Publications

2023

Naylor D, Naasko K, Smith M, Couvillion SP, Nicora C, Trejo J, Fransen S, Danczak RE, McClure RS, Hofmockel KS, Jansson J 2023 Interactive effects of depth and differential irrigation on soil microbiome composition and functioning. Frontiers in Microbiomes. https://doi.org/10.3389/frmbi.2023.1078024

Couvillion SP, Danczak RE, Naylor D,  Smith ML, Stratton KG, Paurus VL, Bloodsworth KJ, Farris Y, Schmidt DJ, Richardson RE, Bramer LM, Fansler SJ, Nakayasu ES, McDermott JE, Metz TO, Lipton MS, Jansson, JK, Hofmockel KS. 2023 Significant remodeling of the soil lipidome following extreme moisture and temperature shifts. Microbiome.  https://doi.org/10.1186/s40168-022-01427-4

Bell SL, Zimmerman AE, Hofmockel KS 2023 Cropping system drives microbial community response to simulated climate change and plant inputs Journal of Soil and Water Conservation DOI: https://doi.org/10.2489/jswc.2023.00069

2022

Jansson J.K. and R. Wu. 2022. Soil Viral Diversity Ecology and Climate Change." Nature Review Microbiology. doi:10.1038/s41579-022-00811-z

Naylor D. R.S. McClure and J.K. Jansson. 2022. Trends in microbial community composition and function by soil depth." Microorganisms. doi:10.3390/microorganisms10030540

Wu R, Smith C, Buchko GW, Blaby IK, Paez-Espino A, Kyrpides NC, Yoshikuni Y, McDermott JE, Hofmockel KS, Cort JR, Jansson JK. 2022. Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase." Nature Communications. (2022)13:5485 https://doi.org/10.1038/s41467-022-32993-8

McClureR, FarrisY, DanczakR, Nelson W, Song H, Kessell A, Lee J, Couvillion S, Henry C, Jansson JK, Hofmockel KS 2022 Interaction Networks are Driven by Community Responsive Phenotypes in a Chitin Degrading Consortium of Soil Microbes. mSystems Oct 26;7(5):e00372-22  DOI: https://doi.org/10.1128/msystems.00372-22

Bhattacharjee A, Qafoku O, Richardson JA, Anderson LN, Schwarz K, Bramer LM, Lomas GX, Orton DJ, Zhu Z, Engelhard MH, Bowden ME, Nelson WC, Jumpponen A, Jansson J, Hofmockel KS, Anderton C Molecular 2022 A Mineral-Doped Micromodel Platform Demonstrates Fungal Bridging of Carbon Hot Spots and Hyphal Transport of Mineral-Derived Nutrients. mSystems  DOI: https://doi.org/10.1128/msystems.00913-22

McClure RS, Garcia MR, Couvillion SP, and Hofmockel KS. 2022. Removal of primary nutrient degrading members severely reduces growth of soil microbial communities even when additional degraders are present. Frontiers in Microbiology, 13 doi: 10.3389/fmicb.2022.1046661

2021

Smercina DN, Bailey VL, Hofmockel KS. 2021 Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function. FEMS Microbiology Ecology. 2021 Jul 5. https://doi.org/10.1093/femsec/fiab091

Graham E, Hofmockel KS 2021 Ecological stoichiometry as a foundation for omics-enabled biogeochemical models of soil organic matter decomposition, Biogeochemistry https://doi.org/10.1007/s10533-021-00851-2

Wu R., M.R. Davison, W.C. Nelson, E.B. Graham, S.J. Fansler, Y. Farris, and S.L. Bell, et al. 2021. "DNA viral diversity, abundance and functional potential vary across grassland soils with a range of historical moisture regimes." mBio 12, no. 6:e02595-21. PNNL-SA-166275. doi:10.1128/mBio.02595-21

Trubl G., J. Kimbrel, J. Liquet-Gonzalez, E. Nuccio, P.K. Weber, J. Pett-Ridge, and J.K. Jansson, et al. 2021. "Active virus-host interactions at sub-freezing temperatures in Arctic peat soil." Microbiome 9. PNNL-SA-162885. doi:10.1186/s40168-021-01154-2

