High Resolution Growth Screen of Ruegeria pomeroyi Transporter Mutants Data September 2021 - June 2022 (C-CoMP Marine Bacterial Transporters project)

Website: https://www.bco-dmo.org/dataset/894179
Data Type: experimental
Version: 1
Version Date: 2023-04-18

Project
» Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites (C-CoMP Marine Bacterial Transporters)

Program
» Center for Chemical Currencies of a Microbial Planet (C-CoMP)
ContributorsAffiliationRole
Moran, Mary AnnUniversity of Georgia (UGA)Principal Investigator
Reisch, Christopher R.University of Florida (UF)Co-Principal Investigator
Mejia, CatalinaUniversity of Florida (UF)Scientist
Trujillo Rodriguez, LidimarieUniversity of Florida (UF-SFRC)Scientist
Schroer, William F.University of Georgia (UGA)Student, Contact
Gray, LauraWoods Hole Oceanographic Institution (WHOI)Data Manager
Newman, SawyerWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
High resolution growth screens were used to confirm the phenotype of Ruegeria pomeroyi DSS-3 transporter knockout mutants. Mutants which had demonstrated growth defects on a given substrate as sole carbon source during an initial growth screen were selected and used here. Each mutant was grown on the substrate(s) of interest along side a wildtype analog (pooled-TnSeq library). Growth curves were generated by reading the optical density at 600 nm hourly. The annotations of a transporter's cognate substrate was confirmed when the mutant of said transporter demonstrated significant defect relative to the wildtype analog on the substrate of interest.


Coverage

Temporal Extent: 2021-09 - 2022-06

Dataset Description

Each column heading provides the treatment condition and replicate. The first 4 letters are substrate abbreviation (provided below) followed by the bacterial identifier. The bacterial identity is either "WT" indicating the wildtype analog (pooled-RBTnSeq library) or four numbers indicating the locus tag of the disrupted gene (e.g. "1234" represents a mutant of "SPO1234").  Finally, the underscore and lowercase letter ("_a",  "_b",  "_c",  "_d") indicates the biological replicate. 

Values are optical density at 600 nm.


Methods & Sampling

Methods & Sampling

Mutant cultures were pre-grown overnight in ½ YTSS medium with 50 mg ml-1 kanamycin. Screens were performed in L1 minimal medium (Guillard and Hargraves 1993) (dx.doi.org/10.17504/protocols.io.jvccn2w) modified to a salinity of 20 ppt and amended with ammonium (3 mM), kanamycin (50 mg ml-1), and phosphorus as PO43- at 36 mM. Overnight cultures of individual mutants were washed 3 times in substrate free medium. Four replicate 200 µl mutant cultures were prepared by inoculating 2 ml of washed  overnight culture into 96 well plates containing 198 ml modified L1 medium and a single substrate at 8 mM carbon. As a positive control, four wells with the same medium were inoculated with washed overnight cultures of the pooled-RB-TnSeq library, used as a proxy for wild-type R. pomeroyi growth but harboring a transposon/kanamycin resistance gene insertion. Cultures were grown at 25oC in a Synergy H1 plate reader (BioTek, Winooski, VT, USA) shaking at 425 rpm for 68-72 h. OD600 readings were collected once each hour.


Data Processing Description

Data Processing Notes from Submitter:

The data were imported into Excel and compiled on a single sheet. Values are OD600, they have not been pathlength corrected, they have not been blank corrected. We recommend blanking each sample to its first time point.

BCO-DMO Processing Notes:

  • Replaced spaces and special characters in column header names with underscores ("_")

 


[ table of contents | back to top ]

Data Files

File
combinedgrowthcurves_bco_dmo3_23_2.csv
(Comma Separated Values (.csv), 35.34 KB)
MD5:66bab205ed3cf81f5e5a42416fc32b5f
Primary data file for dataset ID 894179. File processed with laminar pipeline "894179_v1_high_resolution_screen_growth_curves" at path 894179/1/data/combinedgrowthcurves_bco_dmo3_23_2.csv

[ table of contents | back to top ]

