub 2} supply to mineralize VOCs, which increases process safety and allows for the reuse of the residual gas for inertization purposes in plant. The potential of this technology was evaluated in a biotrickling filter using toluene as a model VOC at loads of 3, 5, 12 and 34 g m{sup −3} h{sup −1} (corresponding to empty bed residence times of 16, 8, 4 and 1.3 min) with a maximum elimination capacity of ∼3 g m{sup −3} h{sup −1}. However, significant differences in the nature and number of metabolites accumulated at each toluene load tested were observed, o- and p-cresol being detected only at 34 g m{sup −3} h{sup −1}, while benzyl alcohol, benzaldehyde and phenol were detected at lower loads. A complete toluene removal was maintained after increasing the inlet toluene concentration from 0.5 to 1 g m{sup −3} (which entailed a loading rate increase from 3 to 6 g m{sup −3} h{sup −1}), indicating that the system was limited by mass transfer rather than by biological activity. A high bacterial diversity was observed, the predominant phyla being Actinobacteria and Proteobacteria.

Fluctuation of microbial activities after influent load variations in a full-scale SBR. Recovery of the biomass after starvation

Energy Technology Data Exchange (ETDEWEB)

Cabezas, Angela; Draper, Patricia; Etchebehere, Claudia [Universidad de la Republica, Montevideo (Uruguay). Catedra de Microbiologia, Facultad de Quimica y Facultad de Ciencias

2009-10-15

Due to variations in the production levels, a full-scale sequencing batch reactor (SBR) for post-treatment of tannery wastewater was exposed to low and high ammonia load periods. In order to study how these changes affected the N-removal capacity, the microbiology of the reactor was studied by a diverse set of techniques including molecular tools, activity tests, and microbial counts in samples taken along 3 years. The recover capacity of the biomass was also studied in a lab-scale reactor operated with intermittent aeration without feeding for 36 days. The results showed that changes in the feeding negatively affected the nitrifying community, but the nitrogen removal efficiencies could be restored after the concentration stress. Species substitution was observed within the nitrifying bacteria, Nitrosomonas europaea and Nitrobacter predominated initially, and after an ammonia overload period, Nitrosomonas nitrosa and Nitrospira became dominant. Some denitrifiers, with nirS related to Alicycliphilus, Azospirillum, and Marinobacter nirS, persisted during long-term reactor operation, but the community fluctuated both in composition and in abundance. This fluctuating community may better resist the continuous changes in the feeding regime. Our results showed that a nitrifying-denitrifying SBR could be operated with low loads or even without feeding during production shut down periods. (orig.)

Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

Science.gov (United States)

Diekmann, Onno E; Serrão, Ester A

2012-04-01

Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. © 2012 Blackwell Publishing Ltd.

High Inter-Individual Diversity of Point Mutations, Insertions, and Deletions in Human Influenza Virus Nucleoprotein-Specific Memory B Cells.

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Sven Reiche

Full Text Available The diversity of virus-specific antibodies and of B cells among different individuals is unknown. Using single-cell cloning of antibody genes, we generated recombinant human monoclonal antibodies from influenza nucleoprotein-specific memory B cells in four adult humans with and without preceding influenza vaccination. We examined the diversity of the antibody repertoires and found that NP-specific B cells used numerous immunoglobulin genes. The heavy chains (HCs originated from 26 and the kappa light chains (LCs from 19 different germ line genes. Matching HC and LC chains gave rise to 43 genetically distinct antibodies that bound influenza NP. The median lengths of the CDR3 of the HC, kappa and lambda LC were 14, 9 and 11 amino acids, respectively. We identified changes at 13.6% of the amino acid positions in the V gene of the antibody heavy chain, at 8.4% in the kappa and at 10.6 % in the lambda V gene. We identified somatic insertions or deletions in 8.1% of the variable genes. We also found several small groups of clonal relatives that were highly diversified. Our findings demonstrate broadly diverse memory B cell repertoires for the influenza nucleoprotein. We found extensive variation within individuals with a high number of point mutations, insertions, and deletions, and extensive clonal diversification. Thus, structurally conserved proteins can elicit broadly diverse and highly mutated B-cell responses.

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

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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

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.

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…

Population genetic diversity and fitness in multiple environments

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McGreevy Thomas J

2010-07-01

Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

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

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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

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.

Large-Scale Spatio-Temporal Patterns of Mediterranean Cephalopod Diversity.

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Stefanie Keller

Full Text Available Species diversity is widely recognized as an important trait of ecosystems' functioning and resilience. Understanding the causes of diversity patterns and their interaction with the environmental conditions is essential in order to effectively assess and preserve existing diversity. While diversity patterns of most recurrent groups such as fish are commonly studied, other important taxa such as cephalopods have received less attention. In this work we present spatio-temporal trends of cephalopod diversity across the entire Mediterranean Sea during the last 19 years, analysing data from the annual bottom trawl survey MEDITS conducted by 5 different Mediterranean countries using standardized gears and sampling protocols. The influence of local and regional environmental variability in different Mediterranean regions is analysed applying generalized additive models, using species richness and the Shannon Wiener index as diversity descriptors. While the western basin showed a high diversity, our analyses do not support a steady eastward decrease of diversity as proposed in some previous studies. Instead, high Shannon diversity was also found in the Adriatic and Aegean Seas, and high species richness in the eastern Ionian Sea. Overall diversity did not show any consistent trend over the last two decades. Except in the Adriatic Sea, diversity showed a hump-shaped trend with depth in all regions, being highest between 200-400 m depth. Our results indicate that high Chlorophyll a concentrations and warmer temperatures seem to enhance species diversity, and the influence of these parameters is stronger for richness than for Shannon diversity.

Honey bee nest thermoregulation: diversity promotes stability.

Science.gov (United States)

Jones, Julia C; Myerscough, Mary R; Graham, Sonia; Oldroyd, Benjamin P

2004-07-16

A honey bee colony is characterized by high genetic diversity among its workers, generated by high levels of multiple mating by its queen. Few clear benefits of this genetic diversity are known. Here we show that brood nest temperatures in genetically diverse colonies (i.e., those sired by several males) tend to be more stable than in genetically uniform ones (i.e., those sired by one male). One reason this increased stability arises is because genetically determined diversity in workers' temperature response thresholds modulates the hive-ventilating behavior of individual workers, preventing excessive colony-level responses to temperature fluctuations.

Embracing "Soft Skill" Diversity in the Workplace (Invited)

Science.gov (United States)

Thomas, T.

2010-12-01

Embracing "Soft Skill" Diversity in the Workplace Terri Thomas, Sr. Director Global Customer Support ShoreTel INRODUCTION Truly successful diversity programs go beyond gender, age, ethnicity, race, sexual orientation and spiritual practice. They include diversity of thought, style, leadership and communication styles, the so called “soft skills”. The increasing need for global workforces is stronger than ever and high performance teams have fully embraced, successfully harnessed and put into practice robust diversity programs than include a “soft skill” focus. Managing diversity presents significant organizational challenges, and is not an easy task, particularly in organizations that are heavily weighted with highly technical professionals such as engineers, accountants etc.. The focus of this presentation is on leveraging the “Soft Skills” diversity in technical work environments to create high performance and highly productive teams. WHY DIVERSITY and WHY NOW? Due to increasing changes in the U.S. population, in order to stay competitive, companies need to focus on diversity and look for ways to become inclusive organizations because diversity has the potential of yielding greater productivity and competitive advantages . Managing and valuing diversity is a key component of effective people management, which can improve workplace productivity (Black Enterprise, 2001). Changing demographics, from organizational restructuring, women in the workplace, equal opportunity legislation and other legal issues, are forcing organizations to become more aggressive in implementing robust diversity practices. However, YOU do not need to wait for your organization to introduce a formal “Diversity” program. There are steps you can take to introduce diversity into your own workgroups. There is no “one single answer” to solve this issue, however this discussion will provide thought provoking ideas, examples of success and failure and a starting point for you

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...

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...

High genetic diversity among and within bitter manioc varieties cultivated in different soil types in Central Amazonia

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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.

Knowledge Diversity, Transfer and Coordination

DEFF Research Database (Denmark)

Laursen, Keld; Moreira, Solon; Markus, Arjan

from the widely accepted view that distant, externally-developed knowledge is difficult to incorporate into the focal firm?s own production. We suggest that high levels of intrafirm network diversity, tie strength, and network density are essential for a diversity of knowledge inputs, knowledge...

Evaluation of simultaneous nutrient and COD removal with polyhydroxybutyrate (PHB) accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis.

Science.gov (United States)

Jena, Jyotsnarani; Kumar, Ravindra; Dixit, Anshuman; Pandey, Sony; Das, Trupti

2015-01-01

Simultaneous nitrate-N, phosphate and COD removal was evaluated from synthetic waste water using mixed microbial consortia in an anoxic environment under various initial carbon load (ICL) in a batch scale reactor system. Within 6 hours of incubation, enriched DNPAOs (Denitrifying Polyphosphate Accumulating Microorganisms) were able to remove maximum COD (87%) at 2 g/L of ICL whereas maximum nitrate-N (97%) and phosphate (87%) removal along with PHB accumulation (49 mg/L) was achieved at 8 g/L of ICL. Exhaustion of nitrate-N, beyond 6 hours of incubation, had a detrimental effect on COD and phosphate removal rate. Fresh supply of nitrate-N to the reaction medium, beyond 6 hours, helped revive the removal rates of both COD and phosphate. Therefore, it was apparent that in spite of a high carbon load, maximum COD and nutrient removal can be maintained, with adequate nitrate-N availability. Denitrifying condition in the medium was evident from an increasing pH trend. PHB accumulation by the mixed culture was directly proportional to ICL; however the time taken for accumulation at higher ICL was more. Unlike conventional EBPR, PHB depletion did not support phosphate accumulation in this case. The unique aspect of all the batch studies were PHB accumulation was observed along with phosphate uptake and nitrate reduction under anoxic conditions. Bioinformatics analysis followed by pyrosequencing of the mixed culture DNA from the seed sludge revealed the dominance of denitrifying population, such as Corynebacterium, Rhodocyclus and Paraccocus (Alphaproteobacteria and Betaproteobacteria). Rarefaction curve indicated complete bacterial population and corresponding number of OTUs through sequence analysis. Chao1 and Shannon index (H') was used to study the diversity of sampling. "UCI95" and "LCI95" indicated 95% confidence level of upper and lower values of Chao1 for each distance. Values of Chao1 index supported the results of rarefaction curve.

Evaluation of simultaneous nutrient and COD removal with polyhydroxybutyrate (PHB accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis.

