Biology subjects

Wutkowska, M.

Publications and source records attributed to Wutkowska, M..

5 recordsLinked to original sources

bioRxiv2025

Soil trace gas oxidizers divergently respond to short- and long-term warming

The upland soil microbiome is dominated by aerobic bacteria that oxidize atmospheric trace gases, including CO, H2, and CH4. As a result, soils are the largest biological sink for these climate-active gases. Whether global warming will enhance or suppress these processes remains unclear. Here, we studied the warming responses of soil trace gas oxidizers by profiling natural geothermal gradients in a subarctic grassland with over 60 years of field warming at +6{degrees}C. We integrate field flux measurements, ex situ biogeochemical assays, metagenomics, and metatranscriptomics to determine ecosystem and cellular-level responses. Our results show that the oxidation of atmospheric CO and H2, but not CH4, increased with long-term warming due to higher cell numbers. However, at the cellular level, trace gas oxidizers, especially methanotrophs, tended to reduce gas consumption and transcription of gas-metabolizing enzymes in response to long-term warming. Our findings suggest that soils may remain a robust sink for trace gases despite lower per-cell activity. This work establishes a framework for interpreting the relationships between temperature and microbial trace gas oxidation on timescales relevant to Earths climate system.

microbiology↗

bioRxiv2025

Uncovering hidden phylo- and ecogenomic diversity of the widespread methanotrophic genus Methylobacter

The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterise the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulphur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognised species diversity within the Methylobacter genus, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.

microbiology↗

bioRxiv2025

Genomic and physiological characterization of 'Candidatus Methylocystis sumavensis', a novel acid-tolerant methanotroph from peatland

Methanotrophic bacteria in peatlands mitigate emissions of methane (CH4), a potent greenhouse gas, yet the mechanisms enabling them to remain active under the acidic conditions typical of many peatlands remain poorly understood. Using enrichment cultivation and single-cell sorting, we isolated a novel peatland methanotroph from Czech soil, Methylocystis sumavensis. This species is moderately acidotolerant and active across broad pH and temperature ranges, with growth optima at pH 6.8 and 24-37 {degrees}C. The genome of M. sumavensis encodes two particulate methane monooxygenase isozymes, a clade I nitrous oxide reductase, multiple terminal oxidases, and two [NiFe]-hydrogenases, including a complete complex of the previously uncharacterised membrane-bound hydrogenase group 4f, indicating substantial metabolic versatility. To link genomic potential with physiological function, we compared transcriptomes under acidic (pH 5.0) and alkaline (pH 9.0) conditions relative to the optimum pH (6.8). Under both stresses, M. sumavensis increased transcription of genes involved in membrane remodelling, ion transport across both membranes, and stress response and repair, while reducing transcription of genes associated with methane oxidation and cell division. Alkaline stress additionally suppressed growth through reduced transcription of the carbon-assimilating Serine cycle. In contrast, acidic stress triggered a coordinated response requiring greater energetic investment. Among the most strongly upregulated genes were those encoding two formate dehydrogenases, the branched-chain alpha-keto-acid dehydrogenase complex, and all seven group 4f [NiFe]-hydrogenase-related genes, suggesting enhanced respiratory redox balancing under elevated external proton concentrations. These results reveal key mechanisms of pH-stress adaptation and highlight metabolic plasticity as a major determinant of methanotroph resilience in ecosystems.

microbiology↗

bioRxiv2021

Linking extreme seasonality and gene expression in arctic marine protists

At high latitudes, strong seasonal differences in light availability affect marine organisms and restrict the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45-10 m protist assemblages sampled over 13 months in a time series station in an arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in arctic samples from Tara Oceans, suggesting that arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.

microbiology↗

bioRxiv2020

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb?

Arctic plants are affected by many stressors. Root-associated fungi are thought to influence plant performance in stressful environmental conditions. However, the relationships are not transparent; do the number of fungal partners, their ecological functions and community composition mediate the impact of environmental conditions and/or influence host plant performance? To address these questions, we used a common arctic plant as a model system: Bistorta vivipara. Whole plants (including root system) were collected from nine locations in Spitsbergen (n=214). Morphometric features were measured as a proxy for performance and combined with metabarcoding datasets of their root-associated fungi (amplicon sequence variants, ASVs), edaphic and meteorological variables. Seven biological hypotheses regarding fungal influence on plant measures were tested using structural equation modelling. The best-fitting model revealed that local temperature affected plants both directly (negatively aboveground and positively below-ground) and indirectly - mediated by fungal richness and the ratio of symbio- and saprotrophic ASVs. Fungal community composition did not impact plant measurements and plant reproductive investment did not depend on any fungal parameters. The lack of impact of fungal community composition on plant performance suggests that the functional importance of fungi is more important than their identity. The influence of temperature on host plants is therefore complex and should be examined further.

microbiology↗