AUTHOR=Mohapatra Balaram , Malhotra Harshit , Phale Prashant S. 

TITLE=Life Within a Contaminated Niche: Comparative Genomic Analyses of an Integrative Conjugative Element ICEnahCSV86 and Two Genomic Islands From Pseudomonas bharatica CSV86T Suggest Probable Role in Colonization and Adaptation

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.928848

DOI=10.3389/fmicb.2022.928848

ISSN=1664-302X

ABSTRACT=<p>Comparative genomic and functional analyses revealed the presence of three genomic islands (GIs, &gt;50 Kb size): ICE<italic>nah</italic>CSV86, <italic>Pseudomonas bharatica</italic> genomic island-1 (PBGI-1), and PBGI-2 in the preferentially aromatic-degrading soil bacterium, <italic>Pseudomonas bharatica</italic> CSV86<sup>T</sup>. Site-specific genomic integration at or near specific transfer RNAs (tRNAs), near-syntenic structural modules, and phylogenetic relatedness indicated their evolutionary lineage to the type-4 secretion system (T4SS) ICE<italic>clc</italic> family, thus predicting these elements to be integrative conjugative elements (ICEs). These GIs were found to be present as a single copy in the genome and the encoded phenotypic traits were found to be stable, even in the absence of selection pressure. ICE<italic>nah</italic>CSV86 harbors naphthalene catabolic (<italic>nah</italic>-<italic>sal</italic>) cluster, while PBGI-1 harbors Co-Zn-Cd (<italic>czc</italic>) efflux genes as cargo modules, whereas PBGI-2 was attributed to as a mixed-function element. The ICE<italic>nah</italic>CSV86 has been reported to be conjugatively transferred (frequency of 7 × 10<sup>–8</sup>/donor cell) to <italic>Stenotrophomonas maltophilia</italic> CSV89. Genome-wide comparative analyses of aromatic-degrading bacteria revealed <italic>nah</italic>-<italic>sal</italic> clusters from several <italic>Pseudomonas</italic> spp. as part of probable ICEs, syntenic to conjugatively transferable ICE<italic>nah</italic>CSV86 of strain CSV86<sup>T</sup>, suggesting it to be a prototypical element for naphthalene degradation. It was observed that the plasmids harboring <italic>nah</italic>-<italic>sal</italic> clusters were phylogenetically incongruent with predicted ICEs, suggesting genetic divergence of naphthalene metabolic clusters in the <italic>Pseudomonas</italic> population. Gene synteny, divergence estimates, and codon-based <italic>Z</italic>-test indicated that ICE<italic>nah</italic>CSV86 is probably derived from PBGI-2, while multiple recombination events masked the ancestral lineage of PBGI-1. Diversifying selection pressure (dN-dS = 2.27–4.31) imposed by aromatics and heavy metals implied the modular exchange-fusion of various cargo clusters through events like recombination, rearrangement, domain reshuffling, and active site optimization, thus allowing the strain to evolve, adapt, and maximize the metabolic efficiency in a contaminated niche. The promoters (P<italic>nah</italic> and P<italic>sal</italic>) of naphthalene cargo modules (<italic>nah</italic>, <italic>sal</italic>) on ICE<italic>nah</italic>CSV86 were proved to be efficient for heterologous protein expression in <italic>Escherichia coli</italic>. GI-based genomic plasticity expands the metabolic spectrum and versatility of CSV86<sup>T</sup>, rendering efficient adaptation to the contaminated niche. Such isolate(s) are of utmost importance for their application in bioremediation and are the probable ideal host(s) for metabolic engineering.</p>