Andrew Allen, Ph.D.

Comparative and functional genomics of eukaryotic marine phytoplankton

Andrew's research group aims to develop new knowledge and new hypotheses related to gene function, biochemical pathways, ecophysiology and other genome-scale characteristics that typify and distinguish the major microeukaryotic phytoplankton lineages.

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Research Description

Marine microbes underpin the function of the earth’s biosphere and serve as indicators of ocean change. Photosynthetic marine microbes account for around half of global photosynthesis annually and together viruses, bacteria and protists account for most of the organic carbon contained within biological entities and are crucial components of coastal and pelagic ecosystems. Knowledge related to microbial diversity and function represents one of the great data gaps in marine observations, despite the fact that marine food web dynamics and associated carbon, nitrogen, silica and other key ocean ecosystem nutrient cycles are largely regulated by microbial activity. Our research group aims to develop new knowledge and new hypotheses related to gene function, biochemical pathways, ecophysiology and other genome-scale characteristics that typify and distinguish the major microeukaryotic phytoplankton lineages. We will develop new resources and protocols for marine microeukaryotic functional genomics and systems biology, and pursue experimental approaches to characterize cellular and genome-scale processes that facilitate adaptation to physiological stress and regulate nutrient biogeochemistry.

Other studies aim to characterize eukaryotic phytoplankton interactions with bacteria and RNA viruses in order to investigate cellular defense, resistance and interaction mechanisms. We will perform ecological genomics experiments to elucidate biogeochemically relevant cellular features that influence the distribution and occurrence of major phytoplankton groups. Together these studies will integrate physiological, bioinformatic, statistical, functional and comparative genomics strategies and data streams to elucidate the regulatory networks that regulate nutrient flux for the major lineages of marine eukaryotic phytoplankton.

Research Impact

Our research group has been organizing and curating the emerging wealth of genomic information for marine microbes, in particular eukaryotic microbes. These computational and bioinformatics resources are enabling data-driven approaches for experimental investigation of cellular features and evolutionary themes that distinguish and characterize major lineages of eukaryotic phytoplankton. Comparative and evolutionary genomics analyses related to the origin and distribution of gene families within and between lineages provide a phylogenetic context for laboratory-based model organism and field-based ecological genomics studies. We are developing and optimizing methods for targeted genetic manipulations which, coupled with systems biology and modeling activities, are generating new information regarding the importance of particular transcripts, proteins and other genetic elements for controlling nutrient homeostasis and metabolism. These developing methods, cell lines and other resources are contributing to a new view of taxonomic and functional diversity and microbially mediated nutrient flux in the marine environment. Given the importance of understanding ecosystem productivity in various ocean regions to a range of scientific fields, these interdisciplinary studies are of broad interest. In particular, they are relevant for numerical modelers interested in ocean biogeochemistry as well as climate responses; microbiologists, plant scientists, evolutionary biologists as well as biogeochemists; paleoceanographers and climatologists; and microbial oceanographers.

Education

Ph.D., Nitrate Uptake by Heterotrophic Bacteria and the Diversity of Bacterial Nitrate Assimilation Genes in Marine Systems
Institute of Ecology, University of Georgia, 2002

B.A., Biology and English
Vassar College, 1996

Awards

Kavli Frontiers of Science Fellow

NSF Postdoctoral Research Fellowship in Microbial Biology, A Partial Genome Microarray for the Study of Fe and N Metabolism in the Coastal Marine Diatom Thalassiosira pseudonana

DIALOG V Symposium Invited Participant
American Society of Limnology and Oceanography

Best Ph.D. student presentation at the University of Georgia, Institute of Ecology Graduate Student Symposium

Award of Distinction for Outstanding Senior Biology Thesis, Effects of Anoxia on Metabolism of the Green Macroalga (Ulva lactuca) and the Brown Algae (Alaria esculenta), Department of Biology, Vassar College, May 1996

Award of Distinction for Outstanding Senior English Thesis, Patriotic Responsibility on the Nationalist Frontier, A Bioregional Literary Analysis of Cooperstown New York
Department of English, Vassar College, May 1996

Papers

Sommer, U., Dupont, C.L, Allen, A.E., Viant, M.R. (2014). Using community metabolomics as a new approach to discriminate marine microbial particulate organic matter in the Western English Channel. Progress in Oceanography (In Press)

Morrissey, J., Tanaka, A., Sutak, R., Moustafa, A., Veluchamy, A., Thomas, Y., Botebol, H., Bouget, F-Y., Trichine, L., Allen, A.E., Lesuisse, E., Bowler, C. (2014). A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and mediates ferric ion uptake. Current Biology (In Press)

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. (2014). Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.The ISME Journal. Advance online publication, 21 October, doi:10.1038/ismej.2014.198

Paerl,R.W., Bertrand,E.M., Allen,A.E., Palenik,B., Azam, F. (2014). Vitamin B1 ecophysiology of marine picoeukaryotic algae: Strain-specific differences and a new role for bacteria in vitamin cycling. Limnology and Oceanography (In Press)

