Summary Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old‐growth forests, ranging from N‐rich Picea abies stands to acidic and N‐poor Pinus sylvestris stands. 454‐pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old‐growth boreal forests.

Summary• Here, species composition and biomass production of actively growing ectomycorrhizal (EM) mycelia were studied over the rotation period of managed Norway spruce (Picea abies) stands in south-western Sweden.• The EM mycelia were collected using ingrowth mesh bags incubated in the forest soil during one growing season. Fungal biomass was estimated by ergosterol analysis and the EM species were identified by 454 sequencing of internal transcribed spacer (ITS) amplicons. Nutrient availability and the fungal biomass in soil samples were also estimated.• Biomass production peaked in young stands (10-30 yr old) before the first thinning phase. Tylospora fibrillosa dominated the EM community, especially in these young stands, where it constituted 80% of the EM amplicons derived from the mesh bags. Species richness increased in older stands.• The establishment of EM mycelial networks in young Norway spruce stands requires large amounts of carbon, while much less is needed to sustain the EM community in older stands. The variation in EM biomass production over the rotation period has implications for carbon sequestration rates in forest soils.

Symbiotic ectomycorrhizal fungi have received increasing attention as regulators of below-ground organic matter storage. They are proposed to promote organic matter accumulation by suppressing saprotrophs, but have also been suggested to play an active role in decomposition themselves. Here we show that exclusion of tree roots and associated ectomycorrhizal fungi in a boreal forest increased decomposition of surface litter by 11% by alleviating nitrogen limitation of saprotrophs-a "Gadgil effect". At the same time, root exclusion decreased Mn-peroxidase activity in the deeper mor layer by 91%. Our results show that ectomycorrhizal fungi may hamper short-term litter decomposition, but also support a crucial role of ectomycorrhizal fungi in driving long-term organic matter oxidation. These observations stress the importance of ectomycorrhizal fungi in regulation of below-ground organic matter accumulation. By different mechanisms they may either hamper or stimulate decomposition, depending upon stage of decomposition and location in the soil profile.

1. Forestry with short stand generations and simplified forest structures has markedly affected forest biodiversity. One group of organisms adversely affected by clear-cutting is ectomycorrhizal (ECM) fungi, as they are associated with the roots of living trees. Retention forestry is a way of reducing logging impacts and enhancing biodiversity conservation. Increasing the proportion of trees retained at harvest may improve ECM fungal diversity.2. We investigated the potential for lifeboating of ECM fungi through the harvesting phase in an experimental field study in a 190-year-old Scots pine forest in northern Sweden. The experiment comprised four levels of tree retention-unlogged forest, plots with 60% or 30% of evenly distributed trees retained and clear-cuts without retained trees. We sampled soils and determined identities, frequencies and relative abundances of ECM fungal species during 3 years following logging through the use of high-throughput sequencing of amplified ITS2 markers.3. We identified 149 ECM fungal species, with the five most abundant species accounting for 50% of the total ECM fungal amplicons. Three years after harvesting, the proportion of ECM sequences in the total amplicon pool had decreased proportionally to the extent of tree removal. In clear-cuts, ECM fungal relative abundance had decreased by 95%, while ECM fungal species richness had declined by 75%, compared to unlogged plots. 4. Tree retention enabled the maintenance of the most frequent ECM species, while more lowly abundant species were progressively lost at random with increasing level of tree removal. Five of the most frequent ECM fungal species remained present after clear-cutting, probably associated with pine seedlings. Synthesis and applications.Tree retention can moderate short-term and potentially also long-term logging impacts on ECM fungi. Local ECM fungal diversity is preserved in proportion to the amount of retained trees. Abundant species may be largely maintained, even by low levels of tree retention and on naturally established seedlings. However, conservation of more infrequent species requires higher levels of tree retention, and our results suggest that around 75% of the ECM species are lost with the forest certification standard of 5% retention trees left at logging. tension limit of the boreal biome, as we wanted to study a diverse ECM fungal community unaffected by modern forestry. Scots pine forest is the most abundant type of forest ecosystem in northern Fennoscandia and commonly monodominant with respect to tree species (Stokland et al., 2003). K E Y W O R D S biodiversity, conservation, ectomycorrhizal fungal community, forest management, highthroughput sequencing, logging, soil, tree retention