Metagenomic, metatranscriptomics and 16S rRNA gene sequence data from diel sampling at Groves Creek Marsh, Skidaway Island, GA during July 2014 (NCEI Accession 0278832)
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title: Metagenomic, metatranscriptomics and 16S rRNA gene sequence data from diel sampling at Groves Creek Marsh, Skidaway Island, GA during July 2014 (NCEI Accession 0278832)
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abstract: This dataset contains chemical and physical data collected at Groves Creek - SkIO during deployment Groves_Creek_2013-2015 from 2014-07-16 to 2014-07-17. These data include Total Dissolved Nitrogen, density, depth, dissolved organic Carbon, salinity calculated from CTD primary sensors, and water temperature. The instruments used to collect these data include Liquid Scintillation Counter, Niskin bottle, Nutrient Autoanalyzer, Shimadzu TOC-V Analyzer, Spectrophotometer, YSI Professional Plus Multi-Parameter Probe, and YSI Sonde 6-Series. These data were collected by Alison Buchan of University of Tennessee as part of the "Collaborative Research: Marine priming effect - molecular mechanisms for the biomineralization of terrigenous dissolved organic matter in the ocean (Marine priming effect)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-03-19. The following is the text of the dataset description provided by BCO-DMO: Metagenomic, metatranscriptomics and 16S rRNA gene sequence data from Groves Creek diel sampling Dataset Description: Groves Creek Marsh (31.972° N, 81.028° W), a temperate salt marsh fringing Skidaway Island, GA served as the field site for this study. During July 16-17, 2014, samples were collected every two hours and four minutes to evenly sample across two tidal cycles and one diurnal cycle. This dataset contains the environmental observations related to the genetic data found at the Joint Genome Institute (JGI) at the following url: https://genome.jgi.doe.gov/portal/Geometdatstreams/Geometdatstreams.info.html?core=genome&query=Geometdatstreams&searchIn=Anything&searchType=Proposals&showAll=false&externallySequenced=true&sortBy=displayNameStr&showRestricted=true&showOnlyPublished=false&showSuperseded=true&sortOrder=asc&rawQuery=false&showFungalOnly=false&activateHighlights=false&programName=all&programYear=all&superkingdom=--any--&status=--any--&scientificProgram=--any--&productCategory=--any--&start=0&rows=50&page=1 (last visited: 2019-03-18)
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title: Buchan, A. (2019) Metagenomic, metatranscriptomics and 16S rRNA gene sequence data from diel sampling at Groves Creek Marsh, Skidaway Island, GA during July 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Dataset version 2019-03-19. https://doi.org/10.1575/1912/bco-dmo.762443.1
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Anchor: http://lod.bco-dmo.org/id/person/51331 Alison Buchan
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LanguageCode: eng; USA
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topicCategory: (MD_TopicCategoryCode) environment
topicCategory: (MD_TopicCategoryCode) oceans
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westBoundLongitude: -81.028
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beginPosition: 2014-07-16
endPosition: 2014-07-17
supplementalInformation: Acquisition Description: Sample collection Surface water samples were collected from approximately 1 m depth using a hand deployed Niskin bottle. Samples for dissolved constituents (dissolved organic carbon, colored dissolved organic matter, and nutrient analyses) were filtered on site through 0.2 m Polycap filters within minutes of collection and then transported to the laboratory for further processing. For cell counts by flow cytometry, samples were transported to the laboratory and fixed using 25% glutaraldehyde. For additional microbial analyses (microbial biomass collection for DNA and RNA extractions and bacterial production) were returned to the laboratory, which was within 10 minutes’ drive of the field site. Salinity was measured for discrete samples collected in the field using a handheld multiparameter probe (YSI, Pro2030). Depth was recorded using a YSI 600OMS V2 Optical Monitoring Sonde deployed on the creek bed. Microbial community analysis sample collection Planktonic microbial cells from surface water samples were collected by filtration. Water was pre-filtered through a GF/D glass fiber filter (~2.7 μM pore size, Whatman, GE Healthcare Life Sciences, Marlborough, MA); 500 mL of the filtrate was passed through a 0.22 μM pore size, 47 mm diameter filter (Millipore, Burlington, MA). Filtration was completed within 30 min of sample collection. After filtration all filters were placed in cryovials and flash frozen in liquid nitrogen. The samples were stored at -80 C until processing. Microbial community analysis sample processing Nucleic acids were extracted from samples following standard methodology. Briefly, for DNA the filters were thawed and placed in a 2 mL tube with 0.3 g glass and zirconia beads (0.2 g glass and 0.1 g zirconia), 0.75 mL CTAB extraction buffer, 0.75 mL phenol:chloroform:isoamyl alcohol (25:24:1, pH 8), internal standards, proteinase K, 10% SDS, and lysozyme for DNA extractions. Samples were vortexed for 10 min to lyse the cells. For RNA extraction, sample tubes were centrifuged for 10 min at 10,000 rpm and 4° C. The lysates were transferred to a sterile 1.5 mL microcentrifuge tube and mixed with 0.75 mL chloroform:isoamyl alcohol (24:1). The aqueous phase was added to a sterile 1.5 mL microcentrifuge with MgCl2, sodium acetate, and isopropanol. This solution was incubated at -80° C for 1.5 hours and then centrifuged at 4° C for 45 min at 10,000 rpm. The supernatant was discarded, and the RNA was washed with 70% EtOH twice. Following RNA extraction Turbo DNase was used to remove residual DNA. For metagenomic samples the lysate was centrifuged at 5,000 rpm for 5 min and washed twice with 0.5 mL of chloroform:isoamyl alcohol by