Laboratory of Microbial Ecology and Evolution

Follow us on twitter @SmallThingsLab


Group Leader

Dr. Rohit Ghai

Lab Members

Dr. Adrian-Stefan Andrei

M.Sc Vinicius Silva Kavagutti

Open postdoc and PhD student positions

We have several open positions for motivated postdocs and PhD students in our upcoming project PELAGICS


Current Projects

Unveiling life strategies of uncultivated viruses in freshwater environments using metagenomics

Project No.: 4828S

Principal Investigator: Rohit Ghai

Financial support: Czech Science Foundation (GACR)

Duration: 2017 - 2019

Viruses are the most abundant biological entities on the planet, at least one order of magnitude more numerous than their host microbes in aquatic environments. Despite their abundance, studying viruses via cultured isolates remains challenging owing to the complexities in obtaining axenic cultures for the abundant microbial groups. The situation is even more acute for freshwaters where the availability of such pure cultures of the dominant phyla is still rather limited. We propose a long-term metagenomics based approach in two well-studied freshwater habitats to enable a first glimpse of the important double-stranded DNA bacteriophages in freshwaters. We will link these uncultured phages to their host both using existing sequence based approaches and also develop novel methods. In particular we will focus on life strategies of free-living viruses developed in the process of co-existence with the host microbes. Moreover, important insights into factors affecting seasonal dynamics of phage and host populations and global biogeography of freshwater phages are expected.


Evolutionary strategies of freshwater phages and their impact on carbon cycling

Project No.: MSM200961801

Financial Support : Programme for research and mobility support of young researchers (CAS)

Principal Investigator: Adrian-Stefan Andrei

Duration: 2018 - 2020


Past Lab Members

Dr. Maliheh Mehrshad, Department of Ecology and Genetics, Limnology, Uppsala University, Sweden



Stefan Neuenschwander (PhD Student), Limnological Station, University of Zurich, Zurich, Switzerland (2016)

Dr. Michaela Salcher (Visiting Scientist), Limnological Station, University of Zurich, Zurich, Switzerland (2016)

Pedro Cabello-Yeves (PhD Student), Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain (2017)

Charlotte Dafni Vavourakis (PhD Student), Dept. of Freshwater and Marine Ecology, University of Amsterdam, Netherlands (2018)

Paul-Adrian Bulzu (PhD Student), Dept. of Molecular Biology and Biotechnology, Babes-Bolyai University, Cluj-Napoca, Romania (2018,2019) 

Dr. Rafael de la Haba (Visiting Scientist), Departamento Microbiologia Y Parasitologia, Facultad Farmacia, Sevilla, Spain  (2018)

Ana-Duran Viseras (PhD Student), Departamento Microbiologia Y Parasitologia, Facultad Farmacia, Sevilla, Spain (2018,2019)

Izabela Mujakic (PhD Student), Laboratory of Anoxygenic Phototrophs, Centrum Algatech, Trebon, Czech Republic (2019)

Dr. Soo-je Park (Visiting Scientist), Microbial Ecology and Genomics Lab, Jeju University, South Korea (2019)

Dr. Felipe H. Coutinho (Post-doc), Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain (2019)

Shohjahon Begmatov (PhD Student), Russian State Agrarian University - Moscow Timiryazev Agricultural Academy


Invited Speakers

Prof. Francisco Rodriguez-Valera, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain 

