Laboratory of Microbial Cultivation and Ecogenomics

Our research focuses on the ecology, evolution, and niche partitioning of freshwater oligotrophs. Small prokaryotes with reduced (streamlined) genomes are the most abundant organisms in the pelagial of freshwater lakes. However, their ecology remains largely elusive because of problems in cultivating environmentally relevant microbes. We apply high-throughput dilution-to-extinction techniques with media mimicking natural conditions to isolate such genome-streamlined oligotrophs and comparative genomics to shed light on their ecological niche, (micro)diversity and evolutionary history.

Group leader

Michaela M. Salcher, PhD

Lab members

Markus Haber, PhD

Cecilia Chiriac, PhD

Hon Lun (Alan) Wong, PhD

Paul Layoun, MSc.

Clafy Fernandes, MSc.

Férová Alžběta, Mgr.

Henriques Vieira Helena, PhD

Current projects

Phage host hunt: finding hosts for freshwater phages

Financial support: Czech Science Foundation (GACR); Project No.: 23-06806S, Duration: 2023-2025

Principal Investigator: Markus Haber

Team Members: Alan Wong, Vojtěch Kasalický, tba, tba

Phages are present in all ecosystems. They impact them by structuring microbial communities through the regulation of host populations and the release of host-bound nutrients through lysis. Metagenomics and -transcriptomics revealed a huge phage diversity in nature but often fail to assign hosts to phages. Especially in freshwater environments, this is partly due to the lack of cultured reference phages. Recent advances in bacterial cultivation enabled the isolation of abundant freshwater bacteria (e.g., Fonsibacter, Methylopumilus, Planktophila). We established a freshwater bacteria culture collection that includes members of these lineages. Here we propose to use these isolates and established high throughput phage isolation protocols to bona-fide identify phage-host pairs. We will study the host range, natural abundance and dynamics of the isolated phages. Finally, we will identify prophage in the genomes of isolates and by long-read metagenomics in environmental bacteria. Our proposed project hence plans to close an important gap in viral ecology by assigning hosts to phages.

This project aims to identify phage-bacteria host pairs and investigate their natural dynamics in a freshwater reservoir using cultivation-dependent and -independent methods.

Phylogeography and ecogenomics of ‘Ca. Fonsibacter’ (SAR11-IIIb)

Financial support: Czech Science Foundation (GACR); Project No.: 22-03662S, Duration: 2022-2024

Principal Investigator: Michaela Salcher

Team Members: Clafy Fernandes, Markus Haber, Cecilia Chiriac, Rohit Ghai

Microbes affiliated to SAR11 (‘Ca. Pelagibacterales’) dominate in marine (SAR11-I, II, IV, V), brackish (SAR11-IIIa) and freshwater (SAR11-IIIb) systems and are challenging to cultivate due to their oligotrophic lifestyle and unusual nutrient requirements. A first culture of freshwater SAR11-IIIb was described only 2 years ago (‘Ca. Fonsibacter’). We have recently isolated 13 SAR11-IIIb strains by high-throughput dilution-to-extinction and aim at 50 additional cultures. State-of-the-art genomics will be combined with experiments to tackle their microdiversity, topdown control by protists and interactions with other microbes (WP1). Sampling of lakes on the southern hemisphere will counterbalance the uneven global sampling of mainly northern countries. Long-read metagenomics will enable sophisticated phylogeographic analyses of highquality genomes of metagenomes (MAGs) and cultures (WP2). The evolution of freshwater SAR11 will be addressed with SAR11 MAGs originating from freshwaters branching within marine lineages and strains gained from the brackish Baltic Sea (WP3).

We aim to characterize the ecology, microdiversity, global biogeography and evolutionary history of ‘Ca. Fonsibacter’ (freshwater SAR11-IIIb) by using high-throughput dilution-toextinction cultivation, experimental characterization, and whole-genome-sequencing together with long-read metagenomics.

