Publications  » 2017   2016   2015   2014   2013   2012   2011


Durham, B. P., S. P. Dearth, S. Sharma, S. A. Amin, C. B. Smith, S. R. Campagna, E. V. Armbrust, and M. A. Moran. 2017. Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. Environmental Microbiology. In press.

Landa, M., A. S. Burns, S. J. Roth, and M. A. Moran. 2017. Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom. ISME Journal. In press.

Satinsky, B. M., C. B. Smith, S. Sharma, M. Landa, P. M. Medeiros, V. J. Coles, P. L. Yager, B. C. Crump, and M. A. Moran. 2017. Bacterial biogeography across the Amazon river-ocean continuum. ISME Journal 11:1852-1864.

Medeiros, P. M, M. Seidel, S. M Gifford, F. Ballantyne, T. Dittmar, W. B Whitman, and M. A. Moran. 2017. Microbially-mediated transformations of estuarine dissolved organic matter. Frontiers in Marine Science 4:69.

Sun, Y., K. E. Powell, W. Sung, M. Lynch, M. A. Moran, and H. Luo. 2017. Spontaneous mutations of a model heterotrophic marine bacterium. ISME Journal 11:1713-1718.


Burns, A.S., H. A. Bullock, C. B. Smith, Q. Huang, W. B. Whitman, and M. A. Moran. 2016. sRNAs expressed during DMSP degradation by a model marine bacterium. Environmental Microbiology Reports 8: 763–773.

Luo, H., Y. Sun, J. T. Hollibaugh, and M. A. Moran. 2016. Low genome content diversity of marine planktonic Thaumarchaeota. Environmental Microbiology 8:501–507.

Rivers, A. R., A. S. Burns, L.-K. Chan, and M. A. Moran. 2016. Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3. Frontiers in Microbiology 7:380.

Moran, M. A., E. B. Kujawinski, A. Stubbins, R. Fatland, L. I. Aluwihare, A. Buchan, B. C. Crump, P. C. Dorrestein, S. T. Dyhrman, N. J. Hess, B. Howe, K. Longnecker, P. M. Medeiros, J. Niggemann, I. Obernosterer, D. J. Repeta, J. R. Waldbauer. Deciphering ocean carbon in a changing world. Proceedings of the National Academy of Sciences 113:3143–3151.

Bendall, M. L., S. L. R. Stevens, L.-K. Chan, S. Malfatti, P. Schwientek, J. Tremblay, W. Schackwitz, J. Martin, A. Pati, B. Bushnell, J. Froula, D. Kang, S. Tringe, S. Bertilsson, M. A. Moran, A. Shade, R. Newton, K. D. McMahon and R. R. Malmstrom. 2016. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME Journal 10:1589–1601.



Moran, M. A. 2015. The global ocean microbiome. Science 350:aac845. Reprint

Satinsky, B. M., C. S. Fortunato, M. Doherty, C. B. Smith, S. Sharma, N. D. Ward, A. V. Krusche, P. L. Yager, J. E. Richey, M. A. Moran, and B. C. Crump. 2015. Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011. Microbiome 3:39.

Amin, S. A., L. R. Hmelo, H. M. van Tol, B. P. Durham, L. T. Carlson, K. R. Heal, R. L. Morales, C. T. Berthiaume, M. S. Parker, B. Djunaedi, A. E. Ingalls, M. R. Parsek, M. A. Moran, and E. V. Armbrust. 2015. Interaction and signaling between a cosmopolitan phytoplankton and associated bacteria. Nature 522: 98–101.

Durham, B. P., S. Sharma, H. Luo, C. B. Smith, S. A. Amin, S. J. Bender, S. P. Dearth, B. A. S. Van Mooy, S. R. Campagna, E. B. Kujawinski, E. V. Armbrust, and M. A. Moran. 2014. Cryptic carbon and sulfur cycling between surface ocean plankton. Proceedings of the National Academy of Sciences 112: 453–457.

Beier, S., A. Rivers, M. A. Moran, and I. Obernosterer. 2015. Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures. ISME Journal 9: 1141-1151.

Medeiros, P. M., M. Seidel, T. Dittmar, W. B. Whitman, and M. A. Moran. 2015. Drought-induced variability in dissolved organic matter composition in a marsh-dominated estuary. Geophysical Research Letters 42:6446–6453.

Luo, H. and M. A. Moran. 2015. How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends in Microbiology 23: 577–584.

