Environmental shaping of codon usage and functional adaptation across microbial communities

Abstract

Microbial communities represent the largest portion of the Earth’s biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species’ boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a ‘functional metagenomics’ platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

“…Fast growing organisms with more abundant tRNA molecules tend to have high CUB for highly expressed genes (Rocha, 2004). Apart from playing a key role in evolution and adaptation biology (Hart, Cortés, Latorre, & Martinez, 2018;Roller, Lucić, Nagy, Perica, & Vlahoviček, 2013;Sharp & Matassi, 1994;Sharp, Emery, & Zeng, 2010), CUB has a prime role in improving the expression level of exogenous genes by the process of codon optimization (Mauro & Chappell, 2014). CUB is species-specific, with many potential environmental and intracellular dynamics affecting the CUB phenomenon (Grantham, Gautier, Gouy, Jacobzone, & Mercier, 1981;Plotkin, Robins, & Levine, 2004).…”

Population structure determined by comparative amplicon gene sequencing in biofilm and planktonic bacterial communities from pesticide-contaminated water

“…In this work, a model was proposed to explain a possible range of characteristics whose expression could confer adaptive advantages over the stressful environment of water tanks used in the washing of agrochemicals. The population fluctuations observed were the result of genetic drift and the capacity for biofilm formation, which involves membrane transport, interaction of signaling molecules and signal transduction, and functional bacterial versatility [58]. The biofilm structure depends on the presence of EPS, which involves the production of glycans and lipid transportation in catabolism.…”

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

“…This suggested that bacterial genera in the same metagenome can exhibit variable codon usage preferences but overall the metagenome is characterized by an accumulative codon bias which differs from the other metagenome samples markedly just like an observation for single microbial species/genome [76,77]. To investigate phyletic independence, the species specific genes common between different metagenome samples were retrieved and distances were calculated between codon usage preferences of each [78]. It was found that codon usage of compared phylogenies showed greater variations between metagenomes than in different species of the same metagenome.…”