Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Saha, Jayanti; Saha, Barnan Kumar; Sarkar, Monalisha; Roy, Vivek; Mandal, Parimal; Pal, Ayon

doi:10.3389/fmicb.2019.02896

Cited by 6 publications

(3 citation statements)

References 124 publications

(147 reference statements)

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“…Earlier, it has been reported that the pqqE gene is highly conserved within genus taxonomic level (Wecksler et al, 2009). The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas (Saha et al, 2019).…”

Section: Phylogenetic Analysismentioning

confidence: 65%

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

et al. 2021

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Plants cannot uptake the insoluble form of phosphate from soil. Phosphate-solubilizing microbes (PSMs) release gluconic acid (C6H12O7) that is synthesized by the interaction between co-factor pyrroloquinoline quinine (PQQ) and glucose dehydrogenase within themselves and hence convert the insoluble phosphate into a soluble form. Phylogenetic analyses based on individual sequences of PqqA–PqqE proteins involved in the PQQ biosynthetic pathway manifested clear clustering formation of the selected species according to their respective genera such as Pantoea, Rouxiella, Rahnella, Kosakonia, Mixta, Cronobacter, and Serratia. In multiple sequence alignment (MSA), numerous semi-conserved sites were identified that indicate acquired mutation during evolution. The selected pqq genes that appeared within an operon system sustain a specified order viz. pqqABCDE for both positive and negative strands. The nucleotide composition of the encoding genes displayed higher content of GCs at different positions of the codons and has also been properly reflected in relative synonymous codon usage (RSCU) values of the codons with few exceptions. The correspondence analysis (COA) based on RSCU proclaimed that the pqqB genes prefer A/U-ending codons over G/C, while for the pqqE gene, G/C-ending codons are comparatively more preferable (except CGU). Mutational pressure contributes to shaping the codon usage pattern for the selected pqq genes evinced from the COAs, while the ENc and neutrality plot gives attestation of natural selection. The higher values of CAI indicate the gene adaptability and codon usage bias. These comprehensive computational studies can be beneficial for further research in molecular phylogenetics, genomics, and proteomics and to better understand the evolutionary dynamics of PQQ.

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Section: Phylogenetic Analysismentioning

confidence: 65%

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

et al. 2021

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“…This value is below the limits for the demarcation of species, commonly accepted (98.65%). Although the comparison of housekeeping genes is very useful for the identification of bacterial species usually isolated in the clinical field, this marker does not allow discrimination in many isolated environmental strains ( Saha et al, 2019 ). Fortunately, the use of bioinformatics tools for the analysis of the whole genome sequence and its content has been revealed as a useful tool for discrimination and taxonomic ordering ( Gutierrez-Albanchez et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions

