Abstract
Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.
Highlights
Species based on 16S RNA assignment B. paralicheniformis B. paralicheniformis B. foraminis B. marisflavi B. halosaccharovorans B. vallismortis B. amyloliquefaciens V. dokdonensis Virgibacillus sp
The premise that species from different environments have unique biosynthetic capabilities is supported by a study that surveyed secondary metabolism gene clusters (SMGCs) in Bacillus genomes and identified classes of SMGCs that are only present in specific Bacillus species[22]
The analysis of the phenotypic and genomic properties of B. thuringiensis resulted in the identification of cry genes and other gene clusters encoding for proteins with toxic phenotypes
Summary
Species based on 16S RNA assignment B. paralicheniformis B. paralicheniformis B. foraminis B. marisflavi B. halosaccharovorans B. vallismortis B. amyloliquefaciens V. dokdonensis Virgibacillus sp. Advancements in next-generation sequencing technologies along with the development of computational genome-annotation tools have facilitated mining whole genomes for functional genes and gene clusters that account for unique metabolic and biosynthetic capabilities[56,57,58,59,60,61] These genome-mining approaches have become important tools in the quest for new proteins and metabolites[62,63], and in the increasingly successful efforts to use microbes as cost-efficient agents for industrial production[64,65,66]. Our results suggest that specific modules of secondary metabolism have evolved in the Red Sea Bacillus due to environmental adaptation, and that several of the isolated strains represent promising platforms for development of MCFs
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