MSc. Michaela Maria Salcher, Ph.D.

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

Contact details

Phone: 387 775 836
Room: 221NB


Research interests

My research focuses on the ecology, evolution, and ecological niche partitioning of the most abundant organisms in lakes: small microbes with reduced (streamlined) genomes. Freshwater microbes are centrally involved in chemical turnover processes, yet individual microbial populations and genotypes greatly differ in their respective metabolic and ecological features. My aim is to get a synoptic view of the functional roles, evolutionary history and phylogeographic distribution patterns of different microbial taxa to identify the main drivers for their success in lakes.

The most abundant microbes in freshwater systems are of conspicuously small size (cell volumes <0.1 μm3) and have streamlined genomes (<1.5 Mbp). Streamlining theory predicts that gene loss is caused by evolutionary selection driven by environmental factors, making these organisms superior competitors for limiting resources under oligotrophic conditions. Ecotype diversification reflects a possible niche-specific adaptation of closely related genotypes and a high degree of microdiversification might be the reason for the observed high total population numbers. Although such streamlined microbes numerically dominate in lakes, they are still poorly studied. Potential auxotrophies and dependencies on co-occurring organisms so far often prevent the establishment of axenic cultures, which, in turn has hampered an in-depth ecological assessment of the reasons for their success in nature. I developed a targeted isolation strategy for bringing these microbes in culture and successfully isolated, e.g., several strains of the highly abundant acI Actinobacteria (Ca. Nanopelagicales’). These isolates are not only of minute cell size but also amongst the most genome-streamlined and abundant microbes in freshwaters. Whole genome sequencing and comparative genomics in combination with high-resolution monitoring of distinct genotypes was applied for identifying microdiversification patterns in these widespread freshwater oligotrophs.

My current project focuses mainly on planktonic methylotrophic Betaproteobacteria. I have a unique collection of strains (>150) that were isolated from the pelagial of different lakes: Ca. Methylopumilus spp.’ (Methylophilaceae, Betaproteobacteria) are small, abundant methylotrophs with streamlined genomes (1.2-1.3 Mb). These strains are ideal models for comparative population-genomics of oligotrophic, highly specialized microbes with streamlined genomes. As their closest relatives can be found in both freshwater sediments and the marine plankton, they also serve as model organisms for studying evolutionary aspects of genome reduction and adaptation to novel environments.

Besides comparative genomics of isolated strains and metagenomics, I am using various single cell techniques such as CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) with subsequent image analysis for a quantification of microbial populations in abundance and biomass, and MAR-FISH (CARD-FISH combined with microautoradiography) to assess substrate incorporations of these microbes. I design novel probes for these techniques (based on 16S or 23S rRNA genes) with a high phylogenetic resolution (genus – species level if possible) to distinguish specific populations in situ. High-frequency and long-term sampling of different lakes provide an ideal framework for recognising recurrent patterns and for identifying seasonal and spatial preferences of different microbial populations. Flow cytometry is applied for a high-throughput analysis of microbial abundances and dilution to extinction techniques in combination with targeted enrichment for the isolation of so far uncultivated microbes.

Curriculum vitae

2019-now       Group leader at the Institute of Hydrobiology, Biology Centre CAS

2017-2018      Group leader at the Limnological Station, University of Zurich, Switzerland

2014-2016      Group leader at the Institute of Hydrobiology, Biology Centre CAS; Straskraba Fellowship for mid-carreer researchers

2010-2014      Postdoctoral fellow at the Limnological Station (University of Zurich, Switzerland); main investigator in the project ‘Functional Role and Ecotype divergence in freshwater Ultramicrobacteria (FREDI)’ funded by the Research Council of European Science Foundation (ESF)

2008-2010      Postdoctoral fellow at the Limnological Station (University of Zurich, Switzerland); main investigator in the project ’Competition as driving force for bacterioplankton successions in lake Zurich’ funded by the Swiss National Science Foundation (SNF 3100A0-117765)

2006-2008      PhD thesis in Microbiology at the University of Zurich, Switzerland

2004-2005      start of PhD thesis at the University of Innsbruck, Austria

1998-2004      Bachelor & Master studies in Ecology, University of Innsbruck, Austria

Current projects:



Google Scholar


12 selected publications, for a full list see Google Scholar or ORCID:

Andrei A-Ş, Salcher MM, Mehrshad M, Rychtecký P, Znachor P & Ghai R (2019). Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. The ISME Journal 13: 1056–1071. doi:10.1038/s41396-018-0332-5

Bulzu P-A, Andrei A-Ş, Salcher MM, Mehrshad M, Inoue K, Kandori H, Beja O, Ghai R & Banciu HL (2019). Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nature Microbiology 4: 1129-1137. doi:10.1038/s41564-019-0404-y

Callieri C, Slabakova V Dzhembekova N, Slabakova N, Peneva E, Cabello-Yeves PJ, Di Cesare A, Eckert EM, Bertoni R, Corno G, Salcher MM, Kamburska L, Bertoni F, Moncheva S (2019). The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global “deep red fluorescence”. The ISME Journal 13: 1676-1687. doi:10.1038/s41396-019-0378-z

