Section 3 update: Cloning 16S rRNA genes and utilization to type bacterial communities

2012 ◽  
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes

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

2009 ◽  
Vol 76 (3) ◽  
pp. 757-768 ◽  
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.

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

2004 ◽  
Vol 70 (9) ◽  
pp. 5057-5065 ◽  
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.

scholarly journals Effect of pH on Isolation and Distribution of Members of Subdivision 1 of the Phylum Acidobacteria Occurring in Soil

2006 ◽  
Vol 72 (3) ◽  
pp. 1852-1857 ◽  
Author(s):  
Michelle Sait ◽  
Kathryn E. R. Davis ◽  
Peter H. Janssen
Keyword(s):  
16S Rrna ◽  
Soil Ph ◽  
Strong Correlation ◽  
Bacterial Communities ◽  
Growth Conditions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Effect Of Ph ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACT The pH strongly influenced the development of colonies by members of subdivision 1 of the phylum Acidobacteria on solid laboratory media. Significantly more colonies of this group formed at pH 5.5 than at pH 7.0. At pH 5.5, 7 to 8% of colonies that formed on plates that were incubated for 4 months were formed by subdivision 1 acidobacteria. These colonies were formed by bacteria that spanned almost the entire phylogenetic breadth of the subdivision, and there was considerable congruence between the diversity of this group as determined by the cultivation-based method and by surveying 16S rRNA genes in the same soil. Members of subdivision 1 acidobacteria therefore appear to be readily culturable. An analysis of published libraries of 16S rRNAs or 16S rRNA genes showed a very strong correlation between the abundance of subdivision 1 acidobacteria in soil bacterial communities and the soil pH. Subdivision 1 acidobacteria were most abundant in libraries from soils with pHs of <6, but rare or absent in libraries from soils with pHs of >6.5. This, together with the selective cultivation of members of the group on lower-pH media, indicates that growth of many members of subdivision 1 acidobacteria is favored by slightly to moderately acidic growth conditions.

scholarly journals Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisa Paruch ◽  
Adam M. Paruch ◽  
Hans Geir Eiken ◽  
Monica Skogen ◽  
Roald Sørheim
Keyword(s):  
16S Rrna ◽  
Seasonal Dynamics ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Seasonal Succession ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Water Ecosystem

Abstract Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.

scholarly journals Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation

2002 ◽  
Vol 68 (11) ◽  
pp. 5537-5548 ◽  
Author(s):  
Wilfred F. M. Röling ◽  
Michael G. Milner ◽  
D. Martin Jones ◽  
Kenneth Lee ◽  
Fabien Daniel ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Oil Spill ◽  
Bacterial Communities ◽  
Inorganic Nutrients ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Oil Degradation ◽  
Beach Sediment ◽  
Wide Range

ABSTRACT Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% ± 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% ± 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% ± 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.

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