Funkce: Vědecký pracovník
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Oddělení mikrobiální ekologie vody
Telefon:
+420 38777 5819
E-mail:
ghai.rohit@gmail.com
Web:
scholar.google.com/citations?user=aVSu92MAAAAJ&hl=en
Místnost:
022
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.
ResearchGate https://www.researchgate.net/profile/Rohit_Ghai
Curriculum Vitae
2009-2015 Postdoctoral Researcher: Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain led by Prof. Francisco Rodriguez-Valera (http://egg.umh.es)
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.
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2016110a.html
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
http://mbio.asm.org/content/7/4/e00805-16.full
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
http://mbio.asm.org/content/6/1/e02083-14.full
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
http://onlinelibrary.wiley.com/doi/10.1111/mec.12985/abstract
Expanding the marine virosphere using metagenomics.
CM Mizuno, F Rodriguez-Valera, NE Kimes, R Ghai. PLoS Genetics 9 (12), e1003987, 2013
http://dx.doi.org/10.1371/journal.pgen.1003987
Boukheloua R.,
Mukherjee I.,
Park H.,
Šimek K.,
Kasalický V., Ngochera M., Grossart H., Picazo-Mozo A., Camacho A. , Cabello-Yeves P.J., Rodriguez-Valera F. , Callieri C., Andrei A.S., Pernthaler J., Posch T., Alfreider A., Sommaruga R., Hahn M., Sonntag B., López-García P., Moreira D., Jardillier L., Lepère C., Biderre-Petit C., Bednarska A., Ślusarczyk M., Tóth V.R., Banciu H.L., Kormas K., Orlić S., Śantić D., Muyzer G., Herlemann D.P.R., Tammert H., Bertilsson S., Langenheder S., Zechmeister T. , Salmaso N., Storelli N., Capelli C., Lepori F. , Lanta V.,
Henriques Vieira H.,
Kostanjšek F.,
Kabeláčová K.,
Chiriac M.,
Haber M.,
Shabarova T.,
Rychtecký P.,
Fernandez C.,
Znachor P.,
Szöke-Nagy T.,
Layoun P.,
Wong H., Kavagutti V.,
Bulzu P.,
Salcher M., Piwosz K., Ghai R. (2024) Global freshwater distribution of Telonemia protists. The ISME Journal
18
: wrae177.
DOI: 10.1093/ismejo/wrae177
|
Henriques Vieira H.,
Bulzu P.,
Kasalický V.,
Haber M.,
Znachor P., Piwosz K., Ghai R. (2024) Isolation of a widespread giant virus implicated in cryptophyte bloom collapse. The ISME Journal
18
: wrae029.
DOI: 10.1093/ismejo/wrae029
|
Layoun P., López-Pérez M., Haro-Moreno J.M.,
Haber M., Thrash J.C., Henson M.W., Kavagutti V., Ghai R.,
Salcher M. (2024) Flexible genomic island conservation across freshwater and marine Methylophilaceae. The ISME Journal
18
: wrad036.
DOI: 10.1093/ismejo/wrad036
|
Park H.,
Bulzu P.,
Shabarova T., Kavagutti V., Ghai R.,
Kasalický V.,
Jezberová J. (2024) Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria. Microbiome
12
: 150.
DOI: 10.1186/s40168-024-01867-0
|
Villena-Alemany C., Mujakic I., Fecskeová L.K., Woodhouse J., Auladell A., Dean J., Hanusová M., Socha M., Gazulla C.R., Sunagawa S., Kavagutti V., Andrei A.S., Grossart H., Ghai R., Koblížek M., Piwosz K. (2024) Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters. Microbiome
12
: 65.
DOI: 10.1186/s40168-024-01786-0
|
Wong H.,
Bulzu P., Ghai R.,
Chiriac M.,
Salcher M. (2024) Ubiquitous genome streamlined Acidobacteriota in freshwater environments. ISME Communications
4
: ycae124.
DOI: 10.1093/ismeco/ycae124
|
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.
DOI: doi.org/10.1002/lno.11401
|
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.
DOI: doi.org/10.1101/2020.05.14.095992
|
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.
DOI: doi.org/10.1128/AEM.01667-20
|
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