Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis

Abstract

Background Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. Results Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. Conclusions Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral’s ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience.

Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches

“…The enriched enzymatic function involving the transfer of aldehyde or ketonic groups suggests a potential linkage to energy metabolism, particularly the reductive pentose phosphate cycle. This nding aligns with the ndings of Doering, et al 30 , who identi ed the complete pathway in coral-associated bacteria. Conversely, the presence of acyltransferases, associated with the phosphate acetyltransferaseacetate kinase pathway, in the seawater bacterial community indicates divergent energy-generation pathways between these two bacterial communities.…”

Unlocking the genomic potential of Red Sea coral probiotics

“…This can be mitigated by obtaining a large number of isolates and meticulously screening and testing them for beneficial traits. Notably, all pBMC examined in this study, even those from the same genus, were distinct and demonstrated potential to contribute to the health and resilience of corals, indicating the need for continued efforts to isolate 64,171 , explore [175][176][177][178][172][173][174]177 and test 173 novel pBMC. We also highlight the discovery of prophages associated with two of the BMCs and their potential role in providing competitive advantage to coral probiotics against other bacteria.…”

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

“… 14 – 18 , 35 – 38 ). Recent advancements include an enhanced understanding of BMC mechanisms, the selection of probiotic strains based on genomic screening, and the exploration of other microbial therapies and bacterial experimental evolution 19 , 39 – 42 .…”