Related Publications

Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites. https://doi.org/10.1101/2023.01.19.524783
Results
Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME Communications, 3(1). https://doi.org/10.1038/s43705-023-00244-6
Results

[ table of contents | back to top ]

Parameters

ParameterDescriptionUnits
time_hours

Sample time

hours
thymWT_a

Thymidine wild type biological replicate a

units
thymWT_b

Thymidine wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thymWT_c

Thymidine wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thymWT_d

Thymidine wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0378_a

Thymidine locas tag 0378 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0378_b

Thymidine locas tag 0378 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0378_c

Thymidine locas tag 0378 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0378_d

Thymidine locas tag 0378 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0379_a

Thymidine locas tag 0379 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0379_b

Thymidine locas tag 0379 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0379_c

Thymidine locas tag 0379 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
thym0379_d

Thymidine locas tag 0379 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cholWT_a

Choline wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cholWT_b

Choline wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cholWT_c

Choline wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cholWT_d

Choline wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
chol1087_a

Choline locas tag 1087 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
chol1087_b

Choline locas tag 1087 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
chol1087_c

Choline locas tag 1087 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
chol1087_d

Choline locas tag 1087 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSPWT_a

DMSP wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSPWT_b

DMSP wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSPWT_c

DMSP wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSPWT_d

DMSP wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
citrWT_a

Citrate wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
citrWT_b

Citrate wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
citrWT_c

Citrate wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
citrWT_d

Citrate wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPSWT_a

DHPS wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPSWT_b

DHPS wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPSWT_c

DHPS wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPSWT_d

DHPS wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glosWT_a

Glucose wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glosWT_b

Glucose wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glosWT_c

Glucose wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glosWT_d

Glucose wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xyloWT_a

Xylose wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xyloWT_b

Xylose wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xyloWT_c

Xylose wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xyloWT_d

Xylose wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taurWT_a

Taurine wild type biological replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taurWT_b

Taurine wild type biological replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taurWT_c

Taurine wild type biological replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taurWT_d

Taurine wild type biological replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSP3186_a

DMSP locas tag 3186 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSP3186_b

DMSP locas tag 3186 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSP3186_c

DMSP locas tag 3186 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DMSP3186_d

DMSP locas tag 3186 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xylo0863_a

Xylose 0863 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xylo0863_b

Xylose 0863 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xylo0863_c

Xylose 0863 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
xylo0863_d

Xylose 0863 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPS0591_a

DHPS locas tag 0591 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPS0591_b

DHPS locas tag 0591 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPS0591_c

DHPS locas tag 0591 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
DHPS0591_d

DHPS locas tag 0591 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glos0863_a

Glucose locas tag 0863 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glos0863_b

Glucose locas tag 0863 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glos0863_c

Glucose locas tag 0863 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glos0863_d

Glucose locas tag 0863 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0676_a

Taurine locas tag 0676 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0676_b

Taurine locas tag 0676 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0676_c

Taurine locas tag 0676 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0676_d

Taurine locas tag 0676 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0674_a

Taurine locas tag 0674 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0674_b

Taurine locas tag 0674 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0674_c

Taurine locas tag 0674 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
taur0674_d

Taurine locas tag 0674 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcNWT_a

GlcNAc biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcNWT_b

GLcNAc biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcNWT_c

GLcNAc biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcNWT_d

GLcNAc biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcN1839_a

GLcNAc locas tag 1839 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcN1839_b

GLcNAc locas tag 1839 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcN1839_c

GLcNAc locas tag 1839 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glcN1839_d

GLcNAc locas tag 1839 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sperWT_a

Spermidine biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sperWT_b

Spermidine biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sperWT_c

Spermidine biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sperWT_d

Spermidine biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cadaWT_a

Cadaverine biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cadaWT_b

Cadaverine biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cadaWT_c

Cadaverine biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cadaWT_d

Cadaverine biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putrWT_a

Putresceine biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putrWT_b

Putresceine biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putrWT_c

Putresceine biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putrWT_d

Putresceine biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ectoWT_a

Ectoine biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ectoWT_b

Ectoine biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ectoWT_c

Ectoine biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ectoWT_d

Ectoine biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sper3469_a

Spermidine locas tag 3469 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sper3469_b

