Dataset: COLI 16S rRNA sequences
Deployment: CH_Sediment_Rowe

16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments.

Principal Investigator:

Annette R. Rowe (University of Southern California, USC)

Co-Principal Investigator:

Dr Kenneth H. Nealson (University of Southern California, USC)

Contact:

Annette R. Rowe (University of Southern California, USC)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transports (PassElectronsThruMarSed)

Current State:

Final no updates expected

Version:

28 Jan 2016

Version Date:

2016-01-28

Data URL:

https://www.bco-dmo.org/dataset-deployment/636876/data

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Description

16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments.

Related Publications:
Rowe, A.R. et al. 2015. Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism. Frontiers in Microbiology (5). doi:10.3389/fmicb.2014.00784

Methods & Sampling

Dataset acquisition description

The microbes isolated during this work were originally enriched from Catalina Harbor sediments from electrodes poised at reducing or electron donating redox potentials. Isolates are obtained from these enrichements based on the oxidation of elemental sulfur, elemental iron, or amorphous FeS. Approximately 30 isolates from 8 phylotypes were obtained. Ribosomal 16S sequences were obtained for all isolates using direct 16S rRNA amplification from pure culture DNA extracts. The universal bacterial primers 27F (5'-AGAGTTTGAT CCTGGCTCAG) and 1492R (5'-GGTTACCTTGTTACGACTT) were used. Approximately 20–40 ng of PCR product from each isolate were purified with a DNA Clean Concentrator Kit (ZymoResearch, Irvine, CA), and Sanger sequencing was per- formed viaGenewiz (La Jolla,CA) or BeckmanCoulter Genomics (Danvers, MA).

Data Processing Description

Dataset Processing Description

These nearly full length sequences were quality checked and assembled using Geneious 7.1© (Biomatters, New Zealand). Alignment of sequences against the Silva database was performed using the SINA aligner (v 1.2.11) (Pruesse et al., 2012; Quast et al., 2013). Nearest cultured representative microbes were also obtained through the Silva database (Quast et al., 2013). Maximum-likelihood estimation trees were constructed from alignments of sequences and nearest neighbors using RaxML (v.8) (Stamatakis, 2014) to assign taxonomy. A identity of 97% was used to designate a specific genera for a given sequence. All full length sequences have been deposited to Genbank (accession numbers KM088025-KM0 88033).

BCO-DMO Processing:
- separated location into lat and lon columns;
- converted degrees and decimal minutes to decimal degrees;
- replaced commas with semi-colons;
- replaces spaces with underscores;
- modified parameter names to conform with BCO-DMO naming conventions.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0939564	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
accession_num	NCBI accession number.	dimensionless	accession_number
species	Species name.	dimensionless	species
lat	Latitude. Positive values = North.	decimal degrees	lat
lon	Longitude. Negative values = West.	decimal degrees	lon
method	Description of sequencing method.	dimensionless	brief_desc
accession_link	Hyperlink to NCBI.	dimensionless	accession_number

Database

Contribute Data

Dataset: COLI 16S rRNA sequences
Deployment: CH_Sediment_Rowe

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: COLI 16S rRNA sequencesDeployment: CH_Sediment_Rowe

Dataset acquisition description

Dataset Processing Description

Dataset: COLI 16S rRNA sequences
Deployment: CH_Sediment_Rowe