Wu R., M.R. Davison, Y. Gao, C.D. Nicora, J.E. McDermott, K.E. Burnum-Johnson, and K.S. Hofmockel, et al. 2021. "Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses." Communications Biology 4, no. 1:992. PNNL-SA-160635. doi:10.1038/s42003-021-02514-2

Ryan M., M. Schloter, B. Schelkle, A. Sessitsch, M. Kazou, I. Sarand, and B.K. Singh, et al. 2021. "Development of Microbiome Biobanks – Challenges and Opportunities." Trends in Microbiology 29, no. 2:89-92. PNNL-SA-151546. doi:10.1016/j.tim.2020.06.009

Weitz K.K., M.L. Smith, K.K. Hixson, E.A. Hill, J.K. Jansson, K.S. Hofmockel, and M.S. Lipton. 2021. "Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems." Journal of the American Society for Mass Spectrometry 32, no. 3:648-652. PNNL-SA-154008. doi:10.1021/jasms.0c00251

Zegeye E., N.C. Sadler, G.X. Lomas, I.K. Attah, J.K. Jansson, K.S. Hofmockel, and C.R. Anderton, et al. 2021. "Activity-based protein profiling of chitin catabolism." Chembiochem 22, no. 4:717-723. PNNL-SA-156004. doi:10.1002/cbic.202000616

Bhattacharjee, A., Anderson, L.N., Alfaro, T., Porras-Alfaro, A., Jumpponen, A., Hofmockel, K.S., Jansson, J.K., Anderton, C.R., Nelson, W.C. (2021)  Draft genome sequence of Fusarium sp. strain DS 682, a novel fungal isolate from the grass rhizosphere. Microbiology Resource Announcements.doi:10.1128/MRA.00884-20

2020

Jansson, J.K., & Hofmockel, K.S. (2020). Soil Microbiomes and Climate Change. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-019-0265-7

Bhattacharjee, A., Velickovic, D., Wietsma, T., Bell, S., Jansson, J., Hofmockel, K., and Anderton, C. (2020) Visualizing microbial community dynamics via a controllable soil environment. mSystems 5.  Feb 11;5(1) https://doi.org/10.1128/mSystems.00645-19

Lee, J., Sadler, N.C., Egbert, R.G., Anderton, C., Hofmockel, K.S., Jansson, J.K., Song, H.S. (2020) Deep Learning Predicts Microbial Interactions from Self-organized Spatiotemporal Patterns. Computational and Structural Biotechnology Journal. 18:1259-1269. https://doi.org/10.1016/j.csbj.2020.05.023.

Martiny, J., Whiteson, K., Bohannan, B., David, L., Hynson, N., McFall-Ngai, M., Rawls, J., Smidt, T., Abdo, Z., Blaser, M.J., Bordenstein, S., Brechot, C., Bull, C., Dorrestein, P., Eisen, J., Garcia-Pichel, F., Gilbert, J., Hofmockel, K., Holtz, M., Knight, R., Welch, D., Mcdonald, D., Methe, B., Mouncey, N., Mueller, N., Pfister, C., Proctor, L., Sachs, J., (2020) The emergence of microbiome centres. Nature Microbiology. Jan;5(1):2-3. https://doi.org/10.1038/s41564-019-0644-x

McClure, R.S., Lee, J.Y., Chowdhury, T.R., Bottos, E.M., White, R.A., Kim, Y.M., Nicora, C.D., Metz, T.O., Hofmockel, K.S., Jansson, J.K., Song, H.S. (2020) Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. Scientific Reports 10. Jul 2;10(1):1-9. https://doi.org/10.1038/s41598-020-67878-7

Naylor, D., Fansler, S., Brislawn, C., Nelson, W.C., Hofmockel, K.S., Jansson, J.K., McClure, R. (2020) Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. mBio. Aug 25;11(4). https://doi.org/10.1128/mBio.01349-20

