Biology subjects

Biasi, C.

Publications and source records attributed to Biasi, C..

4 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

Microbial mechanisms responsible for diurnal dynamics of N2O fluxes in a nutrient-poor subarctic permafrost environment

Diurnal variation of nitrous oxide (N2O) fluxes was recently shown to occur across terrestrial ecosystems, typically with higher daytime emissions. However, the underlying microbial mechanisms remain poorly understood. Here, we investigated the microbial drivers of daily N2O dynamics in a permafrost palsa mire, where a higher net N2O sink has been observed during dark than under light conditions. By integrating day night flux measurements with molecular analyses, we could directly link short-term temporal patterns of N2O exchange with diurnal shifts in microbial activity. Quantitative PCR revealed the presence of denitrification genes nirK and nirS, associated with N2O emissions in soils, and nosZ clades I and II, involved in N2O consumption. However, only nirK and nosZ clade I were transcriptionally active. The diurnal pattern of nirK/nosZ gene expression largely aligned with the diurnal pattern of N2O fluxes, with elevated ratios during daytime, particularly in wet and productive fen habitats. Metatranscriptomic analyses further revealed higher daytime expression ratios of N2O producing relative to N2O reducing genes ((p450nor + norB + hao)/nosZ), in addition to high nirK/nosZ expression ratios. Members of Alphaproteobacteria, particularly Rhizobiales and Bradyrhizobium, consistently expressed both nirK and nosZ across the diel cycle. Analysis of 1,753 metagenome-assembled genomes obtained from the present and previous work further indicate that partial denitrifiers are key players in regulating N2O fluxes in arctic permafrost palsa mire. Together, our results provide new insights into the microbial basis for diurnal N2O dynamics, which should be considered when estimating ecosystem-climate feedback in terrestrial ecosystems in the Arctic and beyond.

microbiology↗

bioRxiv2025

Microbial community composition explains wintertime greenhouse gas fluxes in an oroarctic tundra ecosystem

Microbial communities play a central role in regulating the greenhouse gas balance in soil ecosystems. Microorganisms are active in the cold, snow-covered Arctic tundra soils; however, their contribution to the greenhouse gas budget during the Arctic winter remains poorly understood. To investigate the functional activity of bacterial and archaeal communities in oroarctic tundra soils during late winter, metatranscriptomic samples were collected alongside greenhouse gas (GHG) flux measurements across key vegetation types, which represent pH and moisture gradients. The transcription of central carbohydrate metabolism genes, various stress-related genes, and high carbon dioxide (CO2) fluxes evidenced active microbial metabolism in winter. Vegetation type, soil C/N ratio, pH, and water content explained the functional activity and microbial community composition during winter. The transcription of functional marker genes for methane oxidation and denitrification, coupled with flux data, suggests that shrublands and meadows act as methane (CH4) sinks in winter, while all vegetation types function as small nitrous oxide (N2O) sources. Our results further demonstrate that the soil microbial community has a significant impact on wintertime GHG emissions in the oroarctic tundra, thereby enhancing the explanatory power of a statistical model beyond that of abiotic environmental variables alone. This represents a promising step toward developing microbial-mediated models, which are crucial for improving predictions of ecosystem responses to climate change.

microbiology↗

bioRxiv2022

Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics

Microorganisms are key players in the global cycling of nitrogen (N) and carbon (C), controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide (N2O) and methane (CH4). Characterizing the microbial functional guilds driving these processes is crucial for understanding ecosystem functioning and predicting their responses to environmental changes. Standard sequence-based characterization methods often reveal only a limited fraction of their diversity in nature because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of PCR-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic N and CH4 cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264,000 unique probes. These probes were used to selectively enrich the target genes in shotgun metagenomic libraries. In validation experiments with the mock communities of known microorganisms, targeted metagenomics yielded gene profiles similar to those of the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics from agricultural and wetland soils were significantly correlated, indicating that the targeted approach did not introduce significant quantitative bias. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Notably, shotgun metagenomics detected only three out of the 84 amoA gene phylotypes detected using targeted metagenomics. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes. Manuscript contribution to the fieldMetagenomic sequencing often yields limited numbers of sequences of rare microbial taxa or functional genes, preventing in-depth analyses of specific populations and functional groups. Amplicon-based approaches enable the higher diversity coverage of target populations, but the drawback is the difficulty in designing unbiased primers that cover the highest intra-group diversity. Targeted metagenomics overcomes these challenges and results in similar community structure as traditional amplicon sequencing, while expanding the sequence space in a less biased metagenomic-based approach. Therefore, targeted metagenomics is an invaluable tool for studying the diversity of specific populations within complex natural microbiomes. Here, we present and evaluate a probe library designed for targeted metagenomics of nitrogen and methane cycling genes in complex communities.

microbiology↗