1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:T20b5,

Surface water samples were collected for subsequent microbial community analyses via PCR and shotgun metagenomics. A YSI EXO2 water quality sonde operated by the Smithsonian Environmental Research Center was used to collect physicochemical conditions at time of sample collection.

Shotgun metagenomic DNA and 16S rRNA microbial genes were amplified as described in Sakowski et al. (in revision). Metagenomic DNA was prepped using the Nextera Flex library prep kit. 16S rRNA libraries were prepped by V3-V4 PCR amplification. Both shotgun metagenome and 16S libraries were sequenced on an Illumina MiSeq.

qPCR of 16S rRNA genes and Viral Ribonucleotide Reductase Genes:
Bacterial and viral abundances were estimated by quantitative PCR. For Ribonucleotide Reductase (RNR) quantification, an environmental RNR amplicon was first cloned into chemically competent Escherichia coli cells using the Zero Blunt PCR Cloning Kit (Thermo Scientific) following the manufacturer's protocol. Environmental samples were quantitated for 16S rRNA and RNR gene copy numbers by comparing to a serial dilution of the cloned E. coli cells at known concentrations. All standards and environmental samples were run in triplicate. Three microliters of sample were combined with UltraPure molecular grade water (Thermo, Inc.), SsoAdvanced Universal SYBR Green Supermix (1x final concentration, Bio-Rad Laboratories, Inc.), Forward primer (0.3 mM final concentration), and Reverse primer (0.3 mM final concentration) to a final volume of 25 mL. Samples were amplified on a CFX96 Real-Time PCR Detection System (Bio-Rad Laboratories, Inc.) with the following conditions: denaturing at 98°C for 10 minutes; 45 cycles of denaturing at 98°C for 10 seconds, annealing at 52°C for 30 seconds, and extension at 72°C for 45 seconds; and a final extension of 72°C for 5 minutes.

16S rRNA amplification and sequencing:
16S rRNA genes were amplified from surface water samples in a 25 mL PCR reaction with the following conditions: three microliters of column-purified DNA were combined with UltraPure molecular grade water (Thermo, Inc.), 10X buffer (1x final concentration), dNTPs (0.1mM each final concentration), 16S forward primer 27F (0.3 mM final concentration), 16S reverse primer PE_16S_V4_E786_R (0.3 mM final concentration), bovine serum albumin (0.02 mg/mL final concentration), and Phusion High-Fidelity DNA Polymerase (0.5U; New England BioLabs, Inc. PCR reactions were combined with 150 mL of 4% UMIL EM90 oil (4% UMIL EM90 oil, 0.05% TritonX-100 v/v in mineral oil; Universal Preserv-A-Chem, Inc.) and emulsified by vortexing at max speed (~2,700 rpm) for one minute on a Vortex Genie 2 (MoBio). Emulsions were loaded as 50 mL aliquots and amplified with the following conditions: denaturation at 94°C for 3 minutes; 33 cycles of denaturation at 94°C for 10 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 45 seconds; and a final extension of 72°C for 5 minutes (C1000, BioRad Labs., Inc.).

PCR oil emulsions were broken with isobutanol. Briefly, PCR aliquots were pooled in a 1.5mL microcentrifuge tube and combined with 100 uL of sterile 5M NaCl solution and 1 mL of isobutanol. Samples were vortexed briefly to mix and centrifuged at 16,000 x g for 1 minute. The bottom aqueous layer was retained, and DNA was purified by spin column purification (Zymo, Inc.). DNA was eluted in 20 uL of Tris-HCl.

