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Amplicon sequence variants by sample table from Antarctic methane seeps

Citation

Thurber, Andrew (2020), Amplicon sequence variants by sample table from Antarctic methane seeps, Dryad, Dataset, https://doi.org/10.5061/dryad.0zpc866vh

Abstract

Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70m x 1m) microbial mat formed at 10m water depth in the Ross Sea, Antarctica and we carried out 16S rRNA gene analysis on samples collected one year and five years after the methane seep formed.  The data set attached is the resulting Amplicon Sequence Variant table by sample that we used to track the community composition change during this time and in comparison to other sampling in the McMurdo sound region.  

Methods

To identify the microbial community of the Cinder Cones Seep (CCS; 77° 47.998' S 166° 40.241' E), sediment cores were collected using SCUBA. Sampling points were randomly distributed within patches of white, putative sulfur-oxidizing filamentous bacteria in 2012 (n=3) and 2016 (n=12). Cores were also collected within 2m of the seep (called Reference; n=4) and at Control locations that were downslope, away from seep influence at Cinder Cones and 2 additional sites within McMurdo sound (‘Jetty’: 77° 51.101' S 166° 39.933' E and ‘Turtle Rocks’: 77° 44.615' S 166° 46.297' E; n= 3 at all control sites which were sampled at 20m water depth). A shallow linear microbial mat was also sampled, however with a single core so it is not included in quantitative statistical analysis. Cores were transported at in situ temp (-1.8oC) to McMurdo Station and sliced vertically (intervals given in Figure 4) and the sediment was frozen at -80oC for microbial characterization. A subset of cores had sequential 3cm deep subcores taken vertically for methane analysis and preserved as described below.

DNA was extracted from between 0.25 and 0.5 grams of sediment using the MoBio (now Qiagen) DNeasy PowerSoil kit following manufacturer protocols. Earth Microbiome Project (EMP) Protocols were followed  including amplification with the 515f and 806rb primers. For amplicon sequence variant identification, we used forward reads generated on an Illumina MiSeq (V.2 chemistry and 2x250 paired end sequencing), trimmed to 250 bp and quality filtered using default parameters in QIIME2 2019.10 [29]. Amplicon Sequence Variants (ASVs) were identified using Deblur within Qiime2, and taxonomy assigned by comparison to the Silva v123 database formatted for QIIME (NCBI SRA archive PRJNA387720).  Data analysis pipeline is included as suplamentary material in the manuscript and attached to this dataset.

Funding

National Science Foundation, Award: 1642570

National Science Foundation, Award: 1103428