Environmental Systems Biology – Cellular Processes to Biogeochemical Cycles

Our team is engaged in research at the intersection of biological and microbial oceanography and functional genomics. We are a joint lab group between the Integrative Oceanography Division at Scripps Institution of Oceanography, University of California, San Diego and the Environmental and Microbial Genomics department at the J. Craig Venter Institute (JCVI). We combine laboratory and field studies to investigate the ecology, evolution and biogeochemistry of phytoplankton and other microbes and are motivated by basic research questions related to the function marine ecosystems.

Selected Recent Research

Cross-compartment metaoblic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum

Broddrick J.T., Du N., Smith S.R., Tsuji Y., Jallet D., Ware M.A., Peers G., Matsuda Y., Dupont C.L., Mitchell B.G., Palsson B.O., Allen A.E. (2019) New Phytologist.

Carbonate sensitive phytotransferrin controls high affinity iron uptake in diatoms

McQuaid, J.B., Kustka, A.B., Oborník, M., Horák, A., McCrow, J.P., Karas, B.J., Zheng, H., Andersson, A.J., Barbeau, K.A., Allen, A.E. (2018) Nature.


Biosynthesis of the amnesic shellfish poison domoic acid in a bloom forming diatom

Brunson, J.K., McKinnie, S.M.K., Chekan, J.R., McCrow, J.P., Miles, Z.D., Bertrand, E.M., Bielinski, V.A., Luhavaya, Obornik, M., Smith, G.J., Hutchins, D.A., Allen, A.E., Moore, B.S. (2018) Science.


Pervasive iron limitation at subsurface chlorophyll maxima of the California Current

Hogle S., Dupont, C.L., Hopkinson, B., King, A.L., Buck, K.N., Roe, K.L., Stuart, R.K., Allen, A.E., Mann, E.L., Johnson, Z., Barbeau, K. (2018) Proceedings of the National Academy of Sciences


Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron Biogeochemistry

Bender, S.J., Moran, D., McIlvin, M., Zheng, H., McCrow, J.P., Allen, A.E., Saito, M. (2018) Biogeosciences


Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom

Murik, O., Tirichine, L., Prihoda, J., Thomas, Y., Araújo, W., Allen, A.E., Fernie, A., and Bowler, C. (2018) New Phytologist


Impact of temperature, CO2, and iron on nutrient uptake by a late-season microbial community from the Ross Sea

Spackeen, J.L., Sipler, R.E., Bertrand, E.B., Xu, K., McQuaid, J.B., Walworth, N.G., Hutchins, D.A., Allen, A.E., Bronk, D.A. (2018) Aquatic Microbial Ecology


Stoichiometric N:P ratios, temperature, and iron impact carbon and nitrogen uptake by Ross Sea microbial communities

Spackeen, J.L., Bronk, D.A., Sipler, R.E., Bertrand, E.M., Hutchins, D.A., Allen, A.E. (2018) Journal of Geophysical Research: Biogeosciences


Evolutionary genomics of a cold-adapted diatom, Fragilariopsis cylindrus

Mock, T., Otillar, R.P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., Salamov, S., Sanges, R., Toseland, A., Ward, B.J., Allen, A.E., et al. (2017) Nature


Nitrate reductase knockout uncouples nitrate transport from nitrate assimilation and drives repartitioning of carbon flux in a model pennate diatom

McCarthy, J., Smith, S., McCrow, J., Tan, M., Zheng, H., Beeri, K., Roth, R., Lichtle, C., Goodenough, U., Bowler, C., Dupont, C., Allen, A.E. (2017) The Plant Cell


Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Diner, R.E, Noddings, C.M., Lian, N.C., Kang, A.K., McQuaid, J.B., Jablanovic, J., Nguyen, Anzelmatti, M.A., Espinoza, J.L., Jansson, J., McCrow, J.P., Bielinski, V.A., Karas, B.J., Dupont, C.L., Allen, A.E., Weyman, P.D. (2017) Proceedings of the National Academy of Sciences


Probing the evolution, ecology, and physiology of marine protists using transcriptomics

Caron, D.A., Alexander, H., Allen, A.E., et al. (2017) Nature Reviews Microbiology


Transcriptional orchestration of the global cellular response of a model pennate diatom to diel light cycling under iron limitation

Smith, S.R., Gillard, J.T.F., Kustka, A., McCrow, J.P., Badger, J.H., Zheng, H., Dupont, C.L., Obata, T., Fernie, A.R., Allen, A.E. (2016) PLoS Genetics


Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge

Bertrand, E.M., McCrow, J.P., Moustafa, A., Zheng, H., McQuaid, J., Delmont, T., Post, A.F., Sipler, R., Spackeen, J.L., Xu, K., Bronk, D.A., Hutchins, D.A., Allen, A.E. (2015) Proceedings of the National Academy of Sciences


Designer diatom episomes delivered by bacterial conjugation

Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips APR, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JTF, Beeri K, Ellisman MH, Glass JI, Hutchison III CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD. (2015) Nature Communications


Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Dupont, C.L., Valas, R., McCrow, J.P., Moustafa, A., Walworth, N., U. Goodenaugh, U., Roth, R., Hogle, S., Bai, J. Johnson, Z., Mann, E., Palenik, B., Barbeau, K., Venter, J.C., Allen, A.E. ­­(2015) The ISME Journal