Publications

2022 Wittmers F, Needham DM , Hehenberger E, Giovannoni SJ, Worden AZ. Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers. msystems . e01522-21.

2022 Needham DM , Poirier C, Bachy C, George EE, Wilken S, Yung CMC, Limardo AJ, Morando M, Sudek L, Malmstrom RR, Keeling PJ, Santoro AE, Worden AZ. The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate. Nature Microbiology. 2020 Zimmerman, AE, Howard-Varona C, Needham DM , John SG, Worden AZ, Sullivan MB, Waldbauer JR and Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nature Reviews Microbiology . 18(1). pp. 21-34. DOI 10.1038/s41579-019-0270-x. 

2022 Gu X, Yang Y, Mao F, Lee WL, Armas F, You F, Needham DM , Ng Charmaine, Chen H, Chandra F, Gin KY. A comparative study of flow cytometry-sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant. iMeta . e39.

2022 Bachy C, Hehenberger E, Ling Y, Needham DM , Strauss J, Wilken S, Worden AZ. Marine Protists: A Hitchhiker's Guide to their Role in the Marine Microbiome. In: Stal, LJ, Cretoiu MS. (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham.

2022 Wenshan Z, Zhao S, Yin Y, Zhang H, Needham DM , Evans ED, Dai CL, Lu PJ, Alm EJ, Weitz DA. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. science . 376: eabm1483.

2021 Yeh Y, McNichol J, Needham DM, Fichot EB, Berdjeb L, Fuhrman JA. Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. Environment Microbiol. 23:3240-3250.

2020 Choi C, Jimenez V, Needham DM , Poirier C, Bachy C, Alexander H, Wilken S, Chavez F, Sudek S, Giovannoni SJ and Worden AZ. Seasonal and geographical transitions in eukaryotic phytoplankton community structure in the Atlantic and Pacific Oceans. Open Access Frontiers in Microbiology . 11. Art. No. 542372. DOI 10.3389/fmicb.2020.542372.

2019 Needham DM , Yoshizawa S, Hosaka T, Poirier C, Choi C, Hehenberger E, Irwin NAT, Wilken S, Yung C, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR , Mende D, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences of the United States of America .116. 220574-20583.2019.

2019 Needham DM , Poirier C, Hehenberger E, Swallwell JE, Santoro AE, Worden AZ. Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.Philosophical Transactions of the Royal Society B. 374. 20190086.

2019 Gomez-Consarnau L, Needham DM , Weber PK, Fuhrman JA, Mayali X. Influence of light on particulate organic matter utilization by attached and free-living marine bacteria. Frontiers in Microbiology . 10:1204.

2019 Sieradzki ET, Ignacio-Espinoza JC, Needham DM , Fuhrman JA. Dynamic marine viral infections and major contribution to photosynthetic processes shown by regional and seasonal picoplankton metagranscriptomes. Nature Communications .10:1169.

2018 Needham DM, Fichot EB, Wang E, Berdjeb L, Cram JA, Fichot CG, Fuhrman JA. Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling. The ISME Journal l. 12. 2417-2432.

2018 Berdjeb L, Parada A, Needham DM , Fuhrman JA. Short-term dynamics and interactions of marine protist communities during the spring-summer transition. The ISME Journal . 12. 1907-1917.

2018 Hernando-Morales V, Varela MM, Needham DM , Cram J, Fuhrman JA, Teira E. Vertical and seasonal patterns control bacterioplankton communities at two horizontally coherent coastal upwelling sites of Galicia (NW Spain). Microbial Ecology . 76. 866-884.

2018 Yeh Y, Needham DM , Sieradzki ET, Fuhrman JA. Taxon disappearance from microbiome analysis reinforces the value of mock communities as a standard in every sequencing run. mSystems . 3.e00023-18.

2017 Needham DM , Sachdeva R, Fuhrman JA. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. The ISME Journal . 11. 1614-1629.

2017 Ahlgren NA, Chen Y, Needham DM , Parada AE, Sachdeva R, Trinh V, Chen T and Fuhrman JA. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environmental Microbiology.19. 2434-2452.

2016 Needham DM and Fuhrman JA. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nature Microbiology . 1:16005.

2016 Parada AE, Needham DM , Fuhrman JA. Every base matters: assessing 16SrRNA primers for marine microbiomes with mock communities, time-series and global field samples. Environmental Microbiology . 18.1403-1414.

2015 Cram JA, Xia LC, Needham DM , Sachdeva R, Sun F, Fuhrman JA. Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. The ISME Journal . 9. 2573-2586.

2015 Fuhrman JA, Cram JA, Needham DM. Marine microbial community dynamics and their ecological interpretation. Nature Reviews Microbiology . 13:133-146.

2015 Cram JA, Chow ET, Sachdeva R, Needham DM , Parada AE, Steele JA, Fuhrman JA. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. The ISME Journal . 9. 563-580.

2014 Dixon, AK, Needham, DM , Al-Horani, FA, Chadwick, NE. Microhabitat use and photoacclimation in the clownfish sea anemone Entacmaea quadricolor. Journal of the Marine Biological Association of the United Kingdom . 94(3).473-480.

2013 Needham DM, Chow CE, Cram JA, Sachdeva R, Parada A, Fuhrman. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. The ISME Journal . 7. 1274-1285.

2013 Done B, O'Neil JM, Beckert KA, Cain CJ, Needham DM , Carruthers TJB, Dennison WC. Elucidating terrestrial nutrient sources to a coastal lagoon, Chincoteague Bay, Maryland, USA. Estuarine, Coastal and Shelf Science .116.1-10.

2013 Chow CE, Sachdeva R, Cram JA, Steele JA, Needham DM , Patel A, Parada AE, Fuhrman JA. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. The ISME Journal . 7.2259-2273.

2013 Fuhrman YES,Needham DM , Hewson I. Plankton Viruses. Reference Module in Earth Systems and Environmental Sciences