Nitrogen acquisition from mineral-associated proteins by an ectomycorrhizal fungus

Treatment effects of nitrogen and phosphorus addition on foliar traits in six northern hardwood tree species

Foliar traits can reflect fitness responses to environmental changes, such as changes in nutrient availability. Species may respond differently to these changes due to differences in traits and their plasticity. Traits and community composition together can influence forest nutrient cycling. We compared five traits-foliar N, foliar P, specific leaf area (SLA), leaf dry matter content (LDMC), and leaf carbon isotope ratio (δ13C)-in six northern hardwood tree species (Acer rubrum, Acer saccharum, Betula alleghaniensis, Betula papyrifera, Fagus grandifolia, and Prunus pensylvanica) in a nitrogen (N) and phosphorus (P) fertilization study across 10 mid- and late-successional forest stands in New Hampshire, USA. We also analyzed the response of tree growth to N and P addition. Nutrient addition shifted trait values towards the "acquisitive" side of the spectrum for all traits except δ13C, reflecting a tradeoff between water-use efficiency and nutrient-use efficiency. Treatment responses in relative basal area increment revealed that the Betula species were N-limited, but traits of all species responded to either or both N and P addition in ways that suggest N and P co-limitation. Two species displayed lower foliar P under N addition, and three species displayed lower foliar N under P addition, which also suggests co-limitation. These indications of co-limitation were reflected at the community level. Specific leaf area, LDMC, and δ13C differed with stand age within several species. Examining trait responses of tree species and communities to nutrient availability increases our understanding of biological mechanisms underlying the complex effects of nutrient availability on forests.

Organophosphate esters inhibit enzymatic proteolysis through non-covalent interactions

Enzymatic proteolysis is the key process to produce bioavailable nitrogen in natural terrestrial and aquatic ecosystems for microorganisms and plants. However, little is known on how protein degradation is influenced by organic contaminants. As we known, the overuse of organophosphate esters (OPEs) has caused serious pollution in soil, water, and sediment. Thereby we studied the effect of OPEs on the proteolysis of protein GB1 in aqueous system at neutral pH, and explored the underlying molecular mechanism. Colorimetric ninhydrin methods and SDS-PAGE results revealed that OPEs inhibited the enzymatic hydrolysis of protein GB1. Based on fluorescence quenching experiments, the binding constant (LogKA) were found in order: 6.16 (dibutyl phosphate) > 5.11 (diethyl phosphate) > 1.78 (tributyl phosphate) > 0.876 (triethyl phosphate), proving the interactions between OPEs and protein GB1. Further spectroscopic experiments and molecular docking simulations showed that OPEs could entered the pocket structure of GB1 and induced secondary structural changes and protein folding through non-covalent interactions dominated by hydrogen bonding and van der Waals forces. In addition, organophosphate diesters (di-OPEs) and long-chain OPEs had stronger affinity to GB1, due to the more negative and denser electrostatic surface potential distributions. The deformation of proteins hindered the contact between their active sites and enzymes, leading to the inhibition of GB1 hydrolysis. This study deepened our understanding of the effect of OPEs on protein transformation and degradation, which could further influence the ecological functions and nutrient cycling.

Insights into the Biotic Factors Shaping Ectomycorrhizal Associations

Ectomycorrhizal (EM) associations are essential symbiotic relationships that contribute significantly to the health and functioning of forest ecosystems. This review examines the biotic factors that influence EM associations, focusing on plant and fungal diversity, host specificity, and microbial interactions. Firstly, the diversity of host plants and ectomycorrhizal fungi (EMF) is discussed, highlighting how the richness of these organisms affects the formation and success of EM symbioses. Next, host specificity is explored, with a focus on the complex relationships between EMF and their host plants. Microbial interactions are examined in depth, with sections on both positive and negative influences of bacteria and different fungal groups on EM formation. Overall, this review provides a comprehensive overview of the biotic factors that shape EM associations, offering insights into the mechanisms that underpin these critical ecological interactions and their broader implications for ecosystem management and restoration.

Molecular mechanisms of iron nanominerals formation in fungal extracellular polymeric substances (EPS) layers during fungus-mineral interactions

Extracellular polymeric substances (EPS), which envelop on fungal hyphae surface, interact strongly with minerals and play a crucial role in the formation of nanoscale minerals during biomineralization in nature environments. However, it remains poorly understood about the molecular mechanisms of nanominerals (i.e., iron nanominerals) formation in fungal EPS halos during fungus-mineral interactions. This process is vital because fungi typically grow attached to various mineral surfaces in nature. According to the changes of thickness of the fungal cell and EPS layers during the Trichoderma guizhouense NJAU 4742 and hematite cultivation experiments, we found that fungal biomineralization could trigger the formation of EPS layers. Fe-dominated nanominerals, aromatic C (283-286.1 eV), alkyl C (287.6-288.3 eV), and carboxylic C (288.4-289.1 eV) were the dominant chemical groups on the EPS layers, as determined by nanoscale secondary ion mass spectrometry (NanoSIMS), high-resolution transmission electron microscope (HRTEM), and carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Further, evidence from Fe K-edge X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) spectra indicated that oxygen vacancy (OV) was formed on the Fe-dominated nanomineral surface during fungus-mineral interactions, which played an important role in catalyzing H2O2 decomposition and HO∗ production. Taken together, the intrinsic peroxidase-like activity by reactive oxygen species (ROS) could modulate the Fe-dominated nanominerals formation in EPS layers to newly form a physical barrier between the cell and the external environments around hyphae, providing novel insights into the effects of ROS-mediated fungal-mineral interactions on fungal nutrient recycling, attenuation of contaminants, and biological control in nature environments.