Directory of Open Access Journals (Sweden)

Jyotsnarani Jena

Full Text Available Simultaneous nitrate-N, phosphate and COD removal was evaluated from synthetic waste water using mixed microbial consortia in an anoxic environment under various initial carbon load (ICL in a batch scale reactor system. Within 6 hours of incubation, enriched DNPAOs (Denitrifying Polyphosphate Accumulating Microorganisms were able to remove maximum COD (87% at 2 g/L of ICL whereas maximum nitrate-N (97% and phosphate (87% removal along with PHB accumulation (49 mg/L was achieved at 8 g/L of ICL. Exhaustion of nitrate-N, beyond 6 hours of incubation, had a detrimental effect on COD and phosphate removal rate. Fresh supply of nitrate-N to the reaction medium, beyond 6 hours, helped revive the removal rates of both COD and phosphate. Therefore, it was apparent that in spite of a high carbon load, maximum COD and nutrient removal can be maintained, with adequate nitrate-N availability. Denitrifying condition in the medium was evident from an increasing pH trend. PHB accumulation by the mixed culture was directly proportional to ICL; however the time taken for accumulation at higher ICL was more. Unlike conventional EBPR, PHB depletion did not support phosphate accumulation in this case. The unique aspect of all the batch studies were PHB accumulation was observed along with phosphate uptake and nitrate reduction under anoxic conditions. Bioinformatics analysis followed by pyrosequencing of the mixed culture DNA from the seed sludge revealed the dominance of denitrifying population, such as Corynebacterium, Rhodocyclus and Paraccocus (Alphaproteobacteria and Betaproteobacteria. Rarefaction curve indicated complete bacterial population and corresponding number of OTUs through sequence analysis. Chao1 and Shannon index (H' was used to study the diversity of sampling. "UCI95" and "LCI95" indicated 95% confidence level of upper and lower values of Chao1 for each distance. Values of Chao1 index supported the results of rarefaction curve.

Diversity in Dermatology Residency Programs.

Science.gov (United States)

Van Voorhees, Abby S; Enos, Clinton W

2017-10-01

Given the change in our population to one that is more racially and ethnically diverse, the topic of diversity in dermatology residency programs has gained attention. In a field that has become highly competitive, diversity is lagging behind. What are the reasons for this? The existing diversity among medical school matriculants is reflective of the applicant pool, and although modest, there has been an increase in applications and acceptances from minority populations. However, these proportions do not carry through to the population applying to dermatology residency. Making sense of this and planning how to recruit a more diverse applicant pool will improve the quality and cultural competency of future dermatologists. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

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.

TX-RX isolation method based on polarization diversity, spatial diversity and TX beamforming

DEFF Research Database (Denmark)

Foroozanfard, Ehsan; Carvalho, Elisabeth De; Pedersen, Gert F.

2016-01-01

In this paper, the feasibility of an antenna isolation technique based on null-steer beamforming, polarization diversity and spatial diversity is investigated. The proposed system consists of six patch antennas which are fed by a feeding network to obtain a null-steer beamformer. To achieve spatial...... diversity, antenna elements are located on two layers, facing in a different direction. Moreover, the antenna elements in two layers use different polarization. The measured results of the antenna system present a high TX-RX isolation in the order of 70 dB which shows the feasibility of such a system...

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)

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

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

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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.

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.

Denitrification as an adaptive trait in soil and groundwater bacteria

Energy Technology Data Exchange (ETDEWEB)

Bergwall, C

1997-09-01

The focus of this thesis is on selection and adaptation processes in bacteria with emphasis on denitrifying bacteria in groundwater. Other nitrogen transformation processes such as dissimilatory nitrate reduction to ammonium (nitrate ammonification) and nitrification of forest soil bacteria are briefly discussed. Microcosms with sterile sediment and groundwater were inoculated with single denitrifying strains isolated from three groundwater aquifers, two of which are agricultural aquifers (in situ NO{sub 3}{sup -}-N was 24.1 and 35.2 mg1{sup -1}) and the third which is a pristine lake water infiltration aquifer (in situ NO{sub 3}{sup -}-N was 6.3 mg1{sup -1}). The average denitrification activity for strains from the nitrate contaminated sites were twice as high as the activity of the strains from the pristine site. Denitrification were carbon limited and glucose amendment increased the denitrification activity about a 2-fold for all strains. The strain specific differences in denitrification rates increased to a 2.5-fold after carbon addition indicating that the differences in reduction rates cannot be explained by different carbon utilisation rates but rather reflect innate differences in the reductases of the strains. A preliminary identification of the molecular target for adaptation was performed with artificial electron donors and electron acceptors for all enzymatic steps in the denitrification pathway. Nitrous oxide reductase activity was significantly higher in denitrifiers from the nitrate contaminated sites. This suggests that nos genes may be the molecular target, possibly by mutation or gene duplication for adaptation to high nitrate concentrations. Two anaerobic denitrifiers from each of the contaminated sites were capable of aerobic denitrification indicating that high nitrate concentrations may select for strains that denitrifies in the presence of both oxygen and nitrate. Microcosm experiments with fertilized coniferous forest soil showed that the

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.

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.

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.

Performance and bacterial community structure of a 10-years old constructed mangrove wetland.

Science.gov (United States)

Tian, Tingting; Tam, Nora F Y; Zan, Qijie; Cheung, S G; Shin, Paul K S; Wong, Y S; Zhang, Li; Chen, Zhanghe

2017-11-30

Constructed mangrove wetland has been used for wastewater treatment but its long-term performance has not been reported. One-year monitoring of a 10-years old horizontal subsurface-flow constructed mangrove wetland consisting of three belts, two with mangrove plants and one without, revealed that the system maintained high and stable removal percentages of organic matter and nutrients, and planted belts performed better than unplanted control. Substrates in belts planted with Aegiceras corniculatum or Kandelia obovata had higher abundance of ammonifiers, nitrifiers and denitrifiers but lower total heterotrophic bacteria than unplanted substrate. Denaturing gradient gel electrophoresis showed that microbial diversity in planted substrate was significantly lower than that in unplanted one. The bacteria in substrates, irrespective to belts, were phylogenetically related to Proteobacteria (most dominant), Acidobacteria, Firmicutes, Nitrospirae, Gemmatimonadetes, Chloroflexi and Cyanobacteria. The steady performance of this 10-year old constructed mangrove wetland was affected by the abundance and diversity of bacterial community in substrate. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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)…

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.

Does staff diversity imply openness to diversity?

DEFF Research Database (Denmark)

Lauring, Jakob; Selmer, Jan

2013-01-01

Purpose – Post-secondary educational organizations are currently some of the most diverse settings to be found. However, few educational studies have dealt with staff diversity and hardly any has looked outside the USA. The purpose of this paper is to present a study of members of international...... university departments in Denmark. The authors set out to investigate the relationship between different types of staff diversity and openness to diversity in terms of linguistic, visible, value, and informational heterogeneity. Design/methodology/approach – This study uses responses from 489 staff members......, was unrelated or negatively associated with positive diversity attitudes. Originality/value – Few studies deal with the role of staff diversity and no prior studies the authors know of have examined the link between diversity types and openness to diversity....

Carbohydrates in diversity-oriented synthesis: challenges and opportunities.

Science.gov (United States)

Lenci, E; Menchi, G; Trabocchi, A

2016-01-21

Over the last decade, Diversity-Oriented Synthesis (DOS) has become a new paradigm for developing large collections of structurally diverse small molecules as probes to investigate biological pathways, and to provide a larger array of the chemical space. Drug discovery and chemical biology are taking advantage of DOS approaches to exploit highly-diverse and complex molecular platforms, producing advances in both target and ligand discovery. In this view, carbohydrates are attractive building blocks for DOS libraries, due to their stereochemical diversity and high density of polar functional groups, thus offering many possibilities for chemical manipulation and scaffold decoration. This review will discuss research contributions and perspectives on the application of carbohydrate chemistry to explore the accessible chemical space through appendage, stereochemical and scaffold diversity.

How Should Beta-Diversity Inform Biodiversity Conservation?

Science.gov (United States)

Socolar, Jacob B; Gilroy, James J; Kunin, William E; Edwards, David P

2016-01-01

To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity--the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning. Copyright © 2015 Elsevier Ltd. All rights reserved.

Floristic diversity in fragmented Afromontane rainforests

DEFF Research Database (Denmark)

Schmitt, Christine B.; Denich, Manfred; Demissew, Sebsebe

2010-01-01

Ordination and indicator species analyses showed gradual variations in floristic diversity along the altitudinal gradient with a pronounced shift in species composition at ca. 1830 m. Upper montane forest is characterized by high fern diversity and indicator species that are Afromontane endemics...

Iterative-Transform Phase Retrieval Using Adaptive Diversity

Science.gov (United States)

Dean, Bruce H.

2007-01-01

A phase-diverse iterative-transform phase-retrieval algorithm enables high spatial-frequency, high-dynamic-range, image-based wavefront sensing. [The terms phase-diverse, phase retrieval, image-based, and wavefront sensing are defined in the first of the two immediately preceding articles, Broadband Phase Retrieval for Image-Based Wavefront Sensing (GSC-14899-1).] As described below, no prior phase-retrieval algorithm has offered both high dynamic range and the capability to recover high spatial-frequency components. Each of the previously developed image-based phase-retrieval techniques can be classified into one of two categories: iterative transform or parametric. Among the modifications of the original iterative-transform approach has been the introduction of a defocus diversity function (also defined in the cited companion article). Modifications of the original parametric approach have included minimizing alternative objective functions as well as implementing a variety of nonlinear optimization methods. The iterative-transform approach offers the advantage of ability to recover low, middle, and high spatial frequencies, but has disadvantage of having a limited dynamic range to one wavelength or less. In contrast, parametric phase retrieval offers the advantage of high dynamic range, but is poorly suited for recovering higher spatial frequency aberrations. The present phase-diverse iterative transform phase-retrieval algorithm offers both the high-spatial-frequency capability of the iterative-transform approach and the high dynamic range of parametric phase-recovery techniques. In implementation, this is a focus-diverse iterative-transform phaseretrieval algorithm that incorporates an adaptive diversity function, which makes it possible to avoid phase unwrapping while preserving high-spatial-frequency recovery. The algorithm includes an inner and an outer loop (see figure). An initial estimate of phase is used to start the algorithm on the inner loop, wherein

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

Performance of a reactor containing denitrifying immobilized biomass in removing ethanol and aromatic hydrocarbons (BTEX) in a short operating period

International Nuclear Information System (INIS)

Gusmao, Valquiria Ribeiro; Chinalia, Fabio Alexandre; Sakamoto, Isabel Kimiko; Varesche, Maria Bernadete Amancio

2007-01-01

A horizontal-flow anaerobic immobilized biomass reactor (HAIB) containing denitrifying biomass was evaluated with respect to its ability to remove, separately and in a short operating period (30 days), organic matter, nitrate, and the hydrocarbons benzene (41.4 mg L -1 ), toluene (27.8 mg L -1 ), ethylbenzene (31.1 mg L -1 ), o-xylene (28.5 mg L -1 ), m-xylene (28.4 mg L -1 ) and p-xylene (32.1 mg L -1 ). The purified culture, which was grown in the presence of the specific hydrocarbon, was used as the source of cells to be immobilized in the polyurethane foam. After 30 days of operation, the foam was removed and a new immobilized biomass was grown in the presence of another hydrocarbon. The average hydrocarbon removal efficiency attained was 97%. The organic matter, especially ethanol, was removed with an average efficiency of 83% at a mean influent concentration of 1185.0 mg L -1 . A concomitant removal of 97% of nitrate was observed for a mean influent concentration of 423.4 mg L -1 . The independent removal of each hydrocarbon demonstrated that these contaminants can be biodegraded separately, without the need for a compound to be the primary substrate for the degradation of another. This study proposes the application of the system for treatment of areas contaminated with these compounds, with substitution and formation of a biofilm in a 30-day period

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

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

Extraordinary Genetic Diversity in a Wood Decay Mushroom.

