Scott GeorgeNoah FiererJoseph S. LevyByron J. Adams 2020-12-15 tabular digitial data McMurdo Dry Valleys LTER McMurdo Dry Valleys LTER 10.6073/pasta/a98c5ce00cc51d5424b07aebcfcf9f74 https://mcm.lternet.edu/content/operational-taxonomic-unit-otu-table-characterizing-water-track-and-adjacent-soil-microbial This data package includes the abundance of microbial operational taxonomic units (OTUs) for samples collected during the austral summer of 2012-2013 in the Lake Hoare and Goldman Glacier Basins of Taylor Valley, Antarctica. A total of twenty samples from on- and off-water track soils were collected and analyzed. Samples were collected from the Lake Hoare Basin on 27 December 2012 and from the Goldman Glacier Basin on 4 January 2013. The aim of the study was to identify how variation in the measured physical and chemical environment of water tracks within the two water track systems influenced soil microbial community structure and diversity. Soil bacterial biodiversity was assessed using cultivation independent 16S rRNA gene sequencing. Funding for this study was provided by the National Science Foundation (NSF) as follows:NSF OPP-1637708, LTER: ecosystem Response to Amplified Landscape Connectivity in the McMurdo Dry Valleys, Antarctica, PI: Michael N. GooseffNSF OPP-1341629, Collaborative Research: The Role of Glacial History on the Structure and Functioning of Ecological Communities in the Shackleton Glacier Region of the Transantarctic Mountains, PI: Noah FiererNSF OPP-1847067, CAREER: Linking Antarctic Cold Desert Groundwater to Thermokarst & Chemical Weathering in Partnership with the Geoscience UAV Academy, PI: Joseph S. Levy 2012-12-27 2013-01-04 ground condition As needed Sample A1SLH, where "A1" represents sample 1, collected off the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.940600000000 162.940600000000 -77.639300000000 -77.639300000000 Sample "A2SLH," where "A2" represents sample 2, collected off the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.930300000000 162.930300000000 -77.642800000000 -77.642800000000 Sample A3SGG, where "A3" represents sample 3, collected off the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.925000000000 162.925000000000 -77.666900000000 -77.666900000000 Sample A4WTGG, where "A4" represents sample 4, collected on the water track in Goldman Basin. Coordinates provided by Scott George in December 2020. 162.925800000000 162.925800000000 -77.666800000000 -77.666800000000 Sample A5SLH, where "A5" represents sample 5, collected off the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.934000000000 162.934000000000 -77.632600000000 -77.632600000000 Sample A6WTLH, where "A6" represents sample 6, collected on the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.930000000000 162.930000000000 -77.642700000000 -77.642700000000 Sample A7WTLH, where "A7" represents sample 7, collected on the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.917700000000 162.917700000000 -77.645800000000 -77.645800000000 Sample A8SGG, where "A8" represents sample 8, collected off the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.926200000000 162.926200000000 -77.669000000000 -77.669000000000 Sample A9WTLH, where "A9" represents sample 9, collected on the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.935400000000 162.935400000000 -77.636400000000 -77.636400000000 Sample A10WTLH, where "A10" represents sample 10, collected on the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.940400000000 162.940400000000 -77.639200000000 -77.639200000000 Sample A11WTGG, where "A11" represents sample 11, collected on the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.932500000000 162.932500000000 -77.672000000000 -77.672000000000 Sample A12SLH, where "A12" represents sample 12, collected off the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.918200000000 162.918200000000 -77.646000000000 -77.646000000000 Sample A13WTLH, where "A13" represents sample 13, collected on the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.935100000000 162.935100000000 -77.634500000000 -77.634500000000 Sample A14SLH, where "A14" represents sample 14, collected off the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.935900000000 162.935900000000 -77.636300000000 -77.636300000000 Sample A15WTGG, where "A15" represents sample 15, collected on the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.925600000000 162.925600000000 -77.669000000000 -77.669000000000 Sample A16WTGG, where "A16" represents sample 16, collected on the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.925300000000 162.925300000000 -77.664400000000 -77.664400000000 Sample A17WTLH, where "A17" represents sample 17, collected on the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.935300000000 162.935300000000 -77.636400000000 -77.636400000000 Sample A18SLH, where "A18" represents sample 18, collected off the water track in Lake Hoare Basin. Coordinates provided by Scott George in December 2020. 162.934000000000 162.934000000000 -77.632600000000 -77.632600000000 Sample A19SGG, where "A19" represents sample 19, collected off the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.932200000000 162.932200000000 -77.672100000000 -77.672100000000 Sample A20SGG, where "A20" represents sample 20, collected off the water track in Goldman Glacier Basin. Coordinates provided by Scott George in December 2020. 