Purified DNA was run on a 1.5% agarose gel (UltraPure Agarose, ThermoFisher Scientific). 16S rRNA gene bands were visualized under blue light excitation, extracted, and gel purified (Zymo, Inc.) Purified DNA was eluted into 20 mL of Tris-HCl. Barcodes and Illumina adapters were added to 16S rRNA gene amplicon products in two subsequent limited PCR steps. Barcodes were added as follows: two microliters of purified DNA were combined with UltraPure molecular grade water (Thermo, Inc.), 10X buffer (1x final concentration), dNTPs (0.1mM each final concentration), 16S forward primer PE_16S_V4_U515F (0.3 mM final concentration), 16S rRNA gene reverse primer with 8-mer barcodes PE_IV_XXX (0.3 mM final concentration), and Phusion High-Fidelity DNA Polymerase (0.5U; New England BioLabs, Inc.). Samples were amplified with the following conditions: denaturing at 98°C for 30 seconds; 8 cycles of denaturing at 98°C for 10 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 45 seconds; and a final extension of 72°C for 5 minutes. DNA was purified by spin column purification (Zymo, Inc.) and eluted into 20 mL Tris-HCl. Illumina adapters were then added as above with the following primers: Illumina adapter forward primer PE-III-PCR-F (0.3 mM final concentration) and Illumina adapter reverse primer Barcode_Rev (0.3 mM final concentration). Samples were amplified with the following conditions: denaturing at 98°C for 30 seconds; 5 cycles of denaturing at 98°C for 10 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 45 seconds; and a final extension of 72°C for 5 minutes. DNA was purified by spin column purification (Zymo, Inc.) and eluted into 20 mL Tris-HCl. 16S rRNA gene amplicon libraries were sequenced on an Illumina MiSeq (2 x 300 bp) at the Genetic Core Research Facility at Johns Hopkins University.

Shotgun metagenomic library preparation and sequencing:
Surface water samples were filtered through a 0.2µm PES filter. DNA was extracted from filters for shotgun sequencing from water samples with the DNeasy PowerWater kit (Qiagen) following the manufacturer’s protocol with the following amendment: 20 µL of proteinase K was combined with 1 mL of solution PW1 in the bead tube. The bead tube was incubated at 65°C for ten minutes prior to bead beating. Libraries were prepared with the Nextera DNA Flex Library Prep kit (Illumina, Inc.) following the manufacture's protocol and sequenced on an Illumina MiSeq (2 x 300 bp) at the Genetic Core Research Facility at Johns Hopkins University.

epicPCR of environmental samples:
Surface water glycerol samples (25% v/v) were thawed on ice and one mL was added to three replicate 1.5 mL microcentrifuge tubes per sample. Samples were centrifuged at 25,000 x g for 10 minutes and resuspended after supernatant removal to reduce free viral particles. Thirty microliters of each sample was combined with UltraPure molecular grade water (Thermo, Inc.), 10X buffer (1x final concentration), dNTPs (0.1mM each final concentration), Viral Forward primer (1.0 mM final concentration), Viral Reverse_519R fusion primers (R1 and R2 combined, 0.01 mM each final concentration), 16S Reverseeverse primer (1.0 mM final concentration), bovine serum albumin (0.02 mg/mL final concentration), Tween-20 (0.8% v/v final concentration), and Phusion High-Fidelity DNA Polymerase (1.5U; New England BioLabs, Inc.) to a final volume of 75 mL. PCR reactions were combined with 450 mL of 4% UMIL EM90 oil (4% UMIL EM90 oil, 0.05% TritonX-100 v/v in mineral oil; Universal Preserv-A-Chem, Inc.) and emulsified by vortexing at max speed (~2,700 rpm) for one minute. Emulsions were loaded as 50 mL aliquots and amplified with the following conditions: denaturation at 94°C for 3 minutes; 33 cycles of denaturation at 94°C for 10 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 45 seconds; and a final extension of 72°C for 5 minutes (C1000, BioRad Labs., Inc.).

Amplicons were enriched by nested PCR and subsequently sequenced on a PacBio Sequel with Sequel v3 chemistry (University of Maryland Institute for Genome Sciences). Circular consensus sequences were obtained from raw reads with the following parameters: minimum signal-to-noise ratio (SNR): 3, minimum length: 500bp, minimum passes: 10, minimum read score: 0.75, minimum predicted accuracy: 0.90.

