C-CoMP Publications

C-CoMP Pub. #021

Jo, C., Bernstein, D. B., Vaisman, N., Frydman H. M., & Segrè, D. (2023). Construction and modeling of a coculture microplate for real-time measurement of microbial interactions. mSystems. doi: https://doi.org/10.1128/msystems.00017-21.

Open Access, all data and code are available on GitHub.

C-CoMP Pub. #020

Silverstein, M. R., Segrè, D., & Bhatnagar, J. M. (2023). Environmental microbiome engineering for the mitigation of climate change. Global Change Biology. doi: https://doi.org/10.1111/gcb.16609.

Open Access.

C-CoMP Pub. #019

Kim, H. H., Laufkötter, C., Lovato, T., Doney, S. C., & Ducklow, H. W. (2023). Projected 21st-Century Changes in Marine Heterotrophic Bacteria Under Climate Change. Frontiers in Microbiology, 14, 233. doi: https://doi.org/10.3389/fmicb.2023.1049579.

Open Access, datasets can be found using this CMIP6 Data Search tool in the Earth System Grid Federation website. Please use the experimental IDs listed in the first supplementary table (within supplementary materials) to search for the datasets.

C-CoMP Pub. #018

Nowinski, B., Feng, X., Preston, C. M., Birch, J. M., Luo, H., Whitman, W. B., Moran M. A. (2023). Ecological divergence of synoptic marine bacterial species is shaped by gene content and expression. The ISME Journal, 1-10. doi: https://doi.org/10.1038/s41396-023-01390-4.

Open Access, data are uploaded to the NCBI Sequence Read Archive and available under the Umbrella BioProject PRJNA533622 and BioProject and PRJNA505827. Biological and chemical data are available at BCO-DMO here and here.

C-CoMP Pub. #017

Uchimiya, M., Olofsson, M., Powers, M. A., Hopkinson, B. M., Moran, M. A., & Edison, A. S. (2023). 13C NMR metabolomics: J-resolved STOCSY meets INADEQUATE. Journal of Magnetic Resonance, 347, 107365. doi: https://doi.org/10.1016/j.jmr.2022.107365.

Open Access, original data, processing scripts, and processed files are available at Metabolomics Workbench with Study Identification ST002321 (Project ID: PR001487).

C-CoMP Pub. #016

Ferrer-González, F. X., Hamilton, M., Smith, C. B., Schreier, J. E., Olofsson, M., & Moran, M. A. (2023). Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda. ISME Communications, 3(5). doi: https://doi.org/10.1038/s43705-023-00212-0.

Open Access, raw transcript sequences are uploaded to the NCBI Sequence Read Archive and available under NCBI BioProject PRJNA787291. Data products are available on Zenodo (DOI: 10.5281/zenodo.6812122).

C-CoMP Pub. #015

Schreier, J. E., Smith, C. B., Ioerger, T. R., Moran, M. A. (2023). A mutant fitness assay identifies bacterial interactions in a model ocean hot spot. Proceedings of the National Academy of Sciences, 120(12), 2217200120. doi: https://doi.org/10.1073/pnas.2217200120.

Open Access, analysis code is available on GitHub and Zenodo. Other code, data, and files are linked here: FASTQ Transposon sequencing files, and the Wig formatted file. All other data are included in the article or SI Appendix.

C-CoMP Pub. #013

Dinauer, A., Laufkötter, C., Doney, S. C., & Joos, F. 2022: What controls the large-scale efficiency of carbon transfer through the ocean’s mesopelagic zone? Insights from a new, mechanistic model (MSPACMAM). Global Biogeochemical Cycles, 36, e2021GB007131. doi: https://doi.org/10.1029/2021GB007131.

Open Access, MSPACMAM (Model of Sinking Particles and Cycling of Marine Aggregated Matter) code.

C-CoMP Pub. #012

Fennel, K., Mattern, J. P., Doney, S. C., Bopp, L., Moore, A. M., Wang, B., & Yu, L. 2022: Ocean biogeochemical modelling. Nature Reviews Methods Primers, 2(76). doi: https://doi.org/10.1038/s43586-022-00154-2.

Paper is available from the authors. Example code is available on Zenodo and linked here for the nutrient–phytoplankton–zooplankton–detritus (NPZD) model, parameter optimization and state estimation, and the ensemble Kalman filter application for an ocean biogeochemical model in an idealized 3-dimensional channel.

C-CoMP Pub. #011

Pacheco, A. R., Pauvert, C., Kishore, D., & Segrè, D. (2022). Toward FAIR Representations of Microbial Interactions. mSystems, e00659-22. doi: https://doi.org/10.1128/msystems.00659-22.

