Mark M. Smits

The role of fungi in weathering

No rock at the Earths surface escapes weathering. This process is the primary source of all the essential elements for organisms, except nitrogen and carbon. Since the onset of terrestrial life, weathering has been accelerated under the influence of biota. The study of biological weathering started at the end of the 19th century. Although the role of bacteria (Eubacteria, Archaea) has attracted a lot of interest, until recently the role of fungi has largely been neglected. More recently, however, fungal weathering has become an increasingly important focus of biogeochemical research.

Tree species effects on calcium cycling: The role of calcium uptake in deep soils

Soil acidity and calcium (Ca) availability in the surface soil differ substantially beneath sugar maple (Acer saccharum) and eastern hemlock (Tsuga canadensis) trees in a mixed forest in northwestern Connecticut. We determined the effect of pumping of Ca from deep soil (rooting zone below 20-cm mineral soil) to explain the higher available Ca content in the surface soil beneath sugar maple. We measured the atmospheric input of Ca with bulk deposition collectors and estimated Ca weathering and Ca mineralization in the surface soil (rooting zone above 20-cm mineral soil) from strontium isotope measurements and observed changes in exchangeable Ca in soils during field incubation. Calcium leaching at 20 cm was calculated by combining modeled hydrology with measured Ca soil solution concentrations at 20-cm depth. We measured root length distribution with depth beneath both tree species. Calcium leaching from the surface soil was much higher beneath sugar maple than hemlock and was positively related with the amount of Ca available in the surface soil. Calcium leaching from the surface soil beneath sugar maple was higher than the combined Ca input from atmospheric deposition and soil weathering. Without Ca uptake in the deep soil, surface soils are being depleted in Ca, especially beneath sugar maple. More organically bound Ca was mineralized beneath sugar maple than beneath hemlock. A relatively small part of this Ca release was leached below the surface soil, suggesting that, beneath both tree species, most of the Ca cycling is occurring in the surface soil. Sugar maple had more fine roots in the deep soil than hemlock and a greater potential to absorb Ca in the deep soil. With a simple model, we showed that a relatively small amount of Ca uptake in the deep soil beneath sugar maple is able to sustain high amounts of available Ca in the surface soil.

Rock-eating mycorrhizas: their role in plant nutrition and biogeochemical cycles

A decade ago, tunnels inside mineral grains were found that were likely formed by hyphae of ectomycorrhizal (EcM) fungi. This observation implied that EcM fungi can dissolve mineral grains. The observation raised several questions on the ecology of these “rock-eating” fungi. This review addresses the roles of these rock-eating EcM associations in plant nutrition, biogeochemical cycles and pedogenesis. Research approaches ranged from molecular to ecosystem level scales. Nutrient deficiencies change EcM seedling exudation patterns of organic anions and thus their potential to mobilise base cations from minerals. This response was fungal species-specific. Some EcM fungi accelerated mineral weathering. While mineral weathering could also increase the concentrations of phytotoxic aluminium in the soil solution, some EcM fungi increase Al tolerance through an enhanced exudation of oxalate. Through their contribution to Al transport, EcM hyphae could be agents in pedogenesis, especially podzolisation. A modelling study indicated that mineral tunnelling is less important than surface weathering by EcM fungi. With both processes taken together, the contribution of EcM fungi to weathering may be significant. In the field vertical niche differentiation of EcM fungi was shown for EcM root tips and extraradical mycelium. In the field EcM fungi and tunnel densities were correlated. Our results support a role of rock-eating EcM fungi in plant nutrition and biogeochemical cycles. EcM fungal species-specific differences indicate the need for further research with regard to this variation in functional traits.

Plant-driven fungal weathering: Early stages of mineral alteration at the nanometer scale

Plant-driven fungal weathering is a major pathway of soil formation, yet the precise mechanism by which mycorrhiza alter minerals is poorly understood. Here we report the first direct in situ observations of the effects of a soil fungus on the surface of a mineral over which it grew in a controlled experiment. An ectomycorrhizal fungus was grown in symbiosis with a tree seedling so that individual hyphae expanded across the surface of a biotite flake over a period of three months. Ultramicroscopic and spectroscopic analysis of the fungus-biotite interfaces revealed intimate fungal-mineral attachment, biomechanical forcing, altered interlayer spacings, substantial depletion of potassium (~50 nm depth), oxidation of the biotite Fe(II), and the formation of vermiculite and clusters of Fe(III) oxides. Our study demonstrates the biomechanical-chemical alteration interplay at the fungus-biotite interface at the nanometer scale. Specifically, the weathering process is initiated by physical distortion of the lattice structure of biotite within 1 μm of the attached fungal hypha. Only subsequently does the distorted volume become chemically altered through dissolution and oxidation reactions that lead to mineral neoformation.

The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry.

Soils in boreal forests contain large stocks of carbon. Plants are the main source of this carbon through tissue residues and root exudates. A major part of the exudates are allocated to symbiotic ectomycorrhizal fungi. In return, the plant receives nutrients, in particular nitrogen from the mycorrhizal fungi. To capture the nitrogen, the fungi must at least partly disrupt the recalcitrant organic matter–protein complexes within which the nitrogen is embedded. This disruption process is poorly characterized. We used spectroscopic analyses and transcriptome profiling to examine the mechanism by which the ectomycorrhizal fungus Paxillus involutus degrades organic matter when acquiring nitrogen from plant litter. The fungus partially degraded polysaccharides and modified the structure of polyphenols. The observed chemical changes were consistent with a hydroxyl radical attack, involving Fenton chemistry similar to that of brown-rot fungi. The set of enzymes expressed by Pa. involutus during the degradation of the organic matter was similar to the set of enzymes involved in the oxidative degradation of wood by brown-rot fungi. However, Pa. involutus lacked transcripts encoding extracellular enzymes needed for metabolizing the released carbon. The saprotrophic activity has been reduced to a radical-based biodegradation system that can efficiently disrupt the organic matter–protein complexes and thereby mobilize the entrapped nutrients. We suggest that the released carbon then becomes available for further degradation and assimilation by commensal microbes, and that these activities have been lost in ectomycorrhizal fungi as an adaptation to symbiotic growth on host photosynthate. The interdependence of ectomycorrhizal symbionts and saprophytic microbes would provide a key link in the turnover of nutrients and carbon in forest ecosystems.

