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