Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters

Morales, Sergio E.; Cosart, Theodore F.; Johnson, Jesse V.; Holben, William E.

doi:10.1002/9781118010549.ch16

Cited by 13 publications

(24 citation statements)

References 58 publications

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“…We also calculated the Shannon Diversity indices calculated at the standard 3% level of sequence divergence (Table 2), and these data also support our conclusion that there is greater diversity in the sediments than in the water column (Table 2). These estimates of diversity and richness are within the range reported for other soils and sediments (Jørgensen and Boetius, 2007;Roesch et al, 2007;Morales et al, 2009).…”

Section: Resultssupporting

confidence: 84%

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

et al. 2012

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Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish sitespecific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.

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Section: Resultssupporting

confidence: 84%

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

et al. 2012

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“…Bacterial diversity was higher in beach sands in comparison to the bacterioplankton communities that we sampled (see the supplemental material). Shannon indices place the bacterial communities of beach sands (see Table S1 in the supplemental material) as more diverse than bacterioplankton but not as diverse as the bacterial communities of marine muds or soils (54).…”

Section: Discussionmentioning

confidence: 99%

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

Kostka

Prakash

Overholt

et al. 2011

Appl Environ Microbiol

771

508

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A significant portion of oil from the recent Deepwater Horizon (DH) oil spill in the Gulf of Mexico was transported to the shoreline, where it may have severe ecological and economic consequences. The objectives of this study were (i) to identify and characterize predominant oil-degrading taxa that may be used as model hydrocarbon degraders or as microbial indicators of contamination and (ii) to characterize the in situ response of indigenous bacterial communities to oil contamination in beach ecosystems. This study was conducted at municipal Pensacola Beach, FL, where chemical analysis revealed weathered oil petroleum hydrocarbon (C 8 to C 40 ) concentrations ranging from 3.1 to 4,500 mg kg ؊1 in beach sands. A total of 24 bacterial strains from 14 genera were isolated from oiled beach sands and confirmed as oil-degrading microorganisms. Isolated bacterial strains were primarily Gammaproteobacteria, including representatives of genera with known oil degraders (Alcanivorax, Marinobacter, Pseudomonas, and Acinetobacter). Sequence libraries generated from oiled sands revealed phylotypes that showed high sequence identity (up to 99%) to rRNA gene sequences from the oil-degrading bacterial isolates. The abundance of bacterial SSU rRNA gene sequences was ϳ10-fold higher in oiled (0.44 ؋ 10 7 to 10.2 ؋ 10 7 copies g ؊1 ) versus clean (0.024 ؋ 10 7 to 1.4 ؋ 10 7 copies g ؊1 ) sand. Community analysis revealed a distinct response to oil contamination, and SSU rRNA gene abundance derived from the genus Alcanivorax showed the largest increase in relative abundance in contaminated samples. We conclude that oil contamination from the DH spill had a profound impact on the abundance and community composition of indigenous bacteria in Gulf beach sands, and our evidence points to members of the Gammaproteobacteria (Alcanivorax, Marinobacter) and Alphaproteobacteria (Rhodobacteraceae) as key players in oil degradation there.

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“…This provides snapshots of the predominant bacterial community members, but phylogenetic groups that are present in a low abundance and which may possess important ecosystem functions are not assessed (47). In addition, it has been shown that rich sampling (several thousands of clones) of complex bacterial communities is required to perform robust measurements and estimations of community diversity parameters (37). Thus, the detection bias accompanying analyses of small sample sizes can lead to invalidated assumptions.…”

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confidence: 99%

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

Will

Thürmer

Wollherr

et al. 2010

Appl Environ Microbiol

319

192

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The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H) was higher in the A horizons than in the corresponding B horizons. In addition, the H was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass.

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Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters

Cited by 13 publications

References 58 publications

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

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