Science.gov (United States)

Baranova, Maria A; Logacheva, Maria D; Penin, Aleksey A; Seplyarskiy, Vladimir B; Safonova, Yana Y; Naumenko, Sergey A; Klepikova, Anna V; Gerasimov, Evgeny S; Bazykin, Georgii A; James, Timothy Y; Kondrashov, Alexey S

2015-10-01

Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(-8) (95% CI: 1.1 × 10(-8) to 4.1 × 10(-8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

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.

Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

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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.

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.

Functional Molecular Diversity of Marine Dissolved Organic Matter Is Reduced during Degradation

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Andrea Mentges

2017-06-01

Full Text Available Dissolved organic matter (DOM is a highly diverse mixture of compounds, accounting for one of the world's largest active carbon pools. The surprising recalcitrance of some DOM compounds to bacterial degradation has recently been associated with its diversity. However, little is known about large-scale patterns of marine DOM diversity and its change through degradation, in particular considering the functional diversity of DOM. Here, we analyze the development of marine DOM diversity during degradation in two data sets comprising DOM of very different ages: a three-year mesocosm experiment and highly-resolved field samples from the Atlantic and Southern Ocean. The DOM molecular composition was determined using ultra-high resolution mass spectrometry. We quantify DOM diversity using three conceptually different diversity measures, namely richness of molecular formulas, abundance-based diversity, and functional molecular diversity. Using these measures we find stable molecular richness of DOM with age >1 year, systematic changes in the molecules' abundance distribution with degradation state, and increasing homogeneity with respect to chemical properties for more degraded DOM. Coinciding with differences in sea water density, the spatial field data separated clearly into regions of high and low diversity. The joint application of different diversity measures yields a comprehensive overview on temporal and spatial patterns of molecular diversity, valuable for general conclusions on drivers and consequences of marine DOM diversity.

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.

Flower diversity and bee reproduction in an arid ecosystem

OpenAIRE

Dorado, Jimena; V?zquez, Diego P.

2016-01-01

Background: Diverse flower communities are more stable in floral resource production along the flowering season, but the question about how the diversity and stability of resources affect pollinator reproduction remains open. High plant diversity could favor short foraging trips, which in turn would enhance bee fitness. In addition to plant diversity, greater temporal stability of floral resources in diverse communities could favor pollinator fitness because such communities are likely to occ...

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.

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

African Journals Online (AJOL)

Administrator

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 ...

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.

Cultural diversity, economic development and societal instability

Science.gov (United States)

Nettle, D.; Grace, J.B.; Choisy, M.; Cornell, H.V.; Guegan, J.-F.; Hochberg, M.E.

2007-01-01

Background. Social scientists have suggested that cultural diversity in a nation leads to societal instability. However, societal instability may be affected not only by within-nation on ?? diversity, but also diversity between a nation and its neighbours or ?? diversity. It is also necessary to distinguish different domains of diversity, namely linguistic, ethnic and religious, and to distinguish between the direct effects of diversity on societal instability, and effects that are mediated by economic conditions. Methodology/Principal Findings. We assembled a large cross-national dataset with information on ?? and ?? cultural diversity, economic conditions, and indices of societal instability. Structural equation modeling was used to evaluate the direct and indirect effects of cultural diversity on economics and societal stability. Results show that different type and domains of diversity have interacting effects. As previously documented, linguistic ?? diversity has a negative effect on economic performance, and we show that it is largely through this economic mechanism that it affects societal instability. For ?? diversity, the higher the linguistic diversity among nations in a region, the less stable the nation. But, religious ?? diversity has the opposite effect, reducing instability, particularly in the presence of high linguistic diversity. Conclusions. Within-nation linguistic diversity is associated with reduced economic performance, which, in turn, increases societal instability. Nations which differ linguistically from their neighbors are also less stable. However, religious diversity between, neighboring nations has the opposite effect, decreasing societal instability.

Cultural diversity, economic development and societal instability.

Science.gov (United States)

Nettle, Daniel; Grace, James B; Choisy, Marc; Cornell, Howard V; Guégan, Jean-François; Hochberg, Michael E

2007-09-26

Social scientists have suggested that cultural diversity in a nation leads to societal instability. However, societal instability may be affected not only by within-nation or alpha diversity, but also diversity between a nation and its neighbours or beta diversity. It is also necessary to distinguish different domains of diversity, namely linguistic, ethnic and religious, and to distinguish between the direct effects of diversity on societal instability, and effects that are mediated by economic conditions. We assembled a large cross-national dataset with information on alpha and beta cultural diversity, economic conditions, and indices of societal instability. Structural equation modeling was used to evaluate the direct and indirect effects of cultural diversity on economics and societal stability. Results show that different types and domains of diversity have interacting effects. As previously documented, linguistic alpha diversity has a negative effect on economic performance, and we show that it is largely through this economic mechanism that it affects societal instability. For beta diversity, the higher the linguistic diversity among nations in a region, the less stable the nation. But, religious beta diversity has the opposite effect, reducing instability, particularly in the presence of high linguistic diversity. Within-nation linguistic diversity is associated with reduced economic performance, which, in turn, increases societal instability. Nations which differ linguistically from their neighbors are also less stable. However, religious diversity between neighboring nations has the opposite effect, decreasing societal instability.

Openness to diversity, trust and conflict in multicultural organizations

DEFF Research Database (Denmark)

Lauring, Jakob; Selmer, Jan

2012-01-01

with group trust. The findings of this study suggest that openness to diversity should be highly prioritized by human resource managers in demographically diverse organizations. Possible interventions include organizational culture change programs, diversity training at individual and team levels as well...

Diversity, Adaptability and Ecosystem Resilience

Science.gov (United States)

Keribin, Rozenn; Friend, Andrew

2013-04-01

Our ability to predict climate change and anticipate its impacts depends on Earth System Models (ESMs) and their ability to account for the high number of interacting components of the Earth System and to gauge both their influence on the climate and the feedbacks they induce. The land carbon cycle is a component of ESMs that is still poorly constrained. Since the 1990s dynamic global vegetation models (DGVMs) have become the main tool through which we understand the interactions between plant ecosystems and the climate. While DGVMs have made it clear the impacts of climate change on vegetation could be dramatic, predicting the dieback of rainforests and massive carbon losses from various ecosystems, they are highly variable both in their composition and their predictions. Their treatment of plant diversity and competition in particular vary widely and are based on highly-simplified relationships that do not account for the multiple levels of diversity and adaptability found in real plant ecosystems. The aim of this GREENCYCLES II project is to extend an individual-based DGVM to treat the diversity of physiologies found in plant communities and evaluate their effect if any on the ecosystem's transient dynamics and resilience. In the context of the InterSectoral Impacts Model Intercomparison Project (ISI-MIP), an initiative coordinated by a team at the Potsdam Institute for Climate Impact Research (PIK) that aims to provide fast-track global impact assessments for the IPCC's Fifth Assessment Report, we compare 6 vegetation models including 4 DGVMs under different climate change scenarios and analyse how the very different treatments of plant diversity and interactions from one model to the next affect the models' results. We then investigate a new, more mechanistic method of incorporating plant diversity into the DGVM "Hybrid" based on ecological tradeoffs mediated by plant traits and individual-based competition for light.

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.

Populasi dan aktivitas denitrifikasi serta emisi gas N2 O pada lahan pertanian organik, pertanian intensif, dan hutan

Directory of Open Access Journals (Sweden)

Dwi Agustiyani

2012-10-01

Full Text Available This research investigate the population and potentials denitrification activity from three different soils, organically farmed soil, intensive farmed soil and forest soil. Our objectives were to explore spatial gradients in denitrifier populations, examine whether populations density and its potential activity was related to soil chemical properties (C and N content, and determine the potential emission of gas N2O. Results indicated biological functional differences between these three different soil ecosystems. Forest soil had the highest population density of denitrifying bacteria and also had significant potential denitrifying activities. The highest potentials denitrifying activity in the soil affected to the lowest emission of N2O gas. The lowest population and potential denitrifying activity was measured in the intensive farmed soil. Those conditions might be promoted the potentials emission of N2O.

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

High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography.

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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.

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.

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].

The Implementation of an Innovative High School Mentoring Program Designed to Enhance Diversity and Provide a Pathway for Future Careers in Healthcare Related Fields.

Science.gov (United States)

Patel, Salma I; Rodríguez, Patricia; Gonzales, Rayna J

2015-09-01

Although the population of diverse applicants applying to medical school has increased over recent years (AAMC Diversity in Medical Education: Facts and Figures 2012); efforts persist to ensure the continuance of this increasing trend. Mentoring students at an early age may be an effective method by which to accomplish diversity within the applicant pool. Having a diverse physician population is more likely able to adequately address the healthcare needs of our diverse population. The purpose of this study is to initiate a pipeline program, called the Medical Student Mentorship Program (MSMP), designed to specifically target high school students from lower economic status, ethnic, or racial underrepresented populations. High school students were paired with medical students, who served as primary mentors to facilitate exposure to processes involved in preparing and training for careers in medicine and other healthcare-related fields as well as research. Mentors were solicited from first and second year medical students at the University of Arizona College of Medicine-Phoenix (UACOM-P). Two separate cohorts of mentees were selected based on an application process from a local high school for the school years 2010-2011 and 2011-2012. Anonymous mentee and mentor surveys were used to evaluate the success of the MSMP. A total of 16 pairs of mentees and mentors in the 2010-2011 (Group 1) and 2011-2012 (Group 2) studies participated in MSMP. High school students reported that they were more likely to apply to medical school after participating in the program. Mentees also reported that they received a significant amount of support, helpful information, and guidance from their medical student mentors. Overall, feedback from mentees and mentors was positive and they reported that their participation was rewarding. Mentees were contacted 2 to 3 years post MSMP participation as sophomores or juniors in college, and all reported that they were on a pre-healthcare career track

The interplay of diversity training and diversity beliefs on team creativity in nationality diverse teams

NARCIS (Netherlands)

Homan, A.C.; Buengeler, C.; Eckhoff, R.A.; van Ginkel, W.P.; Voelpel, S.C.

