Advancing coral microbiome manipulation to build long-term climate resilience

Doering, Talisa; Maire, Justin; Oppen, Madeleine J. H. van; Blackall, Linda L.

doi:10.1071/ma23009

Cited by 9 publications

(6 citation statements)

References 30 publications

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“…For bacterial probiotics to be a viable intervention to enhance coral climate resilience, long-term beneficial effects on the coral holobiont must be achieved [ 106 ]. It is therefore important that probiotic bacteria form a stable association with the holobiont.…”

Section: Discussionmentioning

confidence: 99%

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

Doering,

Tandon,

Topa

et al. 2023

Microbiome

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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.

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Section: Discussionmentioning

confidence: 99%

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

Doering,

Tandon,

Topa

et al. 2023

Microbiome

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“…The presence of the bacteria inside both coral epidermal and gastrodermal tissues suggests an endosymbiotic status of the bacteria, which is recognized as a sign of intimate biological relations between microorganisms and cnidarians ( 28 , 29 , 78 ) or metazoans in general ( 79 , 80 ). BMCs that are inherently associated with the coral tissue have also been suggested to be more likely to establish and promote long-term improvements to the holobiont ( 81 ). Additional studies are necessary to explore how long the enrichment of the tissue-associated BMCs Halomonas sp.…”

Section: Discussionmentioning

confidence: 99%

Localization and symbiotic status of probiotics in the coral holobiont

Cardoso,

Hill,

Villela

et al. 2024

mSystems

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Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis . Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome. IMPORTANCE Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.

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“…As climate change increasingly triggers coral bleaching and mortality, novel methods are urgently needed to increase coral climate resilience, including the manipulation of coral-associated microorganisms. Endozoicomonadaceae are great candidates for coral microbiome manipulation approaches [19, 20], due to their prevalence, tissue location ( i.e. more stably associated than bacteria residing in the mucus or skeleton), and putative benefits.…”

Section: Main Textmentioning

confidence: 99%

A novel, tissue-associated and vertically transmitted bacterial symbiont in the coralPocillopora acuta

Maire,

Tsang Min Ching,

Damjanovic

et al. 2023

Preprint

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Coral microhabitats are colonized by a myriad of microorganisms, including diverse bacteria which are essential for host functioning and survival. However, the location, transmission, and functions of individual bacterial species living inside the coral tissues remain poorly studied. Here, we show that a previously undescribed bacterial symbiont of the coral Pocillopora acuta forms cell-associated microbial aggregates (CAMAs) within the mesenterial filaments. CAMAs were found in both adults and larval offspring, providing evidence of vertical transmission. In situ laser capture microdissection of CAMAs followed by 16S rRNA gene metabarcoding and shotgun metagenomics produced a near complete metagenome-assembled genome. We subsequently cultured the CAMA bacteria from P. acuta colonies, and sequenced and assembled their genomes. Phylogenetic analyses showed that the CAMA bacteria belong to an undescribed Endozoicomonadaceae genus and species, which we propose to name Sororendozoicomonas aggregata gen. nov sp. nov. Metabolic pathway reconstruction from its genome sequence suggests this species can synthesize most amino acids, several B vitamins, and antioxidants, which may be beneficial to its coral hosts. This study provides detailed insights into a new member of the widespread Endozoicomonadaceae family, thereby improving our understanding of coral holobiont functioning. Vertically transmitted, tissue-associated bacteria, such as S. aggregata may be key candidates for the development of microbiome manipulation approaches with long-term positive effects on the coral host.

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Advancing coral microbiome manipulation to build long-term climate resilience

Cited by 9 publications

References 30 publications

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

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

Localization and symbiotic status of probiotics in the coral holobiont

A novel, tissue-associated and vertically transmitted bacterial symbiont in the coralPocillopora acuta

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