Klein, A.O., Carlisle, L., Lloyd, M.G., Sayre, N.F,  Bowles, T.M. Understanding farmer knowledge of soil and soil management: a case study of 13 organic farms in an agricultural landscape of northern California. Agroecology and Sustainable Food Systems (link)

Vendig, I., Guzman, A., DeLaCerda, G., Esquivel, K., Mayer, A.C., Ponisio, L., Bowles, T.M. Quantifying direct yield benefits of soil carbon increases from cover cropping. Nature Sustainability. (link)

Smith, M.E., Vico, G., Costa, A., Bowles, T.M., … [31 co-authors] … Bommarco, R. Increasing crop rotational diversity to enhance cereal yields. Communications Earth and Environment 4, 89 (link)

Stanley, P., Spertus, J., Chiartas, J., Stark, P.B., Bowles, T.M. Valid inferences about soil carbon in heterogeneous landscapes. Geoderma 430: 116323 (link)

Thompson, J., Symonds, J., Carlisle, L., Iles, A., Karp, D.S., Ory, J., Bowles, T.M. Remote sensing of hedgerows, windbreaks, and winter cover crops in California’s Central Coast reveals low adoption but hotspots of use. Frontiers in Sustainable Food Systems. 7:1052029. (link)

Breza, L.C., Mooshammer, M., Bowles, T.M., Jin, V.L., Schmer, M.R., Thompson, B., Grandy, A.S. Complex crop rotations improve organic nitrogen cycling. Soil Biology and Biochemistry 177, 108911 (link)


Acevedo, S.E., Waterhouse, H., Barrios-Masias, F., Dierks, J., Renwick, L.R., Bowles, T.M. How does building healthy soils impact the sustainable use of water resources in irrigated agriculture? Elementa: Science of the Anthropocene 10 (1): 00043 (link)

Grandy, A.S., Daly, A.B., Bowles, T.M., Gaudin, A.C.M., Jilling, A., Leptin, A., McDaniel, M.D., Wade, J., Waterhouse, H. The nitrogen gap in soil health concepts and fertility measurements. Soil Biology and Biochemistry 175, 108856 (link)

Salomon, M.J., Watts-Williams, S.J., McLaughlin, M.J., Bücking, H., Singh, B.K., Hutter, I., Schneider, C., Martin, F.M., Vosatka, M., Guo, L., Ezawa, T., Saito, M., Declerck, S., Zhu, Y.-G., Bowles, T., Abbott, L.K., Smith, F.A., Cavagnaro, T.R., van der Heijden, M.G.A., 2022. Establishing a quality management framework for commercial inoculants containing arbuscular mycorrhizal fungi. iScience 25, 104636. (link)

Smith, O.M., Olimpi, E.M., Navarro‐Gonzalez, N., Cornell, K.A., Frishkoff, L.O., Northfield, T.D., Bowles, T.M., Edworthy, M., Eilers, J., Fu, Z., Garcia, K., Gonthier, D.J., Jones, M.S., Kennedy, C.M., Latimer, C.E., Owen, J.P., Sato, C., Taylor, J.M., Wilson‐Rankin, E.E., Snyder, W.E., Karp, D.S., 2022. A trait‐based framework for predicting foodborne pathogen risk from wild birds. Ecological Applications 32. (link)

Debray, R., Socolar, Y., Kaulbach, G., Guzman, A., Hernandez, C.A., Curley, R., Dhond, A., Bowles, T.*, Koskella, B.*, 2022. Water stress and disruption of mycorrhizas induce parallel shifts in phyllosphere microbiome composition. New Phytologist 234, 2018–2031. (link) *co-senior authors

Mooshammer, M., Grandy, A.S., Calderón, F., Culman, S., Deen, B., Drijber, R.A., Dunfield, K., Jin, V.L., Lehman, R.M., Osborne, S.L., Schmer, M., Bowles, T.M., 2022. Microbial feedbacks on soil organic matter dynamics underlying the legacy effect of diversified cropping systems. Soil Biology and Biochemistry 167, 108584. (link)

Bowles, T.M., Jilling, A., Morán-Rivera, K., Schnecker, J., Grandy, A.S., 2022. Crop rotational complexity affects plant-soil nitrogen cycling during water deficit. Soil Biology and Biochemistry 166, 108552. (link)

Chapman, M., Wiltshire, S., Baur, P., Bowles, T., Carlisle, L., Castillo, F., Esquivel, K., Gennet, S., Iles, A., Karp, D., Kremen, C., Liebert, J., Olimpi, E.M., Ory, J., Ryan, M., Sciligo, A., Thompson, J., Waterhouse, H., Boettiger, C., 2022. Social-ecological feedbacks drive tipping points in farming system diversification. One Earth 5, 283–292. (link)

