Nathan Ahlgren

Nathan Ahlgren, Ph.D.

Assistant Professor of Biology
Department of Biology
Clark University
Worcester, MA 01610-1477

Office: #337; Lab #311
Phone: 508.793.7107

Curriculum Vitae
Research Laboratory Website


Professor Ahlgren is a marine microbial ecologist. He is interested in understanding how environmental factors and interactions between microbes and viruses shape the evolution, diversity, and structure of microbial communities. Marine microbial communities are extremely diverse and control globally important cycles in the flow of nutrients and carbon on our planet. A fundamental component to understanding their importance to our planet is knowing what factors control and maintain the diversity and structure of these communities. Professor Ahlgren uses traditional culture isolation and laboratory studies along with cutting-edge DNA sequencing and bioinformatics approaches to elucidate key abiotic and biotic microbial interactions, including the impact of viruses on microbial communities. As such, his work addresses a variety of topics such as biogeographic patterns of microbial populations, models of microbial speciation, virus-host interactions, and the development computational tools for studying virus-host interactions.


Ph.D. University of Washington
M.S. University of Washington
B.S. Massachusetts Institute of Technology

Selected publications

Ahlgren, N. A.*, Ren, J.*, Lu, Y. Y., Fuhrman, J. A., Sun, F. (2016) Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Research. Published online Nov. 28, 2016 (* co-first authors)
Sohm, J.*, Ahlgren, N. A.*, Z. Thomson, C. Williams, J. W. Moffett, M. A. Saito, Rocap, G., Webb, E. (2015) Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, nutrients, and dissolved iron. ISME Journal, 10: 333-345 (* co-first authors)
Ahlgren, N. A., A. Noble, A. P. Patton, K. Roache-Johnson, L. Jackson, D. Robinson, C. McKay, L. R. Moore, M. A. Saito, G. Rocap. (2014) The unique trace metal and macronutrient conditions of the Costa Rica upwelling dome support a distinct and dense community of Synechococcus. Limnology & Oceanography, 59: 2166-2184
Ahlgren, N. A. and G. Rocap. (2012) Diversity and distribution of marine Synechococcus: multiple gene phylogenies for consensus classification and development of qPCR assays for sensitive measurement of clades in the ocean. Frontiers in Microbiology, 3:213
Ahlgren, N.A., A. Schaefer, E. Giraud, C. Harwood, E. P. Greenberg. (2011) Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia. Proceedings of the National Academy of Sciences, 108: 7183-8
Ahlgren, N. A. and G. Rocap. (2006) Culture isolation and culture-independent clone libraries reveal new ecotypes of marine Synechococcus with distinctive light and N physiologies. Applied and Environmental Microbiology, 72: 7193-204
Ahlgren, N. A., G. Rocap. S. W. Chisholm. (2006) Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies. Environmental Microbiology, 72: 723-32
Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser, S. W. Chisholm. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. (2003) Nature, 424:1042-47