Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat - PubMed (original) (raw)

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Victor Kunin et al. Mol Syst Biol. 2008.

Abstract

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.

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Figures

Figure 1

Vertical gradients of gene families or groups of functionally related gene families enriched in the oxic zone (A), anoxic (high H2S) zone (B) and varying across the oxic–anoxic border (low H2S) zone (C). Relative abundance is normalized by the average number of genes in a layer. In most cases, these genes and groups of genes were over-represented relative to other metagenomic data sets (Table I). Error bars denote standard deviations calculated from 1000 bootstrap resamplings of predicted proteins, and points with non-overlapping error bars are treated as significantly different. Lists of gene families used in each group (Photosynthesis-related proteins, Chaperones, Ferredoxins and associated proteins, Sugar degradation pathways, Chemotaxis and Flagella) as well as details of the resampling procedure are given in Supplementary information.

Figure 2

Average isoelectric point (A) and aspartate content (B) of all predicted proteins in the mat layer communities and reference bacteria, archaea, phages and microbiomes available through IMG/M (Markowitz et al, 2006). Genomic average was computed for each genome or microbiome, with 10 layers of the mat treated separately. These values were rounded up to the next (larger value) bin in increments of 0.2 and 0.5 in (A) and (B) respectively, and the distribution of the bins was plotted as a fraction of each data set.

Figure 3

Isoelectric point profiles of predicted proteins (A) and GC content profiles of reads (B) for mat layer communities. In (A), isoelectric point profiles for selected reference genomes are added to highlight the highly overlapping and acid-shifted mat layer profiles.

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Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat - PubMed (original) (raw)