162.926600000000 162.926600000000 -77.664400000000 -77.664400000000 LTER Core Areas population dynamics None <cntperp> <cntper>McMurdo Dry Valleys LTER Information Manager</cntper> </cntperp> <cntemail>im@mcmlter.org</cntemail> Name: Nicholas B. Dragone Role: lab technician Name: Angela Oliverio Role: lab technician Name: Renée F. Brown Role: data manager Not Applicable Not Applicable Field and/or Lab Methods As described in the associated manuscript, soil samples and pore water were collected from the upper 10 cm of the soil horizon using aseptic techniques, and were stored in sterile Whirl-Pack bags at -20°C until processing. Sediment and pore water collected from the darkened portions of water tracks were designated “on-track,” and samples from adjacent lighter soils were classified as “off-track.” Off-track samples were located at least 5 m from the current edge of the water tracks. Wet, on-track soils have a typical albedo of 0.15, while off-track soil albedo is generally 0.22, making them readily distinguishable in the field. DNA extraction and microbial community analyses were conducted using the cultivation-independent 16S rRNA gene sequencing approach as described in Prober et al., 2015 (doi: 10.1111/ele.12381). Total genomic DNA was extracted from each sample using the MoBio PowerSoil DNA Isolation Kit. For microbial analyses, the 4v hypervariable region of the 16S rRNA gene was PCR amplified using the 515f and 806f primer pair which captures both Bacteria and Archaea. Three PCRs were run per sample, with the amplicons from the replicate reactions pooled. Each primer pair included Illumina adapters and 12-bp error-correcting barcodes unique to each sample, as described in the Earth Microbiome Project protocol (Thompson et al., 2017; doi: 10.1038/nature24621). After gel visualization to confirm amplification, PicoGreen dsDNA assay was used to quantify amplicon yields. The amplicons were then pooled together in equimolar concentrations for sequencing on the Illumina MiSeq instrument. DNA sequencing was completed at the University of Colorado Next Generation Sequencing Facility using the 2x150pb paired-end sequencing chemistry. Four DNA extraction and for no-template PCR ‘blanks’ were included in the run to check for potential contamination. Sequences were demultiplexed using a custom Python script (‘prep_fastq_for_uparse.py’, at: https://github.com/leffj/helper-code-for-uparse), with the UPARSE pipeline used for quality filtering and phylotype (i.e. operational taxonomic unit) clustering. Quality filtering was conducted using a maximum e-value of 0.5 with paired-end sequences merged prior to downstream processing. Representative sequences from returned phylotypes that were not ≥75% similar to sequences contained in the Greengenes database were removed; afterwards the raw sequences were mapped to phylotypes at a 97% similarity cutoff. Taxonomic classification of each phylotype was determined using the Ribosomal Database Project classifier against the Greengenes database with a confidence threshold of 0.5. The OTU table for which this metadata describes is the result. The OTU table and eDNA sequences used for this study were from a legacy project, from which only the OTU table remained. As described in the associated manuscript, soil samples and pore water were collected from the upper 10 cm of the soil horizon using aseptic techniques, and were stored in sterile Whirl-Pack bags at -20°C until processing. Sediment and pore water collected from the darkened portions of water tracks were designated “on-track,” and samples from adjacent lighter soils were classified as “off-track.” Off-track samples were located at least 5 m from the current edge of the water tracks. Wet, on-track soils have a typical albedo of 0.15, while off-track soil albedo is generally 0.22, making them readily distinguishable in the field.DNA extraction and microbial community analyses were conducted using the cultivation-independent 16S rRNA gene sequencing approach as described in Prober et al., 2015 (doi: 10.1111/ele.12381). Total genomic DNA was extracted from each sample using the MoBio PowerSoil DNA Isolation Kit. For microbial analyses, the 4v hypervariable region of the 16S rRNA gene was PCR amplified using the 515f and 806f primer pair which captures both Bacteria and Archaea. Three PCRs were run per sample, with the amplicons from the replicate reactions pooled. Each primer pair included Illumina adapters and 12-bp error-correcting barcodes unique to each sample, as described in the Earth Microbiome Project protocol (Thompson et al., 2017; doi: 10.1038/nature24621). After gel visualization to confirm amplification, PicoGreen dsDNA assay was used to quantify amplicon yields. The amplicons were then pooled together in equimolar concentrations for sequencing on the Illumina MiSeq instrument. DNA sequencing was completed at the University of Colorado Next Generation Sequencing Facility using the 2x150pb paired-end sequencing chemistry. Four DNA extraction and for no-template PCR ‘blanks’ were included in the run to check for potential contamination.Sequences were demultiplexed using a custom Python script (‘prep_fastq_for_uparse.py’, at: https://github.com/leffj/helper-code-for-uparse), with the UPARSE pipeline used for quality filtering and phylotype (i.e. operational taxonomic unit) clustering. Quality filtering was conducted using a maximum e-value of 0.5 with paired-end sequences merged prior to downstream processing. Representative sequences from returned phylotypes that were not ≥75% similar to sequences contained in the Greengenes database were removed; afterwards the raw sequences were mapped to phylotypes at a 97% similarity cutoff. Taxonomic classification of each phylotype was determined using the Ribosomal Database Project classifier against the Greengenes database with a confidence threshold of 0.5. The OTU table for which this metadata describes is the result.The OTU table and eDNA sequences used for this study were from a legacy project, from which only the OTU table remained. unknown SOILS_WT_OTU OTU Table Dataset code Internal dataset code The data provider Internal dataset code Operational Taxonomic Unit ID The operational taxonomic unit ID (e.g., “OTU_137”). The data provider The operational taxonomic unit ID (e.g., “OTU_137”). Sample A1SLH Sample A1SLH, where "A1" represents sample 1, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A1SLH, where "A1" represents sample 1, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. A2SLH Sample A2SLH, where "A2" represents sample 2, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A2SLH, where "A2" represents sample 2, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A3SGG Sample A3SGG, where "A3" represents sample 3, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A3SGG, where "A3" represents