Comparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms

Abstract

Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10-2^T, SSBR10-3^T, and SSHM10-5^T) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate-Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.

Keywords: Halobacillus sp.; algicidal activity; comparative genome analysis; halotolerance; stress response.

FIGURE 1

Circular map of (A) (i) Halobacillus shinanisalinarum SSTM10‐2^T, whole chromosome; (ii) Halobacillus salinarum SSBR10‐3^T, whole chromosome; and (iii, iv) Halobacillus amylolyticus SSHM10‐5^T, whole chromosome and plasmid. (B) 16 s rRNA phylogenetic tree and (C) Orthologous Average Nucleotide Identity (ANI). Phylogenetic tree was generated using maximum likelihood method with cutoff value of 50%, constructed using MEGAX based on 16S rRNA sequences. ANI percentage was calculated using OrthoANI in OAT (Orthologous Average Nucleotide Identity Tool).

FIGURE 2

Venn diagram of Halobacillus shinanisalinarum SSTM10‐2^T, Halobacillus salinarum SSBR10‐3^T, and Halobacillus amylolyticus SSHM10‐5^T. Venn diagram was constructed using orthoVenn3 with default settings.

FIGURE 3

COG analysis of core, accessory, and unique genes into four major COG categories (A) and twenty subcategories (B). COG categories: R, General function prediction only; K, Transcription; G, Carbohydrate transport and metabolism; E, Amino acid transport and metabolism; S, Function unknown; V, Defence mechanisms; P, Inorganic ion transport and metabolism; M, Cell wall/membrane/envelope biogenesis; T, Signal transduction mechanisms; C, Energy production and conversion; Q, Secondary metabolites biosynthesis, transport, and catabolism; L, Replication, recombination, and repair; I, Lipid transport and metabolism; H, Coenzyme transport and metabolism; O, Post‐translational modification, protein turnover, and chaperones; J, Translation, ribosomal structure, and biogenesis; N, Cell motility; F, Nucleotide transport and metabolism; U, Intracellular trafficking, secretion, and vesicular transport; and D, Cell cycle control, cell division, and chromosome partitioning.

FIGURE 4

KEGG analysis of core, accessory, and unique gene into six major COG categories (A) and forty subcategories (B).

FIGURE 5

Comparative analysis of COG of strains Halobacillus shinanisalinarum SSTM10‐2^T, Halobacillus salinarum SSBR10‐3^T, and Halobacillus amylolyticus SSHM10‐5^T using multiple tools. (A) RAST annotation, (B) KEGG annotation, and (C) EggNOG annotation.

FIGURE 6

(A) Distribution of ectoine‐related BGC using antiSMASH with default settings. (B) Proposed salt adaptation pathway in Halobacillus shinanisalinarum SSTM10‐2^T, Halobacillus salinarum SSBR10‐3^T, and Halobacillus amylolyticus SSHM10‐5^T.

FIGURE 7

(A) The number of enzymes of each CAZyme family pattern found in genome of Halobacillus shinanisalinarum SSTM10‐2^T, Halobacillus salinarum SSBR10‐3^T, and Halobacillus amylolyticus SSHM10‐5^T. A, auxiliary activity; CE, carbohydrate esterase; GH, glycoside hydrolase; GT, glycosyltransferase; PL, polysaccharide lyase; and CBM, carbohydrate‐binding module. (B) Proposed microcystin degradation pathway. (C) QS pathway of (i) Halobacillus shinanisalinarum SSTM10‐2^T, (ii) Halobacillus salinarum SSBR10‐3^T, and (iii) Halobacillus amylolyticus SSHM10‐5^T with their genetic elements. Green is from the KEGG search, and purple is from the BLAST search. (D) Aromatic compound degradation pathway of Halobacillus shinanisalinarum SSTM10‐2^T, Halobacillus salinarum SSBR10‐3^T, and Halobacillus amylolyticus SSHM10‐5^T with their genetic elements.