Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral‐associated microbes

Abstract

Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral-microbial interactions are lacking. In order to create a framework to examine coral-microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database. From this database, we identified 39 described and candidate phyla of Bacteria and two Archaea phyla associated with corals, demonstrating that corals are one of the most phylogenetically diverse animal microbiomes. Secondly, this new phylogenetic resource shows that certain microorganisms are indeed specific to corals, including evolutionary distinct hosts. Specifically, we identified 2-37 putative monophyletic, coral-specific sequence clusters within bacterial genera associated with the greatest number of coral species (Vibrio, Endozoicomonas and Ruegeria) as well as functionally relevant microbial taxa ("Candidatus Amoebophilus", "Candidatus Nitrosopumilus" and under recognized cyanobacteria). This phylogenetic resource provides a framework for more targeted studies of corals and their specific microbial associates, which is timely given the escalated need to understand the role of the coral microbiome and its adaptability to changing ocean and reef conditions.

Coral microbiome dynamics, functions and design in a changing world

“…As for many plants and animals 38 , a common feature of coral-associated bacterial microbiomes is their specificity to certain coral taxa and sometimes a correlation with the phylogeny of the coral host 36 . For example, the main taxonomic division of the Scleractinia into the robust and complex clades is often reflected in microbiome composition 56 , and speciesspecific microbiomes are frequently observed 12,[56][57][58][59][60] . Tissue and skeletal bacterial microbiomes exhibit phylosymbiosis into deep evolutionary time, but for mucus-associated bacteria the correlation between host evolutionary divergence and microbiome dissimilarities breaks down with increasing divergence times 36 .…”

“…Regardless of the exact definition used, the coral core microbiome likely consists of a small number of taxa that tend to lack host species-specificity 12,59,116 . Core taxa generally occur at low relative abundance 27 (although there are exceptions 117 ), but this notion depends on the taxonomic level that is resolved and used to describe the core microbiome.…”

“…The coral-associated bacteria far outnumber the archaea. Members of two archaeal phyla and at least 39 described and candidate bacterial phyla have been reported 12 . The archaea likely have a role in ammonia oxidation 13 ; little else is known about their contribution to the homeostasis of the coral holobiont.…”

“…Archaeal sequences are abundant in metagenomics studies of many known ecosystems 15 , but fewer metagenomic studies exist in the coral field than in other fields. The most common coral bacteria belong to the phyla Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Tenericutes, whereas the archaea belong to the phyla Thaumarchaeota and Euryarchaeota 12 . Given the recent surge of published studies on coral-associated bacteria and the growing body of data supporting their importance in coral holobiont functioning, we focus the Review on bacteria.…”

Patterns of environmental variability influence coral‐associated bacterial and algal communities on the Mesoamerican Barrier Reef

“…The coral holobiont is comprised of the coral animal and its phylogenetically diverse symbiotic partners including algae, bacteria, archaea, fungi, viruses, and protists (Rohwer, Seguritan, Azam, & Knowlton, 2002). Coral‐associated bacterial communities are incredibly diverse (Huggett & Apprill, 2018; Morrow, Moss, Chadwick, & Liles, 2012; Rohwer, Breitbart, Jara, Azam, & Knowlton, 2001; Sharp, Pratte, Kerwin, Rotjan, & Stewart, 2017; Sunagawa, Woodley, & Medina, 2010) and may play essential roles throughout the coral's life cycle, as different coral life stages correspond with variations in bacterial community structure stability (Apprill, Marlow, Martindale, & Rappé, 2009; Littman, Willis, Pfeffer, & Bourne, 2009; Sharp, Distel, & Paul, 2012; Thompson, Rivera, Closek, & Medina, 2014; Williams, Brown, Putchim, & Sweet, 2015). Bacterial symbionts are involved in sulphur and nitrogen cycling (Rädecker, Pogoreutz, Voolstra, Wiedenmann, & Wild, 2015; Raina, Tapiolas, Willis, & Bourne, 2009), and coral heterotrophy (Bourne, Morrow, & Webster, 2016).…”