characteristics.text: mgm4440040.3
characteristics.characteristic: BROKER_OBJECT_ID
characteristics.text: ERC000024
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-10-11T17:03:08Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-09-20T18:15:15Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104312531
characteristics.characteristic: External Id
characteristics.text: San Diego State University
characteristics.characteristic: INSDC center name
characteristics.text: 2018-10-11T17:03:08Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-09-20T18:15:15Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1937509
characteristics.characteristic: SRA accession
characteristics.text: mgs15104
characteristics.characteristic: Submitter Id
characteristics.text: MGRAST
characteristics.characteristic: broker name
characteristics.text: 2005-08-18
characteristics.characteristic: collection date
characteristics.text: UTC
characteristics.characteristic: collection_timezone
characteristics.text: mgs15104 Taxonomy ID:408172
characteristics.characteristic: description
characteristics.text: 56 M
characteristics.characteristic: diss_org_carb
characteristics.text: ERS1937140
characteristics.characteristic: ebi_id
characteristics.text: marine habitat
characteristics.characteristic: environment (biome)
characteristics.text: marine habitat
characteristics.characteristic: environment (feature)
characteristics.text: marine habitat
characteristics.characteristic: environment (material)
characteristics.text: water
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CHEBI_15377
characteristics.characteristic: environmental package
characteristics.text: wgs_84
characteristics.characteristic: geodetic_system
characteristics.text: USA
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: ~10
characteristics.unit: m
characteristics.characteristic: geographic location (depth)
characteristics.text: 5.866944
characteristics.unit: DD
characteristics.characteristic: geographic location (latitude)
characteristics.text: -162.1278
characteristics.unit: DD
characteristics.characteristic: geographic location (longitude)
characteristics.text: Palmyra Atoll
characteristics.characteristic: geographic location (region and locality)
characteristics.text: metagenome
characteristics.characteristic: investigation type
characteristics.text: 18301735
characteristics.characteristic: isol_growth_condt
characteristics.text: marine
characteristics.characteristic: metagenome_taxonomy
characteristics.text: marine metagenome
characteristics.characteristic: organism
characteristics.text: Northern Line Islands
characteristics.characteristic: project name
characteristics.text: filtering
characteristics.characteristic: samp mat process
characteristics.text: The water for the metagenomes was collected from below the boundary layer (in crevices and against the benthos) to avoid confounding problems with the water column. The sampling was conducted at the same time of day to help minimize diurnal effects. The water was collected from over ~20 m2 of reef using a modified bilge pump connected to low density polyethylene (LDPE) collapsible bags (19 l; Cole-Parmer, Vernon Hills, IL; Figure S1). 1) A large fraction containing mostly microbes, some small eukaryotes (such as dinoflagellates and protists), and a few VLPs, and 2) a small fraction containing mostly VLPs and some small microbes. To obtain these fractions the seawater was processed through a series of filters. The large eukaryotes were removed by filtering the entire sample through 100 m Nitex, into a barrel lined with a clean, high-density polyethylene bag. The filtrate was then concentrated to ~500 ml on a 100 kDa tangential flow filter (TFF), which captured the unicellular eukaryotes, microbes and VLPs (i.e., the water was removed). During the filtration, pressures were kept below 0.6 bar (10 psi) to ensure that the viruses were not destroyed. The concentrated sample was then passed through 0.45 m Sterivex filters (Millipore, Inc) using a 50 ml syringe. In this step, the large metagenomic fraction consisting of microbial cells was caught on the filter (microbiomes) and the filtrate was the small metagenomic fraction (viromes). All filtrations were performed on the research vessel, and the samples were stored for further processing in the laboratory at SDSU. The Sterivex filters were frozen at −80C. The 0.45 m filtrates (i.e., the virome) were extracted with chloroform to kill any residual cells (10% vol:vol; most viruses are resistant to chloroform) and stored at 4C. The viruses in the small metagenomic fractions (i.e., 0.45 m filtrate treated with chloroform) were purified using cesium chloride (CsCl) step gradients to remove free DNA and any cellular material [29], [30]. Viral DNA was isolated using CTAB/phenol:chloroform extractions and amplified in six to eight 18-hour Genomiphi reactions. These reactions were pooled and purified using silica columns (Qiagen Inc, Valencia, CA). The DNA was then precipitated with ethanol and re-suspended in water at a concentration of approximately 300 ng l−1.
characteristics.characteristic: samp_collect_device
characteristics.text: 150 litres
characteristics.characteristic: samp_size
characteristics.text: marine metagenome
characteristics.characteristic: scientific_name
characteristics.text: 454
characteristics.characteristic: sequencing method
characteristics.text: 1.010^63.710^5 VLPs ml−1
characteristics.characteristic: suspend_part_matter
characteristics.text: mgs15104 Taxonomy ID:408172
characteristics.characteristic: title
characteristics.text: water
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CHEBI_15377
characteristics.characteristic: water environmental package