2015-01-01

Attaining value from nationality diversity requires active diversity management, which organizations often employ in the form of diversity training programs. Interestingly, however, the previously reported effects of diversity training are often weak and, sometimes, even negative. This situation

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.

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

A research education program model to prepare a highly qualified workforce in biomedical and health-related research and increase diversity.

Science.gov (United States)

Crockett, Elahé T

2014-09-24

The National Institutes of Health has recognized a compelling need to train highly qualified individuals and promote diversity in the biomedical/clinical sciences research workforce. In response, we have developed a research-training program known as REPID (Research Education Program to Increase Diversity among Health Researchers) to prepare students/learners to pursue research careers in these fields and address the lack of diversity and health disparities. By inclusion of students/learners from minority and diverse backgrounds, the REPID program aims to provide a research training and enrichment experience through team mentoring to inspire students/learners to pursue research careers in biomedical and health-related fields. Students/learners are recruited from the University campus from a diverse population of undergraduates, graduates, health professionals, and lifelong learners. Our recruits first enroll into an innovative on-line introductory course in Basics and Methods in Biomedical Research that uses a laboratory Tool-Kit (a lab in a box called the My Dr. ET Lab Tool-Kit) to receive the standard basics of research education, e.g., research skills, and lab techniques. The students/learners will also learn about the responsible conduct of research, research concept/design, data recording/analysis, and scientific writing/presentation. The course is followed by a 12-week hands-on research experience during the summer. The students/learners also attend workshops and seminars/conferences. The students/learners receive scholarship to cover stipends, research related expenses, and to attend a scientific conference. The scholarship allows the students/learners to gain knowledge and seize opportunities in biomedical and health-related careers. This is an ongoing program, and during the first three years of the program, fifty-one (51) students/learners have been recruited. Thirty-six (36) have completed their research training, and eighty percent (80%) of them have

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.

Diverse crowds using diverse methods improves the scientific dialectic.

Science.gov (United States)

Motyl, Matt; Iyer, Ravi

2015-01-01

In science, diversity is vital to the development of new knowledge. We agree with Duarte et al. that we need more political diversity in social psychology, but contend that we need more religious diversity and methodological diversity as well. If some diversity is good, more is better (especially in science).

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.

Understanding diversity: the importance of social acceptance.

Science.gov (United States)

Chen, Jacqueline M; Hamilton, David L

2015-04-01

Two studies investigated how people define and perceive diversity in the historically majority-group dominated contexts of business and academia. We hypothesized that individuals construe diversity as both the numeric representation of racial minorities and the social acceptance of racial minorities within a group. In Study 1, undergraduates' (especially minorities') perceptions of campus diversity were predicted by perceived social acceptance on a college campus, above and beyond perceived minority representation. Study 2 showed that increases in a company's representation and social acceptance independently led to increases in perceived diversity of the company among Whites. Among non-Whites, representation and social acceptance only increased perceived diversity of the company when both qualities were high. Together these findings demonstrate the importance of both representation and social acceptance to the achievement of diversity in groups and that perceiver race influences the relative importance of these two components of diversity. © 2015 by the Society for Personality and Social Psychology, Inc.

Optimization of multi-branch switched diversity systems

KAUST Repository

Nam, Haewoon

2009-10-01

A performance optimization based on the optimal switching threshold(s) for a multi-branch switched diversity system is discussed in this paper. For the conventional multi-branch switched diversity system with a single switching threshold, the optimal switching threshold is a function of both the average channel SNR and the number of diversity branches, where computing the optimal switching threshold is not a simple task when the number of diversity branches is high. The newly proposed multi-branch switched diversity system is based on a sequence of switching thresholds, instead of a single switching threshold, where a different diversity branch uses a different switching threshold for signal comparison. Thanks to the fact that each switching threshold in the sequence can be optimized only based on the number of the remaining diversity branches, the proposed system makes it easy to find these switching thresholds. Furthermore, some selected numerical and simulation results show that the proposed switched diversity system with the sequence of optimal switching thresholds outperforms the conventional system with the single optimal switching threshold. © 2009 IEEE.

Neutron stars: Observational diversity and evolution

Science.gov (United States)

Safi-Harb, S.

2017-12-01

Ever since the discovery of the Crab and Vela pulsars in their respective Supernova Remnants, our understanding of how neutron stars manifest themselves observationally has been dramatically shaped by the surge of discoveries and dedicated studies across the electromagnetic spectrum, particularly in the high-energy band. The growing diversity of neutron stars includes the highly magnetized neutron stars (magnetars) and the Central Compact Objects shining in X-rays and mostly lacking pulsar wind nebulae. These two subclasses of high-energy objects, however, seem to be characterized by anomalously high or anomalously low surface magnetic fields (thus dubbed as ‘magnetars’ and ‘anti-magnetars’, respectively), and have pulsar characteristic ages that are often much offset from their associated SNRs’ ages. In addition, some neutron stars act ‘schizophrenic’ in that they occasionally display properties that seem common to more than one of the defined subclasses. I review the growing diversity of neutron stars from an observational perspective, then highlight recent and on-going theoretical and observational work attempting to address this diversity, particularly in light of their magnetic field evolution, energy loss mechanisms, and supernova progenitors’ studies.

Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.

Science.gov (United States)

Ishii, Satoshi; Ashida, Naoaki; Ohno, Hiroki; Segawa, Takahiro; Yabe, Shuhei; Otsuka, Shigeto; Yokota, Akira; Senoo, Keishi

2017-06-01

Thirty-nine denitrifying bacterial strains closely related to one another, represented by strains TSA40T and TSA66T, were isolated from rice paddy soils. Strains TSA40T and TSA66T were Gram-stain-negative, slightly curved rod-shaped, and motile by means of polar flagella. They were able to reduce nitrate, nitrite and nitrous oxide, but unable to fix atmospheric N2. While strain TSA66T was able to grow autotrophically by H2-dependent denitrification, strain TSA40T could not. Phylogenetic analysis suggested that they belong to the family Oxalobacteraceae, the order Burkholderiales in the class Betaproteobacteria. Major components in the fatty acids (C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3) and quinone (Q-8) also supported the affiliation of strains TSA40T and TSA66T to the family Oxalobacteraceae. Based on 16S rRNA gene sequence comparisons, strains TSA40T and TSA66T showed the greatest degree of similarity to Herbaspirillum massiliense JC206T, Noviherbaspirillum malthae CC-AFH3T, Noviherbaspirillum humi U15T, Herbaspirillum seropedicae Z67T and Paucimonas lemoignei LMG 2207T, and lower similarities to the members of other genera. Average nucleotide identity values between the genomes of strain TSA40T, TSA66T and H. massiliense JC206T were 75-77 %, which was lower than the threshold value for species discrimination (95-96 %). Based on the 16S rRNA gene sequence analysis in combination with physiological, chemotaxonomic and genomic properties, strains TSA40T (=JCM 17722T=ATCC TSD-69T) and TSA66T (=JCM 17723T=DSM 25787T) are the type strains of two novel species within the genus Noviherbaspirillum, for which the names Noviherbaspirillum denitrificans sp. nov. and Noviherbaspirillum autotrophicum sp. nov. are proposed, respectively. We also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.

Urban tree diversity - Taking stock and looking ahead

DEFF Research Database (Denmark)

Morgenroth, J.; Östberg, Johan; Bosch, C. Konijnendijk van den

2016-01-01

The first International Conference on Urban Tree Diversity hosted in June 2014 by the Swedish University of Agricultural Science in Alnarp, Sweden highlighted the need for a better understanding of the current state of urban tree diversity. Here we present and discuss a selection of urban tree...... diversity themes with the intention of developing and sharing knowledge in a research area that is gaining momentum. We begin by discussing the specific role of species diversity in ecosystem service provision and ecosystem stability. This is followed by exploring the urban conditions that affect species...... richness. Having determined that many ecosystem services depend on urban tree species diversity and that urban environments are capable of supporting high species diversity, we conclude by addressing how to govern for urban tree diversity....

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.

Breeding loggerhead marine turtles Caretta caretta in Dry Tortugas National Park, USA, show high fidelity to diverse habitats near nesting beaches

Science.gov (United States)

Hart, Kristen M.; Zawada, David G.; Sartain-Iverson, Autumn R.; Fujisaki, Ikuko

2016-01-01

We used satellite telemetry to identify in-water habitat used by individuals in the smallest North-west Atlantic subpopulation of adult nesting loggerhead turtles Caretta caretta during the breeding season. During 2010, 2011 and 2012 breeding periods, a total of 20 adult females used habitats proximal to nesting beaches with various levels of protection within Dry Tortugas National Park. We then used a rapid, high-resolution, digital imaging system to map habitat adjacent to nesting beaches, revealing the diversity and distribution of available benthic cover. Turtle behaviour showing measurable site-fidelity to these diverse habitats has implications for managing protected areas and human activities within them. Protecting diverse benthic areas adjacent to loggerhead turtle nesting beaches here and elsewhere could provide benefits for overall biodiversity conservation.

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...

Bacterial diversity and composition during rain events with and without Saharan dust influence reaching a high mountain lake in the Alps.

Science.gov (United States)

Peter, Hannes; Hörtnagl, Paul; Reche, Isabel; Sommaruga, Ruben

2014-12-01

The diversity of airborne microorganisms that potentially reach aquatic ecosystems during rain events is poorly explored. Here, we used a culture-independent approach to characterize bacterial assemblages during rain events with and without Saharan dust influence arriving to a high mountain lake in the Austrian Alps. Bacterial assemblage composition differed significantly between samples with and without Saharan dust influence. Although alpha diversity indices were within the same range in both sample categories, rain events with Atlantic or continental origins were dominated by Betaproteobacteria, whereas those with Saharan dust intrusions were dominated by Gammaproteobacteria. The high diversity and evenness observed in all samples suggests that different sources of bacteria contributed to the airborne assemblage collected at the lake shore. During experiments with bacterial assemblages collected during rain events with Saharan dust influence, cell numbers rapidly increased in sterile lake water from initially ∼3 × 103 cell ml-1 to 3.6-11.1 x105 cells ml-1 within 4-5 days, and initially, rare taxa dominated at the end of the experiment. Our study documents the dispersal of viable bacteria associated to Saharan dust intrusions travelling northwards as far as 47° latitude.

