WorldWideScience

Sample records for heterotrophic bacterial communities

  1. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

    Science.gov (United States)

    Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

    2017-12-01

    Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ( 3 H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the

  2. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... decrease after mercury addition but then slowly increasing throughout the entire experimental period. Pre-exposure levels were not reached within the time span of this investigation. The DGGE band pattern indicated that a shift in the community structure was responsible for recovered diversity. When...

  3. Bacterial abundance, communities and heterotrophic activities in the coastal waters off Tamil Nadu

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Raghukumar, C.; Sheelu, G.; Chandramohan, D.

    Culturable aerobic heterotrophic bacterial (CAHB) numbers, total direct counts (TDC), bacterial generic composition and uptake of labelled glucose by natural microbial assemblages were studied from a few selected coastal sites off Tamil Nadu. A high...

  4. Factors limiting heterotrophic bacterial production in the southern Pacific Ocean

    Directory of Open Access Journals (Sweden)

    F. Van Wambeke

    2008-05-01

    Full Text Available The role of potential factors limiting bacterial growth was investigated along vertical and longitudinal gradients across the South Eastern Pacific Gyre. The effects of glucose, nitrate, ammonium and phosphate additions on heterotrophic bacterial production (using leucine technique were studied in parallel in unfiltered seawater samples incubated under natural daily irradiance. The enrichments realized on the subsurface showed three types of responses. From 141° W (Marquesas plateau to approx 125° W, bacteria were not bottom-up controlled, as confirmed by the huge potential of growth in non-enriched seawater (median of enhancement factor×39 in 24 h. Within the Gyre (125° W–95° W, nitrogen alone stimulated leucine incorporation rates (median×4.2, but rapidly labile carbon (glucose became a second limiting factor (median×37 when the two elements were added. Finally from the border of the gyre to the Chilean upwelling (95° W–73° W, labile carbon was the only factor stimulating heterotrophic bacterial production. Interaction between phytoplankton and heterotrophic bacterial communities and the direct versus indirect effect of iron and macronutrients on bacterial production were also investigated in four selected sites: two sites on the vicinity of the Marquesas plateau, the centre of the gyre and the Eastern border of the gyre. Both phytoplankton and heterotrophic bacteria were limited by availability of nitrogen within the gyre, but not by iron. Iron limited phytoplankton at Marquesas plateau and at the eastern border of the gyre. However 48 h enrichment experiments were not sufficient to show any clear limitation of heterotrophic bacteria within Marquesas plateau and showed a limitation of these organisms by labile carbon in the eastern border of the Gyre.

  5. Heterotrophic bacterial populations in tropical sandy beaches

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, S.; LokaBharathi, P.A.

    Distribution pattern of heterotrophic bacterial flora of three sandy beaches of the west coast of India was studied. The population in these beaches was microbiologically different. Population peaks of halotolerant and limnotolerant forms were...

  6. Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae.

    Directory of Open Access Journals (Sweden)

    Ana Patrícia Graça

    Full Text Available Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA, Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus, fish pathogen (Aliivibrio fischeri and environmentally relevant bacteria (Vibrio harveyi. The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%, Vibrio (22.7% and Bacillus (7.6%. Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I and nonribosomal peptide synthetases (NRPSs genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds.

  7. Heterotrophic free-living and particle-bound bacterial cell size in the ...

    Indian Academy of Sciences (India)

    PRAKASH

    the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible ... seasonal changes in abundance and cell size of heterotrophic ... data, 1995) physiological stress indicated by the presence of small ...

  8. Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

    Science.gov (United States)

    Van Wambeke, France; Pfreundt, Ulrike; Barani, Aude; Berthelot, Hugo; Moutin, Thierry; Rodier, Martine; Hess, Wolfgang R.; Bonnet, Sophie

    2016-06-01

    experiments, suggesting N-limitation of heterotrophic bacteria across the experiment. N2 fixation rates corresponded to 17-37 % of the nitrogen demand of heterotrophic bacteria. Our results suggest that most of the diazotroph-derived nitrogen fuelled the heterotrophic bacterial community through indirect processes generating dissolved organic matter and detritus, like mortality, lysis and grazing of both diazotrophs and non-diazotrophs.

  9. The impact of shrimp farming effluent on bacterial communities in mangrove waters, Ceará, Brazil.

    Science.gov (United States)

    Sousa, O V; Macrae, A; Menezes, F G R; Gomes, N C M; Vieira, R H S F; Mendonça-Hagler, L C S

    2006-12-01

    The effects of shrimp farm effluents on bacterial communities in mangroves have been infrequently reported. Classic and molecular biology methods were used to survey bacterial communities from four mangroves systems. Water temperature, salinity, pH, total heterotrophic bacteria and maximum probable numbers of Vibrio spp. were investigated. Genetic profiles of bacterial communities were also characterized by polymerase chain reaction (PCR) amplification of eubacterial and Vibrio 16S rDNA using denaturing gradient gel electrophoresis (DGGE). Highest heterotrophic counts were registered in the mangrove not directly polluted by shrimp farming. The Enterobacteriaceae and Chryseomonas luteola dominated the heterotrophic isolates. Vibrio spp. pathogenic to humans and shrimps were identified. Eubacterial genetic profiles suggest a shared community structure independent of mangrove system. Vibrio genetic profiles were mangrove specific. Neither microbial counts nor genetic profiling revealed a significant decrease in species richness associated with shrimp farm effluent. The complex nature of mangrove ecosystems and their microbial communities is discussed.

  10. The Heterotrophic Bacterial Response During the Meso-scale Southern Ocean Iron Experiment (SOFeX)

    Science.gov (United States)

    Oliver, J. L.; Barber, R. T.; Ducklow, H. W.

    2002-12-01

    Previous meso-scale iron enrichments have demonstrated the stimulatory effect of iron on primary productivity and the accelerated flow of carbon into the surface ocean foodweb. In stratified waters, heterotrophic activity can work against carbon export by remineralizing POC and/or DOC back to CO2, effectively slowing the biological pump. To assess the response of heterotrophic activity to iron enrichment, we measured heterotrophic bacterial production and abundance during the Southern Ocean Iron Experiment (SOFeX). Heterotrophic bacterial processes primarily affect the latter of the two carbon export mechanisms, removal of DOC to the deep ocean. Heterotrophic bacterial production (BP), measured via tritiated thymidine (3H-TdR) and leucine (3H-Leu) incorporation, increased ~40% over the 18-d observation period in iron fertilized waters south of the Polar Front (South Patch). Also, South Patch BP was 61% higher than in the surrounding unfertilized waters. Abundance, measured by flow cytometry (FCM) and acridine orange direct counts (AODC), also increased in the South Patch from 3 to 5 x 108 cells liter-1, a 70% increase. Bacterial biomass increased from ~3.6 to 6.3 μg C liter-1, a clear indication that production rates exceeded removal rates (bactivory, viral lysis) over the course of 18 days. Biomass within the fertilized patch was 11% higher than in surrounding unfertilized waters reflecting a similar trend. This pattern is in contrast to SOIREE where no accumulation of biomass was observed. High DNA-containing (HDNA) cells detected by FCM also increased over time in iron fertilized waters from 20% to 46% relative to the total population suggesting an active subpopulation of cells that were growing faster than the removal rates. In iron fertilized waters north of the Polar Front (North Patch), BP and abundance were ~90% and 80% higher, respectively, than in unfertilized waters. Our results suggest an active bacterial population that responded to iron fertilization

  11. Bacterial biomass and heterotrophic potential in the waters of the Chesapeake Bay plume and contiguous continental shelf

    Science.gov (United States)

    Kator, H. I.; Zubkoff, P. L.

    1981-01-01

    Seasonal baseline data on bacterial biomass and heterotrophic uptake in the Chesapeake Bay plume and contiguous Atlantic Ocean shelf waters are discussed. Viable count bacterial numbers in surface water samples collected during June 1980 ranged from a maximum of 190,000 MPN (most probable number)/ml at the Bay mouth to a minimum of 7900 MPN/ml offshore. Similarly, direct count densities ranged from 1,800,000 BU (bacterial units)/ml to 24,000 BU/ml. Heterotrophic potential (V max) was largest at the Bay mouth and lowest offshore. Biomass and V max values usually decreased with depth although subsurface maxima were occasionally observed at inshore stations. Correlation of biomass and heterotrophic potential data with selected hydrographic variables was determind with a nonparametric statistic. Results indicate viable counts are positively and significantly correlated with total chlorophyll, temperature, direct count and V max during June 1980; significant negative correlations are obtained with salinity and depth. Calculations of bacterial standing crop are discussed.

  12. Studies on mangrove swamps of Goa 1. Heterotrophic bacterial flora from mangrove swamps

    Digital Repository Service at National Institute of Oceanography (India)

    Matondkar, S.G.P; Mathani, S; Mavinkurve, S

    Heterotrophic bacterial flora from the mangrove swamps of Goa consisted of physiologically active organisms exhibiting cellulolytic, pectinolytic, amylolytic, proteolytic and H2S forming activities, throughout the year. Coryneform and Bacillus were...

  13. Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

    KAUST Repository

    Tian, Ren-Mao

    2014-01-01

    Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2\\',4,4\\'-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.

  14. Biodiversity of culturable heterotrophic bacteria in the Southern Adriatic Sea Italian coastal waters

    Directory of Open Access Journals (Sweden)

    Loredana Stabili

    2004-04-01

    Full Text Available The qualitative and quantitative composition of culturable heterotrophic bacteria in water samples from the Southern Adriatic Sea of Italy was examined. Water samples were collected monthly, for a year, at 16 stations along the coast line between Brindisi and Santa Maria di Leuca. The results obtained described the heterotrophic bacterial community over an annual cycle. Mean values of bacterial densities were 5.3 x 104 CFUml-1 in Brindisi, 5.8 x 104 CFUml-1 in S. Cataldo, 4.3 x 104 CFUml-1 in Otranto and 6.7 x 104 CFUml-1 in S. M. di Leuca. The differences in bacterial densities between the sites considered were estimated. The hydrodynamic circulation, the trophism and the geographical position of the examined sites contribute to justify the different bacterial density trends. The bacterial community consisted mainly of the genera Aeromonas, Pseudomonas, Photobacterium and Flavobacterium. The Enterobacteriaceae represented a considerable fraction of the bacterial community in the Southern Adriatic Sea. Bacilli were predominant among the Gram positive bacteria. The enzymatic versatility of the observed genera suggest their importance in organic matter turnover of this oligotrophic ecosystem.

  15. Dynamics of pollution-indicator and heterotrophic bacteria in sewage treatment lagoons.

    OpenAIRE

    Legendre, P; Baleux, B; Troussellier, M

    1984-01-01

    The spatio-temporal dynamics of pollution-indicator bacteria and aerobic heterotrophic bacteria were studied in the sewage treatment lagoons of an urban wastewater center after 26 months of biweekly sampling at eight stations in these lagoons. Robust statistical methods of time-series analysis were used to study successional steps (through chronological clustering) and rhythmic behavior through time (through contingency periodogram). The aerobic heterotrophic bacterial community showed two ty...

  16. The Response of Heterotrophic Prokaryote and Viral Communities to Labile Organic Carbon Inputs Is Controlled by the Predator Food Chain Structure.

    Science.gov (United States)

    Sandaa, Ruth-Anne; Pree, Bernadette; Larsen, Aud; Våge, Selina; Töpper, Birte; Töpper, Joachim P; Thyrhaug, Runar; Thingstad, Tron Frede

    2017-08-23

    Factors controlling the community composition of marine heterotrophic prokaryotes include organic-C, mineral nutrients, predation, and viral lysis. Two mesocosm experiments, performed at an Arctic location and bottom-up manipulated with organic-C, had very different results in community composition for both prokaryotes and viruses. Previously, we showed how a simple mathematical model could reproduce food web level dynamics observed in these mesocosms, demonstrating strong top-down control through the predator chain from copepods via ciliates and heterotrophic nanoflagellates. Here, we use a steady-state analysis to connect ciliate biomass to bacterial carbon demand. This gives a coupling of top-down and bottom-up factors whereby low initial densities of ciliates are associated with mineral nutrient-limited heterotrophic prokaryotes that do not respond to external supply of labile organic-C. In contrast, high initial densities of ciliates give carbon-limited growth and high responsiveness to organic-C. The differences observed in ciliate abundance, and in prokaryote abundance and community composition in the two experiments were in accordance with these predictions. Responsiveness in the viral community followed a pattern similar to that of prokaryotes. Our study provides a unique link between the structure of the predator chain in the microbial food web and viral abundance and diversity.

  17. Regulation of annual variation in heterotrophic bacterial production in the Schelde estuary (SW Netherlands)

    NARCIS (Netherlands)

    Goosen, N.K.; Van Rijswijk, P.; Kromkamp, J.C.; Peene, J.

    1997-01-01

    Heterotrophic bacterioplankton production (H-3-thymidine incorporation rate) and abundance in the surface water of the Schelde estuary (The Netherlands) were studied during an annual cycle in 1991 along the salinity gradient (0.8 to 33 psu). Bacterial production and numbers increased from the lower

  18. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

    Science.gov (United States)

    Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

    2017-06-01

    While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Bacterial communities in the collection and chlorinated distribution sections of a drinking water system in Budapest, Hungary.

    Science.gov (United States)

    Homonnay, Zalán G; Török, György; Makk, Judit; Brumbauer, Anikó; Major, Eva; Márialigeti, Károly; Tóth, Erika

    2014-07-01

    Bacterial communities of a bank-filtered drinking water system were investigated by aerobic cultivation and clone library analysis. Moreover, bacterial communities were compared using sequence-aided terminal restriction fragment length polymorphism (T-RFLP) fingerprinting at ten characteristic points located at both the collecting and the distributing part of the water supply system. Chemical characteristics of the samples were similar, except for the presence of chlorine residuals in the distribution system and increased total iron concentration in two of the samples. Assimilable organic carbon (AOC) concentration increased within the collection system, it was reduced by chlorination and it increased again in the distribution system. Neither fecal indicators nor pathogens were detected by standard cultivation techniques. Chlorination reduced bacterial diversity and heterotrophic plate counts. Community structures were found to be significantly different before and after chlorination: the diverse communities in wells and the collection system were dominated by chemolithotrophic (e.g., Gallionella and Nitrospira) and oligocarbophilic-heterotrophic bacteria (e.g., Sphingomonas, Sphingopyxis, and Bradyrhizobium). After chlorination in the distribution system, the most characteristic bacterium was related to the facultative methylotrophic Methylocella spp. Communities changed within the distribution system too, Mycobacterium spp. or Sphingopyxis spp. became predominant in certain samples. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Characterization of culturable heterotrophic bacteria in hydrocarbon-contaminated soil from an alpine former military site.

    Science.gov (United States)

    Zhang, Dechao; Margesin, Rosa

    2014-06-01

    We characterized the culturable, heterotrophic bacterial community in soil collected from a former alpine military site contaminated with petroleum hydrocarbons. The physiologically active eubacterial community, as revealed by fluorescence-in situ-hybridization, accounted for 14.9 % of the total (DAPI-stained) bacterial community. 4.0 and 1.2 % of the DAPI-stained cells could be attributed to culturable, heterotrophic bacteria able to grow at 20 and 10 °C, respectively. The majority of culturable bacterial isolates (23/28 strains) belonged to the Proteobacteria with a predominance of Alphaproteobacteria. The remaining isolates were affiliated with the Firmicutes, Actinobacteria and Bacteroidetes. Five strains could be identified as representatives of novel species. Characterization of the 28 strains demonstrated their adaptation to the temperature and nutrient conditions prevailing in the studied soil. One-third of the strains was able to grow at subzero temperatures (-5 °C). Studies on the effect of temperature on growth and lipase production with two selected strains demonstrated their low-temperature adaptation.

  1. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert.

    Science.gov (United States)

    Řeháková, Klára; Chroňáková, Alica; Krištůfek, Václav; Kuchtová, Barbora; Čapková, Kateřina; Scharfen, Josef; Čapek, Petr; Doležal, Jiří

    2015-01-01

    Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies, and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m), in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters) on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter, and Paenibacillus, representing both r- and K-strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850-5000 m) and frost at the highest elevations (5750-5850 m). The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant T. ceaspitosum in a xeric environment and brings important information about

  2. Membrane biofouling in a wastewater nitrification reactor: microbial succession from autotrophic colonization to heterotrophic domination

    KAUST Repository

    Lu, Huijie

    2015-10-22

    Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles.

  3. Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination.

    Science.gov (United States)

    Lu, Huijie; Xue, Zheng; Saikaly, Pascal; Nunes, Suzana P; Bluver, Ted R; Liu, Wen-Tso

    2016-01-01

    Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles. Copyright © 2015 Elsevier Ltd. All

  4. Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring

    KAUST Repository

    Van Nevel, S.

    2017-02-08

    Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.

  5. Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring

    KAUST Repository

    Van Nevel, S.; Koetzsch, S.; Proctor, C.R.; Besmer, M.D.; Prest, E.I.; Vrouwenvelder, Johannes S.; Knezev, A.; Boon, N.; Hammes, F.

    2017-01-01

    Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.

  6. Growth strategy of heterotrophic bacterial population along successional sequence on spoil of brown coal colliery substrate

    Czech Academy of Sciences Publication Activity Database

    Krištůfek, Václav; Elhottová, Dana; Chroňáková, Alica; Dostálková, I.; Picek, T.; Kalčík, Jiří

    2005-01-01

    Roč. 50, č. 5 (2005), s. 427-435 ISSN 0015-5632 R&D Projects: GA ČR(CZ) GA526/03/1259 Institutional research plan: CEZ:AV0Z60660521 Keywords : growth strategy * heterotrophic bacterial population * brown coal colliery spoil Subject RIV: EH - Ecology, Behaviour Impact factor: 0.918, year: 2005

  7. Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

    KAUST Repository

    Tian, R.-M.

    2014-11-04

    Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. IMPORTANCE This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper

  8. Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

    Science.gov (United States)

    Bagatini, Inessa Lacativa; Eiler, Alexander; Bertilsson, Stefan; Klaveness, Dag; Tessarolli, Letícia Piton; Vieira, Armando Augusto Henriques

    2014-01-01

    Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways. PMID:24465807

  9. Light structures phototroph, bacterial and fungal communities at the soil surface.

    Directory of Open Access Journals (Sweden)

    Lawrence O Davies

    Full Text Available The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm and bulk soil (3-12 mm using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

  10. Bacterial community analysis of contaminant soils from Chernobyl

    International Nuclear Information System (INIS)

    Sergeant, C.; Vesvres, M.H.; Chapon, V.; Berthomieu, C.; Piette, L.; Le Marrec, C.; Coppin, F.; Fevrier, L.; Martin-Garin, A.

    2010-01-01

    Complete text of publication follows: Shortly after the Chernobyl accident in 1986, vegetation, contaminated soil and other radioactive debris were buried in situ in trenches. The aims of this work are to analyse the structure of bacterial communities evolving in this environment since 20 years, and to evaluate the potential role of microorganisms in radionuclide migration in soils. Therefore, soil samples exhibiting contrasted radionuclides content were collected in and around the trench number 22. Bacterial communities were examined using a genetic fingerprinting method that allowed a comparative profiling of the samples (DGGE), with universal and group-specific PCR primers. Our results indicate that Chernobyl soil samples host a wide diversity of Bacteria, with stable patterns for Firmicutes and Actinobacteria and more variable for Proteobacteria. A collection of 650 aerobic and anaerobic culturable isolates was also constructed. A phylogenetic analysis of 250 heterotrophic aerobic isolates revealed that 5 phyla are represented: Beta-, Gamma-proteobacteria, Actinobacteria, Bacteroidetes and spore-forming Firmicutes, which is largely dominant. These collection will be screened for the presence of radionuclide-accumulating species in order to estimate the potential influence of microorganisms in radionuclides migration in soils

  11. Rapid bacterial mineralization of organic carbon produced during a phytoplankton bloom induced by natural iron fertilization in the Southern Ocean

    Science.gov (United States)

    Obernosterer, Ingrid; Christaki, Urania; Lefèvre, Dominique; Catala, Philippe; Van Wambeke, France; Lebaron, Philippe

    2008-03-01

    The response of heterotrophic bacteria ( Bacteria and Archaea) to the spring phytoplankton bloom that occurs annually above the Kerguelen Plateau (Southern Ocean) due to natural iron fertilization was investigated during the KErguelen Ocean and Plateau compared Study (KEOPS) cruise in January-February 2005. In surface waters (upper 100 m) in the core of the phytoplankton bloom, heterotrophic bacteria were, on an average, 3-fold more abundant and revealed rates of production ([ 3H] leucine incorporation) and respiration (bacterial metabolic activities were attributable to high-nucleic-acid-containing cells that dominated (≈80% of total cell abundance) the heterotrophic bacterial community associated with the phytoplankton bloom. Bacterial growth efficiencies varied between 14% and 20% inside the bloom and were bacterial activity, due to the stimulation by phytoplankton-derived dissolved organic matter. Within the Kerguelen bloom, bacterial carbon demand accounted for roughly 45% of gross community production. These results indicate that heterotrophic bacteria processed a significant portion of primary production, with most of it being rapidly respired.

  12. Negative consequences of glacial turbidity for the survival of freshwater planktonic heterotrophic flagellates.

    Science.gov (United States)

    Sommaruga, Ruben; Kandolf, Georg

    2014-02-17

    Heterotrophic (phagotrophic) flagellates are key components of planktonic food webs in freshwater and marine ecosystems because they are the main consumers of bacteria. Although they are ubiquitous in aquatic ecosystems, they were numerically undetectable in turbid glacier-fed lakes. Here we show that glacial particles had negative effects on the survival and growth of heterotrophic flagellates. The effect of glacial particles was concentration-dependent and was caused by their interference with bacterial uptake rather than by physical damage. These results are the first to reveal why establishment of heterotrophic flagellates populations is hindered in very turbid glacial lakes. Because glaciers are vanishing around the world, recently formed turbid meltwater lakes represent an excellent opportunity to understand the environmental conditions that probably shaped the establishment of lake communities at the end of the last glaciation.

  13. Succession of Bacterial Communities in a Seasonally Stratified Lake with an Anoxic and Sulfidic Hypolimnion

    Directory of Open Access Journals (Sweden)

    Muhe Diao

    2017-12-01

    Full Text Available Although bacteria play key roles in aquatic food webs and biogeochemical cycles, information on the seasonal succession of bacterial communities in lakes is still far from complete. Here, we report results of an integrative study on the successional trajectories of bacterial communities in a seasonally stratified lake with an anoxic hypolimnion. The bacterial community composition of epilimnion, metalimnion, and hypolimnion diverged during summer stratification and converged when the lake was mixed. In contrast, bacterial communities in the sediment remained relatively stable over the year. Phototrophic Cyanobacteria and heterotrophic Actinobacteria, Alphaproteobacteria and Planktomycetes were abundant in the aerobic epilimnion, Gammaproteobacteria (mainly Chromatiaceae dominated in the metalimnion, and Chlorobi, Betaproteobacteria, Deltaproteobacteria, and Firmicutes were abundant in the anoxic sulfidic hypolimnion. Anoxic but nonsulfidic conditions expanded to the surface layer during fall turnover, when the epilimnion, metalimnion and upper hypolimnion mixed. During this period, phototrophic sulfur bacteria (Chromatiaceae and Chlorobi disappeared, Polynucleobacter (Betaproteobacteria and Methylobacter (Gammaproteobacteria spread out from the former meta- and hypolimnion to the surface layer, and Epsilonproteobacteria dominated in the bottom water layer. Cyanobacteria and Planktomycetes regained dominance in early spring, after the oxygen concentration was restored by winter mixing. In total, these results show large spatio-temporal changes in bacterial community composition, especially during transitions from oxic to anoxic and from sulfidic to nonsulfidic conditions.

  14. Dynamics of pollution-indicator and heterotrophic bacteria in sewage treatment lagoons.

    Science.gov (United States)

    Legendre, P; Baleux, B; Troussellier, M

    1984-09-01

    The spatio-temporal dynamics of pollution-indicator bacteria and aerobic heterotrophic bacteria were studied in the sewage treatment lagoons of an urban wastewater center after 26 months of biweekly sampling at eight stations in these lagoons. Robust statistical methods of time-series analysis were used to study successional steps (through chronological clustering) and rhythmic behavior through time (through contingency periodogram). The aerobic heterotrophic bacterial community showed two types of temporal evolution: in the first four stations, it seems mainly controlled by the nutrient support capacity of the sewage input, whereas in the remaining part of the lagoon, it seems likely that the pollution-indicator bacteria are gradually replaced by other bacterial types that are better adapted to this environment. On the other hand, the pollution-indicator bacteria showed an annual cycle which increased in amplitude at distances further from the wastewater source. The main events in this cycle were produced simultaneously at all stations, indicating control of these bacterial populations by climatic factors, which act through physical and chemical factors, and also through other biological components of this ecosystem (phytoplankton and zooplankton). Finally, we use results from this study to suggest a modified design for a future study program.

  15. Nitrogen removal capacity and bacterial community dynamics of a Canon biofilter system at different organic matter concentrations.

    Science.gov (United States)

    García-Ruiz, María J; Maza-Márquez, Paula; González-López, Jesús; Osorio, Francisco

    2018-02-01

    Three Canon bench-scale bioreactors with a volume of 2 L operating in parallel were configured as submerged biofilters. In the present study we investigated the effects of a high ammonium concentration (320 mgNH 4 + · L -1 ) and different concentrations of organic matter (0, 100 and 400 mgCOD·L -1 ) on the nitrogen removal capacity and the bacterial community structure. After 60 days, the Canon biofilters operated properly under concentrations of 0 and 100 mgCOD·L -1 of organic matter, with nitrogen removal efficiencies up to 85%. However, a higher concentration of organic matter (400 mgCOD·L -1 ) produced a partial inhibition of nitrogen removal (68.1% efficiency). The addition of higher concentrations of organic matter a modified the bacterial community structure in the Canon biofilter, increasing the proliferation of heterotrophic bacteria related to the genera of Thauera, Longilinea, Ornatilinea, Thermomarinilinea, unclassified Chlorobiales and Denitratisoma. However, heterotrophic bacteria co-exist with Nitrosomonas and Candidatus Scalindua. Thus, our study confirms the co-existence of different microbial activities (AOB, Anammox and denitrification) and the adaptation of a fixed-biofilm system to different concentrations of organic matter. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand.

    Science.gov (United States)

    Secker, Nick H; Chua, Jocelyn P S; Laurie, Rebecca E; McNoe, Les; Guy, Paul L; Orlovich, David A; Summerfield, Tina C

    2016-10-01

    New Zealand ephemeral wetlands are ecologically important, containing up to 12% of threatened native plant species and frequently exhibiting conspicuous cyanobacterial growth. In such environments, cyanobacteria and associated heterotrophs can influence primary production and nutrient cycling. Wetland communities, including bacteria, can be altered by increased nitrate and phosphate due to agricultural practices. We have characterized cyanobacteria from the Wairepo Kettleholes Conservation Area and their associated bacteria. Use of 16S rRNA amplicon sequencing identified several operational taxonomic units (OTUs) representing filamentous heterocystous and non-heterocystous cyanobacterial taxa. One Nostoc OTU that formed macroscopic colonies dominated the cyanobacterial community. A diverse bacterial community was associated with the Nostoc colonies, including a core microbiome of 39 OTUs. Identity of the core microbiome associated with macroscopic Nostoc colonies was not changed by the addition of nutrients. One OTU was highly represented in all Nostoc colonies (27.6%-42.6% of reads) and phylogenetic analyses identified this OTU as belonging to the genus Sphingomonas. Scanning electron microscopy showed the absence of heterotrophic bacteria within the Nostoc colony but revealed a diverse community associated with the colonies on the external surface. © 2016 Phycological Society of America.

  17. Distinct responses of bacterial communities to agricultural and urban impacts in temperate southern African estuaries

    Science.gov (United States)

    Matcher, G. F.; Froneman, P. W.; Meiklejohn, I.; Dorrington, R. A.

    2018-01-01

    Worldwide, estuaries are regarded as amongst the most ecologically threatened ecosystems and are increasingly being impacted by urban development, agricultural activities and reduced freshwater inflow. In this study, we examined the influence of different human activities on the diversity and structure of bacterial communities in the water column and sediment in three distinct, temperate permanently open estuarine systems within the same geographic region of southern Africa. The Kariega system is freshwater-deprived and is considered to be relatively pristine; the Kowie estuary is marine-dominated and impacted by urban development, while the Sundays system is fresh-water dominated and impacted by agricultural activity in its catchment. The bacterial communities in all three systems comprise predominantly heterotrophic species belonging to the Bacteroidetes and Proteobacteria phyla with little overlap between bacterioplankton and benthic bacterial communities at the species level. There was overlap between the operational taxonomic units (OTUs) of the Kowie and Kariega, both marine-influenced estuaries. However, lower species richness in the Kowie, likely reflects the impact of human settlements along the estuary. The dominant OTUs in the Sundays River system were distinct from those of the Kariega and Kowie estuaries with an overall decrease in species richness and evenness. This study provides an important snapshot into the microbial population structures of permanently open temperate estuarine systems and the influence of anthropogenic impacts on bacterial diversity and community structure.

  18. Decreases in average bacterial community rRNA operon copy number during succession.

    Science.gov (United States)

    Nemergut, Diana R; Knelman, Joseph E; Ferrenberg, Scott; Bilinski, Teresa; Melbourne, Brett; Jiang, Lin; Violle, Cyrille; Darcy, John L; Prest, Tiffany; Schmidt, Steven K; Townsend, Alan R

    2016-05-01

    Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

  19. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming.

    Directory of Open Access Journals (Sweden)

    Stephen Gang Wu

    2016-04-01

    Full Text Available 13C metabolic flux analysis (13C-MFA has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM, k-Nearest Neighbors (k-NN, and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species.

  20. Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity.

    Science.gov (United States)

    Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

    2018-01-01

    Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile

  1. Microbial pollution indicators and culturable heterotrophic bacteria in a Mediterranean area (Southern Adriatic Sea Italian coasts)

    Science.gov (United States)

    Stabili, L.; Cavallo, R. A.

    2011-05-01

    In the present study we evaluated the degree of microbial water pollution along the coast line between Brindisi and Santa Maria di Leuca (Southern Adriatic Sea) as well as the culturable heterotrophic bacteria abundances and biodiversity in relation to the microbiological quality of the water. A total of 3773 colonies were isolated, subcultured and identified by several morphological, cultural and biochemical methods including the standardized API 20 E and API 20 NE tests. Along the examined coastal tract the microbial pollution indicators were always below the tolerance limits for bathing waters defined by the CEE directive, suggesting a good sanitary quality. Concerning culturable heterotrophic bacteria, different temporal density trends were observed in the four sites in relation to their geographical position. A positive relationship between the bacterial abundances and the temperature was observed in S. Cataldo and Otranto. The culturable bacterial community was mainly composed of the genera Aeromonas, Pseudomonas, Photobacterium and Flavobacterium. The Enterobacteriaceae family represented a conspicuous component of the bacterial community too. Bacilli were predominant among the Gram-positive bacteria. Of interest is the isolation of yeasts (2% at the surface and 1% at the bottom) taking into account their capability of biodegradation of various materials. Because of the low level of microbial pollution recorded, our results are indicative of the natural variation and diversity of the culturable bacterial community in such an oligotrophic ecosystem and could represent a good point of comparison with other ecosystems as well as a baseline for long term studies aimed to evaluate the effects of environmental fluctuations and human impacts on this aspect of biodiversity in coastal areas.

  2. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments.

    Directory of Open Access Journals (Sweden)

    Xuexia Jiang

    Full Text Available Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB. In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III. Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating

  3. Primary productivity, heterotrophy, metabolic indicators of stress and interactions in algal-bacterial mat communities affected by a fluctuating thermal regime

    International Nuclear Information System (INIS)

    Tison, D.L.

    1980-01-01

    Thermal habitats in effluent cooling waters from production nuclear reactors at the Savannah River Plant are unlike natural thermal habitats in that reactor operations are periodically halted, exposing the organisms growing in these thermal habitats to ambient temperatures for unpredictable lengths of time. Rates of primary production, glucose heterotrophy, and the composition of algal-bacterial mat communities growing along a thermal gradient from about 50 to 35 0 C during periods of reactor operation were studied. Cyanobacteria were the only photoautotrophs in mat communities above 40 0 C while cyanobacteria and eucaryotic algae comprised the photoautotrophic component of mat communities below 40 0 C. The heterotrophic component of these communities above 40 0 C was made up of stenothermic and eurythermic thermophilic bacteria while both eurythermic thermophiles and mesophilic bacteria were found in communities below 40 0 C. Net CO 2 -fixation rates during thermal conditions dropped after initial exposure to ambient temperatures. After prolonged exposure of the thermal communities to ambient temperatures, adaptation and colonization by mesophilic algae occurred. Rates of glucose utilization under varying degrees of thermal influence suggested that the heterotrophic component may not have been optimally adapted to thermal conditions. During periods of changing thermal conditions, an increase in the percentage extracellular release of photosynthetically fixed 14 CO 2 by cyanobacteria and algae and an increase in the percentage of glucose mineralized (respired) by the heterotrophic component of the mat communities was observed. Results of temperature shift experiments indicated that the short-term response of the photoautotrophic component of these communities to thermal stress was an increase in the percentage of photosynthate released extracellularly

  4. PO43- dependence of the tolerance of autotrophic and heterotrophic biofilm communities to copper and diuron.

    Science.gov (United States)

    Tlili, Ahmed; Bérard, Annette; Roulier, Jean-Louis; Volat, Bernadette; Montuelle, Bernard

    2010-06-10

    Pollution-induced community tolerance (PICT) concept is based on the assumption that the toxicant exerts selection pressure on the biological communities when exposure reaches a critical level for a sufficient period of time and therefore sensitive species are eliminated. However, induced tolerance of microbial biofilm communities cannot be attributed solely to the presence of toxicants in rivers but also to various environmental factors, such as amount of nutrients. An experimental study was undertaken to highlight the potential impact of a phosphorus gradient on the sensitivity of periphytic microbial community to Cu and diuron. Biofilms were exposed to real-world levels of chronic environmental contamination of toxicants with a phosphorus gradient. Biofilm sensitivity to Cu and diuron was assessed by performing short-term inhibition tests based on photosynthetic efficiency to target photoautotrophs, extracellular enzyme activity (beta-glucosidase and leucine-aminopeptidase) and substrate-induced respiration activity to target heterotrophs. The impact of P-gradient associated to pollution was evaluated by measuring pesticide concentrations in biofilms, biomass parameters (chla, AFDW), bacterial cell density, photosynthetic efficiency and community structure (using 18S and 16S rDNA gene analysis to target eukaryotes and DGGE and HPLC pigment analysis to target bacteria and photoautotrophs). The obtained results show that depending on the studied toxicant and the used structural or functional parameter, the effect of the phosphorus gradient was variable. This highlights the importance of using a range of parameters that target all the biological communities in the biofilm. The PICT method can be regarded as a good tool for assessing anthropogenic environmental contamination, but it is necessary to dissociate the real impact of toxicants from environmental factors.

  5. Coupling of heterotrophic bacteria to phytoplankton bloom development at different pCO2 levels: a mesocosm study

    Directory of Open Access Journals (Sweden)

    R. Thyrhaug

    2008-07-01

    Full Text Available The predicted rise in anthropogenic CO2 emissions will increase CO2 concentrations and decrease seawater pH in the upper ocean. Recent studies have revealed effects of pCO2 induced changes in seawater chemistry on a variety of marine life forms, in particular calcifying organisms. To test whether the predicted increase in pCO2 will directly or indirectly (via changes in phytoplankton dynamics affect abundance, activities, and community composition of heterotrophic bacteria during phytoplankton bloom development, we have aerated mesocosms with CO2 to obtain triplicates with three different partial pressures of CO2 (pCO2: 350 μatm (1×CO2, 700 μatm (2×CO2 and 1050 μatm (3×CO2. The development of a phytoplankton bloom was initiated by the addition of nitrate and phosphate. In accordance to an elevated carbon to nitrogen drawdown at increasing pCO2, bacterial production (BPP of free-living and attached bacteria as well as cell-specific BPP (csBPP of attached bacteria were related to the C:N ratio of suspended matter. These relationships significantly differed among treatments. However, bacterial abundance and activities were not statistically different among treatments. Solely community structure of free-living bacteria changed with pCO2 whereas that of attached bacteria seemed to be independent of pCO2 but tightly coupled to phytoplankton bloom development. Our findings imply that changes in pCO2, although reflected by changes in community structure of free-living bacteria, do not directly affect bacterial activity. Furthermore, bacterial activity and dynamics of heterotrophic bacteria, especially of attached bacteria, were tightly correlated to phytoplankton development and, hence, may also potentially depend on changes in pCO2.

  6. Macroalgal blooms favor heterotrophic diazotrophic bacteria in nitrogen-rich and phosphorus-limited coastal surface waters in the Yellow Sea

    Science.gov (United States)

    Zhang, Xiaoli; Song, Yanjing; Liu, Dongyan; Keesing, John K.; Gong, Jun

    2015-09-01

    Macroalgal blooms may lead to dramatic changes in physicochemical variables and biogeochemical cycling in affected waters. However, little is known about the effects of macroalgal blooms on marine bacteria, especially those functioning in nutrient cycles. We measured environmental factors and investigated bacterial diazotrophs in two niches, surface waters that were covered (CC) and non-covered (CF) with massive macroalgal canopies of Ulva prolifera, in the Yellow Sea in the summer of 2011 using real-time PCR and clone library analysis of nifH genes. We found that heterotrophic diazotrophs (Gammaproteobacteria) dominated the communities and were mostly represented by Vibrio-related phylotypes in both CC and CF. Desulfovibrio-related phylotypes were only detected in CC. There were significant differences in community composition in these two environments (p diazotrophic abundance and community composition and that vibrios and Desulfovibrio-related heterotrophic diazotrophs adapt well to the (N-rich but P-limited) environment during blooming. Potential ecological and microbiological mechanisms behind this scenario are discussed.