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

Summary Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose‐degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition ‘toolbox’ has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.

Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus

The majority of nitrogen in forest soils is found in organic matter–protein complexes. Ectomycorrhizal fungi (EMF) are thought to have a key role in decomposing and mobilizing nitrogen from such complexes. However, little is known about the mechanisms governing these processes, how they are regulated by the carbon in the host plant and the availability of more easily available forms of nitrogen sources. Here we used spectroscopic analyses and transcriptome profiling to examine how the presence or absence of glucose and/or ammonium regulates decomposition of litter material and nitrogen mobilization by the ectomycorrhizal fungus Paxillus involutus. We found that the assimilation of nitrogen and the decomposition of the litter material are triggered by the addition of glucose. Glucose addition also resulted in upregulation of the expression of genes encoding enzymes involved in oxidative degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism. In contrast, the addition of ammonium to organic matter had relatively minor effects on the expression of transcripts and the decomposition of litter material, occurring only when glucose was present. On the basis of spectroscopic analyses, three major types of chemical modifications of the litter material were observed, each correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggest that the expression of the decomposition and nitrogen assimilation processes of EMF can be tightly regulated by the host carbon supply and that the availability of inorganic nitrogen as such has limited effects on saprotrophic activities.

Biological weathering in soil: the role of symbiotic root-associated fungi biosensing minerals and directing photosynthate-energy into grain-scale mineral weathering

Abstract Biological weathering is a function of biotic energy expenditure. Growth and metabolism of organisms generates acids and chelators, selectively absorbs nutrient ions, and applies turgor pressure and other physical forces which, in concert, chemically and physically alter minerals. In unsaturated soil environments, plant roots normally form symbiotic mycorrhizal associations with fungi. The plants provide photosynthate-carbohydrate-energy to the fungi in return for nutrients absorbed from the soil and released from minerals. In ectomycorrhiza, one of the two major types of mycorrhiza of trees, roots are sheathed in fungus, and 15-30% of the net photosynthate of the plants passes through these fungi into the soil and virtually all of the water and nutrients taken up by the plants are supplied through the fungi. Here we show that ectomycorrhizal fungi actively forage for minerals and act as biosensors that discriminate between different grain sizes (53-90 μm, 500-1000 μm) and different minerals (apatite, biotite, quartz) to favour grains with a high surface-area to volume ratio and minerals with the highest P content. Growth and carbon allocation of the fungi is preferentially directed to intensively interact with these selected minerals to maximize resource foraging.

Plant‐driven weathering of apatite – the role of an ectomycorrhizal fungus

Ectomycorrhizal (EcM) fungi are increasingly recognized as important agents of mineral weathering and soil development, with far-reaching impacts on biogeochemical cycles. Because EcM fungi live in a symbiotic relationship with trees and in close contact with bacteria and archaea, it is difficult to distinguish between the weathering effects of the fungus, host tree and other micro-organisms. Here, we quantified mineral weathering by the fungus Paxillus involutus, growing in symbiosis with Pinus sylvestris under sterile conditions. The mycorrhizal trees were grown in specially designed sterile microcosms in which the supply of soluble phosphorus (P) in the bulk media was varied and grains of the calcium phosphate mineral apatite mixed with quartz, or quartz alone, were provided in plastic wells that were only accessed by their fungal partner. Under P limitation, pulse labelling of plants with (14)CO(2) revealed plant-to-fungus allocation of photosynthates, with 17 times more (14)C transferred into the apatite wells compared with wells with only quartz. Fungal colonization increased the release of P from apatite by almost a factor of three, from 7.5 (±1.1) × 10(-10) mol m(-2) s(-1) to 2.2 (±0.52) × 10(-9) mol m(-2) s(-1). On increasing the P supply in the microcosms from no added P, through apatite alone, to both apatite and orthophosphate, the proportion of biomass in roots progressively increased at the expense of the fungus. These three observations, (i) proportionately more plant energy investment in the fungal partner under P limitation, (ii) preferential fungal transport of photosynthate-derived carbon towards patches of apatite grains and (iii) fungal enhancement of weathering rate, reveal the tightly coupled plant-fungal interactions underpinning enhanced EcM weathering of apatite and its utilization as P source.

Ectomycorrhizal weathering, a matter of scale?

Abstract Boreal forest trees influence mineral weathering rates via exudation and uptake processes. Most trees in the boreal forest live in symbiosis with ectomycorrhizal (EcM) fungi that sheath most of the root tips and form the main interface between the tree and the soil. Current weathering models do not take into account the nature and scale of fungal-mineral interactions. Here we show for the first time grain-scale effects of EcM fungi in symbiosis with a host plant on mineral weathering under sterile conditions. EcM fungi actively direct their growth and energy flow towards mineral grains containing essential nutrient elements for the tree and fungus.