Effects of mulching and fertilization on soil nutrients, microbial activity and rhizosphere bacterial community structure determined by analysis of TRFLPs of PCR-amplified 16S rRNA genes

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 After 90 days of incubation, the Gammaproteobacteria were superseded by “Bacilli” and Alphaproteobacteria.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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The Effect of a Sublethal Temperature Elevation on the Structure of Bacterial Communities Associated with the CoralPorites compressa

Journal of Marine Biology ◽

10.1155/2011/969173 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Jennifer L. Salerno ◽

Dan R. Reineman ◽

Ruth D. Gates ◽

Michael S. Rappé

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

16S Rrna Genes ◽

Rrna Genes ◽

Polymorphism Analysis ◽

Significant Shift ◽

Coral Host ◽

Experimental Conditions

Evidence points to a link between environmental stressors, coral-associated bacteria, and coral disease; however, few studies have examined the details of this relationship under tightly controlled experimental conditions. To address this gap, an array of closed-system, precision-controlled experimental aquaria were used to investigate the effects of an abrupt 1°C above summer ambient temperature increase on the bacterial community structure and photophysiology ofPorites compressacorals. While the temperature treatment rapidly impacted the photophysiology of the coral host, it did not elicit a statistically significant shift in bacterial community structure from control, untreated corals as determined by terminal restriction fragment length polymorphism analysis of 16S rRNA genes. Two of three coral colonies harbored more closely related bacterial communities at the time of collection and, despite statistically significant shifts in bacterial community structure for both control and treatment corals during the 10-day acclimation period, maintained this relationship over the course of the experiment. The experimental design used in this study proved to be a robust, reproducible system for investigating coral microbiology in an aquarium setting.

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Axial Dynamics, Stability, and Interspecies Similarity of Bacterial Community Structure in the Highly Compartmentalized Gut of Soil-Feeding Termites (Cubitermes spp.)

Applied and Environmental Microbiology ◽

10.1128/aem.69.10.6018-6024.2003 ◽

2003 ◽

Vol 69 (10) ◽

pp. 6018-6024 ◽

Cited By ~ 65

Author(s):

Dirk Schmitt-Wagner ◽

Michael W. Friedrich ◽

Bianca Wagner ◽

Andreas Brune

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Rflp Analysis ◽

Companion Paper ◽

16S Rrna Genes ◽

Rrna Genes ◽

Molecular Fingerprints ◽

Physicochemical Conditions

ABSTRACT The highly compartmentalized gut of soil-feeding termites is characterized by pronounced axial dynamics in physicochemical conditions and microbial processes. In a companion paper (D. Schmitt-Wagner, M. W. Friedrich, B. Wagner, and A. Brune, Appl. Environ. Microbiol. 69:6007-6017, 2003), we demonstrated that the variety of physicochemical conditions in the different gut compartments of Cubitermes spp. is reflected in the diversity of the respective intestinal microbial communities. Here, we used molecular fingerprints of 16S rRNA genes of the bacterial community, obtained by terminal restriction fragment length polymorphism (T-RFLP) analysis, to describe the axial dynamics of the bacterial community structure in the different gut sections. Comparison of the T-RFLP profiles with the predicted terminal restriction fragments of the clones in clone libraries of the gut segments in Cubitermes orthognathus confirmed that all hindgut sections harbored distinct bacterial communities. Morisita indices of community similarity, calculated by comparing the different patterns, revealed large differences between the bacterial communities of soil, gut, and nest material and also among the individual gut sections. By contrast, comparison of the homologous gut segments of different Cubitermes species indicated that the three termite species investigated possessed a similar, gut-specific microbiota that remained comparatively stable even during several months of maintenance in the laboratory.

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Stratification of Activity and Bacterial Community Structure in Biofilms Grown on Membranes Transferring Oxygen

Applied and Environmental Microbiology ◽

10.1128/aem.70.4.1982-1989.2004 ◽

2004 ◽

Vol 70 (4) ◽

pp. 1982-1989 ◽

Cited By ~ 82

Author(s):

Alina C. Cole ◽

Michael J. Semmens ◽

Timothy M. LaPara

Keyword(s):

Community Structure ◽

Organic Carbon ◽

Bacterial Community ◽

Flow Velocity ◽

Bacterial Community Structure ◽

Respiratory Activity ◽

Denitrifying Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

Biomass Density

ABSTRACT Previous studies have shown that membrane-aerated biofilm (MAB) reactors can simultaneously remove carbonaceous and nitrogenous pollutants from wastewater in a single reactor. Oxygen is provided to MABs through gas-permeable membranes such that the region nearest the membrane is rich in oxygen but low in organic carbon, whereas the outer region of the biofilm is void of oxygen but rich in organic carbon. In this study, MABs were grown under similar conditions but at two different fluid velocities (2 and 14 cm s−1) across the biofilm. MABs were analyzed for changes in biomass density, respiratory activity, and bacterial community structure as functions of biofilm depth. Biomass density was generally highest near the membrane and declined with distance from the membrane. Respiratory activity exhibited a hump-shaped profile, with the highest activity occurring in the middle of the biofilm. Community analysis by PCR cloning and PCR-denaturing gradient gel electrophoresis of 16S rRNA genes demonstrated substantial stratification of the community structure across the biofilm. Population profiles were also generated by competitive quantitative PCR of gene fragments specific for ammonia-oxidizing bacteria (AOB) (amoA) and denitrifying bacteria (nirK and nirS). At a flow velocity of 14 cm s−1, AOB were found only near the membrane, whereas denitrifying bacteria proliferated in the anoxic outer regions of the biofilm. In contrast, at a flow velocity of 2 cm s−1, AOB were either not detected or detected at a concentration near the detection limit. This study suggests that, under the appropriate conditions, both AOB and denitrifying bacteria can coexist within an MAB.

