Dataset Information

Draft Genome Sequence of Alteromonas sp. Strain RKMC-009, Isolated from Xestospongia muta via In Situ Culturing Using an Isolation Chip Diffusion Chamber.

ABSTRACT: We report the draft whole-genome sequence of Alteromonas sp. strain RKMC-009, which was isolated in situ from the sponge Xestospongia muta in San Salvador, The Bahamas, using an isolation chip (ichip). Automated biosynthetic gene cluster analysis using antiSMASH 4.0 predicted the presence of 22 biosynthetic gene clusters.

SUBMITTER: MacIntyre LW

PROVIDER: S-EPMC6588371 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of Alteromonas sp. Strain RKMC-009, Isolated from Xestospongia muta via In Situ Culturing Using an Isolation Chip Diffusion Chamber.

MacIntyre Logan W LW Haltli Bradley A BA Kerr Russell G RG

Microbiology resource announcements 20190620 25

We report the draft whole-genome sequence of Alteromonas sp. strain RKMC-009, which was isolated in situ from the sponge Xestospongia muta in San Salvador, The Bahamas, using an isolation chip (ichip). Automated biosynthetic gene cluster analysis using antiSMASH 4.0 predicted the presence of 22 biosynthetic gene clusters. ...[more]

PMID: 31221650

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Project description:Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to (1) characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs (2) identify which prokaryotic symbiont lineages are metabolically active and, (3) characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling biogeochemistry on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin). These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host-prokaryote interactions.

Project description:Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (? = 0.055) and X. muta (? = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish genetic diversity or as a storehouse of diversity that can be utilized if needed for restoration practices.

Dataset Information

Draft Genome Sequence of Alteromonas sp. Strain RKMC-009, Isolated from Xestospongia muta via In Situ Culturing Using an Isolation Chip Diffusion Chamber.

Publications

Draft Genome Sequence of <i>Alteromonas</i> sp. Strain RKMC-009, Isolated from <i>Xestospongia muta</i> via <i>In Situ</i> Culturing Using an Isolation Chip Diffusion Chamber.

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