| Contributors | Affiliation | Role |
|---|---|---|
| Thurber, Andrew | Oregon State University (OSU-CEOAS) | Principal Investigator |
| Copley, Nancy | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This dataset includes details on 151 marine sediment community samples collected from the Cinder Cones Cold Seep site [-77.8, 166.666] in the Ross Sea region, Antarctica in November 2016. Data are uploaded to the NCBI Sequence Read Archive under submission SUB2655615 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720] with a subset of the data from that archive originating from this project.
Sediment cores were collected from the Cinder Cones site including a methane seep habitat and vertically sectioned into cm intervals with the exterior of the cores discarded to avoid vertical smearing. Sediments were placed in whirlpack bags and kept at -80 until DNA was extracted.
Between 0.25 and 0.5 grams of frozen sediment had DNA extracted using the MoBio (now Qiagen) PowerSoil kits. Primers and amplification procedures follow the Earth Microbiome Project Protocol (http://www.earthmicrobiome.org/protocols-and-standards/16s/) using the updated primers in Apprill et al (2015) following Caporaso et al. (2011). In short, triplicate PCRs were run using the 515FB and the 806RB primers that copy the V4 region if the 16s rRNA gene. These primers were barcoded allowing later in silico separation of pooled samples. Controls and all samples were run on a gel to check for contamination. DNA was cleaned up using the MoBio UltraClean PCR Clean-Up Kit, samples were pooled into equal molar concentrations and submitted for sequencing.
Data were de-multiplexed and primers trimmed. No other data manipulation has been performed.
BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- re-formatted date from m/d/yyyy to yyyy-mm-dd
- split lat and lon into separate columns; converted lat to negative degrees
| File |
|---|
MethaneSeepData2016_MicrobialSampleIdentity.csv (Comma Separated Values (.csv), 24.14 KB) MD5:84b644f2c07befa77639c21b2933a9f6 Primary data file for dataset ID 756997 |
| Parameter | Description | Units |
| accession | NCBI accession number for the archive | unitless |
| sample_name | reference file name used in NCBI | unitless |
| organism | type of organism analyzed: all are marine sediment whose microbial community has been extracted | unitless |
| host | host type: these are environmental samples rather than from individual organisms | unitless |
| collection_date | Date sample was collected formatted as yyyy-mm-dd | unitless |
| geo_loc_name | location sampled | unitless |
| lat | latitude; north is positive | decimal degrees |
| lon | longitude; east is positive | decimal degrees |
| Replicate | Individual identifier for the core | unitless |
| Sediment_Depth_cm | depth range from which microbial community was analyzed | centimeters |
| Habitat | Whether the sample was from an area of active methane seepage or sampled as a control for this habitat. | unitless |
| Dataset-specific Instrument Name | |
| Generic Instrument Name | Automated DNA Sequencer |
| Generic Instrument Description | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
| Dataset-specific Instrument Name | |
| Generic Instrument Name | Thermal Cycler |
| Generic Instrument Description | A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html) |
NSF abstract:
Methane is a potent greenhouse gas that is naturally emitted into the oceans by geologic seeps and microbial production. Based on studies of persistent deep-sea seeps at mid- and northern latitudes, researchers have learned that bacteria and archaea can create a "sediment filter" that oxidizes methane prior to its release. Antarctica is thought to contain large reservoirs of organic carbon buried beneath its ice which could a quantity of methane equivalent to all of the permafrost in the Arctic and yet we know almost nothing about the methane oxidizing microbes in this region. How these microbial communities develop and potentially respond to fluctuations in methane levels is an under-explored avenue of research. A bacterial mat was recently discovered at 78 degrees south, suggesting the possible presence of a methane seep, and associated microbial communities. This project will explore this environment in detail to assess the levels and origin of methane, and the nature of the microbial ecosystem present.
An expansive bacterial mat appeared and/or was discovered at 78 degrees south in 2011. This site, near McMurdo Station Antarctica, has been visited since the mid-1960s, but this mat was not observed until 2011. The finding of this site provides an unusual opportunity to study an Antarctic marine benthic habitat with active methane cycling and to examine the dynamics of recruitment and community succession of seep fauna including bacteria, archaea, protists and metazoans. This project will collect the necessary baseline data to facilitate further studies of Antarctic methane cycling. The concentration and source of methane will be determined at this site and at potentially analogous sites in McMurdo Sound. In addition to biogeochemical characterization of the sites, molecular analysis of the microbial community will quantify the time scales on which bacteria and archaea respond to methane input and provide information on rates of community development and succession in the Southern Ocean. Project activities will facilitate the training of at least one graduate student and results will be shared at both local and international levels. A female graduate student will be mentored as part of this project and data collected will form part of her dissertation. Lectures will be given in K-12 classrooms in Oregon to excite students about polar science. National and international audiences will be reached through blogs and presentations at a scientific conference. The PI's previous blogs have been used by K-12 classrooms as part of their lesson plans and followed in over 65 countries.
| Funding Source | Award |
|---|---|
| NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) |