organism: marine metagenome
description: mgs15659 Taxonomy ID:408172
attributes.tag: BROKER_OBJECT_ID
attributes.value: mgm4440280.3
attributes.tag: ENA first public
attributes.value: 2018-10-11
attributes.tag: ENA last update
attributes.value: 2017-09-20
attributes.tag: External Id
attributes.value: SAMEA104312530
attributes.tag: INSDC center alias
attributes.value: San Diego State University
attributes.tag: INSDC center name
attributes.value: San Diego State University
attributes.tag: INSDC first public
attributes.value: 2018-10-11T17:03:08Z
attributes.tag: INSDC last update
attributes.value: 2017-09-20T18:15:15Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: mgs15659
attributes.tag: broker name
attributes.value: Metagenomics RAST Server
attributes.tag: collection date
attributes.value: 2005-08-11
attributes.tag: collection_timezone
attributes.value: UTC
attributes.tag: diss_org_carb
attributes.value: 42 M
attributes.tag: ebi_id
attributes.value: ERS1937135
attributes.tag: environment (biome)
attributes.value: marine habitat
attributes.tag: environment (feature)
attributes.value: marine habitat
attributes.tag: environment (material)
attributes.value: marine habitat
attributes.tag: environmental package
attributes.value: water
attributes.tag: geodetic_system
attributes.value: wgs_84
attributes.tag: geographic location (country and/or sea)
attributes.value: USA
attributes.tag: geographic location (depth)
attributes.value: ~10
attributes.tag: geographic location (latitude)
attributes.value: 3.82595000
attributes.tag: geographic location (longitude)
attributes.value: -159.34956667
attributes.tag: geographic location (region and locality)
attributes.value: Fanning (Tabuaeran) Atoll
attributes.tag: investigation type
attributes.value: metagenome
attributes.tag: isol_growth_condt
attributes.value: 18301735
attributes.tag: metagenome_taxonomy
attributes.value: marine
attributes.tag: project name
attributes.value: Northern Line Islands
attributes.tag: samp mat process
attributes.value: filtering
attributes.tag: samp_collect_device
attributes.value: 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.
attributes.tag: samp_size
attributes.value: 150 litres
attributes.tag: sample name
attributes.value: mgs15659
attributes.tag: sequencing method
attributes.value: 454
attributes.tag: suspend_part_matter
attributes.value: 2.510^61.210^6 VLPs ml−1
attributes.tag: water environmental package
attributes.value: water