Indranil Mukherjee

Indranil Mukherjee
Biology Centre CAS · Institute of Hydrobiology

MSc, MS, PhD

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23
Publications
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Publications

Publications (23)
Research Proposal
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One PhD student position is open in the Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic within the PhD program in Limnology to study the diversity, dynamics and ecological traits of freshwater eukaryotes using single-cell tec...
Article
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Aim: The aim of the present study was to understand the molecular relationship between nematode (parasite) and fish (host) through codon usage bias (CUB) analysis. Methodology: The Codon usage bias analysis has been performed in fish Carassius gibelio (Prussian carp) and nematode fish parasite Anisakis simplex. The complete coding sequences (CDS) o...
Experiment Findings
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Article
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Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation o...
Article
Full-text available
Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporte...
Article
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Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released from grazing pressure by zooplankton via filtration through 10-µm and 5-µm filters, yi...
Article
Full-text available
Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released from grazing pressure by zooplankton via filtration through 10-µm and 5-µm filters, yi...
Preprint
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Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids...
Article
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We followed seasonal changes in the vertical distribution of protistan communities in Lake Biwa for 2 yr. Heterotrophic nanoflagellates (HNF) and plastidic nanoflagellates (PNF) were enumerated from different depths, and the seasonal community composition of protists was analyzed from the epilimnion and hypolimnion using 18S rRNA gene clone librari...
Article
The objectives of the present study were to evaluate the ecological status of tropical coastal waters using the temperate benthic indices and examine the effect of seasonal variability on the performance of benthic indices. Macrobenthic samples were collected from northwest to southeast coast of India during 2003–2012 and we tested different univar...
Article
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In the Arabian Sea, organic matter produced during the upwelling period reaches the seafloor by the end of the monsoon and during the fall intermonsoon period (FIM). Studies on the benthic community is lacking during this period. Therefore, we predict that the FIM period is critical in structuring the coastal benthic community. Results indicated Co...
Article
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Sea cucumbers (holothurians) are marine invertebrates that are harvested worldwide, mostly for human consumption in Asian countries. To date, only eight species of synaptid holothurians of the genus Protankyra have been reported from the Indian Ocean. The present report forms the first record of Protankyra bidentata (Woodward & Barrett, 1858) from...
Article
Full-text available
In the Arabian Sea, organic matter produced during the upwelling period reaches the seafloor by the end of the monsoon and during the fall intermonsoon period (FIM). Studies on the benthic community is lacking during this period. Therefore, we predict that the FIM period is critical in structuring the coastal benthic community. Results indicated Co...
Article
There is a shift in environmental variables in upwelling region.•There are changes in intensity, direction and network of interactions.•Abiotic factors influenced phytoplankton and bacteria.•Viable bacteria represent a prominent and stable node in the web interactions.•They indirectly yet significantly augment the productivity of upwelling areas.

