HR Excellence in Science

MSc. Rohit Ghai, Ph.D.

Position Research Scientist
Department of Aquatic Microbial Ecology (AME)
Institute of Hydrobiology

Contact details +420 38777 5819


Research interests

My primary research focus is on the fundamental aspects of co-evolution of microbial and phage populations in aquatic ecosystems. The availability of next-generation sequencing technologies has tremendously improved our understanding of the uncultured diversity in the microscopic world, and as a part of our work we aim to understand the breadth and scale of this diversity, processes related to its maintenance and ultimately the consequences for interactions between the microbial and viral components.

We mainly use the freshwater ecosystems as models for our work. Freshwaters (all rivers, lakes and reservoirs together) comprise less than 1% of the total water on earth, but are nevertheless critical for our survival. Remarkably, the vast majority of microbial inhabitants have remained largely unknown and out of bounds of traditional culture-based approaches. Owing to recent developments in sequencing we are now beginning to put together a picture of the microbial communities in these habitats. This has enormous repercussions for microbiology at large, providing us with the ability to partially bypass culture based methods and directly access genomic information, thereby opening a whole new vista of the enormous genetic diversity of these microbes. We use high-resolution sequencing based analyses of freshwater ecosystems to reconstruct genomes of entire natural microbial populations and relate their genomic adapations and dynamics to their environment.

Prokaryotic populations cannot be isolated from the extensive viral world they live in, which is numerically at least ten times as large. Uncultured viruses (frequently of uncultured bacterial hosts) present their own set of challenges to our understanding of the real viral world. If we have now begun to shed light on the vast uncultured microbial majority, estimated to be 99% at the turn of the century, we have barely even begun to scratch the surface of the viral universe. We also use the metagenomic approach towards understanding viral diversity, evolutionary diversifications in natural viral populations and adaptations that affect interactions with their microbial hosts.

We collaborate with several labs, combining metagenomics, genomics, data from cultures of environmentally relevant strains and the environment gained via e.g. specific FISH probes targeting the major bacterioplankton players, interactions with microbial predators etc to refine our understanding and of the microbial communities in aquatic environments.


Curriculum Vitae

2009-2015 Postdoctoral Researcher: Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain led by Prof. Francisco Rodriguez-Valera (

2006-2008 Postdoctoral Researcher:  Institute of Medical Microbiology, University of Giessen, Giessen, Germany, 2006-2008

2003-2006 PhD, Natural Sciences (Dr. rer. nat). University of Giessen, (summa cum laude) . Prof. Dr. Trinad Chakraborty. Institute of Medical Microbiology, University of Giessen, Giessen, Germany, 2003-2006

Selected Recent Publications:

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

R Ghai, M Mehrshad, CM Mizuno, F Rodriguez-Valera. ISME Journal. 2016 Aug 9.


Genomes of Abundant and Widespread Viruses from the Deep Ocean

CM Mizuno, R Ghai, A Saghaï, P López-García, F Rodriguez-Valera. mBio 7 (4), e00805-16


Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics

CM Mizuno, F Rodriguez-Valera, R Ghai. mBio vol. 6 no. 1 e02083-14, 2015


Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing.

R Ghai, CM Mizuno ,A Picazo, A Camacho, F Rodriguez-Valera Molecular Ecology 2014 Oct 30


Expanding the marine virosphere using metagenomics.

CM Mizuno, F Rodriguez-Valera, NE Kimes, R Ghai. PLoS Genetics 9 (12), e1003987, 2013