  7. Survey on Heterotrophic Bacterial Contamination in Bottled Mineral Water by Culture Method

    Directory of Open Access Journals (Sweden)

    Essmaeel Ghorbanalinezhad

    2014-12-01

    Full Text Available Background and Aim: This project focuses on the level of heterotrophic baceria in bottled mineral water which could be a health concern for the elderly, infants, pregnant women and immuno-compromised patients. Materials and Methods: Different brands of bottled water samples were selected randomly and evaluated for their bacteriological quality, using different specific culture media and biochemical tests. Water samples were analyzed within 24 hours of their purchase/collection. Samples were filtered with 0.45 micron and filters were plated in different media. Then media were incubated at 37˚C for 24-48 hours. Results: Morphological study and biochemical tests revealed a number of bacteria in different   brands of  bottled water. Heterotrophic bacteria(Gram positive cocci, Spore forming gram positive bacilli, non spore forming gram positive bacilli, gram negative bacilli, and gram negative coccobacilli; Pseudomonas and Stenotrophomonas counted in 70% of bottled water samples. There were no cases of fecal contamination or the presence of E.coli. Conclusions: Bottled water is not sterile and contains trace amounts of bacteria naturally present or introduced during processing. Testing drinking water for all possible pathogens is complex, time-consuming, and expensive. If only total coliform bacteria are detected in drinking water, the source is probably environmental. Since the significance of non-pathogenic heterotrophic bacteria in relation to health and diseases is not understood, there is an urgent need to establish a maximum limit for the heterotrophic count in the bottled mineral water. Growth conditions play a critical role in the recovery of heterotrophic bacteria in bottled drinking water.

  8. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  9. Bioleaching of Zn, Ni and Fe from contaminated sediments of water reservoir Ružín I with using heterotrophic bacterial strains

    Directory of Open Access Journals (Sweden)

    Katarína Jablonovská

    2012-12-01

    Full Text Available This study investigates the bioleaching of the zinc polluted sediment from water reservoir Ružín I using heterotrophic bacterialstrains ubiquitous in sediment environment. The effect of bacterial activity, pH, iron solubilization and precipitation and bioleachingmedium were evaluated. The pH value controls the bacterial activity during the leaching process. Addition of glucose to the bioleachingmedium accelerated the bioleaching rate. The results indicates, that the leachibility of zinc depend on the geochemical formsand surface interaction between metal and sediment fraction. Sequential chemical extraction confirm, that Zn was predominantly boundto the iron-manganese oxides.

  10. Lentinus (Panus) tigrinus augmentation of a historically contaminated soil: matrix decontamination and structure and function of the resident bacterial community.

    Science.gov (United States)

    Federici, E; Giubilei, M A; Cajthaml, T; Petruccioli, M; D'Annibale, A

    2011-02-28

    The ability of Lentinus tigrinus to grow and to degrade persistent aromatic hydrocarbons in aged contaminated soil was assessed in this study. L. tigrinus extensively colonized the soil; its degradation activity after 60 d incubation at 28°C, however, was mostly limited to dichloroaniline isomers, polychlorinated benzenes and diphenyl ether while the fungus was unable to deplete 9,10-anthracenedione and 7-H-benz[DE]anthracene-7-one which were the major soil contaminants. Although clean-up levels were limited, both density of cultivable heterotrophic bacteria and richness of the resident bacterial community in L. tigrinus microcosms (LtM) increased over time to a significantly larger extent than the respective amended incubation controls (1.9×10(9) CFU g(-1) vs. 1.0×10(9) CFU g(-1) and 37 vs. 16, respectively). Naphthalene- and catechol 2,3-dioxygenase gene copy numbers, however, decreased over time at a higher rate in LtM than in incubation controls likely due to a higher stimulation on heterotrophs than xenobiotics-degrading community members. Copyright © 2010 Elsevier B.V. All rights reserved.

  11. Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima.

    Science.gov (United States)

    Zhang, Fan; Vicente, Jan; Hill, Russell T

    2014-01-01

    Sponges that harbor microalgal or, cyanobacterial symbionts may benefit from photosynthetically derived carbohydrates, which are rich in carbon but devoid of nitrogen, and may therefore encounter nitrogen limitation. Diazotrophic communities associated with two Caribbean sponges, Ircinia strobilina and Mycale laxissima were studied in a time series during which three individuals of each sponge were collected in four time points (5:00 AM, 12:00 noon, 5:00 PM, 10:00 PM). nifH genes were successfully amplified from the corresponding gDNA and cDNA pools and sequenced by high throughput 454 amplicon sequencing. In both sponges, over half the nifH transcripts were classified as from cyanobacteria and the remainder from heterotrophic bacteria. We found various groups of bacteria actively expressing the nifH gene during the entire day-night cycle, an indication that the nitrogen fixation potential was fully exploited by different nitrogen fixing bacteria groups associated with their hosts. This study showed for the first time the dynamic changes in the activity of the diazotrophic bacterial communities in marine sponges. Our study expands understanding of the diazotrophic groups that contribute to the fixed nitrogen pool in the benthic community. Sponge bacterial community-associated diazotrophy may have an important impact on the nitrogen biogeochemical cycle in the coral reef ecosystem.

  12. Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima

    Directory of Open Access Journals (Sweden)

    Fan eZhang

    2014-10-01

    Full Text Available Sponges that harbor microalgal or cyanobacterial symbionts may benefit from photosynthetically derived carbohydrates, which are rich in carbon but devoid of nitrogen, and may therefore encounter nitrogen limitation. Diazotrophic communities associated with two Caribbean sponges, Ircinia strobilina and Mycale laxissima were studied in a time series during which three individuals of each sponge were collected in four time points (5:00 AM, 12:00 noon, 5:00 PM, 10:00 PM. nifH genes were successfully amplified from the corresponding gDNA and cDNA pools and sequenced by high throughput 454 amplicon sequencing. In both sponges, over half the nifH transcripts were classified as from cyanobacteria and the remainder from heterotrophic bacteria. We found various groups of bacteria actively expressing the nifH gene during the entire day-night cycle, an indication that the nitrogen fixation potential was fully exploited by different nitrogen fixing bacteria groups associated with their hosts. This study showed for the first time the dynamic changes in the activity of the diazotrophic bacterial communities in marine sponges. Our study expands understanding of the diazotrophic groups that contribute to the fixed nitrogen pool in the benthic community. Sponge bacterial community-associated diazotrophy may have an important impact on the nitrogen biogeochemical cycle in the coral reef ecosystem.

  13. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    Directory of Open Access Journals (Sweden)

    Annette K. Møller

    2013-04-01

    Full Text Available The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition of the microbial assemblages was different within the snow layers and between snow and freshwater. The highest diversity was seen in snow. In the middle and top snow layers, Proteobacteria, Bacteroidetes and Cyanobacteria dominated, although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacteroidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. Thus, differences in the physicochemical conditions may play an important role in the processes leading to distinctive bacterial community structures in High-Arctic snow and freshwater.

  14. Heterotrophic monitoring at a drinking water treatment plant by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry after different drinking water treatments.

    Science.gov (United States)

    Sala-Comorera, Laura; Blanch, Anicet R; Vilaró, Carles; Galofré, Belén; García-Aljaro, Cristina

    2017-10-01

    The aim of this work was to assess the suitability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for routine heterotrophic monitoring in a drinking water treatment plant. Water samples were collected from raw surface water and after different treatments during two campaigns over a 1-year period. Heterotrophic bacteria were studied and isolates were identified by MALDI-TOF MS. Moreover, the diversity index and the coefficient of population similarity were also calculated using biochemical fingerprinting of the populations studied. MALDI-TOF MS enabled us to characterize and detect changes in the bacterial community composition throughout the water treatment plant. Raw water showed a large and diverse population which was slightly modified after initial treatment steps (sand filtration and ultrafiltration). Reverse osmosis had a significant impact on the microbial diversity, while the final chlorination step produced a shift in the composition of the bacterial community. Although MALDI-TOF MS could not identify all the isolates since the available MALDI-TOF MS database does not cover all the bacterial diversity in water, this technique could be used to monitor bacterial changes in drinking water treatment plants by creating a specific protein profile database for tracking purposes.

  15. Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, Hans C.; Brislawn, Colin J.; Dana, Karl; Flores-Wentz, Tobias; Cory, Alexandra B.; Fansler, Sarah J.; Fredrickson, James K.; Moran, James J.

    2017-10-01

    Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: 1) How does species diversity relate to the rates of primary and heterotrophic productivity? 2) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline Lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope incorporation that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose and acetate, respectively. Bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, energy constraints imposed by changing irradiance over a diel cycle.

  16. Seasonal and spatial patterns of heterotrophic bacterial production, respiration, and biomass in the subarctic NE Pacific

    Science.gov (United States)

    Sherry, Nelson D.; Boyd, Philip W.; Sugimoto, Kugako; Harrison, Paul J.

    1999-11-01

    Heterotrophic bacterial biomass, production, and respiration rates were measured during winter, spring, and summer in the subarctic NE Pacific from September 1995 to June 1997. Sampling took place on six cruises at five hydrographic stations along the east/west line-P transect from slope waters at P4 (1200 m depth) to the open-ocean waters at Ocean Station Papa (OSP) (4250 m depth). Interannual variability was small relative to seasonal and spatial variability. Biomass, derived from cell counts (assuming 20 fg C cell -1), was ca. 12 μg C l -1 in the winter and increased to 20-35 μg C l -1 in the spring and summer all along line-P. Bacterial production from [ 3H]-thymidine and [ 14C]-leucine incorporation rates was lowest in the winter (ca. 0.5 μg C l -1 d -1) with little spatial variability. Production increased 10-fold in spring at P4 (to ca. 4.5 μg C l -1 d -1). In contrast, only a 2-fold increase in bacterial production was observed over this period at the more oceanic stations. Rates of production in late summer were highest over the annual cycle at all stations ranging from ca. 6 at P4 to ca. 2 μg C l -1 d -1 at OSP. Bacterial (rates increased >10-fold to ca. 100 μg C l -1 d -1 at P4 in the summer, but, interestingly, did not increase from spring to summer at the more oceanic stations. Thus bacterial growth efficiency, defined as production/(production+respiration), decreased in the spring westwards from the slope waters (P4) to the open-ocean (OSP), but increased westwards in the summer. Bacterial production was highly correlated with temperature at OSP ( r2=0.88) and less so at P4 ( r2=0.50). The observed temporal and spatial trends presented in this study suggest that seasonal changes in bacterial biomass were greatly affected by changes in loss processes, that bacterial biomass is regulated by different processes than bacterial production, and that bacterial production alone, without respiration measurements, is not a robust proxy for bacterial

  17. Bacterial Community Succession in Pine-Wood Decomposition.

    Science.gov (United States)

    Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

    2016-01-01

    Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  18. Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest

    Directory of Open Access Journals (Sweden)

    Kristin M. Mikkelson

    2017-12-01

    Full Text Available Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH4+ concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions.

  19. Enrichments of methanotrophic-heterotrophic cultures with high poly-β-hydroxybutyrate (PHB) accumulation capacities.

    Science.gov (United States)

    Zhang, Tingting; Wang, Xiaowei; Zhou, Jiti; Zhang, Yu

    2018-03-01

    Methanotrophic-heterotrophic communities were selectively enriched from sewage sludge to obtain a mixed culture with high levels of poly-β-hydroxybutyrate (PHB) accumulation capacity from methane. Methane was used as the carbon source, N 2 as sole nitrogen source, and oxygen and Cu content were varied. Copper proved essential for PHB synthesis. All cultures enriched with Cu could accumulate high content of PHB (43.2%-45.9%), while only small amounts of PHB were accumulated by cultures enriched without Cu (11.9%-17.5%). Batch assays revealed that communities grown with Cu and a higher O 2 content synthesized more PHB, which had a wider optimal CH 4 :O 2 range and produced a high PHB content (48.7%) even though in the presence of N 2 . In all methanotrophic-heterotrophic communities, both methanotrophic and heterotrophic populations showed the ability to accumulate PHB. Although methane was added as the sole carbon source, heterotrophs dominated with abundances between 77.2% and 85.6%. All methanotrophs detected belonged to type II genera, which formed stable communities with heterotrophs of different PHB production capacities. Copyright © 2017. Published by Elsevier B.V.

  20. Microbial plankton communities in the coastal southeastern Black Sea: biomass, composition and trophic interactions

    Directory of Open Access Journals (Sweden)

    Ulgen Aytan

    2018-04-01

    Full Text Available Summary: We investigated biomass and composition of the pico-, nano- and microplankton communities in a coastal station of the southeastern Black Sea during 2011. We also examined trophic interactions within these communities from size-fractionated dilution experiments in February, June and December. Autotrophic and heterotrophic biomasses showed similar seasonal trends, with a peak in June, but heterotrophs dominated throughout the year. Autotrophic biomass was mainly comprised by nanoflagellates and diatoms in the first half of the year, and by dinoflagellates and Synechococcus spp. in the second half. Heterotrophic biomass was mostly dominated by heterotrophic bacteria, followed by nanoflagellates and microzooplankton. Dilution experiments suggest that nano- and microzooplankton were significant consumers of autotrophs and heterotrophic bacteria. More than 100% of bacterial production was consumed by grazers in all experiments, while 46%, 21% and 30% of daily primary production were consumed in February, June and December, respectively. In February, autotrophs were the main carbon source, but in December, it was heterotrophic bacteria. An intermediate situation was observed in June, with similar carbon flows from autotrophs and heterotrophic bacteria. Size-fraction dilution experiments suggested that heterotrophic nanoflagellates are an important link between the high heterotrophic bacterial biomass and microzooplankton. In summary, these results indicate that nano- and microzooplankton were responsible for comprising a significant fraction of total microbial plankton biomass, standing stocks, growth and grazing processes. This suggests that in 2011, the microbial food web was an important compartment of the planktonic food web in the coastal southeastern Black Sea. Keywords: Phytoplankton, Microzooplankton, Carbon biomass, Microbial food web, Grazing, Black Sea

  1. Bacterial community succession in pine-wood decomposition

    Directory of Open Access Journals (Sweden)

    Anna eKielak

    2016-03-01

    Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  2. The influence of the organophosphorus insecticides acephate and parathion upon the heterotrophic bacteria of two freshwater ecosystems

    International Nuclear Information System (INIS)

    Albright, L.J.; Geen, G.H.; Gasith, A.; Mozel, Y.; Perry, A.S.

    1983-01-01

    The effect of acephate and parathion on the heterotrophic bacteria of freshwater ecosystems was studied in a dystrophic west coast Canadian lake and in an eutrophic Israeli fish pond. The limnocorrals were treated with 1-25 ppm of acephate and 30-40 ppb of parathion respectively. Bacterial populations, glucose heterotrophic activities and bacterial and algal productivities were studied using 3 H and 14 C radioisotopes. It is concluded that the two ecosystems are not extensively affected by the pesticide concentrations used

  3. Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation.

    Science.gov (United States)

    Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E

    2012-03-01

    Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The

  4. Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil

    Science.gov (United States)

    Leewis, Mary-Cathrine; Uhlik, Ondrej; Leigh, Mary Beth

    2016-02-01

    Aerobic mineralization of PCBs, which are toxic and persistent organic pollutants, involves the upper (biphenyl, BP) and lower (benzoate, BZ) degradation pathways. The activity of different members of the soil microbial community in performing one or both pathways, and their synergistic interactions during PCB biodegradation, are not well understood. This study investigates BP and BZ biodegradation and subsequent carbon flow through the microbial community in PCB-contaminated soil. DNA stable isotope probing (SIP) was used to identify the bacterial guilds involved in utilizing 13C-biphenyl (unchlorinated analogue of PCBs) and/or 13C-benzoate (product/intermediate of BP degradation and analogue of chlorobenzoates). By performing SIP with two substrates in parallel, we reveal microbes performing the upper (BP) and/or lower (BZ) degradation pathways, and heterotrophic bacteria involved indirectly in processing carbon derived from these substrates (i.e. through crossfeeding). Substrate mineralization rates and shifts in relative abundance of labeled taxa suggest that BP and BZ biotransformations were performed by microorganisms with different growth strategies: BZ-associated bacteria were fast growing, potentially copiotrophic organisms, while microbes that transform BP were oligotrophic, slower growing, organisms. Our findings provide novel insight into the functional interactions of soil bacteria active in processing biphenyl and related aromatic compounds in soil, revealing how carbon flows through a bacterial community.

  5. Comparison of bacterial community structures of terrestrial cyanobacterium Nostoc flagelliforme in three different regions of China using PCR-DGGE analysis.

    Science.gov (United States)

    Han, Pei-pei; Shen, Shi-gang; Jia, Shi-ru; Wang, Hui-yan; Zhong, Cheng; Tan, Zhi-lei; Lv, He-xin

    2015-07-01

    Filamentous Nostoc flagelliforme form colloidal complex, with beaded cells interacting with other bacteria embedded in the complex multilayer sheath. However, the species of bacteria in the sheath and the interaction between N. flagelliforme and associated bacteria remain unclear. In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities of N. flagelliforme from three regions of China. DGGE patterns showed variations in all samples, exhibiting 25 discrete bands with various intensities. The diversity index analysis of bands profiles suggested the high similarity of bacterial communities to each other but also the dependence of microbial composition on each location. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Cyanobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, of which Cyanobacteria was dominant, followed the Proteobacteria. Members of the genus Nostoc were the most abundant in all samples. Rhizobiales and Actinobacteria were identified, whereas, Craurococcus, Caulobacter, Pseudomonas, Terriglobus and Mucilaginibacter were also identified at low levels. Through comparing the bacterial composition of N. flagelliforme from different regions, it was revealed that N. flagelliforme could facilitate the growth of other microorganisms including both autotrophic bacteria and heterotrophic ones and positively contributed to their harsh ecosystems. The results indicated N. flagelliforme played an important role in diversifying the microbial community composition and had potential application in soil desertification.

  6. Diazotrophic Bacterial Community of Degraded Pastures

    Directory of Open Access Journals (Sweden)

    João Tiago Correia Oliveira

    2017-01-01

    Full Text Available Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN of bacteria per gram of sample, in order to determine population density and calculate the Shannon-Weaver diversity index. The diversity of total diazotrophic bacterial community was determined by the technique of Denaturing Gradient Gel Electrophoresis (DGGE of the nifH gene, while the diversity of the culturable diazotrophic bacteria was determined by the Polymerase Chain Reaction (BOX-PCR technique. The increase in the degradation stage of the B. decumbens Stapf. pasture did not reduce the population density of the cultivated diazotrophic bacterial community, suggesting that the degradation at any degree of severity was highly harmful to the bacteria. The structure of the total diazotrophic bacterial community associated with B. decumbens Stapf. was altered by the pasture degradation stage, suggesting a high adaptive capacity of the bacteria to altered environments.

  7. Antibiotics promote aggregation within aquatic bacterial communities

    Directory of Open Access Journals (Sweden)

    Gianluca eCorno

    2014-07-01

    Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

  8. Evaluation on the microbial interactions of anaerobic ammonium oxidizers and heterotrophs in Anammox biofilm

    DEFF Research Database (Denmark)

    Ni, Bing-Jie; Ruscalleda, Mael; Smets, Barth F.

    2012-01-01

    and the affecting factors were evaluated with both experimental and modeling approaches. Fluorescent in situ hybridization (FISH) analysis illustrated that Anammox bacteria and heterotrophs accounted for 77% and 23% of the total bacteria, respectively, even without addition of an external carbon source....... Experimental results showed the heterotrophs could grow both on SMP and decay released substrate from the metabolism of the Anammox bacteria. However, heterotrophic growth in Anammox biofilm (23%) was significantly lower than that of nitrifying biofilm (30–50%). The model predictions matched well...... with the experimental observations of the bacterial distribution, as well as the nitrogenous transformations in batch and continuous experiments. The modeling results showed that low nitrogen surface loading resulted in a lower availability of SMP leading to low heterotrophic growth in Anammox biofilm, but high...

  9. Heterotrophic bacterial responses to the winter–spring phytoplankton bloom in open waters of the NW Mediterranean

    KAUST Repository

    Gomes, Ana

    2014-12-03

    The response of planktonic heterotrophic prokaryotes to the NW Mediterranean winter–spring offshore phytoplankton bloom was assessed in 3 cruises conducted in March, April–May and September 2009. Bulk measurements of phytoplankton and bacterioplankton biomass and production were complemented with an insight into bacterial physiological structure by single-cell analysis of nucleic acid content [low (LNA) vs. high (HNA)] and membrane integrity (“Live” vs. “Dead” cells). Bacterial production empirical conversion factors (0.82±0.25 SE kg C mol leucine−1) were almost always well below the theoretical value. Major differences in most microbial variables were found among the 3 periods, which varied from extremely high phytoplankton biomass and production during the bloom in March (>1 g C m−2 d−1 primary production) to typically oligotrophic conditions during September stratification (<200 mg C m−2 d−1). In both these periods bacterial production was ~30 mg C m−2 d−1 while very large bacterial production (mean 228, with some stations exceeding 500 mg C m−2 d−1) but low biomass was observed during the April–May post-bloom phase. The contribution of HNA (30–67%) and “Live” cells (47–97%) were temporally opposite in the study periods, with maxima in March and September, respectively. Different relationships were found between physiological structure and bottom-up variables, with HNA bacteria apparently more responsive to phytoplankton only during the bloom, coinciding with larger average cell sizes of LNA bacteria. Moderate phytoplankton–bacterioplankton coupling of biomass and activity was only observed in the bloom and post-bloom phases, while relationships between both compartments were not significant under stratification. With all data pooled, bacteria were only weakly bottom-up controlled. Our analyses show that the biomass and production of planktonic algae and bacteria followed opposite paths in the transition from bloom to

  10. Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest.

    Science.gov (United States)

    Mikkelson, Kristin M; Brouillard, Brent M; Bokman, Chelsea M; Sharp, Jonathan O

    2017-12-05

    Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH 4 + concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique "tree-centric" approach, we were able to delineate plots with various tree mortality levels within the same watershed

  11. Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms.

    Science.gov (United States)

    Silva-Bedoya, Lina Marcela; Sánchez-Pinzón, María Solange; Cadavid-Restrepo, Gloria Ester; Moreno-Herrera, Claudia Ximena

    2016-11-01

    The operation of wastewater treatment technologies depends on a combination of physical, chemical and biological factors. Microorganisms present in wastewater treatment plants play essential roles in the degradation and removal of organic waste and xenobiotic pollutants. Several microorganisms have been used in complementary treatments to process effluents rich in fats and oils. Microbial lipases have received significant industrial attention because of their stability, broad substrate specificity, high yields, and regular supply, as well as the fact that the microorganisms producing them grow rapidly on inexpensive media. In Colombia, bacterial community studies have focused on populations of cultivable nitrifying, heterotrophic and nitrogen-fixing bacteria present in constructed wetlands. In this study, culture-dependent methods, culture-independent methods (TTGE, RISA) and enzymatic methods were used to estimate bacterial diversity, to monitor temporal and spatial changes in bacterial communities, and to screen microorganisms that presented lipolytic activity. The dominant microorganisms in the Wastewater Treatment Plant (WWTP) examined in this study belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. The enzymatic studies performed indicated that five bacterial isolates and three fungal isolates possessed the ability to degrade lipids; additionally, the Serratia, Kosakonia and Mucor genera presented lipase-mediated transesterification activity. The implications of these findings in regard to possible applications are discussed later in this paper. Our results indicate that there is a wide diversity of aerobic Gram-negative bacteria inhabiting the different sections of the WWTP, which could indicate its ecological condition, functioning and general efficiency. Copyright © 2016 Elsevier GmbH. All rights reserved.

  12. Bacterial community structure associated with white band disease in the elkhorn coral Acropora palmata determined using culture-independent 16S rRNA techniques.

    Science.gov (United States)

    Pantos, Olga; Bythell, John C

    2006-03-23

    Culture-independent molecular (16S ribosomal RNA) techniques showed distinct differences in bacterial communities associated with white band disease (WBD) Type I and healthy elkhorn coral Acropora palmata. Differences were apparent at all levels, with a greater diversity present in tissues of diseased colonies. The bacterial community associated with remote, non-diseased coral was distinct from the apparently healthy tissues of infected corals several cm from the disease lesion. This demonstrates a whole-organism effect from what appears to be a localised disease lesion, an effect that has also been recently demonstrated in white plague-like disease in star coral Montastraea annularis. The pattern of bacterial community structure changes was similar to that recently demonstrated for white plague-like disease and black band disease. Some of the changes are likely to be explained by the colonisation of dead and degrading tissues by a micro-heterotroph community adapted to the decomposition of coral tissues. However, specific ribosomal types that are absent from healthy tissues appear consistently in all samples of each of the diseases. These ribotypes are closely related members of a group of alpha-proteobacteria that cause disease, notably juvenile oyster disease, in other marine organisms. It is clearly important that members of this group are isolated for challenge experiments to determine their role in the diseases.

  13. Community-acquired bacterial meningitis

    NARCIS (Netherlands)

    van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G.; Wijdicks, Eelco

    2016-01-01

    Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma

  14. Bacterial community affects toxin production by Gymnodinium catenatum.

    Directory of Open Access Journals (Sweden)

    Maria E Albinsson

    Full Text Available The paralytic shellfish toxin (PST-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01 and grown with: 1 complex bacterial communities derived from each of the two parent cultures; 2 simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3 a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell of clonal offspring (134-197 fmol STX cell(-1 was similar to the parent cultures (169-206 fmol STX cell(-1, however cultures grown with single bacterial types contained less toxin (134-146 fmol STX cell(-1 than offspring or parent cultures grown with more complex mixed bacterial communities (152-176 fmol STX cell(-1. Specific toxin production rate (fmol STX day(-1 was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell(-1 day(-1 did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter intracellular STX

  15. Bacterial community affects toxin production by Gymnodinium catenatum.

    Science.gov (United States)

    Albinsson, Maria E; Negri, Andrew P; Blackburn, Susan I; Bolch, Christopher J S

    2014-01-01

    The paralytic shellfish toxin (PST)-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01) and grown with: 1) complex bacterial communities derived from each of the two parent cultures; 2) simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3) a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell) of clonal offspring (134-197 fmol STX cell(-1)) was similar to the parent cultures (169-206 fmol STX cell(-1)), however cultures grown with single bacterial types contained less toxin (134-146 fmol STX cell(-1)) than offspring or parent cultures grown with more complex mixed bacterial communities (152-176 fmol STX cell(-1)). Specific toxin production rate (fmol STX day(-1)) was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell(-1) day(-1)) did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter intracellular STX

  16. Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.

    Science.gov (United States)

    Cassler, M; Peterson, C L; Ledger, A; Pomponi, S A; Wright, A E; Winegar, R; McCarthy, P J; Lopez, J V

    2008-04-01

    In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.

  17. Community respiration/production and bacterial activity in the upper water column of the central Arctic Ocean

    Science.gov (United States)

    Sherr, Barry F.; Sherr, Evelyn B.

    2003-04-01

    Community metabolism (respiration and production) and bacterial activity were assessed in the upper water column of the central Arctic Ocean during the SHEBA/JOIS ice camp experiment, October 1997-September 1998. In the upper 50 m, decrease in integrated dissolved oxygen (DO) stocks over a period of 124 d in mid-winter suggested a respiration rate of ˜3.3 nM O 2 h -1 and a carbon demand of ˜4.5 gC m -2. Increase in 0-50 m integrated stocks of DO during summer implied a net community production of ˜20 gC m -2. Community respiration rates were directly measured via rate of decrease in DO in whole seawater during 72-h dark incubation experiments. Incubation-based respiration rates were on average 3-fold lower during winter (11.0±10.6 nM O 2 h -1) compared to summer (35.3±24.8 nM O 2 h -1). Bacterial heterotrophic activity responded strongly, without noticeable lag, to phytoplankton growth. Rate of leucine incorporation by bacteria (a proxy for protein synthesis and cell growth) increased ˜10-fold, and the cell-specific rate of leucine incorporation ˜5-fold, from winter to summer. Rates of production of bacterial biomass in the upper 50 m were, however, low compared to other oceanic regions, averaging 0.52±0.47 ngC l -1 h -1 during winter and 5.1±3.1 ngC l -1 h -1 during summer. Total carbon demand based on respiration experiments averaged 2.4±2.3 mgC m -3 d -1 in winter and 7.8±5.5 mgC m -3 d -1 in summer. Estimated bacterial carbon demand based on bacterial productivity and an assumed 10% gross growth efficiency was much lower, averaging about 0.12±0.12 mgC m -3 d -1 in winter and 1.3±0.7 mgC m -3 d -1 in summer. Our estimates of bacterial activity during summer were an order of magnitude less than rates reported from a summer 1994 study in the central Arctic Ocean, implying significant inter-annual variability of microbial processes in this region.

  18. 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.

  19. Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions

    International Nuclear Information System (INIS)

    Fernandez-Fontaina, E.; Gomes, I.B.; Aga, D.S.; Omil, F.; Lema, J.M.; Carballa, M.

    2016-01-01

    The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals. - Highlights: • The removal of pharmaceuticals in nitrifying activated sludge (NAS) was studied. • Nitrifying activity increases biotransformation rate of ibuprofen and naproxen. • Hydroxylation of ibuprofen by ammonia monooxygenase of ammonia oxidizing bacteria • Heterotrophic activity enhances biotransformation of sulfamethoxazole in NAS. • Recalcitrance of trimethoprim, diclofenac, carbamazepine and diazepam in NAS

  20. Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Fontaina, E., E-mail: eduardo.fernandez.fontaina@usc.es [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Gomes, I.B. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Aga, D.S. [Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260 (United States); Omil, F.; Lema, J.M.; Carballa, M. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain)

    2016-01-15

    The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals. - Highlights: • The removal of pharmaceuticals in nitrifying activated sludge (NAS) was studied. • Nitrifying activity increases biotransformation rate of ibuprofen and naproxen. • Hydroxylation of ibuprofen by ammonia monooxygenase of ammonia oxidizing bacteria • Heterotrophic activity enhances biotransformation of sulfamethoxazole in NAS. • Recalcitrance of trimethoprim, diclofenac, carbamazepine and diazepam in NAS.

  1. Minerals in soil select distinct bacterial communities in their microhabitats.

    Science.gov (United States)

    Carson, Jennifer K; Campbell, Louise; Rooney, Deirdre; Clipson, Nicholas; Gleeson, Deirdre B

    2009-03-01

    We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova (permanova) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum, and in T. subterraneum, bacterial communities from M and B differed (Ppermanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction (P<0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.

  2. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    of Environmental Biology circleshadowdwnMay 2011circleshadowdwn Introduction The bacteria play a major role in carbon dynamics of marine ecosystems and, the importance of heterotrophic bacteria in marine ecosystem functioning is very well recognized (Azam et al..., 2008). Denaturing gradient gel-electrophoressis (DGGE) based fingerprinting helps estimate the numbers of dominant phylotype in a given sample (Muyzer et al., 1993). Very diverse bacterial assemblages such as those in the soils present many bands...

  3. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River

    International Nuclear Information System (INIS)

    Tiquia, S.M.

    2010-01-01

    The heterotrophic microbial communities of the Rouge River were tracked using Biolog Ecoplates to understand the metabolic diversity at different temporal and spatial scales, and potential link to river pollution. Site less impacted by anthrophogenic sources (site 1), showed markedly lower metabolic diversity. The only substrates that were utilized in the water samples were carbohydrates. Sites more impacted by anthrophogenic sources (sites 8 and 9) showed higher metabolic diversity. Higher functional diversity was linked to the physico-chemical and biological properties of the water samples (i.e. higher concentrations of DO, DOC, chlorophyll, and bacterial density). Biolog analysis was found to be useful in differentiating metabolic diversity between microbial communities; in determining factors that most influence the separation of communities; and in identifying which substrates were most utilized by the communities. It can also be used as an effective ecological indicator of changes in river function attributable to urbanization and pollution. - BIOLOG differentiated metabolic diversity between microbial communities and can be used as ecological indicator of river function attributable to urbanization and pollution.

  5. Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River

    Energy Technology Data Exchange (ETDEWEB)

    Tiquia, S.M., E-mail: smtiquia@umd.umich.ed [Department of Natural Sciences, University of Michigan, 115F Science Building, Dearborn, MI 48128 (United States)

    2010-05-15

    The heterotrophic microbial communities of the Rouge River were tracked using Biolog Ecoplates to understand the metabolic diversity at different temporal and spatial scales, and potential link to river pollution. Site less impacted by anthrophogenic sources (site 1), showed markedly lower metabolic diversity. The only substrates that were utilized in the water samples were carbohydrates. Sites more impacted by anthrophogenic sources (sites 8 and 9) showed higher metabolic diversity. Higher functional diversity was linked to the physico-chemical and biological properties of the water samples (i.e. higher concentrations of DO, DOC, chlorophyll, and bacterial density). Biolog analysis was found to be useful in differentiating metabolic diversity between microbial communities; in determining factors that most influence the separation of communities; and in identifying which substrates were most utilized by the communities. It can also be used as an effective ecological indicator of changes in river function attributable to urbanization and pollution. - BIOLOG differentiated metabolic diversity between microbial communities and can be used as ecological indicator of river function attributable to urbanization and pollution.

  6. Metamorphosis of a butterfly-associated bacterial community.

    Science.gov (United States)

    Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

    2014-01-01

    Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

  7. Metamorphosis of a butterfly-associated bacterial community.

    Directory of Open Access Journals (Sweden)

    Tobin J Hammer

    Full Text Available Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

  8. BACTERIOLOGICAL PROPERTIES OF MARINE WATER IN ADRIATIC FISH FARMS: ENUMERATION OF HETEROTROPHIC BACTERIA

    Directory of Open Access Journals (Sweden)

    Emin Teskeredžić

    2012-12-01

    Full Text Available Aquaculture is currently one of the fastest growing food production sectors in the world. Increase in nutrients and organic wastes lead to general deterioration of water quality. The problem of water quality is associated with both physical and chemical factors, as well as microbiological water quality. Heterotrophic bacteria play an important role in the process of decomposition of organic matter in water environment and indicate eutrophication process. Here we present our experience and knowledge on bacterial properties of marine water in the Adriatic fish farms with European sea bass (Dicentrarchus labrax L., 1758, with an emphasis on enumeration of heterotrophic bacteria in marine water. We applied two temperatures of incubation, as well as two methods for enumeration of heterotrophic bacteria: substrate SimPlate® test and spread plate method on conventional artificial media (Marine agar and Tryptic Soy agar with added NaCl. The results of analysis of bacteriological properties of marine water in the Adriatic fish farms showed that enumeration of heterotrophic bacteria in marine water depends on the applied incubation temperature and media for enumeration. At the same time, the incubation temperature of 22C favours more intense growth of marine heterotrophic bacteria, whereas a SimPlate test gives higher values of heterotrophic bacteria. Volatile values of heterotrophic bacteria during this research indicate a possible deterioration of microbiological water quality in the Adriatic fish farms and a need for regular monitoring of marine water quality.

  9. Upper Arctic Ocean water masses harbor distinct communities of heterotrophic flagellates

    Directory of Open Access Journals (Sweden)

    A. Monier

    2013-06-01

    Full Text Available The ubiquity of heterotrophic flagellates (HFL in marine waters has been recognized for several decades, but the phylogenetic diversity of these small (ca. 0.8–20 μm cell diameter, mostly phagotrophic protists in the upper pelagic zone of the ocean is underappreciated. Community composition of microbes, including HFL, is the result of past and current environmental selection, and different taxa may be indicative of food webs that cycle carbon and energy very differently. While all oceanic water columns can be density stratified due to the temperature and salinity characteristics of different water masses, the Arctic Ocean is particularly well stratified, with nutrients often limiting in surface waters and most photosynthetic biomass confined to a subsurface chlorophyll maximum layer, where light and nutrients are both available. This physically well-characterized system provided an opportunity to explore the community diversity of HFL from different water masses within the water column. We used high-throughput DNA sequencing techniques as a rapid means of surveying the diversity of HFL communities in the southern Beaufort Sea (Canada, targeting the surface, the subsurface chlorophyll maximum layer (SCM and just below the SCM. In addition to identifying major clades and their distribution, we explored the micro-diversity within the globally significant but uncultivated clade of marine stramenopiles (MAST-1 to examine the possibility of niche differentiation within the stratified water column. Our results strongly suggested that HFL community composition was determined by water mass rather than geographical location across the Beaufort Sea. Future work should focus on the biogeochemical and ecological repercussions of different HFL communities in the face of climate-driven changes to the physical structure of the Arctic Ocean.

  10. Diazotrophic Bacterial Community of Degraded Pastures

    OpenAIRE

    João Tiago Correia Oliveira; Everthon Fernandes Figueredo; Williane Patrícia da Silva Diniz; Lucianne Ferreira Paes de Oliveira; Pedro Avelino Maia de Andrade; Fernando Dini Andreote; Júlia Kuklinsky-Sobral; Danúbia Ramos de Lima; Fernando José Freire

    2017-01-01

    Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN) of bacteria per gram ...

  11. Bacterial community changes in an industrial algae production system.

    Science.gov (United States)

    Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

    2018-04-01

    While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

  12. Functional recovery of biofilm bacterial communities after copper exposure

    International Nuclear Information System (INIS)

    Boivin, Marie-Elene Y.; Massieux, Boris; Breure, Anton M.; Greve, Gerdit D.; Rutgers, Michiel; Admiraal, Wim

    2006-01-01

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 μmol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 μmol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 μmol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper

  13. Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit.

