Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

Abstract

Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.

Genomic insights into specialized metabolism in the marine actinomycete Salinispora

“…Inner circle shows the BGCs for which the products are confirmed (black) or predicted (grey) with the corresponding chemical structures numbered and named: 1 sioxanthin, 2 lymphostin, 3 desferrioxamine B, 4 staurosporine, 5 rifamycin S, 6 diterpene, 7 lomaiviticin A, 8 cyanosporaside A, 9 salinilactam, 10 salinosporamide A, 11 salinichelin A, 12 ikarugamycin, 13 sporolide A, 14 rosamicin A, 15 thiolactomycin, 16 arenicolide B, 17 enterocin, 18 tirandalydigin, 19 cyclomarin D, 20 arenimycin A, 21 tambromycin, 22 saliniquinone A, 23 retimycin A, 24 BE43547A1. C. Species phylogeny based on 876 concatenated genes (Millán‐Aguiñaga et al, ). D. Location from which the strain was isolated (see legend).…”

“…The species phylogeny (Fig. ) and the ancestral state reconstructions were based on 876 concatenated genes common to all 119 genome sequences (Millán‐Aguiñaga et al ., ). Maximum likelihood trees for core biosynthetic genes derived from individual BGCs were constructed with default settings in FastTree (Price et al ., ) using a protein alignment (MUSCLE) generated by Geneious Pro v5.5.9.…”

“…Presence‐absence matrix of BGCs in Salinispora spp. The species phylogeny is based on core genes with no evidence of recombination (Millán‐Aguiñaga et al ., ). The perpendicular axis lists the 176 BGCs detected in these strains.…”

“… Table S1. Strain information including 16S sequence types (Freel et al ., ; Vidgen et al ., ; Millán‐Aguiñaga et al ., ) and location of origin (CB: Caribbean, SC: Sea of Cortez, PV: Puerto Vallarta, RS: Red Sea, FJ: Fiji, HI: Hawaii, PM: Palmyra, GU: Guam, PL: Palau, MD: Madeira archipelago, *sponge isolates). Table S2.…”

Extending the Salinilactone Family

“…We recently proposed the designation of six new Salinispora species in addition to the three that have already been described . Consequently, we tracked salinilactone production in members of all nine species as represented by 11 different strains.…”