Abstract
Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers (tufA, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic diversity of the green algae—the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful of endolithic species. We found more than 120 taxonomic units (near species level), including six family-level lineages mostly new to science. The results suggest that the existence of lineages with an endolithic lifestyle predates the existence of modern scleractinian corals by ca. 250my, and that this particular niche was independently invaded by over 20 lineages in green algae evolution. These results highlight the potential of the multi-marker approach to assist in species discovery and, when combined with a phylogenetic framework, clarify the evolutionary origins of host-microbiota associations.
Highlights
Bacteria, fungi and green algae are common inhabitants of coral skeletons
In order to obtain information from eukaryotic and prokaryotic members of the microbiome, we used four metabarcoding markers: the 16S rDNA22, the 18S rDNA23, a fragment of the 23S rDNA that targets algal chloroplasts[24] and a fragment of the elongation factor Tu gene, a DNA barcode recommended and commonly used for green algae due to its ability to distinguish between closely related species[25]
We found a diverse community of cyanobacteria, which was best characterized with the 23S rDNA marker
Summary
Fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. The skeletons of stony corals are populated by endolithic (limestone-boring) bacteria, fungi and a conspicuous layer of green algae[3,4] These organisms are protected from the external environment but endure very low levels of light and extreme daily fluctuations of pH and oxygen levels[5]. Ostreobium (Ulvophyceae, Chlorophyta) is considered to be the most abundant endolithic algal genus in marine habitats and has three described species ( there are some inconsistencies in literature) It is a siphonous alga, meaning that its whole body consists of a single, branched, multinucleate cell[11]. Metabarcoding allows for in-depth microbial composition assessments directly from environmental samples[14] This approach has led to the discovery of an enormous number of microorganisms never isolated or cultured before. The fraction of the biodiversity captured by metabarcoding surveys depends on the markers and primers used, so organisms that are not amplified with the standard methods go undetected even if they are common and play important roles in the ecosystem
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