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Response of bacterioplankton community structure to an artificial gradient of <i>p</i>CO<sub>2</sub> in the Arctic Ocean

Biogeosciences Discussions ◽

10.5194/bgd-9-10645-2012 ◽

2012 ◽

Vol 9 (8) ◽

pp. 10645-10668 ◽

Cited By ~ 9

Author(s):

R. Zhang ◽

X. Xia ◽

S. C. K. Lau ◽

C. Motegi ◽

M. G. Weinbauer ◽

...

Keyword(s):

Species Richness ◽

Community Structure ◽

Bacterial Community ◽

Ocean Acidification ◽

Bacterial Diversity ◽

Bacterial Community Structure ◽

Total Alkalinity ◽

16S Rrna Genes ◽

The Arctic ◽

Rrna Genes

Abstract. The influences of ocean acidification on bacterial diversity were investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples collected from the largest CO2 manipulation mesocosm study that had been performed thus far. Terminal restriction fragment length polymorphism analysis of the PCR amplicons of the 16S rRNA genes revealed that bacterial diversity, species richness and community structure varied with the time of incubation but not the degree of ocean acidification. The phylogenetic composition of the major bacterial assemblage after a 30-day incubation under various pCO2 concentrations did not show clear effects of pCO2 levels. However, the maximum apparent diversity and species richness which occurred during incubation differed in the high and low pCO2 treatments, in which different bacterial community structure harbored. In addition, total alkalinity was one of the contributing factors for the temporal variations in bacterial community structure observed during incubation. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment. Our study suggested that ocean acidification affected the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

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Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches

BMC Microbiology ◽

10.1186/s12866-019-1601-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 5

Author(s):

Niclas Lampert ◽

Aram Mikaelyan ◽

Andreas Brune

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Community Structure ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Feeding Groups ◽

Reducing Conditions ◽

Primary Driver

Abstract Background Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. Results The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites. Conclusion Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

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Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions

Applied and Environmental Microbiology ◽

10.1128/aem.01986-15 ◽

2015 ◽

Vol 81 (20) ◽

pp. 7114-7124 ◽

Cited By ~ 9

Author(s):

Kenly A. Hiller ◽

Kenneth H. Foreman ◽

David Weisman ◽

Jennifer L. Bowen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

16S Rrna ◽

Bacterial Community Composition ◽

Environmental Parameters ◽

Permeable Reactive Barriers ◽

16S Rrna Genes ◽

Rrna Genes ◽

Reactive Barriers

ABSTRACTPermeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole.

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Assessment of total bacterial diversity in whiteleg shrimps and its aquaculture environment in Pangkajene and Banyuwangi, Indonesia

Asia Pacific Journal of Molecular Biology and Biotechnology ◽

10.35118/apjmbb.2021.029.3.04 ◽

2021 ◽

pp. 26-37

Author(s):

Yuni Puji Hastuti ◽

Yuli Siti Fatma ◽

Hardi Pitoyo ◽

Wildan Nurussalam ◽

Jajang Ruhyana

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Community Structure ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Composition ◽

Sequencing Platform ◽

The Difference

Detection of bacterial diversity in whiteleg shrimps and its rearing water is a vital first step in monitoring aquaculture activities. Bacterial community imbalance in whiteleg shrimps and its rearing water influences the quality and quantity of shrimp production. Identifying the bacterial community provides basic information related to dominant bacterial groups in whiteleg shrimps and environments, providing recommendations for proper environmental monitoring and management. In this study, we investigated bacterial community structure in the rearing water and intestinal tract of whiteleg shrimp (Litopenaeus vannamei) collected from two sites, i.e., Pangkajene, South Sulawesi (SU) and Banyuwangi, East Java (BW), Indonesia. The bacterial community was analyzed using amplicon sequencing with Illumina sequencing platform based on the V3-V4 region of the 16S rRNA genes. Bacterial diversity and composition were found differed between the rearing water and the shrimps’ intestines. Bacterial diversity in the rearing water of Banyuwangi (W.BW) was higher than that of Pangkajene (W.SU). Proteobacteria, Bacteroidetes, and Firmicutes were found as the most dominant phyla in rearing water from both farms, while distinct bacterial composition was observed in the shrimps’ intestines. The shrimp intestine from Banyuwangi (U.BW) was dominated by Firmicutes (22.36%), Proteobacteria (22.33%), and Verrucomicrobia (21.11%). In contrast, the shrimp intestine from Pangkajene (U.SU) was highly dominated by Tenericutes (88.54%), followed by Proteobacteria (4.66%), and Firmicutes (2.27%). The difference in bacterial community structure between the rearing water and shrimps’ intestines suggested that the host intestinal environment might have greater selective pressure for bacterial composition inhabiting L.vannamei intestines. Our observations suggest that the shrimps cultured in the rearing water with the similar dominant bacterial group have specific intestinal bacterial diversity.

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