Carlisle, L.*, Esquivel, K.*, Baur, P., Ichikawa, N.F., Olimpi, E.M., Ory, J., Waterhouse, H., Iles, A., Karp, D.S., Kremen, C., Bowles, T.M., 2022. Organic farmers face persistent barriers to adopting diversification practices in California’s Central Coast. Agroecology and Sustainable Food Systems 46, 1145–1172. (link) *co-first authors


Esquivel, K.E.*, Carlisle, L.*, Ke, A., Olimpi, E.M., Baur, P., Ory, J., Waterhouse, H., Iles, A., Karp, D.S., Kremen, C., Bowles, T.M., 2021. The “Sweet Spot” in the Middle: Why Do Mid-Scale Farms Adopt Diversification Practices at Higher Rates? Frontiers in Sustainable Food Systems 5, 1–16. (link) *co-first authors

Salerno, J., Stevens, F.R., Gaughan, A.E., Hilton, T., Bailey, K., Bowles, T., Cassidy, L., Mupeta-Muyamwa, P., Biggs, D., Pricope, N., Mosimane, A.W., Henry, L.M., Drake, M., Weaver, A., Kosmas, S., Woodward, K., Kolarik, N., Hartter, J., 2021. Wildlife impacts and changing climate pose compounding threats to human food security. Current Biology 31, 5077-5085.e6. (link)

Renwick, L.L.R., Deen, W., Silva, L., Gilbert, M.E., Maxwell, T., Bowles, T.M., Gaudin, A.C.M., 2021. Long-term crop rotation diversification enhances maize drought resistance through soil organic matter. Environmental Research Letters 16, 084067. (link)

Socolar, Y., Goldstein, B. R, de Valpine, P., Bowles, T. M. Biophysical and policy factors predict simplified crop rotations in the US Midwest. Environmental Research Letters. (link)

Daly, A.  B., Jilling, A., Bowles, T. M., Buchkowski, R.W., Frey, S. D., Kallenbach, C. M., Keiluweit, M., Mooshammer, M., Schimel, J. P., Grandy, A. S. A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen. Biogeochemistry. (link)

Guzman, A., Montes, M., Hutchins, L., DeLaCerda, G., Yang, P., Kakouridis, A., Dahlquist-Willard, R., Firestone, M., Bowles, T. M., Kremen, C. Crop diversity enriches arbuscular mycorrhizal fungal communities in an intensive agricultural landscape. New Phytologist. (link)

Petersen-Rockney, M., Baur, P., Guzman, A., Bender, S. F., Calo, A., Castillo, F., De Master, K., Dumont, A., Esquivel, K., Kremen, C., LaChance, J., Mooshammer, M., Ory, J., Price, M. J., Socolar, Y., Stanley, P., Iles, A., Bowles,. T. M. Narrow and Brittle or Broad and Nimble? Comparing Adaptive Capacity in Simplifying and Diversifying Farming Systems. Frontiers in Sustainable Food Systems. 5:564900. (link)


Rainey, C., Egerer, M., Herrmann, D., Bowles, T.M. Restoring soil and supporting food sovereignty in an urbanizing world: An interdisciplinary perspective. In: Urban Agroecology – Interdisciplinary Research and Future Directions. Eds Egerer, M., Cohen, H. CRC Press. (book chapter)

Bowles, T. M., Mooshammer, M., Socolar, Y., Calderón, F., Cavigelli, M.A., Culman, S.W., Deen, W., Drury, C.F., Garcia y Garcia, A., Gaudin, A., Harkom, W.S., Lehman, R.M., Osborne, S.L., Robertson, G.P., Salerno, J., Schmer, M.R., Strock, J., and Grandy, A.S. Long-term evidence shows crop rotation diversification increases agricultural resilience to adverse growing conditions in North America. One Earth 2: 1-10 (link)

Wade, J., … Bowles, T.M. … + 32 co-authors. Assessing the sensitivity and repeatability of permanganate oxidizable carbon as a soil health metric: an interlab comparison across soils. Geoderma (link)


Schnecker, J., Bowles, T.M., Hobbie, E., Smith, R.G., Grandy, A.S. Carbon concentration controls decomposition and microbial strategies in a model soil system. Biogeochemistry 144: 47-59.

Jackson, L.E., Bowles, T.M., Ferris, H., Margenot, A., Hollander, A., Garcia-Palacios, P., Duafresne, T., Sánchez-Moreno, S. Plant and soil biodiversity across the borders between arable and forest ecosystems in a Mediterranean landscape. Applied Soil Ecology 136: 122-138.

