Deep sea treasures - Insights from museum archives shed light on coral microbial diversity within deepest ocean ecosystems

Francesco Ricci; William Leggat; Marisa M Pasella; Tom Bridge; Jeremy Horowitz; Peter R Girguis; Tracy Ainsworth

doi:10.1016/j.heliyon.2024.e27513

Deep sea treasures - Insights from museum archives shed light on coral microbial diversity within deepest ocean ecosystems

Heliyon. 2024 Mar 3;10(5):e27513. doi: 10.1016/j.heliyon.2024.e27513. eCollection 2024 Mar 15.

Authors

Francesco Ricci^{1

2

3}, William Leggat⁴, Marisa M Pasella², Tom Bridge^{5

6}, Jeremy Horowitz^{6

7}, Peter R Girguis⁸, Tracy Ainsworth¹

Affiliations

¹ University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, NSW, Australia.
² University of Melbourne, School of Biosciences, Parkville, VIC, Australia.
³ Monash University, Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia.
⁴ University of Newcastle, School of Environmental and Life Sciences, Callaghan, NSW, Australia.
⁵ Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD, Australia.
⁶ ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia.
⁷ Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.
⁸ University of Harvard, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA.

Abstract

Deep sea benthic habitats are low productivity ecosystems that host an abundance of organisms within the Cnidaria phylum. The technical limitations and the high cost of deep sea surveys have made exploring deep sea environments and the biology of the organisms that inhabit them challenging. In spite of the widespread recognition of Cnidaria's environmental importance in these ecosystems, the microbial assemblage and its role in coral functioning have only been studied for a few deep water corals. Here, we explored the microbial diversity of deep sea corals by recovering nucleic acids from museum archive specimens. Firstly, we amplified and sequenced the V1-V3 regions of the 16S rRNA gene of these specimens, then we utilized the generated sequences to shed light on the microbial diversity associated with seven families of corals collected from depth in the Coral Sea (depth range 1309 to 2959 m) and Southern Ocean (depth range 1401 to 2071 m) benthic habitats. Surprisingly, Cyanobacteria sequences were consistently associated with six out of seven coral families from both sampling locations, suggesting that these bacteria are potentially ubiquitous members of the microbiome within these cold and deep sea water corals. Additionally, we show that Cnidaria might benefit from symbiotic associations with a range of chemosynthetic bacteria including nitrite, carbon monoxide and sulfur oxidizers. Consistent with previous studies, we show that sequences associated with the bacterial phyla Proteobacteria, Verrucomicrobia, Planctomycetes and Acidobacteriota dominated the microbial community of corals in the deep sea. We also explored genomes of the bacterial genus Mycoplasma, which we identified as associated with specimens of three deep sea coral families, finding evidence that these bacteria may aid the host immune system. Importantly our results show that museum specimens retain components of host microbiome that can provide new insights into the diversity of deep sea coral microbiomes (and potentially other organisms), as well as the diversity of microbes writ large in deep sea ecosystems.

Keywords: Cyanobacteria; Deep sea; Deep water corals.