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 ...

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.

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.

Anaerobic/oxic/anoxic granular sludge process as an effective nutrient removal process utilizing denitrifying polyphosphate-accumulating organisms.

Science.gov (United States)

Kishida, Naohiro; Kim, Juhyun; Tsuneda, Satoshi; Sudo, Ryuichi

2006-07-01

In a biological nutrient removal (BNR) process, the utilization of denitrifying polyphosphate-accumulating organisms (DNPAOs) has many advantages such as effective use of organic carbon substrates and low sludge production. As a suitable process for the utilization of DNPAOs in BNR, an anaerobic/oxic/anoxic granular sludge (AOAGS) process was proposed in this study. In spite of performing aeration for nitrifying bacteria, the AOAGS process can create anaerobic/anoxic conditions suitable for the cultivation of DNPAOs because anoxic zones exist inside the granular sludge in the oxic phase. Thus, DNPAOs can coexist with nitrifying bacteria in a single reactor. In addition, the usability of DNPAOs in the reactor can be improved by adding the anoxic phase after the oxic phase. These characteristics enable the AOAGS process to attain effective removal of both nitrogen and phosphorus. When acetate-based synthetic wastewater (COD: 600 mg/L, NH4-N: 60 mg/L, PO(4)-P: 10 mg/L) was supplied to a laboratory-scale sequencing batch reactor under the operation of anaerobic/oxic/anoxic cycles, granular sludge with a diameter of 500 microm was successfully formed within 1 month. Although the removal of both nitrogen and phosphorus was almost complete at the end of the oxic phase, a short anoxic period subsequent to the oxic phase was necessary for further removal of nitrogen and phosphorus. As a result, effluent concentrations of NH(4)-N, NO(x)-N and PO(4)-P were always lower than 1 mg/L. It was found that penetration depth of oxygen inside the granular sludge was approximately 100 microm by microsensor measurements. In addition, from the microbiological analysis by fluorescence in situ hybridization, existence depth of polyphosphate-accumulating organisms was further than the maximum oxygen penetration depth. The water quality data, oxygen profiles and microbial community structure demonstrated that DNPAOs inside the granular sludge may be responsible for denitrification in the

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.

Nitrate Removal from Wastewater through Biological Denitrification with OGA 24 in a Batch Reactor

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Federico Rossi

2014-12-01

Full Text Available Nitrates pollution of waters is a worldwide problem and its remediation is a big challenge from the technical and the scientific point of view. One of the most used and promising cleaning techniques is the biological treatment of wastewaters operated by denitrifying bacteria. In this paper we begin a thorough study of denitrifying performances of the bacterium Azospira sp. OGA 24, recently isolated from the highly polluted Sarno river in the south of Italy. Here, the kinetics of nitrates consumption operated by bacteria in a specifically devised batch bioreactor, in anoxic condition and with acetate as the organic substrate, has been characterized. Experimental data were then used in a simplified model of a real wastewater treatment plant to find that OGA 24 can clean water with efficiency up to 90%. The denitrifying performances of OGA 24 match the requirements of Italian laws and make the bacterium suitable for its employment in treatment plants.

Simultaneous removal of sulfide, nitrate and acetate: Kinetic modeling

International Nuclear Information System (INIS)

Wang Aijie; Liu Chunshuang; Ren Nanqi; Han Hongjun; Lee Duujong

2010-01-01

Biological removal of sulfide, nitrate and chemical oxygen demand (COD) simultaneously from industrial wastewaters to elementary sulfur (S 0 ), N 2 , and CO 2 , or named the denitrifying sulfide (DSR) process, is a cost effective and environmentally friendly treatment process for high strength sulfide and nitrate laden organic wastewater. Kinetic model for the DSR process was established for the first time on the basis of Activated Sludge Model No. 1 (ASM1). The DSR experiments were conducted at influent sulfide concentrations of 200-800 mg/L, whose results calibrate the model parameters. The model correlates well with the DSR process dynamics. By introducing the switch function and the inhibition function, the competition between autotrophic and heterotrophic denitrifiers is quantitatively described and the degree of inhibition of sulfide on heterotrophic denitrifiers is realized. The model output indicates that the DSR reactor can work well at 0.5 1000 mg/L influent sulfide, however, the DSR system will break down.

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

NARCIS (Netherlands)

Geisen, Stefan; 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

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.

Science.gov (United States)

Liu, Yang; Chiaromonte, Francesca; Ross, Howard; Malhotra, Raunaq; Elleder, Daniel; Poss, Mary

2015-06-30

Infection with feline immunodeficiency virus (FIV) causes an immunosuppressive disease whose consequences are less severe if cats are co-infected with an attenuated FIV strain (PLV). We use virus diversity measurements, which reflect replication ability and the virus response to various conditions, to test whether diversity of virulent FIV in lymphoid tissues is altered in the presence of PLV. Our data consisted of the 3' half of the FIV genome from three tissues of animals infected with FIV alone, or with FIV and PLV, sequenced by 454 technology. Since rare variants dominate virus populations, we had to carefully distinguish sequence variation from errors due to experimental protocols and sequencing. We considered an exponential-normal convolution model used for background correction of microarray data, and modified it to formulate an error correction approach for minor allele frequencies derived from high-throughput sequencing. Similar to accounting for over-dispersion in counts, this accounts for error-inflated variability in frequencies - and quite effectively reproduces empirically observed distributions. After obtaining error-corrected minor allele frequencies, we applied ANalysis Of VAriance (ANOVA) based on a linear mixed model and found that conserved sites and transition frequencies in FIV genes differ among tissues of dual and single infected cats. Furthermore, analysis of minor allele frequencies at individual FIV genome sites revealed 242 sites significantly affected by infection status (dual vs. single) or infection status by tissue interaction. All together, our results demonstrated a decrease in FIV diversity in bone marrow in the presence of PLV. Importantly, these effects were weakened or undetectable when error correction was performed with other approaches (thresholding of minor allele frequencies; probabilistic clustering of reads). We also queried the data for cytidine deaminase activity on the viral genome, which causes an asymmetric increase

Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

Energy Technology Data Exchange (ETDEWEB)

Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

2010-07-01

Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

Energy Technology Data Exchange (ETDEWEB)

Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra; Barry, Kerrie; Tringe, Susannah G.; Watson, David B.; He, Zhili; Hazen, Terry C.; Tiedje, James M.; Rubin, Edward M.; Zhou, Jizhong

2010-02-15

Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Density and diversity of OpenStreetMap road networks in China

Directory of Open Access Journals (Sweden)

Yingjia Zhang

2015-12-01

Full Text Available OpenStreetMap is a geographic information platform designed to provide real-time updates and user-generated content related to its freely available global map, and it is one of the most widely used examples of volunteered geographic information, a technique associated with so-called neogeography. This paper, based on the data from China’s OpenStreetMap road network in May 2014, taking 340 prefecture-level cities in China as its study area, presents the geometric-related (road density and attribute-related (type diversity spatial patterns of the OpenStreetMap road network, and explores their relationship. The results are as follows. (1 The distribution of OpenStreetMap road density in Shenzhen, Shanghai, Hong Kong, and Macao predominantly obeys a “positive skewness distribution”. OpenStreetMap data for eastern China shows a higher overall and circular structure. In central China, there are noticeable discrepancies in the road density, whereas in western China, the road density is low. (2 The OpenStreetMap road diversity shows a normal distribution. The spatial pattern for the so-called “Hu Huanyong line” was broken by the effect of diplomatic and strategic factors, showing a high diversity along the peripheral border, coastal cities, and core inland cites. (3 China’s OpenStreetMap is partitioned into four parts according to road density and diversity: high density and high diversity; low density and low diversity; high density and low diversity; and low density high diversity. (4 The OpenStreetMap geographical information-collection process and mechanism were analyzed, demonstrating that the road density reflects the preponderance of traffic in the real world. OpenStreetMap road diversity reflects the road-related geographic information demand and value, and it also reflects the interests of users toward to OpenStreetMap geographical information.

Beyond the Diversity Crisis Model: Decentralized Diversity Planning and Implementation

Science.gov (United States)

Williams, Damon A.

2008-01-01

This article critiques the diversity crises model of diversity planning in higher education and presents a decentralized diversity planning model. The model is based on interviews with the nation's leading diversity officers, a review of the literature and the authors own experiences leading diversity change initiatives in higher education. The…

THE EFFECTS OF THE ORGANIZATIONAL CULTURE ON DIVERSITY

Directory of Open Access Journals (Sweden)

Hakan Sezerel

2016-12-01

Full Text Available The success of diversity management practices relies on the combination of a series of variables properly. The relevant literature suggests that diversity management is highly depended on an adequate organizational culture. Thus, a research model that proposes that organizational culture has impact on diversity management perceptions of employees. There are two data sets in this research. The independent variable of the research is organizational culture and the dependent variable of the research is the level of diversity management perceptions. The research is adopted in quantitative method and the data collected via questionnaires. This research which is conducted in a hotel chain finds that the mission dimension of organizational culture impacts all three levels of diversity management.

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.

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.

The population genetics of Quechuas, the largest native South American group: autosomal sequences, SNPs, and microsatellites evidence high level of diversity.

Science.gov (United States)

Scliar, Marilia O; Soares-Souza, Giordano B; Chevitarese, Juliana; Lemos, Livia; Magalhães, Wagner C S; Fagundes, Nelson J; Bonatto, Sandro L; Yeager, Meredith; Chanock, Stephen J; Tarazona-Santos, Eduardo

2012-03-01

Elucidating the pattern of genetic diversity for non-European populations is necessary to make the benefits of human genetics research available to individuals from these groups. In the era of large human genomic initiatives, Native American populations have been neglected, in particular, the Quechua, the largest South Amerindian group settled along the Andes. We characterized the genetic diversity of a Quechua population in a global setting, using autosomal noncoding sequences (nine unlinked loci for a total of 16 kb), 351 unlinked SNPs and 678 microsatellites and tested predictions of the model of the evolution of Native Americans proposed by (Tarazona-Santos et al.: Am J Hum Genet 68 (2001) 1485-1496). European admixture is Quechua or Melanesian populations, which is concordant with the African origin of modern humans and the fact that South America was the last part of the world to be peopled. The diversity in the Quechua population is comparable with that of Eurasian populations, and the allele frequency spectrum based on resequencing data does not reflect a reduction in the proportion of rare alleles. Thus, the Quechua population is a large reservoir of common and rare genetic variants of South Amerindians. These results are consistent with and complement our evolutionary model of South Amerindians (Tarazona-Santos et al.: Am J Hum Genet 68 (2001) 1485-1496), proposed based on Y-chromosome data, which predicts high genomic diversity due to the high level of gene flow between Andean populations and their long-term effective population size. Copyright © 2012 Wiley Periodicals, Inc.