centrifugation at 15,000 rpm for 5 min. The upper aqueous phase was incubated with isopropanol at room temperature for 2 hrs. The DNA was precipitated by centrifugation at 10,000 rpm for an hour and washed with 70% EtOH twice. All sequencing, assembly, and annotation was performed by the DOE Joint Genome Institute (JGI). JGI generated 16S rRNA libraries, metagenomes, and metatranscriptomes. Plate-based DNA library preparation for Illumina sequencing was performed on the PerkinElmer Sciclone NGS robotic liquid handling system using Kapa Biosystems library preparation kit. DNA was sheared to 300 base pairs (bp) using the Covaris LE220 focused-ultrasonicator and size selected using SPRI beads (Beckman Coulter). The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) containing a unique molecular index barcode for each sample library. qPCR was used to determine the concentration of the libraries and were sequenced on the Illumina HiSeq-2500 to yield 150 bp paired-end reads at the DOE Joint Genome Institute. Quality filtered metagenomic sequences for each sample were assembled with metaSPAdes (version 3.10.1; and all contigs >200 bp were uploaded and annotated by the Integrated Microbial Genomes (IMG) pipeline. For metatranscriptomes, a plate-based RNA sample preparation was performed on the PerkinElmer Sciclone NGS robotic liquid handling system using the Illumina Ribo-Zero rRNA Removal Kit (bacteria) and the TruSeq Stranded Total RNA HT sample prep kit following the protocol outlined by Illumina. Total RNA starting material consisted of 100 ng per sample and included 10 cycles of PCR for library amplification. Illumina sequencing was performed as described for metagenome samples. Quality filtered metatranscriptomic sequences for each sample were assembled with Megahit (version 1.10.6), and all contigs > 200 bp were annotated as described for the metagenome samples. Datasets which had assemblies for which the N50 was greater than three standard deviations from mean were not included in further analyses (Supplemental Tables 1 and 2) Resultant assemblies were combined with coding sequences (CDS) using bedtools2 (version 2.27.0) in order to generate an assembly with CDS embedded. Quality controlled raw reads were mapped to the assembly with gene features using bowtie2 (version 2.2.9). Coverage information on the number of reads mapping to each contig was generated using pileup in the BBmap suite of tools. The coverage information was used to normalize read counts to account for the length of reads and the length of CDS. Read counts within KEGG ortholog groups (KO) were summed and normalized as read counts per million mapped to KO-annotated contigs (genes per million [GPM], transcripts per million [TPM]). GPM and TPM were also used in taxonomic analyses.
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Anchor: https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1730 NOAA National Centers for Environmental Information
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electronicMailAddress: NCEI.Info@noaa.gov
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fees: In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
orderingInstructions: Contact NCEI for other distribution options and instructions.
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description: NCEI Accession 0278832 v1.1 was published.
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DateTime: 2023-05-27T05:11:30Z
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acquisitionInformation: (MI_AcquisitionInformation)
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code: multi-parameter water quality sensor
type: multi-parameter water quality sensor
description: used to measure temperature, salinity, dissolved oxygen, and other parameters Instrument used to measure temperature, salinity, dissolved oxygen, and other parameters, often used to measure water quality parameters. Can be a hand-held instrument or a sonde for unattended monitoring. Often used in coastal water monitoring stations. YSI is the preeminent brand (as of 2024).
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code: Niskin bottle
type: Niskin bottle
description: Device for obtaining samples of seawater at a specific depth Why special entry for Niskin bottle but no entry for Nansen bottle?
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code: nutrient autoanalyzer
type: nutrient autoanalyzer
description: Laboratory Instrument Nutrient Autoanalyzer is a generic term describing an automated flow-thru system used to conduct analyses of several different nutrients (nitrate, ammonium, orthophosphate, and silicate) simultaneously from a seawater sample. For example: SEAL AutoAnalyzer 3 HR Continuous Segmented Flow Analyzer
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code: scintillation counter
type: scintillation counter
description: measures ionizing radiation A scintillation counter is an instrument for detecting and measuring ionizing radiation by using the excitation effect of incident radiation on a scintillating material, and detecting the resultant light pulses.
instrument: (MI_Instrument)
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code: spectrophotometer
type: spectrophotometer
description: spectrophotometer, optical spectrometer, spectrograph or spectroscope An optical spectrometer (spectrophotometer, spectrograph or spectroscope) is an instrument used to measure properties of light over a specific portion of the electromagnetic spectrum, typically used in spectroscopic analysis to identify materials. Butler, L. R. P.; Laqua, K. (1995). "Nomenclature, symbols, units and their usage in spectrochemical analysis-IX. Instrumentation for the spectral dispersion and isolation of optical radiation (IUPAC Recommendations 1995)". Pure Appl. Chem. IUPAC. 67 (10): 1725–1744. doi:10.1351/pac199567101725. A spectrometer is the general term for describing a combination of spectral apparatus with one or more detectors to measure the intensity of one or more spectral bands."
