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Our group investigates the ecology of aquatic microorganisms, focusing on their biodiversity and their links to important ecosystem services (e.g., nitrogen cycling) and processes relevant to humans (e.g., water quality and antimicrobial resistance), which are currently exacerbated by global climate change. Our aim is to identify trends and reservoirs of microbial biodiversity and antimicrobial resistance in aquatic systems and the animals living in them at regional to global scales. We use large-scale metagenomic and genomic approaches in combination with longitudinal field studies in temperate to tropical aquatic ecosystems and extensive experimental work in the laboratory.

Scientific Interests

– Climate change microbiology

– Microbial ecology, biodiversity and evolution

– Host-microbe interactions in coral reef ecosystems

– Antimicrobial resistance

– Nitrogen biogeochemical cycle

Current Research Projects

1. Aquatic microbiomes under global climate change
2. Host-microbe interactions in reef fish and their impact on reef ecosystem
3. Biodiversity and evolution of the freshwater sponge microbiome

Selected Publications (total of 45; complete publication list is available in or )

[* corresponding author; ^† co-first authors]

1. 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. , 9:adc9392.
2. 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. , 14: 1384.
3. 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. , 16:1883–1895.
4. 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. , 22:4589–4603.
5. 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. , 114:E7592–E7601.