Centimetre scale functional dispersal limitation of freshwater copiotrophs.

The freshwater microbiome harbours numerous copiotrophic bacteria that rapidly respond to elevated substrate concentrations. We hypothesized that their high centimetre-scale beta diversity in lake water translates into pronounced metabolic variability, and that a large fraction of microbial 'metabolic potential' originates from point sources such as fragile organic aggregates. Three experiments were conducted in pre-alpine Lake Zurich over the course of a harmful cyanobacterial bloom: Spatially explicit 9 ml 'syringe' samples were collected in situ at centimetre distances along with equally sized 'mixed' samples drawn from pre-homogenized lake water and incubated in BIOLOG EcoPlate substrate arrays. Fewer compounds promoted bacterial growth in the syringe than in the mixed samples, in particular during the pre- and late bloom periods. Community analysis of enrichments on three frequently utilized substrates revealed both pronounced heterogeneity and functional redundancy. Bacterial consortia had higher richness in mixed than in syringe samples and differed in composition. Members of the Enterobacter cloacae complex dominated the EcoPlate assemblages during the mid-bloom period irrespective of treatment or substrate. We conclude that small-scale functional dispersal limitation among free-living copiotrophs in lake water reduces local biotransformation potential, and that lacustrine blooms of harmful cyanobacteria can be environmental reservoirs for metabolically versatile potential pathogens.

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%.