Dr. David Needham

Post-Doctoral Researcher

Ocean EcoSystems Biology Group

 

Office:
Room: DW - 321
Phone: +49 431 600-4411
E-Mail: dneedham(at)geomar.de
https://scholar.google.com/citations?hl=en&user=ZN1_hu4AAAAJ

Address:
GEOMAR | Helmholtz Centre for Ocean Research Kiel
Duesternbrooker Weg 20
24105 Kiel, Germany


Research interests

  • Microbe-microbe interactions
  • Microbial community dynamics
  • Biological oceanography
  • Ecological and evolutionary genomics
  • Single cell and meta-omics

Education

Education
2015 PhD Biology    University of Southern California (USC)
2008 BA Biology      Huntingdon College, Montgomery, AL

Postdoctoral Training
2019-pres GEOMAR, Helmholtz Center for Ocean Research
2019-pres Visiting Scientist, Massachusetts Institute of Technology
2017-2019 Monterey Bay Aquarium Research Institute
2015-2017 University of Southern California

Fellowships and Awards

2010       National Science Foundation Graduate Research Fellowship, 3 years
2012       Best Teaching Assistant Award, Cell Biology and Physiology, USC
2019       Best Flash Talk, Marine Particles & Phycospheres Conference, Switzerland
2016       Post-doctoral Conference Travel Award, International Society of Microbial Ecology
2016       Post-doctoral Conference Travel Award from USC, ISME Conference
2010,12  Wrigley Institute of Environmental Science Graduate Research Fellow
2011       International Travel Support, Aquatic Virus Workshop
2011       Graduate Student Travel Award, USC
2011       Graduate Student Travel Award, American Society of Microbiology
2009       Graduate Research Fellowship, USC
2008       Tri-Beta Award, Best Senior Biology Student, Huntingdon College
2007       Everett&Lewis Bishop Award, Best Junior Biology Student, Huntingdon College

Academic Presentations

Oral Presentations
2019 Marine Particles and Phycospheres Conference (Best Talk Award), Switzerland
2018 International Symbiosis Society Congress, USA
2018 ASLO Ocean Sciencea Meeting, USA
2017 EMBO Workshop: Comperative genomics of EUkaryotic Microbes, Spain
2017 Microseminar (Invited), Youtube
2015 ASLO Ocean Sciences, Spain
2014 ASLO (Invited) Aquatic Sciences, Spain
2013 American Society of Microbiology (Young Investigator Award), USA
2011 Aquatic Virus Workshop, USA

Poster Presentations
2019 DOE Ecosystems & Networks Integrated with Genes & Molecular Assemblies (ENIGMA), USA
2019 Marine Particles and Physcospheres Conference, Switzerland
2014 ASLO Ocean Sciences, USA
2013 Aquatic Virus Workshop, USA
2013 Environmental Virus Workshop, USA
2011 American Society of Microbiology General Meeting, USA
2008 ASLO Ocean Sciences, USA

Publications

2020 Zimmerman, AE, Howard-Varona C, NeedhamDM, 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. 

2020 Choi C, Jimenez V, NeedhamDM, 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. Nr. 542372. DOI 10.3389/fmicb.2020.542372.

Zheng W, Zhao S, Yin Y, Zhang H, Needham DM, Evans ED, Dai CL, Lu PJ, Alm EJ, Weitz DA. Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. doi: doi.org/10.1101/2020.12.14.422699. This article is a preprint and has not been certified by peer review.

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. 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  Fertig 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 JA, Needham DM, Hewson I. Plankton Viruses. Reference Module in Earth Systems and Environmental Sciences