1d:Tde2,NSF Abstract: Viruses in the ocean are 10 times more abundant than bacteria and kill 10-66% of bacterial cells daily. Viral infections of bacteria, such as of photosynthetic cyanobacteria that form the base of the food web, impact the flow of energy and carbon within the marine ecosystem. Thus, viral infections dramatically alter important biogeochemical and ecological factors in the ocean, such as how much carbon dioxide is respired or how many fish the ocean ecosystem can sustain. Despite their importance in the ocean ecosystem, researchers do not know the answer to the most basic question of viral biology for most environmental viruses: which bacteria do different viruses infect? Identifying these infections could help researchers understand more about how viruses shape the ecosystem through infections of keystone microbial species, infections of microbes with unique characteristics, or infection patterns that promote microbial community stability. This project is to develop a cost-effective method to substantially increase the number of infections identified within natural microbial communities. The researchers are applying this novel method to determine viral infections in cyanobacteria in the Chesapeake Bay and compare the results to standard approaches to determine viral infections. This technique can be widely used to transform our understanding of how viruses impact many ecosystems, since it is cost-effective, does not need specialized equipment and can be adapted to target different viral populations. Additionally, this project provides research opportunities for undergraduate and high school students, including underrepresented minority students and women. To develop a high-throughput, culture-independent technique to identify infections in the environment, the researchers are optimizing a previously developed method, emulsion paired concatenation-isolation PCR (epicPCR). Adapting epicPCR for viral-host associations will identify interactions by isolating actively infected single cells within a microdroplet to retain the physical proximity of the host and viral DNA during DNA extraction. Next, fusion PCR is done within the microdroplet to allow host rRNA genes to fuse to viral marker genes, such as g20 or ribonucleotide reductase, retained within the same bead. Only rRNA genes successfully fused to viral markers are amplified. Finally, high-throughput sequencing is done on the resulting fusion products. This approach is cultivation-independent, screens a larger fraction of diversity within the sample than traditional approaches, requires little additional equipment compared to microfluidic approaches, and can be scaled up to hundreds of samples because the amount of sequencing required to deeply sample a single environment is low compared to shotgun metagenomic sequencing. Although this technique will be limited to viral marker genes and suffers from the biases of PCR, it still offers great potential to investigate viral-host interactions across a large number of environments. The method is being applied to determine how viral infections influence cynaobacterial blooms in the Chesapeake Bay. The researchers will also compare the results of epicPCR to culture-based, single-cell, and bioinformatics based methods of host-virus associations to identify biases, limitations and caveats of various approaches. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.6:["$","$L1b",null,{"dataset":{"_id":"757405","description":"

Water quality data, gene copy number counts, and 16S analyses from water samples collected from the Rhode River at the Smithsonian Environmental Research Center (SERC) in Edgewater, MD during 2017 and 2018.

\n","problem":"","acquisition":"$1c","processing":"

Data Processing:
\n16S rRNA sequence data were analyzed using the QIIME2 pipeline. Shotgun metagenomes were assembled with metaSPAdes and binned with metaWRAP as described in Sakowski et al. (in revision).

BCO-DMO Processing Notes:
\n- Split the latitude and longitude values into independent columns;
\n- converted longitude from degrees West to degrees East;
\n- reformatted date and time to ISO8601 convention;
\n- added date-time field in UTC;
\n- modified parameter names to conform with BCO-DMO naming conventions;
\n- blank values replaced with no data value 'nd';
\n- concatenated data files from 2017 and 2018.

