What is it about?
metagenome based population genomics
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Why is it important?
The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments. Genes associated with cofactor biosynthesis and one-carbon metabolism showed habitat specificity, and protein-coding genes of unknown function and membrane transport proteins were under positive selection across each habitat. Characterized by different median ratios of nonsynonymous to synonymous evolutionary changes (dN/dS ratios) and a limited but statistically significant negative correlation between the dN/dS ratio and codon usage bias between habitats, the free-living and core genotypes were observed to be evolving under strong purifying selection pressure. Highlighting the potential role of genetic adaptation to the local environment, the two-component system protein-coding genes were highly stable (dN/dS ratio, < 0.03). These results suggest that despite the impact of the habitat on genetic diversity, and hence niche partition, strong environmental selection pressure maintains a conserved core genome for Polynucleobacter populations.
Perspectives
Different in situ functional constraints cause and maintain a conserved core genome in Polynucleobacter populations. Observed patterns of coupling between the dN/dS ratio and CUB highlight that translational fine-tuning likely helps Polynucleobacter bacteria to adapt to subtle metabolic changes in the local environment. However, dominant taxa are known to have complex interspecies metabolic tradeoffs (5) that can influence their genetic evolution, and therefore, understanding the biological factors that influence this habitat-wide genetic conservation remains a challenge for future studies.
Dr Naseer Sangwan
University of Chicago
Read the Original
This page is a summary of: Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations, mSystems, May 2016, ASM Journals,
DOI: 10.1128/msystems.00003-16.
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