Mycorrhizal symbiosis and the nitrogen nutrition of forest trees

Terrestrial plants form primarily mutualistic symbiosis with mycorrhizal fungi based on a compatible exchange of solutes between plant and fungal partners. A key attribute of this symbiosis is the acquisition of soil nutrients by the fungus for the benefit of the plant in exchange for a carbon supply to the fungus. The interaction can range from mutualistic to parasitic depending on environmental and physiological contexts. This review considers current knowledge of the functionality of ectomycorrhizal (EM) symbiosis in the mobilisation and acquisition of soil nitrogen (N) in northern hemisphere forest ecosystems, highlighting the functional diversity of the fungi and the variation of symbiotic benefits, including the dynamics of N transfer to the plant. It provides an overview of recent advances in understanding 'mycorrhizal decomposition' for N release from organic or mineral-organic forms. Additionally, it emphasises the taxon-specific traits of EM fungi in soil N uptake. While the effects of EM communities on tree N are likely consistent across different communities regardless of species composition, the sink activities of various fungal taxa for tree carbon and N resources drive the dynamic continuum of mutualistic interactions. We posit that ectomycorrhizas contribute in a species-specific but complementary manner to benefit tree N nutrition. Therefore, alterations in diversity may impact fungal-plant resource exchange and, ultimately, the role of ectomycorrhizas in tree N nutrition. Understanding the dynamics of EM functions along the mutualism-parasitism continuum in forest ecosystems is essential for the effective management of ecosystem restoration and resilience amidst climate change. KEY POINTS: • Mycorrhizal symbiosis spans a continuum from invested to appropriated benefits. • Ectomycorrhizal fungal communities exhibit a high functional diversity. • Tree nitrogen nutrition benefits from the diversity of ectomycorrhizal fungi.

Native and Alien Antarctic Grasses as a Habitat for Fungi

Biological invasions are now seen as one of the main threats to the Antarctic ecosystem. An example of such an invasion is the recent colonization of the H. Arctowski Polish Antarctic Station area by the non-native grass Poa annua. This site was previously occupied only by native plants like the Antarctic hair grass Deschampsia antarctica. To adapt successfully to new conditions, plants interact with soil microorganisms, including fungi. The aim of this study was to determine how the newly introduced grass P. annua established an interaction with fungi compared to resident grass D. antarctica. We found that fungal diversity in D. antarctica roots was significantly higher compared with P. annua roots. D. antarctica managed a biodiverse microbiome because of its ability to recruit fungal biocontrol agents from the soil, thus maintaining a beneficial nature of the endophyte community. P. annua relied on a set of specific fungal taxa, which likely modulated its cold response, increasing its competitiveness in Antarctic conditions. Cultivated endophytic fungi displayed strong chitinolysis, pointing towards their role as phytopathogenic fungi, nematode, and insect antagonists. This is the first study to compare the root mycobiomes of both grass species by direct culture-independent techniques as well as culture-based methods.

Soil recalcitrant but not labile organic nitrogen mineralization contributes to microbial nitrogen immobilization and plant nitrogen uptake

Soil organic nitrogen (N) mineralization not only supports ecosystem productivity but also weakens carbon and N accumulation in soils. Recalcitrant (mainly mineral-associated organic matter) and labile (mainly particulate organic matter) organic materials differ dramatically in nature. Yet, the patterns and drivers of recalcitrant (MNrec) and labile (MNlab) organic N mineralization rates and their consequences on ecosystem N retention are still unclear. By collecting MNrec (299 observations) and MNlab (299 observations) from 57 15N tracing studies, we found that soil pH and total N were the master factors controlling MNrec and MNlab, respectively. This was consistent with the significantly higher rates of MNrec in alkaline soils and of MNlab in natural ecosystems. Interestingly, our analysis revealed that MNrec directly stimulated microbial N immobilization and plant N uptake, while MNlab stimulated the soil gross autotrophic nitrification which discouraged ammonium immobilization and accelerated nitrate production. We also noted that MNrec was more efficient at lower precipitation and higher temperatures due to increased soil pH. In contrast, MNlab was more efficient at higher precipitation and lower temperatures due to increased soil total N. Overall, we suggest that increasing MNrec may lead to a conservative N cycle, improving the ecosystem services and functions, while increasing MNlab may stimulate the potential risk of soil N loss.

Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.

