2022
DOI: 10.1093/gigascience/giac127
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Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera

Abstract: At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress … Show more

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Cited by 13 publications
(11 citation statements)
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“…The carbon, nitrogen and sulphur metabolic pathways inferred through our analysis support the hypothesis that endolithic bacteria can be considered major nutrient recyclers (Fine & Loya, 2002; Moynihan et al, 2022; Sangsawang et al, 2017; Tandon, Ricci, et al, 2022) and by showing how the abundance of these pathways changes across the skeleton depth gradient, we provide new spatial insight into the coral skeleton biogeochemical cycle. Although the pathways extrapolated from our dataset reflect some of the functional potentials of the endolithic microbial community, further studies are needed to assess their spatial–temporal expression in areas of the skeleton characterized by different O 2 and pH gradients.…”
Section: Resultssupporting
confidence: 75%
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“…The carbon, nitrogen and sulphur metabolic pathways inferred through our analysis support the hypothesis that endolithic bacteria can be considered major nutrient recyclers (Fine & Loya, 2002; Moynihan et al, 2022; Sangsawang et al, 2017; Tandon, Ricci, et al, 2022) and by showing how the abundance of these pathways changes across the skeleton depth gradient, we provide new spatial insight into the coral skeleton biogeochemical cycle. Although the pathways extrapolated from our dataset reflect some of the functional potentials of the endolithic microbial community, further studies are needed to assess their spatial–temporal expression in areas of the skeleton characterized by different O 2 and pH gradients.…”
Section: Resultssupporting
confidence: 75%
“…In darkness, the pH shifts to pre‐illumination values mainly because of CO 2 production through respiration (Shashar & Stambler, 1992), but very few spatially resolved pH measurements have been done in coral skeletons (Reyes‐Nivia et al, 2013; Shashar & Stambler, 1992). There is now increasing evidence for various microbial processes involved in carbon, nitrogen, sulphur and phosphorus transformations in the coral skeleton (Ferrer & Szmant, 1988; Moynihan et al, 2022; Sangsawang et al, 2017; Tandon, Ricci, et al, 2022; Yang et al, 2016; Yang et al, 2019), but quantification of such processes is rare and it remains unknown how the functions of the skeletal microbiome change with depth and skeletal architecture. By using a combination of hyperspectral imaging, planar optode sensors and spatially explicit microbiome characterization (by metabarcoding), the present study explores links between the O 2 and pH microenvironment and the composition and inferred functions of the skeletal microbiome.…”
Section: Introductionmentioning
confidence: 99%
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“…Whether chlamydiae can infect these protists in hospite remains unknown. Four MAGs analyzed in our study were isolated from the coral skeleton [53], and may therefore be derived from Ostreobium or other endolithic protists. One MAG (Pac_F2b) was obtained from bacterial clusters excised from coral epidermis and the strain represented by this MAG therefore likely infects coral cells.…”
Section: Discussionmentioning
confidence: 99%
“…Two additional cnidarian-associated MAGs belonged to the Rhabdochlamydiaceae and Anoxychlamydiaceae. The Anoxychlamydiaceae MAG (PL23a_bin.60) was obtained from coral skeleton, a few centimeters underneath the algal ( Ostreobium) layer [53]. The skeleton is anoxic past the first few centimeters [58], and probably up to the coral tissue layer at night, when phototrophic endoliths ( e.g., Ostreobium , Cyanobacteria) do not photosynthesize [59], and could therefore support anaerobic microorganisms such as Anoxychlamydiaceae [60].…”
Section: Discussionmentioning
confidence: 99%