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

Dr. Michaela M. Salcher

Lab members

Dr. Markus Haber

Dr. Cecilia Chiriac Paul Layoun

Mgr. Monika Okrouhlíková, Ph.D.

Current projects

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

Project No.: 20-12496X

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

Financial support: Czech Science Foundation (GACR)

Duration: 2020-2024

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

Project No.: 19-23469S

Principal Investigator: Michaela Salcher

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

Financial support: Czech Science Foundation (GACR)

Duration: 2019-2021

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

Project No.: 310030_185108

Principal Investigator: Michaela Salcher

Team Members: Markus Haber

Financial support: Money follows Researcher (MFR) grant of the Swiss National Science Foundation (SNSF)

Duration: 2019-2020


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

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