Trees as templates for tropical litter arthropod diversity.

Science.gov (United States)

Donoso, David A; Johnston, Mary K; Kaspari, Michael

2010-09-01

Increased tree species diversity in the tropics is associated with even greater herbivore diversity, but few tests of tree effects on litter arthropod diversity exist. We studied whether tree species influence patchiness in diversity and abundance of three common soil arthropod taxa (ants, gamasid mites, and oribatid mites) in a Panama forest. The tree specialization hypothesis proposes that tree-driven habitat heterogeneity maintains litter arthropod diversity. We tested whether tree species differed in resource quality and quantity of their leaf litter and whether more heterogeneous litter supports more arthropod species. Alternatively, the abundance-extinction hypothesis states that arthropod diversity increases with arthropod abundance, which in turn tracks resource quantity (e.g., litter depth). We found little support for the hypothesis that tropical trees are templates for litter arthropod diversity. Ten tree species differed in litter depth, chemistry, and structural variability. However, the extent of specialization of invertebrates on particular tree taxa was low and the more heterogeneous litter between trees failed to support higher arthropod diversity. Furthermore, arthropod diversity did not track abundance or litter depth. The lack of association between tree species and litter arthropods suggests that factors other than tree species diversity may better explain the high arthropod diversity in tropical forests.

[Formation of microbial populations on the surface of protective coatings].

Science.gov (United States)

Kopteva, Zh P; Zanina, V V; Piliashenko-Novokhatnyĭ, A I; Kopteva, A E; Kozlova, I A

2001-01-01

Formation of microbial cenosis on the surface of polyethylene-, polyurethane- and oil-bitumen-based protective coatings was studied in dynamics during 1, 3, 7, 14 and 21 days. It has been shown that the biofilm was formed on the protective materials during 14 days and consisted of ammonifying, denitrifying, hydrocarbon-oxidizing and sulphate-reducing bacteria referred to Pseudomonas, Arthrobacter, Bacillus and Kesulfovibrio genera. The bacteria which form the biofilm on coatings possess high denitrifying and sulphate-reducing activities. Corrosion inhibitors-biocydes, introduced in composition of oil-bitumen coatings suppressed growth and metabolic activity of corrosion-active bacteria.

Genetic diversity and trait genomic prediction in a pea diversity panel.

Science.gov (United States)

Burstin, Judith; Salloignon, Pauline; Chabert-Martinello, Marianne; Magnin-Robert, Jean-Bernard; Siol, Mathieu; Jacquin, Françoise; Chauveau, Aurélie; Pont, Caroline; Aubert, Grégoire; Delaitre, Catherine; Truntzer, Caroline; Duc, Gérard

2015-02-21

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being

Genotypic Diversity and Short-term Response to Shading Stress in a Threatened Seagrass: Does Low Diversity Mean Low Resilience?

Directory of Open Access Journals (Sweden)

Suzanna M. Evans

2017-08-01

Full Text Available Seagrasses that are predominantly clonal often have low levels of genetic variation within populations and predicting their response to changing conditions requires an understanding of whether genetic variation confers increased resistance to environmental stressors. A higher level of genetic diversity is assumed to benefit threatened species due to the increased likelihood of those populations having genotypes that can persist under environmental change. To test this idea, we conducted an in situ shading experiment with six geographically distinct meadows of the threatened seagrass Posidonia australis that vary in genetic diversity. Different genotypes within meadows varied widely in their physiological and growth responses to reduced light during a simulated short-term turbidity event. The majority of meadows were resistant to the sudden reduction in light availability, but a small subset of meadows with low genotypic diversity were particularly vulnerable to the early effects of shading, showing substantially reduced growth rates after only 3 weeks. Using the photosynthetic performance (maximum quantum yield of known genotypes, we simulated meadows of varying genetic diversity to show that higher diversity can increase meadow resilience to stress by ensuring a high probability of including a high-performing genotype. These results support the hypothesis that complementarity among genotypes enhances the adaptive capacity of a population, and have significant implications for the conservation of declining P. australis meadows close to the species range edge on the east coast of Australia, where the genotypic diversity is low.

Genotypic Diversity and Short-term Response to Shading Stress in a Threatened Seagrass: Does Low Diversity Mean Low Resilience?

Science.gov (United States)

Evans, Suzanna M; Vergés, Adriana; Poore, Alistair G B

2017-01-01

Seagrasses that are predominantly clonal often have low levels of genetic variation within populations and predicting their response to changing conditions requires an understanding of whether genetic variation confers increased resistance to environmental stressors. A higher level of genetic diversity is assumed to benefit threatened species due to the increased likelihood of those populations having genotypes that can persist under environmental change. To test this idea, we conducted an in situ shading experiment with six geographically distinct meadows of the threatened seagrass Posidonia australis that vary in genetic diversity. Different genotypes within meadows varied widely in their physiological and growth responses to reduced light during a simulated short-term turbidity event. The majority of meadows were resistant to the sudden reduction in light availability, but a small subset of meadows with low genotypic diversity were particularly vulnerable to the early effects of shading, showing substantially reduced growth rates after only 3 weeks. Using the photosynthetic performance (maximum quantum yield) of known genotypes, we simulated meadows of varying genetic diversity to show that higher diversity can increase meadow resilience to stress by ensuring a high probability of including a high-performing genotype. These results support the hypothesis that complementarity among genotypes enhances the adaptive capacity of a population, and have significant implications for the conservation of declining P. australis meadows close to the species range edge on the east coast of Australia, where the genotypic diversity is low.

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.

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.

Spatial scale and β-diversity of terrestrial vertebrates in Mexico

OpenAIRE

Ochoa-Ochoa, Leticia M.; Munguía, Mariana; Lira-Noriega, Andrés; Sánchez-Cordero, Víctor; Flores-Villela, Oscar; Navarro-Sigüenza, Adolfo; Rodríguez, Pilar

2014-01-01

Patterns of diversity are scale dependent and beta-diversity is not the exception. Mexico is megadiverse due to its high beta diversity, but little is known if it is scale-dependent and/or taxonomic-dependent. We explored these questions based on the self-similarity hypothesis of beta-diversity across spatial scales. Using geographic distribution ranges of 2 513 species, we compared the beta-diversity patterns of 4 groups of terrestrial vertebrates, across 7 spatial scales (from ~10 km² to 16...

Recruitment, diversity and the influence of constrictions on the ...

African Journals Online (AJOL)

1986-09-15

Sep 15, 1986 ... Eilandvlei has an intermediate diversity with the Wildemess lagoon supporting the most diverse ... deflation basin which has been artificially connected by a .... water levels approached high tide and decreased towards low.

Diversity and distribution of lichen-associated fungi in the Ny-Ålesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing

Science.gov (United States)

Zhang, Tao; Wei, Xin-Li; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2015-01-01

This study assessed the diversity and distribution of fungal communities associated with seven lichen species in the Ny-Ålesund Region (Svalbard, High Arctic) using Roche 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Lichen-associated fungal communities showed high diversity, with a total of 42,259 reads belonging to 370 operational taxonomic units (OTUs) being found. Of these OTUs, 294 belonged to Ascomycota, 54 to Basidiomycota, 2 to Zygomycota, and 20 to unknown fungi. Leotiomycetes, Dothideomycetes, and Eurotiomycetes were the major classes, whereas the dominant orders were Helotiales, Capnodiales, and Chaetothyriales. Interestingly, most fungal OTUs were closely related to fungi from various habitats (e.g., soil, rock, plant tissues) in the Arctic, Antarctic and alpine regions, which suggests that living in association with lichen thalli may be a transient stage of life cycle for these fungi and that long-distance dispersal may be important to the fungi in the Arctic. In addition, host-related factors shaped the lichen-associated fungal communities in this region. Taken together, these results suggest that lichens thalli act as reservoirs of diverse fungi from various niches, which may improve our understanding of fungal evolution and ecology in the Arctic. PMID:26463847

Diversity and distribution of lichen-associated fungi in the Ny-Ålesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing.

Science.gov (United States)

Zhang, Tao; Wei, Xin-Li; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2015-10-14

This study assessed the diversity and distribution of fungal communities associated with seven lichen species in the Ny-Ålesund Region (Svalbard, High Arctic) using Roche 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Lichen-associated fungal communities showed high diversity, with a total of 42,259 reads belonging to 370 operational taxonomic units (OTUs) being found. Of these OTUs, 294 belonged to Ascomycota, 54 to Basidiomycota, 2 to Zygomycota, and 20 to unknown fungi. Leotiomycetes, Dothideomycetes, and Eurotiomycetes were the major classes, whereas the dominant orders were Helotiales, Capnodiales, and Chaetothyriales. Interestingly, most fungal OTUs were closely related to fungi from various habitats (e.g., soil, rock, plant tissues) in the Arctic, Antarctic and alpine regions, which suggests that living in association with lichen thalli may be a transient stage of life cycle for these fungi and that long-distance dispersal may be important to the fungi in the Arctic. In addition, host-related factors shaped the lichen-associated fungal communities in this region. Taken together, these results suggest that lichens thalli act as reservoirs of diverse fungi from various niches, which may improve our understanding of fungal evolution and ecology in the Arctic.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

Science.gov (United States)

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Phylogenetically diverse macrophyte community promotes species diversity of mobile epi-benthic invertebrates

Science.gov (United States)

Nakamoto, Kenta; Hayakawa, Jun; Kawamura, Tomohiko; Kodama, Masafumi; Yamada, Hideaki; Kitagawa, Takashi; Watanabe, Yoshiro

2018-07-01

Various aspects of plant diversity such as species diversity and phylogenetic diversity enhance the species diversity of associated animals in terrestrial systems. In marine systems, however, the effects of macrophyte diversity on the species diversity of associated animals have received little attention. Here, we sampled in a subtropical seagrass-seaweed mixed bed to elucidate the effect of the macrophyte phylogenetic diversity based on the taxonomic relatedness as well as the macrophyte species diversity on species diversity of mobile epi-benthic invertebrates. Using regression analyses for each macrophyte parameter as well as multiple regression analyses, we found that the macrophyte phylogenetic diversity (taxonomic diversity index: Delta) positively influenced the invertebrate species richness and diversity index (H‧). Although the macrophyte species richness and H‧ also positively influenced the invertebrate species richness, the best fit model for invertebrate species richness did not include them, suggesting that the macrophyte species diversity indirectly influenced invertebrate species diversity. Possible explanations of the effects of macrophyte Delta on the invertebrate species diversity were the niche complementarity effect and the selection effect. This is the first study which demonstrates that macrophyte phylogenetic diversity has a strong effect on the species diversity of mobile epi-benthic invertebrates.