EcoFAct – Ecology of abundant freshwater actinobacteria

Financial support: Czech Science Foundation (GACR); Project No.: 21-21990S, Duration: 2021-2023

Principal Investigator: Markus Haber

Team Members: Indranil Mukherjee, Michaela Salcher, Rohit Ghai, Karel Šimek, Vinicius Kavagutti, Cecilia Chiriac

Actinobacteria of the acI lineage (Ca. Nanopelagicales) are ubiquitously present and often among the most abundant microbes in freshwater lakes around the globe. While several hypotheses for their success have been advanced based on culture independent approaches, most remain untested owing to a lack of cultures. Isolation efforts based on the recently reported first successful cultivation of acI strains enabled us to isolate more strains from this group. Here we propose to expand this culture collection and test isolates for physiological and genomic differences related to environmental factors to determine their ecological niches and ecotype diversity. We will address hypotheses pertaining to protection against eukaryotic grazing and phage infection and their interactions with co-occurring auto- and heterotrophic bacteria. Finally, we will examine if their success can be explained by their ability to use light as energy source and its effects on their physiology. Our results will greatly enhance our understanding of the ecological role of this important group.

The proposed research investigates the ecology of acI actinobacteria, one of the most abundant group of freshwater bacteria. Specifically, we will examine niche separation between strains; their interaction with grazer, phages, and sympatric bacteria; and its potential for photoheterotrophy.

Pan-European Lake Sampling - Microbial Eco-genomics (PELAGICS)

Financial support: Czech Science Foundation (GACR); Project No.: 20-12496X, Duration: 2020-2024

Principal Investigator: Rohit Ghai, co-PI: Michaela Salcher

Team Members: Paul Bulzu, Indranil Mukherjee, Alan Wong, Tiberiu Szöke-Nagy, Vojtěch Kasalický, Karel Šimek, Vinicius Kavagutti, Clafy Fernandes, Roudaina Boukheloua, Monika Okrouhlíková, Helena Vieira, Fran Kostanjšek, Petr Macek

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 semi-automated high-throughput isolation we aim for stable cultivation and whole-genome sequencing of 500 prokaryotes and 50 unicellular eukaryotes. Moreover, terabyte scale deep-metagenomic sequencing (ca. 15 TB) will allow recovery of thousands of metagenome-assembled 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.

Eco-genomics of genome-streamlined freshwater methylotrophs

Financial support: Czech Science Foundation (GACR); Project No.: 19-23469S; Duration: 2019-2021

Principal Investigator: Michaela Salcher

Team Members: Markus Haber, Tanja Shabarova, Paul Bulzu, Paul Layoun, Rohit Ghai, Radka Malá

The most abundant planktonic microbes have reduced genomes and streamlining theory predicts that gene loss is caused by evolutionary selection driven by environmental factors. Yet the evolutionary path of streamlining remains unknown because of obstacles in establishing axenic cultures of such microbes. We developed a targeted isolation technique for abundant genome-streamlined freshwater methylotrophs: ‘Ca. Methylopumilus planktonicus’ (Betaproteobacteria, 1.3 Mbp genome size), that are ideal model organisms for studying microdiversification patterns and the evolution of genome-streamlining per se. The closest relatives of ‘Ca. M. planktonicus’ inhabit lake sediments and the pelagial of oceans, and we propose that the evolutionary origin of the family can be traced back to sediment microbes with medium-sized genomes. Whole genome sequencing of 150 strains and deep sequencing of metagenomes will allow comparative population genomics with the aim to disentangle the underlying ecological reasons for the widespread but yet enigmatic phenomenon of genomestreamlining in aquatic microbes.

The aim of the project is using targeted isolation and whole-genome-sequencing of oligotrophic freshwater ‘Ca. Methylopumilus planktonicus’ (Betaproteobacteria) together with metagenomics to study the evolution of genome-streamlining in planktonic microbes. Identifying microdiversification patterns in closely related taxa.

Eco-genomics of freshwater microbes

Financial support: Money follows Researcher (MFR) grant of the Swiss National Science Foundation (SNSF); Project No.: 310030_185108; Duration: 2019-2020

Principal Investigator: Michaela Salcher

Team Members: Markus Haber

Recent publications (2019-now)

