Abigail C. JacksonJesse JornaJohn M. ChastonDiana H. WallByron J. Adams 2021-09-21 tabular digitial data McMurdo Dry Valleys LTER McMurdo Dry Valleys LTER 10.6073/pasta/3380695f50e8f3527c12aba416e86b1f https://mcm.lternet.edu/content/soil-geochemistry-and-microbial-community-data-glaciated-and-potential-glacial-refugia-sites 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. Funding for this work was provided by the National Science Foundation for Long Term Ecological Research, most recently grant #OPP-1637708. 1994-01-03 2019-01-31 ground condition As needed 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 1 241m 1 241m meter 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 241m 241m meter 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 801m 801m meter 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 1 435m 1 435m meter 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 767m 767m meter 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 1 522m 1 522m meter 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 981m 981m meter 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 1 071m 1 071m meter 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 572m 572m meter 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 646m 646m meter 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 706m 706m meter 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 9m 9m meter 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 589m 589m meter 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 873m 873m meter 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 839m 839m meter 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 532m 532m meter 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 852m 852m meter 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 1 537m 1 537m meter LTER Core Areas disturbance inorganic nutrients organic matter population dynamics None <cntperp> <cntper>McMurdo Dry Valleys LTER Information Manager</cntper> </cntperp> <cntemail>im@mcmlter.org</cntemail> Name: Renée F. Brown Role: data manager Not Applicable Not Applicable Field and/or Lab Methods 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. 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. unknown SOILS_REFUGIA_GEOCHEM Geochemistry data DATASET_CODE Internal dataset code. The data provider Internal dataset code. Sequence ID Microbial sequence ID associated with the sample and replicate. The data provider Microbial sequence ID associated with the sample and replicate. Replicate number Sample replicate number. Geochemical parameters were bulked across replicates for each sample. The data provider 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. The data provider 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. The data provider Location where soil sample was collected. VALLEY Valley where soil sample was collected. The data provider Valley where soil sample was collected. SOIL_SAMPLE_ID Code associated with the soil sample. The data provider Code associated with the soil sample. Sequence Tube ID Code written on the sequencing tubes. The data provider Code written on the sequencing tubes. SEASON Field season or seasons when soil sample was collected. The data provider Field season or seasons when soil sample was collected. LATITUDE Latitude of the location where the soil sample was collected. The data provider Latitude of the location where the soil sample was collected. LONGITUDE Longitude of the location where the soil sample was collected. The data provider Longitude of the location where the soil sample was collected. ELEVATION_M Elevation of the location where the soil sample was collected. The data provider meter Distance from coast Distance of the sampling site to the nearest coastline of the continent. The data provider kilometer SITE_CHARACTERIZATION Initial status of the sampling site as a potential refugia or a glaciated (control). The data provider 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. The data provider Designation of the sampling site as a high or low elevation site. Phosphorus Available phosphorus in the soil sample. The data provider milligramsPerLiter (mg/l) Potassium Available potassium in the soil sample. The data provider milligramsPerLiter Soil organic matter Organic matter in the soil sample. The data provider milligramsPerLiter pH pH of the soil sample. The data provider pH of the soil sample. Electric conductivity Electric conductivity of the soil sample. The data provider microSiemensPerCentimeter Nitrate Available nitrate as nitrogen in the soil sample. The data provider milligramsPerLiter Gravimetric water content Gravimetric water content of the soil sample. The data provider percent BioProject Accession NCBI BioProject accession number associated with the sample. The data provider NCBI BioProject accession number associated with the sample. BioSample Accession NCBI BioSample accession number associated with the sample. The data provider NCBI BioSample accession number associated with the sample. McMurdo Dry Valleys LTER The data distributor shall not be liable for innacuracies in the content http 1 0 1 column , https://mcm.lternet.edu/sites/default/files/data/mcmlter-soil-jackson-refugia_geochem-20211118.csv None SOILS_REFUGIA_TAXA 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.  McMurdo Dry Valleys LTER The data distributor shall not be liable for innacuracies in the content http 1 0 1 column , https://mcm.lternet.edu/sites/default/files/data/mcmlter-soil-jackson-refugia_taxa-20211118.zip None 2021-09-21 2021-09-21 McMurdo Dry Valleys LTER http://mcmlter.org/ Biological Data Profile of the Content Standards for Digital Geospatial Metadata devised by the Federal Geographic Data Committee. 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