Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.

The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.

Complete genome of Flavobacterium pectinovorum str. ZE23VCel01 obtained through Nanopore Q20+ chemistry.

This study reports the complete genome of Flavobacterium pectinovorum str. ZE23VCel01 isolated from a freshwater environment. By means of Nanopore Q20+ chemistry, the chromosome was assembled as a circular element with a length of 5.9 Mbp, a GC content of 33.58%, and a coverage of 122×.

A high-quality genome of an undescribed Flavobacterium species uncovered using Q20+ Nanopore chemistry.

Herein, we document the complete genome of the Flavobacterium strain ZE23DGlu08, isolated from Lake Zurich, Switzerland. The circular genome was assembled using long-read Nanopore data (coverage: 226×) with the Q20+ chemistry. The described strain displays a genome size of ~3.9 Mbp with a GC content of 34%.

Pseudomonas kielensis str. Ze23jcel16 complete genome obtained through R10.4.1 Nanopore Flow cell chemistry.

Here, we report the complete genome of Pseudomonas kielensis str. Ze23jcel16 isolated from a freshwater sample. The high-quality chromosome was obtained employing R10.4.1 Nanopore Flow cell chemistry and was assembled as a circular element at 45× coverage, a length of 5.8 Mbp, and a G+C content of 61.15%.

Q20+ Nanopore sequencing data recover a high-quality Asticcacaulis sp. genome.

We present here the complete genome of Asticcacaulis sp. ZE23SCel15. The strain was isolated from the surface water of Lake Zurich, Switzerland. The assembly of high-quality Q20+ Nanopore data yielded a circular genome with ~3.8 Mb (coverage: 34×) and a GC content of 56.81%.