Recently photoassimilated carbon and fungus-delivered nitrogen are spatially correlated in the ectomycorrhizal tissue of Fagus sylvatica

Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms, however, are not fully understood. Here we investigate the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus sylvatica across different spatial scales from the root system to the cellular level. We provided ¹⁵ N-labelled nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a ¹³ CO₂ atmosphere. We analysed the short-term distribution of ¹³ C and ¹⁵ N in the root system with isotope-ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale secondary ion mass spectrometry (NanoSIMS). At the root system scale, plants did not allocate more ¹³ C to root parts that received more ¹⁵ N. Nanoscale secondary ion mass spectrometry imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of ¹³ C and ¹⁵ N at the cellular scale. Our results indicate that, on a coarse scale, plants do not allocate a larger proportion of photoassimilated C to root parts associated with N-delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant-assimilated C and fungus-delivered N were spatially strongly coupled. Here, NanoSIMS visualisation provides an initial insight into the regulation of ectomycorrhizal C and N exchange at the microscale.

A Framework for Investigating Rules of Life Across Disciplines

Clearly and usefully defining the Rules of Life has long been an attractive yet elusive prospect for biologists. Life persists because requirements for existence and successful transmission of hereditary information are met. These requirements are met through mechanisms adopted by organisms, which produce solutions to environmentally imposed constraints on life. Yet, constraints and their suites of potential solutions are typically context-specific, operating at specific levels of organization, or holons, and having cascading effects across multiple levels, or the holarchy. We explore the idea that the interaction of constraints, mechanisms, and requirements within and across levels of organization may produce rules of life that can be productively defined. Although we stop short of listing specific rules, we provide a conceptual framework within which progress toward identifying rules might be made.

How do boreal forest soils store carbon?

Boreal forests store a globally significant pool of carbon (C), mainly in tree biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms underlying C stabilization are not well understood. Here, recently discovered mechanisms behind SOM stabilization, their level of understanding, interrelations, and future directions in the field are provided. A recently unraveled mechanism behind C stabilization via interaction of root-derived tannins with fungal necromass emphasizing fungal necromass chemistry is brought forth. The long-lasting dogma of the stability of SOM on minerals is challenged and the newest insights from the field of soil fauna and their influence on SOM stabilization are provided. In conclusion, mechanisms unraveled during the last decade are crucial steps forward to draw a holistic view of the main drivers of SOM stabilization.

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-021-00793-9.

A widespread mechanism in ectomycorrhizal fungi to access nitrogen from mineral-associated proteins

A large fraction of nitrogen (N) in forest soils is present in mineral-associated proteinaceous compounds. The strong association between proteins and minerals limits microbial accessibility to this source, which is a relatively stable reservoir of soil N. We have shown that the ectomycorrhizal (ECM) fungus Paxillus involutus can acquire N from iron oxide-associated proteins. Using tightly controlled isotopic, spectroscopic and chromatographic experiments, we demonstrated that the capacity to access N from iron oxide-associated bovine serum albumin (BSA) is shared with the ECM fungi Hebeloma cylindrosporum and Piloderma olivaceum. Despite differences in evolutionary history, growth rates, exploration types and the decomposition mechanisms of organic matter, their N acquisition mechanisms were similar to those described for P. involutus. The fungi released N from mineral-associated BSA by direct action of extracellular aspartic proteases on the mineral-associated BSA, without initial desorption of the protein. Hydrolysis was suppressed by the adsorption of proteases to minerals, but this adverse effect was counteracted by the secretion of compounds that conditioned the mineral surface. These data suggest that the enzymatic exudate-driven mechanism to access N from mineral-associated proteins is found in ECM fungi of multiple lineages and exploration types.

Simple Plant and Microbial Exudates Destabilize Mineral-Associated Organic Matter via Multiple Pathways

Most mineral-associated organic matter (MAOM) is protected against microbial attack, thereby contributing to long-term carbon storage in soils. However, the extent to which reactive compounds released by plants and microbes may destabilize MAOM and so enhance microbial access, as well as the underlying mechanisms, remain unclear. Here, we tested the ability of functionally distinct model exudates-ligands, reductants, and simple sugars-to promote microbial utilization of monomeric MAOM, bound via outer-sphere complexes to common iron and aluminum (hydr)oxide minerals. The strong ligand oxalic acid induced rapid MAOM mineralization, coinciding with greater sorption to and dissolution of minerals, suggestive of direct MAOM mobilization mechanisms. In contrast, the simple sugar glucose caused slower MAOM mineralization, but stimulated microbial activity and metabolite production, indicating an indirect microbially-mediated mechanism. Catechol, acting as reductant, promoted both mechanisms. While MAOM on ferrihydrite showed the greatest vulnerability to both direct and indirect mechanisms, MAOM on other (hydr)oxides was more susceptible to direct mechanisms. These findings suggest that MAOM persistence, and thus long-term carbon storage within a given soil, is not just a function of mineral reactivity but also depends on the capacity of plant roots and associated microbes to produce reactive compounds capable of triggering specific destabilization mechanisms.