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Projects

Projects (3)
Project
The main outcome of our project will be a novel, more realistic model of microbial food webs. It will alter the current understanding of rates and efficiencies of carbon and energy transfer in aquatic habitats. This will have a major impact on the present view of the carbon cycle. The innovative methodology that combines cutting-edge molecular and single-cell techniques will reveal yet unknown trophic links between the newly discovered HNF groups.
Project
Freshwater habitats are critical for all terrestrial life, yet the vast majority of their microbial inhabitants (pro- and eukaryotes) remain enigmatic, outside the bounds of cultivation. The recent development of novel cultivation methods, coupled with advances in sequencing now provides an opportunity to finally unravel freshwater microbial diversity. The PELAGICS project plans a coordinated pan-European sampling campaign (70 lakes) with 24 collaborating scientists from 16 European countries. With novel media mimicking natural conditions and semiautomated high-throughput isolation we aim for stable cultivation and whole-genome sequencing of 500 prokaryotes and 50 unicellular eukaryotes. Moreover, terabyte scale deepmetagenomic sequencing (ca. 18 TB) will allow recovery of thousands of metagenomeassembled genomes for pro-, eukaryotes and viruses. This large-scale effort will finally uncover the microbial diversity (pro- and eukaryotes), their natural interactions and ecological roles in aquatic food webs. A Pan-European microbial ecology network is proposed to sample 70 lakes towards the goal of stable cultivation, whole-genome sequencing (500 pro- and 50 unicellular eukaryotes) and terabyte-scale deep-metagenomic sequencing to obtain 1000s of genomes of freshwater pro-, eukaryotes and viruses.
Project
Flagellated protists are fundamental for channeling dissolved organic matter to the microbial food webs via grazing on bacteria. However, knowledge about the community dynamics, trophic interactions and taxonomic affiliation of bacteria and flagellates in situ is still in its infancy and represents one of the “black boxes” of aquatic microbial ecology. Deep freshwater lakes provide ideal sites to examine contrasting trophic interactions at different depths. The Czech-Japanese team has revealed co-dominance of specific microbial communities in epilimnia and hypolimnia of the deep stratified Římov reservoir and Lake Biwa. Since trophic interactions of both flagellate-predator and bacterial-prey communities strongly affect each other we propose a novel “double hybridization technique”, based on specific FISH probes applied in parallel to the flagellates and prey bacteria in their food vacuoles. Concerted activity of the unique international team of specialists facilitates designing new FISH probes, analyzing flagellate food vacuole contents, sequences and metagenomic data. The ecology and trophic interactions of protists in situ, especially of heterotrophic flagellates, is one of the hot topics of aquatic microbial ecology that is severely understudied in freshwater environments. Most studies have focused on protists in the upper water layers of shallow freshwaters while deep lakes and their hypolimnia have remained largely unknown. Moreover, a direct quantification of the real densities and grazing rates of specific phylogenetic groups of bacterivores in relationship to their prey availability has remained elusive (1). The main goal of this project is to target understudied and visually largely undistinguishable groups of freshwater heterotrophic flagellates (major pelagic bacterivores) and to elucidate their population dynamics and feeding preferences on bacteria in situ (2,3) in two different lakes - lake Biwa in Japan and Římov in Czech Republic. This study will be conducted in both the epilimnetic and hypolimnetic water layers, bringing new insights into distinct dynamics, ecophysiology and food preferences of these spatially separated flagellate populations. We intend to combine expertise of both teams, Czech and Japanese, whose specific skills complement each other. The concerted activity will yield in a unique set of methodical approaches that allow addressing the specific goals of the project related to identity and prey preferences of flagellates and to direct in situ detection of single cells at both predator and prey levels. FISH is currently the only reliable method for precise quantification of microbial abundance, and is preferable to amplicon sequencing that is vulnerable to PCR bias. As a result of ongoing studies at these sites (4,5) we already have CARD-FISH probes for several bacterial and flagellate groups, that allow us to use a sophisticated and innovative “double hybridization” approach directly targeting specific microbes in food vacuoles of specific flagellates (reference 2, see also Figure 1 below). We also plan high throughput sequencing (amplicons for 18S, whole metagenome and metatranscriptome) to design additional FISH probes for new flagellate groups. Deep hypolimnetic layers of freshwater lakes are severely understudied. Most studies have used 16S rRNA analysis alone that provides little information regarding food web interactions and metabolic traits of these microbial communities. The bacterial lineage Chloroflexi