Specialized biopolymer degraders structure microbial community assembly through interconnected modes of metabolic cross-feeding.

Communications Biology - Two coinfecting archaeal viruses provide insights into virus-virus interactions

Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

Understanding carbon cycling requires simplifying bacterial diversity into functional groups defined by genetic signatures.

Assistant/Associate/Full Professor Computational Biology

What microbial communities reveal about hierarchy, interdependence, and belonging

Abstract. Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to i

EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...

Long-read sequence assemblies from metagenomes contain frequent errors.

This study maps out the diversity and evolution of the bacterial order Caulobacterales, including the model organism C. crescentus, which reveals widespread phototrophy and illuminates the evolution o...

The story behind the story of our microbial model communities study

Microbial model communities bridge the gap between pure culture and environmental studies, revealing widespread metabolic interdependencies that shape how natural microbial groups thrive and interact ...

AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

Scientific Reports - Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance

All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...

With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses

Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

A few genera of diatoms are widespread in the oceans and form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. A unique feature of the diatom-Richelia symbioses is the symbio...

Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...

A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response to environmental extremes.

Nature Microbiology - The tree of life is a galvanizing image, anchoring biological diversity within a common framework. From a new view in 2016, the tree has continued to grow, and with it, our...

Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum. ### Competing Interest Statement The authors have declared no competing interest.