Age matters: Submersion period shapes community composition of lake biofilms under glyphosate stress

The phosphonate herbicide glyphosate, which is the active ingredient in the commercial formulation Roundup®, is currently the most globally used herbicide. In aquatic ecosystems, periphytic biofilms, or periphyton, are at the base of food webs and are often the first communities to be in direct contact with runoff. Microcosm experiments were conducted to assess the effects of a pulse exposure of glyphosate on community composition and chlorophyll a concentrations of lake biofilms at different colonization stages (2 months, 1 year, and 20 years). This is the first study that uses such contrasting submersion periods. Biofilms were exposed to either environmental levels of pure analytical grade glyphosate (6 μg/L, 65 μg/L, and 600 μg/L) or to corresponding phosphorus concentrations. Community composition was determined by deep sequencing of the 18S and 16S rRNA genes to target eukaryotes and cyanobacteria, respectively. The results showed that submersion period was the only significant contributor to community structure. However, at the taxon level, the potentially toxic genus Anabaena was found to increase in relative abundance. We also observed that glyphosate releases phosphorus into the surrounding water, but not in a bioavailable form. The results of this study indicate that environmental concentrations of glyphosate do not seem to impact the community composition or metabolism of lake biofilms under pulse event conditions.

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Composition and stability of bacterial communities associated with granular activated carbon and anthracite filters in a pilot scale municipal drinking water treatment facility

Journal of Water and Health ◽

10.2166/wh.2012.092 ◽

2012 ◽

Vol 10 (2) ◽

pp. 244-255 ◽

Cited By ~ 6

Author(s):

T. B. Shirey ◽

R. W. Thacker ◽

J. B. Olson

Keyword(s):

Drinking Water ◽

Activated Carbon ◽

Community Structure ◽

Water Treatment ◽

Bacterial Community ◽

16S Rrna ◽

Community Composition ◽

Bacterial Communities ◽

Granular Activated Carbon ◽

Rrna Genes

Granular activated carbon (GAC) is an alternative filter substrate for municipal water treatment as it provides a high surface area suitable for microbial colonization. The resulting microbial growth promotes biodegradation of organic materials and other contaminants from influent waters. Here, the community structure of the bacteria associated with three GAC and two anthracite filters was examined over 12 months to monitor changes in community composition. Nearly complete 16S rRNA genes were polymerase chain reaction amplified for terminal restriction fragment length polymorphism (T-RFLP) analyses. The identity of commonly occurring peaks was determined through the construction of five representative 16S rRNA clone libraries. Based on sequence analysis, the bacterial communities associated with both anthracite and GAC filters appear to be composed of environmentally derived bacteria, with no known human pathogens. Analysis of similarity tests revealed that significant differences in bacterial community structure occurred over time, with filter substrate playing an important role in determining community composition. GAC filters exhibited the greatest degree of bacterial community variability over the sampling period, while anthracite filters showed a lower degree of variability and less change in community composition. Thus, GAC may be a suitable biologically active filter substrate for the treatment of municipal drinking water.

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Effects of Heavy Fuel Oil on the Bacterial Community Structure of a Pristine Microbial Mat

Applied and Environmental Microbiology ◽

10.1128/aem.01352-07 ◽

2007 ◽

Vol 73 (19) ◽

pp. 6089-6097 ◽

Cited By ~ 101

Author(s):

Sylvain Bordenave ◽

María Soledad Goñi-Urriza ◽

Pierre Caumette ◽

Robert Duran

Keyword(s):

Community Structure ◽

Bacterial Community ◽

16S Rrna ◽

Oil Pollution ◽

Microbial Mat ◽

Fuel Oil ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Heavy Fuel Oil

ABSTRACT The effects of petroleum contamination on the bacterial community of a pristine microbial mat from Salins-de-Giraud (Camargue, France) have been investigated. Mats were maintained as microcosms and contaminated with no. 2 fuel oil from the wreck of the Erika. The evolution of the complex bacterial community was monitored by combining analyses based on 16S rRNA genes and their transcripts. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analyses clearly showed the effects of the heavy fuel oil after 60 days of incubation. At the end of the experiment, the initial community structure was recovered, illustrating the resilience of this microbial ecosystem. In addition, the responses of the metabolically active bacterial community were evaluated by T-RFLP and clone library analyses based on 16S rRNA. Immediately after the heavy fuel oil was added to the microcosms, the structure of the active bacterial community was modified, indicating a rapid microbial mat response. Members of the Gammaproteobacteria were initially dominant in the contaminated microcosms. Pseudomonas and Acinetobacter were the main genera representative of this class. After 90 days of incubation, the Gammaproteobacteria were superseded by “Bacilli” and Alphaproteobacteria. This study shows the major changes that occur in the microbial mat community at different time periods following contamination. At the conclusion of the experiment, the RNA approach also demonstrated the resilience of the microbial mat community in resisting environmental stress resulting from oil pollution.

