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

2015 ◽  
Vol 81 (20) ◽  
pp. 7114-7124 ◽  
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.

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

2007 ◽  
Vol 73 (19) ◽  
pp. 6089-6097 ◽  
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.

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

2013 ◽  
Vol 32 (1) ◽  
pp. 17390 ◽  
Author(s):  
Annette K. Møller ◽  
Ditte A. Søborg ◽  
Waleed Abu Al-Soud ◽  
Søren J. Sørensen ◽  
Niels Kroer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Community Structure ◽  
High Arctic ◽  
16S Rrna Genes ◽  
Rrna Genes

scholarly journals The relationship between benthic nutrient fluxes and bacterial community in Aquaculture tail-water treatment systems

2021 ◽  
Author(s):  
Regan Nicholaus ◽  
Betina Lukwambe ◽  
Wen Yang ◽  
Zhongming Zheng
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Constructed Wetland ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Fluxes ◽  
Benthic Nutrient Fluxes ◽  
Tail Water

Constructed-wetlands, Biofilms, and sedimentation are potential aquaculture tail-water treatments however their roles on the distribution of benthic microbial community and the way they affect the interaction between microbial community and inorganic nutrient fluxes have not been fully explored. This study applied 16S rRNA high-throughput sequencing technology to investigate the microbial community distribution and their link with nutrient fluxes in an aquaculture tail- water bioremediation system . Results showed that bacterial community compositions were significantly different in constructed-wetland and biofilm treatments (p<0.05) relative to sedimentation. The composition of the 16S rRNA genes among all the treatments was enriched with Proteobacteria, Bacteroidetes, Firmicutes, and Flavobacteria . NMDS analysis showed that the bacterial composition in constructed-wetland and biofilm samples clustered separately compared to those in sedimentation. The Functional-Annotation-of-Prokaryotic-Taxa analysis indicated that the proportions of sediment-microbial-functional groups (aerobic-chemoheterophy, chemoheterotrophy, and nitrate-ammonification combined) in the constructed-wetland treatment were 47%, 32% in biofilm and 13% in sedimentation system. Benthic-nutrient fluxes for phosphate, ammonium, nitrite, nitrate and sediment oxygen consumption differed markedly among the treatments ( p<0.05 ). Canonical correspondence analysis indicated constructed-wetland had the strongest association between biogeochemical contents and the bacterial community relative to other treatments. This study suggests that the microbial community distributions and their interactions nutrient fluxes were most improved in the constructed-wetland followed by the area under biofilm and sedimentation treatment.

scholarly journals Effect of Elevated Tropospheric Ozone on the Structure of Bacterial Communities Inhabiting the Rhizosphere of Herbaceous Plants Native to Germany

2005 ◽  
Vol 71 (12) ◽  
pp. 7750-7758 ◽  
Author(s):  
Anja B. Dohrmann ◽  
Christoph C. Tebbe
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Poa Pratensis ◽  
Bacterial Community Composition ◽  
16S Rrna Genes ◽  
Herbaceous Plants ◽  
Rrna Genes ◽  
Detectable Effect ◽  
Rrna Gene ◽  
Gene Probe

ABSTRACT Current elevated concentrations of ozone in the atmosphere, as they are observed during summer seasons, can cause severe effects on plant vegetation. This study was initiated to analyze whether ozone-stressed plants also transfer signals below ground and thereby alter the bacterial community composition in their rhizospheres. Herbaceous plants, native to Germany, with tolerance (Anthoxanthum odoratum, Achillea millefolium, Poa pratensis, Rumex acetosa, and Veronica chamaedrys) and sensitivity (Matricaria chamomilla, Sonchus asper, and Tanacetum vulgare) to ozone, raised in the greenhouse, were exposed in open-top chambers to two different ozone regimes, i.e., “summer stress” and a normal ozone background. DNA of bacterial cells from the rhizospheres was directly extracted, and partial sequences of the 16S rRNA genes were PCR amplified with primers targeting the following phylogenetic groups: Bacteria, α-Proteobacteria, Actinobacteria, and Pseudomonas, respectively. The diversity of the amplified products was analyzed by genetic profiling based on single-strand conformation polymorphism (SSCP). Neither the tolerant nor the sensitive plants, the latter with visible above-ground damage, showed ozone-induced differences in any of the SSCP profiles, with the single exception of Actinobacteria-targeted profiles from S. asper. To increase the stress, S. asper was germinated and raised in the continuous presence of an elevated level of ozone. SSCP profiles with Bacteria-specific primers combined with gene probe hybridizations indicated an ozone-related increase in a Xanthomonas-related 16S rRNA gene and a decrease in the respective gene from the plant plastids. The fact that only this latter unrealistic scenario caused a detectable effect demonstrated that ozone stress has a surprisingly small effect on the structural diversity of the bacterial community in rhizospheres.