CL-500-11 comprises a high proportion of the microbial community at the oxygenated hypolimnia of deep freshwater lakes (lake Biwa, > 10% of total cells during the stratification period; Crater Lake, 17-19% of prokaryotic rRNA at 300–500 m depth; and Lake Michigan, 18.1% of microbial community). These are relatively large curved cells, possibly less vulnerable to grazing by small flagellates. Studies on lake Biwa have shown a co-dominance pattern for a particular group of large flagellates (kinetoplastids) with Chloroflexi CL500-11 in the cold hypolimnion (4,5). Kinetoplastids are also found in the hypolimnion of Římov Reservoir. We plan to investigate in detail the possible reasons for the linkage between these two groups by inspecting food vacuole contents (1-3). Notably, this “predator-prey double hybridization” technique (see Figure 1) is a unique in-house approach (developed by the Czech collaborators, (2)), and to our knowledge, currently not available in other institutions. Scientific importance and originality of the project, current state-of-the-art in the field (including relevant literature): An important role of pelagic bacterial communities is to transform dissolved organic material into particulate material making it available to higher trophic levels. Small protists (largely heterotrophic flagellates) are considered to be the major link connecting dissolved organic material, bacteria and the grazers in the food chain (2,3,7). However, strikingly little is known about affiliation and feeding preferences of the core members of this functionally prominent group of bacterivorous protists in freshwaters. Thus, important questions regarding the identities of the bacterioplankton taxa that link the carbon flow to the grazer food chain remain unanswered (1,2,6,7). Moreover, most studies in freshwater lakes have focused on epilimnion as it is the most productive layer (3, 6, 8). In contrast, hypolimnetic waters that constitute the major part of deep lakes, have been studied markedly less although their global importance has been recognized. These layers have cold and stable temperatures and are inhabited by a distinct microbial community (8,9), that is less studied and whose ecological roles and trophic connections are largely unknown. Two key players in this environment (Chloroflexi and kinetoplastids (4,5)), that frequently co-occur might serve as ideal models for trophic interactions and carbon-flow in the hypolimnion. To address these issues we propose a unique study, focusing on flagellated protists and their bacterial prey (based also on our previous collaboration starting in 2015, manuscripts in preparation). We aim to use novel molecular approaches to identify single predator cells and the composition of their bacterial prey in food vacuoles. We suggest a novel approach to detecting the major players at different depths of two deep freshwater ecosystems and elucidating predator-prey trophic interactions (1,6). A combination of high-throughput sequencing (amplicon and metagenome (8,9)) and FISH will be used to overcome the limitations and biases in individual methodologies, e.g. lack of reliable primer sequences for novel groups, PCR bias in amplicon sequencing etc. We aim to answer the following questions: (a) How the flagellate community and its dynamics differ in epilimnion and hypolimnion of two deep lakes with slightly different trophic status, Lake Biwa in Japan and Římov in Czech Republic? (b) What are the food preferences of freshwater flagellates in epilimnion and hypolimnion of both lakes? (c) Can the population dynamics of Chloroflexi in deep water strata be attributed to grazing pressure of prevailing bacterivores, as indicated by spatial co-occurrence of bacterivorous kinetoplastids? References (code numbers valid through the whole project): 1. Šimek, K., et.al. (2013). Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria. ISME J. 7: 1519-1530. 2. Jezbera, J., Horňák, K., Šimek, K. (2005). Food selection by bacterivorous protists: insight from the analysis of the food vacuole content by means of Fluorescence In Situ Hybridization. FEMS Microbiol Ecol. 52: 351-363. 3. Šimek, K., et.al. (2014). A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnol Oceanogr. 59: 1477–1492. 4. Mukherjee, I., Hodoki, Y., Nakano, S. (2015). Kinetoplastid flagellates overlooked by universal primers dominate in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiol Ecol. fiv083. Mukherjee, I., Hodoki, Y., Nakano, S. (2015). Kinetoplastid flagellates overlooked by universal primers dominate in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiol Ecol. fiv083. 5. Okazaki, Y., Nakano, S. (2016). Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan). Environ Microbiol Rep. doi:10.1111/1758-2229.12439. 6. Grujčić V., Kasalický V, Šimek K. (2015). Prey-specific growth responses of freshwater flagellate communities induced by morphologically distinct bacteria from the genus Limnohabitans. Appl Environ Microbiol. 81:4993–5002. 7. Jürgens K., et. al. (2002). Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Anton van Leeu; 81, 413-34. 8. Grossmann L, et.al. (2016). Protistan community analysis: key findings of a large-scale molecular sampling. ISME J. 10, 2269–79. 9. Giner CR., et al. (2016). Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes. Appl Environ Microbiol; AEM-00560.