    Science.gov (United States)

    Diaby, N; Dold, B; Rohrbach, E; Holliger, C; Rossi, P

    2015-11-15

    Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation

  14. Soil bacterial community shifts associated with sugarcane straw removal

    Science.gov (United States)

    Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

    2017-04-01

    In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

  15. Bacterial Communities Associated with the Lichen Symbiosis▿ †

    Science.gov (United States)

    Bates, Scott T.; Cropsey, Garrett W. G.; Caporaso, J. Gregory; Knight, Rob; Fierer, Noah

    2011-01-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and “algae” (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N2 fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2 fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses. PMID:21169444

  16. The Effect of Light on Bacterial Activity in a Seaweed Holobiont.

    Science.gov (United States)

    Coelho-Souza, Sergio A; Jenkins, Stuart R; Casarin, Antonio; Baeta-Neves, Maria Helena; Salgado, Leonardo T; Guimaraes, Jean R D; Coutinho, Ricardo

    2017-11-01

    Holobionts are characterized by the relationship between host and their associated organisms such as the biofilm associated with macroalgae. Considering that light is essential to macroalgae survival, the aim of this study was to verify the effect of light on the heterotrophic activity in biofilms of the brown macroalgae Sargassum furcatum during its growth cycle. Measurements of heterotrophic activity were done under natural light levels at different times during a daily cycle and under an artificial extinction of natural light during the afternoon. We also measured Sargassum primary production under these light levels in the afternoon. Both measurements were done with and without photosynthesis inhibitor and antibiotics. Biofilm composition was mainly represented by bacteria but diatoms, cyanobacteria, and other organisms were also common. When a peak of diatom genera was recorded, the heterotrophic activity of the biofilm was higher. Heterotrophic activity was usually highest during the afternoon and the presence of a photosynthesis inhibitor caused an average reduction of 17% but there was no relationship with Sargassum primary production. These results indicate that autotrophic production in the biofilm was reduced by the inhibitor with consequences on bacterial activity. Heterotrophic activity was mainly bacterial and the antibiotics chloramphenicol and penicillin were more effective than streptomycin. We suggest primary producers in the biofilm are more important to increase bacterial activity than the macroalgae itself because of coherence of the peaks of heterotrophic and autotrophic activity in biofilm during the afternoon and the effects of autotrophic inhibitors on heterotrophic activity.

  17. Mineral phosphate solubilizing bacterial community in agro-ecosystem

    African Journals Online (AJOL)

    Mineral phosphate solubilizing bacterial community in agro-ecosystem. N Saha, S Biswas. Abstract. The present communication deals with the assessment of phosphate solubilizing bacterial community structure across artificially created fertility gradient with regards to N, P and K status of soil in the experimental site.

  18. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    Energy Technology Data Exchange (ETDEWEB)

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  19. Bacterial community structure in the Cerasus sachalinensis Kom ...

    African Journals Online (AJOL)

    Jane

    2011-07-21

    Jul 21, 2011 ... The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial ...

  20. Occurrence of heterotrophic and coliform bacteria in liquid hand soaps from bulk refillable dispensers in public facilities.

    Science.gov (United States)

    Chattman, Marisa; Gerba, Sheri L; Maxwell, Charles P

    2011-03-01

    The goal of the study discussed in this article was to determine the occurrence of heterotrophic and coliform bacteria in liquid soap from bulk refillable dispensers, obtained from restrooms in a variety of public facilities. A total of 541 samples was collected from five U.S. cities. Liquid soap from dispensers in public areas was found to contain heterotrophic and coliform bacterial numbers averaging more than 106 CFU/mL in 24.8% of the dispensers.

  1. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  2. Microbiological assessment of house and imported bottled water by comparison of bacterial endotoxin concentration, heterotrophic plate count, and fecal coliform count.

    Science.gov (United States)

    Reyes, Mayra I; Pérez, Cynthia M; Negrón, Edna L

    2008-03-01

    Consumers increasingly use bottled water and home water treatment systems to avoid direct tap water. According to the International Bottled Water Association (IBWA), an industry trade group, 5 billion gallons of bottled water were consumed by North Americans in 2001. The principal aim of this study was to assess the microbial quality of in-house and imported bottled water for human consumption, by measurement and comparison of the concentration of bacterial endotoxin and standard cultivable methods of indicator microorganisms, specifically, heterotrophic and fecal coliform plate counts. A total of 21 brands of commercial bottled water, consisting of 10 imported and 11 in-house brands, selected at random from 96 brands that are consumed in Puerto Rico, were tested at three different time intervals. The Standard Limulus Amebocyte Lysate test, gel clot method, was used to measure the endotoxin concentrations. The minimum endotoxin concentration in 63 water samples was less than 0.0625 EU/mL, while the maximum was 32 EU/mL. The minimum bacterial count showed no growth, while the maximum was 7,500 CFU/mL. Bacterial isolates like P. fluorescens, Corynebacterium sp. J-K, S. paucimobilis, P. versicularis, A. baumannii, P. chlororaphis, F. indologenes, A. faecalis and P. cepacia were identified. Repeated measures analysis of variance demonstrated that endotoxin concentration did not change over time, while there was a statistically significant (p bacterial count over time. In addition, multiple linear regression analysis demonstrated that a unit change in the concentration of endotoxin across time was associated with a significant (p bacterial growth was not detected in some water samples, endotoxin was present. Measurement of Gram-negative bacterial endotoxins is one of the methods that have been suggested as a rapid way of determining bacteriological water quality.

  3. Heterotrophic bacterial production, respiration, and growth efficiency associated with upwelling intensity in the Ulleung Basin, East Sea

    Science.gov (United States)

    Kim, Bomina; Kim, Sung-Han; Kwak, Jung Hyun; Kang, Chang-Keun; Lee, Sang Heon; Hyun, Jung-Ho

    2017-09-01

    We investigated bacterial production (BP) and respiration (BR), as well as the physico-chemical properties of the water column, to elucidate the effect of upwelling on heterotrophic bacterial metabolic activities and growth efficiency (BGE) in July 2012 and May 2013 in the Ulleung Basin (UB), East/Japan Sea. The upwelled conditions were characterized by higher chlorophyll-a (Chl-a) concentrations resulting from the upward shift of the nitracline compared to that of the non-upwelled condition. Analyses of the size fractions of Chl-a and pigment composition revealed that large size phytoplankton (> 20 μm), mainly consisting of diatoms, appeared to be the major phytoplankton component. BP and BR were significantly correlated with Chl-a (P 0.05). These results suggest that bacterial metabolic activities are stimulated by the availability of organic resources enhanced by upwelling in the UB. Further statistical analysis showed that the difference in BP and BGE with variations in upwelling intensity were significant (P = 0.018 for BP, P = 0.035 for BGE), but the difference in BR was not significant (P = 0.321). These results suggest that metabolic energy is partitioned more for BP under a strong upwelling condition, i.e. high nutrient and Chl-a conditions. In contrast, the energy generated via respiration was partitioned more for maintaining metabolism rather than for biomass production under weakly or non-upwelled conditions, i.e. stratified and low Chl-a conditions. Overall, our results suggest that any changes in upwelling intensity would significantly affect the carbon cycle associated with the fate of primary production, and the role of the microbial loop in the UB where changes in the intensity and frequency of upwelling associated with climatic changes are in progress.

  4. Development of a novel artificial medium based on utilization of algal photosynthetic metabolites by symbiotic heterotrophs.

    Science.gov (United States)

    Watanabe, K; Imase, M; Aoyagi, H; Ohmura, N; Saiki, H; Tanaka, H

    2008-09-01

    (i) Quantitative and qualitative analyses of photosynthetic metabolites of Chlorella sorokiniana and elucidation of the mechanism of their utilization by algal symbionts. (ii) Development of artificial medium that imitates photoautotroph-heterotroph interaction and investigation of its suitability for isolation of novel microbes from the environment. Various components, including free dissolved carbohydrates, nitrogenous compounds and vitamin, were detected and together contributed 11.1% (as carbon content) of the total photosynthetic metabolites in the medium. Utilization of these photosynthetic metabolites in algal culture broth by algal symbionts was studied. Many symbionts showed specific utilization patterns. A novel artificial extracellular released organic carbon medium, which imitated the nutritional conditions surrounding algae, was developed based on the pattern of utilization of the algal metabolites by the symbiotic heterotrophs. About 42.9% of the isolates were closely related to photoautotrophic-dependent and oligotrophic bacteria. With the novel artificial medium, it was possible to selectively isolate some bacterial strains. Synthetic bacterial growth medium is an important and basic tool for bacterial isolation from environmental samples. The current study shows that preferential separation of typical bacterial subset can be achieved by using artificial medium that mimics photosynthetic metabolites.

  5. Ice formation and growth shape bacterial community structure in Baltic Sea drift ice.

    Science.gov (United States)

    Eronen-Rasimus, Eeva; Lyra, Christina; Rintala, Janne-Markus; Jürgens, Klaus; Ikonen, Vilma; Kaartokallio, Hermanni

    2015-02-01

    Drift ice, open water and under-ice water bacterial communities covering several developmental stages from open water to thick ice were studied in the northern Baltic Sea. The bacterial communities were assessed with 16S rRNA gene terminal-restriction fragment length polymorphism and cloning, together with bacterial abundance and production measurements. In the early stages, open water and pancake ice were dominated by Alphaproteobacteria and Actinobacteria, which are common bacterial groups in Baltic Sea wintertime surface waters. The pancake ice bacterial communities were similar to the open-water communities, suggesting that the parent water determines the sea-ice bacterial community in the early stages of sea-ice formation. In consolidated young and thick ice, the bacterial communities were significantly different from water bacterial communities as well as from each other, indicating community development in Baltic Sea drift ice along with ice-type changes. The thick ice was dominated by typical sea-ice genera from classes Flavobacteria and Gammaproteobacteria, similar to those in polar sea-ice bacterial communities. Since the thick ice bacterial community was remarkably different from that of the parent seawater, results indicate that thick ice bacterial communities were recruited from the rarer members of the seawater bacterial community. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

    Science.gov (United States)

    Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle

    2017-07-05

    Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.

  7. Microbial Functioning and Community Structure Variability in the Mesopelagic and Epipelagic Waters of the Subtropical Northeast Atlantic Ocean

    NARCIS (Netherlands)

    Baltar, F.; Aristegui, J.; Gasol, J.M.; Herndl, G.J.

    2012-01-01

    We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0

  8. Bacterial community diversity of the deep-sea octocoral Paramuricea placomus

    Directory of Open Access Journals (Sweden)

    Christina A. Kellogg

    2016-09-01

    Full Text Available Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

  9. Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

    Directory of Open Access Journals (Sweden)

    Jacob D. Hosen

    2017-08-01

    Full Text Available Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition

  10. Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

    Science.gov (United States)

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

    2013-01-01

    Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

  11. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Chroňáková, Alica; Krištůfek, Václav; Kuchtová, B.; Čapková, K.; Scharfen, J.; Čapek, P.; Doležal, J.

    2015-01-01

    Roč. 6, April (2015), Article 304 ISSN 1664-302X Institutional support: RVO:60077344 Keywords : heterotrophic microbial community * subnival soil * life strategy * Ladakh * mountains * Himalayas Subject RIV: EE - Microbiology, Virology Impact factor: 4.165, year: 2015

  12. Strong, weak, and missing links in a microbial community of the N.W. Mediterranean Sea.

    Science.gov (United States)

    Bettarel, Y; Dolan, J R; Hornak, K; Lemée, R; Masin, M; Pedrotti, M-L; Rochelle-Newall, E; Simek, K; Sime-Ngando, T

    2002-12-01

    Planktonic microbial communities often appear stable over periods of days and thus tight links are assumed to exist between different functional groups (i.e. producers and consumers). We examined these links by characterizing short-term temporal correspondences in the concentrations and activities of microbial groups sampled from 1 m depth, at a coastal site of the N.W. Mediterranean Sea, in September 2001 every 3 h for 3 days. We estimated the abundance and activity rates of the autotrophic prokaryote Synechococcus, heterotrophic bacteria, viruses, heterotrophic nanoflagellates, as well as dissolved organic carbon concentrations. We found that Synechococcus, heterotrophic bacteria, and viruses displayed distinct patterns. Synechococcus abundance was greatest at midnight and lowest at 21:00 and showed the common pattern of an early evening maximum in dividing cells. In contrast, viral concentrations were minimal at midnight and maximal at 18:00. Viral infection of heterotrophic bacteria was rare (0.5-2.5%) and appeared to peak at 03:00. Heterotrophic bacteria, as % eubacteria-positive cells, peaked at midday, appearing loosely related to relative changes in dissolved organic carbon concentration. Bacterial production as assessed by leucine incorporation showed no consistent temporal pattern but could be related to shifts in the grazing rates of heterotrophic nanoflagellates and viral infection rates. Estimates of virus-induced mortality of heterotrophic bacteria, based on infection frequencies, were only about 10% of cell production. Overall, the dynamics of viruses appeared more closely related to Synechococcus than to heterotrophic bacteria. Thus, we found weak links between dissolved organic carbon concentration, or grazing, and bacterial activity, a possibly strong link between Synechococcus and viruses, and a missing link between light and viruses.

  13. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

    Directory of Open Access Journals (Sweden)

    Lidianne L. Rocha

    2016-01-01

    Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

  14. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

    Science.gov (United States)

    Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

    2016-01-01

    We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

  15. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  16. Impact of disinfection on drinking water biofilm bacterial community.

    Science.gov (United States)

    Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-11-01

    Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

  17. Growth of legionella and other heterotrophic bacteria in a circulating cooling water system exposed to ultraviolet irradiation

    International Nuclear Information System (INIS)

    Kusnetsov, J.M.; Miettinen, I.T.; Martikainen, P.J.; Keskitalo, P.J.; Ahonen, H.E.; Tulkki, A.I.

    1994-01-01

    The effect of ultraviolet irradiation on the growth and occurrence of legionella and other heterotrophic bacteria in a circulating cooling water system was studied. Water of the reservoir was circulated once in 28 h through a side-stream open channel u.v. radiator consisting of two lamps. Viable counts of legionellas and heterotrophic bacteria in water immediately after the u.v. treatment were 0-12 and 0.7-1.2% of those in the reservoir, respectively. U.v. irradiation increased the concentration of easily assimilable organic carbon. In the u.v. irradiated water samples incubated in the laboratory the viable counts of heterotropic bacteria reached the counts in reservoir water within 5 d. The increase in viable counts was mainly due to reactivation of bacterial cells damaged by u.v. light, not because of bacterial multiplication. Despite u.v. irradiation the bacterial numbers in the reservoir water, including legionellas, did not decrease during the experimental period of 33 d. The main growth of bacteria in the reservoir occurred in biofilm and sediment, which were never exposed to u.v. irradiation. (Author)

  18. Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

    Science.gov (United States)

    Wu, M.; Wang, H.; Wang, N.; Wang, M.

    2017-12-01

    Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

  19. Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system.

    Science.gov (United States)

    She, Siyuan; Niu, Jiaojiao; Zhang, Chao; Xiao, Yunhua; Chen, Wu; Dai, Linjian; Liu, Xueduan; Yin, Huaqun

    2017-03-01

    Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

  20. Studies on phytoplankton-bacterial interactions

    Digital Repository Service at National Institute of Oceanography (India)

    DeCosta, P.M.

    community was most diverse during the pre- monsoon period. Heterotrophic dinoflagellates were abundant in the water column as well as sediment. A seasonal cycling between vegetative and resting cysts of autotrophic and heterotrophic dinoflagellates... governed by the environmental characteristics of the study area was observed. Temperature, salinity and Suspended Particulate Matter (SPM) were the main factors affecting dinoflagellate community structure in both the water column and sediment...

  1. The bacterial community of entomophilic nematodes and host beetles.

    Science.gov (United States)

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. © 2016 John Wiley & Sons Ltd.

  2. Strategies for managing rival bacterial communities: Lessons from burying beetles.

    Science.gov (United States)

    Duarte, Ana; Welch, Martin; Swannack, Chris; Wagner, Josef; Kilner, Rebecca M

    2018-03-01

    The role of bacteria in animal development, ecology and evolution is increasingly well understood, yet little is known of how animal behaviour affects bacterial communities. Animals that benefit from defending a key resource from microbial competitors are likely to evolve behaviours to control or manipulate the animal's associated external microbiota. We describe four possible mechanisms by which animals could gain a competitive edge by disrupting a rival bacterial community: "weeding," "seeding," "replanting" and "preserving." By combining detailed behavioural observations with molecular and bioinformatic analyses, we then test which of these mechanisms best explains how burying beetles, Nicrophorus vespilloides, manipulate the bacterial communities on their carcass breeding resource. Burying beetles are a suitable species to study how animals manage external microbiota because reproduction revolves around a small vertebrate carcass. Parents shave a carcass and apply antimicrobial exudates on its surface, shaping it into an edible nest for their offspring. We compared bacterial communities in mice carcasses that were either fresh, prepared by beetles or unprepared but buried underground for the same length of time. We also analysed bacterial communities in the burying beetle's gut, during and after breeding, to understand whether beetles could be "seeding" the carcass with particular microbes. We show that burying beetles do not "preserve" the carcass by reducing bacterial load, as is commonly supposed. Instead, our results suggest they "seed" the carcass with bacterial groups which are part of the Nicrophorus core microbiome. They may also "replant" other bacteria from the carcass gut onto the surface of their carrion nest. Both these processes may lead to the observed increase in bacterial load on the carcass surface in the presence of beetles. Beetles may also "weed" the bacterial community by eliminating some groups of bacteria on the carcass, perhaps through

  3. Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages

    Directory of Open Access Journals (Sweden)

    ANTONIUS SUWANTO

    2010-04-01

    Full Text Available Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages. Biodiversitas 11 (2: 65-68.Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to monitor the dynamics of the bacterial communities associated with early developmental stages of white shrimp (Litopenaeus vannamei larvae. Samples for analysis were egg, hatching nauplii, 24 hours old nauplii, and 48 hours old nauplii which were collected from one cycle of production at commercial hatchery. T-RFLP results indicated that the bacterial community associated with early stages of shrimp development might be transferred vertically from broodstock via egg. There was no significant difference between bacterial communities investigated, except the bacterial community of 48 hours old nauplii. Diversity analyses showed that the bacterial community of egg had the highest diversity and evenness, meanwhile the bacterial community of 48 hours old nauplii had the lowest diversity. Nine phylotypes were found at all stages with high abundance. Those TRFs were identified as γ- proteobacteria, α-proteobacteria, and bacteroidetes group.

  4. Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters.

    Science.gov (United States)

    Farnelid, Hanna; Harder, Jens; Bentzon-Tilia, Mikkel; Riemann, Lasse

    2014-10-01

    The wide distribution of diverse nitrogenase (nifH) genes affiliated with those of heterotrophic bacteria in marine and estuarine waters indicates ubiquity and an ecologically relevant role for heterotrophic N2 -fixers (diazotrophs) in aquatic nitrogen (N) cycling. However, the lack of cultivated representatives currently precludes an evaluation of their N2 -fixing capacity. In this study, microoxic or anoxic N-free media were inoculated with estuarine Baltic Sea surface water to select for N2 -fixers. After visible growth and isolation of single colonies on oxic plates or in anoxic agar tubes, nifH gene amplicons were obtained from 64 strains and nitrogenase activity, applying the acetylene reduction assay, was confirmed for 40 strains. Two strains, one Gammaproteobacterium affiliated with Pseudomonas and one Alphaproteobacterium affiliated with Rhodopseudomonas were shown to represent established members of the indigenous diazotrophic community in the Baltic Sea, with abundances of up to 7.9 × 10(4) and 4.7 × 10(4)  nifH copies l(-1) respectively. This study reports media for successful isolation of heterotrophic diazotrophs. The applied methodology and the obtained strains will facilitate future identification of factors controlling heterotrophic diazotrophic activity in aquatic environments, which is a prerequisite for understanding and evaluating their ecology and contribution to N cycling at local and regional scales. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. Architectural design drives the biogeography of indoor bacterial communities.

    Science.gov (United States)

    Kembel, Steven W; Meadow, James F; O'Connor, Timothy K; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G Z; Bohannan, Brendan J M; Green, Jessica L

    2014-01-01

    Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.

  6. Characterization of Bioaerosol Bacterial Communities During Hazy and Foggy Weather in Qingdao, China

    Science.gov (United States)

    Qi, Jianhua; Li, Mengzhe; Zhen, Yu; Wu, Lijing

    2018-06-01

    This study was conducted to evaluate the impact of hazy and foggy weather on the bacterial communities in bioaerosols, for which samples were collected from the Qingdao coastal region on sunny, foggy, and hazy days in January and March 2013. Bacterial community compositions were determined using polymerase chain reaction denaturing gradient gel electrophoresis (PCRDGGE). The bacterial community diversity was found to be high on foggy and hazy days, and the dominant species differed during hazy weather. The Shannon-Wiener index revealed that the bacterial community diversity of coarse particles was higher than that of fine particles in the bioaerosols. The bacterial community diversity of fine particles significantly correlated with relative humidity (RH; r 2 = 0.986). The cluster analysis results indicated that the bacterial communities on sunny days differed from those on hazy and foggy days. Compared with sunny days, the bacterial communities in the fine particles during hazy weather exhibited greater changes than those in the coarse particles. Most of the sequenced bacteria were found to be closely affiliated with uncultured bacteria. During hazy weather, members of the classes Bacilli and Gammaproteobacteria ( Pseudomonas and Acinetobacter) were dominant. The DGGE analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, and their relative percentages to all the measured species changed significantly on hazy days, particularly in the fine particles. Haze and fog had a significant impact on the bacterial communities in bioaerosols, and the bacterial community diversity varied on different hazy days.

  7. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Chroňáková, A.; Krištůfek, V.; Kuchtová, B.; Čapková, Kateřina; Scharfen, J.; Čapek, P.; Doležal, Jiří

    2015-01-01

    Roč. 6, č. 304 (2015), s. 1-16 ISSN 1664-302X R&D Projects: GA ČR GA13-13368S Institutional support: RVO:67985939 Keywords : heterotrophic microbial community * hesubnival soil * life strategy Subject RIV: EF - Botanics Impact factor: 4.165, year: 2015

  8. Assessing Interactions of Multiple Agrichemicals by Using Bacterial Assemblages in a Wetland Mesocosm System

    Directory of Open Access Journals (Sweden)

    Bruce Libman

    2005-08-01

    Full Text Available Agrichemicals may enter wetlands located adjacent to or downstream from agricultural fields. We investigated the individual and interactive effects of three agrichemicals [atrazine, chlorpyrifos, and monosodium acid methanearsonate (MSMA] and methyl mercury on abundance and heterotrophic potential of wetland heterotrophic bacteria assemblages. We used a factorial experimental design, in which chemicals were introduced in all possible combinations to 66 500-liter mesocosms at the Biological Field Station of the University of Mississippi. Methyl mercury was added to bring the total mercury (HG concentration to 0.4 mg/Kg wet weight at the sediment surface. Atrazine, chlorpyrifos, and MSMA were added at concentrations of 192, 51, and 219μg/L, respectively. Over 32 days of exposure, microbial heterotrophic activity was sensitive to only the interactive effect of HG*ATR*CPF in the sediments and only CPF in the water. Total bacterial numbers did not exhibit any significant treatment effects. Therefore, the effects of agrichemicals were reflected on cell-specific bacterial heterotrophic activity rather than bacterial population size.

  9. Seasonal and spatial variations in heterotrophic nanoflagellate and bacteria abundances in sediments of a freshwater littoral zone

    NARCIS (Netherlands)

    Starink, Mathieu; Bär-Gilissen, M.J.; Cappenberg, T.E.

    1996-01-01

    We studied seasonal variation in heterotrophic nanoflagellates (HNAN) and bacterial, densities at different depths in the sediment of two freshwater littoral stations. Station 1 was in a reed bed of Phragmites australis; station 2 was outside the reed zone in open water. Benthic HNAN abundances

  10. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  11. Formation of Chromophoric Dissolved Organic Matter by Bacterial Degradation of Phytoplankton-Derived Aggregates

    Directory of Open Access Journals (Sweden)

    Joanna D. Kinsey

    2018-01-01

    Full Text Available Organic matter produced and released by phytoplankton during growth is processed by heterotrophic bacterial communities that transform dissolved organic matter into biomass and recycle inorganic nutrients, fueling microbial food web interactions. Bacterial transformation of phytoplankton-derived organic matter also plays a poorly known role in the formation of chromophoric dissolved organic matter (CDOM which is ubiquitous in the ocean. Despite the importance of organic matter cycling, growth of phytoplankton and activities of heterotrophic bacterial communities are rarely measured in concert. To investigate CDOM formation mediated by microbial processing of phytoplankton-derived aggregates, we conducted growth experiments with non-axenic monocultures of three diatoms (Skeletonema grethae, Leptocylindrus hargravesii, Coscinodiscus sp. and one haptophyte (Phaeocystis globosa. Phytoplankton biomass, carbon concentrations, CDOM and base-extracted particulate organic matter (BEPOM fluorescence, along with bacterial abundance and hydrolytic enzyme activities (α-glucosidase, β-glucosidase, leucine-aminopeptidase were measured during exponential growth and stationary phase (~3–6 weeks and following 6 weeks of degradation. Incubations were performed in rotating glass bottles to keep cells suspended, promoting cell coagulation and, thus, formation of macroscopic aggregates (marine snow, more similar to surface ocean processes. Maximum carbon concentrations, enzyme activities, and BEPOM fluorescence occurred during stationary phase. Net DOC concentrations (0.19–0.46 mg C L−1 increased on the same order as open ocean concentrations. CDOM fluorescence was dominated by protein-like signals that increased throughout growth and degradation becoming increasingly humic-like, implying the production of more complex molecules from planktonic-precursors mediated by microbial processing. Our experimental results suggest that at least a portion of open

  12. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  13. Production of heterotrophic bacteria inhabiting macroscopic organic aggregates (marine snow) from surface waters

    International Nuclear Information System (INIS)

    Alldredge, A.L.; Cole, J.J.; Caron, D.A.

    1986-01-01

    Macroscopic detrital aggregates, known as marine snow, are a ubiquitous and abundant component of the marine pelagic zone. Descriptions of microbial communities occurring at densities 2-5 orders of magnitude higher on these particles than in the surrounding seawater have led to the suggestion that marine snow may be a site of intense heterotrophic activity. The authors tested this hypothesis using incorporation of [ 3 H]thymidine into macromolecules as a measure of bacterial growth occurring on marine snow from oceanic waters in the North Atlantic and from neritic waters off southern California. Abundances of marine snow ranged from 0.1 to 4.3 aggregates per liter. However, only 0.1-4% ration per cell on aggregates was generally equal to or lower than that of bacteria found free-living in the surrounding seawater, indicating that attached bacteria were not growing more rapidly than free-living bacteria. Bacteria inhabiting aggregates were up to 25 times larger than free-living forms

  14. Polyphasic bacterial community analysis of an aerobic activated sludge removing phenols and thiocyanate from coke plant effluent

    Energy Technology Data Exchange (ETDEWEB)

    Felfoldi, T.; Szekely, A.J.; Goral, R.; Barkacs, K.; Scheirich, G.; Andras, J.; Racz, A.; Marialigeti, K. [Eotvos Lorand University, Budapest (Hungary). Dept. of Microbiology

    2010-05-15

    Biological purification processes are effective tools in the treatment of hazardous wastes such as toxic compounds produced in coal coking. In this study, the microbial community of a lab-scale activated sludge system treating coking effluent was assessed by cultivation-based (strain isolation and identification, biodegradation tests) and culture-independent techniques (sequence-aided T-RFLP, taxon-specific PCR). The results of the applied polyphasic approach showed a simple microbial community dominated by easily culturable heterotrophic bacteria. Comamonas badia was identified as the key microbe of the system, since it was the predominant member of the bacterial community, and its phenol degradation capacity was also proved. Metabolism of phenol, even at elevated concentrations (up to 1500 mg/L), was also presented for many other dominant (Pseudomonas, Rhodanobacter, Oligella) and minor (Alcaligenes, Castellaniella, Microbacterium) groups, while some activated sludge bacteria (Sphingomonas, Rhodopseudomonas) did not tolerate it even in lower concentrations (250 mg/L). In some cases, closely related strains showed different tolerance and degradation properties. Members of the genus Thiobacillus were detected in the activated sludge, and were supposedly responsible for the intensive thiocyanate biodegradation observed in the system. Additionally, some identified bacteria (e.g. C. badia and the Ottowia-related strains) might also have had a significant impact on the structure of the activated sludge due to their floc-forming abilities.

  15. Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

    Science.gov (United States)

    Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

    2015-01-01

    Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

  16. Heterotrophic bacteria in soils of Larsemann Oasis of East Antarctica

    Science.gov (United States)

    Churilin, Nikita; Soina, Vera

    2015-04-01

    The study of diversity and functional state of microorganisms in subsurface rocks layers, their participation in the biochemical weathering and formation of organic horizons of soils is important for understanding ecology and microorganisms in Antarctic soils. The study of cultured forms of microorganisms and their potential viability is still relevant to characterize the physiological state, biological activity and resilience of microorganisms involved in the initial soil formation. Improvement of isolation techniques of viable bacteria from the extreme habitats has a particular importance for rising the efficiency of environmental monitoring. The aim of the study was to investigate the viable heterotrophic bacteria involved in the formation of soils from wet valleys Larsemann Oasis, which is one of the warmest ice-free space of East Antarctica. Soil samples were taken from the intermountain humid valleys, where silt-gravelly substrates formed moss, algae, lichen cover. We used nutrient solutions (trypticase soy, R2A and glucose-peptone) to isolate cultured bacteria and study their morphological types in the light microscope. The total number of microorganisms was determined by fluorescent microscopy with acridine orange. SEM was used for morphological studies of bacterial communities in situ. To activate the growth processes we added into nutrient solutions various regulatory metabolites that have dose-dependence and operate at the community level. Physiological and functional conditions were determined by the duration of the lag phase and specific growth rate of bacterial communities in nutrient solutions containing various organic substrates. Soils form under protection of «stone pavement» and organisms leave the surface, so the forming organo-mineral horizon occurs inside of rock, thus the microprofile can form on both sides of the organic horizons. UV radiation, lack of moisture and strong wind are main limiting factors for microorganisms' growth in

  17. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

    Science.gov (United States)

    Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.

    2014-01-01

    The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376

  18. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

    Directory of Open Access Journals (Sweden)

    Justin Wright

    2017-11-01

    Full Text Available The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM, has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26 with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration

  19. Characterisation of the bacterial community structures in the intestine of Lampetra morii.

    Science.gov (United States)

    Li, Yingying; Xie, Wenfang; Li, Qingwei

    2016-07-01

    The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response.

  20. Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

    Science.gov (United States)

    Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

    2017-11-01

    The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

  1. Variation of a benthic heterotrophic bacteria community with different respiratory metabolisms in Coyuca de Benítez coastal lagoon (Guerrero, Mexico

    Directory of Open Access Journals (Sweden)

    María Jesús Ferrara-Guerrero

    2007-03-01

    Full Text Available The fluctuations of the number, biomass and composition of the heterotrophic community were studied daily for two days, according to depth, pH, Eh, O2 and organic carbon concentration within a zone of the canal between the Coyuca de Benítez lagoon (Guerrero, Mexico and the coastal waters. At the three moments of the day studied (6 am, 2 pm and 10 pm, the oxygen concentrations in the overlying water and in the superficial sediment layer were near air-saturation in the diurnal samplings (582 µM at 6 am and 665 µM at 2 pm, and sub-satured during the night (158 µM. In the sediments, the models of vertical distribution of Eh and organic carbon distributions were very irregular due to the bio-perturbation of the benthic, meio- and macrofauna, whose activity allows the superficial organic carbon to migrate towards sediment deeper layers. Vertical distribution of the different viable bacteria populations seems to be related to the hydrodynamic patterns of the communicating canal and sediments heterogeneity. In the sediment column, the heterotrophic bacteria total number varied from 6.8 to 20.3 x 108 cells cm-3. The highest heterotrophic bacterial biomass values were encountered during the diurnal samplings (39.2 µgC.l-1 at 6 am and 34.4 µgC.l-1 at 2 pm and the lowest during the night (9.7 µgC.l-1. The fluctuations of viable heterotrophic bacteria populations with different respiratory metabolisms (aerobic, microaerophilic and anaerobic can be explained by the existence of suboxic microniches that appear when particles of sediment are resuspended due to the water circulation and the benthic infauna excavating activity, that allows the supernatant water oxygen to penetrate through its galleries towards deeper sediment zones. The statistical analysis (Multiple lineal regression model r²≥ 0.5 showed that the on the whole, the hydrological parameters are not influence over the bacterial number and bacterial biomass distribution (r²≤ 0

  2. Plants of the fynbos biome harbour host species-specific bacterial communities.

    Science.gov (United States)

    Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

    2016-08-01

    The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Analysis of soil whole- and inner-microaggregate bacterial communities

    Energy Technology Data Exchange (ETDEWEB)

    Mummey, D L; Stahl, P D [University of Wyoming, Laramie, WY (United States). Dept. of Renewable Resources

    2004-07-01

    Although soil structure largely determines energy flows and the distribution and composition of soil microhabitats, little is known about how microbial community composition is influenced by soil structural characteristics and organic matter compartmentalization dynamics. A UV irradiation-based procedure was developed to specifically isolate inner-microaggregate microbial communities, thus providing the means to analyze these communities in relation to their environment. Whole- and inner-microaggregate fractions of undisturbed soil and soils reclaimed after disturbance by surface coal mining were analyzed using 16S rDNA terminal restriction fragment polymorphism (T-RFLP) and sequence analyses to determine salient bacterial community structural characteristics. We hypothesized that inner-microaggregate environments select for definable microbial communities and that, due to their sequestered environment, inner-microaggregate communities would not be significantly impacted by disturbance. However, T-RFLP analysis indicated distinct differences between bacterial populations of inner-microaggregates of undisturbed and reclaimed soils. While both undisturbed and reclaimed inner-microaggregate bacterial communities were dominated by Actinobacteria, undisturbed soils contained only Actinobacteridae, while in inner-microaggregates of reclaimed soils Rubrobacteridae predominate. Spatial stratification of division-level lineages within microaggregates was also seen. The fractionation methods employed in this study therefore represent a valuable tool for defining relationships between biodiversity and soil structure.

  4. Parental material and cultivation determine soil bacterial community structure and fertility.

    Science.gov (United States)

    Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu

    2015-01-01

    Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate

  5. Microbial Community Composition and Ultrastructure of Granules from a Full-Scale Anammox Reactor

    KAUST Repository

    Gonzalez-Gil, Graciela

    2014-12-11

    Granules in anammox reactors contain besides anammox bacteria other microbial communities whose identity and relationship with the anammox bacteria are not well understood. High calcium concentrations are often supplied to anammox reactors to obtain sufficient bacterial aggregation and biomass retention. The aim of this study was to provide the first characterization of bacterial and archaeal communities in anammox granules from a full-scale anammox reactor and to explore on the possible role of calcium in such aggregates. High magnification imaging using backscattered electrons revealed that anammox bacteria may be embedded in calcium phosphate precipitates. Pyrosequencing of 16S rRNA gene fragments showed, besides anammox bacteria (Brocadiacea, 32 %), substantial numbers of heterotrophic bacteria Ignavibacteriacea (18 %) and Anaerolinea (7 %) along with heterotrophic denitrifiers Rhodocyclacea (9 %), Comamonadacea (3 %), and Shewanellacea (3 %) in the granules. It is hypothesized that these bacteria may form a network in which heterotrophic denitrifiers cooperate to achieve a well-functioning denitrification system as they can utilize the nitrate intrinsically produced by the anammox reaction. This network may provide a niche for the proliferation of archaea. Hydrogenotrophic methananogens, which scavenge the key fermentation product H2, were the most abundant archaea detected. Cells resembling the polygon-shaped denitrifying methanotroph Candidatus Methylomirabilis oxyfera were observed by electron microscopy. It is hypothesized that the anammox process in a full-scale reactor triggers various reactions overall leading to efficient denitrification and a sink of carbon as biomass in anammox granules.

  6. Microbial community composition and ultrastructure of granules from a full-scale anammox reactor.

    Science.gov (United States)

    Gonzalez-Gil, Graciela; Sougrat, Rachid; Behzad, Ali R; Lens, Piet N L; Saikaly, Pascal E

    2015-07-01

    Granules in anammox reactors contain besides anammox bacteria other microbial communities whose identity and relationship with the anammox bacteria are not well understood. High calcium concentrations are often supplied to anammox reactors to obtain sufficient bacterial aggregation and biomass retention. The aim of this study was to provide the first characterization of bacterial and archaeal communities in anammox granules from a full-scale anammox reactor and to explore on the possible role of calcium in such aggregates. High magnification imaging using backscattered electrons revealed that anammox bacteria may be embedded in calcium phosphate precipitates. Pyrosequencing of 16S rRNA gene fragments showed, besides anammox bacteria (Brocadiacea, 32%), substantial numbers of heterotrophic bacteria Ignavibacteriacea (18%) and Anaerolinea (7%) along with heterotrophic denitrifiers Rhodocyclacea (9%), Comamonadacea (3%), and Shewanellacea (3%) in the granules. It is hypothesized that these bacteria may form a network in which heterotrophic denitrifiers cooperate to achieve a well-functioning denitrification system as they can utilize the nitrate intrinsically produced by the anammox reaction. This network may provide a niche for the proliferation of archaea. Hydrogenotrophic methananogens, which scavenge the key fermentation product H2, were the most abundant archaea detected. Cells resembling the polygon-shaped denitrifying methanotroph Candidatus Methylomirabilis oxyfera were observed by electron microscopy. It is hypothesized that the anammox process in a full-scale reactor triggers various reactions overall leading to efficient denitrification and a sink of carbon as biomass in anammox granules.