The Bacterial Community Composition of the Bovine Rumen Detected Using Pyrosequencing of 16S rRNA Genes

Metagenomics ◽  
2012 ◽  
Vol 1 ◽  
pp. 1-11 ◽  
Author(s):  
Sitao Wu ◽  
Ransom L. Baldwin ◽  
Weizhong Li ◽  
Congjun Li ◽  
Erin E. Connor ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bovine Rumen

scholarly journals Spatial and Temporal Analysis of the Microbial Community in Slow Sand Filters Used for Treating Horticultural Irrigation Water

2003 ◽  
Vol 69 (4) ◽  
pp. 2116-2125 ◽  
Author(s):  
Leo A. Calvo-Bado ◽  
Tim R. Pettitt ◽  
Nick Parsons ◽  
Geoff M. Petch ◽  
J. Alun W. Morgan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Plant Pathogen ◽  
Temporal Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Global Changes ◽  
Rrna Gene ◽  
Microbial Composition

ABSTRACT An experimental slow sand filter (SSF) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, Phytophthora cryptogea. Passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. To monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the ATP content was measured. PCR amplification of 16S rRNA genes and denaturing gradient gel electrophoresis (DGGE) were used to study the dynamics of the bacterial community in detail. The top layer (1 cm) of the SSF column was dominated by a variable and active microbial population, whereas the middle (50 cm) and bottom (80 cm) layers were dominated by less active and diverse bacterial populations. The major changes in the microbial populations occurred during the first week of filter operation, and these populations then remained to the end of the study. Spatial and temporal nonlinear mapping of the DGGE bands provided a useful visual representation of the similarities between SSF samples. According to the DGGE profile, less than 2% of the dominating bands present in the SSF column were represented in the culturable population. Sequence analysis of DGGE bands from all depths of the SSF column indicated that a range of bacteria were present, with 16S rRNA gene sequences similar to groups such as Bacillus megaterium, Cytophaga, Desulfovibrio, Legionella, Rhodococcus rhodochrous, Sphingomonas, and an uncharacterized environmental clone. This study describes the characterization of the performance, and microbial composition, of SSFs used for the treatment of water for use in the horticultural industry. Utilization of naturally suppressive population of microorganisms either directly or by manipulation of the environment in an SSF may provide a more reproducible control method for the future.

scholarly journals Microbial Community Structure in Midgut and Hindgut of the Humus-Feeding Larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae)

2003 ◽  
Vol 69 (11) ◽  
pp. 6659-6668 ◽  
Author(s):  
Markus Egert ◽  
Bianca Wagner ◽  
Thorsten Lemke ◽  
Andreas Brune ◽  
Michael W. Friedrich
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Companion Paper ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Gene Frequencies ◽  
Fermentation Products

ABSTRACT The guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. In a companion paper (T. Lemke, U. Stingl, M. Egert, M. W. Friedrich, and A. Brune, Appl. Environ. Microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle Pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and the presence of a diverse, yet unstudied microbial community. Here, we report on the community structure of bacteria and archaea in the midgut, hindgut, and food soil of P. ephippiata larvae, determined with cultivation-independent techniques. Clone libraries and terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that the intestines of P. ephippiata larvae contain a complex gut microbiota that differs markedly between midgut and hindgut and that is clearly distinct from the microbiota in the food soil. The bacterial community is dominated by phylogenetic groups with a fermentative metabolism (Lactobacillales, Clostridiales, Bacillales, and Cytophaga-Flavobacterium-Bacteroides [CFB] phylum), which is corroborated by high lactate and acetate concentrations in the midgut and hindgut and by the large numbers of lactogenic and acetogenic bacteria in both gut compartments reported in the companion paper. Based on 16S rRNA gene frequencies, Actinobacteria dominate the alkaline midgut, while the hindgut is dominated by members of the CFB phylum. The archaeal community, however, is less diverse. 16S rRNA genes affiliated with mesophilic Crenarchaeota, probably stemming from the ingested soil, were most frequent in the midgut, whereas Methanobacteriaceae-related 16S rRNA genes were most frequent in the hindgut. These findings agree with the reported restriction of methanogenesis to the hindgut of Pachnoda larvae.

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