Temporal and spatial dynamics of microbial communities

Extreme climate events, such as intense rainfall and flooding, are expected to increase significantly in Northern sub-boreal habitats. Flooding alters soil hydrology, impacting soil greenhouse gas (GHG) cycling, which is mediated by microbial communities and their adaptation to climate change. This study examined the effects of a two-week flash flood during the growing season on bacterial, archaeal, and fungal communities, as well as microbial processes linked to GHG fluxes, in riparian alder (Alnus incana (L.) Moench) forests. Soil samples were collected before, during, and after experimental flooding and analysed using quantitative polymerase chain reaction (qPCR) and sequencing techniques to assess microbial community dynamics. Physicochemical characteristics and in-situ GHG emissions were concurrently measured. Flooding reduced nitrate accumulation in soil, promoting dinitrogen-fixing and nifH gene-carrying bacteria, such as Geomonas. Anaerobic bacteria (Oleiharenicola, Pelotalea) increased during the flood, while soil N2O emissions were negatively related to soil moisture levels. However, drier patches within the flooded area acted as N2O sources, suggesting nitrification. A diverse AMF community was detected, including genera Acaulospora, Archaeospora, Claroideoglomus, Diversispora, and Paraglomus. Flooding increased the abundance of fungal genera Naucoria, Russula, and Tomentella, as well as the family Thelephoraceae, which form symbiotic relationships with alder trees, aiding nitrogen uptake and carbon sequestration. Overall, flash flooding during the active growing season significantly affects nitrogen-fixing and nitrifying microbes and alters symbiotic fungal community composition. Flooding creates spatial variability in GHG emissions, enhancing CH4 oxidation in waterlogged areas while promoting nitrification-driven N2O emissions in drier, elevated zones.