MSc. Markus Haber, Ph.D.

Funkce: Vědecký asistent - Oddělení mikrobiální ekologie vody

Kontaktní údaje

Telefon: +420 387 77 5836
Místnost: 221 NB


My research aims to identify the roles of microbes in chemical turnover processes in aquatic ecosystems and investigate which adaptations make microbes successful in their environment.

My current research investigates the ecology of a group of highly abundant freshwater actinobacteria: Ca. Nanopelagicales (also known as acI clade). These microbes are among the most abundant bacteria in freshwater lakes around the globe. They are of small size (cell volumes <0.1 μm3) and have highly streamlined genomes (<1.5 Mbp). Using a Ca. Nanopelagicales strain collection, I am examining niche separation between strains; their interaction with grazer, phages, and sympatric bacteria; and the role of photoheterotrophy in these bacteria. Besides cultivation and cultivation-based experiments, I am using comparative genomics, single-cell techniques such as CARD-FISH and metagenomic analyses to advance our understanding of the ecology of this group.

Odborný životopis

Jun 2019 – nowAssociated Scientist at the Institute of Hydrobiology, Biology Centre CAS

2014 – Mar 2019Postdoc at Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Israel; Advisor: Dr. Laura Steindler

2006 – 2013PhD at Tel Aviv University, Israel. Supervisor: Prof. Micha Ilan; Thesis: Chemical ecology and bacterial symbionts of Axinella sponges.

1998 – 2003Bachelor & Master studies in Biology, University of Münster, Germany


Participation in research projects

GAČR - Czech Science Foundation (2021 – 2023). EcoFAct – Ecology of abundant freshwater actinobacteria. PI: Dr. Markus Haber.

GAČR - Czech Science Foundation (2019 - 2021). Ecogenomics of genome-streamlined freshwater methylotrophs. PI: Dr. Michaela Salcher. Team member

Swiss National Science Foundation (2019 - 2020). Ecogenomics of freshwater bacteria. PI: Dr. Michaela Salcher. Team member

Israel Science Foundation – INCPM (2016 - 2017). Genomes of Mediterranean marine microbes. PI: Dr. Laura Steindler. Team member

Israel Science Foundation (2012 - 2016). Photoheterotrophy: Physiological and genetic characterization of how dominant heterotrophic bacteria channel light energy into the ocean. PI: Dr. Laura Steindler. Team member

European Commission - FP6 Marie Curie Research and Training Network (2005 – 2008). BIOCAPITAL - Cope with the Challenges and Opportunities of the 21st Century: Integrated Basic and Applied Training in a Success-oriented Bioprospecting. PhD student at Tel Aviv University, Israel, and research assistant at Instituto di Chimica Biomoleculare, Consiglio Nazionale delle Ricerche, Pozzuoli-Napoli, Italy.



Publications as member of the Institute of Hydrobiology are listed below. A full list of publications can be found in the following online research profiles:

Google Scholar

ORCID: 0000-0003-2591-6210

Research ID: AAG-5640-2020

SCOPUS ID: 36113783600


Celkem nalezeno: 12 záznamů
Henriques Vieira H., Bulzu P., Kasalický V., Haber M., Znachor P., Piwosz K., Ghai R. (2024) Isolation of a widespread giant virus implicated in cryptophyte bloom collapse. The ISME Journal 18 : wrae029.
DOI: 10.1093/ismejo/wrae029
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
Bar-Shalom R., Rozenberg A., Lahyani M., Hassanzadeh B., Sahoo G., Haber M., Burgsdorf I., Tang X., Squatrito V., Gómez-Consarnau L., Béjà O., Steindler L. (2023) Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota. ISME 17 : 1063–1073.
DOI: 10.1038/s41396-023-01412-1
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., 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
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
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
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.
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
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.
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: doi:10.1111/1462-2920.15210


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