Download URLhttps://www.bco-dmo.org/dataset/636859/data/download
Media Type text/tab-separated-values
Created January 28, 2016
Modified August 19, 2016
State Final no updates expected
Brief Description

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

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).

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.



accession_num [accession number]

NCBI accession number.

Database identifier assigned by repository and linked to GenBank or other repository.
species [species]
Species name.

a taxonomic binomial that consists of a genus name followed by the species name of an organism

lat [latitude]
Latitude. Positive values = North.

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Longitude. Negative values = West.

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

method [brief_desc]

Description of sequencing method.

brief description, open ended, specific to the data set in which it appears

accession_link [accession number]

Hyperlink to NCBI.

Database identifier assigned by repository and linked to GenBank or other repository.

Dataset Maintainers

Annette R. RoweUniversity of Southern California (USC)
Kenneth H. NealsonUniversity of Southern California (USC)
Shannon RauchUniversity of Southern California (USC)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transports
Acronym PassElectronsThruMarSed
Created January 28, 2016
Modified January 28, 2016
Project Description

Description from C-DEBI:
One of the major questions in subsurface biology is understanding how microrganisms in the subsurface are “making a living”. However, there is a dearth of knowledge concerning the physiology of major microbial groups that likely dominate the subsurface, including the lithotrophic or “rock-eating” microbes. This, in turn, makes one of the major research goals of C-DEBI, identifying and assessing activity in the deep subsurface biosphere, extremely difficult for these processes (i.e. not identified via “meta-omic” based studies) and in many cases these metabolisms are probably overlooked. Through my C-DEBI fellowship I was able to develop techniques for electrochemical cultivation of lithotrophic microbes to help facilitate identification and further study of microbial groups with these abilities. As part of this work I targeted cultivation of several groups of facultative lithotrophs that are phylogenetically related to organisms that are genetically tractable, and I’m currently in the process of building draft genomes for these microbes. It is my goal to use these microbes as model systems for understanding and biochemically characterizing the physiology of lithotrophs that will lead to better genetic markers to identify these physiologies in the environment. The work done through this fellowship has currently resulted in one publication in “Frontiers in Microbiology” on the electrochemical cultivation and isolation of facultative lithotrophs and tracking the physiology of cathode oxidizing microbes is the publication that will be submitted this summer. One of the most exciting results from this work is that the majority of microbes isolated from the one marine sediment tested, appear to have different redox potential where they catalyze the oxidation of a cathode suggesting a variety of different protein pathways used. This highlights both the unknown nature of these processes and the diversity of potential lithotrophic metabolic pathways.

This project was funded by a C-DEBI Postdoctoral Fellowship.

Data Project Maintainers
Annette R. RoweUniversity of Southern California (USC)Principal Investigator
Kenneth H. NealsonUniversity of Southern California (USC)Co-Principal Investigator