Dataset Information

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.

ABSTRACT: Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.

SUBMITTER: West KM

PROVIDER: S-EPMC7722930 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.

West Katrina M KM Richards Zoe T ZT Harvey Euan S ES Susac Robert R Grealy Alicia A Bunce Michael M

Scientific reports 20201208 1

Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S gene ...[more]

PMID: 33293686

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Project description:BackgroundDinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates.ResultsStratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5-30 m assemblages and the 130-150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0-30 m, and the abundance of rare taxa was highest within 130-150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives.ConclusionsDinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and-morphospecies.

Dataset Information

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.

Publications

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.

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