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

Abstract

Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.

Unlocking the genomic potential of Red Sea coral probiotics

“…Following the classification of each pBMC for identification and phylogenomic analysis, we screened the pBMC genomes for genes encoding proteins that are potentially beneficial for corals. We screened for genes related to catalase, urease, and siderophore production; phosphate assimilation; and nitrogen cycle and DMSP degradation through biochemical tests and PCR assays 44 , which are typically employed for BMC selection. We also detected genes involved in other potential beneficial traits (Table S3 ), including those related to oxidative stress, such as superoxide dismutases (all pBMC genomes), which exert an antioxidant effect by catalyzing the dismutation of superoxide (an ROS molecule that causes cell damage) 86 ; catalase KatE (all pBMC genomes) and catalase-peroxidase KatG (pBMC1, pBMC2, pBMC5, and pBMC6 genomes), both of which protect cells from the toxic effects of H 2 O 2 and aerated growth conditions 87 – 91 ; manganese catalase (pBMC5 and pBMC6 genomes), which is also involved in the protection of cells from H 2 O 2 92 , 93 ; and glutathione synthetase (all pBMC genomes except for pBMC6), which produces glutathione that can subsequently be used by glutathione peroxidase (all pBMC genomes except for pBMC3 and pBMC4) to scavenge ROS, such as H 2 O 2 94 , 95 .…”

“…pBMC strains were isolated from coral fragments (± 5 cm long) of Pocillopora verrucosa, Galaxea fascicularis, and Stylophora pistillata Clade IV. The fragments were collected between February and April 2021 from Al Fahal reef (22°18′18.4′′N, 38°57′52.5′′E), Aquarium reef (22°23′15.6′′N, 38°55′07.2′′E), and Tahala reef (22°15′46.9′′N, 39°03′05.9′′E) in the eastern central Red Sea, Saudi Arabia, as described by Delgadillo-Ordoñez and colleagues 44 .…”

Molecular hydrogen can minimize negative effects of heat stress on the hard coral genusAcropora

“…Another possibility to provide thermal-stressed corals with hydrogen is supplementation via other approaches. Microbiome interventions particularly reshaping the microbiome through probiotics are emerging as very promising tools for coral reef conservation [91,92,93,94]. Given the widespread abundance of hydrogen-producing bacteria [95] and their likely presence within the coral microbiome, identifying these bacteria could reveal new beneficial microorganisms potentially further supporting the development of effective probiotics.…”