Nelson, W.C., Anderson, L.N., Wu, R., McDermott, J.E., Bell, S.L., Jumpponen, A., Fansler, S.J., Tyrrell, K.J., Farris, Y., Hofmockel, K.S., Jansson, J.K. (2020) Terabase Metagenome Sequencing of Grassland Soil Microbiomes. Microbiology Resource Announcements. Aug 6;9(32). https://doi.org/10.1128/MRA.00718-20

Velickovic D., R.K. Chu, G.L. Myers, A. Ahkami, and C.R. Anderton. 2020. "An Approach For Visualizing The Spatial Metabolome Of An Entire Plant Root System Inspired by the Swiss-rolling Technique." Journal of Mass Spectrometry 55, no. 4:Article Number e4363. PNNL-SA-142631. doi:10.1002/jms.4363

Berg, G., Rybakova, D., Fischer, D., Cernava, T., Champomier-Vergès, M.C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Herrero-Corral, G., Kazou, M., Kinkel, L., Lange, L., Lima, N., Loy, A., Macklin, J.A., Maguin, E., Mauchline, T., McClure, R., Mitter, B., Ryan, M., Sarand, I., Smidt, H., Schelkle, B., Roume, H., Kiran, S.G., Selvin, J., de Souza, R.S.C., van Overbeek, L., Singh, B., Wagner, M., Walsh, A., Sessitsch, A., Schloter, M. (2020). Microbiome definition re-visited: old concepts and new challenges. Microbiome, 8(103):1-22. https://doi.org/10.1186/s40168-020-00875-0

Ryan, M.J., Schloter, M., Berg, G., Kostic, T., Kinkel, L.L., Eversole, K., Macklin, J.A., Schelkl, B., Kazou, M., Sarand, I., Singh, B.K., Fischer, D., Maguin, E., Ferrocino, I., Lima, N., McClure, R.S., Charles, T.C., de Souza, R.S.C., Kiran, G.S., Krug, H.L., Taffner, L., Roume, H., Selvin, J., Smith, D., Rybakova, D., Sessitsch, A. (2020). Requirements for the development of microbiome biobanks. Trends in Microbiology. https://doi.org/10.1016/j.tim.2020.06.009

Ahamed F., M. Singh, H. Song, P. Doshi, C. Ooi, and Y. Ho. 2020. "On The Use of Sectional Techniques for the Solution of Depolymerization Population Balances: Results on a Discrete-Continuous Mesh." Powder Technology 31, no. 7:2669-2679. PNNL-SA-132415. doi:10.1016/j.apt.2020.04.032

Naylor, D., Sadler, N., Bhattacharjee, A., Graham, E., Anderton, C., McClure, R., Lipton, M., Hofmockel, K., Jansson, J.K. (2020) Soil Microbiomes under Climate Change and Implications for Carbon Cycling. Annual Review of Environment and Resources. Oct 1;45. https://doi.org/10.1146/annurev-environ-012320-082720

Anderton C.R., J.M. Mobberley, J.K. Cole, J. Nunez, R.F. Starke, A.A. Boaro, and Y. Yesiltepe, et al. 2020. "Nitrogen source governs community carbon metabolism in a model hypersaline benthic phototrophic biofilm." mSystems 5, no. 3:Article No. e00260-20. PNNL-SA-145330. doi:10.1128/mSystems.00260-20

McClure, R., Naylor, D., Farris, Y., Davison, M., Fansler, S.J., Hofmockel, K.S., Jansson, J.K. (2020) Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome. Frontiers in Microbiology. Aug 26;11:1987.https://doi.org/10.3389/fmicb.2020.01987

Bhattacharjee, A., Thompson, A.M., Schwarz, K.C., Burnet, M.C., Kim, Y.M., Nunez, J.R., Fansler, S.J., Farris, Y., Brislawn, C.J., Metz, T.O., McClure, R.S. (2020) Soil microbial EPS resiliency is influenced by carbon source accessibility. Soil Biology and Biochemistry. Dec 1;151 https://doi.org/10.1016/j.soilbio.2020.108037

