Roger D. Finlay

Ectomycorrhizal (ECM) fungi play an important role in biological mineral weathering and show increased mycelial base cation content when grown with minerals. However, the mechanisms underlying base cation mobilisation and uptake remain poorly understood. With a focus on the mineral weathering ECM genus Suillus, we investigated evolutionary expansions and contractions of base cation transporter gene families across a phylogeny of 108 Agaricomycetes species. We also quantified base cation uptake by ECM and saprotrophic fungal species, including Suillus, under pure culture conditions with and without mineral additions, and assessed correlations between uptake and base cation transporter family copy numbers. We hypothesised that (1) greater base cation uptake depends on higher gene copy numbers of base cation transporter families resulting from evolutionary expansions, (2) weathering of mineral additions enhances base cation uptake by Suillus, and (3) Suillus species exhibit greater base cation uptake in mineral amended conditions compared to other fungi. We identified 25 base cation transporter families with significant expansions and contractions across the phylogeny, and many within Suillus, underscoring the ecological importance of base cation transport in this genus. Suillus and Piloderma, another ECM genus, showed higher mycelial cation concentrations when grown with minerals compared to nutrient limited conditions, confirming mineral-derived uptake. Nine significant positive correlations were detected between base cation uptake and base cation transporter gene family copy numbers in mineral amended conditions. This indicates that in some cases, such as for the Mg²⁺ transporter-E family, expansions in transporter families likely support enhanced base cation acquisition. Overall, these findings suggest that Suillus species have undergone rapid evolutionary changes in base cation transporter family copy numbers, potentially linked to their mineral weathering abilities. Further studies integrating transcriptional regulation of transporter genes will be essential to elucidate the mechanisms governing base cation mobilisation and uptake in Suillus and other ECM fungi.

Summary: Ericaceous understory shrubs and ericoid mycorrhizal fungal communities are ubiquitous in boreal forests, and their interactions with ectomycorrhizal and saprotrophic fungi may determine organic matter dynamics in forest soils. We followed decomposition of pine needle litter and mor‐layer humus over 3 yr in a factorial shrub removal‐ and pine root exclusion experiment in an old‐growth Scots pine (Pinus sylvestris) forest, to evaluate effects of fungal guilds on mass loss. Litter mass loss was 23% greater when ectomycorrhizal fungi were excluded suggesting increased saprotrophic activity, independently of ericoid shrub presence. However, this ‘Gadgil effect’ was only found after 17 months following a summer drought. By contrast, humus mass loss was overall stimulated by ectomycorrhizal fungi, while ericoid mycorrhizal shrubs appeared to counteract this effect, potentially caused by simultaneous addition of recalcitrant organic matter and inhibition of ectomycorrhizal decomposers. We conclude that competitive saprotrophic–ectomycorrhizal fungal interactions may slow early‐stage litter decomposition, but this effect was small and inconsistent. Furthermore, interactions between ecto‐ and ericoid mycorrhizal guild members appear to determine the late‐stage organic matter balance of boreal forest humus.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

The role of ectomycorrhizal (ECM) fungi in biological mineral weathering is increasingly recognised, although the quantitative significance of microbially mediated mineral dissolution for plant growth is debated. Species within the ECM genus Suillus are found to preferentially inhabit mineral soils and are frequently reported to possess mineral weathering capabilities. Though studies growing ECM fungi with minerals have shown heightened mycelial nutrient content compared to growth without minerals, the mechanistic understanding of nutrient mobilisation and uptake associated with weathering remains largely unknown. We examined copy numbers of 173 transporter gene families present in 108 Agaricomycetes species, and analysed evolutionary expansions and contractions of base cation transporter gene families across the phylogeny. We also quantified mycelial base cation uptake by ECM species in the genera Suillus and Piloderma, and two saprotrophic fungi, when grown in pure culture with and without minerals. We hypothesised that 1) greater base cation uptake is dependent on evolutionary expansions in copy-numbers of base cation transporter genes, 2) mineral weathering results in base cation uptake by Suillus growing in pure culture with mineral additions, 3) base cation uptake by Suillus growing in pure culture with mineral additions will be greater compared to other fungal species, and 4) base cation uptake will correlate with base cation transporter gene family copy numbers. We showed that 25 transporter gene families are significantly expanding and contracting in the genus Suillus, 10 of which correspond to base cation transporter families and two of which are accessories to base cation transport, highlighting the importance of base cation uptake and transport in the life strategy of Suillus species. Additionally, there are significant expansions in the Fungal Mating-type Pheromone Receptor (MAT-PR) Family in Suillus species, suggesting that these species are adapting to their environment. For all elements there were examples of higher mycelial concentrations after growth in pure culture with mineral additions as compared to the nutrient limited treatment for Suillus species but also for some Piloderma species, confirming that mineral weathering resulted in base cation uptake in pure culture. For 40 % of the significantly expanding and/or contracting base cation gene transporters families, copy numbers were significantly correlated with uptake of mineral elements, and most of the significant correlations were positive. This suggested that members of the genus Suillus are rapidly evolving, and that the expansions and/or contractions in these transporter families are likely to be related to the requirement of base cation uptake, underpinned by the finding that mycelial uptake of elements in the presence of minerals often increased with base cation transporter family copy numbers. Further work into other levels of regulation, e.g. through transcriptional regulation of transporter proteins, would be useful to gain a deeper understanding of base cation uptake regulation and its role in mineral weathering by Suillus species, and ECM fungi in general.

Summary: Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C‐ and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N‐related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.