Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha)

Abstract

Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of the B. pumilus group and aquatic-derived B. pumilus representatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of the Plakina cyanorosea holobiont.

Evaluation of the Marine Bacterial Population in the Great Bitter Lake, Egypt, as a Source of Antimicrobial Secondary Metabolites

“…The antimicrobial protein BLDZ1 from marine B. licheniformis inhibits the biofilm formation of microbial pathogens such as P. aeurginosa [51]. The genome mining of a marine B. pumilus strain showed at least twelve BGCs, including PKS-I, PKS-II, and NRPS which indicates a high bioactivity potential [52]. Marine B. pumilus was reported to produce an active non-ribosomal lipopeptide Pumilacidin (~3 KD) with anti-Staphylococcus aureus activity [53].…”

Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated micro-organisms

“…2018; Freitas‐Silva et al. 2021). For example , Bacillus pumilus strain 64–1, isolated from the marine sponge Plakina cyanorosea , showed broad antimicrobial activity against antibiotic‐resistant Gram‐positive and Gram‐negative pathogens.…”

“…The genome mining of this strain showed at least 12 BGCs, including PKS‐I, PKS‐II and NRPS (Freitas‐Silva et al. 2021).…”

“…Many BGCs encoding antimicrobial metabolites have been reported in the genomes of marine firmicutes. The genome of Bacillus includes several BGCs, such as PKS-I, PKS-II, PKS-III, terpene, NRPS, siderophore, Trans AT PKS/NRPS, lassopeptide, lanthipeptide, bacteriocins and others (Othoum et al 2018;Freitas-Silva et al 2021). For example, Bacillus pumilus strain 64-1, isolated from the marine sponge Plakina cyanorosea, showed broad antimicrobial activity against antibiotic-resistant Gram-positive and Gram-negative pathogens.…”

“…For example, Bacillus pumilus strain 64-1, isolated from the marine sponge Plakina cyanorosea, showed broad antimicrobial activity against antibiotic-resistant Gram-positive and Gram-negative pathogens. The genome mining of this strain showed at least 12 BGCs, including PKS-I, PKS-II and NRPS (Freitas-Silva et al 2021).…”