Practicality of diversion path analysis

International Nuclear Information System (INIS)

Murphey, W.M.; Schleter, J.C.

1974-07-01

One can define the safeguards system for nuclear material as the set of all protective actions taken to prevent or to deter attempts to divert nuclear material to unauthorized use. Maintenance of effective safeguards requires a program for routine assessment of plant safeguards systems in terms of their capabilities to satisfy safeguards aims. Plant internal control systems provide capabilities for detection of unprevented diversion and can provide assurance that diversion has not occurred. A procedure called Diversion Path Analysis (DPA) enables routine assessment of the capabilities of internal control systems in this regard and identification of safeguards problem areas in a plant. A framework for safeguards system design is also provided which will allow flexibility to accommodate individual plant circumstances while maintaining acceptable diversion detection capability. The steps of the procedure are described and the practicality of the analytical method is shown by referring to a demonstration test for a high throughput process where plant personnel were major participants. The boundary conditions for the demonstration case are given, along with some conclusions about the general procedure. (U.S.)

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.

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.

Impact of chloride on denitrification potential in roadside wetlands

International Nuclear Information System (INIS)

Lancaster, Nakita A.; Bushey, Joseph T.; Tobias, Craig R.; Song, Bongkeun; Vadas, Timothy M.

2016-01-01

Developed landscapes are exposed to changes in hydrology and water chemistry that limit their ability to mitigate detrimental impacts to coastal water bodies, particularly those that result from stormwater runoff. The elevated level of impervious cover increases not only runoff but also contaminant loading of nutrients, metals, and road salt used for deicing to water bodies. Here we investigate the impact that road salt has on denitrification in roadside environments. Sediments were collected from a series of forested and roadside wetlands and acclimated with a range of Cl − concentrations from 0 to 5000 mg L −1 for 96 h. Denitrification rates were measured by the isotope pairing technique using 15 N–NO 3 − , while denitrifying community structures were compared using terminal restriction fragment length polymorphism (T-RFLP) of nitrous oxide reductase genes (nosZ). Chloride significantly (p < 0.05) inhibited denitrification in forested wetlands at a Cl − dosage of 2500 or 5000 mg L −1 , but the decrease in denitrification rates was less and not significant for the roadside wetlands historically exposed to elevated concentrations of Cl − . The difference could not be attributed to other significant changes in conditions, such as DOC concentrations, N species concentrations, or pH levels. Denitrifying communities, as measured by T-RFs of the nosZ gene, in the roadside wetlands with elevated concentration of Cl − were distinctly different and more diverse compared to forested wetlands, and also different in roadside wetlands after 96 h exposures to Cl − . The shifts in denitrifying communities seem to minimize the decrease in denitrification rates in the wetlands previously exposed to Cl. As development results in more Cl − use and exposure to a broad range of natural or manmade wetland structures, an understanding of the seasonal effect of Cl on denitrification processes in these systems would aid in design or mitigation of the effects on

Effect of Plant Diversity on Diversity and Abundance of Arthropods in Winter Wheat Fields

Directory of Open Access Journals (Sweden)

A Khodashenas

2011-02-01

Full Text Available Abstract Plant biomass and diversity play an important role in enhancing of biodiversity of other trophic levels, specially arthropods in terrestrial ecosystems. In order to determine the effects of plants on diversity and abundance of arthropods, a study was carried out in three regions of Razavi and northern Khorasan provinces, Shirvan, Mashhad and Gonabad. In each region, high and low input fields of winter wheat and a natural system for comparison were selected. In ripening stage of wheat growth (90 stage of Zadoks, sampling was done by use of quadrate in each system with five replications. Plants in each quadrate were counted and species richness of plants was determined. Insect sampling was done by sweep net from surface of plants, then species richness and abundance of collected insects were determined. As a result, agricultural practices decreased plant species richness but diversity and abundance of insects and spiders increased in agricultural systems. Our finding revealed that abundance of insects and spiders were not affected by plant species richness and plant biomass was the main factor affecting on species richness and abundance of insects, spiders and beneficial insects. Therefore, decreasing plant species richness that arose from agricultural practices doesn’t effect on arthropods diversity and abundance and doesn’t decrease sustainability of agricultural systems. Irregular use of chemical inputs, specially pesticides, is the main factor to decreasing of plants and arthropods species richness in agricultural systems. Keywords: Plant diversity, Arthropod diversity, Arthropod abundance, Plant-insect interactions, Agricultural systems

A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

Directory of Open Access Journals (Sweden)

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

Construction of 1,3,4-Oxadiazole and 1,3,4-Thiadiazole Library with a High Level of Skeletal Diversity Based on Branching Diversity-Oriented Synthesis on Solid-Phase Supports.

Science.gov (United States)

Ha, Ji-Eun; Yang, Seung-Ju; Gong, Young-Dae

2018-02-12

An efficient solid-phase synthetic route for the construction of 1,3,4-oxadiazole and 1,3,4-thiadiazole libraries based on branching diversity-oriented synthesis (DOS) has been developed in this study. The core skeleton resins, 1,3,4-oxadiazole and 1,3,4-thiadiazole, were obtained through desulfurative and dehydrative cyclizations of thiosemicarbazide resin, respectively. Various functional groups have been introduced to the core skeleton resins, such as aryl, amine, amide, urea, thiourea, and an amino acid. Most of the libraries were purified by simple trituration without extraction or column chromatography after cleavage of the products from the solid-supported resin. As a result, we obtained high yields of pure 1,3,4-oxadiazole and 1,3,4-thiadiazole derivatives (total numbers = 128). Finally, we confirmed the drug-like properties of our library by calculation of physicochemical properties, displays of the skeletal diversities of the library in 3D-space, and occupation of a broad range of areas by their functional groups.

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...

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

Ethnic diversity and employment growth in English cities.

Science.gov (United States)

Lee, Neil

2011-01-01

There are many reasons why cities with diverse populations may grow faster. Ethnic diversity might attract human capital, tourists or firms, increase productivity through diverse approaches to problem-solving or ethnic minority entrepreneurship. Yet there are also reasons to believe that diversity could be harmful, by leading to sub-optimal provision of public goods or reducing trust or social capital. Or it may be irrelevant, being merely a proxy for class. A number of studies have shown both positive and negative relationships between diversity and growth, using a range of different measures for "diversity." This paper asks two questions: have more diverse English cities grown faster? And does measurement matter: is it important to have a multinational population or an ethnically diverse one? To answer these questions, in this paper a range of models are estimated for employment growth for 53 English cities between 1981 and 2001. The evidence suggests that cities with a high proportion of their populations born abroad in 1981 grew faster in the subsequent 10 years. Neither diversity by country of birth nor ethnic diversity is significant in the period 1991-2001. However, when variables accounting for both are included together, it appears that cities with a large number of migrants saw higher employment growth in the 1990s, but that ethnically diverse cities were less successful. The results presented here suggest that considerable attention needs to be paid to the variable used to indicate "diversity" in these studies and that the impact of diversity varies according to nature of the groups any indicator for "diversity" is representing.

Mapping global diversity patterns for migratory birds.

Directory of Open Access Journals (Sweden)

Marius Somveille

Full Text Available Nearly one in five bird species has separate breeding and overwintering distributions, and the regular migrations of these species cause a substantial seasonal redistribution of avian diversity across the world. However, despite its ecological importance, bird migration has been largely ignored in studies of global avian biodiversity, with few studies having addressed it from a macroecological perspective. Here, we analyse a dataset on the global distribution of the world's birds in order to examine global spatial patterns in the diversity of migratory species, including: the seasonal variation in overall species diversity due to migration; the contribution of migratory birds to local bird diversity; and the distribution of narrow-range and threatened migratory birds. Our analyses reveal a striking asymmetry between the Northern and Southern hemispheres, evident in all of the patterns investigated. The highest migratory bird diversity was found in the Northern Hemisphere, with high inter-continental turnover in species composition between breeding and non-breeding seasons, and extensive regions (at high latitudes where migratory birds constitute the majority of the local avifauna. Threatened migratory birds are concentrated mainly in Central and Southern Asia, whereas narrow-range migratory species are mainly found in Central America, the Himalayas and Patagonia. Overall, global patterns in the diversity of migratory birds indicate that bird migration is mainly a Northern Hemisphere phenomenon. The asymmetry between the Northern and Southern hemispheres could not have easily been predicted from the combined results of regional scale studies, highlighting the importance of a global perspective.

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.

Managing Workplace Diversity

Directory of Open Access Journals (Sweden)

Harold Andrew Patrick

2012-04-01

Full Text Available Diversity management is a process intended to create and maintain a positive work environment where the similarities and differences of individuals are valued. The literature on diversity management has mostly emphasized on organization culture; its impact on diversity openness; human resource management practices; institutional environments and organizational contexts to diversity-related pressures, expectations, requirements, and incentives; perceived practices and organizational outcomes related to managing employee diversity; and several other issues. The current study examines the potential barriers to workplace diversity and suggests strategies to enhance workplace diversity and inclusiveness. It is based on a survey of 300 IT employees. The study concludes that successfully managing diversity can lead to more committed, better satisfied, better performing employees and potentially better financial performance for an organization.

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

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.

Managing a culturally diverse workforce : Diversity perspectives in organizations

NARCIS (Netherlands)

Podsiadlowski, Astrid; Gröschke, Daniela; Kogler, Marina; Springer, Cornelia; van der Zee, Karen

The authors conducted two studies to analyze why and how organizations approach and manage cultural diversity in the Austrian workplace and to identify organizations' diversity perspectives. In Study 1, 29 interviews revealed insights into organizational approaches to diversity and how these

Teaching for Diversity: Addressing Diversity Issues in Responsive ESL Instruction

Science.gov (United States)

Fu, Jing

2013-01-01

Student diversity has become a typical phenomenon in American public schools. The impact of increasing diversity on literacy instruction is unchallenged. Teachers reinforce this message by often citing ESL student diversity as a barrier for literacy teaching. In order to better understand the complexity of diversity issues, I explored two ESL…

Relationship of subseafloor microbial diversity to sediment age and organic carbon content

Science.gov (United States)

Walsh, E. A.; Kirkpatrick, J. B.; Sogin, M. L.; D'Hondt, S. L.

