Understanding how tree species interact within forest stands and how these interactions influence forest functioning—particularly biotic interactions with soil microbes—is crucial for informing forest management strategies under a rapidly changing climate.Altering tree species composition can shift soil fungal community structure and affect tree performance and competitive outcomes. For instance, enriching monospecific beech forests with conifers (mainly spruce or the non-native Douglas fir) can improve beech growth and stress resistance, especially under drought conditions, and it has more recently been linked to higher fungal diversity. Although several mechanisms have been proposed to explain these positive effects on beech growth, site conditions likely play a major role, and potentially also feedback with fungi, such as mycorrhizal symbionts.Here, we investigated whether belowground fungal communities may act as mediators of tree species interactions in mixed beech–conifer forests. Specifically, we hypothesized that variation in fungal community composition is associated with variation in the intensity of tree species interactions, focusing on European beech. To show how beech growth differs under interspecific competition in beech-spruce and beech-Douglas fir forests, we calculated the relative interaction index (RII). We further hypothesize that the effects of site conditions on beech RII are indirect and mediated by fungal communities.We calculated diameter increment of beech trees between 2017 and 2024 in pure beech stands and in mixed beech–spruce and beech–Douglas fir stands. Tree growth was estimated using allometric equations to derive annual aboveground biomass increment, which was used as the performance metric for calculating beech RII in mixed stands with either spruce or Douglas fir as competitors.Soil- and root-associated fungal communities were characterized using DNA metabarcoding. Fungal community composition was analysed separately for soil and root samples using principal coordinates analysis (PCoA), and it was used to predict RII while accounting for the effects of site and stand covariates (e.g., stand age, stand density, and soil properties). To disentangle the relationships among soil environment, fungal community composition, and beech RII, we applied a stepwise regression framework reflecting a hypothesized causal pathway. We further examined associations between beech RII and differentially abundant fungal taxa putatively involved in mediating tree species interactions.We found that beech RII was associated with fungal community composition but only in beech–spruce forests, indicating a strong neighbour identity effect. In beech–spruce stands, the influence of site conditions on beech RII was mediated by both soil and root fungal communities. Additionally, ectomycorrhizal fungal taxa which significantly differed in relative abundance between beech–spruce and pure beech forests were negatively correlated with beech RII, making them candidates involved in or responding to shifts in tree species interactions.Overall, our results demonstrate that fungal communities are tightly coupled to tree species interactions in beech–spruce forests but not in beech–Douglas fir forests, where alternative mechanisms beyond soil conditions may predominantly regulate tree interactions.

Tropical rainforests harbor exceptional biodiversity and function, but are increasingly threatened by agricultural expansion. Whether landscape heterogeneity mitigates these impacts, as in temperate systems, remains unclear. Here, we quantified how local land use and landscape heterogeneity shape multidiversity and ecosystem multifunctionality, using 34 biodiversity metrics and 21 functions across 128 plots in Sumatra. Relative to rainforests, plantations reduced multidiversity and multifunctionality by ~25%, with stronger aboveground declines, lower plant and animal but higher microbial diversity. Contrary to temperate systems, landscape heterogeneity did not buffer local land-use effects but exacerbated declines in multidiversity and multifunctionality, and benefits of surrounding-rainforest cover were confined to rainforest fragments rather than plantations. Our results highlight the irreplaceability of continuous tropical rainforests, and the limited transferability of temperate-based landscape conservation strategies.

Arbuscular mycorrhizal fungi (AMF) form symbioses with crops, enhancing nutrient uptake and stress tolerance. However, their responses to agronomic practices such as cover cropping and microbial grain inoculation remain poorly understood under field conditions. For maize, one of the world’s most important crops, it is still unclear how these management strategies influence AMF colonization, diversity, and community composition across growth stages and seasons, and whether they ultimately affect yield. We investigated maize root AMF colonization and community structure under cover cropping and microbial inoculation in two subsequent years with field rotation. In the first year, AMF colonization and richness followed a clear temporal pattern, peaking at the vegetative stage and declining toward maturity, while no seasonality was observed in the second year. These patterns likely reflected differences in environmental conditions (weather, soil fertility) between the field rotations. Contrary to expectations, cover crops did not enhance AMF colonization. The AMF species used for maize grain inoculation were also part of the resident community and colonized roots, being most abundant in the drier season, yet inoculation did not increase overall colonization. Shannon diversity was unaffected by crop growth stage but declined under both cover cropping and inoculation, indicating moderate changes in community composition rather than dominance by single taxa. Multivariate analyses showed that cover crops modified community composition in one year, though responses of individual taxa were limited. Despite these shifts, neither cover cropping nor inoculation consistently improved maize yield. The highest yields occurred in non-inoculated plots, with cover crops supporting productivity only in the wetter year and reducing it under stress. AMF colonization and community composition in maize were driven by crop phenology and environmental conditions, whereas cover cropping and inoculation did not consistently enhance yield. These treatments modulated AMF diversity and composition in ways that may promote soil resilience under changing climatic conditions. Aligning AMF- and cover crop–based practices with site-specific environments can support more sustainable maize production.