\n","bcodmoProcessing":"","title":"Water quality data, gene copy number counts, and 16S analyses from Rhode River samples collected at SERC during 2017 and 2018","nickname":"SERC time series","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"2","version_date":"2020-12-03T05:00:00.000Z","abstract":"Water quality data, gene copy number counts, and 16S analyses from Rhode River samples collected at SERC during 2017 and 2018.","citation":"Preheim, S. (2020) Water quality data, gene copy number counts, and 16S analyses from Rhode River samples collected at SERC during 2017 and 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2020-12-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.757405.2 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.757405.2","versionDate":"2020-12-03","versionId":"2","year":"2020","title":"Water quality data, gene copy number counts, and 16S analyses from Rhode River samples collected at SERC during 2017 and 2018","authors":"Preheim, S.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.757405.2","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2017-05-17T04:00:00.000Z","end":"2018-12-27T05:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1494993600","label":"2017-05-17"},"end":{"value":"1545886800","label":"2018-12-27"}},"spatial_extent":{"shape":"point","center":{"latitude":38.8869,"longitude":-76.5418},"wkt":" POINT (-76.5418 38.8869)","north":0,"east":0,"south":0,"west":0},"dataset_type":["Other Field Results"],"keywords":["oceans"],"data_files":[{"id":"902461","title":"WQ_log.csv","url":"https://datadocs.bco-dmo.org/dataset/757405/file/vmmwyj1ILQ71jg/WQ_log.csv","showTableUrl":"https://www.bco-dmo.org/dataset/757405/data/view/902461","description":"Primary data file for dataset ID 757405","filename":"WQ_log.csv","bytesize":8029,"checksum":{"value":"c0886b6121000810139c015fd09d6d53","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"755239","name":"Sarah Preheim"},"performedAtOrganization":{"_id":"665365","name":"Johns Hopkins University"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"708682","name":"Mathew Biddle"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"51498","name":"Shannon Rauch"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[],"funding":[{"_id":"755236","name":"OCE-1820652","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1820652"}],"instruments":[{"_id":"832990","name":"Illumina MiSeq","description":"","type_id":"649","type_name":"Automated DNA Sequencer","type_desc":"A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.","type_acronym":"Automated Sequencer"},{"_id":"832989","name":"CFX96 Real-Time PCR Detection System","description":"","type_id":"707569","type_name":"qPCR Thermal Cycler","type_desc":"An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).","type_acronym":"qPCR"},{"_id":"757431","name":"YSI EXO2 water quality sonde","description":"YSI EXO2 water quality sonde operated by the Smithsonian Environmental Research Center","type_id":"666","type_name":"YSI Professional Plus Multi-Parameter Probe","type_desc":"The YSI Professional Plus handheld multiparameter meter provides for the measurement of a variety of combinations for dissolved oxygen, conductivity, specific conductance, salinity, resistivity, total dissolved solids (TDS), pH, ORP, pH/ORP combination, ammonium (ammonia), nitrate, chloride and temperature. More information from the manufacturer.","type_acronym":"YSI ProPlus"}],"parameters":[{"_id":"832943","name":"Sample","format":"","frictionlessType":"string","description":"

Sample date and identifer

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"832944","name":"ISO_DateTime_EST","format":"","frictionlessType":"string","description":"

Date and time (EST) of observation formatted to ISO8601 standard: YYYY-MM-DDThh:mm

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"832945","name":"ISO_DateTime_UTC","format":"","frictionlessType":"string","description":"

Date and time (UTC) of observation formatted to ISO8601 standard: YYYY-MM-DDThh:mm

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

"}},{"_id":"832946","name":"Temp","format":"","frictionlessType":"string","description":"

Water Temperature

","units":{"_id":"","name":"degrees Celsius"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"832947","name":"Conductivity","format":"","frictionlessType":"string","description":"

Conductivity

","units":{"_id":"","name":"millisiemens per centimeter (mS/cm)"},"type":{"_id":"779","name":"conductivity","description":"

Conductivity. Units and collection methods may vary. Often reported in Siemens/meter.

When used in a JGOFS/GLOBEC project this is the conductivity in Siemens/meter for the primary conductivity sensor on a CTD.

"}},{"_id":"832948","name":"DO_pcnt","format":"","frictionlessType":"string","description":"

Water Dissolved Oxygen % air saturation

","units":{"_id":"","name":"unitless (percent)"},"type":{"_id":"910","name":"dissolved Oxygen","description":"

dissolved oxygen concentration

"}},{"_id":"832949","name":"Pressure","format":"","frictionlessType":"string","description":"

Water pressure

","units":{"_id":"","name":"psi"},"type":{"_id":"732","name":"pressure","description":"

water pressure at measurement; depth reported as pressure; positive number increasing with water depth

"}},{"_id":"832950","name":"pH","format":"","frictionlessType":"string","description":"

Water pH

","units":{"_id":"","name":"pH scale"},"type":{"_id":"1892","name":"pH","description":"

pH: The measure of the acidity or basicity of an aqueous solution

"}},{"_id":"832951","name":"Chlorophyll_RFU","format":"","frictionlessType":"string","description":"

Water Chlorophyll

","units":{"_id":"","name":"RFU"},"type":{"_id":"766","name":"chlorophyll a","description":"

Total chlorophyll a pigment. See dataset for units of measurement; often reported in: milligrams per cubic meter (mg/m3); micrograms/liter (ug/L); nanograms/liter (ng/L).