Open Access.

C-CoMP Pub. #010

Howard-Varona, C., Roux, S., Bowen, B. P., Silva, L. P., Lau, R., Schwenck, S. M., Schwartz, S., Woyke, T., Northen, T. Sullivan, M. B., & Floge, S. A. (2022). Protist impacts on marine cyanovirocell metabolism. ISME Communications, 2(1), 1-14. doi: https://doi.org/10.1038/s43705-022-00169-6.

Open Access, Raw data, calculations, scripts, & statistical tests are deposited in Cyverse. Metabolomics analysis scripts are located on GitHub.

C-CoMP Pub. #009

Forchielli, E., Sher, D., & Segrè, D. (2022). Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies. mSystems, e00070-22. doi: https://doi.org/10.1128/msystems.00070-22.

Open Access, Raw data and code are available on GitHub.

C-CoMP Pub. #008

Holderman, N. R., Ferrer‐Gonzalez, F., Glushka, J., Moran, M. A., & Edison, A. S. (2022). Dissolved organic metabolite extraction from high salt media. NMR in Biomedicine, e4797. doi: https://doi.org/10.1002/nbm.4797.

Open Access, Data are linked here: NMR data.

C-CoMP Pub. #007

Walworth, N. G., Saito, M. A., Lee, M. D., McIlvin, M. R., Moran, D. M., Kellogg, R. M., Fu, F. X., Hutchins, D. A., & Webb, E. A. (2021). Why Environmental Biomarkers Work: Transcriptome–Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. Journal of Proteome Research, 21(1), 77-89. doi: https://doi.org/10.1021/acs.jproteome.1c00517.

Open Access on PubMed here. Data and code are linked here: RNA-seq data, Protein Spectral Count data, Raw mass spectra, RNA-protein model code.

C-CoMP Pub. #006

Zomorrodi, A. R., Hemez, C., Arranz-Gibert, P., Wu, T., Isaacs, F. J., & Segrè, D. (2022). Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. iScience, 104562. doi: https://doi.org/10.1016/j.isci.2022.104562.

Open Access, Data and Code available on Zenodo (DOI: 10.5281/zenodo.6569900).

C-CoMP Pub. #005

Goldford, J. E., George, A. B., Flamholz, A. I., & Segrè, D. (2022). Protein cost minimization promotes the emergence of coenzyme redundancy. Proceedings of the National Academy of Sciences, 119(14), e2110787119. doi: https://doi.org/10.1073/pnas.2110787119.

Open Access, Data and Code available on GitHub.

C-CoMP Pub. #004

Olofsson, M., Ferrer-González, F. X., Uchimiya, M., Schreier, J. E., Holderman, N. R., Smith, C. B., Edison, A. S., & Moran, M. A. (2022). Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy. ISME Communications, 2(1), 1-9. doi: https://doi.org/10.1038/s43705-022-00116-5.

Open Access. Data are linked here: Transcriptome Data, Metabolomics Data, Additional Data Products and Metadata.

C-CoMP Pub. #003

Moran, M. A., Ferrer‐González, F. X., Fu, H., Nowinski, B., Olofsson, M., Powers, M. A., Schreier, J. E., Schroer, W. F., Smith, C. B., & Uchimiya, M. (2022). The Ocean's labile DOC supply chain. Limnology and Oceanography, 9999, 1-15. doi: https://doi.org/10.1002/lno.12053.

Open Access. Model Code.

C-CoMP Pub. #002

Uchimiya, M., Schroer, W., Olofsson, M., Edison, A. S., & Moran, M. A. (2021). Diel investments in metabolite production and consumption in a model microbial system. The ISME Journal, 1-12. doi: https://doi.org/10.1038/s41396-021-01172-w.

Open Access. Data are linked here: Sequencing Data, Metabolomics Data.

C-CoMP Pub. #001

Moran, M. A., Kujawinski, E. B., Schroer, W. F., Amin, S. A., Bates, N. R., Bertrand, E. M., Braakman, R., Brown, C. T., Covert, M. W., Doney, S. C., Dyhrman, S. T., Edison, A. S., Eren, A. M., Levine, N. M., Li, L., Ross, A. C., Saito, M. A., Santoro, A. E., Segré, D., Shade, A., Sullivan, M. B., & Vardi, A. (2022). Microbial metabolites in the marine carbon cycle. Nature Microbiology, 7(4), 508-523. doi: https://doi.org/10.1038/s41564-022-01090-3.

A read-only version is available at here. A pre-print version is available for download here.

Names of C-CoMP members are emboldened. Publications are ordered numerically by their C-CoMP Publication number (C-CoMP Pub. ###).