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.

Figure 1

Sequences in the Coral Microbial Database. (21,100 Sanger‐produced sequences from archaeal and bacterial SSU rRNA genes) classified to phyla, candidate phyla and phyla‐level lineages from cultivated cells and environmental samples (uncultivated), based on the Silva reference taxonomy (Pruesse et al., 2007). Phyla that are also represented in next‐generation sequencing data available in the Coral Microbiome Portal are denoted (*).

Figure 2

Abundances of archaeal and bacterial SSU rRNA gene sequences in the Coral Microbial Database according to most detailed taxonomic lineage. The colours reflect the representation of these sequences across different species of coral.

Figure 3

Phylogeny of coral‐specific clusters within the Gammaproteobacteria genus Vibrio and related sequences, based on 16S ribosomal RNA genes. The displayed tree is a maximum likelihood tree constructed based on long (> 1200 bp) sequences only; shorter coral‐associated sequences (indicated by dashed lines) were added using the ARB Parsimony (Quick add marked) tool in ARB. Filled circles indicate bootstrap support (maximum parsimony, with 1000 resamplings) of > 90%, and open circles represent > 75% support. Bar indicates 10% sequence divergence. The numbers of sequences in each cluster are indicated in brackets and the coral host genera for each cluster are listed adjacent to clusters, and microbial species name in bold and described or type species in culture. Accession numbers for specific sequences are shown in brackets, where accession numbers are absent none were available. ATCC, American Type Culture Collection.

Figure 4

Phylogeny of coral‐specific clusters within the Gammaproteobacteria genus Endozoicomonas and related sequences, based on 16S ribosomal RNA genes. The displayed tree is a maximum likelihood tree constructed based on long (> 1200 bp) sequences only; shorter coral‐associated sequences (indicated by dashed lines) were added using the ARB Parsimony (Quick add marked) tool. Filled circles indicate bootstrap support (maximum parsimony, with 1000 resamplings) of > 90%, and open circles represent > 75% support. Bar indicates 5% sequence divergence. The numbers of sequences in each cluster are indicated in brackets and the coral host genera for each cluster are listed adjacent to clusters, and microbial species name in bold and described or type species in culture. Accession numbers for specific sequences are shown in brackets, where accession numbers are absent none were available.

Figure 5

Phylogeny of coral‐specific clusters within the Alphaproteobacteria genus Ruegeria and related sequences, based on 16S ribosomal RNA genes. The displayed tree is a maximum likelihood tree constructed based on long (> 1200 bp) sequences only; shorter coral‐associated sequences (indicated by dashed lines) were added using the ARB Parsimony (Quick add marked) tool. Filled circles indicate bootstrap support (maximum parsimony, with 1000 resamplings) of > 90%, and open circles represent > 75% support. Bar indicates 10% sequence divergence. The numbers of sequences in each cluster are indicated in brackets and the coral host genera for each cluster are listed adjacent to clusters, and microbial species name in bold and described or type species in culture. Accession numbers for specific sequences are shown in brackets, where accession numbers are absent none were available. ATCC, American Type Culture Collection. NBRC, NTE (National Institute of Technology and Evaluation) Biological Resource Centre.

Figure 6

Phylogeny of coral‐specific clusters within the Bacteroidetes genus “Candidatus Amoebophilus” and related sequences, based on 16S ribosomal RNA genes. The displayed tree is a maximum likelihood tree constructed based on long (> 1200 bp) sequences only; shorter coral‐associated sequences (indicated by dashed lines) were added using the ARB Parsimony (Quick add marked) tool. Filled circles indicate bootstrap support (maximum parsimony, with 1000 resamplings) of > 90%, and open circles represent > 75% support. Bar indicates 10% sequence divergence. The numbers of sequences in each cluster are indicated in brackets and the coral host genera for each cluster are listed adjacent to clusters, and microbial species name in bold and described or type species in culture. Accession numbers for specific sequences are shown in brackets, where accession numbers are absent none were available.

Figure 7

Phylogeny of coral‐specific clusters within the Thaumarchaeota Marine Group II “Candidatus Nitrosopumilus” and related sequences, based on 16S ribosomal RNA genes. The displayed tree is a maximum likelihood tree constructed based on long (> 1200 bp) sequences only; shorter coral‐associated sequences (indicated by dashed lines) were added using the ARB Parsimony (Quick add marked) tool. Filled circles indicate bootstrap support (maximum parsimony, with 1000 resamplings) of > 90%, and open circles represent > 75% support. Bar indicates 10% sequence divergence. The numbers of sequences in each cluster are indicated in brackets and the coral host genera for each cluster are listed adjacent to clusters, and microbial species name in bold and described or type species in culture. Accession numbers for specific sequences are shown in brackets, where accession numbers are absent none were available.

Figure 8

Phylogeny of coral‐specific clusters within the Cyanobacterial ‘Family I’ and related sequences, based on 16S ribosomal RNA genes. The displayed tree is a maximum likelihood tree constructed based on long (> 1200 bp) sequences only; shorter coral‐associated sequences (indicated by dashed lines) were added using the ARB Parsimony (Quick add marked) tool. Filled circles indicate bootstrap support (maximum parsimony, with 1000 resamplings) of > 90%, and open circles represent > 75% support. Bar indicates 10% sequence divergence. The numbers of sequences in each cluster are indicated in brackets and the coral host genera for each cluster are listed adjacent to clusters. Accession numbers for specific sequences are shown in brackets, where accession numbers are absent none were available.