Varaljay, V. A., J. Robidart, C. M. Preston, S. M. Gifford, B. P. Durham, A. S. Burns, J. P. Ryan, R. Marin, R. P. Kiene, J. P. Zehr, C. A. Scholin, & M. A. Moran. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal 9: 1677-1686.

Alivisatos, A. P., M. J. Blaser, E. L. Brodie, M. Chun, J. L. Dangl, T. J. Donohue, and the Unified Microbiome Initiative Consortium. 2015. A unified initiative to harness Earth’s microbiomes: Transition from description to causality and engineering. Science 350:507-508.

Chernyh, N. A., A. V. Mardanov, V. M. Gumerov, M. L. Miroshnichenko, A. V. Lebedinsky, A. Y. Merkel, D. Crowe, N. V. Pimenov, I. I. Rusanov, N. V. Ravin,· M. A. Moran, and E. A. Bonch‐Osmolovskaya. 2015. Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka. Extremophiles 19: 1157-1171.


Luo, H., and M. A. Moran. 2014. Evolutionary ecology of the marine Roseobacter clade. Microbiology and Molecular Biology Reviews 78:573-587.

Satinsky, B M, B C Crump, C B Smith, S Sharma, B Zielinski, M Doherty, J Meng, S Sun, P M Medeiros, J H Paul, V J Coles, P L Yager, and M A Moran. 2014. Microspatial gene expression patterns in the Amazon River Plume. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1402782111.

Vila-Costa, M, J M Rinta-Kanto, R S Poretsky, S Sun, R P Kiene, and M A Moran. 2014. Microbial controls on DMSP degradation and DMS formation in the Sargasso Sea. Biogeochemistry 120:295-305.

Keeling, P J and 80 co-authors. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology. doi: 10.1371/journal.pbio.1001889.

Rivers, A R, C B Smith, and M A Moran. 2014. An updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3. Standards in Genome Science. In press.

Beier, S, A R Rivers, M A Moran, and I Obernosterer. 2014. The transcriptional response of prokaryotes to phytoplankton-derived DOM in seawater. Environmental Microbiology. doi: 10.1111/1462-2920.12434.

Luo, H, B K Swan, R Stepanauskas, A L Hughes, and M A Moran. 2014. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. ISME Journal 8:1428-1439.

Luo, H, B K Swan, R Stepanauskas, A . Hughes, and M A Moran. 2014. Comparing effective population sizes of dominant marine alphaproteobacteria lineages. Environmental Microbiology Reports. doi: 10.1111/1758-2229.12129.

Luo, H, B B Tolar, B K Swan, C L Zhang, R Stepanauskas, M A Moran, and J T Hollibaugh. 2014. Single cell genomics shedding light on marine Thaumarchaeota diversification. ISME Journal 8:732-736.

Satinsky, B M, B L Zielinski, M Doherty, C B Smith, S Sharma, J H Paul, B C Crump, and M A Moran. 2014. The Amazon Continuum Dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010. Microbiome 2:17.

Gifford, S M, S Sharma, and M A Moran. 2014. Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community. Frontiers in Aquatic Microbiology 5:185.


Hollibaugh, J T, S M Gifford, M A Moran, M J Ross, S Sharma, and B B Tolar. 2013. Seasonal variation in the metatranscriptomes of a Thaumarchaeota population from southeastern US coastal waters. ISME Journal 8:685–698.

Reisch, C R, W M Crabb, S M Gifford, Q Teng, M J Stoudemyer, M A Moran, and W B Whitman. 2013. Metabolism of dimethylsulfoniopropionate carbon by Ruegeria pomeroyi DSS-3. Molecular Microbiology 89:774-791.

Vila-Costa, M, A Barberan, J-C Auguet, S Sharma, M A Moran, and E Casamayor. 2013. Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios. FEMS Microbiology Ecology 84:387–397.

Vila-Costa, M, S Sharma, M A Moran, and E O Casamayor. 2013. Diel gene expression profiles of a phosphorus limited mountain lake using metatranscriptomics. Environmental Microbiology 15:1190 – 1203.

Gifford, S M, S Sharma, M Booth, and M A Moran. 2013. Expression patterns reveal niche diversification in a marine microbial assemblage. ISME Journal 7:281-298.

Luo, H, M Csürös, A L Hughes, and M A Moran. 2013. Evolution of divergent life history strategies in marine alphaproteobacteria. mBio 4:4.

Luo, H and M A Moran. 2013. Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton. Environmental Microbiology Reports 5:686-696

Gifford, S M, B Satinsky, and M A Moran. 2013. Quantitative microbial metatranscriptomics. In: I Paulsen and A J Holmes, eds. Environmental Microbiology: Methods in Molecular Biology. Chapter 17, pp. 213-229.