Total found: 36 records
Kavagutti V., Bulzu P., Chiriac M., Salcher M., Mukherjee I., Shabarova T., Grujčić V., Mehrshad M., Kasalický V., Andrei A.S., Jezberová J., Seďa J., Rychtecký P., Znachor P., Šimek K., Ghai R. (2023) High‑resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome 11: 15.
DOI: 10.1186/s40168-022-01451-4
Kavagutti V., Chiriac M., Ghai R., Salcher M., Haber M. (2023) Isolation of phages infecting the abundant freshwater Actinobacteriota order ‘Ca. Nanopelagicales’. The ISME Journal 17: 943–946.
DOI: 10.1038/s41396-023-01400-5
Ngugi D.K., Salcher M., Andrei A.S., Ghai R., Klotz F., Chiriac M., Ionescu D., Büsing P., Grossart H., Xing P., Priscu J.C., Alymkulov S., Pester M. (2023) Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. Sciences Advances 9: eadc9392.
DOI: 10.1126/sciadv.adc9392
Šimek K., Mukherjee I., Szöke-Nagy T., Haber M., Salcher M., Ghai R. (2023) Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores. ISME Journal 17: 84–94.
DOI: 10.1038/s41396-022-01326-4
Bulzu P., Kavagutti V., Andrei A.S., Ghai R. (2022) The evolutionary kaleidoscope of rhodopsins. mSystems 7: e00405-22.
DOI: 10.1128/msystems.00405-22
Chiriac M., Bulzu P., Andrei A.S., Okazaki Y., Nakano S., Haber M., Kavagutti V., Layoun P., Ghai R., Salcher M. (2022) Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR. Microbiome 10: 84.
DOI: 10.1186/s40168-022-01274-3
Bulzu P., Kavagutti V., Chiriac M., Vavourakis C.D. , Inoue K. , Kandori H. , Andrei A.S., Ghai R. (2021) Heliorhodopsin evolution is driven by photosensory promiscuity in monoderms. mSphere 6: e00661-21.
DOI: 10.1128/mSphere.00661-21
Durán-Viseras A., Andrei A., Vera-Gargallo B., Ghai R., Sánchez-Porro C., Ventosa A. (2021) Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis. Environmental Microbiology 23: 3418–3434.
DOI: 10.1111/1462-2920.15082
Mujakic I., Andrei A., Shabarova T., Kolesár Fecskeová L., Salcher M., Piwosz K., Ghai R., Koblížek M. (2021) Common presence of phototrophic Gemmatimonadota in temperate freshwater lakes. mSystems 6: e01241-20.
DOI: 10.1128/mSystems.01241-20
Saha S., Bulzu P., Urajová P., Mareš J., Konert G., Manoel J.C., Macho M. , Ewe D., Hrouzek P., Masojídek J., Ghai R., Sourav K. (2021) Quorum-sensing signals from epibiont mediate the induction of novel microviridins in the mat-forming cyanobacterial genus Nostoc. mSphere 6: e00562-21.
DOI: 10.1128/mSphere.00562-21
Cabello-Yeves P.J., Zemskaya T.I., Zakharenko A.S., Sakirko M.V., Ivanov V.G., Ghai R., Rodriguez-Valera F. (2020) Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat Limnology and Oceanography 65: 1471–1488.
Inoue K. , Tsunoda S.P., Singh M., Tomida S., Hososhima S., Konno M., Nakamura R., Watanabe H. , Bulzu P.A., Banciu H.L., Andrei A., Uchihashi T., Ghai R., Béjà O., Kandori H. (2020) Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps Science Advances 6: eaaz2441.
DOI: 10.1126/sciadv.aaz2441
Mukherjee I., Salcher M., Andrei A., Kavagutti V., Shabarova T., Grujčić V., Haber M., Layoun P., Hodoki Y., Nakano S., Šimek K., Ghai R. (2020) A freshwater radiation of diplonemids Environmental Microbiology 22: 4658–4668.
Park S.J., Andrei A., Bulzu P., Kavagutti V., Ghai R., Mosier A.C. (2020) Expanded diversity and metabolic versatility of marine nitrite-oxidizing bacteria revealed by cultivation-and genomics-based approaches. Applied and Environmental Microbiology 86: e01667-20.
Salcher M., Andrei A., Bulzu P., Keresztes Z.G., Banciu H.L., Ghai R. (2020) Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) mSphere 5: e00686-20.
Andrei A., Salcher M., Mehrshad M., Rychtecký P., Znachor P., Ghai R. (2019) Niche-directed evolution modulates genome architecture in freshwater Planctomycetes ISME Journal 13: 1056–1071.
DOI: 10.1038/s41396-018-0332-5
Bulzu P.A., Andrei A., Salcher M., Mehrshad M., Inoue K. , Kandori H. , Béjà O., Ghai R., Banciu H.L. (2019) Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche Nature Microbiology 4: 1129–1137 .
DOI: 10.1038/s41564-019-0404-y
Durán-Viseras A., Andrei A., Ghai R., Sánchez-Porro C., Ventosa A. (2019) New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea Frontiers in Microbiology 10: 1928.
DOI: 10.3389/fmicb.2019.01928
Flores-Uribe J., Hevroni G. , Ghai R., Pushkarev A. , Inoue K. , Kandori H. , Béjà O. (2019) Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity Environmental Microbiology Reports 11: 419-424.
DOI: 10.1111/1758-2229.12730
Kavagutti V., Andrei A., Mehrshad M., Salcher M., Ghai R. (2019) Phage-centric ecological interactions in aquatic ecosystems revealed through ultradeep metagenomics Microbiome 7: 135.
DOI: 10.1186/s40168-019-0752-0

More publications


Biology Centre CAS
Branišovská 1160/31
370 05 České Budějovice
Data box: r84nds8


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+420 387 775 051 (secretariat)
+420 778 468 552 (for media)

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