SOILS_REFUGIA English utf8 dataset McMurdo Dry Valleys LTER Information Manager im@mcmlter.org pointOfContact 2021-09-21 ISO 19115-2 Geographic Information - North American Profile Metadata - Data with Biological Extensions ISO 19115-2:2009(E) Soil geochemistry and microbial community data from glaciated and potential glacial refugia sites in the McMurdo Dry Valleys, Antarctica (1993-2019) 2021-09-21 publication Abigail Jackson Brigham Young University ajackson260@gmail.com pointOfContact Jesse Jorna Brigham Young University jjgjorna@outlook.com pointOfContact John Chaston Brigham Young University (801) 422-4553 College of Life Sciences Provo UT 84602 US john_chaston@byu.edu http://chastonlab.byu.edu/ pointOfContact Diana Wall Colorado State University http://www.colostate.edu Johnson Hall 107 Fort Collins CO 80523 US Diana.Wall@colostate.edu http://wp.natsci.colostate.edu/walllab/ pointOfContact Byron Adams Brigham Young University byron_adams@byu.edu https://biology.byu.edu/adams-lab pointOfContact documentDigital A study was conducted to examine soil microbial communities and associated geochemical parameters at potential glacial refugia and glaciated control sites throughout the McMurdo Dry Valleys region of Antarctica. Soil samples were collected as part of ongoing long-term monitoring efforts by the McMurdo Dry Valleys Long Term Ecological Research program (MCM LTER). The oldest samples used in this study were collected during the 1993-1994 austral summer, and the newest from the 2018-2019 austral summer. "Refugia" sites were selected based on geographical positions and elevations indicative of potential glacial refugia status. Each refugia site was paired with a lower elevation "glaciated" site in the same dry valley that was not likely to have functioned as a refugium. Six replicate soils per sampling site were sequenced with 16S primers following Earth Microbiome Project protocols, filtered using the DADA2 pipeline, and clustered to amplicon sequence variant using the SILVA reference database to generate the microbial classification table included herein. Soil samples were also analyzed for various geochemical parameters as part of this study, which include P, K, NO3-, gravimetric water content, percent organic matter, pH, and electroconductivity. Name: Renée F. Brown Role: data manager completed McMurdo Dry Valleys LTER Information Manager im@mcmlter.org pointOfContact disturbance inorganic nutrients organic matter population dynamics theme LTER Core Areas English Soil sample associated with the refugia dataset. Sample was collected during the 2003-2004 austral summer from Battleship Promontory, Alatna Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 161.081433000000 161.081433000000 -76.922350000000 -76.922350000000 Soil sample associated with the refugia dataset. Sample was collected during the 2005-2006 austral summer from Lake Brownworth, Upper Wright Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 162.728803000000 162.728803000000 -77.438633000000 -77.438633000000 Soil sample associated with the refugia dataset. Sample was collected during the 2005-2006 austral summer from the Dais, Wright Valley (Soil Sample ID: DAIS 3 3-5). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 161.236417000000 161.236417000000 -77.547767000000 -77.547767000000 Soil sample associated with the refugia dataset. Sample was collected during the 2010-2011 austral summer from Hawkins Cirque (Soil Sample ID: UNN2). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 160.578597000000 160.578597000000 -77.510192000000 -77.510192000000 Soil sample associated with the refugia dataset. Sample was collected during the 2005-2006 austral summer from the Labyrinth in Upper Wright Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 160.954581000000 160.954581000000 -77.557614000000 -77.557614000000 Soil sample associated with the refugia dataset. Sample was collected during the 2018-2019 austral summer from Levy Cirque, Beacon Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 160.615478000000 160.615478000000 -77.797233000000 -77.797233000000 Soil sample associated with the refugia dataset. Sample was collected during the 1995-1996 austral summer from Lower Alatna Valley (Soil Sample ID: A1). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 161.139150000000 161.139150000000 -76.894650000000 -76.894650000000 Soil sample associated with the refugia dataset. Sample was collected during the 2018-2019 austral summer from Lower Beacon Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 160.688703000000 160.688703000000 -77.810944000000 -77.810944000000 Soil sample associated with the refugia dataset. Sample was collected during the 2011-2012 austral summer from Lower Garwood Valley (Soil Sample ID: GR36). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 163.851208000000 163.851208000000 -78.026478000000 -78.026478000000 Soil sample associated with the refugia dataset. Sample was collected during the 2011-2012 austral summer from Lower Miers Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 163.809119000000 163.809119000000 -78.100597000000 -78.100597000000 Soil sample associated with the refugia dataset. Sample was collected during the 2008-2009 austral summer from Lower Mount Seuss (Soil Sample ID: UNN Recon 4). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 161.738569000000 161.738569000000 -77.017808000000 -77.017808000000 Soil sample associated with the refugia dataset. Sample was collected sometime between 2001-2003 from Lower Taylor Valley (Soil Sample ID: F6A1). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 163.250683000000 163.250683000000 -77.607694000000 -77.607694000000 Soil sample associated with the refugia dataset. Sample was collected sometime between 2001-2003 from Taylor Valley (Soil Sample ID: MtF A1). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 163.158597000000 163.158597000000 -77.573172000000 -77.573172000000 Soil sample associated with the refugia dataset. Sample was collected sometime between 2010-2013 from Mount Seuss. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 161.710119000000 161.710119000000 -77.036628000000 -77.036628000000 Soil sample associated with the refugia dataset. Sample was collected during the 2011-2012 austral summer from Upper Garwood Valley (Soil Sample ID: GR21). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 163.850603000000 163.850603000000 -78.038600000000 -78.038600000000 Soil sample associated with the refugia dataset. Sample was collected during the 2011-2012 austral summer from Upper Miers Valley (Soil Sample ID: MR21). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 163.750792000000 163.750792000000 -78.116672000000 -78.116672000000 Soil sample associated with the refugia dataset. Sample was collected during the 1993-1994 austral summer from Upper Victoria Valley. Location info provided by Jesse Jorna and Abby Jackson in September 2021. 161.687022000000 161.687022000000 -77.342122000000 -77.342122000000 Soil sample associated with the refugia dataset. Sample was collected sometime between 2010-2012 from Wall Valley (Soil Sample ID: BA2). Location info provided by Jesse Jorna and Abby Jackson in September 2021. 160.871031000000 160.871031000000 -77.493617000000 -77.493617000000 ground condition 1994-01-03 2019-01-31 Funding for this work was provided by the National Science Foundation for Long Term Ecological Research, most recently grant #OPP-1637708. https://mcm.lternet.edu/sites/default/files/data/mcmlter-soil-jackson-refugia_geochem-20211118.csv SOILS_REFUGIA_GEOCHEM eng; US McMurdo Dry Valleys LTER SOILS_REFUGIA_GEOCHEM Data Source Definition : Geochemistry data Number of Header Lines : 1 Number of Footer Lines : 0 Orientation : Column Field Delimiter : , false DATASET_CODE Internal dataset code. SEQUENCE_ID Microbial sequence ID associated with the sample and replicate. REPLICATE Sample replicate number. Geochemical parameters were bulked across replicates for each sample. PAIR Number designating the paired low- and high- elevation sites from each Valley. E.g., m388 is a 1 and m810 is also a 1, meaning they are a direct comparison. LOCATION Location where soil sample was collected. VALLEY Valley where soil sample was collected. SOIL_SAMPLE_ID Code associated with the soil sample. SEQ_TUBE_ID Code written on the sequencing tubes. SEASON Field season or seasons when soil sample was collected. LATITUDE Latitude of the location where the soil sample was collected. LONGITUDE Longitude of the location where the soil sample was collected. ELEVATION_M Elevation of the location where the soil sample was collected. COAST_DIST_KM Distance of the sampling site to the nearest coastline of the continent. SITE_CHARACTERIZATION Initial status of the sampling site as a potential refugia or a glaciated (control). ELEVATION_TYPE Designation of the sampling site as a high or low elevation site. P_MGL Available phosphorus in the soil sample. K_MGL Available potassium in the soil sample. OM_MGL Organic matter in the soil sample. PH pH of the soil sample. EC_USCM Electric conductivity of the soil sample. NO3N_MGL