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

Applied and Environmental Microbiology ◽

10.1128/aem.67.4.1893-1901.2001 ◽

2001 ◽

Vol 67 (4) ◽

pp. 1893-1901 ◽

Cited By ~ 195

Author(s):

Gesche Braker ◽

Héctor L. Ayala-del-Rı́o ◽

Allan H. Devol ◽

Andreas Fesefeldt ◽

James M. Tiedje

Keyword(s):

Community Structure ◽

Restriction Fragment Length Polymorphism ◽

16S Rrna ◽

Fragment Length Polymorphism ◽

Puget Sound ◽

Rflp Analysis ◽

16S Rrna Genes ◽

Rrna Genes ◽

Restriction Fragment Length ◽

Redox Gradients

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

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Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.569020 ◽

2021 ◽

Vol 12 ◽

Author(s):

Li Ma ◽

Geng Wu ◽

Jian Yang ◽

Liuqin Huang ◽

Dorji Phurbu ◽

...

Keyword(s):

Community Structure ◽

Hydrogen Production ◽

16S Rrna ◽

High Throughput Sequencing ◽

Hot Springs ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

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Identification and analysis of PCB dechlorinating anaerobic enrichments by amplification: accuracy of community structure based on restriction analysis and partial sequencing of 16S rRNA genes

Journal of Applied Microbiology ◽

10.1046/j.1365-2672.1998.00508.x ◽

1998 ◽

Vol 84 (6) ◽

pp. 1156-1162 ◽

Cited By ~ 12

Author(s):

LaMontagne ◽

Davenport ◽

Hou ◽

Dutta

Keyword(s):

Community Structure ◽

16S Rrna ◽

Restriction Analysis ◽

16S Rrna Genes ◽

Rrna Genes ◽

Partial Sequencing

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Vertical variation in Vibrio community composition in Sansha Yongle Blue Hole and its ability to degrade macromolecules

Marine Life Science & Technology ◽

10.1007/s42995-019-00003-4 ◽

2019 ◽

Vol 2 (1) ◽

pp. 60-72 ◽

Cited By ~ 4

Author(s):

Bei Li ◽

Jiwen Liu ◽

Shun Zhou ◽

Liang Fu ◽

Peng Yao ◽

...

Keyword(s):

Organic Carbon ◽

16S Rrna ◽

Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Tween 20 ◽

Rrna Gene ◽

Free Living ◽

Blue Hole ◽

Gene Copies

Abstract With the advantages of wide distribution, fast growth, and broad metabolic spectrum to organic carbon compounds, Vibrio may play an important role in organic carbon cycling. However, the ecological roles of Vibrio in many marine environments have not been explored. Here, the world’s deepest ‘blue hole’, the Sansha Yongle Blue Hole (SYBH) in the South China Sea, which is a geographically semi-enclosed environment featuring unique chemical characters, was investigated. The abundance, diversity and carbon source utilization capability of Vibrio were studied by quantification and high-throughput sequencing of Vibrio specific 16S rRNA genes and cultivation methods. The abundance of Vibrio in water column of the SYBH ranged from 3.78 × 104 to 7.35 × 106 16S rRNA gene copies L−1. Free-living Vibrio was more abundant than particle-associated Vibrio (~ 1.20 × 106 versus~ 2.68 × 105 gene copies L−1), indicating that Vibrio prefers a free-living life style. The Vibrio assemblages showed clear vertical stratification and could be divided into three groups: aerobic-transition, middle anaerobic and bottom anaerobic zones. Dissolved oxygen (DO), temperature, pH and salinity were the main environmental factors affecting the abundance and community composition. Cultivated Vibrio demonstrated a degrading capability to various macromolecular substrates, including starch, Tween 20/40/80, DNA, gelatin, alginate, casein, chitin, lecithin, κ-carrageenan, mannan, xylan and hyaluronic acid. This suggests that Vibrio could produce a variety of highly active extracellular enzymes. Our study provides new insights into the distribution pattern and possible role in carbon cycle of Vibrio in the unique environment of a ‘blue hole’.