Spermidine locas tag 3469 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sper3469_c

Spermidine locas tag 3469 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
sper3469_d

Spermidine locas tag 3469 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cada3469_a

Cadaverine locas tag 3469 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cada3469_b

Cadaverine locas tag 3469 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cada3469_c

Cadaverine locas tag 3469 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cada3469_d

Cadaverine locas tag 3469 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putr3469_a

Putresceine locas tag 3469 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putr3469_b

Putresceine locas tag 3469 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putr3469_c

Putresceine locas tag 3469 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
putr3469_d

Putresceine locas tag 3469 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ecto1147_a

Ectoine locas tag 1147 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ecto1147_b

Ectoine locas tag 1147 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ecto1147_c

Ectoine locas tag 1147 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
ecto1147_d

Ectoine locas tag 1147 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
malaWT_a

Malate biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
malaWT_b

Malate biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
malaWT_c

Malate biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
malaWT_d

Malate biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succWT_a

Succinate biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succWT_b

Succinate biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succWT_c

Succinate biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succWT_d

Succinate biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumrWT_a

Fumarate biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumrWT_b

Fumarate biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumrWT_c

Fumarate biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumrWT_d

Fumarate biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2626_a

Malate locus tag 2626 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2626_b

Malate locus tag 2626 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2626_c

Malate locus tag 2626 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2626_d

Malate locus tag 2626 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2628_a

Malate locus tag 2628 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2628_b

Malate locus tag 2628 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2628_c

Malate locus tag 2628 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2628_d

Malate locus tag 2628 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2630_a

Malate locus tag 2630 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2630_b

Malate locus tag 2630 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2630_c

Malate locus tag 2630 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
mala2630_d

Malate locus tag 2630 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2626_a

Succinate locus tag 2626 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2626_b

Succinate locus tag 2626 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2626_c

Succinate locus tag 2626 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2626_d

Succinate locus tag 2626 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2628_a

Succinate locus tag 2628 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2628_b

Succinate locus tag 2628 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2628_c

Succinate locus tag 2628 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2628_d

Succinate locus tag 2628 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2630_a

Succinate locus tag 2630 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2630_b

Succinate locus tag 2630 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2630_c

Succinate locus tag 2630 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
succ2630_d

Succinate locus tag 2630 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2626_a

Fumarate locus tag 2626 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2626_b

Fumarate locus tag 2626 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2626_c

Fumarate locus tag 2626 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2626_d

Fumarate locus tag 2626 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2628_a

Fumarate locus tag 2628 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2628_b

Fumarate locus tag 2628 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2628_c

Fumarate locus tag 2628 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2628_d

Fumarate locus tag 2628 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2630_a

Fumarate locus tag 2630 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2630_b

Fumarate locus tag 2630 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2630_c

Fumarate locus tag 2630 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
fumr2630_d

Fumarate locus tag 2630 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cystWT_a

Cysteate biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cystWT_b

Cysteate biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cystWT_c

Cysteate biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cystWT_d

Cysteate biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glycWT_a

Glycerol biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glycWT_b

Glycerol biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glycWT_c

Glycerol biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glycWT_d

Glycerol biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3040_a

Cysteate locus tag 3040 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3040_b

Cysteate locus tag 3040 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3040_c

Cysteate locus tag 3040 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3040_d

Cysteate locus tag 3040 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glyc0608_a

Glycerol locus tag 0608 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glyc0608_b

Glycerol locus tag 0608 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glyc0608_c

Glycerol locus tag 0608 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
glyc0608_d

Glycerol locus tag 0608 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3041_a

Cysteate locus tag 3041 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3041_b

Cysteate locus tag 3041 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3041_c

Cysteate locus tag 3041 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
cyst3041_d

Cysteate locus tag 3041 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
isetWT_a

Isethionate biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
isetWT_b

Isethionate biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
isetWT_c

Isethionate biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
isetWT_d

Isethionate biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2357_a

Isethionate locus tag 2357 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2357_b

