C-CoMP Publications

Pre-prints

C-CoMP Pub. #038

Doney, S. C., Mitchell, K. A., Henson, S. A., Cavan, E. L., DeVries, T., Gruber, N., Hauck, J., Mouw, C. B., Müller, J. D., & Primeau, F. W. (2024). Observational and numerical modeling constraints on the global ocean biological carbon pump. Authorea Preprints. doi: https://doi.org/10.22541/essoar.170983384.44030316/v1.

C-CoMP Pub. #037

McParland, E. L., Wittmers, F., Bolanos, L. M., Carlson, C. A., Giovannoni, S. J., Michelsen, M. Parsons, R. J., Kido Soule, M. C., Swarr, G. J., Temperton, B., Vergin, K. Worden, A. Z., Longnecker, K. & Kujawinski, E. B. (2024). Seasonal exometabolites are regulated by essential microbial metabolisms in the oligotrophic ocean. bioRxiv, 2024-03. doi: https://doi.org/10.1101/2024.03.05.583599.

C-CoMP Pub. #031

Gregor, R., Szabo, R. E., Vercelli, G. T., Gralka, M., Reynolds, R., Qu, E. B., Levine, N. M., & Cordero, O. X. (2023). Widespread B-vitamin auxotrophy in marine particle-associated bacteria. bioRxiv, 2023-10. doi: https://doi.org/10.1101/2023.10.16.562604.

C-CoMP Pub. #024

Veseli, I., Cooper, Z. S., DeMers, M. A., Schechter, M. S., Miller, S., Weber, L., Smith, C. B., Rodriguez, L. T., Schroer, W. F., McIlvin, M. R., Lopez, P. Z., Saito, M., Dyhrman, S., Eren, A. M., Moran, M. A., & Braakman, R. (2024). Digital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms. bioRxiv, 2024-01. doi: https://doi.org/10.1101/2024.01.16.575828.

Peer-reviewed publications

C-CoMP Pub. #039

Herbst, K., Wang, T., Forchielli, E. J., Thommes, M., Paschalidis, I. C., & Segrè, D. (2024). Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations. Communications Biology, 7(1), 407. doi: https://doi.org/10.1038/s42003-024-06093-w.

Open access, data and code are available on the MASS GitHub repository and within the supplemental methods of the paper.

C-CoMP Pub. #034

Howard-Varona, C., Lindback, M. M., Fudyma, J. D., Krongauz, A., Solonenko, N. E., Zayed, A. A. Andreopoulos, W. B., Olsen, H. M., Kim, Y., Kyle, J. E., Glavina del Rio, T., Adkins, J. N., Tfaily, M. M., Paul, S., Sullivan, M. B., & Duhaime, M. B. (2024). Environment-specific virocell metabolic reprogramming. The ISME Journal, wrae055. doi: https://doi.org/10.1093/ismejo/wrae055.

Open access, Genomes are available at Joint Genome Institute’s portal for Integrated Microbial Genomes/Virus or GenBank and are listed in the data availability statement of the paper. Supplementary datasets are available on Zenodo.

C-CoMP Pub. #032

Kujawinski, E. B., Braakman, R., Longnecker, K., Becker, J. W., Chisholm, S. W., Dooley, K., Kido Soule, M. C., Swarr, G. J., & Halloran, K. (2023). Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. Msystems, 8(5), e01261-22. doi: https://doi.org/10.1128/msystems.01261-22.

Open access, targeted metabolomics data are available from MetaboLights (MTBLS567). Code used to find KEGG compound information for Prochlorococcus strains is available on the Pro_mtabs GitHub repository.

C-CoMP Pub. #029

Paoletti, M. M., Fournier, G. P., Dolan, E. L., & Saito, M. A. (2023). Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein Portal. Journal of Proteome Research, 22(9),2775-3102. doi: https://doi.org/10.1021/acs.jproteome.3c00152.

