In situ devices can culture the microbial dark matter of corals

Flúvio Modolon; Júnia Schultz; Gustavo Duarte; Caren Leite Spindola Vilela; Torsten Thomas; Raquel Silva Peixoto

doi:10.1016/j.isci.2023.108374

In situ devices can culture the microbial dark matter of corals

iScience. 2023 Nov 13;26(12):108374. doi: 10.1016/j.isci.2023.108374. eCollection 2023 Dec 15.

Authors

Flúvio Modolon¹, Júnia Schultz², Gustavo Duarte², Caren Leite Spindola Vilela¹, Torsten Thomas³, Raquel Silva Peixoto^{1

2}

Affiliations

¹ Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
² King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia.
³ Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.

Abstract

Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.

Keywords: Marine biotechnology; Marine organism; Microbiology; Zoology.