C-CoMP Publications

C-CoMP Pub. #058

DeVries, T., Yamamoto, K., Wanninkhof, R., Gruber, N., Hauck, J., Müller, J. D., ... & Zeng, J. (2023). Magnitude, trends, and variability of the global ocean carbon sink from 1985 to 2018. Global Biogeochemical Cycles, 37(10), e2023GB007780. doi: https://doi.org/10.1029/2023GB007780.

Open access.

C-CoMP Pub. #049

Eren, A. M., & Banfield, J. F. (2024). Modern microbiology: Embracing complexity through integration across scales. Cell, 187(19), 5151-5170. doi: https://doi.org/10.1016/j.cell.2024.08.028.

Open access.

C-CoMP Pub. #047

Sher, D., Segrè, D., & Follows, M. J. (2024). Quantitative principles of microbial metabolism shared across scales. Nature Microbiology, 1-14. doi: https://doi.org/10.1038/s41564-024-01764-0.

C-CoMP Pub. #045

Doney, S. C., Wolfe, W. H., McKee, D. C., & Fuhrman, J. G. (2024). The science, engineering, and validation of marine carbon dioxide removal and storage. Annual Review of Marine Science, 17. doi: https://doi.org/10.1146/annurev-marine-040523-014702.

Open access in January 2025.

C-CoMP Pub. #044

Silverstein, M. R., Bhatnagar, J. M., & Segrè, D. (2024). Metabolic complexity drives divergence in microbial communities. Nature Ecology & Evolution, 1-12. doi: https://doi.org/10.1038/s41559-024-02440-6.

Raw sequencing data and metadata are available on the NCBI Sequence Read Archive and available under NCBI BioProject PRJNA1074799. Processed data and analysis and simulation code are available on the Metabolic Complexity Divergence GitHub repository.

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. #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. Global Biogeochemical Cycles, 38(7), e2024GB008156. doi: https://doi.org/10.1029/2024GB008156.

Open access

C-CoMP Pub. #036

Rao, D., Füssy, Z., Brisbin, M. M., McIlvin, M. R., Moran, D. M., Allen, A. E., Follows, M. J. & Saito, M. A. (2024). Flexible B12 ecophysiology of Phaeocystis antarctica due to a fusion B12–independent methionine synthase with widespread homologues. Proceedings of the National Academy of Sciences, 121(6), e2204075121. doi: https://doi.org/10.1073/pnas.2204075121.

P. antarctica CCMP1871 mass spectrometry culture proteomics data and transcriptome-derived FASTA files are available on PRIDE under accession number PXD031524. Code for the statistical analysis is available on the Phaeo-Fe-B12 GitHub repository as well as in the paper within relevant figure captions and supporting information.

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. #030

Hamilton, M., Ferrer‐González, F. X., & Moran, M. A. (2024). Heterotrophic bacteria trigger transcriptome remodelling in the photosynthetic picoeukaryote Micromonas commoda. Environmental Microbiology Reports, 16(3), e13285. doi: https://doi.org/10.1111/1758-2229.13285.

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.5822680)

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. #024

Veseli, I., DeMers, M. A., Cooper, Z. S., 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, M. A., Moran, M. A., & Braakman, R. (2024). Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms. Scientific Data, 11(1), 967. doi: https://doi.org/10.1038/s41597-024-03778-z.

Open access, Reproducible workflows for the generation and analyses of the Digital Microbes can be accessed at on the digital-microbe repository on GitHub. The R pomeroyi and Alteromonas Digital Microbes are available on Zenodo (https://doi.org/10.5281/zenodo.7304959 and https://doi.org/10.5281/zenodo.7430118, respectively). The R. pomeroyi raw proteomics data is available on PRIDE under project PXD045824 with accompanying metadata and processed data available in BCO-DMO dataset 927507. The accompanying raw transcriptomic expression data is available under the NCBI BioProject PRJNA972985 with metadata available in BCO-DMO dataset 916134.

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. #014

Pfeifer, M. A., Zajic, C. J., Isaacs, J. M., Erickson, O. A., & Dolan, E. L. (2024). Beyond performance, competence, and recognition: forging a science researcher identity in the context of research training. International Journal of STEM Education, 11(1), 19. doi: https://doi.org/10.1186/s40594-024-00479-2.  

Open access, interview questions and codebook are available in additional file one.

C-CoMP Pub. #013