sea anemone metagenome
project_name
Preliminary assessment of Edwardsiella andrillae Microbiome
submitted_to_insdc
NCBI-SRA
investigation_type
miens-survey
geo_loc_name
Antarctica: Coulman High Site, Ross Ice Shelf
lat_lon
77.5266667 S 171.3350000 E
collection_date
2010-12
env_biome
ice shelf
env_feature
ice shelf bottom
env_material
ice and seawater
env_package
host-associated
host
Edwardsiella andrillae
subspecf_gen_lin
bacteria
source_mat_id
Anemone.E.A.4
oxy_stat_samp
aerobic
samp_collect_device
ROV SCINI
samp_mat_process
preserved in ethanol
samp_size
1 individual
nucl_acid_ext
http://www.ncbi.nlm.nih.gov/pubmed/8979338
nucl_acid_amp
A single-step 30 cycle PCR using HotStarTaq Plus Master Mix Kit (Qiagen, Valencia, CA) were used under the following conditions: 94oC for 3 minutes, followed by 28 cycles of 94oC for 30 seconds; 53oC for 40 seconds and 72oC for 1 minute; after which a final elongation step at 72oC for 5 minutes was performed. Following PCR, all amplicon products from different samples were mixed in equal concentrations and purified using Agencourt Ampure beads (Agencourt Bioscience Corporation, MA, USA). Samples were sequenced utilizing Roche 454 FLX titanium instruments and reagents and following manufacturer’s guidelines
target_gene
16S rRNA
target_subfragment
V1-2
seq_meth
454 pyrosequencing
pcr_primers
27Fmod:GRGTTTGATCMTGGCTCAG, 519R:GWATTACCGCGGCKGCTG
pcr_cond
initial denaturation: 94degC_3min; 28 cycles: denaturation=94degC_30sec, annealing=53degC_40sec, elongation=72degC_1min; final elongation: 72degC_5min
depth
256 m
host_common_name
Anemone
host_taxid
1821226
host_subject_id
E.A.4
host_life_stage
Adult
host_body_site
whole specimen
host_substrate
ice
samp_salinity
34.573 PSU
std_deviation_of_salinity
0.017
oxy_stat_samp
aerobic
temp
-1.949 degree Celcius
std_deviation_of_temp
0.053
samp_store_temp
4 degree Celcius
samp_store_dur
5 years
diss_react_phos
65 mg m^-3
nitrate_as_nitro
419 mg m^-3
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.host-associated