  7. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

    DEFF Research Database (Denmark)

    Bergauer, Kristin; Fernandez-Guerra, Antonio; Garcia, Juan A L

    2018-01-01

    The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter...... as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities...... collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted...

  8. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

    Science.gov (United States)

    Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

    2016-01-01

    Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

  9. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

    Directory of Open Access Journals (Sweden)

    Laura Delgado-Balbuena

    Full Text Available Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826 accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485 inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100% > earthworms applied (92% > organic material applied (77% > untreated soil (57% > surfactant applied (34% after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil

  10. Antibiotic resistance in triclosan heterotrophic plate count bacteria from sewage water / Ilsé Coetzee

    OpenAIRE

    Coetzee, Ilsé

    2015-01-01

    The concentration of triclosan in antiseptics, disinfectants and preservatives in products exceeds the minimal lethal levels. Extensive use of triclosan and antibiotics results in bacterial resistance to their active ingredients. The precise relationship between use and resistance, however, has been challenging to define. The aim of the study was to identify and determine antibiotic resistance profiles of triclosan tolerant heterotrophic plate count bacteria isolates from sewag...

  11. Changes in the bacterial community of soybean rhizospheres during growth in the field.

    Science.gov (United States)

    Sugiyama, Akifumi; Ueda, Yoshikatsu; Zushi, Takahiro; Takase, Hisabumi; Yazaki, Kazufumi

    2014-01-01

    Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

  12. Invasive lionfish harbor a different external bacterial community than native Bahamian fishes

    Science.gov (United States)

    Stevens, J. L.; Olson, J. B.

    2013-12-01

    The introduction and subsequent spread of lionfish into the Atlantic Ocean and Caribbean Sea has become a worldwide conservation issue. These highly successful invaders may also be capable of introducing non-native microorganisms to the invaded regions. This study compared the bacterial communities associated with lionfish external tissue to those of native Bahamian fishes and ambient water. Terminal restriction fragment length polymorphism analyses demonstrated that lionfish bacterial communities were significantly different than those associated with three native Bahamian fishes. Additionally, all fishes harbored distinct bacterial communities from the ambient bacterioplankton. Analysis of bacterial clone libraries from invasive lionfish and native squirrelfish indicated that lionfish communities were more diverse than those associated with squirrelfish, yet did not contain known fish pathogens. Using microscopy and molecular genetic approaches, lionfish eggs were examined for the presence of bacteria to evaluate the capacity for vertical transmission. Eggs removed from the ovaries of gravid females were free of bacteria, suggesting that lionfish likely acquire bacteria from the environment. This study was the first examination of bacterial communities associated with the invasive lionfish and indicated that they support different communities of environmentally derived bacteria than Caribbean reef fishes.

  13. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

    Science.gov (United States)

    Luo, Gang; Angelidaki, Irini

    2014-09-01

    The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier

  14. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

    DEFF Research Database (Denmark)

    Jurburg, Stephanie D.; Nunes, Ines Marques; Stegen, James C.

    2017-01-01

    The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In ord...... diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery....... to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days...... slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme...

  15. Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

    Science.gov (United States)

    Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

    2011-01-01

    Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

  16. The Role of Heterotrophic Microbial Communities in Estuarine C Budgets and the Biogeochemical C Cycle with Implications for Global Warming: Research Opportunities and Challenges.

    Science.gov (United States)

    Anderson, O Roger

    2016-05-01

    Estuaries are among the most productive and economically important marine ecosystems at the land-ocean interface and contribute significantly to exchange of CO2 with the atmosphere. Estuarine microbial communities are major links in the biogeochemical C cycle and flow of C in food webs from primary producers to higher consumers. Considerable attention has been given to bacteria and autotrophic eukaryotes in estuarine ecosystems, but less research has been devoted to the role of heterotrophic eukaryotic microbes. Current research is reviewed here on the role of heterotrophic eukaryotic microbes in C biogeochemistry and ecology of estuaries, with particular attention to C budgets, trophodynamics, and the metabolic fate of C in microbial communities. Some attention is given to the importance of these processes in climate change and global warming, especially in relation to sources and sinks of atmospheric CO2 , while also documenting the current paucity of research on the role of eukaryotic microbes that contribute to this larger question of C biogeochemistry and the environment. Some recommendations are made for future directions of research and opportunities of applying newer technologies and analytical approaches to a more refined analysis of the role of C in estuarine microbial community processes and the biogeochemical C cycle. © 2015 The Author Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

  17. Tank bromeliad water: similar or distinct environments for research of bacterial bioactives?

    Science.gov (United States)

    Carmo, F L; Santos, H F; Peixoto, R S; Rosado, A S; Araujo, F V

    2014-01-01

    The Atlantic Rainforest does not have a uniform physiognomy, its relief determines different environmental conditions that define the composition of its flora and fauna. Within this ecosystem, bromeliads that form tanks with their leaves hold water reservoirs throughout the year, maintaining complex food chains, based mainly on autotrophic and heterotrophic bacteria. Some works concluded that the water held by tank bromeliads concentrate the microbial diversity of their ecosystem. To investigate the bacterial diversity and the potential biotechnology of these ecosystems, tank bromeliads of the Neoregelia cruenta species from the Atlantic Rainforest in Brazil were used as models for this research. Bacteria isolated from these models were tested for production of bioactive compounds. DGGE of the water held by tank bromeliads was performed in different seasons, locations and sun exposure to verify whether these environmental factors affect bacterial communities. The DGGE bands profile showed no grouping of bacterial community by the environmental factors tested. Most of the isolates demonstrated promising activities in the tests performed. Collectively, these results suggest that tank bromeliads of the N. cruenta species provide important habitats for a diverse microbial community, suggesting that each tank forms a distinct micro-habitat. These tanks can be considered excellent sources for the search for new enzymes and/or new bioactive composites of microbial origin.

  18. Assessing the impact of fungicide enostroburin application on bacterial community in wheat phyllosphere.

    Science.gov (United States)

    Gu, Likun; Bai, Zhihui; Jin, Bo; Hu, Qing; Wang, Huili; Zhuang, Guoqiang; Zhang, Hongxun

    2010-01-01

    Fungicides have been used extensively for controlling fungal pathogens of plants. However, little is known regarding the effects that fungicides upon the indigenous bacterial communities within the plant phyllosphere. The aims of this study were to assess the impact of fungicide enostroburin upon bacterial communities in wheat phyllosphere. Culture-independent methodologies of 16S rDNA clone library and 16S rDNA directed polymerase chain reaction with denaturing gradient gel electrophoresis (PCR-DGGE) were used for monitoring the change of bacterial community. The 16S rDNA clone library and PCR-DGGE analysis both confirmed the microbial community of wheat plant phyllosphere were predominantly of the gamma-Proteobacteria phyla. Results from PCR-DGGE analysis indicated a significant change in bacterial community structure within the phyllosphere following fungicide enostroburin application. Bands sequenced within control cultures were predominantly of Pseudomonas genus, but those bands sequenced in the treated samples were predominantly strains of Pantoea genus and Pseudomonas genus. Of interest was the appearance of two DGGE bands following fungicide treatment, one of which had sequence similarities (98%) to Pantoea sp. which might be a competitor of plant pathogens. This study revealed the wheat phyllosphere bacterial community composition and a shift in the bacterial community following fungicide enostroburin application.

  19. Recolonization by heterotrophic bacteria after UV irradiation or ozonation of seawater; a simulation of ballast water treatment.

    Science.gov (United States)

    Hess-Erga, Ole-Kristian; Blomvågnes-Bakke, Bente; Vadstein, Olav

    2010-10-01

    Transport of ballast water with ships represents a risk for introduction of foreign species. If ballast water is treated during uptake, there will be a recolonization of the ballast water by heterotrophic bacteria during transport. We investigated survival and succession of heterotrophic bacteria after disinfection of seawater in the laboratory, representing a model system of ballast water treatment and transport. The seawater was exposed to ultraviolet (UV) irradiation, ozone (2 doses) or no treatment, incubated for 16 days and examined with culture-dependent and -independent methods. The number of colony-forming units (CFU) was reduced below the detection level after disinfection with UV and high ozone dose (700 mV), and 1% of the initial level for the low ozone dose (400 mV). After less than 3 days, the CFU was back or above the starting point for the control, UV and low ozone treatment, whereas it took slightly more than 6 days for the high ozone treatment. Disinfection increased substrate availability and reduced cell densities. Lack of competition and predation induced the recolonization by opportunistic bacteria (r-strategists), with significant increase in bacterial numbers and a low diversity (based on DGGE band pattern). All cultures stabilized after the initial recolonization phase (except Oz700) where competition due to crowding and nutrient limitation favoured bacteria with high substrate affinity (K-strategists), resulting in higher species richness and diversity (based on DGGE band pattern). The bacterial community was significantly altered qualitatively and quantitatively and may have a higher potential as invaders in the recipient depending on disinfection method and the time of release. These results have implications for the treatment strategy used for ballast water. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Patterning bacterial communities on epithelial cells.

    Directory of Open Access Journals (Sweden)

    Mohammed Dwidar

    Full Text Available Micropatterning of bacteria using aqueous two phase system (ATPS enables the localized culture and formation of physically separated bacterial communities on human epithelial cell sheets. This method was used to compare the effects of Escherichia coli strain MG1655 and an isogenic invasive counterpart that expresses the invasin (inv gene from Yersinia pseudotuberculosis on the underlying epithelial cell layer. Large portions of the cell layer beneath the invasive strain were killed or detached while the non-invasive E. coli had no apparent effect on the epithelial cell layer over a 24 h observation period. In addition, simultaneous testing of the localized effects of three different bacterial species; E. coli MG1655, Shigella boydii KACC 10792 and Pseudomonas sp DSM 50906 on an epithelial cell layer is also demonstrated. The paper further shows the ability to use a bacterial predator, Bdellovibriobacteriovorus HD 100, to selectively remove the E. coli, S. boydii and P. sp communities from this bacteria-patterned epithelial cell layer. Importantly, predation and removal of the P. Sp was critical for maintaining viability of the underlying epithelial cells. Although this paper focuses on a few specific cell types, the technique should be broadly applicable to understand a variety of bacteria-epithelial cell interactions.

  1. Spatial variation of bacterial community composition near the Luzon ...

    African Journals Online (AJOL)

    Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis ... chain reaction (PCR)-amplified bacterial 16S ribosomal deoxyribonucleic acid (DNA) gene fragments and interpreted the results; its relationship with physical and ...

  2. Canopy soil bacterial communities altered by severing host tree limbs

    Directory of Open Access Journals (Sweden)

    Cody R. Dangerfield

    2017-09-01

    Full Text Available Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

  3. Temperature adaptation of bacterial communities in experimentally warmed forest soils.

    Science.gov (United States)

    Rousk, Johannes; Frey, Serita D; Bååth, Erland

    2012-10-01

    A detailed understanding of the influence of temperature on soil microbial activity is critical to predict future atmospheric CO 2 concentrations and feedbacks to anthropogenic warming. We investigated soils exposed to 3-4 years of continuous 5 °C-warming in a field experiment in a temperate forest. We found that an index for the temperature adaptation of the microbial community, T min for bacterial growth, increased by 0.19 °C per 1 °C rise in temperature, showing a community shift towards one adapted to higher temperature with a higher temperature sensitivity (Q 10(5-15 °C) increased by 0.08 units per 1 °C). Using continuously measured temperature data from the field experiment we modelled in situ bacterial growth. Assuming that warming did not affect resource availability, bacterial growth was modelled to become 60% higher in warmed compared to the control plots, with the effect of temperature adaptation of the community only having a small effect on overall bacterial growth (bacterial growth, most likely due to substrate depletion because of the initially higher growth in warmed plots. When this was factored in, the result was similar rates of modelled in situ bacterial growth in warmed and control plots after 3 years, despite the temperature difference. We conclude that although temperature adaptation for bacterial growth to higher temperatures was detectable, its influence on annual bacterial growth was minor, and overshadowed by the direct temperature effect on growth rates. © 2012 Blackwell Publishing Ltd.

  4. Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

    Science.gov (United States)

    Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

    2017-12-19

    Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

  5. Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy.

    Science.gov (United States)

    Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin; Lamendella, Regina

    2016-06-15

    Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial

  6. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing

    DEFF Research Database (Denmark)

    Luo, Gang; Angelidaki, Irini

    2014-01-01

    with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature......The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community...... showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor...

  7. Bacterial community composition of a wastewater treatment system reliant on N{sub 2} fixation

    Energy Technology Data Exchange (ETDEWEB)

    Reid, N.M.; Bowers, T.H.; Lloyd-Jones, G. [Scion, Rotorua (New Zealand)

    2008-05-15

    The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N{sub 2} fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by {alpha}-Proteobacteria and {beta}-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system. (orig.)

  8. Meteorological factors had more impact on airborne bacterial communities than air pollutants.

    Science.gov (United States)

    Zhen, Quan; Deng, Ye; Wang, Yaqing; Wang, Xiaoke; Zhang, Hongxing; Sun, Xu; Ouyang, Zhiyun

    2017-12-01

    Airborne bacteria have gained increasing attention because they affect ecological balance and pose potential risks on human health. Recently, some studies have focused on the abundance and composition of airborne bacteria under heavy, hazy polluted weather in China, but they reached different conclusions about the comparisons with non-polluted days. In this study, we tested the hypothesis that meteorological factors could have a higher impact on shaping airborne bacterial communities than air pollutants by systematically monitoring the communities for 1year. Total suspended particles in Beijing were sampled for 20 consecutive days in each season of 2015. Bacterial abundance varied from 8.71×10 3 to 2.14×10 7 ribosomal operons per cubic meter according to the quantitative PCR analysis. There were relatively higher bacterial counts in spring and in autumn than in winter and summer. Airborne bacterial communities displayed a strong seasonality, according to the hierarchical cluster analysis. Only two exceptions overtook the seasonal trend, and both occurred in or after violent meteorological changes (sandstorm or rain). Aggregated boosted tree analysis performed on bacterial abundance showed that the dominant factors shaping bacterial communities were meteorological. They were air pressure in winter, air temperature and relative humidity in spring, RH in summer, and vapor pressure in autumn. Variation partition analysis on community structure showed that meteorological factors explained more variations than air pollutants. Therefore, both of the two models verified our hypothesis that the differences in airborne bacterial communities in polluted days or non-polluted days were mainly driven by the discrepancies of meteorological factors rather than by the presence of air pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Safe-site effects on rhizosphere bacterial communities in a high-altitude alpine environment.

    Science.gov (United States)

    Ciccazzo, Sonia; Esposito, Alfonso; Rolli, Eleonora; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2014-01-01

    The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P floristic communities rhizospheres on their soil bacterial communities.

  10. Bacterial community from gut of white shrimp, Penaeus vannamei, cultured in earthen ponds

    Directory of Open Access Journals (Sweden)

    Supamattaya, K.

    2007-05-01

    Full Text Available The Fluorescent in situ hybridization (FISH technique and conventional method were used to analyse the bacterial community in the gut of white shrimp cultured in earthen ponds. Samples were collectedfrom three parts, hepatopancreas, anterior intestine and posterior intestine. Gut bacterial community was enumerated by 15 probes in FISH and 3 bacterial culture technique media. The results showed that bacteriaspecific probes determined bacterial community and Eubacteria as the dominant group of microbial community in the studied gut portions. β-Proteobacteria group (29.53±5.39% and γ-Proteobacteria group (26.18±6.88% were major groups of bacterial flora in the hepatopancreas. In contrast, low G+C gram positive bacteria group (LGC was the most abundant group detected in anterior intestine (36.40±3.53% andposterior intestine (30.32±4.63%. Vibrio spp. were detected very less in hepatopancreas (0.25±0.43% and were present in 3 of 9 samples. In the case of bacterial detection using cultivation method, the number ofbacterial groups verified by TSA, TCBS and MRS showed high variation in every part of the studied digestive tract portions; however, no vibrio or lactic acid bacteria were present in the hepatopancreas ofhealthy shrimp. This study reveals the proportion of bacterial community in the digestive tract of white shrimp which can be used as important database for studying the change of the bacterial community in an abnormal condition including the efficiency of probiotics in the gut (in vivo of white shrimp.

  11. Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Shih-Hsiung; Chen, Mu-Hsuan; Chen, Chien-Cheng; Chen, Colin S [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Chen, Jiun-Hong [Department of Life Science, National Taiwan University, Taipei, Taiwan (China); Chen, Ssu Ching, E-mail: osycchna@ksts.seed.net.tw [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)

    2010-12-30

    The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

  12. Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

    International Nuclear Information System (INIS)

    Liang, Shih-Hsiung; Chen, Mu-Hsuan; Chen, Chien-Cheng; Chen, Colin S.; Chen, Jiun-Hong; Chen, Ssu Ching

    2009-01-01

    The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

  13. Bacterial communities of disease vectors sampled across time, space, and species.

    Science.gov (United States)

    Jones, Ryan T; Knight, Rob; Martin, Andrew P

    2010-02-01

    A common strategy of pathogenic bacteria is to form close associations with parasitic insects that feed on animals and to use these insects as vectors for their own transmission. Pathogens interact closely with other coexisting bacteria within the insect, and interactions between co-occurring bacteria may influence the vector competency of the parasite. Interactions between particular lineages can be explored through measures of alpha-diversity. Furthermore, general patterns of bacterial community assembly can be explored through measures of beta-diversity. Here, we use pyrosequencing (n=115,924 16S rRNA gene sequences) to describe the bacterial communities of 230 prairie dog fleas sampled across space and time. We use these communinty characterizations to assess interactions between dominant community members and to explore general patterns of bacterial community assembly in fleas. An analysis of co-occurrence patterns suggests non-neutral negative interactions between dominant community members (Pspace (phylotype-based: R=0.418, Pspace and time.

  14. Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting.

    Science.gov (United States)

    Huhe; Jiang, Chao; Wu, Yanpei; Cheng, Yunxiang

    2017-12-01

    During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high-throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed. Bacterial and fungal community diversity and relative abundance varied significantly, and inversely, over time. Relationships between physicochemical factors and microbial community compositions were evaluated by redundancy analysis. The variation in bacterial community composition was significantly related to water-soluble organic carbon (WSOC), and pile temperature and moisture (p composts. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  15. Effects of remediation on the bacterial community of an acid mine drainage impacted stream.

    Science.gov (United States)

    Ghosh, Suchismita; Moitra, Moumita; Woolverton, Christopher J; Leff, Laura G

    2012-11-01

    Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

  16. Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

    Science.gov (United States)

    Flues, Sebastian; Bass, David; Bonkowski, Michael

    2017-08-01

    Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Bacterial communities in the fruit bodies of ground basidiomycetes

    Science.gov (United States)

    Zagryadskaya, Yu. A.; Lysak, L. V.; Chernov, I. Yu.

    2015-06-01

    Fruit bodies of basidiomycetes at different stages of decomposition serve as specific habitats in forest biocenoses for bacteria and differ significantly with respect to the total bacterial population and abundance of particular bacterial genera. A significant increase in the total bacterial population estimated by the direct microscopic method with acridine orange staining and in the population of saprotrophic bacteria (inoculation of glucose peptone yeast agar) in fruit bodies of basidiomycetes Armillaria mellea and Coprinus comatus was recorded at the final stage of their decomposition in comparison with the initial stage. Gramnegative bacteria predominated in the tissues of fruit bodies at all the stages of decomposition and were represented at the final stage by the Aeromonas, Vibrio, and Pseudomonas genera (for fruit bodies of A. mellea) the Pseudomonas genus (for fruit bodies of C. comatus). The potential influence of bacterial communities in the fruit bodies of soil basidiomycetes on the formation of bacterial communities in the upper soil horizons in forest biocenoses is discussed. The loci connected with the development and decomposition of fruit bodies of basidiomycetes on the soil surface are promising for targeted search of Gram-negative bacteria, the important objects of biotechnology.

  18. Simultaneous heterotrophic nitrification and aerobic denitrification by the marine origin bacterium Pseudomonas sp. ADN-42.

    Science.gov (United States)

    Jin, Ruofei; Liu, Tianqi; Liu, Guangfei; Zhou, Jiti; Huang, Jianyu; Wang, Aijie

    2015-02-01

    Recent research has highlighted the existence of some bacteria that are capable of performing heterotrophic nitrification and have a phenomenal ability to denitrify their nitrification products under aerobic conditions. A high-salinity-tolerant strain ADN-42 was isolated from Hymeniacidon perleve and found to display high heterotrophic ammonium removal capability. This strain was identified as Pseudomonas sp. via 16S rRNA gene sequence analysis. Gene cloning and sequencing analysis indicated that the bacterial genome contains N2O reductase function (nosZ) gene. NH3-N removal rate of ADN-42 was very high. And the highest removal rate was 6.52 mg/L · h in the presence of 40 g/L NaCl. Under the condition of pure oxygen (DO >8 mg/L), NH3-N removal efficiency was 56.9 %. Moreover, 38.4 % of oxygen remained in the upper gas space during 72 h without greenhouse gas N2O production. Keeping continuous and low level of dissolved oxygen (DO <3 mg/L) was helpful for better denitrification performance. All these results indicated that the strain has heterotrophic nitrification and aerobic denitrification abilities, which guarantee future application in wastewater treatment.

  19. Biogeography of cryoconite bacterial communities on glaciers of the Tibetan Plateau.

    Science.gov (United States)

    Liu, Yongqin; Vick-Majors, Trista J; Priscu, John C; Yao, Tandong; Kang, Shichang; Liu, Keshao; Cong, Ziyuang; Xiong, Jingbo; Li, Yang

    2017-06-01

    Cryoconite holes, water-filled pockets containing biological and mineralogical deposits that form on glacier surfaces, play important roles in glacier mass balance, glacial geochemistry and carbon cycling. The presence of cryoconite material decreases surface albedo and accelerates glacier mass loss, a problem of particular importance in the rapidly melting Tibetan Plateau. No studies have addressed the microbial community composition of cryoconite holes and their associated ecosystem processes on Tibetan glaciers. To further enhance our understanding of these glacial ecosystems on the Tibetan Plateau and to examine their role in carbon cycling as the glaciers respond to climate change, we explored the bacterial communities within cryoconite holes associated with three climatically distinct Tibetan Plateau glaciers using Illumina sequencing of the V4 region of the 16S rRNA gene. Cryoconite bacterial communities were dominated by Cyanobacteria, Chloroflexi, Betaproteobacteria, Bacteroidetes and Actinobacteria. Cryoconite bacterial community composition varied according to their geographical locations, exhibiting significant differences among glaciers studied. Regional beta diversity was driven by the interaction between geographic distance and environmental variables; the latter contributed more than geographic distance to the variation in cryoconite microbial communities. Our study is the first to describe the regional-scale spatial variability and to identify the factors that drive regional variability of cryoconite bacterial communities on the Tibetan Plateau. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra

    Directory of Open Access Journals (Sweden)

    Congcong eShen

    2015-06-01

    Full Text Available The elevational diversity pattern for microorganisms has received great attention recently but is still understudied, and phylogenetic relatedness is rarely studied for microbial elevational distributions. Using a bar-coded pyrosequencing technique, we examined the biodiversity patterns for soil bacterial communities of tundra ecosystem along 2000–2500 m elevations on Changbai Mountain in China. Bacterial taxonomic richness displayed a linear decreasing trend with increasing elevation. Phylogenetic diversity and mean nearest taxon distance (MNTD exhibited a unimodal pattern with elevation. Bacterial communities were more phylogenetically clustered than expected by chance at all elevations based on the standardized effect size of MNTD metric. The bacterial communities differed dramatically among elevations, and the community composition was significantly correlated with soil total carbon, total nitrogen, C:N ratio, and dissolved organic carbon. Multiple ordinary least squares regression analysis showed that the observed biodiversity patterns strongly correlated with soil total carbon and C:N ratio. Taken together, this is the first time that a significant bacterial diversity pattern has been observed across a small-scale elevational gradient. Our results indicated that soil carbon and nitrogen contents were the critical environmental factors affecting bacterial elevational distribution in Changbai Mountain tundra. This suggested that ecological niche-based environmental filtering processes related to soil carbon and nitrogen contents could play a dominant role in structuring bacterial communities along the elevational gradient.

  1. Submerged macrophytes modify bacterial community composition in sediments in a large, shallow, freshwater lake.

    Science.gov (United States)

    Zhao, Da-Yong; Liu, Peng; Fang, Chao; Sun, Yi-Meng; Zeng, Jin; Wang, Jian-Qun; Ma, Ting; Xiao, Yi-Hong; Wu, Qinglong L

    2013-04-01

    Submerged aquatic macrophytes are an important part of the lacustrine ecosystem. In this study, the bacterial community compositions in the rhizosphere sediments from three kinds of submerged macrophytes (Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans) were investigated to determine whether submerged macrophytes could drive the variation of bacterial community in the eutrophic Taihu Lake, China. Molecular techniques, including terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries, were employed to analyze the bacterial community compositions. Remarkable differences of the T-RFLP patterns were observed among the different samples, and the results of LIBSHUFF analysis also confirmed that the bacterial community compositions in the rhizosphere sediments of three kinds of submerged macrophytes were statistically different from that of the unvegetated sediment. Acidobacteria, Deltaproteobacteria, and Betaproteobacteria were the dominant bacterial groups in the rhizosphere sediments of Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans, respectively, accounting for 15.38%, 29.03%, and 18.00% of the total bacterial abundances. Our study demonstrated that submerged macrophytes could influence the bacterial community compositions in their rhizosphere sediments, suggesting that macrophytes have an effect on the cycling and transportation of nutrients in the freshwater lake ecosystem.

  2. Storm-scale dynamics of bacterial community composition in throughfall and stemflow

    Science.gov (United States)

    Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

    2017-12-01

    Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

  3. Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Shih-Hsiung; Chen, Mu-Hsuan; Chen, Chien-Cheng; Chen, Colin S. [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Chen, Jiun-Hong [Department of Life Science, National Taiwan University, Taipei, Taiwan (China); Chen, Ssu Ching, E-mail: osycchna@ksts.seed.net.tw [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)

    2009-12-30

    The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

  4. Structure of the Bacterial Community in Different Stages of Early Childhood Caries.

    Science.gov (United States)

    Ximenes, Marcos; Armas, Rafael Dutra de; Triches, Thaisa Cezária; Cardoso, Mariane; Vieira, Ricardo de Souza

    2018-01-15

    To characterise in vivo the structure of bacterial communities in decayed and sound primary teeth. Samples of biofilms were collected from three groups of patients with complete and exclusively primary dentition (n = 45): G1: sound teeth (n = 15); G2: enamel lesion (n = 15); G3: dentin lesion (n = 15). DNA was extracted (CTAB 2%) from the biofilm, the partial 16S rRNA gene was amplified with Bacteria Universal Primers (BA338fGC - UN518r) and subjected to DGGE (denaturing gradient gel electrophoresis). Multidimensional scaling and ANOSIM (analysis of similarity) were employed to determine the structure of the bacterial communities. The amplicon richness was determined by averaging amplicons, with the differences between treatments determined with ANOVA, while means were compared using Tukey's test (p < 0.05). Compared to sound teeth, a greater variety of bacterial communities was found in decayed teeth. Despite the differences between the bacterial communities of sound teeth and decayed teeth, the Venn diagram showed that the samples had 38 amplicons in common. Greater amplicon richness was observed in samples of decayed teeth (enamel: 20.5 ± 2.7; dentin: 20.1 ± 2.8) compared with the sound samples (12.0 ± 4.3) (p <0.05), indicating enhanced growth for specific groups of bacteria on decayed teeth. Although there is less bacterial diversity on sound than ECC-decayed teeth, the bacterial communities are very similar.

  5. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    Science.gov (United States)

    Comte, J.; Lovejoy, C.; Crevecoeur, S.; Vincent, W. F.

    2016-01-01

    Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north-south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial "keystone species". These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

  6. Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

    Directory of Open Access Journals (Sweden)

    Carolina Chiellini

    2013-01-01

    Full Text Available Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution.

  7. Shifts in the metabolic function of a benthic estuarine microbial community following a single pulse exposure to silver nanoparticles

    International Nuclear Information System (INIS)

    Echavarri-Bravo, Virginia; Paterson, Lynn; Aspray, Thomas J.; Porter, Joanne S.; Winson, Michael K.; Thornton, Barry; Hartl, Mark G.J.

    2015-01-01

    The increasing use of silver nanoparticles (AgNPs) as a biocidal agent and their potential accumulation in sediments may threaten non-target natural environmental bacterial communities. In this study a microcosm approach was established to investigate the effects of well characterized OECD AgNPs (NM-300) on the function of the bacterial community inhabiting marine estuarine sediments (salinity 31‰). The results showed that a single pulse of NM-300 AgNPs (1 mg L −1 ) that led to sediment concentrations below 6 mg Ag kg −1 dry weight inhibited the bacterial utilization of environmentally relevant carbon substrates. As a result, the functional diversity changed, but recovered after 120 h under the experimental conditions. This microcosm study suggests that AgNPs under environmentally relevant experimental conditions can negatively affect bacterial function and provides an insight into the understanding of the bacterial community response and resilience to AgNPs exposure, important for informing relevant regulatory measures. - Highlights: • AgNPs affected the bacterial community function in estuarine marine sediments. • AgNPs inhibited the bacterial utilization of environmentally relevant substrates. • Heterotrophic bacterial groups showed resilience to AgNPs after 120 h exposure. • AgNPs did not affect the bacterial community structure in sediments. - AgNPs inhibited the bacterial utilization of environmentally relevant substrates and caused temporary shifts in the bacterial functional diversity in marine estuarine sediments

  8. [Progress of heterotrophic studies on symbiotic corals].

    Science.gov (United States)

    Yang, Yang-Chu-Qiao; Hong, Wen Ting; Wang, Shu Hong

    2017-12-01

    Heterotrophy of zooxanthellae symbiotic corals refers to the nutrition directly coming from food absorption, not the nutrition obtained from photosynthesis. Most ex situ propagation of symbiotic corals focused on the effects of irradiation, flow rate and water quality on corals, few of them involved in the demand and supply of coral heterotrophic nutrition. This paper reviewed the significance of heterotrophic nutrient supply to symbiotic corals from the sources of coral heterotrophic nutrition, the factors affecting the supply of coral heterotrophic nutrient, and the methods of how to study the coral heterotrophy. In general, the research of coral heterotrophy is just at the beginning stage, and future studies should focus on the inherent mechanism of coral feeding selection and developing more effective research methods.

  9. Identification of the Bacterial Community Responsible for ...

    African Journals Online (AJOL)

    Identification of bacteria community responsible for decontaminating Eleme petrochemical industrial effluent using 16S PCR denaturing gradient gel electrophoresis (DGGE) was determined. Gene profiles were determined by extracting DNA from bacterial isolates and amplified by polymerase chain reaction (PCR) using ...

  10. Temporal dynamics of bacterial and fungal communities in a genetically modified (GM) rice ecosystem.

    Science.gov (United States)

    Lee, Seung-Hoon; Kim, Chang-Gi; Kang, Hojeong

    2011-04-01

    We assessed the temporal dynamics of bacterial and fungal communities in a soil ecosystem supporting genetically modified (GM) rice (Oryza sativa L., ABC-TPSP; fusion of trehalose-6-phosphate synthase and phosphatase). Using terminal restriction fragment length polymorphism analysis and real-time quantitative PCR, we compared bacterial and fungal communities in the soils underlying GM rice (ABC-TPSP), and its host cultivar (Nakdong) during growing seasons and non-growing seasons. Overall, the soils supporting GM and non-GM rice did not differ significantly in diversity indices, including ribotype numbers, for either bacteria or fungi. The diversity index (H) in both the bacterial and fungal communities was correlated with water content, dissolved organic carbon (DOC), and ammonium nitrogen, and the correlation was stronger in fungi than in bacteria. Multivariate analysis showed no differences in microbial community structures between the two crop genotypes, but such differences did appear in time, with significant changes observed after harvest. Gene copy number was estimated as 10(8)~10(11) and 10(5)~10(7) per gram of soil for bacteria and fungi, respectively. As observed for community structure, the rice genotypes did not differ significantly in either bacterial- or fungal-specific gene copy numbers, although we observed a seasonal change in number. We summarize the results of this study as follows. (1) GM rice did not influence soil bacterial and fungal community structures as compared to non-GM rice in our system, (2) both bacterial and fungal communities changed with the growth stage of either rice genotype, (3) fungal communities were less variable than bacterial communities, and (4) although several environmental factors, including ammonium nitrogen and DOC correlated with shifts in microbial community structure, no single factor stood out.

  11. Influence of technological treatments on bacterial communities in ...

    African Journals Online (AJOL)

    Influence of technological treatments on bacterial communities in tilapia ( Oreochromis niloticus ) as determined by 16S rDNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)

  12. The bacterial communities of Drosophila suzukii collected from undamaged cherries

    Directory of Open Access Journals (Sweden)

    James Angus Chandler

    2014-07-01

    Full Text Available Drosophila suzukii is an introduced pest insect that feeds on undamaged, attached fruit. This diet is distinct from the fallen, discomposing fruits utilized by most other species of Drosophila. Since the bacterial microbiota of Drosophila, and of many other animals, is affected by diet, we hypothesized that the bacteria associated with D. suzukii are distinct from that of other Drosophila. Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. We find that the bacterial communities associated with these samples of D. suzukii contain a high frequency of Tatumella. Gluconobacter and Acetobacter, two taxa with known associations with Drosophila, were also found, although at lower frequency than Tatumella in four of the five samples examined. Sampling D. suzukii from different locations and/or while feeding on different fruits is needed to determine the generality of the results determined by these samples. Nevertheless this is, to our knowledge, the first study characterizing the bacterial communities of this ecologically unique and economically important species of Drosophila.

  13. Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

    Science.gov (United States)

    Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

    2014-04-01

    With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

  14. The effects of wastewater effluent and river discharge on benthic heterotrophic production, organic biomass and respiration in marine coastal sediments

    International Nuclear Information System (INIS)

    Burd, B.; Macdonald, T.; Bertold, S.

    2013-01-01

    Highlights: • High river particulate flux results in low sediment P/B due to large burrowers. • Sewage deposition results in high P/B from biomass depletion and bacterial increase. • Heterotrophic production was 56% of oxidized OC flux with 35% growth efficiency. • Production was correlated with organic/inorganic flux – biomass was not. • δ 15 N patterns illustrate feeding strategies of key taxa near the outfall. -- Abstract: We examine effects of high river particulate flux and municipal wastewater effluent on heterotrophic organic carbon cycling in coastal subtidal sediments. Heterotrophic production was a predictable (r 2 = 0.95) proportion (56%) of oxidized OC flux and strongly correlated with organic/inorganic flux. Consistent growth efficiencies (36%) occurred at all stations. Organic biomass was correlated with total, OC and buried OC fluxes, but not oxidized OC flux. Near the river, production was modest and biomass high, resulting in low P/B. Outfall deposition resulted in depleted biomass and high bacterial production, resulting in the highest P/B. These patterns explain why this region is production “saturated”. The δ 15 N in outfall effluent, sediments and dominant taxa provided insight into where, and which types of organisms feed directly on fresh outfall particulates, on older, refractory material buried in sediments, or utilize chemosynthetic symbiotic bacteria. Results are discussed in the context of declining bottom oxygen conditions along the coast

  15. Spatial and vertical distribution of bacterial community in the northern South China Sea.

    Science.gov (United States)

    Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

    2015-10-01

    Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

  16. Biogeographical distribution and diversity of bacterial communities in surface sediments of the South China Sea.

    Science.gov (United States)

    Li, Tao; Wang, Peng

    2013-05-01

    This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

  17. Supraglacial bacterial community structures vary across the Greenland ice sheet

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Zarsky, Jakub D.

    2016-01-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across...... the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related...... to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community...

  18. Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

    Science.gov (United States)

    Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

    2017-01-01

    The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

  19. Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

    Directory of Open Access Journals (Sweden)

    Yinhong Hu

    2018-02-01

    Full Text Available The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete, permeable pavement (bricks with round holes, shrub coverage (Buxus megistophylla Levl., lawns (Festuca elata Keng ex E. Alexeev, and roadside trees (Sophora japonica Linn. in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC, and soil moisture content (SMC. The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and

  20. Clostridium difficile is an autotrophic bacterial pathogen.

    Directory of Open Access Journals (Sweden)

    Michael Köpke

    Full Text Available During the last decade, Clostridium difficile infection showed a dramatic increase in incidence and virulence in the Northern hemisphere. This incessantly challenging disease is the leading cause of antibiotic-associated and nosocomial infectious diarrhea and became life-threatening especially among elderly people. It is generally assumed that all human bacterial pathogens are heterotrophic organisms, being either saccharolytic or proteolytic. So far, this has not been questioned as colonization of the human gut gives access to an environment, rich in organic nutrients. Here, we present data that C. difficile (both clinical and rumen isolates is also able to grow on CO2+H2 as sole carbon and energy source, thus representing the first identified autotrophic bacterial pathogen. Comparison of several different strains revealed high conservation of genes for autotrophic growth and showed that the ability to use gas mixtures for growth decreases or is lost upon prolonged culturing under heterotrophic conditions. The metabolic flexibility of C. difficile (heterotrophic growth on various substrates as well as autotrophy could allow the organism in the gut to avoid competition by niche differentiation and contribute to its survival when stressed or in unfavorable conditions that cause death to other bacteria. This may be an important trait for the pathogenicity of C. difficile.

