AUTHOR=Dahar Ghulam Yaseen , Wang Huan Wei , Rajer Faheem Uddin , Jin Pengfie , Xu Peidong , Abro Manzoor Ali , Qureshi Abdul Sattar , Karim Asad , Miao Weiguo 

TITLE=Comparative genomic analysis of Bacillus atrophaeus HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities

JOURNAL=Frontiers in Microbiology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1384691

DOI=10.3389/fmicb.2024.1384691

ISSN=1664-302X

ABSTRACT=<p><italic>Bacillus atrophaeus</italic> HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of <italic>B. atrophaeus</italic> HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of <italic>B. atrophaeus</italic> HAB-5 with other strains, <italic>Bacillus amyloliquefaciens</italic> DSM7, <italic>B. atrophaeus</italic> SRCM101359, <italic>Bacillus velezensis</italic> FZB42, <italic>B. velezensis</italic> HAB-2, and <italic>Bacillus subtilis</italic> 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the <italic>B. atrophaeus</italic> HAB-5 strain. Many gene clusters in the <italic>B. atrophaeus</italic> HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes (<italic>trpA, trpB, trpC, trpD, trpE, trpS, ywkB, miaA,</italic> and <italic>nadE</italic>), there are probable genes that produce volatile chemicals (<italic>acoA, acoB, acoR, acuB,</italic> and <italic>acuC</italic>). Moreover, HAB-5 contained genes linked to iron transportation (<italic>fbpA, fetB, feuC, feuB, feuA,</italic> and <italic>fecD</italic>), sulfur metabolism (<italic>cysC, sat, cysK, cysS,</italic> and <italic>sulP</italic>), phosphorus solubilization (<italic>ispH, pstA, pstC, pstS, pstB</italic>, <italic>gltP,</italic> and <italic>phoH</italic>), and nitrogen fixation (<italic>nif3-like, gltP, gltX, glnR, glnA, nadR, nirB, nirD, nasD, narl, narH, narJ,</italic> and <italic>nark</italic>). In conclusion, this study provides a comprehensive genomic analysis of <italic>B. atrophaeus</italic> HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of <italic>B. atrophaeus</italic> and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.</p>