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

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P - Mol. Syst. Biol. (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA.

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.

Show MeSH
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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2483411&req=5

f2: 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.

Mentions: The average isoelectric points of the mat layer communities are conspicuously acid-shifted when compared with most bacteria and microbiomes that are non-halophilic (Figure 2A). We determined this to be due primarily to an enrichment in the acidic amino acid aspartate (Figure 2B). Furthermore, the isoelectric profiles of all 10 layers converge on a common acid-shifted profile (Figure 3A) despite a significant variation in GC content between layers (Figure 3B), reflecting differing phylogenetic composition. The latter is consistent with aspartate usage being GC-independent as it can be encoded by both GC-rich and GC-poor codons (GAC and GAT, respectively). As each metagenomic read pair is likely derived from different species and no single species dominates the mat community, we conclude that a significant fraction of the community has converged on the enrichment of low isoelectric point proteins.


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

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P - Mol. Syst. Biol. (2008)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483411&req=5

f2: 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.
Mentions: The average isoelectric points of the mat layer communities are conspicuously acid-shifted when compared with most bacteria and microbiomes that are non-halophilic (Figure 2A). We determined this to be due primarily to an enrichment in the acidic amino acid aspartate (Figure 2B). Furthermore, the isoelectric profiles of all 10 layers converge on a common acid-shifted profile (Figure 3A) despite a significant variation in GC content between layers (Figure 3B), reflecting differing phylogenetic composition. The latter is consistent with aspartate usage being GC-independent as it can be encoded by both GC-rich and GC-poor codons (GAC and GAT, respectively). As each metagenomic read pair is likely derived from different species and no single species dominates the mat community, we conclude that a significant fraction of the community has converged on the enrichment of low isoelectric point proteins.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA.

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.

Show MeSH