  1. Bacterial community profile of contaminated soils in a typical antimony mining site.

    Science.gov (United States)

    Wang, Ningning; Zhang, Suhuan; He, Mengchang

    2018-01-01

    The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb DGT , As DGT , potential ecological risk index (RI), TC, TN), among which pH, Sb DGT , and As DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

  2. The abundance and diversity of heterotrophic bacteria as a function of harvesting frequency of duckweed (Lemna minor L.) in recirculating aquaculture systems.

    Science.gov (United States)

    Ardiansyah, A; Fotedar, R

    2016-07-01

    Duckweed (Lemna minor L.) is a potential biofilter for nutrient removal and acts as a substrate for heterotrophic bacteria in recirculating aquaculture systems (RAS). Here, we determined the effects of harvesting frequency of duckweed on heterotrophic bacteria in RAS. Twelve independent RAS consisting of fish-rearing tank, biofilter tank and waste-collection tank were used to study the interactions between duckweed harvest frequencies up to 6 days and the composition, abundance and diversity of heterotrophic bacteria. After 36 days, heterotrophic bacteria in the biofilter tank were primarily Gram-negative cocci or ovoid, coccobacilli, Gram-negative bacilli and Gram-positive bacilli. Most bacterial genera were Bacillus and Pseudomonas while the least common was Acinetobacter. Duckweed harvested after every 2 days produced the highest specific growth rates (SGR) and total harvested biomass of duckweed, but harboured less abundant bacteria, whereas 6-day harvests had a higher growth index (GI) of duckweed than 2-day harvests, but caused a poor relationship between SGR and biomass harvest with the abundance and diversity of heterotrophic bacteria. Stronger correlations (R(2)  > 0·65) between duckweed SGR and biomass harvest with the heterotrophic bacteria diversity were observed at 4-day harvest frequency and the control. This study provides significant information on the interaction between the harvest frequency of duckweed and the composition, abundance and diversity of heterotrophic bacteria in recirculating aquaculture systems (RAS). Different harvest frequencies significantly influence the abundance and diversity of heterotrophic bacteria, which in turn may influence the nitrogen uptake efficiency of the system. The research is useful in improving the efficiency of removing nitrogenous metabolites in RAS directly by the duckweed and associated heterotrophic bacteria. © 2016 The Society for Applied Microbiology.

  3. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (PPCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (Pmicrobial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water based on CCA analysis, while NO3 was the only factor in sediment. Published by Elsevier B.V.

  4. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

    Science.gov (United States)

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-08-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

  5. Bacterial social interactions and the emergence of community-intrinsic properties

    DEFF Research Database (Denmark)

    Madsen, Jonas Stenløkke; Sørensen, Søren Johannes; Burmølle, Mette

    2018-01-01

    Bacterial communities are dominated and shaped by social interactions, which facilitate the emergence of properties observed only in the community setting. Such community-intrinsic properties impact not only the phenotypes of cells in a community, but also community composition and function...... on community composition and interactions in multispecies biofilms. We hereby wish to emphasize the importance of studying social interactions in settings where community-intrinsic properties are likely to emerge....

  6. Pyridine-type alkaloid composition affects bacterial community composition of floral nectar.

    Science.gov (United States)

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T; Halpern, Malka

    2015-06-30

    Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness.

  7. Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

    Science.gov (United States)

    Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

    2017-12-01

    Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

  8. Changes in bacterial community after application of three different herbicides.

    Science.gov (United States)

    Moretto, Jéssica Aparecida Silva; Altarugio, Lucas Miguel; Andrade, Pedro Avelino; Fachin, Ana Lúcia; Andreote, Fernando Dini; Stehling, Eliana Guedes

    2017-07-06

    The native soil microbiota is very important to maintain the quality of that environment, but with the intensive use of agrochemicals, changes in microbial biomass and formation of large quantities of toxic waste were observed in soil, groundwater and surface water. Thereby, the goal of this study was to evaluate if the selective pressure exerted by the presence of the herbicides atrazine, diuron and 2,4-D changes the bacterial community structure of an agricultural soil, using denaturing gradient gel electrophoresis technique. According to PERMANOVA analysis, a greater effect of the herbicide persistence time in the soil, the effect of the herbicide class and the effect of interaction between these two factors (persistence time and herbicide class) were observed. In conclusion, the results showed that the selective pressure exerted by the presence of these herbicides altered the composition of the local microbiota, being atrazine and diuron that most significantly affected the bacterial community in soil, and the herbicide 2,4-D was the one that less altered the microbial community and that bacterial community was reestablished first. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. An Amoebal Grazer of Cyanobacteria Requires Cobalamin Produced by Heterotrophic Bacteria.

    Science.gov (United States)

    Ma, Amy T; Beld, Joris; Brahamsha, Bianca

    2017-05-15

    Amoebae are unicellular eukaryotes that consume microbial prey through phagocytosis, playing a role in shaping microbial food webs. Many amoebal species can be cultivated axenically in rich media or monoxenically with a single bacterial prey species. Here, we characterize heterolobosean amoeba LPG3, a recent natural isolate, which is unable to grow on unicellular cyanobacteria, its primary food source, in the absence of a heterotrophic bacterium, a Pseudomonas species coisolate. To investigate the molecular basis of this requirement for heterotrophic bacteria, we performed a screen using the defined nonredundant transposon library of Vibrio cholerae , which implicated genes in corrinoid uptake and biosynthesis. Furthermore, cobalamin synthase deletion mutations in V. cholerae and the Pseudomonas species coisolate do not support the growth of amoeba LPG3 on cyanobacteria. While cyanobacteria are robust producers of a corrinoid variant called pseudocobalamin, this variant does not support the growth of amoeba LPG3. Instead, we show that it requires cobalamin that is produced by the Pseudomonas species coisolate. The diversity of eukaryotes utilizing corrinoids is poorly understood, and this amoebal corrinoid auxotroph serves as a model for examining predator-prey interactions and micronutrient transfer in bacterivores underpinning microbial food webs. IMPORTANCE Cyanobacteria are important primary producers in aquatic environments, where they are grazed upon by a variety of phagotrophic protists and, hence, have an impact on nutrient flux at the base of microbial food webs. Here, we characterize amoebal isolate LPG3, which consumes cyanobacteria as its primary food source but also requires heterotrophic bacteria as a source of corrinoid vitamins. Amoeba LPG3 specifically requires the corrinoid variant produced by heterotrophic bacteria and cannot grow on cyanobacteria alone, as they produce a different corrinoid variant. This same corrinoid specificity is also

  10. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events.

    Science.gov (United States)

    Sison-Mangus, Marilou P; Jiang, Sunny; Kudela, Raphael M; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  11. Phytoplankton-associated bacterial community composition and succession during toxic diatom bloom and non-bloom events

    Directory of Open Access Journals (Sweden)

    Marilou P. Sison-Mangus

    2016-09-01

    Full Text Available Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6%-65% as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12%- 86% dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in 3 independent bloom events. Other

  12. Investigation of bacterial communities in peat land of the Gahai Lake natural conservation area

    Science.gov (United States)

    Bai, Yani; Wang, Jinchang; Zhan, Zhigao; Guan, Limei; Jin, Liang; Zheng, Guohua

    2017-10-01

    Peat is involved in the global carbon cycle and water conservation; therefore, it is implicated in global environmental change. Microorganisms play an important role in the function of peat. To investigate the bacterial communities in peat of Gahai Lake, different locations and depths were sampled and Illumina Miseq sequencing was used to analyze the microbial community. Chemical properties of peat samples were analyzed by China state standard methods (GB methods). The results showed that bacterial communities were affected by depth, with bacterial diversity and community structure at 90 and 120 cm significantly different from that at 10, 30 and 50 cm depth from the peat surface. Chemical properties of peat land including organic matter, total nitrogen and humus content did not significantly influence bacterial community structure in peat, with only one group from genus Rhizomicrobium that was significantly correlated with total nitrogen. A substantial proportion of the bacterial sequences were unclassified (1.4%), which indicates the great application potential of peat in the Gahai Lake natural conservation area in the future.

  13. Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination.

    Science.gov (United States)

    Jia, Shuyu; Shi, Peng; Hu, Qing; Li, Bing; Zhang, Tong; Zhang, Xu-Xiang

    2015-10-20

    For comprehensive insights into the effects of chlorination, a widely used disinfection technology, on bacterial community and antibiotic resistome in drinking water, this study applied high-throughput sequencing and metagenomic approaches to investigate the changing patterns of antibiotic resistance genes (ARGs) and bacterial community in a drinking water treatment and distribution system. At genus level, chlorination could effectively remove Methylophilus, Methylotenera, Limnobacter, and Polynucleobacter, while increase the relative abundance of Pseudomonas, Acidovorax, Sphingomonas, Pleomonas, and Undibacterium in the drinking water. A total of 151 ARGs within 15 types were detectable in the drinking water, and chlorination evidently increased their total relative abundance while reduced their diversity in the opportunistic bacteria (p < 0.05). Residual chlorine was identified as the key contributing factor driving the bacterial community shift and resistome alteration. As the dominant persistent ARGs in the treatment and distribution system, multidrug resistance genes (mainly encoding resistance-nodulation-cell division transportation system) and bacitracin resistance gene bacA were mainly carried by chlorine-resistant bacteria Pseudomonas and Acidovorax, which mainly contributed to the ARGs abundance increase. The strong correlation between bacterial community shift and antibiotic resistome alteration observed in this study may shed new light on the mechanism behind the chlorination effects on antibiotic resistance.

  14. Effective bioleaching of chromium in tannery sludge with an enriched sulfur-oxidizing bacterial community.

    Science.gov (United States)

    Zeng, Jing; Gou, Min; Tang, Yue-Qin; Li, Guo-Ying; Sun, Zhao-Yong; Kida, Kenji

    2016-10-01

    In this study, a sulfur-oxidizing community was enriched from activated sludge generated in tannery wastewater treatment plants. Bioleaching of tannery sludge containing 0.9-1.2% chromium was investigated to evaluate the effectiveness of the enriched community, the effect of chromium binding forms on bioleaching efficiency, and the dominant microbes contributing to chromium bioleaching. Sludge samples inoculated with the enriched community presented 79.9-96.8% of chromium leaching efficiencies, much higher than those without the enriched community. High bioleaching efficiencies of over 95% were achieved for chromium in reducible fraction, while 60.9-97.9% were observed for chromium in oxidizable and residual fractions. Acidithiobacillus thiooxidans, the predominant bacteria in the enriched community, played an important role in bioleaching, whereas some indigenous heterotrophic species in sludge might have had a supporting role. The results indicated that A. thiooxidans-dominant enriched microbial community had high chromium bioleaching efficiency, and chromium binding forms affected the bioleaching performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Influence of river discharge on abundance and dissemination of heterotrophic, indicator and pathogenic bacteria along the East Coast of India.

    Science.gov (United States)

    Prasad, V R; Srinivas, T N R; Sarma, V V S S

    2015-06-15

    In order to examine the influence of discharge from different rivers from peninsular India and urban sewage on intensity and dissemination of heterotrophic, indicator and pathogenic bacteria, a study was carried out during peak discharge period along coastal Bay of Bengal. The coastal Bay received freshwater inputs from the river Ganges while Godavari and Krishna contributed to the south. Contrasting difference in salinity, temperature, nutrients and organic matter was observed between north and south east coast of India. The highest heterotrophic, indicator and pathogenic bacterial abundance was observed in the central coastal Bay that received urban sewage from the major city. Intensity and dissemination of heterotrophic, indicator and pathogenic bacteria displayed linear relation with magnitude of discharge. The coliform load was observed up to 100km from the coast suggesting that marine waters were polluted during the monsoon season and its impact on the ecosystem needs further studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ 13C pulse-chase method

    OpenAIRE

    Miyatake, T.; Moerdijk-Poortvliet, T.C.W.; Stal, L.J.; Boschker, H.T.S.

    2014-01-01

    Carbon flow from benthic diatoms to heterotrophic bacterial was traced in an intertidal sediment for 5 consecutive days. 13C-labeled bicarbonate was sprayed onto the sediment surface during low tide and 13C-label incorporation in major carbon pools, intermediate metabolites, and biomarkers were monitored. Phospholipid-derived fatty acid (PLFA) and ribosomal ribonucleic acid (rRNA) were used to identify the responsible members of the microbial community at class and family phylogenetic resolut...

  17. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  18. Bacterial community dynamics and product distribution during pH-adjusted fermentation of vegetable wastes.

    Science.gov (United States)

    Ye, N-F; Lü, F; Shao, L-M; Godon, J-J; He, P-J

    2007-10-01

    To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.

  19. Bacterial communities in ancient permafrost profiles of Svalbard, Arctic.

    Science.gov (United States)

    Singh, Purnima; Singh, Shiv M; Singh, Ram N; Naik, Simantini; Roy, Utpal; Srivastava, Alok; Bölter, Manfred

    2017-12-01

    Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50 × 10 3 to 2.22 × 10 5 CFU g -1 , total bacterial numbers range from 1.14 × 10 5 to 5.52 × 10 5 cells g -1 soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A. sulfonivorans, A. bergeri, P. mandelii, and P. jessenii as the dominant species. Other species belong to genera Acinetobacter, Bacillus, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Rhodococcus, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus. To the best of our knowledge, genera Acinetobacter, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus are the first northernmost records from Arctic permafrost. The present study fills the knowledge gap of culturable bacterial communities and their chronological characterization from permafrost soils of Ny-Ålesund (79°N), Arctic. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Science.gov (United States)

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  1. Bacterial community survey of sediments at Naracoorte Caves, Australia

    Directory of Open Access Journals (Sweden)

    Ball Andrew S.

    2012-07-01

    Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

  2. Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses

    DEFF Research Database (Denmark)

    Matsumoto, S.; Katoku, M.; Saeki, G.

    2010-01-01

    of these groups also became evident from a 16S rRNA clone library. Microprofiles of NH4+, NO2-, NO3- and O-2 concentrations measured with microelectrodes showed good agreement with the spatial organization of nitrifying bacteria. One- and two-dimensional numerical biofilm models were constructed to explain......This study evaluates the community structure in nitrifying granules (average diameter of 1600 mu m) produced in an aerobic reactor fed with ammonia as the sole energy source by a multivalent approach combining molecular techniques, microelectrode measurements and mathematical modelling...... the observed granule development as a result of the multiple bacteria-substrate interactions. The interaction between nitrifying and heterotrophic bacteria was evaluated by assuming three types of heterotrophic bacterial growth on soluble microbial products from nitrifying bacteria. The models described well...

  3. Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

    Science.gov (United States)

    Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-02-01

    Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

  4. Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration.

    Science.gov (United States)

    Sun, Shan; Li, Song; Avera, Bethany N; Strahm, Brian D; Badgley, Brian D

    2017-07-15

    Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery

  5. Impact of enzymatic digestion on bacterial community composition in CF airway samples.

    Science.gov (United States)

    Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

    2017-01-01

    Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

  6. Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance.

    Science.gov (United States)

    Frenk, Sammy; Hadar, Yitzhak; Minz, Dror

    2018-02-15

    Anthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified as Bacilli These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certain Bacteroidetes and proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs. IMPORTANCE This report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a

  7. Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

    Science.gov (United States)

    Blasiak, Leah C.; Schmidt, Alex W.; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L.; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P.; Schmidt, Thomas M.; Hill, Russell T.

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas. PMID:24465484

  8. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    DEFF Research Database (Denmark)

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob

    2014-01-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High......-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized...... that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide...

  9. A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

    Science.gov (United States)

    Shang, Shuanghua; Yi, Yanli

    2015-12-01

    The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

  10. Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

    Science.gov (United States)

    Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

    2013-01-01

    The Pampa biome is considered one of the main hotspots of the world's biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

  11. Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

    Science.gov (United States)

    Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Hélène; Guisan, Antoine; van der Meer, Jan Roelof

    2016-11-01

    Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km 2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700

  12. Simplified and representative bacterial community of maize roots.

    Science.gov (United States)

    Niu, Ben; Paulson, Joseph Nathaniel; Zheng, Xiaoqi; Kolter, Roberto

    2017-03-21

    Plant-associated microbes are important for the growth and health of their hosts. As a result of numerous prior studies, we know that host genotypes and abiotic factors influence the composition of plant microbiomes. However, the high complexity of these communities challenges detailed studies to define experimentally the mechanisms underlying the dynamics of community assembly and the beneficial effects of such microbiomes on plant hosts. In this work, from the distinctive microbiota assembled by maize roots, through host-mediated selection, we obtained a greatly simplified synthetic bacterial community consisting of seven strains ( Enterobacter cloacae , Stenotrophomonas maltophilia, Ochrobactrum pituitosum, Herbaspirillum frisingense, Pseudomonas putida, Curtobacterium pusillum , and Chryseobacterium indologenes ) representing three of the four most dominant phyla found in maize roots. By using a selective culture-dependent method to track the abundance of each strain, we investigated the role that each plays in community assembly on roots of axenic maize seedlings. Only the removal of E. cloacae led to the complete loss of the community, and C. pusillum took over. This result suggests that E. cloacae plays the role of keystone species in this model ecosystem. In planta and in vitro, this model community inhibited the phytopathogenic fungus Fusarium verticillioides , indicating a clear benefit to the host. Thus, combined with the selective culture-dependent quantification method, our synthetic seven-species community representing the root microbiome has the potential to serve as a useful system to explore how bacterial interspecies interactions affect root microbiome assembly and to dissect the beneficial effects of the root microbiota on hosts under laboratory conditions in the future.

  13. Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats

    Science.gov (United States)

    Ni, Jiajia; Yu, Yuhe; Zhang, Tanglin; Gao, Lei

    2012-09-01

    The intestinal bacteria of vertebrates form a close relationship with their host. External and internal conditions of the host, including its habitat, affect the intestinal bacterial community. Similarly, the intestinal bacterial community can, in turn, influence the host, particularly with respect to disease resistance. We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake. We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes, from which 66 different operational taxonomic units were identified. Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination, we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish, except for DF-7, and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities (Mantel one-tailed test, R=0.157, P=0.175). Cetobacterium appeared more frequently in the intestine of grass carp collected from pond. A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  14. Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton

    Science.gov (United States)

    Shelford, Emma J.; Suttle, Curtis A.

    2018-02-01

    Lytic infection of bacteria by viruses releases nutrients during cell lysis and stimulates the growth of primary producers, but the path by which these nutrients flow from lysates to primary producers has not been traced. This study examines the remineralisation of nitrogen (N) from Vibrio lysates by heterotrophic bacterioplankton and its transfer to primary producers. In laboratory trials, Vibrio sp. strain PWH3a was infected with a lytic virus (PWH3a-P1) and the resulting 36.0 µmol L-1 of dissolved organic N (DON) in the lysate was added to cultures containing cyanobacteria (Synechococcus sp. strain DC2) and a natural bacterial assemblage. Based on the increase in cyanobacteria, 74 % (26.5 µmol L-1 N) of the DON in the lysate was remineralised and taken up. Lysate from Vibrio sp. strain PWH3a labeled with 15NH4+ was also added to seawater containing natural microbial communities, and in four field experiments, stable isotope analysis indicated that the uptake of 15N was 0.09 to 0.70 µmol N µg-1 of chlorophyll a. The results from these experiments demonstrate that DON from lysate can be efficiently remineralised and transferred to phytoplankton, and they provide further evidence that the viral shunt is an important link in nitrogen recycling in aquatic systems.

  15. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

    KAUST Repository

    Tian, Renmao

    2014-08-29

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. The Arbuscular Mycorrhizal Fungus Funneliformis mosseae Alters Bacterial Communities in Subtropical Forest Soils during Litter Decomposition

    Directory of Open Access Journals (Sweden)

    Heng Gui

    2017-06-01

    Full Text Available Bacterial communities and arbuscular mycorrhizal fungi (AMF co-occur in the soil, however, the interaction between these two groups during litter decomposition remains largely unexplored. In order to investigate the effect of AMF on soil bacterial communities, we designed dual compartment microcosms, where AMF (Funneliformis mosseae was allowed access (AM to, or excluded (NM from, a compartment containing forest soil and litterbags. Soil samples from this compartment were analyzed at 0, 90, 120, 150, and 180 days. For each sample, Illumina sequencing was used to assess any changes in the soil bacterial communities. We found that most of the obtained operational taxonomic units (OTUs from both treatments belonged to the phylum of Proteobacteria, Acidobacteria, and Actinobacteria. The community composition of bacteria at phylum and class levels was slightly influenced by both time and AMF. In addition, time and AMF significantly affected bacterial genera (e.g., Candidatus Solibacter, Dyella, Phenylobacterium involved in litter decomposition. Opposite to the bacterial community composition, we found that overall soil bacterial OTU richness and diversity are relatively stable and were not significantly influenced by either time or AMF inoculation. OTU richness at phylum and class levels also showed consistent results with overall bacterial OTU richness. Our study provides new insight into the influence of AMF on soil bacterial communities at the genus level.

  17. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Dai, Minhan; Jiao, Nianzhi; Herndl, Gerhard J

    2014-01-01

    To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and 16S rRNA gene (V1-3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S rRNA vs. rDNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance-decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay. PMID:24684298

  18. Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

    Directory of Open Access Journals (Sweden)

    Sonia Ciccazzo

    2014-01-01

    Full Text Available The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05 on 16S rRNA gene diversity revealed significant differences (P<0.05 between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  19. Microbial activity and bacterial community structure during degradation of microcystins

    DEFF Research Database (Denmark)

    Christoffersen, K.; Lyck, Susanne; Winding, A.

    2002-01-01

    experiments were analysed by polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE) of 16S rDNA, which showed that the indigenous bacterial community responded quickly to the addition of lysates. Our study confirms that bacteria can efficiently degrade microcystins in natural waters....... It was hypothesised that the bacterial community from a lake with frequent occurrence of toxic cyanobacteria can degrade microcystin along with other organic compounds. The initial dissolved microcystin concentrations ranged between 10 and 136 mug 1(-1) (microcystin-LR equivalents) in the laboratory experiment, using...... experiment to evaluate the effects of organic lysates on bacterial proliferation in the absence of microcystin. An exponential decline of the dissolved toxins was observed in all cases with toxins present, and the degradation rates ranged between 0.5 and 1.0 d(-1). No lag phases were observed but slow...

  20. Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake.

    Directory of Open Access Journals (Sweden)

    Timothy J Colston

    Full Text Available Vertebrates are metagenomic organisms in that they are composed not only of their own genes but also those of their associated microbial cells. The majority of these associated microorganisms are found in the gastrointestinal tract (GIT and presumably assist in processes such as energy and nutrient acquisition. Few studies have investigated the associated gut bacterial communities of non-mammalian vertebrates, and most rely on captive animals and/or fecal samples only. Here we investigate the gut bacterial community composition of a squamate reptile, the cottonmouth snake, Agkistrodon piscivorus through pyrosequencing of the bacterial 16S rRNA gene. We characterize the bacterial communities present in the small intestine, large intestine and cloaca. Many bacterial lineages present have been reported by other vertebrate gut community studies, but we also recovered unexpected bacteria that may be unique to squamate gut communities. Bacterial communities were not phylogenetically clustered according to GIT region, but there were statistically significant differences in community composition between regions. Additionally we demonstrate the utility of using cloacal swabs as a method for sampling snake gut bacterial communities.

  1. Hydrocephalus in adults with community-acquired bacterial meningitis

    NARCIS (Netherlands)

    Soemirien Kasanmoentalib, E.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2010-01-01

    Objective: To evaluate the occurrence, treatment, and outcome of hydrocephalus complicating community-acquired bacterial meningitis in adults. Methods: Case series from a prospective nationwide cohort study from Dutch hospitals from 2006 to 2009. Results: Hydrocephalus was diagnosed in 26 of 577

  2. Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

    Directory of Open Access Journals (Sweden)

    Wolf Sarah

    2011-09-01

    Full Text Available Abstract Background Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2 and Fibrisoma limi (BUZ 3 with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82 were studied in mixed cultures under nutrient rich (carbon source present in medium and poor (carbon source absent in medium conditions. Findings F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc. The growth and survival of tested heterotrophs was enhanced by the presence of Nostoc or its metabolites, suggesting that the heterotrophs could utilize the autotrophs and its products as a nutrient source. However, the autotroph could withstand and out-compete the heterotrophs under nutrient poor conditions. Conclusions Our results suggest that the nutrients in cultivation media, which boost or reduce the number of heterotrophs, were the important factor influencing the outcome of the interplay between filamentous heterotrophs and autotrophs. For better understanding of these interactions, additional research is needed. In particular, it is necessary to elucidate the mode of action for lysis by heterotrophs, and the possible defense mechanisms of the autotrophs.

  3. Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia.

    Science.gov (United States)

    Khoo, Jing-Jing; Chen, Fezshin; Kho, Kai Ling; Ahmad Shanizza, Azzy Iyzati; Lim, Fang-Shiang; Tan, Kim-Kee; Chang, Li-Yen; AbuBakar, Sazaly

    2016-07-01

    Ticks are vectors in the transmission of many important infectious diseases in human and animals. Ticks can be readily found in the semi-forested areas such as the settlements of the indigenous people in Malaysia, the Orang Asli. There is still minimal information available on the bacterial agents associated with ticks found in Malaysia. We performed a survey of the bacterial communities associated with ticks collected from domestic animals found in two Orang Asli villages in Malaysia. We collected 62 ticks, microscopically and molecularly identified as related to Haemaphysalis wellingtoni, Haemaphysalis hystricis and Haemaphysalis bispinosa. Bacterial 16s rRNA hypervariable region (V6) amplicon libraries prepared from the tick samples were sequenced on the Ion Torrent PGM platform. We detected a total of 392 possible bacterial genera after pooling and sequencing 20 samples, indicating a diverse bacterial community profile. Dominant taxa include the potential tick endosymbiont, Coxiella. Other dominant taxa include the tick-associated pathogen, Rickettsia, and environmental bacteria such as Bacillus, Mycobacterium, Sphingomonas and Pseudomonas. Other known tick-associated bacteria were also detected, including Anaplasma, Ehrlichia, Rickettsiella and Wolbachia, albeit at very low abundance. Specific PCR was performed on selected samples to identify Rickettsia and Coxiella. Sequence of Rickettsia felis, which causes spotted fever in human and cats, was identified in one sample. Coxiella endosymbionts were detected in three samples. This study provides the baseline knowledge of the microbiome of ticks in Malaysia, focusing on tick-associated bacteria affecting the Orang Asli communities. The role of the herein found Coxiella and Rickettsia in tick physiology or disease transmission merits further investigation. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

  4. Bacterial Isolates andAntibiotic Sensitivity in Community Acquired ...

    African Journals Online (AJOL)

    Objective: The objective of the studywas to determine bacterial causes of community acquired pneumonia and their antibiotic sensitivity pattern amongst patients admitted intomedicalwards inAminu Kano Teaching Hospital, Kano, Nigeria Methods: The study incorporated patients aged fifteen years and above admitted into ...

  5. Mixotrophic organisms become more heterotrophic with rising temperature

    NARCIS (Netherlands)

    Wilken, S.; Huisman, J.; Naus-Wiezer, S.; van Donk, E.

    2013-01-01

    The metabolic theory of ecology predicts that temperature affects heterotrophic processes more strongly than autotrophic processes. We hypothesized that this differential temperature response may shift mixotrophic organisms towards more heterotrophic nutrition with rising temperature. The hypothesis

  6. Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients.

    Science.gov (United States)

    Zhang, Qian; Goberna, Marta; Liu, Yuguo; Cui, Ming; Yang, Haishui; Sun, Qixiang; Insam, Heribert; Zhou, Jinxing

    2018-04-24

    The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e. relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling for elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e. climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Distinct bacterial communities in surficial seafloor sediments following the 2010 Deepwater Horizon blowout

    Directory of Open Access Journals (Sweden)

    Tingting Yang

    2016-09-01

    Full Text Available A major fraction of the petroleum hydrocarbons discharged during the 2010 Macondo oil spill became associated with and sank to the seafloor as marine snow flocs. This sedimentation pulse induced the development of distinct bacterial communities. Between May 2010 and July 2011, full-length 16S rRNA gene clone libraries demonstrated bacterial community succession in oil-polluted sediment samples near the wellhead area. Libraries from early May 2010, before the sedimentation event, served as the baseline control. Freshly deposited oil-derived marine snow was collected on the surface of sediment cores in September 2010, and was characterized by abundantly detected members of the marine Roseobacter cluster within the Alphaproteobacteria. Samples collected in mid-October 2010 closest to the wellhead contained members of the sulfate-reducing, anaerobic bacterial families Desulfobacteraceae and Desulfobulbaceae within the Deltaproteobacteria, suggesting that the oil-derived sedimentation pulse triggered bacterial oxygen consumption and created patchy anaerobic microniches that favored sulfate-reducing bacteria. Phylotypes of the polycyclic aromatic hydrocarbon-degrading genus Cycloclasticus, previously found both in surface oil slicks and the deep hydrocarbon plume, were also found in oil-derived marine snow flocs sedimenting on the seafloor in September 2010, and in surficial sediments collected in October and November 2010, but not in any of the control samples. Due to the relative recalcitrance and stability of polycyclic aromatic compounds, Cycloclasticus represents the most persistent microbial marker of seafloor hydrocarbon deposition that we could identify in this dataset. The bacterial imprint of the DWH oil spill had diminished in late November 2010, when the bacterial communities in oil-impacted sediment samples collected near the Macondo wellhead began to resemble their pre-spill counterparts and spatial controls. Samples collected in summer

  8. Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

    Science.gov (United States)

    Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

    2016-01-01

    Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

  9. Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem.

    Science.gov (United States)

    Hao, Yi; Ma, Chuanxin; Zhang, Zetian; Song, Youhong; Cao, Weidong; Guo, Jing; Zhou, Guopeng; Rui, Yukui; Liu, Liming; Xing, Baoshan

    2018-01-01

    The aim of this study was to compare the toxicity effects of carbon nanomaterials (CNMs), namely fullerene (C 60 ), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs), on a mini-ecosystem of rice grown in a loamy potted soil. We measured plant physiological and biochemical parameters and examined bacterial community composition in the CNMs-treated plant-soil system. After 30 days of exposure, all the three CNMs negatively affected the shoot height and root length of rice, significantly decreased root cortical cells diameter and resulted in shrinkage and deformation of cells, regardless of exposure doses (50 or 500 mg/kg). Additionally, at the high exposure dose of CNM, the concentrations of four phytohormones, including auxin, indoleacetic acid, brassinosteroid and gibberellin acid 4 in rice roots significantly increased as compared to the control. At the high exposure dose of MWCNTs and C 60 , activities of the antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) in roots increased significantly. High-throughput sequencing showed that three typical CNMs had little effect on shifting the predominant soil bacterial species, but the presence of CNMs significantly altered the composition of the bacterial community. Our results indicate that different CNMs indeed resulted in environmental toxicity to rice and soil bacterial community in the rhizosphere and suggest that CNMs themselves and their incorporated products should be reasonably used to control their release/discharge into the environment to prevent their toxic effects on living organisms and the potential risks to food safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH

    Directory of Open Access Journals (Sweden)

    Yuting Zhang

    2017-07-01

    Full Text Available Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007–2014 of applying chemical nitrogen, phosphorus and potassium (NPK fertilizers, composted manure or their combination to acidic (pH 5.8, near-neutral (pH 6.8 or alkaline (pH 8.4 Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (% of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%, Actinobacteria (19.7%, Chloroflexi (15.3% and Acidobacteria (12.6%; the medium dominant phyla were Bacterioidetes (5.3%, Planctomycetes (4.8%, Gemmatimonadetes (4.5%, Firmicutes (3.4%, Cyanobacteria (2.1%, Nitrospirae (1.8%, and candidate division TM7 (1

  11. Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH.

    Science.gov (United States)

    Zhang, Yuting; Shen, Hong; He, Xinhua; Thomas, Ben W; Lupwayi, Newton Z; Hao, Xiying; Thomas, Matthew C; Shi, Xiaojun

    2017-01-01

    Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1

  12. Lesion bacterial communities in American lobsters with diet-induced shell disease.

    Science.gov (United States)

    Quinn, Robert A; Metzler, Anita; Tlusty, Michael; Smolowitz, Roxanna M; Leberg, Paul; Chistoserdov, Andrei Y

    2012-04-26

    In southern New England, USA, shell disease affects the profitability of the American lobster Homarus americanus fishery. In laboratory trials using juvenile lobsters, exclusive feeding of herring Clupea harengus induces shell disease typified initially by small melanized spots that progress into distinct lesions. Amongst a cohabitated, but segregated, cohort of 11 juvenile lobsters fed exclusively herring, bacterial communities colonizing spots and lesions were investigated by denaturing gradient gel electrophoresis of 16S rDNA amplified using 1 group-specific and 2 universal primer sets. The Bacteroidetes and Proteobacteria predominated in both spots and lesions and included members of the orders Flavobacteriales (Bacteriodetes), Rhodobacterales, Rhodospirillales and Rhizobiales (Alphaproteobacteria), Xanthomonadales (Gammaproteobacteria) and unclassified Gammaproteobacteria. Bacterial communities in spot lesions displayed more diversity than communities with larger (older) lesions, indicating that the lesion communities stabilize over time. At least 8 bacterial types persisted as lesions developed from spots. Aquimarina 'homaria', a species commonly cultured from lesions present on wild lobsters with epizootic shell disease, was found ubiquitously in spots and lesions, as was the 'Candidatus Kopriimonas aquarianus', implicating putative roles of these species in diet-induced shell disease of captive lobsters.

  13. Influence of the Drilling Mud Formulation Process on the Bacterial Communities in Thermogenic Natural Gas Wells of the Barnett Shale▿†

    Science.gov (United States)

    Struchtemeyer, Christopher G.; Davis, James P.; Elshahed, Mostafa S.

    2011-01-01

    The Barnett Shale in north central Texas contains natural gas generated by high temperatures (120 to 150°C) during the Mississippian Period (300 to 350 million years ago). In spite of the thermogenic origin of this gas, biogenic sulfide production and microbiologically induced corrosion have been observed at several natural gas wells in this formation. It was hypothesized that microorganisms in drilling muds were responsible for these deleterious effects. Here we collected drilling water and drilling mud samples from seven wells in the Barnett Shale during the drilling process. Using quantitative real-time PCR and microbial enumerations, we show that the addition of mud components to drilling water increased total bacterial numbers, as well as the numbers of culturable aerobic heterotrophs, acid producers, and sulfate reducers. The addition of sterile drilling muds to microcosms that contained drilling water stimulated sulfide production. Pyrosequencing-based phylogenetic surveys of the microbial communities in drilling waters and drilling muds showed a marked transition from typical freshwater communities to less diverse communities dominated by Firmicutes and Gammaproteobacteria. The community shifts observed reflected changes in temperature, pH, oxygen availability, and concentrations of sulfate, sulfonate, and carbon additives associated with the mud formulation process. Finally, several of the phylotypes observed in drilling muds belonged to lineages that were thought to be indigenous to marine and terrestrial fossil fuel formations. Our results suggest a possible alternative exogenous origin of such phylotypes via enrichment and introduction to oil and natural gas reservoirs during the drilling process. PMID:21602366

  14. The effect of antibiotics on associated bacterial community of stored product mites.

    Directory of Open Access Journals (Sweden)

    Jan Kopecky

    Full Text Available Bacteria are associated with the gut, fat bodies and reproductive organs of stored product mites (Acari: Astigmata. The mites are pests due to the production of allergens. Addition of antibiotics to diets can help to characterize the association between mites and bacteria.Ampicillin, neomycin and streptomycin were added to the diets of mites and the effects on mite population growth (Acarus siro, Lepidoglyphus destructor and Tyrophagus putrescentiae and associated bacterial community structure were assessed. Mites were treated by antibiotic supplementation (1 mg g(-1 of diet for 21 days and numbers of mites and bacterial communities were analyzed and compared to the untreated control. Bacterial quantities, determined by real-time PCR, significantly decreased in antibiotic treated specimens from 5 to 30 times in A. siro and T. putrescentiae, while no decline was observed in L. destructor. Streptomycin treatment eliminated Bartonella-like bacteria in the both A. siro and T. putrescentiae and Cardinium in T. putrescentiae. Solitalea-like bacteria proportion increased in the communities of neomycin and streptomycin treated A. siro specimens. Kocuria proportion increased in the bacterial communities of ampicillin and streptomycin treated A. siro and neomycin and streptomycin treated L. destructor.The work demonstrated the changes of mite associated bacterial community under antibiotic pressure in pests of medical importance. Pre-treatment of mites by 1 mg g(-1 antibiotic diets improved mite fitness as indicated accelerated population growth of A. siro pretreated streptomycin and neomycin and L. destructor pretreated by neomycin. All tested antibiotics supplemented to diets caused the decrease of mite growth rate in comparison to the control diet.

  15. Effects of biofloc promotion on water quality, growth, biomass yield and heterotrophic community in Litopenaeus vannamei (Boone, 1931 experimental intensive cultures

    Directory of Open Access Journals (Sweden)

    Irasema E. Luis-Villaseñor

    2015-08-01

    Full Text Available Six 1.2-m3 tanks were stocked with an initial biomass of 500 g m-3 of Litopenaeus vannamei juveniles (individual weight: 1.0±0.3 g, to evaluate the effect of biofloc promotion on water quality and on shrimp growth and production, and to identify the dominant taxa in the heterotrophic communities present in experimental closed cultures. Feeding was ad libitum twice daily with 35% protein shrimp feed. Three tanks were managed as biofloc technology (BFT systems, adding daily an amount of cornmeal equivalent to 50% of the shrimp feed supplied. The remaining three received only shrimp feed and served as controls. Experiment lasted 21 days. The mean concentrations of P-PO4 3- and inorganic dissolved N species (TAN, N-NO2 -, N-NO3 - were significantly lower (P<0.5 in BFT than in the control. The individual final weight, increase in biomass, food, and protein conversion rates were significantly better in BFT than in the control (P<0.05. The mean N content of the shrimp biomass gained in the BFT cultures was equivalent to 45.7% of the protein-N added as feed, and was significantly higher than the 34.7% recycled into shrimp biomass in the control cultures. Bacterial concentrations were not significantly different. Vibrionaceae dominated in both systems; in both some isolates were potential pathogens, and diversity was higher in the control than in the BFT treatment. The advantages of BFT technology are confirmed by the significantly lower TAN and N-NO2 - concentrations, as well as by the better shrimp performance in terms of growth, biomass yield, and food and protein conversion efficiency.

