organism: sediment metagenome
description: This Dirty mat biomass is dominated by gliding filamentous Beggiatoaceae giant bacteria, but it also contains some sediment inhabiting bacteria, ciliated protozoans and some metazoans that saturated the Eukarya library. This biomass is detonated as Dirty just because some sediment particles become carried over and metazoans were visible.
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. With no further cleaning process the Dirty mat biomass was one of this subsamples. This biomass contained visible sediment particles and some metazoans. 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: Dirty 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