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

Bowen, Jennifer L.; Morrison, Hilary G.; Hobbie, John E.; Sogin, Mitchell L.

doi:10.1038/ismej.2012.47

Cited by 86 publications

(64 citation statements)

References 33 publications

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“…In previous studies (Horner-Devine et al, 2004; Có rdova-Kreylos et al, 2011), salt marsh inhabiting bacterial communities were described at deep sequencing resolution (Bowen et al, 2012) and at continental scales (Martiny et al, 2011). Moreover, their response to external nutrients has been recorded (Bowen et al, 2009).…”

Section: Discussionmentioning

confidence: 98%

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

et al. 2014

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The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic b-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

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Section: Discussionmentioning

confidence: 98%

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

et al. 2014

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“…DGGE has been suggested as a good prescreening approach that could enhance and inform the application of next-generation sequencing (NGS) methods (Hanning & Ricke 2011). On the one hand, the resolution of DGGE was sufficient to reveal seasonal variation within the same lake; however, it is clear that deep sequencing of 16S rDNA gene fragments using NGS technologies would enable rare species to be better resolved (Bowen et al 2012). On the other hand, it is clear that current methods based on NGS technologies do not reveal the true diversity of complex microbial communities (Lundin et al 2012), and more robust methods should be applied to estimate the true richness of environmental communities (Haegeman et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Homogeneous microbial diversity in the upper sediment layers of a shallow lake

Tšertova¹,

Kisand

Baty³

et al. 2013

Aquat. Microb. Ecol.

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The variability and patchiness in composition of bacterial communities were studied in a large eutrophic boreal lake (280 km 2 ) with a mean depth of < 3 m. The present study was undertaken to determine the factors that influence species dispersal in the sediment environment of large shallow lakes and to test the hypothesis that species dispersal in the sediment is heterogeneous. Surficial sediment samples were collected according to both transect and 'log-wise' sampling designs. For the vertical slicing of sediment samples, steps were chosen according to average deposition rates. Bacterial community composition (BCC) was examined by denaturing gradient gel electrophoresis (DGGE) of PCR amplification products from DNA extracted from the total community. The relationships of the DGGE fingerprint to space, bacterial abundance, production, and dry weight of the sediment were analyzed using multivariate statistical methods. The BCC was found to be uniform over both the 1 to 1000 m ('log-wise') and kilometer (>10 km transect) scales. An increase in bacterial diversity from the river bed to mid-lake corresponded to the sediment type and was related to an increase in productivity. Vertically, the bacterial diversity decreased with sediment depth while the bacterial community in the upper 2 to 5 cm of sediment was almost homogeneous. These data suggest that BCC of organic-rich sediment is very homogeneous horizontally, and the upper centimeters of the sediment undergo frequent mixing, leading to similar homogeneity.

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“…Essentially, we cannot measure what we cannot detect. The detection of rare taxa will have relatively high variability, not necessarily because they are ecologically more variable (though they may be) but because of challenges with consistent detection and making observations near the limits of measurement (Anders & Huber 2010, Dickie 2010, Reeder & Knight 2010, Bowen et al 2012, Lan et al 2012, Albertsen et al 2013, Haegeman et al 2013, Hugoni et al 2013, Delmont et al 2015. For example, rare members are often only present in either the rRNA gene pool or the rRNA pool but not both (İnceog lu et al 2015), suggesting a combination of technical detection limitation, high variability in activity/transcripts, and a large contribution of dormant taxa to the rRNA gene pool that collectively overwhelms signals from the rare biosphere.…”

Section: Detection Bias Against Rare Taxamentioning

confidence: 99%

“…along environmental gradients) are driven by true environmental constraints or are a byproduct of non-exhaustive or biased sampling efforts. A study in salt marsh sediment suggested that replicated detection of the rare biosphere can be consistent, at least for some habitats (Bowen et al 2012). Many of the rare biosphere members observed using cultivation-independent methods are presumed to be as yet uncultivable.…”

Section: Detection Bias Against Rare Taxamentioning

confidence: 99%

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

Newton¹,

Shade²

2016

Aquat. Microb. Ecol.

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There are patterns in the dynamics of rare taxa that lead to hypotheses about their lifestyles. For example, persistently rare taxa may be oligotrophs that are adapted for efficiency in resource-limiting environments, while conditionally rare or blooming taxa may be copiotrophs that are adapted to rapid growth when resources are available. Of course, the trophic strategies of microorganisms have direct ecological implications for their abundances, contributions to community structure, and role in nutrient turnover. We summarize general frameworks for separately considering rarity and heterotrophy, pulling examples from a variety of ecosystems. We then integrate these 2 topics to discuss the technical and conceptual challenges to understanding their precise linkages. Because much has been investigated especially in marine aquatic environments, we finally extend the discussion to lifestyles of rarity for freshwater lakes by offering case studies of Lake Michigan lineages that have rare and prevalent patterns hypothesized to be characteristic of oligotrophs and copiotrophs. To conclude, we suggest moving forward from assigning dichotomies of rarity/prevalence and oligotrophs/copiotrophs towards their more nuanced continua, which can be linked via genomic information and coupled to quantifications of microbial physiologies during cell maintenance and growth.

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

Cited by 86 publications

References 33 publications

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

Homogeneous microbial diversity in the upper sediment layers of a shallow lake

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

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