CAUTION Within JGOFS MERGED water column products: this parameter is derived from HPLC methodology and the units are nanograms/liter; however; this parameter name is also used for a variety of water and nonwater column sampling; derived via the fluorometric method; units will also vary.

"}},{"_id":"832952","name":"BGA_PE_RFU","format":"","frictionlessType":"string","description":"

Water Total Algae

","units":{"_id":"","name":"RFU"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"832953","name":"FDOM_RFU","format":"","frictionlessType":"string","description":"

Fluorescent Dissolved Organic Matter

","units":{"_id":"","name":"RFU"},"type":{"_id":"835","name":"fluorescence","description":"

Fluorescence. Indirect measure of pigment concentration.

Units and collection method may vary. Units often reported in milligrams/meter^3 (mg/m3) or micromoles per liter (ug/L). Sometimes reported after being calibrated against extracted pigment concentrations.

In JGOFS/GLOBEC projects fluorescence is measured from CTD instrument sensor.

"}},{"_id":"832954","name":"Specific_Conductivity","format":"","frictionlessType":"string","description":"

Water Specific Conductivity

","units":{"_id":"","name":"millisiemens per centimeter (mS/cm)"},"type":{"_id":"1894","name":"specific conductance","description":"

Electrical conductivity is a measure of a water’s ability to conduct electricity, and therefore a measure of the water’s ionic activity and content. The higher the concentration of ionic (dissolved) constituents, the higher the conductivity. Conductivity of the same water changes substantially as its temperature changes. This can have a confounding effect on attempts to compare this feature across different waters, or seasonal changes in this parameter for a particular body of water. The use of specific conductance [SC; units of microSiemens per centimeter (µS·cm-1) or miliSiemens per centimeter (mS·cm-1], the conductivity normalized to temperature of 25 ºC, eliminates this complication and allows valuable comparisons to be made.

"}},{"_id":"832955","name":"Salinity","format":"","frictionlessType":"string","description":"

Water Salinity

","units":{"_id":"","name":"psu"},"type":{"_id":"955","name":"sal","description":"

Salinity: The amount (mass or quantity of matter) of salt per amount (volume or mass) of a body of water.

"}},{"_id":"832956","name":"DO","format":"","frictionlessType":"string","description":"

Water Dissolved Oxygen

","units":{"_id":"","name":"milligrams per Liter (mg/L)"},"type":{"_id":"910","name":"dissolved Oxygen","description":"

dissolved oxygen concentration

"}},{"_id":"832957","name":"Depth","format":"","frictionlessType":"string","description":"

Probe Depth

","units":{"_id":"","name":"meters (m)"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"832958","name":"Turbidity","format":"","frictionlessType":"string","description":"

Water Turbidity

","units":{"_id":"","name":"FNU"},"type":{"_id":"1728","name":"turbidity","description":"

Turbidity is the cloudiness or haziness of a fluid caused by individual particles

"}},{"_id":"832959","name":"Chlorophyll","format":"","frictionlessType":"string","description":"

Water Chlorophyll

","units":{"_id":"","name":"micrograms per Liter (ug/L)"},"type":{"_id":"766","name":"chlorophyll a","description":"

Total chlorophyll a pigment. See dataset for units of measurement; often reported in: milligrams per cubic meter (mg/m3); micrograms/liter (ug/L); nanograms/liter (ng/L).

"}},{"_id":"832960","name":"BGA_PE","format":"","frictionlessType":"string","description":"

Water Total Algae

","units":{"_id":"","name":"micrograms per Liter (ug/L)"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"832961","name":"FDOM","format":"","frictionlessType":"string","description":"

Fluorescent Dissolved Organic Matter

","units":{"_id":"","name":"ppb QSE"},"type":{"_id":"835","name":"fluorescence","description":"

Fluorescence. Indirect measure of pigment concentration.

In JGOFS/GLOBEC projects fluorescence is measured from CTD instrument sensor.

