Download URLhttps://www.bco-dmo.org/dataset/650224/data/download
Media Type text/tab-separated-values
Created June 28, 2016
Modified August 19, 2016
State Final with updates expected
Brief Description

GenBank accession numbers and links for microbial isolates from sediment samples collected at Paleochori Bay, Milos island, Greece

Acquisition Description

Samples were collected at the shallow-water hydrothermal vent sites at Paleochori Bay, Milos Island, Greece. Sequence data (bacterial ssrRNA) was obtained using the Ion Torrent platform from total RNA extracted from 32 sediment and microbial biofilm samples characterized along a transect. Sequence data are currently being generated and analyzed, they will be deposited in GenBank prior to publication and will be made available to the scientific community.

Processing Description

BCO-DMO Processing:

– added conventional header with dataset name, PI name, version date, reference information
– renamed parameters to BCO-DMO standard
– created links to GenBank accession pages


Instance Description

Ion Torrent platform

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Instance Description

push cores were collected by SCUBA divers

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/


sample [sample]
sample: species name or source material

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

analysis [unknown]
type of genetic analysis
association with a community-wide standard parameter is not yet defined
description [brief_desc]
description of product

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

database [unknown]
name of repository
association with a community-wide standard parameter is not yet defined
GenBank_acc [accession number]
GenBank accession number
Database identifier assigned by repository and linked to GenBank or other repository.
reference_paper [reference_paper]

A list of papers referred to as a data column.

Dataset Maintainers

Costantino VetrianiRutgers University (Rutgers IMCS)
Nancy CopleyRutgers University (Rutgers IMCS)

BCO-DMO Project Info

Project Title Autotrophic carbon fixation at a shallow-water hydrothermal system: Constraining microbial activity, isotopic and geochemical regimes
Acronym Hydrothermal Autotrophic Carbon Fixation
Created January 8, 2014
Modified June 3, 2015
Project Description

In this project we studied the shallow-water hydrothermal vent sites at Milos Island (Greece) to better understand the extent of autotrophic carbon fixation and its chemical and isotopic signature along environmental (redox/thermal) gradients. This was a 12-day long expedition (May 18 to 30, 2012) to sample vent fluids, gases and retrieve sediment cores at Paleochori Bay by using SCUBA diving at 8-10 m depth. In addition to the submarine vent sites, two subaerial locations of venting were identified at 36o 40′ 28″N – 24o 31′ 14″ E and 36o 40′ 25″ N – 24o 30′ 44″ E. Both the subaerial and submarine sites are located on the same fracture zone that likely controls the hydrothermal circulation of evolved meteoritic water and seawater within the magmatic zone of Milos Island. To this end, the geochemistry of the fluids and gases emitted from subaerial sites provide important information towards identifying the linkage between the subaerial and submarine magmatic activity and provide insights on the metabolic functions (e.g. H2 oxidation, Fe(III) reduction, C and S cycling) of the subsurface microbial community. 

Currently, there is only limited information on the identity and activity of the microorganisms carrying out CO2-fixation in situ, despite the fact that these organisms form the basis of their respective ecosystems. Representatives that are able to grow autotrophically are known to exist in almost all major groups of prokaryotes, and these organisms play essential roles in ecosystems by providing a continuous supply of organic carbon for heterotrophs. Microorganisms present in extreme environments utilize CO2- fixation pathways other than the Calvin-Benson-Bassham (CBB) cycle. At present, five alternative autotrophic CO2 fixation pathways are known. Different carbon fixation pathways result in distinct isotopic signatures of the produced biomass due to the isotopic discrimination between light (12C) and heavy (13C) carbon by the carboxylating enzymes. Thus, inferences about the carbon fixation pathway predominantly utilized by the microbial community can also be made based on the stable carbon isotopic composition of the organic matter, in extant systems as well as in the geological record. However, at present little is known about the systematics and extents of fractionation during carbon fixation by prokaryotic organisms, and to our knowledge no studies exist that have systematically studied the relationship between the operation of different carbon fixation pathways and how this is reflected in the stable carbon isotopic composition in a natural system. This is a 2-year interdisciplinary, international research program that employs a powerful combination of cutting-edge research tools aiming to improve our understanding of autotrophic carbon fixation and its chemical and isotopic signature along environmental gradients in a natural hydrothermal system. The following hypotheses are addressed:

1. The diversity of microorganisms present along a thermal and redox gradient, and rates of CO2 fixation, will reflect adaptation to in situ temperatures and geochemical conditions

2. Microorganisms utilizing the CBB cycle for autotrophic CO2-fixation will represent a smaller percentage of the chemolithoautotrophic community at higher temperatures, where microorganisms utilizing alternative CO2-fixation pathways dominate

3. Isotopic values of biomass and specific biomarker molecules will vary along a thermal and redox gradient from zones characterized by a higher hydrothermal fluid flux and thus higher temperatures to the surrounding, cooler areas, corresponding to the physiology of the microorganisms utilizing different pathways for carbon fixation

The PIs will use a multidisciplinary approach to delineate the relative contribution of the different carbon fixation pathways along an environmental gradient by combining metagenomic analyses coupled with: 1) an assessment of the frequency and the expression of specific key genes involved in carbon fixation, and 2) with the measurement of carbon fixation rates. These data will be integrated with the determination of stable C isotopic composition of biomass, DIC, and specific hydrocarbons/lipids. Due to its easy accessibility, well-established environmental gradients, and extensive background information, the shallow-water vents off Milos (Greece) will be used as a natural laboratory to perform these studies.

Intellectual Merit. The data generated in this study will allow constraints on the relationship between autotrophic carbon fixation and the resulting isotopic signatures of biomass and specific biomarker molecules (e.g. CH4, C2+ alkanes, lipids) in a natural system. This has implications for assessing the importance of carbon fixation in extant ecosystems, and it will also provide a tool to improve the interpretation of isotopic values in the geological record.

Data Project Maintainers
Costantino VetrianiRutgers UniversityCo-Principal Investigator
Stefan M. SievertWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Dionysis I. FoustoukosCarnegie Institution for Science (CIS)Co-Principal Investigator