Available nitrate as nitrogen in the soil sample. GWC_PCT Gravimetric water content of the soil sample. BIOPROJ_ACCN NCBI BioProject accession number associated with the sample. BIOSAMP_ACCN NCBI BioSample accession number associated with the sample. DBF https://mcm.lternet.edu/sites/default/files/data/mcmlter-soil-jackson-refugia_geochem-20211118.csv https://mcm.lternet.edu/sites/default/files/data/mcmlter-soil-jackson-refugia_taxa-20211118.zip SOILS_REFUGIA_TAXA eng; US McMurdo Dry Valleys LTER SOILS_REFUGIA_TAXA Data Source Definition : Feature classification table that contains every observed ASV in the 16S sequencing products, the number of copies of that ASV across every sample, as well as the taxonomic classification of that sample using the SILVA reference database. m388-m864 correspond to the Sequence ID in the geochemical dataset.  Number of Header Lines : 1 Orientation : Column Field Delimiter : , false DBF https://mcm.lternet.edu/sites/default/files/data/mcmlter-soil-jackson-refugia_taxa-20211118.zip dataset Soil samples were collected in various field seasons between 1993-1994 and 2018-2019 according to the protocols established in the McMurdo Dry Valleys in 1993 (Freckman and Virginia 1993). Sequencing and analyses were performed in April 2021. DNA extraction was on each sample using the provided standard protocol with DNeasy PowerSoil Kit (Qiagen). For each sample 0.25 grams of homogenized whole soil was used for each extraction, replicated 6-fold per sample. A total of 5 negative controls were also performed on pure PCR-grade water and one reagent-only control. Sequencing libraries were prepared from each sample following established protocols (Kozich et al. 2013). 4 ul of extracted DNA was added to a 96 well plate including sample-specific primers with 17 ul of AccuPrime Pfx Supermix, and 2 ul of each paired set of duel-indexed primers for the V4 region of the 16S rRNA gene supplied by the Earth Microbiome Project. To prevent evaporation, a drop of mineral oil was added to each well. The plate was amplified in individual 20 ul reactions on a thermocycler at 95 °C for 2 minutes followed by 30 cycles of 95 °C for 20 seconds, 55 °C for 15 seconds, and 72 °C for 5 minutes, then 72 °C for 10 minutes and held at 4 °C. Amplified DNA was run on gel electrophoresis using 4 ul of amplified DNA and 4 ul of loading dye in a 1% agarose gel at 100v for 60 minutes alongside a ladder. PCR amplicons were normalized and pooled using the Charm Biotech’s Just-a-PlateTM Normalization kit to 20ng/ul of total DNA per sample. These amplicons were submitted for sequencing on a MiSeq, 2x250v2 chemistry at the Arizona State University genomics core sequencing center. All post-extraction steps included a reagent only negative control to remove contaminant sequences in data analysis. Environmental analyses were performed by the BYU Environmental Analytics Lab. In short, pH was measured using a Thermo Orion Model 410A+ by Thermo Electron, Waltham, MA. Organic matter content was detected using chromic acid titration (Walkley and Black, 1934) and nitrate content measured following the methods described in Keeney and Welson (1982) on a Fialyzer 2000, FIALAb, Seattle, WA. Phosphorous and Potassium content were extracted using 0.5M sodium bicarbonate following the Olsen et al. (1954) and Schoenau and Karamos (1993) protocols respectively. References cited: Freckman, D. W., and R. A. Virginia. 1993. Extraction of nematodes from Dry Valley Antarctic soils. Polar Biology 13:483–487. Keeney, D.R., and D.W. Nelson. Nitrogen - Inorganic forms. pp. 643-698. In: A.L. Page (ed.), Methods of Soil Analysis Part 2. 1982. American Society of Agronomy, Inc. Madison, WI. Kozich, J. J., S. L. Westcott, N. T. Baxter, S. K. Highlander, and P. D. Schloss. 2013. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology 79:5112–5120. Olsen, S.R., C.V. Cole, F.S. Watanabe, and L.A. Dean. 1954. Estimation of available phosphorus in soil by extraction with sodium bicarbonate. USDA Cir. No. 939. Schoenau, J.J., and R.E. Karamonos. Sodium Bicarbonate Extractable P, K, and N. pp. 51-58. In: M.R. Carter (ed.), Soil Sampling and Methods of Analysis. 1993. Canadian Society of Soil Science. Ottawa, Ontario, Canada. Walkley, A., and I.A. Black. 1934. An examination of the Degtjareff method for determining soil organic matter and a proposed modification of the chromic acid titration method. Soil Science 37:29-38. Metadata Access Constraints: none Metadata Use Constraints: none annually McMurdo Dry Valleys LTER http://mcmlter.org/ pointOfContact