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

Reduction-dependent siderophore assimilation in a model pennate diatom

Coale, T.H., Horák, A., Obornik, M., Allen, A.E. (2019). Proceedings of the National Academy of Sciences


Euphotic zone nitrification in the California Current Ecosystem

Stephens, B.M., Wankel, S.D., Beman, J.M., Rabines, A., Allen, A.E., Aluwihare, L.I. (2019). Limnology and Oceanography


Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

Smith, S.R., Dupont, C.L., McCarthy, J.K., Broddrick, J.T., Oborník, M., Aleš Horák, A., Füssy, Z., Cihlář, J., Zheng, H., McCrow, J.P., Hixson, Kleessen, S., Araújo, W., Nunes-Nesi, A., Fernie, A., Nikoloski Z., Palsson, B.O., Allen, A.E. (2019) Nature Communications


Manganese and iron deficiency in Phaeocystis antarctica and the implications for Southern Ocean productivity

Wu, M., McCain, S.P., Rowland, E., Middag, R., Sandgren, M., Allen, A.E., Bertrand, E.B. (2019) Nature Communications


Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection

Kolody, B., McCrow, J., Zeigler-Allen, L., Aylward, F., Fontanez, K., Moustafa, A., Moniruzzaman, M., Chavez, F., Scholin, C., Allen, E., Worden, A., DeLong, E.F., Allen, A.E (2019) The ISME Journal

Silicon limitation facilitates virus infection and mortality of diatoms

Kranzler, C.F., Krause, J.W., Brzenzinski,, M.A., Edwards, B.R., Biggs, W.P., Maniscalco, M., McCrow, J.P., Van Mooy, B.A.S., Bidle, K.D., Allen, A.E., Thamatrakoln, K. (2019) Nature Microbiology


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

Latest News

Diatoms Have Found a Way to Pirate Bacterial Iron Sources, JCVI Scientists use CRISPR Technology to Discover How

Ph.D. student John Brunson awarded the 2019 Edward A. Frieman Prize for Excellence in Graduate Student Research

New A.E. Allen Lab Grant Funded: National Science Foundation, Division of Ocean Sciences - Iron Bioavailability in High-CO2 Oceans: New Perspectives on Iron Acquisition Mechanisms in Diatoms

New A.E. Allen Lab Grant Funded: National Science Foundation, Division of Molecular and Cellular Biosciences - Defining the Competitive Edge: Cellular Systems that Enable Nitrate Assimilation in Marine Diatoms

A. E Allen gives talk, Compartmentalized metabolic networks in a model photosynthetic eukaryotic microbe, at The Donald Danforth Plant Science Center, Fall Symposium 2018: Bioengineering: Synthetic Circuits to Sustainable Agriculture

Diatoms on the podcast This Week in Microbiology (TWiM)! The TWiM hosts discuss a carbonate-sensitive phytotransferrin in diatoms that controls iron uptake.

Dr. Jeff McQuaid Presents Poster on Carbonate Control of Iron Uptake in Diatoms at SCAR Conference

A.E. Allen is ASM Microbe 2018 Outstanding Abstract Award Winner for, Iron bioavailability in high-CO2 oceans: A new view of iron acquisition mechanisms in diatoms

Ph.D. student Jeffrey McQuaid awarded the 2018 Edward A. Frieman Prize for Excellence in Graduate Student Research

A.E. Allen discusses the impact of ocean acidification on ocean carbon storage on Radio Ecoshock