Marine Microbial Ecology | GEOMAR
Our group develops and applies molecular and experimental approaches to study the dynamics and interactions between marine microbes and their implications on the ocean ecosystem.
Research
Our research -- at the intersection of oceanography, ecology, microbiology, and genomics -- aims to contribute to an understanding of the role of the full microbial community (microbial eukaryotes, bacteria, archaea, and viruses) on ocean ecosystem function and productivity, elemental cycles, and sensitivity to changing ocean conditions due to, for example, climate change.
*Hover over images for more information.
Our research embeds in diverse time-series locations with an expertise in baseline microbiological measurements such as molecular-based diversity assessments, biomass quantification, and microbial interactions. On-going work includes systematic analyses in the Baltic Sea (including at Boknis Eck) and Tropical Atlantic (Cabo Verde Ocean Observatory).
Time series
Phytoplankton are highly diverse and produce complex and distinctive species-specific suits of compounds. The degree to which sympatric bacterial consortia interact with phytoplankton in species-specific ways and how that varies over space and time is still largely unknown. Enrichment experiments allow a platform to address these questions including via isolations and synthetic communities.
Phytoplankton-bacteria
interactions
Our research embeds in diverse time-series locations where our expertise in baseline microbiological measurements such as biomass quantification, molecular-based diversity assessment, and activity. Past contributions include research at the San Pedro Ocean Time-series, Bermuda Atlantic Time-series, and Monterey Bay Time-Series and we have plans to follow on this research at Boknis Eck, Helgoland, and Cabo Verde.
Time series
Genomics
Single cell resolution
Microbe-to-microbe interactions, for example predation and parasitisms, dictate the fate of energy and elemental cycles in the ocean but studying the microbial diversity in traditional size fractionation-based filtration muddles information about these natural associations. Single cell genomics and other single cell resolved techniques allow detection of high and low frequency interactions and the genetic potential of the interacting partners.
With most environmental microbes resistant to cultivation, community shotgun sequencing (metagenomics), single cell genomics, and metatranscriptomic sequencing make up a valuable toolkit to support our explorations into the lifestyles and evolution of microbial life in the ocean. We apply novel applications of state-of-the-art bioinformatic techniques to explore genomic diversity of viruses, prokaryotes, and microbial eukaryotes.
Genomics
Our group has a deep understanding of high throughput single-gene sequencing approaches and applies these to a variety of sample types. One of the most common applications is for the rRNA gene for which we apply a universal three-domain primer set optimized to amplify 16S of bacteria, archaea, (including phytoplankton chloroplasts), 18S and eukaryotes. This analysis is routine in our group and allows high throughput surveys from a multitude of plankton and host-associated microbiomes.
Amplicon sequencing
Our group endeavors to grow, isolate, and/or enrich novel micro-organisms from the marine environment which allows for mechanistic understanding of microbial interactions as well as physiological, functional, and genomic characterizations. Current targets and successes include ammonia oxidizing archaea, diatoms, cryptophytes, dinoflagellates, and nitrogen fixing bacteria.
Photo: Colormetric detection of nitrite produced by novel ammonia oxidizing archaaea.
Microbial Cultivation
People
Alyzza Calayag, PhD student
Jana Hinz, Bachelor student
Elisa D'Agostino, PhD student
Sookyoung Kim, Masters student
Lara Schroeder, Bachelor student
Please get in touch to discuss opportunities to work in our group
Our group operates within the international
Affiliations
GEOMAR is a leading oceanographic research with research foci spanning Ocean Circulation and Climate Dynamics; Seafloor Dynamics, Hazards and Resources; Marine Biogeochemistry; and Marine Ecology. GEOMAR scientists lead international oceanographic research cruises around the world from the Baltic Sea, Tropical Atlantic and beyond. The diverse expertise at GEOMAR allow for integrative research foci such as on marine carbon sinks, Atlantic Tropical Upwelling, and ocean biogeochemistry.
GEOMAR offers Masters and PhD degrees through association with the University of Kiel. Students with an interest in a PhD and/or Masters are encouraged to contact me. Masters students can apply through the M. Sc. Biological Oceanography program at the University of Kiel.
Pictured: Kiel Fjord from GEOMAR East Shore Campus
Values
Our group strives to foster and support a diverse, equitable, and inclusive research environment that celebrates diversity as a moral value through our teaching, mentorship, & research. We also recognize that diverse backgrounds, different life experiences, & global perspectives are essential to tackling grand challenges & research excellence. We aspire to a stimulating, collaborative, & open research environment, inspired by our individual and shared passions and curiosities about nature.
Map includes some past affiliations, current, or planned collaborations of OEB. Join us!
Field work
Baltic Sea, AL592: We participated once again in the annual GEOMAR fisheries spring time-series cruises in the Baltic Sea. These cruises are important and on-going to assess stocks of cod and other fisheries in the Baltic Sea. Our contributions are assessment of the microbial food web components on which these stocks depend. Alyzza Calayag particpiated in the cruise and took many samples for her PhD research which focuses on developing and applying cultivation-independent techniques for detecting microbial interactions in the plankton.
