URLhttps://www.bco-dmo.org/dataset/567215
Download URLhttps://www.bco-dmo.org/dataset/567215/data/download
Media Type text/tab-separated-values
Created September 16, 2015
Modified August 19, 2016
State Final no updates expected
Brief Description

Microbial cell counts in sediment cores collected during KN195-03.

Acquisition Description

Coring systems used:
EQP-01: Multi Corer, Piston Corer (long core)
EQP-02: Multi Corer, Gravity Corer
EQP-03: Gravity Corer
EQP-03a: Multi Corer, Gravity Corer (used long core system as a gravity corer)
EQP-04: Multi Corer, Gravity Corer (used long core system as a gravity corer), Piston Corer (long core)
EQP-05: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-06: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-06a: Gravity Corer
EQP-07: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-08: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-09: Gravity Corer
EQP-10: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-11: Multi Corer, Gravity Corer, Piston Corer (long core)

Excerpt from Kallmeyer et al. (2012) Supplemental Information:
For each cell enumeration, we took 2-cm3 samples from the center of a freshly cut core end using a sterile cutoff 3-cm3 syringe. We carried out cell counts according to the method of Kallmeyer et al. (2008). We extruded the 2-cm3 sediment plug into a sterile 15-mL centrifuge tube containing 8 mL of 2.5% (wt/vol) NaCl solution with 2% (vol/vol) formalin as a fixative and then thoroughly shook the tube to form a homogenous suspension. In cases where cell densities were high enough (> 105 cells/cm−3), we made direct cell counts by staining this slurry with SYBR Green I, placing a small aliquot of the slurry directly on a 0.2-μm pore size filter and enumerating manually under a fluorescence microscope (Noble and Fuhrman, 1998). Counts obtained with SYBR Green I have been found to be indistinguishable from acridine orange direct counts (AODCs) (Morono et al., 2009).

References:
Kallmeyer, J., Smith, D.C., D’Hondt, S.L., & Spivack, A.J. 2008. New cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr Methods 6:236–245. doi:10.4319/lom.2008.6.236

Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., & D’Hondt, S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences, 109(40), 16213-16216. doi:10.1073/pnas.1203849109

Noble, R.T., Fuhrman, J.A. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14(2):113–118. doi:10.3354/ame014113

Morono, Y., Terada, T., Masui, N., & Inagak,i F. 2009. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J 3:503–511. doi:10.1038/ismej.2009.1

Processing Description

Excerpt from Kallmeyer et al. (2012) Supplemental Information:
Independent of the stain used, direct counting has a minimum detection limit (MDL) around 105 cells/cm−3 (Kallmeyer, 2011). For samples with lower cell abundances, we found it necessary to detach and separate the cells from the mineral matrix using a cell extraction protocol (Kallmeyer et al. 2008). Most counts at North Pacific Gyre sites were of extracted cells because gyre cell abundances drop below the direct count MDL within decimeters to meters below the seafloor; for the same reason, a few counts of the deepest equatorial Pacific sediment were also of cell extracts.

References:
Kallmeyer J. 2011. Detection and quantification of microbial cells in subsurface sediments. Advances in Applied Microbiology, eds Laskin AI, Sariaslani S, Gadd GM (Elsevier, San Diego), Vol 76. doi:10.1016/B978-0-12-387048-3.00003-9

Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., & D’Hondt, S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences, 109(40), 16213-16216. doi:10.1073/pnas.1203849109

Kallmeyer, J., Smith, D.C., D’Hondt, S.L., & Spivack, A.J. 2008. New cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr Methods 6:236–245. doi:10.4319/lom.2008.6.236

BCO-DMO Processing:
– Modified parameter names to conform with BCO-DMO naming conventions;
– Converted lat and lon from degrees and decimal minutes to decimal degrees.

Instruments

fluorescence microscope [Microscope-Fluorescence]
Details
Instance Description (fluorescence microscope)

Direct cell counts were obtained by placing a small aliquot of the slurry directly on a 0.2-um pore size filter and enumerating manually under a fluorescence microscope.

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

Multi Corer [Multi Corer]
Details
The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408.
Piston Corer (Long Core) [Piston Corer]
Details
The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.
Gravity Corer [Gravity Corer]
Details
The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079).

Parameters

cruise_id [cruise_id]
Details
cruise_id

Cruise identification number.

cruise designation; name
station_id [station]
Details
station_id

Station identification number.

Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.

lat [latitude]
Details
lat
Latitude of station.

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

lon [longitude]
Details
lon
Longitude of station.

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

MBSF [unknown]
Details
MBSF

Meters Below Seafloor (MBSF).

association with a community-wide standard parameter is not yet defined
cell_density [unknown]
Details
cell_density
Cell density.
association with a community-wide standard parameter is not yet defined
Details
st_dev

Standard deviation of cell density.

Generic standard deviation value, taking on the units of the parameter that it is tied to.

Dataset Maintainers

NameAffiliationContact
Steven L. D'HondtUniversity of Rhode Island (URI-GSO)
David C. SmithUniversity of Rhode Island (URI-GSO)
Robert PockalnyUniversity of Rhode Island (URI-GSO)
Arthur J. SpivackUniversity of Rhode Island (URI-GSO)
Jens KallmeyerHelmholtz Centre Potsdam (GFZ)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Oceanographic control and global distributions of subseafloor microbial life and activity
Acronym Subseafloor Microbial Life
URLhttps://www.bco-dmo.org/project/2182
Created November 8, 2011
Modified January 18, 2012
Project Description

Recent studies of subseafloor life, that is microbes living deep below the ocean&aposs seafloor, have produced astonishing results that challenge fundamental ideas about the limits and distributions of life. These include: (1) that the microbial biomass of subseafloor sediments is spatially much more variable and possibly much smaller than previously believed; (2) that rates of subseafloor sedimentary microbial activity are far below the rate required for cell maintenance, implying that either most subseafloor cells are inactive or that the energy required for their cellular maintenance is lower than anticipated; and (3) the global distributions of subseafloor sedimentary microbes and their activities are significantly affected by the oceanographic properties of the overlying water column. This proposal will conduct fieldwork to test these ideas at a range of sites in the equatorial Pacific. To do this the principal investigators will conduct a transect study where the following samples and measurements will be taken: (1) coring the sediment to ~18 meter or more below seafloor (mbsf) at 12 sites in the Pacific Ocean; (2) conducting extensive microbiological and biogeochemical analyses of these cores; (3) surveying the oceanographic and geologic characteristics of each site; and (4) using the results to test and refine models for the global distribution of subseafloor microbial abundances and their metabolic activities. Using these data the investigators will then address four important questions: (1) What are the principal controls on the magnitude and geographic distribution of subseafloor sedimentary cell abundance and steady-state rates of microbial activities? (2) Can we accurately estimate the magnitude and global distribution of subseafloor sedimentary cell abundance? (3) Can we accurately estimate the global distribution of organic carbon-fueled microbial activity in subseafloor sediment? and (4) Do different subseafloor sediments with very different cell abundances and rates of metabolic activity characterized by different groups of organisms? This study will significantly advance our understanding of life in the subseafloor ocean and will provide samples for diverse independent studies, including the International Census of Marine Microbes. This project will also have a strong research and training impact at both the graduate and undergraduate levels as the inherently multidisciplinary nature of subsurface life provides an ideal entry into collaborative modern science.

Data Project Maintainers
NameAffiliationRole
Steven L. D'HondtUniversity of Rhode Island (URI-GSO)Principal Investigator
David C. SmithUniversity of Rhode Island (URI-GSO)Co-Principal Investigator
Robert PockalnyUniversity of Rhode Island (URI-GSO)Co-Principal Investigator
Arthur J. SpivackUniversity of Rhode Island (URI-GSO)Co-Principal Investigator
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