Salcher MM, Schaefle D, Kaspar M, Neuenschwander SM & Ghai R (2019). Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. The ISME Journal. doi:10.1038/s41396-019-0471-3

Grujcic V, Nuy JK, Salcher MM, Shabarova T, Kasalicky V, Boenigk J, Jensen M & Simek K (2018). Cryptophyta as major bacterivores in freshwater summer plankton. The ISME Journal 12: 1668-1681. doi:10.1038/s41396-018-0057-5

Mehrshad M, Salcher MM, Okazaki Y, Nakano S-i, Šimek K, Andrei A-S & 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 SM, Ghai R, Pernthaler J & Salcher MM (2018). Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. The ISME Journal 12: 185. doi:10.1038/ismej.2017.156

Salcher MM, Neuenschwander SM, Posch T & Pernthaler J (2015). The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign. The ISME Journal 9: 2442-2453. doi:10.1038/ismej.2015.55

Salcher MM (2014) Same same but different: ecological niche partitioning of planktonic freshwater prokaryotes. J Limnol 73: 74-87. doi:10.4081/jlimnol.2014.813

Salcher MM, Posch T & Pernthaler J (2013). In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake. The ISME Journal 7: 896-907. doi:10.1038/ismej.2012.162

Posch T, Koster O, Salcher MM & Pernthaler J (2012). Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming. Nature Climate Change 2: 809-813. doi:10.1038/nclimate1581

Salcher MM, Pernthaler J & Posch T (2011). Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves' (LD12). The ISME Journal 5: 1242-1252. doi:10.1038/ismej.2011.8

Total found: 30 records
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
Okazaki Y., Fujinaga S., Salcher M., Callieri C., Tanaka A., Kohzu A., Oyagi H., Tamaki H., Nakano S. (2021) Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. Microbiome 9 : DOI: 10.1186/s40168-020-00974-y
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
Shabarova T., Salcher M., Porcal P., Znachor P., Nedoma J., Grossart H., Seďa J., Hejzlar J., Šimek K. (2021) Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession. Nature Microbiology 6 : 479–488.
DOI: 10.1038/s41564-020-00852-1
Di Cesare A., Dzhembekova N., Cabello-Yeves P.J., Eckert E.M., Slabakova V., Slabakova N., Peneva E., Bertoni R., Corno G., Salcher M., Kamburska L., Bertoni F., Rodriguez-Valera F. , Moncheva S., Callieri C. (2020) Genomic comparison and spatial distribution of different Synechococcus phylotypes in the Black Sea Frontiers in Microbiology 11 : 1979.
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.
Piwosz K., Shabarova T., Pernthaler J., Posch T., Šimek K., Porcal P., Salcher M. (2020) Bacterial and eukaryotic small-subunit amplicon data do not provide a quantitative picture of microbial communities, but they are reliable in the context of ecological interpretations mSphere 5 : e00052-20.
DOI: 10.1128/mSphere.00052-20
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.
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.
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
Callieri C., Slabakova V., Dzhembekova N., Slabakova N., Peneva E., Cabello-Yeves P.J., Di Cesare A., Eckert E.M., Bertoni R., Corno G., Salcher M., Kamburska L., Bertoni F., Moncheva S. (2019) The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global “deep red fluorescence” ISME Journal 13 : 1676-1687.
DOI: 10.1038/s41396-019-0378-z
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
Salcher M., Schaefle D., Kaspar M., Neuenschwander S., Ghai R. (2019) Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae ISME Journal 13 : 2764–2777.
DOI: 10.1038/s41396-019-0471-3
Alfreider A., Grimus V., Luger M., Ekblad A., Salcher M., Summerer M. (2018) Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes FEMS Microbiology Ecology 94 : 163.
DOI: 10.1093/femsec/fiy163
Bock K., Salcher M., Jensen M. , Pandey R.V., Boenigk J. (2018) Synchrony of eukaryotic and prokaryotic planktonic communities in three seasonally sampled Austrian lakes Frontiers in Microbiology 9 : 1290.
DOI: 10.3389/fmicb.2018.01290
Grujčić V., Nuy J. K., Salcher M., Shabarova T., Kasalický V., Boenigk J., Jensen M. , Šimek K. (2018) Cryptophyta as major bacterivores in freshwater summer plankton ISME Journal 12 : 1668-1681.
DOI: 10.1038/s41396-018-0057-5
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
Šimek K., Grujčić V., Hahn M., Horňák K., Jezberová J., Kasalický V., Nedoma J., Salcher M., Shabarova T. (2018) Bacterial prey food characteristics modulate community growth response of freshwater bacterivorous flagellates Limnology and Oceanography 63 : 484–502.
DOI: 10.1002/lno.10759
Alfreider A., Baumer A., Bogensperger T., Posch T., Salcher M., Summerer M. (2017) CO2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs Environmental Microbiology 19 : 2754–2768.
DOI: 10.1111/1462-2920.13786

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

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