Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential

Abstract

The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.

Keywords: Streptomyces; comparative genomics; environmental adaptation; marine sponge bacteria; secondary metabolite biosynthetic gene clusters; single molecule real-time sequencing.

FIGURE 1

Genome maps of the SM17 and the SM18 chromosomes (A,B), and the SM17 plasmids pSM17A (C), pSM17B (D), pSM17C (E), generated using the Artemis and DNAplotter programs. All the molecules were in silico-determined to be linear, although they are represented in a circular fashion, and the sizes are not representative of the scale. The following are represented from the outer to the inner circles: the nucleotide position; coding sequences (CDSs) in the forward strand (in blue); CDSs in the reverse strand (in cyan); regions of putative secondary metabolite biosynthetic gene clusters (smBGCs, in orange); tRNA and rRNA genes (in gray and green, respectively); GC% plot on default settings (above average in olive and below average in purple). In (A,B), detailed in red are the regions determined to be the terminal inverted repeats (TIRs).

FIGURE 2

Phylogenetic tree of the concatenated nucleotide sequence of the 16S rRNA gene, plus the housekeeping genes atpD, gyrB, recA, rpoB, and tyrB. Including in this analysis are the SM17 and SM18 isolates, plus 60 Streptomyces isolates with complete genomes available in the GenBank database. Generated using MrBayes and MEGA X, with a posterior probability cut off of 95%.

FIGURE 3

Differential growth assessment of marine and terrestrial Streptomyces strains. From left to right, (A) S. albus J1074 and SM17 on ISP2 agar medium; (B) S. albus J1074 and SM17 on ISP2 + ASW agar medium; (C) S. pratensis ATCC 33331 and SM18 on ISP2 agar medium; (D) S. pratensis ATCC 33331 and SM18 on ISP2 + ASW agar medium, following 3 days growth.

FIGURE 4

Gene clusters families (GCFs) analysis using antiSMASH (version 4), BiG-SCAPE (version 20181005), MIBiG database (version 1.4), and CytoScape. Each node represents a smBGC predicted in the respective organism (labeled in different colors), and the interactions represent cluster similarity. Annotations of the MIBiG database smBGCs are labeled accordingly. Singletons, i.e., smBGCs without similarities with the smBGCs in the MIBiG database, or without similarities with the smBGCs predicted in the other genomes analyzed in this study, are not included in this figure.

FIGURE 5

Venn diagram representation of GCFs presence/absence analysis using BiG-SCAPE.

FIGURE 6

Venn diagram representing the presence/absence of orthologous genes in the SM17, SM18, S. albus J1074, and the S. pratensis ATCC 33331 genomes. Orthologous genes that are present commonly in the marine sponge-derived isolates SM17 and SM18, while absent in their terrestrial counterparts J1074 and ATCC 33331, are circled in red.

FIGURE 7

Graphical representation of the gene synteny of the partial nuo-operon present in the genomes of the marine isolates Streptomyces sp. SM17, Streptomyces sp. SM18, Salinispora arenicola CNS-205, Salinispora tropica CNB-440, and Kocuria flava S43, while absent in the terrestrial isolates Streptomyces albus J1074 and Streptomyces pratensis ATCC 33331. Each of the three lines represent a reading frame and the arrows represent a gene, with their respective gene names. Genes with the same color are homologs, while the ones in white are hypothetical proteins with no homologs in the UniProt or PDB databases.