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.
Highlights
The symbiotic relationship between marine invertebrates and microorganisms is among the oldest, most faithfully maintained, and functionally sophisticated within the realm of animal microbiomes (Petersen and Osvatic, 2018)
A total of 3,705 coding sequences (CDS), five rRNA and 45 tRNA-coding genes were assigned, with an estimated coding ratio of 88.3% (Supplementary Table 1). These results were comparable with data derived from other B. pumilus genomes deposited in the National Center for Biotechnology Information (NCBI) GenBank database, for which the average values comprise a genome size of 3.83 Mbp, with a GC content of 41.3% and around 3,784 protein-coding genes
The isolate was confirmed to have the type strain of the B. pumilus clade (B. pumilus ATCC 7061T) and other aquatic-derived B. pumilus strains (B. pumilus RI0695 and B. pumilus Ha06YP001) as its closest relatives, following phylogenetic and genome-based taxonomic analyses. Together with these related strains, it appears to have an open pangenome, with a dominant core component and specific accessory genes distributed throughout these strains
Summary
The symbiotic relationship between marine invertebrates and microorganisms is among the oldest, most faithfully maintained, and functionally sophisticated within the realm of animal microbiomes (Petersen and Osvatic, 2018). It is still important to isolate and genetically characterize sponge-associated bacteria to gain further insights into their role within the overall functioning of the sponge holobiont (Laport, 2018; Pita et al, 2018) as well as their potential to produce bioactive compounds with pharmaceutical applications, together with enzymes and biosurfactants with industrial utility (Santos-Gandelman et al, 2014). A diverse range of antibacterial and antifungal substances, together with enzymes and inhibitors, biosurfactants and compounds with bioremediation, bioleaching or cytotoxic potentials have been isolated from sponge-derived Bacillus (SantosGandelman et al, 2014; Indraningrat et al, 2016; Laport, 2018; Ortiz and Sansinenea, 2019)
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