MSc. Michaela Maria Salcher, Ph.D.

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

Contact details

Phone: 387 775 836
Room: C221


Research interests

My research focuses on the ecology, evolution, and ecological niche separation of the most abundant organisms in lakes: small microbes with reduced (streamlined) genomes. Freshwater microbes are centrally involved in chemical turnover processes, yet individual populations greatly differ in their ecology and role in the environment. My aim is to get a synoptic view of the functional roles, evolutionary history, ecological and genomic adaptations to freshwaters, and phylogeographic distribution 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 characterization. I developed a targeted isolation strategy for bringing these microbes in culture and successfully isolated, e.g., strains of the highly abundant acI Actinobacteria (Ca. Nanopelagicales’), the freshwater sister lineage of SAR11 (Ca. Fonsibacter’) and methylotrophic Burkholderiales (Ca. Methylopumilus’). These taxa are not only of minute cell and genome size but also amongst the most abundant microbes in freshwaters.

In the pursuit of a comprehensive understanding of aquatic microbial ecology, I advocate for a multifaceted approach integrating various methodologies ranging from in situ experiments and field surveys explored by cutting-edge meta-omics to experiments with relevant model organisms. For this purpose, my lab established a large culture collection of typical freshwater genera (>7000 axenic strains, thereof >500 genome-sequenced) from ~100 lakes from five continents spanning all major climatic zones and biomes. Our strain collection includes a high diversity of undescribed taxa known only from environmental sequences, a large number of hard-to-grow oligotrophs and almost all known freshwater copiotrophs. While the last five years have been spent obtaining this treasure trove, it is now ready to be exploited to its full use and serve as model to elucidate the role of oligotrophs and copiotrophs in natural environments.

Ongoing and past projects focus on the global distribution and ecology of ‘Ca. Fonsibacter’ (GAČR 22-03662S), the evolutionary history and genomic microdiversity of ‘Ca. Methylopumilus’ (GAČR 19-23469S, 2019-2022) and a European-wide sampling of 77 lakes in 15 countries for isolating and genome-sequencing of diverse pro- and eukaryotes together with Tb-scale metagenomic sequencing (GAČR 20-12496X). Besides, I’m co-PI in a project studying the combined effects of warming and pollutants on nutrient flows and lower trophic levels in freshwater communities (GAČR 24-11779S).

Curriculum vitae

2019-now       Senior researcher at the Institute of Hydrobiology, Biology Centre CAS

2017-2018      Senior researcher at the Limnological Station, University of Zurich, Switzerland

2014-2016      Researcher 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 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:

Past projects:


10 selected publications, for a full list see Google Scholar or ORCID, papers with IHB affiliation are listed below:

Layoun P, López-Pérez M, Haro-Moreno JM, Haber M, Thrash JC, Henson MW, Kavagutti VS, Ghai R, Salcher MM (2024). Flexible genomic island conservation across freshwater and marine Methylophilaceae. The ISME Journal wrad036. doi:10.1093/ismejo/wrad036.

Chiriac M-C, Haber M, Salcher MM (2023) Adaptive genetic traits in pelagic freshwater microbes. Environmental Microbiology 25:606-641. doi:10.1111/1462-2920.16313. Invited Review article

Shabarova T, Salcher MM, Porcal P, Znachor P, Nedoma J, Grossart H-P, 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

Bulzu P-A, Andrei A-S, 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

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 13:2764-2777. doi:10.1038/s41396-019-0471-3

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, 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


Scientific profiles with full publication lists:


Google Scholar

ORCID: 0000-0003-1063-6523

Researcher ID: A-1141-2013

SCOPUS ID: 8380561300

Total found: 40 records
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
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
Chiriac M., Haber M., Salcher M. (2023) Adaptive genetic traits in pelagic freshwater microbes. Environmental Microbiology 25 : 606–641.
DOI: 10.1111/1462-2920.16313
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
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
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
Dirren-Pitsch G., Bühler D., Salcher M., Bassin B., Le Moigne A., Schuler M., Pernthaler J., Posch T. (2022) FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates. Frontiers in Microbiology 13 : 1070232.
DOI: 10.3389/fmicb.2022.1070232
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

More publications


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

Staff search