Ecology and exploration of the rare biosphere

Lynch, Michael D. J.; Neufeld, Josh D.

doi:10.1038/nrmicro3400

Cited by 886 publications

(779 citation statements)

References 178 publications

(188 reference statements)

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“…Prokaryotic communities in natural environments usually contain extremely high species-level diversity; however, the mechanisms maintaining such high diversity are still unclear (Torsvik et al, 2002;Lynch and Neufeld, 2015). We observed a sharp increase of explained variation when grouping otu97 into otu94 and broader taxa (for example, at least 50% increase in R 2 from otu97 to otu94 for soil cases; Figure 3), suggesting that under conditions of strong habitat filtering, some sequence-derived finely resolved taxa might exhibit similar responses to environmental conditions and behave as the same ecologically cohesive units (Philippot et al, 2009(Philippot et al, , 2010.…”

Section: Discussionmentioning

confidence: 99%

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Yeh

Sastri

et al. 2016

The ISME Journal

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We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community-environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community-environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community-environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community-environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches.

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Section: Discussionmentioning

confidence: 99%

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Yeh

Sastri

et al. 2016

The ISME Journal

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“…Fierer and Jackson 2006;Tedersoo et al 2014). While a limited number of species are frequently detected from soils, a vast majority of microorganisms appear at very low frequencies and are referred to as "rare biosphere" (Sogin et al 2006;Lynch and Neufeld 2015). On a global scale these rare taxa contribute to a nearly limitless pool of genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

Yeast diversity and species recovery rates from beech forest soils

et al. 2016

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“…This fraction is currently defined at arbitrary thresholds of 0.1 to 0.01% (Lynch and Neufeld, 2015). Although the definition of rare taxa will always remain partially based on ad hoc assumptions (Haegeman et al, 2013), several bioinformatics-based tools have shown the substantial impact of varying rarity thresholds on community analyses (Gobet et al, 2010).…”

mentioning

confidence: 99%

Absolute quantification of microbial taxon abundances

et al. 2016

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High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). Our results highlight that both relative and absolute abundances should be considered for a comprehensive biological interpretation of microbiome surveys. The ISME Journal (2017) 11, 584-587; doi:10.1038/ismej.2016 published online 9 September 2016 Recent advancements in high-throughput sequencing of marker genes, such as the 16S rRNA gene, have provided microbial ecologists the tools to accurately infer the relative composition of microbial communities (Franzosa et al., 2015). This resulted in a widespread application of the technology in longitudinal studies where shifts in community structure are related to environmental variables and functional outputs (Faust et al., 2015;Wilhelm et al., 2015). An inherent limitation of the sequencing technology is that the calculated taxon abundances comprise relative values (Widder et al., 2016). Hence, caution must be taken with the biological interpretation of these values, since inter-sample differences in cell density are not considered. To our knowledge, there are no descriptive studies that assess the extent to which relative abundances deliver a skewed image of the actual microbial community dynamics. In this study, we combined robust cell density measurements from flow cytometry (Prest et al., 2013;Van Nevel et al., 2013) with the relative abundances derived from 16S rRNA gene amplicon sequencing. We performed two extensive longitudinal surveys on the central water reservoir of a cooling water system. This engineered freshwater ecosystem was subjected to highly controlled operational phases (Supplementary Information and data set). We quantified the absolute taxon abundances and assessed whether additional insights could be attained with the combined approach.Based on the sample-specified total cell density, the absolute taxon abundances were calculated for each time point. Individual taxon densities ranged from 0.5 to 1 679 cells per μl. Several inter-taxon differences became apparent by performing ordinary least squares regression analysis between the relative and absolute abundances. We focused on the three most abundant taxa, which ...

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Ecology and exploration of the rare biosphere

Cited by 886 publications

References 178 publications

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Yeast diversity and species recovery rates from beech forest soils

Absolute quantification of microbial taxon abundances

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