Open access, mass spectrometry and protein sequence files from Saunders et al. (2022) are deposited in ProteomeXchange (PRIDE) (dataset ID PXD030684) as well as through the Ocean Protein Portal under expedition FK160115. Metagenomic sequences can be accessed on JGI's IMG database (IDs: Gp0055157, Gp0055156, Gp0055136, Gp0055135, Gp0055134, and Gp0055133). Supporting Information includes seed sequences and tree files.

C-CoMP Pub. #028

Anderson, S. R., Blanco-Bercial, L., Carlson, C. A., & Harvey, E. L. (2024). Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean. ISME communications, 4(1), ycae014. doi: https://doi.org/10.1093/ismeco/ycae014.

Open access, all files and code can be found on the BATS-parasites GitHub repository. 18S rRNA sequences are deposited under BioProject PRJNA769790 on the Sequence Read Archive.

C-CoMP Pub. #027

Kishore, D., Birzu, G., Hu, Z., DeLisi, C., Korolev, K. S., & Segrè, D. (2023). Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation. Msystems, e00961-22. doi: https://doi.org/10.1128/msystems.00961-22.

Open access, code for making the pipeline is available on the MiCoNE repository on GitHub. Documentation is provided on the MiCoNE - Microbial Co-occurrence Network Explorer Read the Docs webpage. Data and scripts are available on the MiCoNE pipeline-paper repository on GitHub. Synthetic data and scripts are available on the MiCoNE-synthetic-data repository on GitHub.

C-CoMP Pub. #026

Pfeifer, M. A., & Dolan, E. L. (2023). Venturing into Qualitative Research: A Practical Guide to Getting Started. Scholarship and Practice of Undergraduate Research, 7(1), 10-20. doi: https://doi.org/10.18833/spur/7/1/2.

Open access

C-CoMP Pub. #025

Skalnik, C. J., Cheah, S. Y., Yang, M. Y., Wolff, M. B., Spangler, R. K., Talman, L., Morrison, J. H., Peirce, S. M., Agmon, E. & Covert, M. W. (2023). Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. PLOS Computational Biology, 19(6), e1011232. doi: https://doi.org/10.1371/journal.pcbi.1011232.

Open access, full source code is available on the vivarium-ecoli repository on GitHub. Results can be reproduced by running on the version of the code archived at Zenodo (DOI 10.5281/zenodo.7709618). The data files used to generate all figures are deposited at Zenodo (DOI 10.5281/zenodo.7709450).

C-CoMP Pub. #023

Gregor, R., Johnson, J., Coe L. S. Y., Evans, N. Forsythe, D., Jones, R., Muratore, D., Rodrigues de Oliveira, B. F., Szabo, R., Wan, Y., Williams, J., Chappell, C. R., Matsuda, S. B., Alvarez de la Campa, M. O., Queer and Trans in Microbiology Consortium, Weismann, J. L. (2023). Building a queer- and trans-inclusive microbiology conference. mSystems. doi: https://doi.org/10.1128/msystems.00433-23.

Open access

C-CoMP Pub. #022

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), 37. doi: https://doi.org/10.1038/s43705-023-00244-6.

Open access, all growth and RB-TnSeq data are available on BCO-DMO (Project 884792). All raw NMR data, processing scripts, and processed files are available on Metabolomics Workbench (Study ID ST002381).

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 (Dataset CTD 2016 and Dataset NIskin 2016).

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 the TnSeq Phycosphere Interactions GitHub repository and TnSeq Phycosphere Interactions Zenodo webpage. 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.

A read-only version of Ocean Biogeochemical modelling paper. 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 the Cyano_phage_grazer_omics Cyverse folder. Metabolomics analysis scripts are located on the Metabolomics_CyanophageGrazer GitHub repository.

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 the marine_heterotrophs GitHub repository.

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: Resource Partitioning of Diatom Metabolites that Support Bacterial Heterotrophy in the Ocean 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. 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 the coenzymes GitHub repository.

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 is available on the Labile_DOC_supply_chain GitHub repository.

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.

Read-only version. Pre-print version.

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