Research Focus Overview
Our team studies aquatic microbes from the perspective of biodiversity, their relationship to ecosystem functions (e.g., nitrogen cycling) and their impact on water quality in aquatic ecosystems affected by climate change. Our aim is to understand, from a regional and global perspective, how changes in microbial biodiversity due to environmental change affect ecosystem services and the development of antimicrobial resistance, including the animals living in them. To this end, we employ large-scale meta- and genomic analyses and combine them with temporal field studies in temperate and tropical waters and extensive laboratory experiments.
Expertise
– Microbial biodiversity and evolution
– Microbial ecophysiology
– Nitrogen cycling
– Host-microbe interactions
– Metagenomics
Current projects
(1) Aquatic microbiomes under global climate change
The aquatic environment is changing rapidly due to the threat of climate change. In freshwater systems, animal biodiversity has declined four times faster than in the marine environment. However, the microbial biodiversity of inland freshwater ecosystems, which face unprecedented anthropogenic threats and where planktonic prokaryotes form the basis of the food web and provide important ecosystem services, such as detoxification of ammonia and other pollutants, is still poorly understood.
We will catalogue the genetic diversity of marine and freshwater microorganisms using metagenomes collected worldwide and assess temporal trends using metagenomes collected over 20 years. Using predictive models, we will assess the determinants of microbial biodiversity trends at regional and global scales. Our aim is to understand the biodiversity dynamics of key ecosystem service providers to inform ecosystem management and conservation.
Sampling of microbial biodiversity in aquatic systems, including European temperate lakes, where nitrifying prokaryotes have evolved clonally over millennia. Picture credit: David Ngugi
(2) Microbiomes of herbivorous fishes and their ecological impact on the reef ecosystem
Marine piscine herbivores are the “cows of the ocean”. They feed on a wide variety of marine macroalgae and thus influence the biogeochemical processes and the ecology of the reef ecosystem. As each species is specialized to the algal species it feeds on, we are investigating the functional diversity of its microbiome using metagenomics and assessing potential activities using metatranscriptomics as well as in vivo and field experiments. Our aim is to understand the role of the gut microbiome in the assimilation of marine algae and the impact these gut processes have on the reef biogeochemical cycles.
Stomach content of herbivorous surgeonfishes
(3) Biodiversity and evolution of the freshwater sponge microbiome
Freshwater lakes can have large sponge populations that multiply in summer. They filter large volumes of water daily and can remove up to 95% of bacteria and suspended particles. Some bacteria are ingested as food, while others evolve as part of the sponge microbiome.
We are studying the genetic diversity of sponge-associated microbes worldwide to learn more about their role in freshwater systems, particularly as reservoirs of antimicrobial resistance. We also study the evolution of the freshwater sponge holobiont, focusing on the microbiome and its impact on host development and habitat acclimation.
The metagenomes of freshwater sponges are underrepresented in public sequence databases. Their marine counterparts are a “hotspot” of antimicrobial resistance (Ngugi et al., in prep.). Photo credits: Thorsten Reusch/ Michelle Fernandes
Other On-going Projects (External)
- Identity, infection strategy, and biogeochemical impact of nitrifier-infecting viruses [SPP2330, Project PE2147/5-1]
- Ecological relevance of nucleotide salvage pathways in aquatic environments: significance in microbial bioenergetics and nutrient dynamics [DFG, PN44123226]
Current Group Members
Sunwoo Lee (MSc Student, CAU)
Dr. Basak Öztürk (vising scientist)
Sabrina Jung (technical assistant)
Justyna Barys (external PhD candidate, TU Braunschweig)
János Papendorf (external PhD candidate, TU Braunschweig)
5 Key Publications (total of 45; complete publication list is available in Google Scholar or ORCID)
- Ngugi DK, Salcher MM, Andrei A-S, Ghai R, Klotz F, Chiriac M-C, Ionescu D, Buesing P, Grossart H-P, Xing P, Priscu JC, Alymkulov S, and Pester M. (2023). Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. Science Advances, 9:adc9392.
- Ngugi DK, Silvia GA, Sánchez P, Gasol JM, Agusti S, Karl DM, and Duarte CM. (2023). Abiotic selection of microbial genome size in the global ocean. Nature Communication, 14: 1384.
- Pogoreutz C, Oakley CA, Raedecker N, Cárdenas A, Perna G, Peng L, Davy SK, Ngugi DK, and Voolstra CR. (2022). Coral holobiont cues prime Endozoicomonas to a symbiotic lifestyle. The ISME Journal, 16:1883–1895.
- Duarte CM, Ngugi DK, Alam I, Pearman J, Kamau A, Eguiluz VM, Gojobori T, Acinas S, Gasol JM, Bajic VB, and Irigoien X. (2020). Sequencing effort dictates gene discovery in marine microbial metagenomes. Environmental Microbiology, 22:4589–4603.
- Ngugi DK, Miyake S, Cahill MJ, Vinu M, Hackmann TJ, Blom J, Tietbohl M., Berumen M., and Stingl U. (2017). Genomic diversification of giant enteric symbionts reflects host dietary lifestyle. PNAS, 114:E7592–E7601.
Open positions
We are currently looking for enthusiastic students to join our group, including students interested in a BSc and MSc thesis. Research interns are also welcome. If you are interested in any of our research topics (e.g., antibiotic resistance, host-microbe interactions, microbial biodiversity, metagenomics) or have any cool ideas, please come along or email us (David Ngugi, dngugi(at)geomar.de). We can also help PhD students to apply for fellowships/scholarships to support their research work in our lab.
Current Collaborators
Prof. Dr. Michael Pester, Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), Braunschweig, Germany
Prof. Dr. Lesego Molale-Tom, North-West University, South Africa
Prof. Dr. Hans-Peter Grossart, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
Dr. Michaela M. Salcher, Institute of Hydrobiology, Biology Center CAS, Czechia
Prof. Daniel Abel Shilla, University of Dar es Salaam, Tanzania
Dr. Adrian Stefan-Andrea, Limnological Station, University of Zurich, Switzerland
Dr. Anncarol Karanja, Kenyatta University, Nairobi, Kenya
Prof. Carlos M. Duarte, King Abdullah University of Science & Technology, Saudi Arabia
Dr. Silvia G. Acinas, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
Prof. Dr. Christian Voolstra, University of Konstanz, Germany
Prof. Dr. Sarahi L. Garcia, University of Oldenburg, Germany