et al. 2022

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SAICEUPSMT strain was isolated from soils in the mining district of Almadén (Ciudad Real, Spain), subjected to a high concentration of mercury. Using the plant model of lupinus, the strain was inoculated into the rhizosphere of the plant in a soil characterized by a high concentration of mercury (1,710 ppm) from an abandoned dump in the mining district of Almadén (Ciudad Real, Spain). As a control, a soil with a minimum natural concentration of mercury, from a surrounding area, was used. Under greenhouse conditions, the effect that the inoculum of the SAICEUPSMT strain had on the antioxidant capacity of the plant was studied, through the quantification of the enzymatic activity catalase (CAT), ascorbate peroxidase (APX), superoxide dismutase (SOD), and glutathione reductase (GR). Likewise, the capacity of the plant to bioaccumulate mercury in the presence of the inoculum was studied, as well as the effect on the biometric parameters total weight (g), shoot weight (g), root weight (g), shoot length (cm), root length (cm), total number of leaves (N), and total number of secondary roots (No). Finally, in view of the results, the SAICEUPSMT strain was identified from the phenotypic and genotypic point of view (housekeeping genes and complete genome sequencing). The inoculum with the SAICEUPSMT strain in the presence of mercury produced a significant reduction in the enzymatic response to oxidative stress (CAT, APX, and SOD). It can be considered that the strain exerts a phytoprotective effect on the plant. This led to a significant increase in the biometric parameters total plant weight, root weight and the number of leaves under mercury stress, compared to the control without abiotic stress. When analyzing the mercury content of the plant with and without bacterial inoculum, it was found that the incorporation of the SAICEUPSMT strain significantly reduced the uptake of mercury by the plant, while favoring its development in terms of biomass. Given the positive impact of the SAICEUPSMT strain on the integral development of the plant, it was identified, proving to be a Gram negative bacillus, in vitro producer of siderophores, auxins and molecules that inhibit stress precursors. The most represented fatty acids were C16:0 (33.29%), characteristic aggregate 3 (22.80%) comprising C16:1 ω7c and C16: 1ω6c, characteristic aggregate 8 (13.66%) comprising C18:1 ω7c, and C18: 1 cycle ω6c and C 17:0 (11.42%). From the genotypic point of view, the initial identification of the strain based on the 16S rRNA gene sequence classified it as Pseudomonas iranensis. However, genome-wide analysis showed that average nucleotide identity (ANI, 95.47%), DNA-DNA in silico hybridization (dDDH, 61.9%), average amino acid identity (AAI, 97.13%), TETRA (0.99%) and intergenic distance (0.04) values were below the established thresholds for differentiation. The results of the genomic analysis together with the differences in the phenotypic characteristics and the phylogenetic and chemotaxonomic analysis support the proposal of the SAICEUPSMT strain as the type strain of a new species for which the name Pseudomonas mercuritolerans sp. is proposed. No virulence genes or transmissible resistance mechanisms have been identified, which reveals its safety for agronomic uses, under mercury stress conditions.

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“…Multiple sequence alignment (MSA) [45] of the 16S rRNA genes was generated using the tool Clustal Omega [46]. Phylogeny was inferred using the maximum likelihood (ML) method [47] after a detailed model selection analysis based on Bayesian Information Criterion (BIC) score [48] and employing 1000 bootstrap replicates [49] using MEGA X [50]. Model selection has the utmost priority for deciphering the substitution pattern during evolution [51].…”

Section: Molecular Identification By 16s Rrna Gene and Phylogenetic A...mentioning

confidence: 99%

Study of mercury resistance and Fourier transform infrared spectroscopy‐based metabolic profiling of a potent Bacillus tropicus strain from forest soil

Saha,

Roy,

Saha

et al. 2023

J Basic Microbiol

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Mercury (Hg) is a highly toxic heavy metal and Hg‐resistant indigenous bacterial isolates may offer a green and cost‐effective bioremediation strategy to counter Hg contamination. In this study, a potent Hg‐resistant bacterium was isolated from the forest soil of a bird sanctuary. Identification using matrix‐assisted laser desorption ionization‐time of flight mass spectrometry depicted the isolate as a strain of Bacillus tropicus, validated by morphological, biochemical, and molecular studies. The isolate demonstrated biological Hg removal efficiency and capacity of 50.67% and 19.76 mg g−1, respectively. The plasmid borne resistance determinant, merA, encoding mercuric reductase, was detected in the bacterium endowing it with effective Hg volatilization and resistance capability. A Fourier‐transform infrared spectroscopic comparative metabolic profiling revealed the involvement of various functional groups like –COOH, ‐CH2, ‐OH, PO4− and so on, resulting in differential spectral patterns of the bacterium both in control and Hg‐exposed situations. A temporal variance in metabolic signature was also observed during the early and mid‐log phase of growth in the presence of Hg. The bacterium described in this study is the first indigenous Hg‐resistant strain isolated from the Uttar Dinajpur region, which could be further explored and exploited as a potent bioresource for Hg remediation.

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Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Cited by 6 publications

References 124 publications

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions

Study of mercury resistance and Fourier transform infrared spectroscopy‐based metabolic profiling of a potent Bacillus tropicus strain from forest soil

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