  16. Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

    Science.gov (United States)

    Kumar, Arvind; Rai, Lal Chand

    2017-07-01

    Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

  17. Isolation of amoebic-bacterial consortia capable of degrading trichloroethylene

    International Nuclear Information System (INIS)

    Tyndall, R.L.; Ironside, K.; Little, C.D.; Katz, S.; Kennedy, J.

    1990-01-01

    Groundwater from a waste disposal site contaminated with chlorinated alkenes was examined for the presence of amoebic-bacterial consortia capable of degrading the suspected carcinogen, trichloroethylene (TCE). Consortia were readily isolated from all of four test wells. They contained free-living amoebae, and heterotrophic and methylotrophic bacteria. Electron microscopic examination showed bacteria localized throughout the amoebic cytoplasm and an abundance of hyphomicrobium, but not Type I methanotrophs. The presence of Type II methanotrophs was indirectly indicated by lipid analysis of one consortium. The consortia have been passaged for over two years on mineral salts media in a methane atmosphere, which would not be expected to maintain the heterotrophs or amoebae separately. The methanotrophic bacteria apparently provided a stable nutrient source, allowing the persistence of the various genera. By use of 14 C-radiotracer techniques, the degradation of TCE by the consortia was observed with 14 C eventuating predominantly in CO 2 and water-soluble products. In a more detailed examination of one consortia, the amoebae and heterotrohic components did not degrade TCE, while a mixed culture of heterotrophs and methanotrophs did degrade TCE, suggesting the latter component was the primary cause for the consortium's ability to degrade TCE. Amoebic-bacterial consortia may play a role in stabilizing and preserving methylotrophic bacteria in hostile environments

  18. Comparison of bacterial and fungal communities between natural and planted pine forests in subtropical China.

    Science.gov (United States)

    Nie, Ming; Meng, Han; Li, Ke; Wan, Jia-Rong; Quan, Zhe-Xue; Fang, Chang-Ming; Chen, Jia-Kuan; Li, Bo

    2012-01-01

    To improve our understanding of the changes in bacterial and fungal diversity in natural pine and planted forests in subtropical region of China, we examined bacterial and fungal communities from a native and a nearby planted pine forest of the Mt. Lushan by constructing clone libraries of 16S and 18S rRNA genes. For bacterial communities, Proteobacteria and Acidobacteria were dominant bacterial taxa in both two types of forest soils. The Shannon-Wiener diversity index, rarefaction curve analysis, and LibShuff analysis suggest that these two forests contained similar diversity of bacterial communities. Low soil acidity (pH ≈ 4) of our study forests might be one of the most important selection factors determining growth of acidophilic Acidobacteria and Proteobacteria. However, the natural forest harbored greater level of fungal diversity than the planted forest according to the Shannon-Wiener diversity index and rarefaction curve analysis. Basidiomycota and Ascomycota were dominant fungal taxa in the soils of natural and planted forests, respectively. Our results suggest that fungal community was more sensitive than the bacterial community in characterizing the differences in plant cover impacts on the microbial flora in the natural and planted forests. The natural and planted forests may function differently due to the differences in soil fungal diversity and relative abundance.

  19. Exploring the plant-associated bacterial communities in Medicago sativa L

    Directory of Open Access Journals (Sweden)

    Pini Francesco

    2012-05-01

    Full Text Available Abstract Background Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti. However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti level. Results Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40% between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system. Conclusions In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may

  20. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  1. Hydrological pulse regulating the bacterial heterotrophic metabolism between Amazonian mainstems and floodplain lakes

    Directory of Open Access Journals (Sweden)

    Luciana Oliveira Vidal

    2015-09-01

    Full Text Available We evaluated in situ rates of bacterial carbon processing in Amazonian floodplain lakes and mainstems, during both high and low water phases (p < 0.05. Our results showed that Bacterial Production (BP was lower and more variable than Bacterial Respiration (BR, determined as total respiration. Bacterial Carbon Demand (BCD was mostly accounted by BR and presented the same pattern that BR in both water phases. Bacterial growth efficiency showed a wide range (0.2–23% and low mean value of 3 and 6 %, (in high and low water respectively suggesting that dissolved organic carbon (DOC was mostly allocated to catabolic metabolism. However, BGE was regulated by BP in low water phase. Consequently, changes in BGE showed the same pattern that BP. In addition, the hydrological pulse effects on mainstems and floodplains lakes connectivity were found for BP and BGE in low water. Multiple correlation analyses revealed that indexes of organic matter quality (chlorophyll-a, N stable isotopes and C/N ratios were the strongest seasonal drivers of bacterial carbon metabolism. Our work indicated that: (1 the bacterial metabolism was mostly driven by respiration in Amazonian aquatic ecosystems resulting in low BGE in either high and low water phase; (2 the hydrological pulse regulated

  2. Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Ito, Isao [Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan); Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: isaoito@kuhp.kyoto-u.ac.jp; Ishida, Tadashi [Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan)], E-mail: ishidat@kchnet.or.jp; Togashi, Kaori [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: ktogashi@kuhp.kyoto-u.ac.jp; Niimi, Akio [Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: niimi@kuhp.kyoto-u.ac.jp; Koyama, Hiroshi [General Internal Medicine, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa-Mukohatacho, Fushimi-ku, Kyoto 612-8555 (Japan)], E-mail: hkoyama-kyt@umin.ac.jp; Ishimori, Takayoshi [Department of Radiology, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan)], E-mail: ti10794@kchnet.or.jp; Kobayashi, Hisataka [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan); Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, Room 1B40, MSC1088, 10 Center Drive, Bethesda, MD 20892-1088 (United States)], E-mail: kobayash@mail.nih.gov; Mishima, Michiaki [Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: mishima@kuhp.kyoto-u.ac.jp

    2009-12-15

    Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age {+-} S.D.: 61.1 {+-} 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would

  3. Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

    International Nuclear Information System (INIS)

    Ito, Isao; Ishida, Tadashi; Togashi, Kaori; Niimi, Akio; Koyama, Hiroshi; Ishimori, Takayoshi; Kobayashi, Hisataka; Mishima, Michiaki

    2009-01-01

    Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age ± S.D.: 61.1 ± 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would not

  4. Evolution of bacterial communities in the Gironde Estuary (France) according to a salinity gradient

    Science.gov (United States)

    Prieur, D.; Troussellier, M.; Romana, A.; Chamroux, S.; Mevel, G.; Baleux, B.

    1987-01-01

    Three surveys were performed in the Gironde Estuary (France) in August 1981, March 1982 and July 1982. For each campaign, seventy samples were taken by helicopter, in order to follow the tide along the estuary. Of the parameters that were studied, salinity appeared to be the most important and which controls the bacterial communities along the estuary. This paper deals with the evolution of bacterial communities along a salinity gradient. The information obtained from various bacteriological parameters (total bacterial counts, viable counts on salted and unsalted media, functional evenness) were convergent. The bacterial community is dominated by an halotolerant microflora. In the estuary, a continental microflora is followed by a marine microflora. The succession zone between these two microflora is located between 5 and 10‰ areas of salinity.

  5. Experimental warming effects on the bacterial community structure and diversity

    Science.gov (United States)

    Kim, W.; Han, S.; Adams, J.; Son, Y.

    2014-12-01

    The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

  6. Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington

    KAUST Repository

    Lee, O. O.

    2009-04-10

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  7. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs.

    Science.gov (United States)

    Frade, Pedro R; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.

  8. Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils

    Directory of Open Access Journals (Sweden)

    Jing eLi

    2015-02-01

    Full Text Available Copper contamination on China’s arable land could pose severe economic, ecological and healthy consequences in the coming decades. As the drivers in maintaining ecosystem functioning, the responses of soil microorganisms to long-term copper contamination in different soil ecosystems are still debated. This study investigated the impacts of copper gradients on soil bacterial communities in two agricultural fields with contrasting soil properties. Our results revealed consistent reduction in soil microbial biomass carbon (SMBC with increasing copper levels in both soils, coupled by significant declines in bacterial abundance in most cases. Despite of contrasting bacterial community structures between the two soils, the bacterial diversity in the copper-contaminated soils showed considerably decreasing patterns when copper levels elevated. High-throughput sequencing revealed copper selection for major bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Chloroflexi were highly sensitive to copper. The thresholds that bacterial communities changed sharply were 800 and 200 added copper mg kg-1 in the fluvo-aquic soil and red soil, respectively, which were similar to the toxicity thresholds (EC50 values characterized by SMBC. Structural equation model (SEM analysis ascertained that the shifts of bacterial community composition and diversity were closely related with the changes of SMBC in both soils. Our results provide field-based evidence that copper contamination exhibits consistently negative impacts on soil bacterial communities, and the shifts of bacterial communities could have largely determined the variations of the microbial biomass.

  9. Threshold concentration of glucose for bacterial growth in soil

    NARCIS (Netherlands)

    Reischke, Stephanie; Kumar, Manoj G.K.; Baath, Erland

    The activity of heterotrophic soil microorganisms is usually limited by the availability and quality of carbon (C). Adding organic substances will thus trigger a microbial response. We studied the response in bacterial growth and respiration after the addition of low amounts of glucose. First we

  10. Temporal distribution of bacterial community structure in the Changjiang Estuary hypoxia area and the adjacent East China Sea

    International Nuclear Information System (INIS)

    Liu Min; Huang Huiqin; Bao Shixiang; Xiao Tian; Zhang Wuchang; Wu Ying; Zhou Feng

    2012-01-01

    Bacterial community structure and the effects of environmental factors on the microbial community distribution were investigated in the Changjiang Estuary hypoxia area and its adjacent area in the East China Sea (ECS) in June, August and October, 2006. Profiles of bacterial communities were generated by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes followed by DNA sequence analysis. The dominant bacterial groups were affiliated to Gammaproteobacteria, Cytophaga–Flavobacteria–Bacteroides (CFB), Deltaproteobacteria, Cyanobacteria and Firmicutes, which were mostly from the marine seawater ecosystem. Effects of environmental factors on the bacterial community distribution were analyzed by the ordination technique of canonical correspondence analysis (CCA). The environmental factors significantly influencing bacterial community structure were different in the three months; dissolved organic carbon (DOC) and temperature in June and nitrite in August. No environmental variables displayed significant influence on the bacterial community at the 5% level in October. The seasonal environmental heterogeneity in the Changjiang Estuary and the adjacent ECS, such as seasonal hydrodynamic conditions and riverine input of nutrients, might be the reason for the difference in the key environmental factors determining the bacterial community in the three months. (letter)

  11. Temperature-driven adaptation of the bacterial community in peat measured by using thymidine and leucine incorporation

    OpenAIRE

    Ranneklev, Sissel Brit; Bååth, Erland

    2001-01-01

    The temperature-driven adaptation of the bacterial community in peat was studied, by altering temperature to simulate self-heating and a subsequent return to mesophilic conditions. The technique used consisted of extracting the bacterial community from peat using homogenization-centrifugation and measuring the rates of thymidine (TdR) or leucine (Leu) incorporation by the extracted bacterial community at different temperatures. Increasing the peat incubation temperature from 25°C to 35, 45, o...

  12. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    Science.gov (United States)

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  13. Differential response of marine flagellate communities to prokaryotic food quality

    Science.gov (United States)

    De Corte, D.; Paredes, G.; Sintes, E.; Herndl, G. J.

    2016-02-01

    Marine prokaryotes play a major role in the biogeochemical cycles. The main predators of prokaryotes are heterotrophic nanoflagellates (HNF). HNF are thus a major link connecting dissolved organic material through prokaryotic grazing to the higher trophic levels. However, little is known about the grazing specificity of HNF on specific prokaryotic taxa. Bacterial and archaeal microbes may have different nutritive values for the HNF communities, thus affecting growth rates and community composition of HNFs. In this study we investigated the influence of prey food quality on Cafeteria roenbergensis and on a natural HNF community isolated in the northern Adriatic Sea. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains and two fast growing marine Bacteria (Pseudomonas marina and Marinobacter algicola) were fed to the HNFs. The two fast growing bacterial strains resulted in high growth rates of Cafeteria roenbergensis and the mixed HNF community, while the two Nitrosococcus strains did not. Cafeteria roenbergensis fed on N. adriaticus but it did not graze N. piranensis, suggesting that the subtle metabolic and physiological differences between these two closely related thaumarchaeal strains affect the grazing pressure to which they are exposed. Our study also indicates that prokaryotic community composition influences the composition of the HNF community.

  14. Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs

    Directory of Open Access Journals (Sweden)

    Brandon J. Varela

    2018-02-01

    Full Text Available Research on the amphibian skin microbiota has focused on identifying bacterial taxa that deter a pathogenic chytrid fungus, and on describing patterns of microbiota variation. However, it remains unclear how environmental variation affects amphibian skin bacterial communities, and whether the overall functional diversity of the amphibian skin microbiota is associated to such variation. We sampled skin microbial communities from one dendrobatoid frog species across an environmental gradient along the Panama Canal, and from three dendrobatoid frog species before and after the onset of the wet season in one site. We found frog skin microbial alpha diversity to be highest in frogs from sites with low soil pH, but no clear effect of the onset of the wet season. However, we found frog skin microbial community structure to be affected by soil pH and the onset of the wet season, which also resulted in a decrease in between-sample variation. Across the sampled frog species, bacterial functional groups changed with the onset of the wet season, with certain bacterial functional groups entirely disappearing and others differing in their relative abundances. In particular, we found the proportion of Bd-inhibitory bacteria to correlate with mean soil pH, and to increase in two of the frog species with the onset of the wet season. Taken together, our results suggest that structure and predicted function of amphibian bacterial skin communities may be influenced by environmental variables such as pH and precipitation, site effects, and host effects.

  15. An investigation of total bacterial communities, culturable antibiotic-resistant bacterial communities and integrons in the river water environments of Taipei city.

    Science.gov (United States)

    Yang, Chu-Wen; Chang, Yi-Tang; Chao, Wei-Liang; Shiung, Iau-Iun; Lin, Han-Sheng; Chen, Hsuan; Ho, Szu-Han; Lu, Min-Jheng; Lee, Pin-Hsuan; Fan, Shao-Ning

    2014-07-30

    The intensive use of antibiotics may accelerate the development of antibiotic-resistant bacteria (ARB). The global geographical distribution of environmental ARB has been indicated by many studies. However, the ARB in the water environments of Taiwan has not been extensively investigated. The objective of this study was to investigate the communities of ARB in Huanghsi Stream, which presents a natural acidic (pH 4) water environment. Waishuanghsi Stream provides a neutral (pH 7) water environment and was thus also monitored to allow comparison. The plate counts of culturable bacteria in eight antibiotics indicate that the numbers of culturable carbenicillin- and vancomycin-resistant bacteria in both Huanghsi and Waishuanghsi Streams are greater than the numbers of culturable bacteria resistant to the other antibiotics tested. Using a 16S rDNA sequencing approach, both the antibiotic-resistant bacterial communities (culture-based) and the total bacterial communities (metagenome-based) in Waishuanghsi Stream exhibit a higher diversity than those in Huanghsi Stream were observed. Of the three classes of integron, only class I integrons were identified in Waishuanghsi Stream. Our results suggest that an acidic (pH 4) water environment may not only affect the community composition of antibiotic-resistant bacteria but also the horizontal gene transfer mediated by integrons. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas.

    Directory of Open Access Journals (Sweden)

    Rachael E Antwis

    Full Text Available Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects.

  17. Bacterial community structure in aquifers corresponds to stratigraphy

    Science.gov (United States)

    Beyer, Andrea; Möller, Silke; Neumann, Stefan; Burow, Katja; Gutmann, Falko; Lindner, Julia; Müsse, Steffen; Kothe, Erika; Büchel, Georg

    2014-05-01

    So far, groundwater microbiology with respect to different host rocks has not been well described in the literature. However, factors influencing the communities would be of interest to provide a tool for mapping groundwater paths. The Thuringian Basin (Germany) studied here, contains formations of the Permian (Zechstein) and also Triassic period of Buntsandstein, Muschelkalk and Keuper, all of which can be found to crop out at the surface in different regions. We analyzed the bacterial community of nine natural springs and sixteen groundwater wells of the respective rock formations as well as core material from the Zechstein salts. For that we sampled in a mine 3 differnet salt rock samples (carnallitite, halite and sylvinitite). To validate the different approaches, similar rock formations were compared and a consistent microbial community for Buntsandstein could be verified. Similary, for Zechstein, the presence of halophiles was seen with cultivation, isolation directly from the rock material and also in groundwater with DNA-dependent approaches. A higher overlap between sandstone- and limestone-derived communities was visible as if compared to the salt formations. Principal component analysis confirmed formation specific patterns for Muschelkalk, Buntsandstein and Zechstein for the bacterial taxa present, with some overlaps. Bacilli and Gammaproteobacteria were the major groups, with the genera Pseudomonas, Marinomonas, Bacillus, Marinobacter and Pseudoalteromonas representing the communities. The bacteria are well adapted to their respective environment with survival strategies including a wide range of salinity which makes them suitable as tracers for fluid movement below the ground. The results indicate the usefulness and robustness of the approach taken here to investigate aquifer community structures in dependence of the stratigraphy of the groundwater reservoir.

  18. Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm.

    Science.gov (United States)

    Nocker, Andreas; Lepo, Joe E; Snyder, Richard A

    2004-11-01

    We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the gamma- and delta-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated

  19. Molecular assessment of the bacterial community associated with Cassava (Manihot esculenta Crantz) cultivation in Cameroon.

    Science.gov (United States)

    Sarr, Papa Saliou; Sugiyama, Akifumi; Begoude, Aime Didier Boyogueno; Yazaki, Kazufumi; Araki, Shigeru; Nawata, Eiji

    2017-04-01

    Bacterial communities play an important role in nutrient cycles and plant development. Their distribution and activity may depend on location and environmental heterogeneity. This study characterized soil bacterial communities in cassava fields of Eastern (Andom) and Southern (Bityili) Cameroon using molecular tools. In both sites, two improved varieties (TMS-96/1414; TMS-92/0326) and a local variety (Local) were grown in a randomized block design. Composite bulk soils were collected at 10months after planting from cassava plots. The 16S rDNA region was amplified, MiSeq was performed and sequence data analyzed. The same 17 bacterial phyla were present in both Andom and Bityili, while Chlorobi and Deinococcus-Thermus were only specific to Andom. The phyla Proteobacteria, Planctomycetes, Actinobacteria and Acidobacteria were dominant. Although both sites shared similar phyla, the principal coordinate analysis revealed significant variations in their composition, suggesting that the functions of the bacteria in nutrients cycling are likely to differ between Andom and Bityili. Cassava yields were generally higher in Andom which also displayed a higher diversity of bacterial communities. This study provides useful information on the composition of bacterial communities in cassava fields in two agro-ecologies of Cameroon. It constitutes to our knowledge the first report describing soil bacterial communities in association with cassava growth in the country, using molecular tools. Copyright © 2017 Elsevier GmbH. All rights reserved.

  20. Correlations between cyanobacterial density and bacterial transformation to the viable but nonculturable (VBNC) state in four freshwater water bodies.

    Science.gov (United States)

    Chen, Huirong; Shen, Ju; Pan, Gaoshan; Liu, Jing; Li, Jiancheng; Hu, Zhangli

    2015-10-01

    Nutrient concentrations, phytoplankton density and community composition, and the viable but nonculturable (VBNC) state of heterotrophic bacteria were investigated in three connected reservoirs and a small isolated lake in South China to study the relationship between biotic and abiotic factors and the VBNC state in bacteria. Nutrient concentrations in the reservoirs increased in the direction of water flow, whereas Wenshan Lake was more eutrophic. Cyanobacterial blooms occurred in all four water bodies, with differing seasonal trends and dominant species. In Xili and Tiegang Reservoirs, the VBNC ratio (percent of VBNC state bacteria over total viable bacteria) was high for most of the year and negatively correlated with cyanobacterial density. Laboratory co-culture experiments were performed with four heterotrophic bacterial species isolated from Wenshan Lake (Escherichia coli, Klebsiella peneumoniae, Bacillus megaterium and Bacillus cereus) and the dominant cyanobacterial species (Microcystis aeruginosa). For the first three bacterial species, the presence of M. aeruginosa induced the VBNC state and the VBNC ratio was positively correlated with M. aeruginosa density. However, B. cereus inhibited M. aeruginosa growth. These results demonstrate that cyanobacteria could potentially regulate the transformation to the VBNC state of waterborne bacteria, and suggest a role for bacteria in cyanobacterial bloom initiation and termination.

  1. Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef.

    Science.gov (United States)

    Säde, Elina; Penttinen, Katri; Björkroth, Johanna; Hultman, Jenni

    2017-04-01

    Understanding the factors influencing meat bacterial communities is important as these communities are largely responsible for meat spoilage. The composition and structure of a bacterial community on a high-O 2 modified-atmosphere packaged beef product were examined after packaging, on the use-by date and two days after, to determine whether the communities at each stage were similar to those in samples taken from different production lots. Furthermore, we examined whether the taxa associated with product spoilage were distributed across production lots. Results from 16S rRNA amplicon sequencing showed that while the early samples harbored distinct bacterial communities, after 8-12 days storage at 6 °C the communities were similar to those in samples from different lots, comprising mainly of common meat spoilage bacteria Carnobacterium spp., Brochothrix spp., Leuconostoc spp. and Lactococcus spp. Interestingly, abundant operational taxonomic units associated with product spoilage were shared between the production lots, suggesting that the bacteria enable to spoil the product were constant contaminants in the production chain. A characteristic succession pattern and the distribution of common spoilage bacteria between lots suggest that both the packaging type and the initial community structure influenced the development of the spoilage bacterial community. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Balanced Fertilization Decreases Environmental Filtering on Soil Bacterial Community Assemblage in North China

    Directory of Open Access Journals (Sweden)

    Youzhi Feng

    2017-12-01

    Full Text Available Although increasing evidences have emerged for responses of soil microorganisms to fertilizations, the knowledge regarding community assemblages that cause variations in composition is still lacking, as well as the possible feedback to soil fertility. Phylogenetic conservatism of species indicates their similar environmental preferences and/or function traits and phylogenetic signals further can infer community assemblages and influenced ecological processes. Here, we calculated the mean pairwise phylogenetic distance and nearest relative index, characterizing phylogenetic signal and the undergone ecological process to evaluate the community assembly of soil bacterial phylotypes in 20-year fertilized soils. The bacterial community assembly is structured by environmental filtering, regardless of fertilization regime. Soil phosphorous (P availability imposes selection on community assemblage and influences their community turnover among fertilizations. When P nutrient lacks, the effect of environmental filtering becomes stronger, hence bacterial functional traits become more coherent; this process results into increased intraspecific interactions characterized by co-occurrence network analysis. In contrast, when P nutrient becomes abundant, the environmental selection is mitigated; function traits are evened. This process reduces intraspecific interactions and increases carbon sequestration efficiency, which is finally of great favor to the increases in soil fertility. This study has made the first attempt, at the bacterial level, to understand how fertilization affects agroecosystems. When more phylogenetic information on how nutrient cycling-related microbes respond to fertilization becomes available, the systematic knowledge will eventually provide guidance to optimal fertilization strategies.

  3. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs.

    Directory of Open Access Journals (Sweden)

    Pedro R Frade

    Full Text Available Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%. About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater, host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.

  4. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    Science.gov (United States)

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-12-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

  5. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

    Science.gov (United States)

    Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

    2009-09-01

    Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

  6. Characterizing changes in soil bacterial community structure in response to short-term warming

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Jinbo [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing China; School of Marine Sciences, Ningbo University, Ningbo China; Sun, Huaibo [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing China; Peng, Fei [Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou China; Zhang, Huayong [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing China; Xue, Xian [Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou China; Gibbons, Sean M. [Argonne National Laboratory Biosciences Division, Argonne IL USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago IL USA; Gilbert, Jack A. [Argonne National Laboratory Biosciences Division, Argonne IL USA; Department of Ecology and Evolution, University of Chicago, Chicago IL USA; Chu, Haiyan [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing China

    2014-02-18

    High altitude alpine meadows are experiencing considerably greater than average increases in soil surface temperature, potentially as a result of ongoing climate change. The effects of warming on plant productivity and soil edaphic variables have been established previously, but the influence of warming on soil microbial community structure has not been well characterized. Here, the impact of 15 months of soil warming (both + 1 and + 2 degrees C) on bacterial community structure was examined in a field experiment on a Tibetan plateau alpine meadow using bar-coded pyrosequencing. Warming significantly changed (P < 0.05) the structure of the soil bacterial community, but the alpha diversity was not dramatically affected. Changes in the abundance of the Actinobacteria and Alphaproteobacteria were found to contribute the most to differences between ambient (AT) and artificially warmed conditions. A variance partitioning analysis (VPA) showed that warming directly explained 7.15% variation in bacterial community structure, while warming-induced changes in soil edaphic and plant phenotypic properties indirectly accounted for 28.3% and 20.6% of the community variance, respectively. Interestingly, certain taxa showed an inconsistent response to the two warming treatments, for example Deltaproteobacteria showed a decreased relative abundance at + 1 degrees C, but a return to AT control relative abundance at + 2 degrees C. This suggests complex microbial dynamics that could result from conditional dependencies between bacterial taxa.

  7. Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

    Science.gov (United States)

    Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

    2015-08-01

    Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

  8. Spatial variation of bacterial community composition near the Luzon ...

    African Journals Online (AJOL)

    use

    2011-11-23

    Nov 23, 2011 ... However, little information of spatial variation of bacterial community ... GF/F glass fiber (0.45 µm, 47 mm diameter, Whatman Japan. Limited., Tokyo ... the research vessel using a CTD system (Sea-Bird Electronics, Inc.,. USA).

  9. Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere.

    Directory of Open Access Journals (Sweden)

    Erika Yashiro

    Full Text Available We studied the effect of many years of streptomycin use in apple orchards on the proportion of phyllosphere bacteria resistant to streptomycin and bacterial community structure. Leaf samples were collected during early July through early September from four orchards that had been sprayed with streptomycin during spring of most years for at least 10 years and four orchards that had not been sprayed. The percentage of cultured phyllosphere bacteria resistant to streptomycin at non-sprayed orchards (mean of 65% was greater than at sprayed orchards (mean of 50% (P = 0.0271. For each orchard, a 16S rRNA gene clone library was constructed from leaf samples. Proteobacteria dominated the bacterial communities at all orchards, accounting for 71 of 104 OTUs (determined at 97% sequence similarity and 93% of all sequences. The genera Massilia, Methylobacterium, Pantoea, Pseudomonas, and Sphingomonas were shared across all sites. Shannon and Simpson's diversity indices and Pielou's evenness index were similar among orchards regardless of streptomycin use. Analysis of Similarity (ANOSIM indicated that long-term streptomycin treatment did not account for the observed variability in community structure among orchards (R = -0.104, P = 0.655. Other variables, including time of summer, temperature and time at sampling, and relative distance of the orchards from each other, also had no significant effect on bacterial community structure. We conclude that factors other than streptomycin exposure drive both the proportion of streptomycin-resistant bacteria and phylogenetic makeup of bacterial communities in the apple phyllosphere in middle to late summer.

  10. Bacterial community structure in the Cerasus sachalinensis Kom ...

    African Journals Online (AJOL)

    The results showed that the bacterial community diversity in the cultivated C. sachalinensis rhizosphere was always higher than the wild, while the evenness and dominance indices followed a different pattern as compared to band richness in the wild and cultivated conditions. The plant growth stages also had an influence ...

  11. Changes in Soil Bacterial Communities and Diversity in ...

    Science.gov (United States)

    Silver-induced selective pressure is becoming increasingly important due to the growing use of silver (Ag) as an antimicrobial agent in biomedical and commercial products. With demonstrated links between environmental resistomes and clinical pathogens, it is important to identify microbial profiles related to silver tolerance/resistance. We investigated the effects of ionic Ag stress on soil bacterial communities and identified resistant/persistant bacterial populations. Silver treatments of 50 - 400 mg Ag kg-1 soil were established in five soils. Chemical lability measurements using diffusive gradients in thin-film devices confirmed that significant (albeit decreasing) labile Ag concentrations were present throughout the 9-month incubation period. Synchrotron X-ray absorption near edge structure spectroscopy demonstrate that this decreasing lability was due to changes in Ag speciation to less soluble forms such as Ag0 and Ag2S. Real-time PCR and Illumina MiSeq screening of 16S rRNA bacterial genes showed β-diversity in response to Ag pressure, and immediate and significant reductions in 16S rRNA gene counts with varying degrees of recovery. These effects were more strongly influenced by exposure time than by Ag dose at these rates. Ag-selected dominant OTUs principally resided in known persister taxa (mainly Gram positive), including metal-tolerant bacteria and slow-growing Mycobacteria. Soil microbial communities have been implicated as sources of an

  12. Bacterial community composition in the water column of a lake formed by a former uranium open pit mine.

    Science.gov (United States)

    Edberg, Frida; Andersson, Anders F; Holmström, Sara J M

    2012-11-01

    Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

  13. Temperature-driven adaptation of the bacterial community in peat measured by using thymidine and leucine incorporation.

    Science.gov (United States)

    Ranneklev, S B; Bååth, E

    2001-03-01

    The temperature-driven adaptation of the bacterial community in peat was studied, by altering temperature to simulate self-heating and a subsequent return to mesophilic conditions. The technique used consisted of extracting the bacterial community from peat using homogenization-centrifugation and measuring the rates of thymidine (TdR) or leucine (Leu) incorporation by the extracted bacterial community at different temperatures. Increasing the peat incubation temperature from 25 degrees C to 35, 45, or 55 degrees C resulted in a selection of bacterial communities whose optimum temperatures for activity correlated to the peat incubation temperatures. Although TdR and Leu incorporations were significantly correlated, the Leu/TdR incorporation ratios were affected by temperature. Higher Leu/TdR incorporation ratios were found at higher temperatures of incubation of the extracted bacterial community. Higher Leu/TdR incorporation ratios were also found for bacteria in peat samples incubated at higher temperatures. The reappearance of the mesophilic community and disappearance of the thermophilic community when the incubation temperature of the peat was shifted down were monitored by measuring TdR incorporation at 55 degrees C (thermophilic activity) and 25 degrees C (mesophilic activity). Shifting the peat incubation temperature from 55 to 25 degrees C resulted in a recovery of the mesophilic activity, with a subsequent disappearance of the thermophilic activity. The availability of substrate for bacterial growth varied over time and among different peat samples. To avoid confounding effects of substrate availability, a temperature adaptation index was calculated. This index consisted of the log(10) ratio of TdR incorporation at 55 and 25 degrees C. The temperature index decreased linearly with time, indicating that no thermophilic activity would be detected by the TdR technique 1 month after the temperature downshift. There were no differences between the slopes of the

  14. Effects of triclosan on bacterial community composition and ...

    Science.gov (United States)

    Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

  15. Temporal and Spatial Diversity of Bacterial Communities in Coastal Waters of the South China Sea

    Science.gov (United States)

    Du, Jikun; Xiao, Kai; Li, Li; Ding, Xian; Liu, Helu; Lu, Yongjun; Zhou, Shining

    2013-01-01

    Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns. PMID:23785512

  16. Bacterial carbon cycling in a subarctic fjord

    DEFF Research Database (Denmark)

    Middelboe, Mathias; Glud, Ronnie Nøhr; Sejr, M.K.

    2012-01-01

    of viruses on bacterial mortality (4–36% of cell production) and carbon cycling. Heterotrophic bacterial consumption was closely coupled with autochthonous BDOC production, and the majority of the primary production was consumed by pelagic bacteria at all seasons. The relatively low measured BGE emphasized......In this seasonal study, we examined the environmental controls and quantitative importance of bacterial carbon consumption in the water column and the sediment in the subarctic Kobbefjord, Greenland. Depth-integrated bacterial production in the photic zone varied from 5.0 ± 2.7 mg C m−2 d−1...... in February to 42 ± 28 mg C m−2 d−1 in May and 34 ± 7 mg C m−2 d−1 in September, corresponding to a bacterial production to primary production ratio of 0.34 ± 0.14, 0.07 ± 0.04, and 0.08 ± 0.06, respectively. Based on measured bacterial growth efficiencies (BGEs) of 0.09–0.10, pelagic bacterial carbon...

  17. Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz.

    Science.gov (United States)

    Coelho, Francisco J R C; Louvado, António; Domingues, Patrícia M; Cleary, Daniel F R; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R; Cunha, Ângela; Gomes, Newton C M

    2016-10-20

    The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

  18. Bacterial communities in sediment of a Mediterranean marine protected area.

    Science.gov (United States)

    Catania, Valentina; Sarà, Gianluca; Settanni, Luca; Quatrini, Paola

    2017-04-01

    Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) "Capo Gallo-Isola delle Femmine" was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.

  19. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  20. Transient shifts in bacterial communities associated with the temperate gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Marie La Rivière

    Full Text Available BACKGROUND: Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. METHODOLOGY/PRINCIPAL FINDINGS: The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed. CONCLUSION/SIGNIFICANCE: This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals

  1. Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill.

    Science.gov (United States)

    Engel, Annette Summers; Liu, Chang; Paterson, Audrey T; Anderson, Laurie C; Turner, R Eugene; Overton, Edward B

    2017-10-15

    Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria , Firmicutes , Bacteroidetes , and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria ( Rhizobiales ), Chloroflexi ( Dehalococcoidia ), and Planctomycetes Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts. IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial

  2. Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor.

    Science.gov (United States)

    Ishizawa, Hidehiro; Kuroda, Masashi; Morikawa, Masaaki; Ike, Michihiko

    2017-01-01

    Duckweed (family Lemnaceae ) has recently been recognized as an ideal biomass feedstock for biofuel production due to its rapid growth and high starch content, which inspired interest in improving their productivity. Since microbes that co-exist with plants are known to have significant effects on their growth according to the previous studies for terrestrial plants, this study has attempted to understand the plant-microbial interactions of a duckweed, Lemna minor , focusing on the growth promotion/inhibition effects so as to assess the possibility of accelerated duckweed production by modifying co-existing bacterial community. Co-cultivation of aseptic L. minor and bacterial communities collected from various aquatic environments resulted in changes in duckweed growth ranging from -24 to +14% compared to aseptic control. A number of bacterial strains were isolated from both growth-promoting and growth-inhibitory communities, and examined for their co-existing effects on duckweed growth. Irrespective of the source, each strain showed promotive, inhibitory, or neutral effects when individually co-cultured with L. minor . To further analyze the interactions among these bacterial strains in a community, binary combinations of promotive and inhibitory strains were co-cultured with aseptic L. minor , resulting in that combinations of promotive-promotive or inhibitory-inhibitory strains generally showed effects similar to those of individual strains. However, combinations of promotive-inhibitory strains tended to show inhibitory effects while only Aquitalea magnusonii H3 exerted its plant growth-promoting effect in all combinations tested. Significant change in biomass production was observed when duckweed was co-cultivated with environmental bacterial communities. Promotive, neutral, and inhibitory bacteria in the community would synergistically determine the effects. The results indicate the possibility of improving duckweed biomass production via regulation of co

  3. Hydrogeochemical characteristics and bacterial community diversity in leachate from animal carcass disposal

    Science.gov (United States)

    Kaown, D.; Kim, H.; Lee, S.; Hyun, Y.; Moon, H.; Ko, K.; Lee, K.

    2012-12-01

    The release of leachate from animal carcass disposal can potentially contaminate soil and groundwater. During the Korea's foot-and-mouth disease (FMD) outbreak in 2010-2011, about 3.53 million of pigs and cattle were slaughtered and 4,538 burial sites were constructed. The objectives of this study are to determine the hydrogeochemical characteristics and bacterial community diversity in leachate from animal carcass disposal. Hydrogeochemical characteristics and bacterial community diversity in leachate from animal carcass burial facilities were monitored to prevent further soil and groundwater contamination and to build effective plans for stabilization of the burial site. Two burial sites were investigated in this study. An animal carcass disposal site is located in a flat area and another disposal site is found in mountain area. The hydrogeochemical and hydrogeological characteristics were analyzed to identify groundwater contamination by leachate from livestock burial sites. After 5-6 months of burial, the concentrations of NH4+, Cl-, and HCO3- in leachate were decreased since the leachate was regularly pumped and treated. However, high concentrations of major contaminants (NH4+, Cl-, and HCO3-) were still observed in landfill leachate of mountain area even though pumping and treatment of leachate were continuously conducted. Bacterial community diversity over time in leachate from animal carcass disposal was analyzed using 16S rRNA gene-based pyrosequencing. The impact of landfill leachate on change of bacterial community in soil and groundwater were monitored for a year.

  4. Bacterial Community Development in Experimental Gingivitis

    Science.gov (United States)

    Kistler, James O.; Booth, Veronica; Bradshaw, David J.; Wade, William G.

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1–V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344 267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  5. Bacterial community development in experimental gingivitis.