Polarstern 135/2 Mindelo-Bremerhaven: We participated in a Polarstern transit cruise from Mindelo, Cabo Verde to Bremerhaven. On this cruise, we collected size-fractionated microbial biomass samples from the surface to just meters above the seafloor (down to 5000m!), including samples from long-term time series stations Cabo Verde Ocean Observatory (CVOO) and European Station for Time-Series in the Ocean of the Canary Islands (ESTOC). The cruise enabled training of the WASCAL Masters students as they rotated through modules focused on Microbiology, Oceanography, Ecology, and Biogeochemistry.
São Vicente, Cabo Verde March 2023: In March 2023, supporting two masters students in the WASCAL masters program, we sampled around São Vicente to assess microbial diversity in the near shore environment, off shore environment, as well as in associated with wild caught fish.
Bergen, Norway: In spring 2022, we collected samples to understand the effect of enhanced alkalinity as a form of carbon capture on microbial diversity via large-scale mesocosm experiments. This work is a collaboration with the KOSMOS (Kiel Off-Shore Mesocosms for Ocean Simulations) team lead by Ulf Riebesell.
Mindelo, Cabo Verde: In summer 2022, in collaboration with the WASCAL program (West African Science Service Centre on Climate Change and Adapted Land Use) our group co-lead a two week class on Marine Microbiology in Mindelo, Cabo Verde. In connection with the class ,we sampled the local and offshore environments with the students to help understand the controls on productivity in this important region.
Baltic Sea: in collaboration with the Marine Ecology research Unit at GEOMAR, our group participated in a 10-day cruise in the southwest Baltic Sea aboard the R/V Alkor.
Publications
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. 2022. Msystems. e01522-21.
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. 2022. Nature Microbiology.
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. 2022. iMeta. e39.
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. 2022. In: Stal, LJ, Cretoiu MS. (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham.
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. 2022. Science. 376: eabm1483.
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. 2022. Environ Microbiol. 23:3240-3250.
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. 2021. Environ Microbiol. 23:3240-3250.
Bachy C, Yung C, Needham DM, Gazitúa MC, Roux S, Limardo AJ, Choi CJ, Jorgens DM, Sullivan MB, Worden AZ. Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. 2021. The ISME Journal. 15:3129-3147.
Choi CJ, Jimenez V, Needham DM, Poirier C, Bachy C, Alexander H, Wilken S, Chavez FP, Sudek S, Giovannoni SJ, Worden AZ. Seasonal and geographical transitions in eukaryotic phytoplankton community structure in the Atlantic and Pacific oceans. 2020. Frontiers in Microbiology. 11:2187.
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. 2019. PNAS.116. 220574-20583.
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. 2019. Philosophical Transactions of the Royal Society B. 374. 20190086.
Zimmerman AE, Howard-Varona C., Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. 2019. Nature Reviews Microbiology. 18:21-34.
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. 2019. Frontiers in Microbiology. 10:1204.
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. 2019. Nature Communications.10:1169.
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. 2018. The ISME Journal. 12. 2417-2432.
Berdjeb L, Parada A, Needham DM, Fuhrman JA. Short-term dynamics and interactions of marine protist communities during the spring-summer transition. 2018. The ISME Journal. 12. 1907-1917.
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). 2018. Microbial Ecology. 76. 866-884.
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. 2018. mSystems. 3. e00023-18.
Needham DM, Sachdeva R, Fuhrman JA. 2017. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. The ISME Journal. 11: 1614-1629.
Ahlgren, NA, Chen, Y.,Needham DM, Parada, AE, Sachdeva, R., Trinh, V., Chen, T. and Fuhrman, JA. (2017), Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environmental Microbiology, 19: 2434–2452.
Needham DM and Fuhrman JA. 2016. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nature Microbiology.1(16005).
Parada AE, Needham DM, Fuhrman JA. 2016. Every base matters: assessing 16S rRNA primers for marine microbiomes with mock communities, time-series and global field samples. Environmental Microbiology. 18(5).1403-1414.
Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA. 2015. Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. The ISME Journal. 9. 2573-2586.
Fuhrman JA, Cram JA, Needham DM. 2015. Marine microbial community dynamics and their ecological interpretation. Nature Reviews Microbiology. 13:133-146.
Cram JA, Chow ET, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA. 2015. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. The ISME Journal, 9:563-580.
Dixon, AK, Needham DM, Al-Horani, FA, Chadwick, NE. 2014. 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.
Needham DM, Chow CE, Cram JA, Sachdeva R, Parada A, Fuhrman. 2013. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. The ISME Journal, 7:1274-1285.
Fertig B, O’Neil JM, Beckert KA, Cain CJ, Needham DM, Carruthers TJB, Dennison WC. 2013. Elucidating terrestrial nutrient sources to a coastal lagoon, Chincoteague Bay, Maryland, USA. Estuarine, Coastal and Shelf Science, 116: 1-10.
Chow CE, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, Parada AE, Fuhrman JA. 2013. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. The ISME Journal, 7:2259:2273.
Fuhrman JA, Needham DM, Hewson I. 2013. Plankton Viruses. Reference Module in Earth Systems and Environmental Sciences.