sample 3, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A4WTGG Sample A4WTGG, where "A4" represents sample 4, collected on the water track in Goldman Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A4WTGG, where "A4" represents sample 4, collected on the water track in Goldman Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A5SLH Sample A5SLH, where "A5" represents sample 5, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A5SLH, where "A5" represents sample 5, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A6WTLH Sample A6WTLH, where "A6" represents sample 6, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A6WTLH, where "A6" represents sample 6, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A7WTLH Sample A7WTLH, where "A7" represents sample 7, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A7WTLH, where "A7" represents sample 7, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A8SGG Sample A8SGG, where "A8" represents sample 8, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A8SGG, where "A8" represents sample 8, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A9WTLH Sample A9WTLH, where "A9" represents sample 9, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A9WTLH, where "A9" represents sample 9, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A10WTLH Sample A10WTLH, where "A10" represents sample 10, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A10WTLH, where "A10" represents sample 10, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A11WTGG Sample A11WTGG, where "A11" represents sample 11, collected on the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A11WTGG, where "A11" represents sample 11, collected on the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A12SLH Sample A12SLH, where "A12" represents sample 12, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A12SLH, where "A12" represents sample 12, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A13WTLH Sample A13WTLH, where "A13" represents sample 13, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A13WTLH, where "A13" represents sample 13, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A14SLH Sample A14SLH, where "A14" represents sample 14, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A14SLH, where "A14" represents sample 14, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A15WTGG Sample A15WTGG, where "A15" represents sample 15, collected on the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A15WTGG, where "A15" represents sample 15, collected on the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A16WTGG Sample A16WTGG, where "A16" represents sample 16, collected on the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A16WTGG, where "A16" represents sample 16, collected on the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A17WTLH Sample A17WTLH, where "A17" represents sample 17, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A17WTLH, where "A17" represents sample 17, collected on the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A18SLH Sample A18SLH, where "A18" represents sample 18, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A18SLH, where "A18" represents sample 18, collected off the water track in Lake Hoare Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A19SGG Sample A19SGG, where "A19" represents sample 19, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A19SGG, where "A19" represents sample 19, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Sample A20SGG Sample A20SGG, where "A20" represents sample 20, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. The data provider Sample A20SGG, where "A20" represents sample 20, collected off the water track in Goldman Glacier Basin. Values represent the number of raw (i.e., not rarefied) sequence reads for each OTU within this sample. Taxonomic Domain Taxonomic Domain of the OTU (e.g., “k_Bacteria”). Unclassified values indicated by “Unclassified”. The data provider Taxonomic Domain of the OTU (e.g., “k_Bacteria”). Unclassified values indicated by “Unclassified”. Taxonomic Phylum Taxonomic Phylum of the OTU (i.e. “p_Proteobacteria”). Missing values indicated by blank cell. The data provider Taxonomic Phylum of the OTU (i.e. “p_Proteobacteria”). Missing values indicated by blank cell. Taxonomic Class Taxonomic Class of the OTU (e.g., “c_Gammaproteobacteria”). Missing values indicated by blank cell, or “c__” if class could not be identified. The data provider Taxonomic Class of the OTU (e.g., “c_Gammaproteobacteria”). Missing values indicated by blank cell, or “c__” if class could not be identified. Taxonomic Order Taxonomic Order of the OTU (e.g., “o_Pseudomonadales”). Missing values indicated by blank cell, or “o__” if order could not be identified. The data provider Taxonomic Order of the OTU (e.g., “o_Pseudomonadales”). Missing values indicated by blank cell, or “o__” if order could not be identified. Taxonomic Family Taxonomic Family of the OTU (e.g., “f_Pseudomonadaceae”). Missing values indicated by blank cell, or “f__” if family could not be identified. The data provider Taxonomic Family of the OTU (e.g., “f_Pseudomonadaceae”). Missing values indicated by blank cell, or “f__” if family could not be identified. Taxonomic Genus Taxonomic Genus of the OTU (e.g., “g_Pseudomonas”). Missing values indicated by blank cell, or “g__” if genus could not be identified. The data provider Taxonomic Genus of the OTU (e.g., “g_Pseudomonas”). Missing values indicated by blank cell, or “g__” if genus could not be identified. Taxonomic Species Taxonomic Species of the OTU (e.g., “s_viridiflava”). Missing values indicated by blank cell, or “s__” if species could not be identified. The data provider Taxonomic Species of the OTU (e.g., “s_viridiflava”). Missing values indicated by blank cell, or “s__” if species could not be identified. 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/SOILS_WT_OTU.csv None 2020-12-15 2020-12-15 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. Drupal Ecological information Management Systems, version D7, Biological Data Profile module