Isethionate locus tag 2357 repilicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2357_c

Isethionate locus tag 2357 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2357_d

Isethionate locus tag 2357 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2358_a

Isethionate locus tag 2358 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2358_b

Isethionate locus tag 2358 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2358_c

Isethionate locus tag 2358 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
iset2358_d

Isethionate locus tag 2358 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butrWT_a

3-Hydroxybutyrate biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butrWT_b

3-Hydroxybutyrate biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butrWT_c

3-Hydroxybutyrate biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butrWT_d

3-Hydroxybutyrate biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carnWT_a

Carnitine biological wild type replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carnWT_b

Carnitine biological wild type replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carnWT_c

Carnitine biological wild type replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carnWT_d

Carnitine biological wild type replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537A_a

3-Hydroxybutyrate locus tag 537A replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537A_b

3-Hydroxybutyrate locus tag 537A replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537A_c

3-Hydroxybutyrate locus tag 537A replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537A_d

3-Hydroxybutyrate locus tag 537A replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537B_a

3-Hydroxybutyrate locus tag 537B replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537B_b

3-Hydroxybutyrate locus tag 537B replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537B_c

3-Hydroxybutyrate locus tag 537B replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
butr537B_d

3-Hydroxybutyrate locus tag 537B replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2995_a

Carnitine locus tag 2995 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2995_b

Carnitine locus tag 2995 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2995_c

Carnitine locus tag 2995 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2995_d

Carnitine locus tag 2995 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2996_a

Carnitine locus tag 2996 replicate a

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2996_b

Carnitine locus tag 2996 replicate b

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2996_c

Carnitine locus tag 2996 replicate c

Number of sequence counts (barcodes) that mapped to each gene in the treatment.
carn2996_d

Carnitine locus tag 2996 replicate d

Number of sequence counts (barcodes) that mapped to each gene in the treatment.


[ table of contents | back to top ]

Instruments

Dataset-specific Instrument Name
Synergy H1 plate reader (BioTek, Winooski, VT, USA)
Generic Instrument Name
plate reader
Dataset-specific Description
Cultures were grown at 25oC in a Synergy H1 plate reader (BioTek, Winooski, VT, USA) shaking at 425 rpm for 68-72 h. OD600 readings were collected once each hour.
Generic Instrument Description
Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.


[ table of contents | back to top ]

Project Information

Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites (C-CoMP Marine Bacterial Transporters)


Project:

Observing expression of marine bacterial transporter systems with transcriptomic or proteomic tools can provide valuable information about the metabolomic environment. However, these ‘omics approaches are limited by the low rate of transporter gene annotation. Here, a barcoded, arrayed, mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 is employed in high throughput screens to identify the target substrates of 13 transporter systems. A set of 156 isolated putative transporter mutants were screened for growth on minimal medium with 63 substrates, each as a sole carbon source. Mutants that demonstrated a growth defect on a specific substrate were selected for secondary, higher resolution, growth screening. Mutants that continued to demonstrate growth defect relative to the pooled-mutant library (pooled-BarSeq, used as an analog for wildtype) were screened for their ability to drawdown the target substate. Gene annotations were made when mutants of the given transporter demonstrated both growth and drawdown defects on the target substrate.

In addition to the isolated mutant screens, the pooled barcoded transposon mutant library (pooled-BarSeq) was grown on minimal medium with selected substrates, each as sole carbon source, such that the relative enrichment or depletion of each mutant could demonstrate its fitness cost associated with the loss of each disrupted gene when grown on each substrate. The results of pooled-BarSeq screens had mixed consistency with the isolated mutant screens, demonstrating the value of isolated mutants for transporter annotation.

Program:

The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere.



[ table of contents | back to top ]

Program Information

Center for Chemical Currencies of a Microbial Planet (C-CoMP)


Coverage: North Atlantic, BATS, global/other


Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.

Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

The Program's Data Management Plan (DMP) is available as a PDF document.



[ table of contents | back to top ]

Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
Simons Foundation (Simons)

[ table of contents | back to top ]