2013-12-01

Our tag pyrosequencing investigation of four globally distant sites reveals sediment age and total organic carbon content to be significant components in understanding subseafloor diversity. Our sampling locations include two sites from high-productivity regions (Indian Ocean and Bering Sea) and two from moderate-productivity (eastern and central equatorial Pacific Ocean). Sediment from the high-productivity sites has much higher TOC than sediment from the moderate-productivity equatorial sites. We applied a high-resolution 16S V4-V6 tag pyrosequencing approach to 24 bacterial and 17 archaeal samples, totaling 602,502 reads. We identified1,291 archaeal and 15,910 bacterial OTUs (97%) from these reads. We analyzed bacterial samples from all four sites in addition to archaeal samples from our high productivity sites. These high productivity, high TOC sites have a pronounced methane-rich sulfate-free zone at depth from which archaea have been previously considered to dominate (Biddle et al., 2006). At all four locations, microbial diversity is highest near the seafloor and drops rapidly to low but stable values with increasing sediment depth. The depth at which diversity stabilizes varies greatly from site to site, but the age at which it stabilizes is relatively constant. At all four sites, diversity reaches low stable values a few hundred thousand years after sediment deposition. The sites with high total organic carbon (high productivity sites) generally exhibit higher diversity at each sediment age than the sites with lower total organic carbon (moderate-productivity sites). Archaeal diversity is lower than bacterial diversity at every sampled depth. Biddle, J.F., Lipp, J.S., Lever, M.A., Lloyd, K.G., Sørensen, K.B., Anderson, R. et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. PNAS 103: 3846-3851.

NASFAA Diversity and Inclusion: Recommendations of the Professional Diversity Caucus

Science.gov (United States)

National Association of Student Financial Aid Administrators, 2015

2015-01-01

NASFAA's Diversity and Inclusion Report emphasizes the importance of diversity and inclusivity to NASFAA. Included in this report is a diversity statement developed by NASFAA's Professional Diversity Caucus, and approved by NASFAA's Board in March of 2015. The Caucus convened in the summer of 2014 to better understand issues related to diversity…

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

Capturing the Diversity in Lexical Diversity

Science.gov (United States)

Jarvis, Scott

2013-01-01

The range, variety, or diversity of words found in learners' language use is believed to reflect the complexity of their vocabulary knowledge as well as the level of their language proficiency. Many indices of lexical diversity have been proposed, most of which involve statistical relationships between types and tokens, and which ultimately…

High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing.

Science.gov (United States)

Rahman, Abdur; Cailliez-Grimal, Catherine; Bontemps, Cyril; Payot, Sophie; Chaillou, Stéphane; Revol-Junelles, Anne-Marie; Borges, Frédéric

2014-07-01

Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Diversity Management

DEFF Research Database (Denmark)

Ravazzani, Silvia

2018-01-01

This entry provides an overview of diversity management which, in the context of organizations, consists in the strategic process of harnessing the potential of all employees to create an inclusive environment and, at the same time, contribute to meeting organizational goals. The entry first...... describes the complex construct of diversity that has been variously conceptualized in the literature, embracing multiple social and informational diversity dimensions such as gender, age, culture, values, and workstyle. This is followed by illustration of the historical development of diversity-management...... discourse and practice, and possible overarching approaches guiding organizations. It goes on to elucidate elements linked to the implementation of diversity management: positive and negative outcomes, most spread practices including communication, and contingency factors shaping the understanding...

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

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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.

Do inclusive leaders help to reduce turnover in diverse groups? The moderating role of leader-member exchange in the diversity to turnover relationship.

Science.gov (United States)

Nishii, Lisa H; Mayer, David M

2009-11-01

This research examines leader-member exchange (LMX) at the group level as a moderator of the relationships between demographic (i.e., race, age, gender) and tenure diversity and group turnover. Drawing primarily from LMX, social categorization, and expectation states theories, we hypothesized that through the pattern of LMX relationships that they develop with followers, group managers influence inclusion and status differentials within groups such that the positive relationship between diversity and group turnover will be weaker when the group mean on LMX is high or when group differentiation on LMX is low. Results from a sample of supermarket departments (N = 348) yielded general support for the study hypotheses. We also found evidence for a 3-way interaction involving demographic diversity, LMX mean, and LMX differentiation such that the interaction between demographic diversity and LMX differentiation was only significant when LMX mean was high. These findings highlight the important role that leaders play in influencing the relationship between diversity and turnover through the patterns of inclusion that they create in their units.

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

High genetic diversity among Mycobacterium tuberculosis strains in Tehran, Iran

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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

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.

Subgenomic Diversity Patterns Caused by Directional Selection in Bread Wheat Gene Pools

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Kai Voss-Fels

2015-07-01

Full Text Available Genetic diversity represents the fundamental key to breeding success, providing the basis for breeders to select varieties with constantly improving yield performance. On the other hand, strong selection during domestication and breeding have eliminated considerable genetic diversity in the breeding pools of major crops, causing erosion of genetic potential for adaptation to emerging challenges like climate change. High-throughput genomic technologies can address this dilemma by providing detailed knowledge to characterize and replenish genetic diversity in breeding programs. In hexaploid bread wheat ( L., the staple food for 35% of the world’s population, bottlenecks during allopolyploidisation followed by strong artificial selection have considerably narrowed diversity to the extent that yields in many regions appear to be unexpectedly stagnating. In this study, we used a 90,000 single nucleotide polymorphism (SNP wheat genotyping array to assay high-frequency, polymorphic SNP markers in 460 accessions representing different phenological diversity groups from Asian, Australian, European, and North American bread wheat breeding materials. Detailed analysis of subgroup diversity at the chromosome and subgenome scale revealed highly distinct patterns of conserved linkage disequilibrium between different gene pools. The data enable identification of genome regions in most need of rejuvenation with novel diversity and provide a high-resolution molecular basis for genomic-assisted introgression of new variation into chromosome segments surrounding directionally selected metaloci conferring important adaptation and quality traits.

Animal ecosystem engineers modulate the diversity-invasibility relationship.

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Nico Eisenhauer

Full Text Available Invasions of natural communities by non-indigenous species are currently rated as one of the most important global-scale threats to biodiversity. Biodiversity itself is known to reduce invasions and increase stability. Disturbances by ecosystem engineers affect the distribution, establishment, and abundance of species but this has been ignored in studies on diversity-invasibility relationships.We determined natural plant invasion into 46 plots varying in the number of plant species (1, 4, and 16 and plant functional groups (1, 2, 3, and 4 for three years beginning two years after the establishment of the Jena Experiment. We sampled subplots where earthworms were artificially added and others where earthworm abundance was reduced. We also performed a seed-dummy experiment to investigate the role of earthworms as secondary seed dispersers along a plant diversity gradient. Horizontal dispersal and burial of seed dummies were significantly reduced in subplots where earthworms were reduced in abundance. Seed dispersal by earthworms decreased with increasing plant species richness and presence of grasses but increased in presence of small herbs. These results suggest that dense vegetation inhibits the surface activity of earthworms. Further, there was a positive relationship between the number of earthworms and the number and diversity of invasive plants. Hence, earthworms decreased the stability of grassland communities against plant invasion.Invasibility decreased and stability increased with increasing plant diversity and, most remarkably, earthworms modulated the diversity-invasibility relationship. While the impacts of earthworms were unimportant in low diverse (low earthworm densities and high diverse (high floral structural complexity plant communities, earthworms decreased the stability of intermediate diverse plant communities against plant invasion. Overall, the results document that fundamental processes in plant communities like plant seed

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...

Rethinking Diversity.

Science.gov (United States)

1996

These three papers were presented at a symposium on rethinking diversity in human resource development (HRD) moderated by Neal Chalofsky at the 1996 conference of the Academy of Human Resource Development. "Diversity: A Double-Edged Sword" (Sally F. Angus) presents the notion of work force diversity through two differing perspectives in order to…

Organizational strategy and diversity management: diversity-sensitive orientation as a moderating influence.

Science.gov (United States)

Dansky, Kathryn H; Weech-Maldonado, Robert; De Souza, Gita; Dreachslin, Janice L

2003-01-01

Empirical studies on diversity suggest that health care organizations have been slow to embrace diversity management. We propose that sensitivity to diversity, at the corporate level, moderates strategic decision making, which influences human resource management practices such as diversity initiatives. This study of 203 hospitals explored the relationships among organizational strategy, organizational sensitivity to diversity, and diversity management practices.

An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation

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Suzanne L. Ishaq

2017-10-01

Full Text Available Sub-acute ruminal acidosis (SARA is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs but not diversity (Inverse Simpson, Shannon, but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05 affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction for protozoa

Genetic diversity of endangered populations of Butia capitata ...

African Journals Online (AJOL)

The flora and fauna of the Cerrado biome in central Brazil both show great diversity and high levels of endemism. Butia capitata is a palm native to this biome that has significant economic, social, and environmental value. We sought to identify and quantify the genetic diversity of four fragmented populations of B. capitata ...

The diversity of Klebsiella pneumoniae surface polysaccharides.

Science.gov (United States)

Follador, Rainer; Heinz, Eva; Wyres, Kelly L; Ellington, Matthew J; Kowarik, Michael; Holt, Kathryn E; Thomson, Nicholas R

2016-08-01

Klebsiella pneumoniae is considered an urgent health concern due to the emergence of multi-drug-resistant strains for which vaccination offers a potential remedy. Vaccines based on surface polysaccharides are highly promising but need to address the high diversity of surface-exposed polysaccharides, synthesized as O-antigens (lipopolysaccharide, LPS) and K-antigens (capsule polysaccharide, CPS), present in K. pneumoniae . We present a comprehensive and clinically relevant study of the diversity of O- and K-antigen biosynthesis gene clusters across a global collection of over 500 K. pneumoniae whole-genome sequences and the seroepidemiology of human isolates from different infection types. Our study defines the genetic diversity of O- and K-antigen biosynthesis cluster sequences across this collection, identifying sequences for known serotypes as well as identifying novel LPS and CPS gene clusters found in circulating contemporary isolates. Serotypes O1, O2 and O3 were most prevalent in our sample set, accounting for approximately 80 % of all infections. In contrast, K serotypes showed an order of magnitude higher diversity and differ among infection types. In addition we investigated a potential association of O or K serotypes with phylogenetic lineage, infection type and the presence of known virulence genes. K1 and K2 serotypes, which are associated with hypervirulent K. pneumoniae , were associated with a higher abundance of virulence genes and more diverse O serotypes compared to other common K serotypes.

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

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

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Flávio de Oliveira Francisco

2013-01-01

Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

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...

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity.

Science.gov (United States)

Jurasinski, Gerald; Retzer, Vroni; Beierkuhnlein, Carl

2009-02-01

Almost half a century after Whittaker (Ecol Monogr 30:279-338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative--depending on the organism(s) or ecosystems investigated--this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term "inventory diversity." Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness ("key concept" vs. "abstruse concept"). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, "differentiation diversity" (first group) and "proportional diversity" (second group). Thus, we propose to use the terms "inventory diversity" for within-sample diversity, "differentiation diversity" for compositional similarity between samples, and "proportional diversity" for the

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.