    Directory of Open Access Journals (Sweden)

    James O Kistler

    Full Text Available Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp, and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs per sample. Principal coordinates analysis (PCoA plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new

  6. Bacterial community development in experimental gingivitis.

    Science.gov (United States)

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  7. A decadal (2002-2014 analysis for dynamics of heterotrophic bacteria in an Antarctic coastal ecosystem: variability and physical and biogeochemical forcings

    Directory of Open Access Journals (Sweden)

    Hyewon Kim

    2016-11-01

    Full Text Available We investigated the dynamics of heterotrophic bacteria in the coastal western Antarctic Peninsula (WAP, using decadal (2002-2014 time series of two bacterial variables, bacterial production (BP via 3H-leucine incorporation rates and bacterial biomass (BB via bacterial abundance, collected at Palmer Antarctica Long Term Ecological Research (LTER Station B (64.8°S, 64.1°W over a full austral growing season (October-March. Strong seasonal and interannual variability in the degree of bacterial coupling with phytoplankton processes were observed with varying lags. On average, BP was only 4% of primary production (PP, consistent with low BP:PP ratios observed in polar waters. BP was more strongly correlated with chlorophyll (Chl, than with PP, implying that bacteria feed on DOC produced from a variety of trophic levels (e.g. zooplankton sloppy feeding and excretion as well as directly on phytoplankton-derived DOC. The degree of bottom-up control on bacterial abundance was moderate and relatively consistent across entire growing seasons, suggesting that bacteria in the coastal WAP are under consistent DOC limitation. Temperature also influenced BP rates, though its effect was weaker than DOC. We established generalized linear models (GLMs for monthly composites of BP and BB via stepwise regression to explore a set of physical and biogeochemical predictors. Physically, high BP and large BB were shaped by a stratified water-column, similar to forcing mechanisms favoring phytoplankton blooms, but high sea surface temperature (SST also significantly promoted bacterial processes. High BP and large BB were influenced by high PP and bulk DOC concentrations. Based on these findings, we suggest an increasingly important role of marine heterotrophic bacteria in the coastal WAP food-web as climate change introduces a more favorable environmental setting for promoting BP, with increased DOC from retreating glaciers, a more stabilized upper water-column from ice

  8. Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure.

    Science.gov (United States)

    Pérez, María Teresa; Sommaruga, Ruben

    2007-09-01

    We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24-48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition.

  9. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

    Science.gov (United States)

    Brouchkov, Anatoli; Kabilov, Marsel; Filippova, Svetlana; Baturina, Olga; Rogov, Victor; Galchenko, Valery; Mulyukin, Andrey; Fursova, Oksana; Pogorelko, Gennady

    2017-12-15

    Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Functional diversity and redundancy across fish gut, sediment and water bacterial communities.

    Science.gov (United States)

    Escalas, Arthur; Troussellier, Marc; Yuan, Tong; Bouvier, Thierry; Bouvier, Corinne; Mouchet, Maud A; Flores Hernandez, Domingo; Ramos Miranda, Julia; Zhou, Jizhong; Mouillot, David

    2017-08-01

    This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand.

    Science.gov (United States)

    Rangjaroen, Chakrapong; Rerkasem, Benjavan; Teaumroong, Neung; Sungthong, Rungroch; Lumyong, Saisamorn

    2014-01-01

    Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.

  12. Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

    Science.gov (United States)

    Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

    2013-06-01

    Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

  13. [Analysis of the bacterial community developing in the course of Sphagnum moss decomposition].

    Science.gov (United States)

    Kulichevskaia, I S; Belova, S E; Kevbrin, V V; Dedysh, S N; Zavarzin, G A

    2007-01-01

    Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 x 10(7) cells ml(-1). About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Phanctomycetes. The population sizes of Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.

  14. Self-sustaining, solar-driven bioelectricity generation in micro-sized microbial fuel cell using co-culture of heterotrophic and photosynthetic bacteria

    Science.gov (United States)

    Liu, Lin; Choi, Seokheun

    2017-04-01

    Among many energy harvesting techniques with great potential, microbial fuel cell (MFC) technology is arguably the most underdeveloped. Even so, excitement is building, as microorganisms can harvest electrical power from any biodegradable organic source (e.g. wastewater) that is readily available in resource-limited settings. Nevertheless, the requirement for endless introduction of organic matter imposes a limiting factor to this technology, demanding an active feeding system and additional power. Here, we demonstrated self-sustaining bioelectricity generation from a microliter-scale microbial fuel cell (MFC) by using the syntrophic interaction between heterotrophic exoelectrogenic bacteria and phototrophs. The MFC continuously generated light-responsive electricity from the heterotrophic bacterial metabolic respiration with the organic substrates produced by photosynthetic bacteria. Without additional organic fuel, the mixed culture in a 90-μL-chamber MFC generated self-sustained current for more than 13 days, while the heterotrophic culture produced current that decreased dramatically within a few hours. The current from the mixed culture was about 70 times greater than that of the device with only photosynthetic bacteria. The miniaturization provided a short start-up time, a well-controlled environment, and small internal resistance. Those advantages will become the general design platform for micropower generation.

  15. Impact of enzymatic digestion on bacterial community composition in CF airway samples

    Directory of Open Access Journals (Sweden)

    Kayla M. Williamson

    2017-05-01

    Full Text Available Background Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF. We sought to evaluate the effect of enzymatic digestion (EnzD prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP samples from patients with CF. Methods DNA from 81 samples (39 sputum and 42 OP collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA of individual genera for paired samples with and without EnzD. Results Shannon Diversity Index (alpha-diversity decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn, whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella (p < 0.01, Streptococcus (p < 0.01, and Rothia (p < 0.01. Staphylococcus (p < 0.01 was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella (p < 0.01, Granulicatella (p < 0.01, Prevotella (p < 0.01, and Gemella (p = 0.02. In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. Discussion We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP

  16. Bacterial levels in the Nyl River system, Limpopo province, South ...

    African Journals Online (AJOL)

    Heterotrophic plate counts, faecal coliform counts and total coliform counts indicated that the system was stressed. The Modimolle sewage treatment works and local agricultural activities were found to be the point and diffuse sources of bacterial contamination, respectively. African Journal of Aquatic Science 2010, 35(1): ...

  17. Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake

    Science.gov (United States)

    Navarro, J.B.; Moser, D.P.; Flores, A.; Ross, C.; Rosen, Michael R.; Dong, H.; Zhang, G.; Hedlund, B.P.

    2009-01-01

    Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of 1 ?????106 cells ml-1 of culturable heterotrophs was replaced by a dense population of more than 1????????109 cells ml-1, which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria. ?? 2008 Springer Science+Business Media, LLC.

  18. Long- term manure exposure increases soil bacterial community potential for plasmid uptake

    DEFF Research Database (Denmark)

    Musovic, Sanin; Klümper, Uli; Dechesne, Arnaud

    2014-01-01

    Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and main......Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive...... and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent...

  19. Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment.

    Science.gov (United States)

    Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N

    2014-02-01

    The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0-6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α- and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  20. Bacterial activity in a reservoir determined by autoradiography and its relationships to phyto- and zooplankton

    International Nuclear Information System (INIS)

    Simek, K.

    1986-01-01

    In the drinking water reservoir Rimov (Southern Bohemia) bacterioplankton was studied during 1983. Special attention was given to the relationships between parameters of bacterial abundance, total and individual activity. Bacterial counts and biomass was assessed and autoradiographic determinations of the proportion of active bacteria incorporating thymidine (Th) and a mixture of amino acids (AA) and total uptake rate of AA were made over a year in the surface layer and during summer stratification from the thermocline and 15 m depth. Specific activity of metabolically active bacteria and specific activity per unit of biomass were negatively correlated with counts of metabolizing cells and with bacterial biomass, respectively. Total and individual heterotrophic activity and counts of bacteria coincided with the changes of phytoplankton biomass, whereas bacteria incorporating Th were more tightly correlated with primary production. The most significant relation of metabolically active bacteria was found to cladoceran biomass. Thus, this part of heterotrophic bacterial activity seems to be stimulated by leakage of dissolved organic matter from phytoplankton being disrupted and incompletely digested by cladocerans rather than from healthy photosynthetizing cells. (author)

  1. Bacterial and archaeal communities in sediments of the north Chinese marginal seas.

    Science.gov (United States)

    Liu, Jiwen; Liu, Xiaoshou; Wang, Min; Qiao, Yanlu; Zheng, Yanfen; Zhang, Xiao-Hua

    2015-07-01

    Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the surface sediment of four sea areas including the Bohai Sea (BS), North Yellow Sea (NYS), South Yellow Sea (SYS), and the north East China Sea (NECS) were surveyed by 16S ribosomal RNA (rRNA) gene pyrosequencing and quantitative PCR. The results showed that microbial communities of the four geographic areas were distinct from each other at the operational taxonomic unit (OTU) level, whereas the microbial communities of the BS, NYS, and SYS were more similar to each other than to the NECS at higher taxonomic levels. Across all samples, Bacteria were numerically dominant relative to Archaea, and among them, Gammaproteobacteria and Euryarchaeota were predominant in the BS, NYS, and SYS, while Deltaproteobacteria and Thaumarchaeota were prevalent in the NECS. The most abundant bacterial genera were putative sulfur oxidizer and sulfate reducer, suggesting that sulfur cycle processes might prevail in these areas, and the high abundance of dsrB (10(7)-10(8) copies g(-1)) in all sites verified the dominance of sulfate reducer in the north Chinese marginal seas. The differences in sediment sources among the sampling areas were potential explanations for the observed microbial community variations. Furthermore, temperature and dissolved oxygen of bottom water were significant environmental factors in determining both bacterial and archaeal communities, whereas chlorophyll a in sediment was significant only in structuring archaeal community. This study presented an outline of benthic microbial communities and provided insights into understanding the biogeochemical cycles in sediments of the north Chinese marginal seas.

  2. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

    NARCIS (Netherlands)

    Frade, P.R.; Roll, K.; Bergauer, K.; Herndl, G.

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associatedwith the surface mucus layer of corals have rarely taken place. It has thereforeremained enigmatic whether mucus-associated archaeal and bacterial communities exhibita similar specificity towards coral hosts

  3. Restructuring of endophytic bacterial communities in grapevine yellows-diseased and recovered Vitis vinifera L. plants.

    Science.gov (United States)

    Bulgari, Daniela; Casati, Paola; Crepaldi, Paola; Daffonchio, Daniele; Quaglino, Fabio; Brusetti, Lorenzo; Bianco, Piero Attilio

    2011-07-01

    Length heterogeneity-PCR assays, combined with statistical analyses, highlighted that the endophytic bacterial community associated with healthy grapevines was characterized by a greater diversity than that present in diseased and recovered plants. The findings suggest that phytoplasmas can restructure the bacterial community by selecting endophytic strains that could elicit a plant defense response.

  4. Hydrocephalus is a rare outcome in community-acquired bacterial meningitis in adults

    DEFF Research Database (Denmark)

    Bodilsen, Jacob; Schønheyder, Henrik Carl; Nielsen, Henrik I

    2013-01-01

    BACKGROUND: Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid in this ......BACKGROUND: Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid...... in this field of research we set out to ascertain the risk and outcome of hydrocephalus in patients with community-acquired bacterial meningitis (CABM) in North Denmark Region. METHODS: We conducted a retrospective population-based cohort study of CABM cases above 14 years of age. Cases diagnosed during a 13......-year period, 1998 through 2010, were identified in a laboratory register and data were acquired through patient records. Cases not confirmed by culture met other strict inclusion criteria. The diagnosis of hydrocephalus relied upon the radiologists' reports on cranial imaging. Outcome was graded...

  5. Heterotrophic cultivation of microalgae for pigment production: A review.

    Science.gov (United States)

    Hu, Jianjun; Nagarajan, Dillirani; Zhang, Quanguo; Chang, Jo-Shu; Lee, Duu-Jong

    Pigments (mainly carotenoids) are important nutraceuticals known for their potent anti-oxidant activities and have been used extensively as high end health supplements. Microalgae are the most promising sources of natural carotenoids and are devoid of the toxic effects associated with synthetic derivatives. Compared to photoautotrophic cultivation, heterotrophic cultivation of microalgae in well-controlled bioreactors for pigments production has attracted much attention for commercial applications due to overcoming the difficulties associated with the supply of CO 2 and light, as well as avoiding the contamination problems and land requirements in open autotrophic culture systems. In this review, the heterotrophic metabolic potential of microalgae and their uses in pigment production are comprehensively described. Strategies to enhance pigment production under heterotrophic conditions are critically discussed and the challenges faced in heterotrophic pigment production with possible alternative solutions are presented. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation.

    Science.gov (United States)

    Xu, Xihui; Zhang, Zhou; Hu, Shunli; Ruan, Zhepu; Jiang, Jiandong; Chen, Chen; Shen, Zhenguo

    2017-01-01

    Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH 4 + -N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.

  7. Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms.

    Science.gov (United States)

    Sun, Fu-Lin; Fan, Lei-Lei; Xie, Guang-Jian

    2016-08-01

    The anaerobic-anoxic-aerobic (A2O) process is a highly efficient sewage treatment method, which uses complex bacterial communities. However, the effect of copper on this process and the bacterial communities involved remains unknown. In this study, a systematic investigation of the effect of persistent exposure of copper in the A2O wastewater treatment system was performed. An A2O device was designed to examine the effect of copper on the removal efficiency and microbial community compositions of activated sludge that was continuously treated with 10, 20, and 40 mg L(-1) copper, respectively. Surprisingly, a decrease in chemical oxygen demand (COD) and ammonia nitrogen (NH4N) removal efficiency was observed, and the toxicity of high copper concentration was significantly greater at 7d than at 1d. Proteobacteria, Bacteroidetes, Acidobacteria, Chlorobi, and Nitrospirae were the dominant bacterial taxa in the A2O system, and significant changes in microbial community were observed during the exposure period. Most of the dominant bacterial groups were easily susceptible to copper toxicity and diversely changed at different copper concentrations. However, not all the bacterial taxa were inhibited by copper treatment. At high copper concentration, many bacterial species were stimulated and their abundance increased. Cluster analysis and principal coordinate analysis (PCoA) based on operational taxonomic units (OTUs) revealed clear differences in the bacterial communities among the samples. These findings indicated that copper severely affected the performance and key microbial populations in the A2O system as well as disturbed the stability of the bacterial communities in the system, thus decreasing the removal efficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  9. Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

    Science.gov (United States)

    Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

    2016-11-01

    Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

  10. Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times.

    Science.gov (United States)

    Neher, Deborah A; Weicht, Thomas R; Bates, Scott T; Leff, Jonathan W; Fierer, Noah

    2013-01-01

    Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

  11. Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River

    Science.gov (United States)

    Fan, Limin; Song, Chao; Meng, Shunlong; Qiu, Liping; Zheng, Yao; Wu, Wei; Qu, Jianhong; Li, Dandan; Zhang, Cong; Hu, Gengdong; Chen, Jiazhang

    2016-01-01

    Bacterioplankton and archaeaplankton communities play key roles in the biogeochemical processes of water, and they may be affected by many factors. In this study, we used high-throughput 16S rRNA gene sequencing to profile planktonic bacterial and archaeal community compositions in the upper section of the tidal reach in Yangtze River. We found that the predominant bacterial phyla in this river section were Proteobacteria, Firmicutes, and Actinobacteria, whereas the predominant archaeal classes were Halobacteria, Methanomicrobia, and unclassified Euryarchaeota. Additionally, the bacterial and archaeal community compositions, richnesses, functional profiles, and ordinations were affected by the spatial heterogeneity related to the concentration changes of sulphate or nitrate. Notably, the bacterial community was more sensitive than the archaeal community to changes in the spatial characteristics of this river section. These findings provide important insights into the distributions of bacterial and archaeal communities in natural water habitats. PMID:27966673

  12. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    Science.gov (United States)

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  13. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    Directory of Open Access Journals (Sweden)

    Tao Ding

    Full Text Available Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  14. Archaeal and bacterial community analysis of several Yellowstone National Park hot springs

    Science.gov (United States)

    Colman, D. R.; Takacs-Vesbach, C. D.

    2012-12-01

    The hot springs of Yellowstone National Park (YNP) are home to a diverse assemblage of microorganisms. Culture-independent studies have significantly expanded our understanding of the diversity of both Bacteria and Archaea present in YNP springs as well as the geochemical and ecological controls on communities. While the ecological analysis of Bacteria among the physicochemically heterogenous springs of YNP has been previously conducted, less is known about the extent of diversity of Archaeal communities and the chemical and ecological controls on their populations. Here we report a culture-independent analysis of 31 hot spring archaeal and bacterial communities of YNP springs using next generation sequencing. We found the phylogenetic diversity of Archaea to be generally comparable to that of co-occurring bacterial communities although overall, in the springs we investigated, diversity was higher for Bacteria than Archaea. Chemical and physical controls were similar for both domains with pH correlating most strongly with community composition. Community differences reflected the partitioning of taxonomic groups in low or high pH springs for both domains. Results will be discussed in a geochemical and ecological context.

  15. Impact of Anthracene Exposure on Bacterial Community Composition and Function in an Egyptian Marine Environment

    International Nuclear Information System (INIS)

    Zakaria, A.E.M.; Lappin-Scott, H.

    2013-01-01

    The application of bioremediation technology for pollution treatment requires more knowledge about how do microbial communities respond to pollutant exposure. The main goals of this study are to investigate the behavior of natural bacterial microflora of Suez Gulf (SGM) in response to exposure to different concentrations of Polycyclic Aromatic Hydrocarbons (PAHs) for different periods. In this study, anthracene, as a model of (PAHs) was added in different concentrations, (30,150 and 500 ppm) to fertilized Suez Gulf water in shaking microcosms to examine the possible shifts in bacterial community composition and function. Changes in bacterial community composition was followed up after different periods of exposure (0, 6, 12, and 18) days to the above mentioned concentrations of anthracene by profiling the amplified product of 16S rDNA via denaturing gradient gel electrophoresis (DGGE) of SGM in treated microcosm separately. DGGE profiles revealed remarkable changes in diversity due to exposure concentration and duration to anthracene. A diverse relationship between anthracene concentration and bacterial diversity was detected. On the other hand, changes in community function were determined by testing the biodegradation capabilities of the consortia after different exposures separately in microcosms containing 50 ppm of anthracene for 14 days. The remaining anthracene was extracted and monitored by high performance liquid chromatography (HPLC) and DGGE profiles of amplified 16S rDNA extracted from parallel biodegradation microcosms were examined to indicate the effects of pre-exposure to different concentrations for different periods to PAHs on the bacterial community compositions. The results confirm that the long term effects of pre exposure to high concentrations of PAH on the bacterial community composition, suggesting that that some organisms can be used as a bio marker indicating the exposures of the marine environment to high concentrations of PAHs. HPLC

  16. Analysis of bacterial and fungal community structure in replant ...

    African Journals Online (AJOL)

    High quality DNA is the basis of analyzing bacterial and fungal community structure in replant strawberry rhizosphere soil with the method of denaturing gradient gel electrophoresis (DGGE). DNA of soil microorganisms was extracted from the rhizosphere soil of strawberries planted in different replanted years (0, two, ...

  17. Comparison of bacterial communities of tilapia fish from Cameroon ...

    African Journals Online (AJOL)

    Comparison of bacterial communities of tilapia fish from Cameroon and Vietnam using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) ... The different PCR-DGGE 16S rDNA banding profiles obtained were analysed and results showed that there were specific bands for each geographical ...

  18. The bacterial community composition of the surface microlayer in a high mountain lake.

    Science.gov (United States)

    Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

    2010-09-01

    The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.

  19. Shifts in soil bacterial community after eight years of land-use change.

    Science.gov (United States)

    Suleiman, Afnan Khalil Ahmad; Manoeli, Lupatini; Boldo, Juliano Tomazzoni; Pereira, Marcos G; Roesch, Luiz Fernando Wurdig

    2013-03-01

    The interaction between plants, soil and microorganisms is considered to be the major driver of ecosystem functions and any modification of plant cover and/or soil properties might affect the microbial structure, which, in turn, will influence ecological processes. Assuming that soil properties are the major drivers of soil bacterial diversity and structure within the same soil type, it can be postulated whether plant cover causes significant shifts in soil bacterial community composition. To address this question, this study used 16S rRNA pyrosequencing to detect differences in diversity, composition and/or relative abundance of bacterial taxa from an area covered by pristine forest, as well as eight-year-old grassland surrounded by the same forest. It was shown that a total of 69% of the operational taxonomic units (OTUs) were shared between environments. Overall, forest and grassland samples presented the same diversity and the clustering analysis did not show the occurrence of very distinctive bacterial communities between environments. However, 11 OTUs were detected in statistically significant higher abundance in the forest samples but in lower abundance in the grassland samples, whereas 12 OTUs occurred in statistically significant higher abundance in the grassland samples but in lower abundance in the forest samples. The results suggested the prevalence of a resilient core microbial community that did not suffer any change related to land use, soil type or edaphic conditions. The results illustrated that the history of land use might influence present-day community structure. Copyright © 2012 Elsevier GmbH. All rights reserved.

  20. Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process.

    Science.gov (United States)

    Bulgari, Daniela; Casati, Paola; Quaglino, Fabio; Bianco, Piero A

    2014-07-21

    Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic. Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality. Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured

  1. Pole-to-pole biogeography of surface and deep marine bacterial communities

    Science.gov (United States)

    Ghiglione, Jean-François; Galand, Pierre E.; Pommier, Thomas; Pedrós-Alió, Carlos; Maas, Elizabeth W.; Bakker, Kevin; Bertilson, Stefan; Kirchman, David L.; Lovejoy, Connie; Yager, Patricia L.; Murray, Alison E.

    2012-01-01

    The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation. PMID:23045668

  2. Lead pollution in a large, prairie-pothole lake (Rush Lake, WI, USA): Effects on abundance and community structure of indigenous sediment bacteria

    International Nuclear Information System (INIS)

    Grandlic, Christopher J.; Geib, Ian; Pilon, Renee; Sandrin, Todd R.

    2006-01-01

    Rush Lake (WI, USA), the largest prairie-pothole lake east of the Mississippi River, has been contaminated with lead pollution as a result of over 140 years of waterfowl hunting. We examined: (1) the extent of lead pollution in Rush Lake sediments and (2) whether lead pollution in Rush Lake is affecting the abundance and community structure of indigenous sediment bacteria. Sediment lead concentrations did not exceed 59 mg Pb kg -1 dry sediment. No relationship was observed between sediment lead concentration and the abundance of aerobic (P = 0.498) or anaerobic (P = 0.416) heterotrophic bacteria. Similarly, lead did not appear to affect bacterial community structure when considering both culturable and nonculturable community members. In contrast, the culturable fraction of sediment bacteria in samples containing 59 mg Pb kg -1 exhibited a unique community structure. While factors other than lead content likely play roles in determining bacterial community structure in the sediments of Rush Lake, these data suggest that the culturable fraction of sediment bacterial communities is affected by elevated lead levels. - Low levels of lead pollution in Rush Lake are not impinging upon the abundance of indigenous sediment bacteria, but may be affecting the community structure of the culturable fraction of these bacteria

  3. Microbial interactions with the cyanobacterium Microcystis aeruginosa and their dependence on temperature

    DEFF Research Database (Denmark)

    Dziallas, Claudia; Grossart, Hans-Peter

    2012-01-01

    and their associated community often masked this temperature effect. Both macro- and microenvironment of active cyanobacterial strains were characterized by high pH and oxygen values creating a unique habitat that potentially affects microbial diversity and function. For example, archaea including ‘anaerobic......Associated heterotrophic bacteria alter the microenvironment of cyanobacteria and potentially influence cyanobacterial development. Therefore, we studied interactions of the unicellular freshwater cyanobacterium Microcystis aeruginosa with heterotrophic bacteria. The associated bacterial community...... was greatly driven by temperature as seen by DNA Wngerprinting. However, the associated microbes also closely interacted with the cyanobacteria indicating changing ecological consequence of the associated bacterial community with temperature. Whereas concentration of dissolved organic carbon in cyanobacterial...

  4. Time-scales of hydrological forcing on the geochemistry and bacterial community structure of temperate peat soils

    Science.gov (United States)

    Nunes, Flavia L. D.; Aquilina, Luc; De Ridder, Jo; Francez, André-Jean; Quaiser, Achim; Caudal, Jean-Pierre; Vandenkoornhuyse, Philippe; Dufresne, Alexis

    2015-10-01

    Peatlands are an important global carbon reservoir. The continued accumulation of carbon in peatlands depends on the persistence of anoxic conditions, in part induced by water saturation, which prevents oxidation of organic matter, and slows down decomposition. Here we investigate how and over what time scales the hydrological regime impacts the geochemistry and the bacterial community structure of temperate peat soils. Peat cores from two sites having contrasting groundwater budgets were subjected to four controlled drought-rewetting cycles. Pore water geochemistry and metagenomic profiling of bacterial communities showed that frequent water table drawdown induced lower concentrations of dissolved carbon, higher concentrations of sulfate and iron and reduced bacterial richness and diversity in the peat soil and water. Short-term drought cycles (3-9 day frequency) resulted in different communities from continuously saturated environments. Furthermore, the site that has more frequently experienced water table drawdown during the last two decades presented the most striking shifts in bacterial community structure, altering biogeochemical functioning of peat soils. Our results suggest that the increase in frequency and duration of drought conditions under changing climatic conditions or water resource use can induce profound changes in bacterial communities, with potentially severe consequences for carbon storage in temperate peatlands.

  5. Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils.

    Science.gov (United States)

    Li, Jing; Hu, Hang-Wei; Ma, Yi-Bing; Wang, Jun-Tao; Liu, Yu-Rong; He, Ji-Zheng

    2015-07-01

    Nickel pollution imposes deleterious effects on soil ecosystem. The responses of soil microorganisms to long-term nickel pollution under field conditions remain largely unknown. Here, we used high-throughput sequencing to elucidate the impacts of long-term nickel pollution on soil bacterial communities in two contrasting agricultural soils. Our results found that the soil microbial biomass carbon consistently decreased along the nickel gradients in both soils. Nickel pollution selectively favored or impeded the prevalence of several dominant bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Planctomycetes displayed sensitivity. Despite the apparent shifts in the bacterial community composition, no clear tendency in the bacterial diversity and abundance was identified along the nickel gradients in either soil. Collectively, we provide evidence that long-term nickel pollution shifted the soil bacterial communities, resulting in the decrease of microbial biomass although the bacterial diversity was not significantly changed.

  6. Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls

    Science.gov (United States)

    Bienhold, Christina; Wenzhöfer, Frank; Rossel, Pamela E.; Boetius, Antje

    2017-01-01

    Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100–1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time

  7. Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls.

    Directory of Open Access Journals (Sweden)

    Petra Pop Ristova

    Full Text Available Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m, but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were

  8. Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia.

    Science.gov (United States)

    Balmonte, John Paul; Arnosti, Carol; Underwood, Sarah; McKee, Brent A; Teske, Andreas

    2016-01-01

    Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities

  9. Riverine bacterial communities reveal environmental disturbance signatures within the Betaproteobacteria and Verrucomicrobia

    Directory of Open Access Journals (Sweden)

    John Paul Balmonte

    2016-09-01

    Full Text Available Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa versus land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2010, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- versus post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in

  10. Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves.

    Science.gov (United States)

    Dias, Juliana; Marcondes, Marcos I; Noronha, Melline F; Resende, Rafael T; Machado, Fernanda S; Mantovani, Hilário C; Dill-McFarland, Kimberly A; Suen, Garret

    2017-01-01

    At birth, calves display an underdeveloped rumen that eventually matures into a fully functional rumen as a result of solid food intake and microbial activity. However, little is known regarding the gradual impact of pre-weaning diet on the establishment of the rumen microbiota. Here, we employed next-generation sequencing to investigate the effects of the inclusion of starter concentrate (M: milk-fed vs. MC: milk plus starter concentrate fed) on archaeal, bacterial and anaerobic fungal communities in the rumens of 45 crossbred dairy calves across pre-weaning development (7, 28, 49, and 63 days). Our results show that archaeal, bacterial, and fungal taxa commonly found in the mature rumen were already established in the rumens of calves at 7 days old, regardless of diet. This confirms that microbiota colonization occurs in the absence of solid substrate. However, diet did significantly impact some microbial taxa. In the bacterial community, feeding starter concentrate promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea , and Succinivribrio ). Shifts in the ruminal bacterial community also correlated to changes in fermentation patterns that favored the colonization of Methanosphaera sp. A4 in the rumen of MC calves. In contrast, M calves displayed a bacterial community dominated by taxa able to utilize milk nutrients (e.g., Lactobacillus, Bacteroides , and Parabacteroides ). In both diet groups, the dominance of these milk-associated taxa decreased with age, suggesting that diet and age simultaneously drive changes in the structure and abundance of bacterial communities in the developing rumen. Changes in the composition and abundance of archaeal communities were attributed exclusively to diet, with more highly abundant Methanosphaera and less abundant Methanobrevibacter in MC calves. Finally, the fungal community was dominated by members of the genus SK3 and Caecomyces . Relative

  11. Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves

    Science.gov (United States)

    Dias, Juliana; Marcondes, Marcos I.; Noronha, Melline F.; Resende, Rafael T.; Machado, Fernanda S.; Mantovani, Hilário C.; Dill-McFarland, Kimberly A.; Suen, Garret

    2017-01-01

    At birth, calves display an underdeveloped rumen that eventually matures into a fully functional rumen as a result of solid food intake and microbial activity. However, little is known regarding the gradual impact of pre-weaning diet on the establishment of the rumen microbiota. Here, we employed next-generation sequencing to investigate the effects of the inclusion of starter concentrate (M: milk-fed vs. MC: milk plus starter concentrate fed) on archaeal, bacterial and anaerobic fungal communities in the rumens of 45 crossbred dairy calves across pre-weaning development (7, 28, 49, and 63 days). Our results show that archaeal, bacterial, and fungal taxa commonly found in the mature rumen were already established in the rumens of calves at 7 days old, regardless of diet. This confirms that microbiota colonization occurs in the absence of solid substrate. However, diet did significantly impact some microbial taxa. In the bacterial community, feeding starter concentrate promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea, and Succinivribrio). Shifts in the ruminal bacterial community also correlated to changes in fermentation patterns that favored the colonization of Methanosphaera sp. A4 in the rumen of MC calves. In contrast, M calves displayed a bacterial community dominated by taxa able to utilize milk nutrients (e.g., Lactobacillus, Bacteroides, and Parabacteroides). In both diet groups, the dominance of these milk-associated taxa decreased with age, suggesting that diet and age simultaneously drive changes in the structure and abundance of bacterial communities in the developing rumen. Changes in the composition and abundance of archaeal communities were attributed exclusively to diet, with more highly abundant Methanosphaera and less abundant Methanobrevibacter in MC calves. Finally, the fungal community was dominated by members of the genus SK3 and Caecomyces. Relative

  12. Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves

    Directory of Open Access Journals (Sweden)

    Juliana Dias

    2017-08-01

    Full Text Available At birth, calves display an underdeveloped rumen that eventually matures into a fully functional rumen as a result of solid food intake and microbial activity. However, little is known regarding the gradual impact of pre-weaning diet on the establishment of the rumen microbiota. Here, we employed next-generation sequencing to investigate the effects of the inclusion of starter concentrate (M: milk-fed vs. MC: milk plus starter concentrate fed on archaeal, bacterial and anaerobic fungal communities in the rumens of 45 crossbred dairy calves across pre-weaning development (7, 28, 49, and 63 days. Our results show that archaeal, bacterial, and fungal taxa commonly found in the mature rumen were already established in the rumens of calves at 7 days old, regardless of diet. This confirms that microbiota colonization occurs in the absence of solid substrate. However, diet did significantly impact some microbial taxa. In the bacterial community, feeding starter concentrate promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea, and Succinivribrio. Shifts in the ruminal bacterial community also correlated to changes in fermentation patterns that favored the colonization of Methanosphaera sp. A4 in the rumen of MC calves. In contrast, M calves displayed a bacterial community dominated by taxa able to utilize milk nutrients (e.g., Lactobacillus, Bacteroides, and Parabacteroides. In both diet groups, the dominance of these milk-associated taxa decreased with age, suggesting that diet and age simultaneously drive changes in the structure and abundance of bacterial communities in the developing rumen. Changes in the composition and abundance of archaeal communities were attributed exclusively to diet, with more highly abundant Methanosphaera and less abundant Methanobrevibacter in MC calves. Finally, the fungal community was dominated by members of the genus SK3 and Caecomyces

  13. Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days.

    Science.gov (United States)

    Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2018-05-01

    The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM 2.5 [airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions ( R = 0.157, P airborne bacterial community composition. Only six genera increased across PM 10 samples ( Dokdonella , Caenimonas , Geminicoccus , and Sphingopyxis ) and PM 2.5 samples ( Cellulomonas and Rhizobacter ), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus , Kocuria , and Sphingomonas Network analysis indicated that Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days. IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus , Tumebacillus , and Desulfurispora ) increased significantly on heavy-haze days. In addition, Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Accurate and real

  14. [Algo-bacterial communities of the Kulunda steppe (Altai region, Russia) soda lakes].

    Science.gov (United States)

    Samylina, O S; Sapozhnikov, F V; Gaĭnanova, O Iu; Riabova, A V; Nikitin, M A; Sorokin, D Iu

    2015-01-01

    The composition and macroscopic structure of the floating oxygenic phototrophic communities from Kulunda steppe soda lakes (Petukhovskoe sodovoe, Tanatara VI, and Gorchiny 3) was described based on the data of the 2011 and 2012 expeditions (Winogradsky Institute of Microbiology). The algo-bacterial community with a green alga Ctenocladus circinnatus as an edificator was the typical one. Filamentous Geitlerinema sp. and Nodosilinea sp. were the dominant cyanobacteria. Apart from C. circinnatus, the algological component of the community contained unicellular green algae Dunaliella viridis and cf. Chlorella minutissima, as well as diatoms (Anomeoneis sphaerophora, Brchysira brebissonii, Brachysira zellensis, Mastogloia pusilla var. subcapitata, Nitzschia amphibia, Nitzschia communis, and Nitzschia sp.1). The latter have not been previously identified in the lakes under study. In all lakes, a considerable increase in salinity was found to result in changes in the composition and macroscopic structure of algo-bacterial communities.

  15. Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

    2017-08-16

    Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

  16. Activity and stability of a complex bacterial soil community under simulated Martian conditions

    Science.gov (United States)

    Hansen, Aviaja Anna; Merrison, Jonathan; Nørnberg, Per; Aagaard Lomstein, Bente; Finster, Kai

    2005-04-01

    A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.

  17. Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

    Science.gov (United States)

    Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

    2015-02-15

    Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa.

    Science.gov (United States)

    Klepac-Ceraj, Vanja; Lemon, Katherine P; Martin, Thomas R; Allgaier, Martin; Kembel, Steven W; Knapp, Alixandra A; Lory, Stephen; Brodie, Eoin L; Lynch, Susan V; Bohannan, Brendan J M; Green, Jessica L; Maurer, Brian A; Kolter, Roberto

    2010-05-01

    Polymicrobial bronchopulmonary infections in cystic fibrosis (CF) cause progressive lung damage and death. Although the arrival of Pseudomonas aeruginosa often heralds a more rapid rate of pulmonary decline, there is significant inter-individual variation in the rate of decline, the causes of which remain poorly understood. By coupling culture-independent methods with ecological analyses, we discovered correlations between bacterial community profiles and clinical disease markers in respiratory tracts of 45 children with CF. Bacterial community complexity was inversely correlated with patient age, presence of P. aeruginosa and antibiotic exposure, and was related to CF genotype. Strikingly, bacterial communities lacking P. aeruginosa were much more similar to each other than were those containing P. aeruginosa, regardless of antibiotic exposure. This suggests that community composition might be a better predictor of disease progression than the presence of P. aeruginosa alone and deserves further study.

  19. Development of bacterial communities in biological soil crusts along a revegetation chronosequence in the Tengger Desert, northwest China

    Science.gov (United States)

    Liu, Lichao; Liu, Yubing; Zhang, Peng; Song, Guang; Hui, Rong; Wang, Zengru; Wang, Jin

    2017-08-01

    Knowledge of structure and function of microbial communities in different successional stages of biological soil crusts (BSCs) is still scarce for desert areas. In this study, Illumina MiSeq sequencing was used to assess the compositional changes of bacterial communities in different ages of BSCs in the revegetation of Shapotou in the Tengger Desert. The most dominant phyla of bacterial communities shifted with the changed types of BSCs in the successional stages, from Firmicutes in mobile sand and physical crusts to Actinobacteria and Proteobacteria in BSCs, and the most dominant genera shifted from Bacillus, Enterococcus and Lactococcus to RB41_norank and JG34-KF-361_norank. Alpha diversity and quantitative real-time polymerase chain reaction (PCR) analysis indicated that bacterial richness and abundance reached their highest levels after 15 years of BSC development. Redundancy analysis showed that silt + clay content and total K were the prime determinants of the bacterial communities of BSCs. The results suggested that bacterial communities of BSCs recovered quickly with the improved soil physicochemical properties in the early stages of BSC succession. Changes in the bacterial community structure may be an important indicator in the biogeochemical cycling and nutrient storage in early successional stages of BSCs in desert ecosystems.

  20. 2,4,6-Trinitrotoluene mineralization and bacterial production rates of natural microbial assemblages from coastal sediments

    International Nuclear Information System (INIS)

    Montgomery, Michael T.; Coffin, Richard B.; Boyd, Thomas J.; Smith, Joseph P.; Walker, Shelby E.; Osburn, Christopher L.

