Combined Amplicon Pyrosequencing Assays Reveal Presence of the Apicomplexan “type-N” (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia

Abstract

BackgroundThe coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. “type-N” symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring.Methods & Principal FindingsWe investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa - Chromera velia . Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens ( Cryptosporidium and Cryptococcus ). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C . velia , respectively.SignificanceThis is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these organisms but also identify their potential as pathogens.

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

“…In order to examine if the phyla-based distribution of sequences in this database are representative of those available in next-generation sequencing studies, we examined phyla-based diversity of 715,114 coralmicrobial sequences spanning nine studies and 23 coral species from the Alcyonacea as well as complex and robust Scleractinian lineages available within the Coral Microbiome Portal (CMP) (https://vamps2.mbl.edu/portals/ CMP) (Sunagawa et al, 2010;Barott et al, 2011;Morrow et al, 2012;Apprill et al, 2013;Bayer et al, 2013a, b;Bourne et al, 2013;Šlapeta and Linares, 2013;Lesser and Jarett, 2014). We identified high consistency between the two types of sequence data, with three lineages represented in the next-generation studies that were not present in the Sanger database (Candidate division OP10, TG-1 and WS6), and five lineages in the Sanger sequencing based Coral MD database (BD1-5, Elusimicrobia, NPL-UPA2, SHA-109 and WCHB1-60) which were absent from the CMP.…”

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

“…Phylogenetic placements of query OTU representatives that were taxonomically assigned to the Apicomplexa were conducted using a full-length reference multiple sequence alignment and corresponding phylogeny comprising 190 taxa from all major Alveolate clades (see Supplementary Data 3 and 4 for GenBank accession numbers, sequences and clade assignments). The taxon sampling was collated from a range of publications relating to eukaryotic diversity in general and Alveolata diversity and phylogeny in particular; for example, refs 20,[63][64][65][66][67][68][69] . It is also acknowledged that single gene trees are unable to resolve the backbone of the Alveolate phylogeny.…”

Increased growth and pigment content ofChromera veliain mixotrophic culture

“…Recently, a new alveolate microalga, Chromera velia, was discovered in association with stony corals of Sydney Harbour and the Great Barrier Reef, Australia. Chromera velia has been isolated from and detected in coral tissue and has been experimentally demonstrated to infect coral larvae (Moore et al, 2008;Cumbo et al, 2012;Janou skovec et al, 2012;Slapeta & Linares, 2013). The coral holobiont is a nutrient-rich system involving complex interactions between the predominant coral host and symbiotic zooxanthellae partners together with a poorly defined milieu of associated microorganisms such as bacteria, viruses and eukaryotes, including C. velia (Bourne et al, 2009;Janou skovec et al, 2012).…”