Biology subjects

Siljanen, H. M. P.

Publications and source records attributed to Siljanen, H. M. P..

4 recordsLinked to original sources

bioRxiv2026

Vegetation increases CH4 emissions and methanotroph diversity in marine sediments

Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH) emissions, whose microbial and environmental descriptors in Zostera noltei meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH fluxes, CH-producing and consuming microbial communities and sediment physico-chemical parameters in Z. noltei meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH fluxes were measured at low tide and microbial communities were characterised using targeted metagenomics of three functional genes (mcrA, mmoX, pmoA) and quantitative PCR. CH fluxes were higher in vegetated than bare sediments (24.4 {+/-} 2.6 vs. 9.4 {+/-} 0.7 {micro}mol m-{superscript 2} d-{superscript 1}). Mixed linear models and random forest analyses identified C accumulation rate and CO2 flux as the strongest positive descriptors of CH fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera (mcrA-Methanolobus, mmoX-Methylocella, pmoA-Methylococcus, Methyloglobulus) emerged as abundant, seagrass-associated, correlated with CH fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH fluxes than gene abundance or a specific genus. Findings indicate Z. noltei meadows enhance C burial and CH emission, with methanotroph diversity potentially mitigating CH emissions. Our results provide the first integrated assessment of CH fluxes and their descriptors in Z. noltei meadows, highlighting the intertwined nature of C burial and CH emissions and the need to account for both in blue C climate assessments.

ecology↗

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↗

bioRxiv2023

Activity and abundance of nitrous oxide consuming bacteria in Platismatia glauca cryptogamic lichen in boreal Finnish spruce forest.

The boreal spruce forest soil can assimilate atmospheric N2O through symbiotic relationships with mycorrhizae or with bacteria, especially during spring and autumn, when aerobic microsites to soil can form. In cold soils with large field capacity (FCD), high humidity and absence of fertilisation, a balance between absorption and emission of nitrous oxide and dinitrogen was observed to be close to zero, and even to assume negative values in some cases, thus suggesting that forest soils absorb more N2O than they emit. Furthermore, in the presence of cryptogamic coverings of mosses and lichens, the absorption value was observed to be greater than in forests with less coverage; although the main role in N2O absorption is played by soil and root system. However, the role played by epiphytic organisms in N2O absorption in the boreal forests has not been uncovered yet. We studied, N2O dynamics of the lichen, Platismatia glauca, showing that N2O is consumed especially at lower incubation temperatures. The quantitative analysis with real-time PCR of nitrous oxide reductase gene fragment nosZ, showed that enzyme is present in the lichen and the gene is more transcribed under lower incubation temperature. The presented results unveil that cryptogamic covers consume nitrous oxide (with values between 0.1 and 0.4 ng N2O-C/g (ww)/h) at the atmospheric concentration via complete dissimilatory denitrification when nitrogen is limited.

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↗