MSc. Indranil Mukherjee, Ph.D.

Job Position: Postdoc - Department of Aquatic Microbial Ecology (AME)

Contact details

Phone: +420 387 77 5885
Room: 23


My primary research interest is to understand the ecological role of flagellated protists (microbial eukaryotes) in aquatic ecosystems. My research focuses on understanding the diversity, seasonal dynamics, bacterivory and selective grazing, and evolution of important groups of flagellated protists mainly from freshwater lakes and reservoirs. I use a wide range of microscopic (fluorescence staining, CARD-FISH, FLB tracer techniques, etc.) and molecular techniques (cloning, amplicon sequencing, metagenomics, metatranscriptomics, etc.) to study these abundant and important organisms, which are still poorly understood. I am currently developing culture techniques to isolate these less known organisms from various European lakes and to understand them through genomics.


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Curriculum vitae


Postdoctoral researcher in Institute of Hydrobiology, Biology Centre, Czech Academy of Sciences (CAS), Czech Republic (2019-Till now).

Postdoctoral researcher in Center for Ecological Research, Kyoto University, Japan (2016-2018).

Postdoctoral researcher in Institute of Hydrobiology, Biology Centre, Czech Academy of Sciences (CAS), Czech Republic (08.2016-09.2016).

Research student in Center for Ecological Research, Kyoto University (04.2011-09.2011).

Project assistant in National Institute of Oceanography (CSIR), Goa, India (2009-2011).


Educational Qualifications

Ph.D. in Biological sciences (specialization in Microbial Ecology) from Kyoto University, Japan (2013-2016)

M.S. in Biological sciences (specialization in Microbial Ecology) from Kyoto University, Japan (2011-2013)

M.Sc. in Marine Biology from Pondicherry University, India (2007-2009)

B.Sc. in Microbiology, Genetics, Chemistry from Osmania University, India (2003-2006)



Mukherjee I, Salcher MM, Andrei AS, Kavagutti VS, 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.

Šimek K, Grujčić V, Mukherjee I, Kasalický V, Salcher MM, Nedoma J, Mehrshad M (2020). Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes. FEMS Microbiology Ecology: 96, fiaa121.

Mukherjee I, Hodoki Y, Okazaki Y, Fujinaga S, Ohbayashi K, Nakano S (2019). Widespread dominance of kinetoplastids and unexpected presence of diplonemids in deep freshwater lakes. Frontiers in Microbiology: 10, 2375.

Mukherjee I, Hodoki Y, Nakano S (2017). Seasonal dynamics of heterotrophic and plastidic protists in the water column of Lake Biwa, Japan. Aquatic Microbial Ecology: 80, 123-137.

Sanitha K. Sivadas, Rahul Nagesh, G.V.M. Gupta, Udaykumar Gaonkar, Indranil Mukherjee, Darwin Ramteke, Baban S. Ingole (2016). Testing the efficiency of temperate benthic biotic indices in accessing the ecological status of a tropical ecosystem. Marine Pollution Bulletin: 106, 62-76.

Deshmukh A, Ingole B, Mukherjee I, Sanita Sivdas (2015). First record of the synaptid holothurian Protankyra bidentata (Woodward & Barrett, 1858) from the Indian Ocean. Indian Journal of Fisheries: 62, 157-160.

Mukherjee I, Hodoki Y, Nakano S (2015). Kinetoplastid flagellates overlooked by universal primers dominate in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiology Ecology: 91, fiv083.

Malik A, Fernandes CEG, Gonsalves M-JBD, Subina NS, Mamatha SS, Krishna K, Varik S, Kumari R, Gauns M, Cejoice RP, Pandey SS, Jineesh VK, Kamaleson AS, Vijayan V, Mukherjee I, Subramanyan S, Nair S, Ingole B, LokaBharathi PA (2015). Interactions between trophic levels in upwelling and non-upwelling regions during summer monsoon. Journal of Sea Research: 95, 56–69.

Ingole BS, Gaonkar UV, Deshmukh A, Mukherjee I, Sivadas SK, Gophane A (2014). Macrobenthic community structure of coastal Arabian Sea during the Fall intermonsoon. Indian Journal of Geo-Marine Sciences: 43, 2223-2232.

Total found: 9 records
Mukherjee I., Grujčić V., Salcher M., Znachor P., Seďa J., Devetter M., Rychtecký P., Šimek K., Shabarova T. (2024) Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir. Environmental Microbiome 19 : 31.
DOI: 10.1186/s40793-024-00574-5
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
Park H., Shabarova T., Salcher M., Kosová L., Rychtecký P., Mukherjee I., Šimek K., Porcal P., Seďa J., Znachor P., Kasalický V. (2023) In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model. Microbiome 11 : 112.
DOI: 10.1186/s40168-023-01522-0
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
Ahmed W., Gupta S., Mukherjee I., Babu V., Singh R. (2022) Comparative studies of codon usage profile of Anisakis simplex (Nematoda) and Carassius gibelio (Prussian carp). Journal of Environmental Biology 43 : 123-132.
DOI: 10.22438/jeb/43/1/MRN-1845
Šimek K., Mukherjee I., Nedoma J., Pires de Paula C., Jezberová J., Sirová D., Vrba J. (2022) CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes. Environmental Microbiology 24 : 4256–4273.
DOI: 10.1111/1462-2920.15846
Piwosz K., Mukherjee I., Salcher M., Grujčić V., Šimek K. (2021) CARD-FISH in the sequencing era: Opening a new universe of protistan ecology. Frontiers in Microbiology 12 : 640066.
DOI: 10.3389/fmicb.2021.640066
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.
Šimek K., Grujčić V., Mukherjee I., Kasalický V., Nedoma J., Posch T., Mehrshad M., Salcher M. (2020) Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes FEMS Microbiology Ecology 96 : fiaa121.


Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

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