Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
Highlights
Soil, from the biological point of view, can be considered as one of the great ecological component or a system where a vast majority of microorganisms exists, albeit unexplored (Daniel, 2005; Stefanis et al, 2013; Jansson and Hofmockel, 2018)
The lowest deviation of Nc within the genome was observed in Clostridium butyricum JKY6D1 (SD = ±3.34), a Gram positive bacteria isolated from pit mud whereas the highest deviation in Nc was observed in Azotobacter chroococcum NCIMB 8003 (SD = ±7.17), a Gram negative soil bacterium
Our study revealed signature codon usage trend in the 92 soil bacteria where all the housekeeping genes were found to be under selectional pressure
Summary
From the biological point of view, can be considered as one of the great ecological component or a system where a vast majority of microorganisms exists, albeit unexplored (Daniel, 2005; Stefanis et al, 2013; Jansson and Hofmockel, 2018). Each of the different types of bacteria residing in the soil owns distinct morphological, physiological, biochemical, and ecological characteristics, and the variation in the structure and composition of different soil types impart a great influence on the diversity of the microbial community that the soil retain (Fierer and Jackson, 2006; Berg and Smalla, 2009). Many studies relating to soil microbial ecology has already revealed the immense diversity of soil bacteria, and it is a very common hypothesis that plant species as well as the soil type have a substantial influence on the structure and function of the rhizosphere associated bacterial populations (Berg and Smalla, 2009; Pérez-Valera et al, 2015). Some of the major soil inhabiting bacterial genera which are of great interest include different species of the genera Bacillus, Clostridium, Pseudomonas, Streptomyces, Micromonospora, Nitrosomonas, Nitrobacter, Vibrio, and Thiobacillus (Shimp et al, 1993; Lehman et al, 2015)
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