MSc. Markus Haber, Ph.D.
Research Scientist
Department of Aquatic Microbial Ecology (AME)
Institute of Hydrobiology
+420 387 77 5836
markus.haber@hbu.cas.cz
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. One current research project investigates the ecology of the highly abundant freshwater actinobacteria order Ca. Nanopelagicales (also known as acI clade). These microbes are among the most abundant bacteria in freshwater lakes around the globe. They are small (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. In a recently funded project, we are expanding the search for phages to other abundant freshwater bacteria. Phages play crucial roles in biogeochemical cycles (e.g. releasing nutrients from their hosts through lysis). Using flow cytometry based high-throughput cultivation and a unique freshwater bacteria collection, we aim to isolate and genome sequence phages of some of the most abundant freshwater lineages such as Ca. Fonsibacter, Ca. Planktophila, Limnohabitans, and others. This bona fide identification will allow us to investigate the dynamics of the isolated phages and their hosts in our long-term sampling site, the Rimov reservoir, via metagenomics. Jun 2023 – now Research Scientist at the Institute of Hydrobiology, Biology Centre CAS Jun 2019 – May 2023 Associated Scientist at the Institute of Hydrobiology, Biology Centre CAS 2014 – Mar 2019 Postdoc at Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Israel; Advisor: Dr. Laura Steindler 2006 – 2013 PhD at Tel Aviv University, Israel. Supervisor: Prof. Micha Ilan; Thesis: Chemical ecology and bacterial symbionts of Axinella sponges. 1998 – 2003 Bachelor & Master studies in Biology, University of Münster, Germany GAČR - Czech Science Foundation (2024 – 2026). MATISSE: Microbial Activity in Time and Space during Spring Ecological Succession. PI: Dr. Rohit Ghai. Team member GAČR - Czech Science Foundation (2023 – 2025). Phage host hunt: finding hosts for freshwater phages. PI: Markus Haber. GAČR - Czech Science Foundation (2022 – 2024). Phylogeography and ecogenomics of ‘Ca. Fonsibacter’ (SAR11-IIIb). PI: Dr. Michaela Salcher. Team member 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:
Participation in research projects
Publications
