title: Metagenome or environmental sample from Clean mat biomass
organism: sediment metagenome
description: This Clean mat biomass is dominated by gliding filamentous Beggiatoaceae giant bacteria, but it also contains some others bacteria and ciliated protozoans. This biomass is detonated as Clean because sample processing include some steps aimed to reduce the carry over of sediment particles, non attached flora and any metazoans inhabiting the mat.
attributes.tag: isolation_source
attributes.value: Mat covering of sea bed underneath a salmon farm in southern Chile
attributes.tag: collection_date
attributes.value: 2012-01-31
attributes.tag: geo_loc_name
attributes.value: Chile: Estero Pichicolo, Los Lagos
attributes.tag: lat_lon
attributes.value: 42.037 S 72.593 W
attributes.tag: ref_biomaterial
attributes.value: Aranda et al. 2015. Sulphur-cycling bacteria and ciliated protozoans in a Beggiatoaceae mat covering organically enriched sediments beneath a salmon farm in a southern Chilean fjord. Marine Pollution Bulletin. Submission MPB-D-15-00052
attributes.tag: rel_to_oxygen
attributes.value: microaerophilic
attributes.tag: samp_collect_device
attributes.value: Sediment mini-cores (24 mm diameter) sampled by scuba divers.
attributes.tag: samp_mat_process
attributes.value: After retrieving, the overlying sea water of mini core was gently extracted and replaced with sterile oxic sea water (SOSW) and then cold incubated in the dark to allow oxygen consumption and gliding of mat forming cells in the overlaying-sea water. Gliding filamentous mat-forming cells were gently aspirated with a disposable Pasteur pipette, and then transferred to 100 ml polypropylene flasks filled with SOSW. Filaments were gently dispersed by pipetting followed by flushing with SOSW. Samples were then incubated for 3 hours to allow for the decantation of filaments and chemotactic self-aggregation. Mat biomass collected from 9 mini-cores at the study site were segregated into two subsamples for independent downstream processing. The Clean mat biomass was obtained by three times dispersion in fresh SOSW followed by cell self-aggregations steps. This process was intended to reduce the carry over of sediment particles, flora not attached to the gliding filamentous cells and observed polychaetes and oligochaetes that could saturate the Eukarya library. Total DNA was extracted using a Power Soil DNA isolation Kit (MO BIO Laboratories, Inc., CA) according to the manufacturer's specifications.
attributes.tag: samp_size
attributes.value: Approximately 300 microliters of mat biomass. It is half of the mat biomass collected by combination of 9 mini-cores (24 mm diameter each).
attributes.tag: source_material_id
attributes.value: Clean mat biomass
attributes.tag: depth
attributes.value: 0-1 cm
attributes.tag: env_biome
attributes.value: marine neritic biome
attributes.tag: elev
attributes.value: - 40 m
attributes.tag: env_feature
attributes.value: fjord
attributes.tag: env_material
attributes.value: sediment
attributes.tag: BioSampleModel
attributes.value: Metagenome or environmental