Prof. Gerard Muyzer, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam

Prof. Gerald Koudelka, Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA 









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.
Vavourakis C.D. , Mehrshad M., Balkema C., van Hall R., Andrei A., Ghai R., Sorokin D., Muyzer G. (2019) Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake BMC Biology 17 : 69. DOI:10.1186/s12915-019-0688-7
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
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
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
Mehrshad M., Rodriguez-Valera F. , Amoozegar M. A., López-García P., Ghai R. (2018) The enigmatic SAR202 cluster up close: Shedding light on a globally distributed dark ocean lineage involved in sulfur cycling The ISME Journal 12 : 655-668 .
DOI: 10.1038/s41396-017-0009-5
Mehrshad M., Salcher M.M., Okazaki Y., Nakano S., Šimek K., Andrei A., Ghai R. (2018) Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome 6 : 176.
DOI: 10.1186/s40168-018-0563-8
Neuenschwander S., Ghai R., Pernthaler J., Salcher M. (2018) Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria ISME Journal 12 : 185-198 .
DOI: 10.1038/ismej.2017.156
Vavourakis C.D. , Andrei A., Mehrshad M., Ghai R., Sorokyn D. Y., Muyzer G. (2018) A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments Microbiome 6 : 168.
DOI: 10.1186/s40168-018-0548-7
Al-Qahtani A.A., Al-Anazi M.R., Nazir N., Ghai R., Abdo A.A. , Sanai F.M. , Al-Hamoudi W.K. , Alswat K.A. , Al-Ashgar H.I. , Khan M.Q. , Albenmousa A., Cruz D.D. , Bohol M.F.F. , Al-Ahdal M.N. (2017) Hepatitis B virus (HBV) X gene mutations and their association with liver disease progression in HBV-infected patients Oncotarget 8 : 105115-105125.
DOI: 10.18632/oncotarget.22428
Cabello-Yeves P.J., Ghai R., Mehrshad M., Picazo A., Camacho A. , Rodriguez-Valera F. (2017) Reconstruction of diverse Verrucomicrobial genomes from metagenome datasets of freshwater reservoirs Frontiers in Microbiology 8 : 2131.
DOI: 10.3389/fmicb.2017.02131
Cabello-Yeves P.J., Haro-Moreno J.M., Martin-Cuadrado A.B., Ghai R., Picazo A., Camacho A. , Rodriguez-Valera F. (2017) Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs Frontiers in Microbiology 8 : 1151.
DOI: 10.3389/fmicb.2017.01151
Carda-Diegez M. , Ghai R., Rodriguez-Valera F. , Amaro C. (2017) Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. Microbiome 5 : 162.
DOI: 10.1186/s40168-017-0376-1
Ghai R., Mehrshad M., Megumi Mizuno C., Rodriguez-Valera F. (2017) Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria. ISME Journal 11 : 304–308.
DOI: 10.1038/ismej.2016.110
Koh H. W., Hur M., Kang M. S., Ku Y. B., Ghai R., Park S. J. (2017) Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans Scientific Reports 7 : 15007 .
DOI: 10.1038/s41598-017-15164-4
Shevchenko V., Mager T., Kovalev K., Polovinkin V., Alekseev A., Juettner J., Chizhov I., Bamann C., Vavourakis C., Ghai R., Gushchin I., Borshchevskiy V., Rogachev A. , Melnikov I. , Popov A. , Balandin T. , Rodriguez-Valera F., Manstein D.J., Bueldt G., Bamberg E., Gordeliy V. (2017) Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach Science Advances 3 : e1603187 .
DOI: 10.1126/sciadv.1603187
Ghai R., Mehrshad M., Mizuno C., Rodriguez-Valera F. (2016) Metagenomic recovery of phage genomes of uncultured freshwater Actinobacteria The ISME Journal DOI: doi:10.1038/ismej.2016.110
Mizuno C., Ghai R., López-García P., Rodriguez-Valera F. (2016) Genomes of Abundant and Widespread Viruses from the Deep Ocean mBio 7 : e00805-16.
DOI: doi:10.1128/mBio.00805-16
Alexe M. , Şerban G., Baricz A. , Andrei A., Cristea A., Battes K.P., Cîmpean M. , Momeu L., Muntean V. , Porav S.A. , Banciu H.L. (2018) Limnology and plankton diversity of salt lakes from Transylvanian Basin (Romania): A review Journal of Limnology 77 : 17-34.
DOI: 10.4081/jlimnol.2017.1657
Cristea A., Baricz A, Leopold N., Floare C.G. , Borodi G. , Kacso I., Tripon S., Bulzu P.A., Andrei A., Cadar O., Levei E.A., Banciu H.L. (2018) Polyhydroxybutyrate production by an extremely halotolerant Halomonas elongata strain isolated from the hypersaline meromictic Fără Fund Lake (Transylvanian Basin, Romania) Journal of Applied Microbiology 125 : 1343-1357.
DOI: 10.1111/jam.14029
Mehrshad M., Salcher M.M., Okazaki Y., Nakano S., Šimek K., Andrei A., Ghai R. (2018) Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome 6 : 176.
DOI: 10.1186/s40168-018-0563-8
Andrei A., Baricz A. , Robeson M.S., Pǎuşan M.R., Tǎmaş T., Chiriac C., Szekeres E., Barbu-Tudoran L., Levei E.A., Coman C., Podar M., Banciu H.L. (2017) Hypersaline sapropels act as hotspots for microbial dark matter Scientific Reports 7 : 6150.
DOI: 10.1038/s41598-017-06232-w
Andrei A., Pausan M.R., Tamas T., Har N., Barbu-Tudoran L., Leopold N., Banciu H.L. (2017) Diversity and biomineralization potential of the epilithic bacterial communities inhabiting the oldest public stone monument of Cluj-Napoca (Transylvania, Romania) Frontiers in Microbiology 8 : 372.
DOI: 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Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

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