Abstract:

Marine nematode microbiomes were studied by isolating host-associated microbial taxa in nematodes from the Gulf of Mexico. A two‐gene metabarcoding approach was used to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1–V2 region of the 18S rRNA gene targeting microbial eukaryotes. This dataset contains nematode taxonomic identifications, video images, and 18S rRNA, 16S rRNA, NGS reads (fastq) from samples collected in the Gulf of Mexico in June and July of 2007. This dataset supports the publications: Schuelke, T., Pereira, T.J., Hardy, S.M., & Bik, H.M. (2018). Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Molecular Ecology, 27(8): 1930-1951. doi: 10.1111/mec.14539; and Pereira, T. J., De Santiago, A., Schuelke, T., Hardy, S. M., & Bik, H. M. (2020). The impact of intragenomic rRNA variation on metabarcoding‐derived diversity estimates: A case study from marine nematodes. Environmental DNA. doi:10.1002/edn3.77

Suggested Citation:

Holly Bik. 2018. Dataset for: Nematode‐associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7959G4X

Publications:

Schuelke, T., Pereira, T. J., Hardy, S. M., & Bik, H. M. (2018). Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Molecular Ecology, 27(8), 1930–1951. doi:10.1111/mec.14539

Pereira, T. J., De Santiago, A., Schuelke, T., Hardy, S. M., & Bik, H. M. (2020). The impact of intragenomic rRNA variation on metabarcoding‐derived diversity estimates: A case study from marine nematodes. Environmental DNA. doi:10.1002/edn3.77

Purpose:

To investigate patterns in marine nematode microbiomes, by characterizing host‐associated microbial taxa in worms isolated from a range of habitat types (deep‐sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and the Gulf of Mexico).

Data Parameters and Units:

MEMB_Specimens: Video capture images of nematode specimens OTU_Tables: 18S rRNA, 16S rRNA, NGS reads (fastq) Nematode-Samples_GOMRI_19July2018.csv: Sample ID, Nematode Order, Nematode Family, Nematode Genus, Nematode ID, Feeding Group, Morph voucher, Year, Ocean region (Gulf of Mexico), Habitat, Depth, Latitude (decimal degrees), Longitude (decimal degrees), Sample site, Genbank ID. Raw Illumina metabarcoding data (18S rRNA gene amplicons generated from single nematodes) have been deposited in the NCBI Sequence Read Archive (BioProject PRJNA422296 and SRA accession SRP128131). Full-length 18S rRNA gene sequences newly generated via Sanger sequencing have been deposited on GenBank (Accession Numbers: MN250033–MN250142) Metabarcoding primer constructs and QIIME mapping files are available on Figshare (https://doi.org/10.6084/m9.figshare.5701090). QIIME outputs (ASV/OTU tables), and all scripts used for processing and analyzing the data in the present study are available on GitHub (https://github. com/BikLab/nematode-rRNA-variants).

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