Weyman, P.D., Beeri, K., Lefebvre, S.C., Rivera, J., Heuberger, A., Peers, G., Allen, A.E., Dupont, C.L. (2014). Inactivation of Phaeodactylum tricornutum urease gene using TALEN-based targeted mutagenesis. Plant Biotechnology Journal. Article first published online: 10 Oct, doi: 10.1111/pbi.12254

Dupont, C.L., Larsson, J., Yooseph,S., Ininbergs, Goll, J., Asplund-Samuelsson, J., McCrow, J.P., Celepli, N., Allen, L.Z., Ekman, M., Lucas, A.J., Hagström, Å., Thiagarajan, M., Brindefalk, B., Richter, R.A., Andersson, A.F., Tenney, A., Lundin, D., Tovchigrechko, A., Nylander, J.A.A., Brami, D., Badger, J.H., Allen, A.E., Rusch, D.B., Hoffman, J., Norrby, E., Friedman, R., Pinhassi, J., Venter, J.C., Bergman, B. (2014). Functional tradeoffs underpin salinity-driven divergence in microbial community composition. Ploss ONE. Published: February 27, 2014, doi: 10.1371/journal.pone.008954

Karas, B.J., Molparia, B., Jablanovic, J., Hermann, W.J., Lin,Y-C., Dupont, C.L., Tagwerker, C., Yonemoto, I.T., Vladimir, N.N., Chuang, R-Y., Allen, A.E., Glass, J.I., Hutchison III, C.A., Smith, H.O., Venter, J.C., Weyman, P.D. (2013). Assembly of eukaryotic algal chromosomes in yeast. J Biol Eng. Dec 10;7(1):30. doi: 10.1186/1754-1611-7-30

Smith, D.R., Arrigo, K., Alderkamp, Anne-Carlijn, Allen, A.E. (2013). Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes in Phaeocystis algae. Mol Phylogenet Evol. Nov 8;71C:36-40. doi: 10.1016/j.ympev.2013.10.018. [Epub ahead of print]

Allen, A.E., Allen, LZ. McCrow, J.P. (2013). Lineage specific gene family enrichment at the microscale in marine systems. Current Opinion in Microbiology. Available online 23 October. doi: 10.1016/j.mib.2013.10.001

Noble, A.E., Moran, D.M, Allen, A.E., Saito, M.A. (2013). Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice: basal sea ice communities as a capacitor for iron. Frontiers and in Microbiological Chemistry. Online early. doi: 10.3389/fchem.2013.00025

McLean, J.S., Lombardo, M.J., Badger, J.H., Edlund, A., Novotny, M., Yee-Greenbaum, J., Vyahhi, N., Hall, A., Dupont, C.L., Ziegler, M.G., Chitsaz, H., Allen, A.E., Tesler, G., Yooseph, S., Pevzner, P.A., Friedman, R., Nealson, K.H., Venter, J.C., Lasken, R.S. (2013). Sequencing “dark matter of life” within a biofilm from hospital restroom reveals a candidate division TM6 genome representing a new class of proteobacteria. Proceedings of the National Academy of Sciences. Online June 10, 2013. doi: 10.1073/pnas.1219809110

Veluchamy, A., Lin, X., Maumus, F., Rivarola, M., Bhaysar, J., Creasy, T., O’brien, K., Sengamalay, N., Tallom, L.J., Simth, A.D., Rayko, E., Ahmed, I., Crom, S., Farrant, G., Sgro, J.Y., Sue, O., Bondurant, S.P., Allen, A.E., Rabinowicz, P., Sussman, M., Bowler, C. (2013). Insights into the role of DNA methylation in Diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nature Communications 2013, 4, 2091, doi: 10.1038/ncomms3091

Smith, M.W., Allen, L.Z., Allen, A.E., Herfort, L., Simon, H.M. (2013). Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Frontiers in Microbiology, 4:120. doi: 10.3389/fmicb.2013.00120

Bertrand, E.M., Moran, D.M., McIlvin, M.R., Hoffman, J.M., Allen, A.E., Saito, M.A. (2013). Methionine synthase interreplacement in diatom cultures and communities: Implications for the persistence of B₁₂ use by eukaryotic phytoplankton. Limnology and Oceanography, 58(4), 1431-1450.

Read, B.A., et al. (2013). Emiliania’s pan genome drives the phytoplankton’s global distribution. Nature. Jul 11;499(7457):209-13. doi: 10.1038/nature12221. Epub 2013 Jun 12.

Kontchick, T., Dupont, C.L., Valas, R.E., Badger, J.H., Allen, A.E. (2013). Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. New Phytologist; 198(2):398-407. doi: 10.1111/nph.12160. Epub 2013 Mar 13.

Cock, M., Sterck, L., Ahmed, S., Allen, A.E., et al. (2012). The Ectocarpus genome and brown algal genomics. Advances in Botanical Research 64: 141-184.

