Dataset: Subseafloor Microbial Cell Counts

Name: Microbial cell counts in sediment cores collected during R/V Knorr cruise KN195-03 in the Pacific Ocean in 2009 (Subseafloor Microbial Life project)
Published: 2015-09-16
Keywords: oceans

Cite This Dataset

Spatial Extent: N:30.3553 E:-86.1882 S:-4.2365 W:-157.8705

Project:

Oceanographic control and global distributions of subseafloor microbial life and activity (Subseafloor Microbial Life)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Steven L. D'Hondt (University of Rhode Island, URI-GSO)

Co-Principal Investigator:

Robert Pockalny (University of Rhode Island, URI-GSO)

David C. Smith (University of Rhode Island, URI-GSO)

Arthur J. Spivack (University of Rhode Island, URI-GSO)

Contact:

Dr Jens Kallmeyer (Helmholtz Centre Potsdam, GFZ)

BCO-DMO Data Manager:

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

Version:

16 Sept 2015

Version Date:

2015-09-16

Validated:

Yes

Current State:

Final no updates expected

Microbial cell counts in sediment cores collected during R/V Knorr cruise KN195-03 in the Pacific Ocean in 2009 (Subseafloor Microbial Life project)

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Description

Microbial cell counts in sediment cores collected during KN195-03 (Equatorial Pacific 86˚W to 148˚W and North Pacific Gyre 15˚N to 30˚N and 149˚W to 158˚W); cell counts from 12 coring stations.

Methods & Sampling

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

Data 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., 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.

Data Files

File
KN195-03_cell_counts.csv (Comma Separated Values (.csv), 25.97 KB) MD5:10b8c7bc2891f7f3cf0815fb01856a4c Primary data file for dataset ID 567215

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0752336

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KN195-03	EQP Equatorial Pacific	2009-01-12	R/V Knorr	Steven L. D'Hondt (Chief Scientist)	data info

Instruments

Fluorescence Microscope

Supplied Name: fluorescence microscope

Supplied Description:

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.

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic Description:

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.

Gravity Corer

Supplied Description:

Instrument Type

Generic Name: Gravity Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

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).

Multi Corer

Supplied Description:

Instrument Type

Generic Name: Multi Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

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

Supplied Name: Piston Corer (Long Core)

Supplied Description:

Instrument Type

Generic Name: Piston Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	Cruise identification number.	dimensionless	cruise_id
station_id	Station identification number.	dimensionless	station
lat	Latitude of station.	decimal degrees	lat
lon	Longitude of station.	decimal degrees	lon
MBSF	Meters Below Seafloor (MBSF).	meters	no_bcodmo_term
cell_density	Cell density.	cells per cubic centimeter (cells cm-3)	no_bcodmo_term
st_dev	Standard deviation of cell density.	cells per cubic centimeter (cells cm-3)	std_dev

Status message

Database

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Dataset: Subseafloor Microbial Cell Counts