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Archaeal and Bacterial Communities Respond Differently to Environmental Gradients in Anoxic Sediments of a California Hypersaline Lake, the Salton Sea

Applied and Environmental Microbiology ◽

10.1128/aem.02409-09 ◽

2009 ◽

Vol 76 (3) ◽

pp. 757-768 ◽

Cited By ~ 78

Author(s):

Brandon K. Swan ◽

Christopher J. Ehrhardt ◽

Kristen M. Reifel ◽

Lilliana I. Moreno ◽

David L. Valentine

Keyword(s):

Community Structure ◽

16S Rrna ◽

Bacterial Communities ◽

Environmental Gradients ◽

Total Carbon ◽

Salton Sea ◽

16S Rrna Genes ◽

Rrna Genes ◽

Hypersaline Lake ◽

Anoxic Sediments

ABSTRACT Sulfidic, anoxic sediments of the moderately hypersaline Salton Sea contain gradients in salinity and carbon that potentially structure the sedimentary microbial community. We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, and Crenarchaeota. Community structure and diversity were evaluated by terminal restriction fragment length polymorphism (T-RFLP), quantitative analysis of gene (16S rRNA) frequencies of dominant microorganisms, and cloning and sequencing of 16S rRNA. Archaea were numerically dominant at all depths and exhibited a lesser response to environmental gradients than that of Bacteria. The relative abundance of Crenarchaeota was low (0.4 to 22%) at all depths but increased with decreased carbon content and increased salinity. Salinity structured the bacterial community but exerted no significant control on archaeal community structure, which was weakly correlated with total carbon. Partial sequencing of archaeal 16S rRNA genes retrieved from three sediment depths revealed diverse communities of Euryarchaeota and Crenarchaeota, many of which were affiliated with groups previously described from marine sediments. The abundance of these groups across all depths suggests that many putative marine archaeal groups can tolerate elevated salinity (5.0 to 11.8% [wt/vol]) and persist under the anaerobic conditions present in Salton Sea sediments. The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains.

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Comparison of Diversities and Compositions of Bacterial Populations Inhabiting Natural Forest Soils

Applied and Environmental Microbiology ◽

10.1128/aem.70.9.5057-5065.2004 ◽

2004 ◽

Vol 70 (9) ◽

pp. 5057-5065 ◽

Cited By ~ 144

Author(s):

Evelyn Hackl ◽

Sophie Zechmeister-Boltenstern ◽

Levente Bodrossy ◽

Angela Sessitsch

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Community Composition ◽

Forest Soils ◽

Bacterial Communities ◽

Pine Forests ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Bacterial Communities ◽

Soil Bacterial

ABSTRACT The diversity and composition of soil bacterial communities were compared among six Austrian natural forests, including oak-hornbeam, spruce-fir-beech, and Austrian pine forests, using terminal restriction fragment length polymorphism (T-RFLP, or TRF) analysis and sequence analysis of 16S rRNA genes. The forests studied differ greatly in soil chemical characteristics, microbial biomass, and nutrient turnover rates. The aim of this study was to relate these differences to the composition of the bacterial communities inhabiting the individual forest soils. Both TRF profiling and clone sequence analysis revealed that the bacterial communities in soils under Austrian pine forests, representing azonal forest types, were distinct from those in soils under zonal oak-hornbeam and spruce-fir-beech forests, which were more similar in community composition. Clones derived from an Austrian pine forest soil were mostly affiliated with high-G+C gram-positive bacteria (49%), followed by members of the α-Proteobacteria (20%) and the Holophaga/Acidobacterium group (12%). Clones in libraries from oak-hornbeam and spruce-fir-beech forest soils were mainly related to the Holophaga/Acidobacterium group (28 and 35%), followed by members of the Verrucomicrobia (24%) and the α-Proteobacteria (27%), respectively. The soil bacterial communities in forests with distinct vegetational and soil chemical properties appeared to be well differentiated based on 16S rRNA gene phylogeny. In particular, the outstanding position of the Austrian pine forests, which are determined by specific soil conditions, was reflected in the bacterial community composition.

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