URLhttps://www.bco-dmo.org/dataset/551070
Download URLhttps://www.bco-dmo.org/dataset/551070/data/download
Media Type text/tab-separated-values
Created February 18, 2015
Modified August 19, 2016
State Final no updates expected
Brief Description

Organic carbon and nitrogen in near-vent sediment samples, Paleochori Bay, Milos Island, Greece

Acquisition Description

Samples were collected by push cores along a transect from the hottest part of the venting area towards the unaffected, colder sediments, i.e., at 0 cm, 50 cm, 100 cm, 150 cm, 200 cm, and 300 cm. On shore, the push cores were sliced in 2 cm intervals, frozen on dry ice, and subsequently stored at -80ºC. DNA was extracted using a commercially available extraction kit. We were able to successfully sequence 16S rRNA amplicons for Bacteria and Archaea from a total of 26 samples. Sequence data are currently being analyzed and will be deposited in GenBank prior to publication and will be made available to the scientific community. For TOC and TON analyses, dried sediment samples were weighed into methanol rinsed silver boats (4 x 6 mm, Costech). 96 well glass plates (combusted 4 hrs @ 450C) holding these samples were placed in a vacuum desiccator that also contained an open dish with about 50 ml fresh, concentrated (12N) HCl. An inverted crystallization dish was placed over the samples to protect them from water that can condense and rain down from the desiccator top during heating. The desiccator was closed and pumped out with an air driven aspirator, to a reading of about ~0.5 atm and the desiccator is placed in an oven kept between 60 and 65 C. Acidification was allowed to run for 60 to 72 hours. The samples were then transferred to another vacuum desiccator, this time charged with indicating silica gel (Fisher S162-500, activated by heating to 450ºC overnight, and pumped down again and dried for about 24 hours before use. Immediately before analysis, samples are wrapped in tin boats (Costech, 4×6, methanol rinsed). 

Processing Description

We have used a commercially available extraction kit for extracting the DNA. 16S rRNA amplicons for Bacteria and Archaea were generated using 454 sequence technology. Obtained sequences are currently being analyzed using the QIIME pipeline. The reads are being dereplicated, denoised, screened for chimeric sequences and taxonomically classified using the RDP and GreenGenes databases. Multivariate ordination techniques are being used to discriminate among samples with similar community structures. For TOC and TON analyses, samples are analyzed in triplicate using a Fisons 1108 Elemental Analyzer equipped with a Costech “Zero Blank” sample carousel. Effluent gases from the EA flow into a Finnigan-MAT Conflo-II interface attached to a DeltaPlus Isotope Ratio Mass Spectrometer. Standard materials (USGS-40 glutamic acid, IAEA-N1 ammonium sulfate, NBS-19 limestone, as well as known glycine and calcites) are used to determine the area response and calibrate the isotopic reference gas. 

Instruments

Spectrometer [Spectrometer]
Details
Instance Description (Spectrometer)

Finnigan-MAT Conflo-II interface attached to a DeltaPlus Isotope Ratio Mass Spectrometer

A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.

Elemental Analyzer [CHN Elemental Analyzer]
Details
Instance Description (Elemental Analyzer)

Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel

A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.

Parameters

location [region]
Details
location
sampling location

geographical area of sampling

lat [latitude]
Details
lat
latitude; north is positive

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

lon [longitude]
Details
lon

longitude; east is positive

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

site [site]
Details
site
sampling site number
Sampling site identification.
date [date]
Details
date
sampling date

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

distance [unknown]
Details
distance
distance from transect origin
association with a community-wide standard parameter is not yet defined
comment [comment]
Details
comment
comment
free text comments, may only have meaning to submitting PI
sediment_horizon [unknown]
Details
sediment_horizon
sediment horizon
association with a community-wide standard parameter is not yet defined
TOC [TOC]
Details
TOC
total organic carbon mean percent
total organic Carbon
Details
TOC_sd
total organic carbon standard deviation
Generic standard deviation value, taking on the units of the parameter that it is tied to.
TOC_n [numb_obs]
Details
TOC_n
number of samples for total organic carbon

number of observations

TON [TON]
Details
TON
total organic nitrogen mean percent
total organic Nitrogen
Details
TON_st
total organic nitrogen standard deviation
Generic standard deviation value, taking on the units of the parameter that it is tied to.
TON_n [numb_obs]
Details
TON_n
number of samples for total organic nitrogen

number of observations

C_N [C_to_N]
Details
C_N
carbon:nitrogen ratio
Carbon to Nitrogen ratio; CAUTION; file dependent
d13C_org [unknown]
Details
d13C_org
organic d13C concentration
association with a community-wide standard parameter is not yet defined
d13C_org_sd [standard deviation]
Details
d13C_org_sd
organic d13C standard deviation
Generic standard deviation value, taking on the units of the parameter that it is tied to.
d13C_org_n [numb_obs]
Details
d13C_org_n
number of samples for organic d13C

number of observations

d15N_org [unknown]
Details
d15N_org
organic d15N concentration
association with a community-wide standard parameter is not yet defined
d15N_org_sd [standard deviation]
Details
d15N_org_sd
organic d15N standard deviation
Generic standard deviation value, taking on the units of the parameter that it is tied to.
d15N_org_n [numb_obs]
Details
d15N_org_n
number of samples for organic d15N

number of observations

DNA [unknown]
Details
DNA
whether DNA was extracted from the samples for subsequent microbial community analyses
association with a community-wide standard parameter is not yet defined
rRNA [unknown]
Details
rRNA
whether 16S rRNA Sequence Data for Bacteria and Archaea was collected
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Stefan M. SievertWoods Hole Oceanographic Institution (WHOI)
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)

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
URLhttps://www.bco-dmo.org/project/473892
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. 

Abstract:
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
NameAffiliationRole
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
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