Šimek K.Mukherjee I.Szöke-Nagy T., Haber M., Salcher M.Ghai R. (2023) Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores. The ISME Journal 17 : 84–94. DOI: 10.1038/s41396-022-01326-4
Briddon C.L., Szekeres E. , Hegedüs A., Nicoară M., Chiriac M., Stockenreiter M., Drugă B. (2022) The combined impact of low temperatures and shifting phosphorus availability on the competitive ability of cyanobacteria. Scientific Report12 : 16409.
DOI: 10.1038/s41598-022-20580-2
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
Chiriac M.Bulzu P., Andrei A.S., Okazaki Y., Nakano S., Haber M.Kavagutti V.Layoun P.Ghai R., Salcher M.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.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
Drugă B., Ramm E., Szekeres E. , Chiriac M., Hegedüs A., Stockenreiter M. (2021) Long-term acclimation might enhance the growth and competitive ability of Microcystis aeruginosa in warm environments. Freshwater Biology 67 : 589–602. DOI: 10.1111/fwb.13865
Haber M., Rosenberg D.R., Lalzar M., Burgsdorf I., Saurav K., Lionheart R., Lehahn Y., Aharonovich D., Gómez-Consarnau L., Sher D., Krom M.D., Steindler L. (2022) Spatiotemporal variation of microbial communities in the ultra-oligotrophic Eastern Mediterranean Sea. Frontiers in Microbiology 13 : 867694. DOI: 10.3389/fmicb.2022.867694
Johnson M.S., Burns B.P., Herdean A., Angeloski A., Ralph P., Morris T., Kindler G., Wong H., Kuzhiumparambil U., Sedger L.M., Larkum A.W.D. (2022) A cyanobacteria enriched layer of Shark Bay stromatolites reveals a new Acaryochloris strain living in near infrared light. Microorganisms 10 : 1035. DOI: 10.3390/microorganisms10051035
Kindler G.S., Wong H., Larkum A.W.D., Johnson M., MacLeod F.I., Burns B.P. (2022) Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay. FEMS Microbiology Ecology 98 : fiab158. DOI: 10.1093/femsec/fiab158
Nobs S.J., MacLeod F.I., Wong H., Burns B.P. (2022) Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life? Trends in Microbiology 30 : 421-431. DOI: 10.1016/j.tim.2021.11.003
Ray A.E., Zaugg J., Benaud N., Chelliah D.S., Bay S., Wong H., Leung P.M., Ji M., Terauds A., Montgomery K., Greening C., Cowan D.A., Kong W., Williams T.J., Hugenholtz P., Ferrari B.C. (2022) Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. The ISME Journal 16 : 2547–2560. DOI: 10.1038/s41396-022-01298-5
Vadaq N., Schirmer M., Tunjungputri R.N., Vlamakis H., Chiriac M., Ardiansyah E., Gasem M.H., Joosten L.A.B., de Groot P.G., Xavier R.J., Netea M.G., van der Ven A., de Mast Q. (2022) Untargeted plasma metabolomics and gut microbiome profiling provide novel insights into the regulation of platelet reactivity in healthy individuals. Thrombosis and Haemostasis 122 : 529-539. DOI: 10.1055/a-1541-3706

Haber M., Burgsdorf I., Handley K.M., Rubin-Blum M., Steindler L. (2021) Genomic insights into the lifestyles of Thaumarchaeota inside sponges. Frontiers in Microbiology 11 : 622824. DOI:

Mujakic I., Andrei A., Shabarova T., Kolesár Fecskeová L., Salcher M.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.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.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
Rosenberg D.R., Haber M., Goldford J., Lalzar M., Aharonovich D., Al-Ashhab A., Lehahn Y., Segrè D., Steindler L., Sher D. (2021) Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors. Environmental Microbiology 23 : 4295-4308. DOI: 10.1111/1462-2920.15611
Shabarova T., Salcher M.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.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. DOI:
Kust A., Řeháková K., Vrba J., Maicher V., Mareš J., Hrouzek P., Chiriac M.C., Benedová Z., Tesařová M., Saurav K. (2020) Insight into unprecedented diversity of cyanopeptides in eutrophic ponds using an MS/MS networking approach Toxins 12 : 561. DOI: doi:10.3390/toxins12090561
Mukherjee I., Salcher M.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:
Piwosz K., Shabarova T., Pernthaler J., Posch T., Šimek K., Porcal P., Salcher M.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.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. DOI:

Sizikov S., Burgsdorf I., Handley K.M., Lahyani M., Haber M., Steindler L. (2020), Characterization of sponge‐associated Verrucomicrobia: microcompartment‐based sugar utilization and enhanced toxin–antitoxin modules as features of host‐associated Opitutales. Environmental Microbiology 22: 4669-4688. DOI:
Šimek K., Grujčić V., Mukherjee I., Kasalický V., Nedoma J., Posch T., Mehrshad M., Salcher M.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. DOI:
Andrei A., Salcher M.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.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.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.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.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


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

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