Moran, M A, B Satinsky, S M Gifford, H Luo, A Rivers, L-. Chan, . Meng, B P Durham, C Shen, V A Varaljay, C B Smith, P L Yager, and B M Hopkinson. 2013. Sizing up metatranscriptomics. ISME Journal 7:237-243.

Rivers, A R, S Sharma, S G Tringe , J Martin, S Joye, and M A Moran. 2013. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME Journal 7:2315-2329.

Satinsky, B M, S M Gifford, and M A Moran. 2013. Use of internal standards for quantitative metatranscriptome and metagenome analysis. Methods in Enzymology 531: 237-250.

Swan, B K, B Tupper, . Sczyrba, F M Lauro, M Martinez-Garcia, J M González, . Luo, J J Wright, Z C Landry, N W Hanson, B P Thompson, N J Poulton, P Schwientek, S G Acinas, S J Giovannoni, M A Moran, S J Hallam, R Cavicchioli, T Woyke, and R Stepanauskas. 2013. Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. Proceedings of the National Academy of Sciences 110: 11463-11468.


Chan, L K, R J Newton, S Sharma, C B Smith, P Rayapati, A J Limardo, et al. 2012. Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. Frontiers in Aquatic Microbiology 3:159.

Levine, N M, V A Varaljay, D A Toole, J W H Dacey, S C Doney, M A Moran. 2012. Environmental, biochemical, and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea. Environmental Microbiology 14:1210-23.

Luo, H, A Löytynoja, M A Moran. 2012. Genome content of uncultivated marine Roseobacters in the surface ocean. Environmental Microbiology 14:41-51.

Moran, M A, C R Reisch, R P Kiene, W B Whitman. 2012. Genomic insights into bacterial DMSP transformations. Annual Review of Marine Science 4:523-542.

Rinta-Kanto, J, S Sun, S Sharma, R P Kiene, M A Moran. 2012. Bacterial community transcription patterns during a marine phytoplankton bloom. Environmental Microbiology 14:228-239.

Schuller, D J, C R Reisch, M A Moran, W B Whitman, and W N Lanzilotta. 2012. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelegabacter ubique. Protein Science 21: 289-298.

Varaljay, V A, S M Gifford, S T Wilson, S Sharma, D M Karl, M. A. Moran. 2012. Bacterial dimethylsulfoniopropionate-degrading genes in the oligotrophic North Pacific Subtropical Gyre. Applied and Environmental Microbiology 78:2775-2782.

Vila-Costa, M, J M Gasol, S Sharma, M Moran. 2012. Community analysis of high-and low-nucleic acid-containing bacteria in NW Mediterranean coastal waters using 16S rDNA pyrosequencing. Environmental Microbiology 14:1390-402.


Gifford, S M, S Sharma, J M Rinta-Kanto, and M A Moran. 2011. Quantitative analysis of a deeply-sequenced marine microbial metatranscriptome. ISME Journal 5:461-472.

Hollibaugh, J T, S Gifford, S Sharma, N Bano, M A Moran. 2011. Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. ISME Journal 5:866-878.

Howard, E C, S Sun, C R Reisch, D A del Valle, H Bürgmann, R P Kiene, and M A Moran. 2011. Changes in DMSP demethylase gene assemblages in response to an induced phytoplankton bloom. Applied and Environmental Microbiology 77:524-531.

Jansson, J K, J D Neufeld, M A Moran, and J A Gilbert. 2011. Omics for understanding microbial functional dynamics. Environmental Microbiology 14:1-3.

Mou, X, M Vila-Costa, S Sun, W Zhao, S Sharma, and M A Moran. 2011. Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton. Environmental Microbiology 3:798-806.

Reisch, C R, M J Stoudemayer, V A Varaljay, I J Amster, M A Moran, and W B Whitman. 2011. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473:208-211.

Reisch, C R, M A Moran, and W B Whitman. 2011. Bacterial catabolism of dimethylsulfoniopropionate (DMSP). Frontiers in Microbial Physiology and Metabolism 2:172.

Robbins, S, J Jacob, X Lu, M A Moran, and X Mou. 2011. Bromodeoxyuridine (BrdU) labeling and subsequent fluorescence activated cell sorting for culture-independent identification of dissolved organic carbon-degrading bacterioplankton. Journal of Visualized Experiments 55 doi:10.3791/2855.

Back to top