Renwick, L.R., Bowles, T.M., Deen W., Gaudin, ACM. Potential of increased temporal crop diversity to improve resource use efficiencies: exploiting water and nitrogen linkages. In: Agroecosystem Diversity: Reconciling Contemporary Agriculture and Environmental Quality. (peer-reviewed book chapter).


Bowles, T.M., Atallah, S.S., Campbell, E.E, Gaudin, A.C.M., Wieder, W.R., Grandy, A.S. Addressing agricultural nitrogen losses in a changing climate. Nature Sustainability 1: 399-408

Herrmann, D.L., Chuang, W.-C., Schwarz, K., Bowles, T.M., Garmestani, A.S., Schuster, W., Eason, T., Hopton, M.E., Allen, C.R. Agroecology for the shrinking city. Sustainability 10: 1-14.

Bowles, T.M., Jackson, L.E., Cavagnaro, T.R. Mycorrhizal fungi modulate plant and nitrogen loss responses to varying amounts and patterns of water supply. Global Change Biology 24: e171-e182.


Bowles, T.M., Jackson, L.E., Loeher, M., Cavagnaro, T.R. Ecological intensification and arbuscular mycorrhizas: a meta-analysis of tillage and cover crop effects. Journal of Applied Ecology 54: 1785-1793.


Hurriso, T.T., Culman, S.W., Horwath, W.R., Wade, J., Beniston, J.W., Bowles, T.M., Grandy, A.S., Frankluebbers., A.J., Schipanski, M.E., Lucas, S., Ugarte, C. Comparison of permanganate oxidizable carbon and mineralized C to assess organic matter stabilization and mineralization. Soil Science Society of America Journal 80:1352-1364

Bowles, T.M., Barrios-Masias, F.H., Carlisle, E.A., Cavagnaro, T.R., Jackson, L.E. Effects of arbuscular mycorrhizae on tomato yield, nutrient uptake, water relations, and soil carbon dynamics under deficit irrigation in field conditions. Science of the Total Environment 566-567: 1223-1234

Schimdt, J.E., Bowles, T.M., Gaudin, A.C.M. Using ancient traits to convert soil health into crop yield: Impact of selection on maize root and rhizosphere function. Frontiers in Plant Science 7:373. (Link)


Bowles, T.M., Hollander, A.D., Steenwerth, K., Jackson, L.E. Tightly-coupled plant-soil nitrogen cycling: Comparison of organic farms across an agricultural landscape. PLoS ONE 10(6):e0131888 (Link)

Margenot, A.J., Calderón, F.J., Bowles, T.M., Parikh, S.J., Jackson, L.E. Soil organic matter functional group composition in relation to organic C, N, and P fractions in organically-managed tomato fields characterized by mid-infrared spectroscopy. Soil Science Society of American Journal 79: 772-782.

Bowles, T.M., Raab, P., Jackson, L.E. Root expression of nitrogen metabolism genes reflects soil nitrogen cycling in an organic agroecosystem. Plant and Soil 392: 175-189.


Bowles, T.M., Acosta-Martínez, V., Calderón, F.J., Jackson, L.E. Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape. Soil Biology and Biochemistry 68, 252-262.

Prior to 2014

Du, W., Josephrajan, A., Adhikary, S., Bowles, T., Bielinsky, A.K., Eichman, B.F. Mcm10 self-association is mediated by an N-terminal coiled-coil domain. PLoS ONE, 8(7), e70518. (Link)

Jackson, L.E., Bowles, T.M., Hodson A.K., Lazcano, C. Soil microbial-root and –microbial-rhizosphere processes to increase nitrogen availability and retention in agroecosystems. Current Opinion in Environmental Sustainability 4, 517-522.

Bowles, T.*, Metz, A.H.*, O’Quin, J., Wawrzak, Z., Eichman B.F. Structure and DNA binding of alkylation response protein AidB.  Proc. Natl. Acad. Sci., USA, 105, 15299-15304. (*equal contribution) (PDF)

Kendall, A., McDonald, M., Bian, W., Bowles, T., Baumgarten, S.C., Shi, J., Stewart, P.L., Bullitt, E., Gore, D., Irving, T.C., Havens, W.M., Ghabrial, S.A., Wall, J.S., Stubbs, G. Structure of flexible filamentous plant viruses. J Virol. 82, 9546-54.

Stubbs, G., Kendall, A., McDonald, M., Bian, W., Bowles, T., Baumgarten, S., McCullough, I., Shi, J., Stewart, P., Bullitt, E., Gore, D. and Ghabrial, S. Flexible filamentous virus structures from fiber diffraction. Powder Diffraction 23, 113-117.