    2011-01-01

    The nitrogenous energetic constituent, 2,4,6-Trinitrotoluene (TNT), is widely reported to be resistant to bacterial mineralization (conversion to CO 2 ); however, these studies primarily involve bacterial isolates from freshwater where bacterial production is typically limited by phosphorus. This study involved six surveys of coastal waters adjacent to three biome types: temperate broadleaf, northern coniferous, and tropical. Capacity to catabolize and mineralize TNT ring carbon to CO 2 was a common feature of natural sediment assemblages from these coastal environments (ranging to 270+/-38 μg C kg -1 d -1 ). More importantly, these mineralization rates comprised a significant proportion of total heterotrophic production. The finding that most natural assemblages surveyed from these ecosystems can mineralize TNT ring carbon to CO 2 is consistent with recent reports that assemblage components can incorporate TNT ring carbon into bacterial biomass. These data counter the widely held contention that TNT is recalcitrant to bacterial catabolism of the ring carbon in natural environments. - Highlights: → TNT mineralization is a common feature of natural bacterial assemblages in coastal sediments. → TNT mineralization rates comprised a significant proportion of total heterotrophic production. → These data counter the widely held contention that TNT is recalcitrant to bacterial catabolism of the ring carbon in natural environments. - The capacity to mineralize TNT ring carbon to CO 2 is a common feature of natural bacterial assemblages in coastal sediment.

  1. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-05-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  2. Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production

    KAUST Repository

    Belila, Abdelaziz

    2016-02-18

    Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m3/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during

  3. Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics

    DEFF Research Database (Denmark)

    Pellicer i Nàcher, Carles; Franck, Stephanie; Gülay, Arda

    2014-01-01

    Membrane-aerated biofilm reactors performing autotrophic nitrogen removal can be successfully applied to treat concentrated nitrogen streams. However, their process performance is seriously hampered by the growth of nitrite oxidizing bacteria (NOB). In this work we document how sequential aeration...... (rich in oxygen) and AnAOB in regions neighbouring the liquid phase. Both communities were separated by a transition region potentially populated by denitrifying heterotrophic bacteria. AOB and AnAOB bacterial groups were more abundant and diverse than NOB, and dominated by the r......-strategists Nitrosomonas europaea and Ca. Brocadia anammoxidans, respectively. Taken together, the present work presents tools to better engineer, monitor and control the microbial communities that support robust, sustainable and efficient nitrogen removal....

  4. Bacterial community composition and potential driving factors in different reef habitats of the Spermonde Archipelago, Indonesia

    DEFF Research Database (Denmark)

    Kegler, Hauke F.; Lukman, Muhammad; Teichberg, Mirta

    2017-01-01

    Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along...... a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross shelf environmental and water quality gradient. The main research questions were: (1) How do water....../Shigella (Gammaproteobacteria) and Raistonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes...

  5. Thermal adaptation of heterotrophic soil respiration in laboratory microcosms.

    Science.gov (United States)

    Mark A. Bradford; Brian W. Watts; Christian A. Davies

    2010-01-01

    Respiration of heterotrophic microorganisms decomposing soil organic carbon releases carbon dioxide from soils to the atmosphere. In the short term, soil microbial respiration is strongly dependent on temperature. In the long term, the response of heterotrophic soil respiration to temperature is uncertain. However, following established evolutionary tradeoffs, mass-...

  6. Partitioning autotrophic and heterotrophic respiration at Howland Forest

    Science.gov (United States)

    Carbone, Mariah; Hollinger, Dave; Davidson, Eric; Savage, Kathleen; Hughes, Holly

    2015-04-01

    Terrestrial ecosystem respiration is the combined flux of CO2 to the atmosphere from above- and below-ground, plant (autotrophic) and microbial (heterotrophic) sources. Flux measurements alone (e.g., from eddy covariance towers or soil chambers) cannot distinguish the contributions from these sources, which may change seasonally and respond differently to temperature and moisture. The development of improved process-based models that can predict how plants and microbes respond to changing environmental conditions (on seasonal, interannual, or decadal timescales) requires data from field observations and experiments to distinguish among these respiration sources. We tested the viability of partitioning of soil and ecosystem respiration into autotrophic and heterotrophic components with different approaches at the Howland Forest in central Maine, USA. These include an experimental manipulation using the classic root trenching approach and targeted ∆14CO2 measurements. For the isotopic measurements, we used a two-end member mass balance approach to determine the fraction of soil respiration from autotrophic and heterotrophic sources. When summed over the course of the growing season, the trenched chamber flux (heterotrophic) accounted for 53 ± 2% of the total control chamber flux. Over the four different 14C sampling periods, the heterotrophic component ranged from 35-55% and the autotrophic component ranges 45-65% of the total flux. Next steps will include assessing the value of the flux partitioning for constraining a simple ecosystem model using a model-data fusion approach to reduce uncertainties in estimates of NPP and simulation of future soil C stocks and fluxes.

  7. Two-stage heterotrophic and phototrophic culture strategy for algal biomass and lipid production.

    Science.gov (United States)

    Zheng, Yubin; Chi, Zhanyou; Lucker, Ben; Chen, Shulin

    2012-01-01

    A two-stage heterotrophic and phototrophic culture strategy for algal biomass and lipid production was studied, wherein high density heterotrophic cultures of Chlorellasorokiniana serve as seed for subsequent phototrophic growth. The data showed growth rate, cell density and productivity of heterotrophic C.sorokiniana were 3.0, 3.3 and 7.4 times higher than phototrophic counterpart, respectively. Hetero- and phototrophic algal seeds had similar biomass/lipid production and fatty acid profile when inoculated into phototrophic culture system. To expand the application, food waste and wastewater were tested as feedstock for heterotrophic growth, and supported cell growth successfully. These results demonstrated the advantages of using heterotrophic algae cells as seeds for open algae culture system. Additionally, high inoculation rate of heterotrophic algal seed can be utilized as an effective method for contamination control. This two-stage heterotrophic phototrophic process is promising to provide a more efficient way for large scale production of algal biomass and biofuels. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers

    DEFF Research Database (Denmark)

    Edwards, Arwyn; Mur, Luis A. J.; Girdwood, Susan E.

    2014-01-01

    Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction...... revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine...... fragment length polymorphism and Fourier transform infrared metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids...

  9. Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

    DEFF Research Database (Denmark)

    Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana

    2017-01-01

    Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid......-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse...... and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha(-1). We used culture-based enumerations of general bacteria, Pseudomonas...

  10. Diversity of bacterial communities along a petroleum contamination gradient in desert soils.

    Science.gov (United States)

    Abed, Raeid M M; Al-Kindi, Sumaiya; Al-Kharusi, Samiha

    2015-01-01

    Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.

  11. Mechanism of uranium (VI) removal by two anaerobic bacterial communities

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Monica [Centro de Ciencias do Mar, Universidade do Algarve, FCT-DQF (edificio 8), Campus de Gambelas, 8005-139 Faro (Portugal); Faleiro, Maria Leonor [IBB - Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, FCT, Campus de Gambelas, 8005-139 Faro (Portugal); Costa, Ana M. Rosa da [Centro de Investigacao em Quimica do Algarve, Universidade do Algarve, FCT, DQF, Campus de Gambelas, 8005-139 Faro (Portugal); Chaves, Sandra; Tenreiro, Rogerio [Universidade de Lisboa, Faculdade de Ciencias, Centro de Biodiversidade, Genomica Integrativa e Funcional (BioFIG), Campus de FCUL, Campo Grande, 1749-016 Lisboa (Portugal); Matos, Antonio Pedro [Servico de Anatomia Patologica, Hospital Curry Cabral, Lisboa (Portugal); Costa, Maria Clara, E-mail: mcorada@ualg.pt [Centro de Ciencias do Mar, Universidade do Algarve, FCT-DQF (edificio 8), Campus de Gambelas, 8005-139 Faro (Portugal)

    2010-12-15

    The mechanism of uranium (VI) removal by two anaerobic bacterial consortia, recovered from an uncontaminated site (consortium A) and other from an uranium mine (consortium U), was investigated. The highest efficiency of U (VI) removal by both consortia (97%) occurred at room temperature and at pH 7.2. Furthermore, it was found that U (VI) removal by consortium A occurred by enzymatic reduction and bioaccumulation, while the enzymatic process was the only mechanism involved in metal removal by consortium U. FTIR analysis suggested that after U (VI) reduction, U (IV) could be bound to carboxyl, phosphate and amide groups of bacterial cells. Phylogenetic analysis of 16S rRNA showed that community A was mainly composed by bacteria closely related to Sporotalea genus and Rhodocyclaceae family, while community U was mainly composed by bacteria related to Clostridium genus and Rhodocyclaceae family.

  12. Mechanism of uranium (VI) removal by two anaerobic bacterial communities

    International Nuclear Information System (INIS)

    Martins, Monica; Faleiro, Maria Leonor; Costa, Ana M. Rosa da; Chaves, Sandra; Tenreiro, Rogerio; Matos, Antonio Pedro; Costa, Maria Clara

    2010-01-01

    The mechanism of uranium (VI) removal by two anaerobic bacterial consortia, recovered from an uncontaminated site (consortium A) and other from an uranium mine (consortium U), was investigated. The highest efficiency of U (VI) removal by both consortia (97%) occurred at room temperature and at pH 7.2. Furthermore, it was found that U (VI) removal by consortium A occurred by enzymatic reduction and bioaccumulation, while the enzymatic process was the only mechanism involved in metal removal by consortium U. FTIR analysis suggested that after U (VI) reduction, U (IV) could be bound to carboxyl, phosphate and amide groups of bacterial cells. Phylogenetic analysis of 16S rRNA showed that community A was mainly composed by bacteria closely related to Sporotalea genus and Rhodocyclaceae family, while community U was mainly composed by bacteria related to Clostridium genus and Rhodocyclaceae family.

  13. Bacterial diversity in a tropical crude oil-polluted soil undergoing ...

    African Journals Online (AJOL)

    The bacterial diversity in a tropical soil experimentally polluted with crude oil during a 57 days bioremediation was investigated in five 1 m2 plots using total culturable hydrocarbon utilizing bacteria, heterotrophic bacteria and gas chromatographic analyses. Four out of the five experimental plots received each 4 L of Bonny ...

  14. A pilot study of bacterial regrowth in water pipelines.

    Science.gov (United States)

    Mancini, Laura; Marcheggiani, Stefania; Grasso, Cinzia; Romanelli, Cristina; Mistretta, Antonio; Marranzano, Marina

    2016-01-01

    Bacterial regrowth in water distribution systems results in deterioration of bacteriological quality of drinking water, as well as accelerated corrosion of the pipelines. The aim of the present study was to analyze the phenomena of colonization and bacterial regrowth in source water and in the water distribution systems of three distribution networks in the province of Catania (Sicily, Italy). The BART™ (Biological Activity Reaction Test) method was used, which is also capable of determining the potential aggressiveness of microbial species in water. We searched for sulfate reducing bacteria, iron-related bacteria, nitrifying and denitrifying bacteria, heterotrophic bacteria, slime-forming bacteria and fluorescent Pseudomonads. A high concentration of heterotrophic bacteria was found in almost every water sample analyzed. Sulfate reducing bacteria and iron-related bacteria were found in all three distribution networks, while non-fluorescing Pseudomonas were detected in source water of only one of the distribution networks. The BART™ method was found to be a practical and easy to use tool to detect the different bacteria groups involved in regrowth phenomena.

  15. Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.

    Science.gov (United States)

    Kuehn, Joanna S; Gorden, Patrick J; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J; Wang, Chong; Phillips, Gregory J

    2013-01-01

    Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1-V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.

  16. Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium

    Science.gov (United States)

    de Andrade, Pedro Avelino Maia; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

    2017-01-01

    Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil. PMID:28686690

  17. Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie.

    Directory of Open Access Journals (Sweden)

    Joseph D Coolon

    Full Text Available Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion. The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have

  18. Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times.

    Directory of Open Access Journals (Sweden)

    Jun Zhao

    Full Text Available Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October. All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005 and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production.

  19. Changes in soil bacterial communities induced by the invasive plant Pennisetum setaceum in a semiarid environment

    Science.gov (United States)

    Rodriguez-Caballero, Gema; Caravaca, Fuensanta; del Mar Alguacil, María; Fernández-López, Manuel; José Fernández-González, Antonio; García-Orenes, Fuensanta; Roldán, Antonio

    2016-04-01

    Invasive alien species are considered as a global threat being among the main causes of biodiversity loss. Plant invasions have been extensively studied from different disciplines with the purpose of identifying predictor traits of invasiveness and finding solutions. However, less is known about the implication of the rhizosphere microbiota in these processes, even when it is well known the importance of the interaction between plant rhizosphere and microbial communities. The objective of this study was to determine whether native and invasive plants support different bacterial communities in their rhizospheres and whether there are bacterial indicator species that might be contributing to the invasion process of these ecosystems. We carried out a study in five independent locations under Mediterranean semiarid conditions, where the native Hyparrhenia hirta is being displaced by Pennisetum setaceum, an aggressive invasive Poaceae and soil bacterial communities were amplified and 454-pyrosequenced. Changes in the composition and structure of the bacterial communities, owing to the invasive status of the plant, were detected when the richness and alpha-diversity estimators were calculated as well as when we analyzed the PCoA axes scores. The Indicator Species Analysis results showed a higher number of indicators for invaded communities at all studied taxonomic levels. In conclusion, the effect of the invasiveness and its interaction with the soil location has promoted shifts in the rhizosphere bacterial communities which might be facilitating the invader success in these ecosystems.

  20. Bacterial Community Associated with Healthy and Diseased Pacific White Shrimp (Litopenaeus vannamei) Larvae and Rearing Water across Different Growth Stages.

    Science.gov (United States)

    Zheng, Yanfen; Yu, Min; Liu, Jiwen; Qiao, Yanlu; Wang, Long; Li, Zhitao; Zhang, Xiao-Hua; Yu, Mingchao

    2017-01-01

    Bacterial communities are called another "organ" for aquatic animals and their important influence on the health of host has drawn increasing attention. Thus, it is important to study the relationships between aquatic animals and bacterial communities. Here, bacterial communities associated with Litopenaeus vannamei larvae at different healthy statuses (diseased and healthy) and growth stages (i.e., zoea, mysis, and early postlarvae periods) were examined using 454-pyrosequencing of the 16S rRNA gene. Bacterial communities with significant difference were observed between healthy and diseased rearing water, and several bacterial groups, such as genera Nautella and Kordiimonas could also distinguish healthy and diseased shrimp. Rhodobacteraceae was widely distributed in rearing water at all growth stages but there were several stage-specific groups, indicating that bacterial members in rearing water assembled into distinct communities throughout the larval development. However, Gammaproteobacteria , mainly family Enterobacteriaceae , was the most abundant group (accounting for more than 85%) in shrimp larvae at all growth stages. This study compared bacterial communities associated with healthy and diseased L . vannamei larvae and rearing water, and identified several health- and growth stage-specific bacterial groups, which might be provided as indicators for monitoring the healthy status of shrimp larvae in hatchery.

  1. Bacterial Community Associated with Healthy and Diseased Pacific White Shrimp (Litopenaeus vannamei Larvae and Rearing Water across Different Growth Stages

    Directory of Open Access Journals (Sweden)

    Yanfen Zheng

    2017-07-01

    Full Text Available Bacterial communities are called another “organ” for aquatic animals and their important influence on the health of host has drawn increasing attention. Thus, it is important to study the relationships between aquatic animals and bacterial communities. Here, bacterial communities associated with Litopenaeus vannamei larvae at different healthy statuses (diseased and healthy and growth stages (i.e., zoea, mysis, and early postlarvae periods were examined using 454-pyrosequencing of the 16S rRNA gene. Bacterial communities with significant difference were observed between healthy and diseased rearing water, and several bacterial groups, such as genera Nautella and Kordiimonas could also distinguish healthy and diseased shrimp. Rhodobacteraceae was widely distributed in rearing water at all growth stages but there were several stage-specific groups, indicating that bacterial members in rearing water assembled into distinct communities throughout the larval development. However, Gammaproteobacteria, mainly family Enterobacteriaceae, was the most abundant group (accounting for more than 85% in shrimp larvae at all growth stages. This study compared bacterial communities associated with healthy and diseased L. vannamei larvae and rearing water, and identified several health- and growth stage-specific bacterial groups, which might be provided as indicators for monitoring the healthy status of shrimp larvae in hatchery.

  2. Functional Potential of Bacterial Communities using Gene Context Information

    Directory of Open Access Journals (Sweden)

    Anwesha Mohapatra

    2017-12-01

    Full Text Available Estimation of the functional potential of a bacterial genome can be determined by accurate annotation of its metabolic pathways. Existing homology based methods for pathway annotation fail to account for homologous genes that participate in multiple pathways, causing overestimation of gene copy number. Mere presence of constituent genes of a candidate pathway which are dispersed on a genome often results in incorrect annotation, thereby leading to erroneous gene abundance and pathway estimation. Clusters of evolutionarily conserved coregulated genes are characteristic features in bacterial genomes and their spatial arrangement in the genome is constrained by the pathway encoded by them. Thus, in order to improve the accuracy of pathway prediction, it is important to augment homology based annotation with gene organization information. In this communication, we present a methodology considering prioritization of gene context for improved pathway annotation. Extensive literature mining was performed to confirm conserved juxtaposed arrangement of gene components of various pathways. Our method was utilized to identify and analyse the functional potential of all available completely sequenced bacterial genomes. The accuracy of the predicted gene clusters and their importance in metabolic pathways will be demonstrated using a few case studies. One of such case study corresponds to butyrate production pathways in gut bacteria where it was observed that gut pathogens and commensals possess a distinct set of pathway components. In another example, we will demonstrate how our methodology improves the prediction accuracy of carbohydrate metabolic potential in human microbial communities. Applicability of our method for estimation of functional potential in bacterial communities present in diverse environments will also be illustrated.

  3. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters.

    Science.gov (United States)

    Bacosa, Hernando P; Liu, Zhanfei; Erdner, Deana L

    2015-01-01

    Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.

  4. Seasonal variations and resilience of bacterial communities in a sewage polluted urban river.

    Directory of Open Access Journals (Sweden)

    Tamara García-Armisen

    Full Text Available The Zenne River in Brussels (Belgium and effluents of the two wastewater treatment plants (WWTPs of Brussels were chosen to assess the impact of disturbance on bacterial community composition (BCC of an urban river. Organic matters, nutrients load and oxygen concentration fluctuated highly along the river and over time because of WWTPs discharge. Tag pyrosequencing of bacterial 16S rRNA genes revealed the significant effect of seasonality on the richness, the bacterial diversity (Shannon index and BCC. The major grouping: -winter/fall samples versus spring/summer samples- could be associated with fluctuations of in situ bacterial activities (dissolved and particulate organic carbon biodegradation associated with oxygen consumption and N transformation. BCC of the samples collected upstream from the WWTPs discharge were significantly different from BCC of downstream samples and WWTPs effluents, while no significant difference was found between BCC of WWTPs effluents and the downstream samples as revealed by ANOSIM. Analysis per season showed that allochthonous bacteria brought by WWTPs effluents triggered the changes in community composition, eventually followed by rapid post-disturbance return to the original composition as observed in April (resilience, whereas community composition remained altered after the perturbation by WWTPs effluents in the other seasons.

  5. Soil Bacterial Community Was Changed after Brassicaceous Seed Meal Application for Suppression of Fusarium Wilt on Pepper

    Directory of Open Access Journals (Sweden)

    Gaidi Ren

    2018-02-01

    Full Text Available Application of Brassicaceous seed meal (BSM is a promising biologically based disease-control practice but BSM could directly and indirectly also affect the non-target bacterial communities, including the beneficial populations. Understanding the bacterial response to BSM at the community level is of great significance for directing plant disease management through the manipulation of resident bacterial communities. Fusarium wilt is a devastating disease on pepper. However, little is known about the response of bacterial communities, especially the rhizosphere bacterial community, to BSM application to soil heavily infested with Fusarium wilt pathogen and cropped with peppers. In this study, a 25-day microcosm incubation of a natural Fusarium wilt pathogen-infested soil supplemented with three BSMs, i.e., Camelina sativa ‘Crantz’ (CAME, Brassica juncea ‘Pacific Gold’ (PG, and a mixture of PG and Sinapis alba cv. ‘IdaGold’ (IG (PG+IG, 1:1 ratio, was performed. Then, a further 35-day pot experiment was established with pepper plants growing in the BSM treated soils. The changes in the bacterial community in the soil after 25 days of incubation and changes in the rhizosphere after an additional 35 days of pepper growth were investigated by 454 pyrosequencing technique. The results show that the application of PG and PG+IG reduced the disease index by 100% and 72.8%, respectively, after 35 days of pepper growth, while the application of CAME did not have an evident suppressive effect. All BSM treatments altered the bacterial community structure and decreased the bacterial richness and diversity after 25 days of incubation, although this effect was weakened after an additional 35 days of pepper growth. At the phylum/class and the genus levels, the changes in specific bacterial populations resulting from the PG and PG+IG treatments, especially the significant increase in Actinobacteria-affiliated Streptomyces and an unclassified genus and

  6. Particulate organic matter predicts bacterial productivity in a river dominated estuary

    Science.gov (United States)

    Crump, B. C.

    2015-12-01

    Estuaries act as coastal filters for organic and inorganic fluvial materials in which microbial, biogeochemical, and ecological processes combine to transform organic matter and nutrients prior to export to the coastal ocean. The function of this estuarine 'bioreactor' is linked to the residence times of those materials and to rates of microbial heterotrophic activity. Our ability to forecast the impact of global change on estuarine bioreactor function requires an understanding of the basic controls on microbial community activity and diversity. In the Columbia River estuary, the microbial community undergoes a dramatic seasonal shift in species composition during which a spring bacterioplankton community, dominated by Flavobacteriaceae and Oceanospirillales, is replaced by a summer community, dominated by Rhodobacteraceae and several common marine taxa. This annual shift occurs in July, following the spring freshet, when river flow and river chlorophyll concentration decrease and when estuarine water residence time increases. Analysis of a large dataset from 17 research cruises (1990-2014) showed that the composition of particulate organic matter in the estuary changes after the freshet with decreasing organic carbon and nitrogen content, and increasing contribution of marine and autochthonous estuarine organic matter (based on PO13C and pigment ratios). Bacterial production rates (measured as leucine or thymidine incorporation rates) in the estuary respond to this change, and correlate strongly with labile particulate nitrogen concentration and temperature during individual sampling campaigns, and with the concentration of chlorophyll in the Columbia River across all seasons. Regression models suggest that the concentration of labile particulate nitrogen and the rate of bacterial production can be predicted from sensor measurements of turbidity, salinity, and temperature in the estuary and chlorophyll in the river. These results suggest that the quality of

  7. Spatial Distribution of Bacterial Communities Driven by Multiple Environmental Factors in a Beach Wetland of the Largest Freshwater Lake in China

    Directory of Open Access Journals (Sweden)

    Xia eDing

    2015-02-01

    Full Text Available The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction and vertical (sediment depth gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH4+ concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

  8. Structure and Composition of Leachfield Bacterial Communities: Role of Soil Texture, Depth and Septic Tank Effluent Inputs

    Directory of Open Access Journals (Sweden)

    Janet A. Atoyan

    2012-09-01

    Full Text Available Although groundwater quality depends on microbial processes in the soil treatment area (STA of onsite wastewater treatment systems (OWTS, our understanding of the development of these microbial communities is limited. We examined the bacterial communities of sand, sandy loam, and clay STAs at different depths in response to septic tank effluent (STE addition using mesocosms. Terminal restriction fragment length polymorphism (TRFLP analysis was used to compare the bacterial community structure and composition of STE, native soil prior to STE addition (UNX and soil exposed to STE (EXP. Principal component analysis separated communities with depth in sand but not in sandy loam or clay. Indices of richness, diversity, and evenness followed the order: sandy loam > sand > clay. Analysis of TRF peaks indicated that STE contributed least to the composition of STA bacterial communities (5%–16%, followed by UNX soil (18%–48%, with the highest proportion of the community made up of TRFs not detected previously in either UNX or STE (50%–82% for all three soils. Soil type and depth can have a marked effect on the structure and composition of STA bacterial communities, and on the relative contribution of native soil and STE to these communities.

  9. Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora.

    Directory of Open Access Journals (Sweden)

    Jie Li

    Full Text Available Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.

  10. Influence of Uranium on Bacterial Communities: A Comparison of Natural Uranium-Rich Soils with Controls

    Science.gov (United States)

    Mondani, Laure; Benzerara, Karim; Carrière, Marie; Christen, Richard; Mamindy-Pajany, Yannick; Février, Laureline; Marmier, Nicolas; Achouak, Wafa; Nardoux, Pascal; Berthomieu, Catherine; Chapon, Virginie

    2011-01-01

    This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil. PMID:21998695

  11. The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar

    Science.gov (United States)

    Samuni-Blank, Michal; Izhaki, Ido; Laviad, Sivan; Bar-Massada, Avi; Gerchman, Yoram; Halpern, Malka

    2014-01-01

    Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that “everything is everywhere, but the environment selects”. Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs. PMID:24922317

  12. Effects Of Palm Oil Mill Effluents (Pome) On Soil Bacterial Flora And ...

    African Journals Online (AJOL)

    Sandy loam soil in Egbema, Rivers State was impacted with POME at different levels and analyzed for bacteriological quality and soil enzyme activities. Light application caused significant increase in total heterotrophic, phosphate solibilizing, nitrifying and lipolytic bacterial counts while heavy application caused a decrease ...

  13. Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum).

    Science.gov (United States)

    Williams-Newkirk, Amanda Jo; Rowe, Lori A; Mixson-Hayden, Tonya R; Dasch, Gregory A

    2014-01-01

    The lone star tick (Amblyomma americanum) is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5-3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii) and an obligate Coxiella symbiont, together accounting for 6.7-100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (pmales containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of the bacterial community change during the tick life cycle and that some sex-specific attributes may be detectable in nymphs.

  14. Bacterial community dynamics in a rumen fluid bioreactor during in-vitro cultivation.

    Science.gov (United States)

    Zapletalová, Martina; Kašparovská, Jitka; Křížová, Ludmila; Kašparovský, Tomáš; Šerý, Omar; Lochman, Jan

    2016-09-20

    To study the various processes in the rumen the in vitro techniques are widely used to realize more controlled and reproducible conditions compared to in vivo experiments. Mostly, only the parameters like pH changes, volatile fatty acids content or metabolite production are monitored. In this study we examine the bacterial community dynamics of rumen fluid in course of ten day cultivation realize under standard conditions described in the literature. Whereas the pH values, total VFA content and A/P ratio in bioreactor were consistent with natural conditions in the rumen, the mean redox-potential values of -251 and -243mV were much more negative. For culture-independent assessment of bacterial community composition, the Illumina MiSeq results indicated that the community contained 292 bacterial genera. In course of ten days cultivation a significant changes in the microbial community were measured when Bacteroidetes to Firmicutes ratio changed from 3.2 to 1.2 and phyla Proteobacteria and Actinobacteria represented by genus Bifidobacterium and Olsenella significantly increased. The main responsible factor of these changes seems to be very low redox potential in bioreactor together with accumulation of simple carbohydrates in milieu as a result of limited excretion of fermented feed and absence of nutrient absorbing mechanisms. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

    Science.gov (United States)

    Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

    2018-01-01

    As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem

  16. Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

    Directory of Open Access Journals (Sweden)

    Baneshwar Singh

    2018-01-01

    Full Text Available As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m and temporal (3–732 days dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples, the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples, the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding

  17. Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis.

    Science.gov (United States)

    Li, Meiju; Zhou, Mi; Adamowicz, Elizabeth; Basarab, John A; Guan, Le Luo

    2012-02-24

    Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (∼1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Bacterial community structure in two permafrost wetlands on the Tibetan Plateau and Sanjiang Plain, China.

    Science.gov (United States)

    Yun, Juanli; Ju, Yiwen; Deng, Yongcui; Zhang, Hongxun

    2014-08-01

    Permafrost wetlands are important methane emission sources and fragile ecosystems sensitive to climate change. Presently, there remains a lack of knowledge regarding bacterial communities, especially methanotrophs in vast areas of permafrost on the Tibetan Plateau in Northwest China and the Sanjiang Plain (SJ) in Northeast China. In this study, 16S rRNA-based quantitative PCR (qPCR) and 454 pyrosequencing were used to identify bacterial communities in soils sampled from a littoral wetland of Lake Namco on the Tibetan Plateau (NMC) and an alluvial wetland on the SJ. Additionally, methanotroph-specific primers targeting particulate methane monooxygenase subunit A gene (pmoA) were used for qPCR and pyrosequencing analysis of methanotrophic community structure in NMC soils. qPCR analysis revealed the presence of 10(10) 16S rRNA gene copies per gram of wet soil in both wetlands, with 10(8) pmoA copies per gram of wet soil in NMC. The two permafrost wetlands showed similar bacterial community compositions, which differed from those reported in other cold environments. Proteobacteria, Actinobacteria , and Chloroflexi were the most abundant phyla in both wetlands, whereas Acidobacteria was prevalent in the acidic wetland SJ only. These four phyla constituted more than 80 % of total bacterial community diversity in permafrost wetland soils, and Methylobacter of type I methanotrophs was overwhelmingly dominant in NMC soils. This study is the first major bacterial sequencing effort of permafrost in the NMC and SJ wetlands, which provides fundamental data for further studies of microbial function in extreme ecosystems under climate change scenarios.

  19. Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments

    KAUST Repository

    Fodelianakis, Stylianos

    2016-09-23

    Previous studies have shown that the response of bacterial communities to disturbances depends on their environmental history. Historically fluctuating habitats host communities that respond better to disturbance than communities of historically stable habitats. However, the exact ecological mechanism that drives this dependency remains unknown. Here, we experimentally demonstrate that modifications of niche optima and niche breadths of the community members are driving this dependency of bacterial responses to past environmental conditions. First, we develop a novel, simple method to calculate the niche optima and breadths of bacterial taxa regarding single environmental gradients. Then, we test this method on sediment bacterial communities of three habitats, one historically stable and less loaded and two historically more variable and more loaded habitats in terms of historical chlorophyll-α water concentration, that we subject to hypoxia via organic matter addition ex situ. We find that communities containing bacterial taxa differently adapted to hypoxia show different structural and functional responses, depending on the sediment\\'s environmental history. Specifically, in the historically less fluctuating and loaded sediments where we find more taxa poorly adapted to hypoxic conditions, communities change a lot over time and organic matter is not degraded efficiently. The opposite is true for the historically more fluctuating and loaded sediments where we find more taxa well adapted to hypoxia. Based on the community responses observed here, we also propose an alternative calculation of community resistance that takes into account how rapidly the communities respond to disturbances and not just the initial and final states of the community.

  20. Determination and Variation of Core Bacterial Community in a Two-Stage Full-Scale Anaerobic Reactor Treating High-Strength Pharmaceutical Wastewater.

    Science.gov (United States)

    Ma, Haijun; Ye, Lin; Hu, Haidong; Zhang, Lulu; Ding, Lili; Ren, Hongqiang

    2017-10-28

    Knowledge on the functional characteristics and temporal variation of anaerobic bacterial populations is important for better understanding of the microbial process of two-stage anaerobic reactors. However, owing to the high diversity of anaerobic bacteria, close attention should be prioritized to the frequently abundant bacteria that were defined as core bacteria and putatively functionally important. In this study, using MiSeq sequencing technology, the core bacterial community of 98 operational taxonomic units (OTUs) was determined in a two-stage upflow blanket filter reactor treating pharmaceutical wastewater. The core bacterial community accounted for 61.66% of the total sequences and accurately predicted the sample location in the principal coordinates analysis scatter plot as the total bacterial OTUs did. The core bacterial community in the first-stage (FS) and second-stage (SS) reactors were generally distinct, in that the FS core bacterial community was indicated to be more related to a higher-level fermentation process, and the SS core bacterial community contained more microbes in syntrophic cooperation with methanogens. Moreover, the different responses of the FS and SS core bacterial communities to the temperature shock and influent disturbance caused by solid contamination were fully investigated. Co-occurring analysis at the Order level implied that Bacteroidales, Selenomonadales, Anaerolineales, Syneristales, and Thermotogales might play key roles in anaerobic digestion due to their high abundance and tight correlation with other microbes. These findings advance our knowledge about the core bacterial community and its temporal variability for future comparative research and improvement of the two-stage anaerobic system operation.

  1. Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

    Directory of Open Access Journals (Sweden)

    Ditte V. Vestergaard

    2018-05-01

    Full Text Available Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05. Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05, including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables

  2. Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

    Science.gov (United States)

    Vestergaard, Ditte V.; Holst, Gitte J.; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P. G.

    2018-01-01

    Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear

  3. Pig Farmers' Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes.

    Science.gov (United States)

    Vestergaard, Ditte V; Holst, Gitte J; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P G

    2018-01-01

    Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building's occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers' homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3-V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers' homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers' homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium , and Lactobacillus . Pig stables had significantly lower airborne bacterial diversity than farmers' homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear to

  4. Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

    Directory of Open Access Journals (Sweden)

    Raymon S Shange

    Full Text Available Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of

  5. Adaptations in bacterial and fungal communities to termite fungiculture

    DEFF Research Database (Denmark)

    Otani, Saria

    in the bacterial and fungal communities. To do this, we used pyrosequencing, fluorescent in situ hybridisation, light and confocal microscopy, enzymatic assays, chemical extractions, in vitro assays, and feeding experiments in this thesis work to elucidate these predicted changes in fungus-growing termite...... in the proportion of fungal material provided to the cockroaches. However, gut microbiotas remained distinct from those of termites after Termitomyces-feeding, indicating that a fungal diet can play a role in structuring gut community composition, but at the same time exemplifies how original community compositions......, and possibly gut microenvironment constrain the magnitude of change. This thesis also characterises the fungus comb fungal communities (mycobiotas) in fungusgrowing termites, and shows that non-Termitomyces fungi were essentially absent in combs, and that Termitomyces fungal crops are maintained...

  6. The Effectiveness of Heterotrophic Bacteria Isolated from Dumai Marine Waters of Riau, Used as Antibacterial against Pathogens in Fish Culture

    Science.gov (United States)

    Feliatra, F.; Nursyirwani; Tanjung, A.; Adithiya, DS; Susanna, M.; Lukystyowati, I.

    2018-02-01

    Heterotrophic bacteria have an important role as decomposer of organic compounds (mineralization) derived from industrial waste, decomposition of unconsumed feed, faecal, excretion of fish, and have the ability to inhibit the growth of pathogenic bacteria. We investigated the role of heterotrophic bacteria used as antibacterial against pathogens in fish culture.This research was conducted from January until March 2017. The phylogenitic of the isolated bacterial was determined by 16S rDNA sequences analysis. Antagonism test showed that the bacteria had the ability to inhibit the growth of pathogenic bacteria (Vibrio alginolyticus, Aeromonas hydrophila and Pseudomonas sp.) Three isolates (Dm5, Dm6 and Dm4) indicated high inhibition zones which were classified into strong category with the average from 10.5 to 11.8 mm toward V. alginolitycus. Other isolates were classified into medium and weak category. Based on DNA analysis of heterotrophic bacteria isolated from marine waters of industrial area and low salinity of estuarine waters twelve strains of bacteria were identified, and all had highest level of homology to Bacillus sp.,one isolates has similarity to Enterobacter cloacae, other isolates to Clostridium cetobutylicum. Most of isolated bacteria obtained from the waters of industrial area due to it received much of nutrients that very influenced the growth of bacteria.

  7. Carbon, metals and grain size correlate with bacterial community composition in sediments of a high arsenic aquifer

    Directory of Open Access Journals (Sweden)

    Teresa eLegg

    2012-03-01

    Full Text Available Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As. This has globally important implications since As toxicity in drinking water affects the health of millions of people worldwide, including in the Ganges-Brahmaputra Delta region of Bangladesh where geogenic groundwater arsenic concentrations can be more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across environmental gradients in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flowpath, at a range of depths between 1.5 and 15 m. We identified significant shifts in bacterial community composition along the groundwater flowpath in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C, manganese (Mn, and iron (Fe concentrations. Deltaproteobacteria and Chloroflexi were more abundant in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were more abundant in sediments with higher concentrations of sand and Si, and lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance- reducers in the high C and metal sediments. It is well-documented that C, Mn and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

  8. Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

    Science.gov (United States)

    Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

    2015-01-01

    The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

  9. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables.

    Science.gov (United States)

    Jackson, Colin R; Randolph, Kevin C; Osborn, Shelly L; Tyler, Heather L

    2013-12-01

    Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional

  10. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

    Science.gov (United States)

    2013-01-01

    Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by

  11. Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

    Directory of Open Access Journals (Sweden)

    Román eZapién-Campos

    2015-05-01

    Full Text Available Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion.

  12. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    Directory of Open Access Journals (Sweden)

    Amy Apprill

    Full Text Available Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae, and examine the potential for a core bacterial community and its variability with host (endogenous or geographic/environmental (exogenous specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding, suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp., as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could

  13. Restructuring of Endophytic Bacterial Communities in Grapevine Yellows-Diseased and Recovered Vitis vinifera L. Plants ▿

    Science.gov (United States)

    Bulgari, Daniela; Casati, Paola; Crepaldi, Paola; Daffonchio, Daniele; Quaglino, Fabio; Brusetti, Lorenzo; Bianco, Piero Attilio

    2011-01-01

    Length heterogeneity-PCR assays, combined with statistical analyses, highlighted that the endophytic bacterial community associated with healthy grapevines was characterized by a greater diversity than that present in diseased and recovered plants. The findings suggest that phytoplasmas can restructure the bacterial community by selecting endophytic strains that could elicit a plant defense response. PMID:21622794

  14. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  15. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria