Dataset: Buoyant single cell densities of marine bacterial isolates

Name: Buoyant single cell densities of marine bacterial isolates in pure water, deuterated water and artificial seawater (Bacterioplankton single-cell growth project)
Published: 2016-10-19
Keywords: biota, oceans

Cite This Dataset

Project:

Linking Single-Cell Growth Rates and Genomics (Bacterioplankton single-cell growth)

Principal Investigator:

Dr Martin Polz (Massachusetts Institute of Technology, MIT)

Co-Principal Investigator:

Scott Manalis (Massachusetts Institute of Technology, MIT)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2016-10-19

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Buoyant single cell densities of marine bacterial isolates in pure water, deuterated water and artificial seawater (Bacterioplankton single-cell growth project)

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Description

Mass and density measurements of single cells from 8 microbial strains measured in pure water, deuterated water and artificial seawater.

These data are to appear in a paper entitled "Direct single-cell biomass estimates for marine bacteria via Archimedes' principle" by Nathan Cermak, Jamie W. Becker, Scott M. Knudsen, Sallie W. Chisholm, Scott R. Manalis, and Martin F. Polz. ISME Journal (In Press)

Methods & Sampling

We measured single cell buoyant mass (cell mass minus the mass of the fluid it displaces) using a suspended microchannel resonator. This is a custom-fabricated silicon microfluidic chip with a fluid-filled resonator. When a cell flows through the resonator in a fraction of a second, it briefly changes the resonator's total mass, which changes its resonant frequency. By tracking the resonator's resonant frequency, we can weigh single cells. The baseline frequency of the resonator is also proportional to the fluid density, and we quantify this relationship in advance using sodium-chloride solutions as density standards.

In this measurement, cells were grown in either 2216 marine broth (13B01) or dilute seawater-based media (all others). Cells were taken from exponential growth phase (except for 13B01 which was measured in both stationary and exponential phases) and fixed with either formaldehyde or glutaraldehyde.

Data Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added 'cell_id' parameter name

Data Files

File
cell_densities.csv (Comma Separated Values (.csv), 757.87 KB) MD5:d691fd86f920b7667dbff23f4d947923 Primary data file for dataset ID 661577

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1129359

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Polz_lab		2011-09-01	MIT	Dr Martin Polz (Principal Investigator)	data info

Instruments

Suspended Microchannel Resonator

Supplied Name:

Supplied Description:

A custom-fabricated silicon microfluidic chip with a fluid-filled resonator to measure mass and density of single cells.

Instrument Type

Generic Name: Suspended Microchannel Resonator

Acronym: SMR

Generic Description:

A high-precision instrument for measuring single-cell mass, volume, and density using one or two resonators connected by a serpentine fluidic channel. During operation of the dual SMR, a dilute cell population suspended in cell media, Fluid 1, is delivered to the sample bypass via pressure-driven flow (Figure 2A, Supplementary Figure 1), and single cells flow into the first SMR (SMR1) for the first buoyant mass measurement. The cells then travel through a microchannel to a cross-junction, where a second fluid of different density is introduced. After the cross-junction, cells continue through a long serpentine channel, which facilitates mixing of the two fluids. The cells next enter a second cantilever (SMR2) for a buoyant mass measurement in the mixed fluid, Fluid 2. As cells flow through each cantilever, a change in resonance frequency is recorded (Figure 2B), which is determined by each cell's buoyant mass in each cantilever's corresponding fluid.

Reference: Bryan, A.K. et al. (2015) Measuring single cell mass, volume, and density with dual suspended microchannel resonators. Proc Natl Acad Sci USA 108: 10992–10996 doi:10.1073/pnas.1104651108. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895367/

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
baselineFrequency_hz	The resonator's baseline frequency at the time of measurement	hertz	no_bcodmo_term
buoyantMass_fg	The cell's buoyant mass	femtograms (fg)	mass
cell_id	Cell identification number	unitless	sample
fluid	Type of fluid the cells were measured in: H2O is pure water; D2O is pure deuterated water; and ASW is artificial seawater (made from sea salts from sigma aldrich).	unitless	treatment
fluidDensity_gpermL	The density of the fluid in which the cell was immersed; calculated based on the resonator's baseline frequency	grams/milliliter (g/ml)	no_bcodmo_term
strain	Bacterial strain	unitless	taxon
time_hr	The time elative to the start of the experiment at which the cell was measured	hours	time_elapsed

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Database

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Dataset: Buoyant single cell densities of marine bacterial isolates