"}},{"_id":"832962","name":"Location","format":"","frictionlessType":"string","description":"

Name of sample site

","units":{"_id":"","name":"unitless"},"type":{"_id":"1124","name":"site","description":"

Sampling site identification.

"}},{"_id":"832963","name":"Lat","format":"","frictionlessType":"string","description":"

Site Latitude with North being positive

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"832964","name":"Lon","format":"","frictionlessType":"string","description":"

Site longitude with west being negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

"}},{"_id":"832965","name":"Instrumentation","format":"","frictionlessType":"string","description":"

Name/type of sensor used for measurements

","units":{"_id":"","name":"unitless"},"type":{"_id":"864","name":"instrument","description":"

instrument used to collect or process data, definition is specific to the data set in which it appears

"}},{"_id":"832966","name":"Sample_ID","format":"","frictionlessType":"string","description":"

Unique Sample Identifier

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"832967","name":"Genes_16S_1","format":"","frictionlessType":"string","description":"

16S qPCR Gene Copy Number Mean

","units":{"_id":"","name":"gene copy nmuber mean per milliliter (per mL)"},"type":{"_id":"680873","name":"genetic_conc","description":"

Concentration or count of genetic material.

"}},{"_id":"832968","name":"Genes_16S_2","format":"","frictionlessType":"string","description":"

16S qPCR Gene Copy Number Standard Error

","units":{"_id":"","name":"gene copy number standard error per mL"},"type":{"_id":"680873","name":"genetic_conc","description":"

Concentration or count of genetic material.

"}},{"_id":"832969","name":"RNR_Genes_1","format":"","frictionlessType":"string","description":"

RNR qPCR Gene Copy Number Mean

","units":{"_id":"","name":"gene copy number mean per mL"},"type":{"_id":"680873","name":"genetic_conc","description":"

Concentration or count of genetic material.

"}},{"_id":"832970","name":"RNR_Genes_2","format":"","frictionlessType":"string","description":"

RNR qPCR Gene Copy Number Standard Error

","units":{"_id":"","name":"gene copy number standard error per mL"},"type":{"_id":"680873","name":"genetic_conc","description":"

Concentration or count of genetic material.

"}},{"_id":"832971","name":"Library_Accession_Number_16S","format":"","frictionlessType":"string","description":"

NCBI Accession Numbers for 16S Libraries

","units":{"_id":"","name":"unitless"},"type":{"_id":"1971","name":"accession number","description":"

Database identifier assigned by repository and linked to GenBank or other repository.

"}},{"_id":"832972","name":"Shotgun_Metagenome_Library_Accession_Number","format":"","frictionlessType":"string","description":"

NCBI Accession Numbers for Shotgun Metagenome Libraries

","units":{"_id":"","name":"unitless"},"type":{"_id":"1971","name":"accession number","description":"

Database identifier assigned by repository and linked to GenBank or other repository.

"}},{"_id":"832973","name":"Fusion_Amplicon_Accession_Numbers","format":"","frictionlessType":"string","description":"

NCBI Accession Numbers for 16S/RNR Fusion Libraries

","units":{"_id":"","name":"unitless"},"type":{"_id":"1971","name":"accession number","description":"

Database identifier assigned by repository and linked to GenBank or other repository.

"}}],"related_publications":[],"related_datasets":[{"_id":"821955","name":"SERC 2019 viral dilution incubations","url":"","relation_type":"IsRelatedTo","type_desc":"

The dataset is related to another dataset.

\n","relation_desc":"","citation":"Preheim, S. (2020) Gene copy number counts and 16S analyses of July 2019 Rhode River surface water incubated with or without viral dilution. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-08-25 doi:10.26008/1912/bco-dmo.821955.1"}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/757405/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/757405/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/757405/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/757405/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"755237","name":"EAGER: High-throughput, culture-independent technique identifying cyanobacteria infections to improve understanding of carbon biogeochemical cycling","acronym":"identify cyano infections","description":"$1d"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.757405.2","url":"https://doi.org/10.26008/1912/bco-dmo.757405.2","date_assigned":"2020-12-07","version_date":"2020-12-03","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":288},"downloads":{"count":320}}},"fileId":"902461"}]