Bertrand, E.M., Allen, A.E. (2012). Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton. Front. Microbio. 3:375. doi: 10.3389/fmicb.2012.00375

Shrestha, R.P., Tesson, B., Norden-Krichmar, T., Federowicz, S., Hildebrand, M., Allen, A.E. (2012). Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana. BMC Genomics 13:499. Sep 20;13(1):499. [Epub ahead of print] doi: 10.1186/1471-2164-13-499

Brown, M.V., Lauro, F.M., Muir, L., Wilkins, D., DeMaere, M.Z., Thomas, T., Riddle, M., Fuhrman, J., Andrews-Pfankoch, C., Lewis, M., Hoffman, J.M., Allen, A.E., Rintoul, S.R., Cavicchioli, R. (2012). Temperature defined biogeographic boundaries in marine bacteria. Molecular Systems Biology 8:595. Published online 2012 July 17. doi: 10.1038/msb.2012.28

Loper, J.E., (29 co-authors), Allen, A.E., Paulsen, I.T. (2012). Comparative genomics of plant-associated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genetics 8(7): e1002784. doi: 10.1371/journal.pgen.1002784

Bertrand, EM, Allen, A.E., Dupont, C.L., Norden-Krichmar, T.M., Bai, J., Valas, R.E., Saito, M.A. (2012). Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein. Proceedings of the National Academy of Sciences. Published ahead of print May 31, 2012, doi: 10.1073/pnas.1201731

Fernie, A.R., Obata, T., Allen, A.E., Araújo, W.L., Bowler, C. (2012). Leveraging metabolomics for functional investigations in sequenced marine diatoms. Trends in Plant Science. Published online March 30, 2012. doi: 10.1016/j.tplants.2012.02.005

Allen, L.Z., Allen, E.A., Badger, J.H., McCrow, J.P., Paulsen, I.T., Elbourne, L.D.H., Thiagarajan, M., Rusch, D.B., Nealson, K.H., Williamson, S.J., Venter, J.C., Allen, A.E. (2012). Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME Journal. Published online January 26, 2012. doi: 10.1038/ismej.2011.201

Marchetti, A., Schruth, D.M., Durkin, C.A., Parker, M.S., Kodner, R. Berthiaume, C.T., Morales, R., Allen, A.E., Armbrust, E.V. (2012). Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proceedings of the National Academy of Sciences of the United States of America, USA. Published online January 18, 2012. doi: 10.1073/pnas. 1118408109

Allen, A.E., A. Moustafa, A. Montsant, A. Eckert, P.G. Kroth, C. Bowler. (2011). Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms. Molecular Biology and Evolution. (2012) 29:367-379, first published online September 368, 2011 doi: 2010.1093/molbev/msr

Norden-Krichmar, T.M., Allen, A.E., Gaasterland, T., Hildebrand, M. (2011). Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS ONE 6(8): e22870. doi: 10.1371/journal.pone.002870

Worden, A.Z., Dupont, C.L., Allen, A.E. (2011). Genomes of uncultured eukaryotes: sorting FACS from fiction. Genome Biology, 12:117.

Allen, A.E., Dupont,C.L., Oborník, M., Horák, A., Nunes-Nesi, A., McCrow, J.P., Zheng, H., Johnson, D.A., Hu, H., Fernie, A.F., Bowler, C. (2011). Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature 473(7346):203-7.

Tachibana, M., Allen, A.E., Kikutani, S., Endo, Y., Bowler, C., Matsuda. (2011). Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. Photosynthesis Research. Advance access published March 2, 2011, doi: 10.1007/s11120-011-9634-4

Hopkinson, B.M., Dupont, C.L., Allen, A.E., Morel, F.M.M. (2011). Efficiency of the CO2-concentrating mechanisms of diatoms. Proceedings of the National Academy of Sciences of the United States of America, USA. 108(10):3830-7.

Yooseph, S., Nealson, K., Rusch, D.B., McCrow, J.P., Kim, M., Johnson, J., Montgomery, R., Ferriera, S., Beeson, K., Williamson, S.J., Tovchigrechko, A., Allen, A.E., Dupont, C.L., Zeigler, L.A., Sutton, G., Eisenstadt, E., Rogers, Y.H., Friedman, R., Frazier, M., Venter, J.C. (2010.) Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 468, 60-66.

Worden, A.Z., Allen, A.E. (2010). Voyage of the microbial eukaryote. Current Opinion in Microbiology 13(5), 652-660.

Cuvelier M.L., Allen A.E., Monier A., McCrow J., et al. (2010). Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences of the United States of America, USA 107, 14679-14684

Cock, M., Sterck, L., Rouze, P., Scornet, D., Allen, A.E., et al. (2010). The Ectocarpus genome and the independent evolution of mulicellularity in the brow algae. Nature 465, 617-621.

Maheswari U., Jabbari K., Petit J.L., Porcel B.M., Allen A.E., Cadoret J.P., De Martino A., Heijde M., La Roche J., Lopez P.J., Martin-Jezequel V., Mock T., Parker M.S., Vardi A., Armbrust E.V., Weissenbach J., Katinka M., Bowler C. (2010). Digital expression profiling of novel diatom transcripts provides insights into their biological functions. Genome Biology 11:R85

Bowler, C., Vardi, A., Allen, A.E. (2010). Oceanographic and biogeochemical insights from diatom genomes. Annual Review of Marine Sciences. 2:333-365

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