Zegeye, E.K., Sadler, N.C., Lomas, G.X., Attah, I.K., Jansson, J.K., Hofmockel, K.S., Anderton, C.R., Wright, A.T. (2020) Activity‐based protein profiling of chitin catabolism. ChemBioChem. Oct 13. https://doi.org/10.1002/cbic.202000616

Weitz, K.K., Smith, M.L., Hixson, K.K., Hill, E. A., Jansson, J.K., Hofmockel, K.S., Lipton, M.S. (2020) Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems. Journal of the American Society for Mass Spectrometry. Dec 1. https://doi.org/10.1021/jasms.0c00251

Lee J., S. Haruta, S. Kato, H. Bernstein, S.R. Lindemann, D. Lee, and J.K. Fredrickson, et al. 2020. "Prediction of Neighbor-dependent Microbial Interactions from Limited Population Data." Frontiers in Microbiology 10. PNNL-SA-144026. doi:10.3389/fmicb.2019.03049

2019

Boiteau, R.M., Fansler, S.J., Farris, Y., Shaw, J.B., Koppenaal, D.W., Pasa-Tolic, L., Jansson, J.K. (2019). Siderophore profiling of co-habitating soil bacteria by ultra-high resolution mass spectrometry. Metallomics, 11(1), 166-175. https://dx.doi.org/10.1039/c8mt00252e

Graham, E., Paez-Espino, D., Brislawn, C., Neches, R., Hofmockel, K., Wu, R., Kyrpides, N., Jansson, J., Mcdermott, J. (2019) Untapped Viral Diversity in Global Soil Metagenomes. bioRxiv. https://doi.org/10.1101/583997

Song, H.-S., Lee, J.-Y., Haruta, S., Nelson, W.C., Lee, D.-Y., Lindemann, S.R., et al. (2019). Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities. Frontiers in Microbiology, 10. https://dx.doi.org/10.3389/fmicb.2019.01264

Hutchins, D.A., Jansson, J.K., Remais, J.V., Rich, V. I., Singh, B.K., Trivedi, P. (2019). Climate change microbiology — problems and perspectives. Nature Reviews Microbiology, 17(6), 391-396. https://dx.doi.org/10.1038/s41579-019-0178-5

McClure, R.S. (2019). Toward a Better Understanding of Species Interactions through Network Biology. mSystems, 4(3). https://dx.doi.org/10.1128/mSystems.00114-19

Cavicchioli, R., Ripple, W.J., Timmis, K.N., Azam, F., Bakken, L.R., Baylis, M., et al. (2019). Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology. https://dx.doi.org/10.1038/s41579-019-0222-5

Chowdhury, T.R., Lee, J.Y., Bottos, E.M., Brislawn, C.J., White, R.A., 3rd, Bramer, L.M., et al. (2019). Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations. mSystems, 4(4). https://dx.doi.org/10.1128/mSystems.00061-19

Zegeye, E.K., Brislawn, C.J., Farris, Y., Fansler, S.J., Hofmockel, K.S., Jansson, J.K., et al. (2019). Selection, Succession, and Stabilization of Soil Microbial Consortia. mSystems, 4(4). https://dx.doi.org/10.1128/mSystems.00055-19

Lee, J.Y., Haruta, S., Kato, S., Bernstein, H.C., Lindemann, S., Lee, D.Y., Fredrickson, J.K., Song, H.S. (2019) Prediction of Neighbor-dependent Microbial Interactions from Limited Population Data. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.03049

2018

Jansson, J.K.,  Hofmockel, K.S. (2018). The soil microbiome – from metagenomics to metaphenomics. Current Opinion in Microbiology, 43, 162-168. https://dx.doi.org/10.1016/j.mib.2018.01.013

Colby, S.M., McClure, R.S., Overall, C.C., Renslow, R.S., McDermott, J.E. (2018). Improving network inference algorithms using resampling methods. BMC Bioinformatics, 19(1), 376. https://dx.doi.org/10.1186/s12859-018-2402-0

Song, H.S. (2018). Special issue: Microbial community modeling: Prediction of microbial interactions and community dynamics. Processes, 6(5). Editorial. https://dx.doi.org/10.3390/pr6050041