Abstract:

We profiled the bacterial communities (“microbiomes”) and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA as part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity. It was found that bacteria in the genera Moritella and Pseudoalteromonas genera dominated whole larval microbiomes, and adult skin and gut microbiomes. It was also found from 16S rDNA sequencing results that symbionts did not constantly show host specificity and provided confirmation of the formerly published identity of ceratioid bioluminescent symbionts. Bioluminescent symbiont amplicon sequence variants (ASVs) were found at all depths in the seawater, with the highest abundance found at mesopelagic depths absent from larval ceratioid samples but were absent from larval ceratioid samples. The hypothesis that bioluminescent symbionts are not present throughout host development, and that ceratioids acquire their bioluminescent symbionts from the environment was supported by findings of this study. This dataset supports the publication: Freed, L. L., Easson, C., Baker, L. J., Fenolio, D., Sutton, T. T., Khan, Y., Blackwelder, P., Hendry, T.A. & Lopez, J.V. (2019). Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the Gulf of Mexico. FEMS Microbiology Ecology. doi:10.1093/femsec/fiz146

Suggested Citation:

Freed, Lindsay; Easson, Cole; Lopez, Jose. 2019. Dataset for: Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the Gulf of Mexico. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/531X8N14

Publications:

Freed, L. L., Easson, C., Baker, L. J., Fenolio, D., Sutton, T. T., Khan, Y., … Lopez, J. V. (2019). Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the gulf of mexico. FEMS Microbiology Ecology. doi:10.1093/femsec/fiz146

Purpose:

To characterize the microbial communities in six families of anglerfish (suborder Ceratioidei), including the bioluminescent bacteria characterized from esca.

Data Parameters and Units:

GenBank Accession, sample ID name, CruiseNum, Station, Date, Trawl Depth (m), StartLon, EndLat, StartLat.

Methods:

The 806R and 515F primers were used for PCR amplification of the V4 region of the 16S rRNA gene (Caporaso et al. 2011). The V4 region of the 16S rRNA gene was amplified using 806R and 515F primers (Caporaso et al. 2011). Sequencing of amplicons was with an Illumina MiSeq using the V2 500-cycle cartridge across three runs (Caporaso et al. 2012). Trimmomatic 0.36 was used to remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10), low-quality leading and trailing bases (LEADING: 3, TRAILING 3), reads with an average base quality below 15 (SLIDINGWINDOW:4:15) and reads below 24 bases long (MINLEN:24).

Instruments:

MiSeq Illumina

Provenance and Historical References:

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., … Knight, R. (2010). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108(Supplement_1), 4516–4522. doi:10.1073/pnas.1000080107 Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., … Knight, R. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal, 6(8), 1621–1624. doi:10.1038/ismej.2012.8

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