Publications
Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations
Nature Communications
Calayag, AM, Priest, T., Oldenburg, E, Muschiol J, Wietz M, Needham DM
2025
More realistic plankton simulation models will improve projections of ocean ecosystem responses to global change
Nature Ecology & Evolution
Flynn KJ, Atkinson A, Beardall J, Berges JA, Boersma M, Brunet C, Calbet A, Caron DA, Dam HG, Glibert PM, Hansen PJ, ...et al
2025
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Science
Wenshan Z, Zhao S, Yin Y, Zhang H, Needham DM, Evans ED, Dai CL, Lu PJ, Alm EJ, Weitz DA
2022
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators
PNAS
Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi C, Hehenberger E, Irwin NAT, Wilken S, Yung C,Bachy C, ..., Shirouzu M, Iwasaki W, Worden AZ
2019
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
Environmental Microbiology
Parada AE, Needham DM, Fuhrman JA
2016
Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems
Nature Reviews Microbiology
Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML
2020
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate
Nature Microbiology
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
2022
Basin-scale dynamics and enrichment-enabled genomics of marine nitrifiers: seasonality, niches, interac8ons, and genomic uniqueness
bioRxiv
Kim S, D'Agostino E, Needham DM
From Microscale to Microbial Insights: Validating High-Throughput Microvolume Extraction Methods (HiMEx) for Microbial Ecology
bioRxiv
Ghotbi M, Ghotbi M, D'Agostino E, Kanitz M, Needham DM
Elucidating terrestrial nutrient sources to a coastal lagoon, Chincoteague Bay, Maryland, USA
Estaurine, Coastal, and Shelf Science
Fertig B, O’Neil JM, Beckert KA, Cain CJ, Needham DM, Carruthers TJB, Dennison WC
2013
Short-term observations of marine bacterial and viral communities: patterns, connections and resilience
ISME Journal
Needham DM, Chow CE, Cram JA, Sachdeva R, Parada A, Fuhrman JA
2013
Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight
ISME Journal
Chow CE, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, Parada AE, Fuhrman JA
2013
Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years
ISME Journal
Cram JA, Chow ET, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA
2015
Marine microbial community dynamics and their ecological interpretation
Nature Reviews Microbiology
Fuhrman JA, Cram JA, Needham DM
2015
Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes
ISME Journal
Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA
2015
Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom
Nature Microbiology
Needham DM, Fuhrman JA
2016
Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters
ISME Journal
Needham DM, Sachdeva R, Fuhrman JA
2017
Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems
Environmental Microbiology
Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA
2017
Vertical and seasonal patterns control bacterioplankton communities at two horizontally coherent coastal upwelling sites off Galicia (NW Spain)
Microbial Ecology
Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E
2018
Short-term dynamics and interactions of marine protist communities during the spring–summer transition
ISME Journal
Berdjeb L, Parada A, Needham DM, Fuhrman JA
2018
Taxon disappearance from microbiome analysis reinforces the value of mock communities as a standard in every sequencing run
Msystems
Yeh Y, Needham DM, Sieradzki ET, Fuhrman JA
2018
Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling
ISME Journal
Needham DM, Fichot EB, Wang E, Berdjeb L, Cram JA, Fichot CG, Fuhrman JA
2018
Influence of light on particulate organic matter utilization by attached and free-living marine bacteria
Frontiers in Microbiology
Gomez-Consarnau L, Needham DM, Weber PK, Fuhrman JA, Mayali X
2019
Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes
Nature Communications
Sieradzki ET, Ignacio-Espinoza JC, Needham DM, Fuhrman JA
2019
Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes
Phil. Trans. Roy. Soc. B
Needham DM, Poirier C, Hehenberger E, Swallwell JE, Santoro AE, Worden AZ
2019
Seasonal and geographical transitions in eukaryotic phytoplankton community structure in the Atlantic and Pacific Oceans
Frontiers in Microbiology
Choi CJ, Jimenez V, Needham DM, Poirier C, Bachy C, Alexander H, Wilken S, Chavez FP, Sudek S, Giovannoni SJ, Worden AZ
2020
Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S
Environmental Microbiology
Yeh Y, McNichol J, Needham DM, Fichot EB, Berdjeb L, Fuhrman JA
2021
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts
ISME Journal
Bachy C, Yung C, Needham DM, Gazitúa MC, Roux S, Limardo AJ, Choi CJ, Jorgens DM, Sullivan MB, Worden AZ
2021
A comparative study of flow cytometry‐sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant
Imeta
Gu X, Yang Y, Mao F, Lee WL, Armas F, You F, Needham DM, Ng Charmaine, Chen H, Chandra F, Gin KY
2022
Marine protists: a Hitchhiker's guide to their role in the marine microbiome
The marine Microbiome
Bachy C, Hehenberger E, Ling Y, Needham DM, Strauss J, Wilken S, Worden AZ
2022
Genomes from uncultivated pelagiphages reveal multiple phylogenetic clades exhibiting extensive auxiliary metabolic genes and cross-family multigene transfers
Msystems
Wittmers F, Needham DM, Hehenberger E, Giovannoni SJ, Worden AZ
2022
Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding
Biogeosciences
Min MA, Needham DM, Sudek S, Truelove NK et al.,
2023
Non-photosynthetic lineages sibling to Cyanobacteria associate with eukaryotes in the open ocean
Current Biology
Wittmers F, Comstock J, Poirier C, Needham DM, Schulz F, Malmstrom R, Carlson CA, Worden AZ
2024