Biology subjects

Pitkanen, J.-M.

Publications and source records attributed to Pitkanen, J.-M..

3 recordsLinked to original sources

bioRxiv2026

Soil microbiome structure and function reflect environmental variation rather than reindeer presence in a northern peatland

Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect the soil microorganisms driving methane (CH) and nitrous oxide (N2O) cycling. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while the effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.

microbiology↗

bioRxiv2026

Scalable isolation of soil genomic DNA from microbes to multicellular micro- and mesofauna

Global initiatives emphasize the need for harmonized soil biodiversity assessments. Efficient DNA extraction methods that accommodate larger soil volumes are essential for capturing higher trophic levels than bacteria and fungi and supporting extensive sampling campaigns. We developed and evaluated a scalable, cost-efficient, and automation-ready soil DNA isolation technique alongside commercial protocols. Three starting soil amounts (0.25 g, 2.5 g, and 5 g) were tested using widely used Qiagen kits, the developed isolation method, or combinations thereof. Lysis volumes ranged from 800 {micro}l to 15 ml, and purification employed either silica membrane or carboxyl-coated magnetic beads. Four different types of soil, both agricultural and forest soil, samples were sequenced on an Illumina MiSeq platform using universal eukaryotic primers targeting the 18S rRNA SSU region, enabling detection of non-fungal eukaryotes such as soil mesofauna and protozoa. The developed protocol, which combined a tenfold increase in sample volume with hybrid purification steps, yielded the highest DNA recovery and consistently improved detected richness in several soil types. Species richness patterns varied by soil type and organism group: for eukaryotes and protozoa, commercial maxiprep methods along with the combination methods outperformed the miniprep approach in agricultural soils, while the developed technique excelled in coarse xeric forest soils. For metazoans, larger extraction volumes were associated with higher richness in forest soils. Our findings indicate that at least a tenfold increase in soil input compared to conventional 0.2-0.3 g is required to reliably capture mesofaunal diversity, with preliminary evidence suggesting further benefits at 20-fold volumes. We confirm that extraction volume is a key factor shaping detection of both soil metazoan and protozoan community compositions, with effects varying by soil type and organism group. The developed scalable approach offers a practical solution for large-scale soil biodiversity assessments, aligning with global monitoring goals and enabling integration of higher trophic levels into eDNA-based frameworks.

microbiology↗

bioRxiv2019

Can school children support ecological research? Lessons from the ‘Oak bodyguard’ citizen science project

Scientific knowledge in the field of ecology is increasingly enriched by data acquired by the general public participating in citizen science (CS) programs. Yet, doubts remain about the reliability of such data, in particular when acquired by school children. We built upon an ongoing CS program - Oak bodyguards - to assess the ability of European schoolchildren to accurately estimate the strength of biotic interactions in terrestrial ecosystems. We used standardized protocols to estimate predation rates on artificial caterpillars and insect herbivory on oak leaves and compared estimates made by school children, trained and untrained professional scientists (with no or limited expertise in predation or herbivory assessment). Compared to trained scientists, both schoolchildren and untrained professional scientists overestimated predation rates, but assessments made by the latter were more consistent. School children overestimated insect herbivory, as did untrained professional scientists. Thus, raw data acquired by school children participating in CS programs cannot be used and require several quality checks. However, such data are of no less value than data collected by untrained professional scientists and can be calibrated for bias.

scientific communication and education↗