Climate change poses significant challenges to forests, requiring adaptive forest management. In Central Europe, beech ( Fagus sylvatica L.) is a dominant tree species with a wide ecological range. It is widely used for reforestation and the conversion of monospecific conifer into mixed forests. Selecting superior populations for establishing climate‐resilient European beech forests is critical, but whether and to what extent populations differ in their ecological adaptedness and adaptability remains unclear. Beech tree roots host diverse fungal communities, including symbiotrophic and saprotrophic fungi, which are essential for nitrogen acquisition and tree growth. However, it is still unclear whether these fungal associations also contribute to enhanced seedling biomass and adaptability across variable environmental conditions. Our findings indicate that ecological adaptedness in beech seedlings was generally low. In contrast, adaptability to different environments varied among populations, with only one population exhibiting low adaptability while the others demonstrated the potential to perform well across a range of environmental conditions. Root‐associated fungi did not show clear effects on beech adaptability, but they significantly influenced seedling biomass, primarily through their impact on total nitrogen content and nitrogen uptake, which together accounted for over 60% of the observed effect on biomass. Notably, there was a clear contrast in the roles of fungal guilds: symbiotrophic fungi had a positive influence on biomass, whereas saprotrophic fungi exerted a negative effect. Synthesis and applications . The results reveal low adaptedness but high adaptability among beech seedlings, supporting mixed plantings of local and climate‐matched non‐local populations to strengthen forest resilience. Root‐associated fungi strongly influenced seedling growth through nitrogen uptake, with mycorrhizal fungi having positive effects and saprotrophs negative ones. These results emphasise the importance of integrating both genetic diversity and microbial associations into climate‐smart forest management strategies.

Salinity stress is a growing global challenge. We investigated how Populus euphratica, a salinity-adapted tree, acclimates to NaCl from cellular to whole-plant levels. Photosynthesis and aboveground growth declined, but root length and biomass remained stable under salinity. Unlike lateral roots (LRs), main roots (MRs) displayed hyperplastic growth, with a twofold increase in tip diameter due to additional cortical cell layers but without changes in cell volume. This root thickening was Na*-specific and absent under KCl exposure. MRs accumulated high Na* levels, while LRs did not, consistent with strong Na* extrusion capacity and elevated expression of Na* transporters in LRs, indicating specialized ion management within the root system. Transcriptomic analysis revealed stronger salinity responses in LRs, with enrichment of transcripts involved in stress defense, transport, and transcriptional regulation. In contrast, MRs upregulated genes related to mitotic cell division, steroid biosynthesis, and cell wall organization, supporting hyperplasia. Root phytohormones showed increased ABA and JA, especially in MRs, while auxin declined. Long-term salinity led to downregulation of stress responses in MRs, suggesting acclimation, whereas LRs maintained active defense pathways. GO enrichment highlighted distinct developmental programs: MRs prioritized cell proliferation and structural remodeling, while LRs focused on stress tolerance and salt extrusion. These results suggest that P. euphratica employs a dual salt-coping strategy: MRs undergo hyperplastic growth for structural resilience and ion buffering, while LRs dynamically exclude Na* and transmit stress signals. This opens new perspectives on mechanisms of salt tolerance in plants, supporting that root-level specialization enables efficient salinity adaptation in halophytes.

Mycorrhizal symbiosis shapes plant growth and stress resilience. Here, we compared physiological and molecular responses of poplars (P. x canescens) colonised by Paxillus involutus (Pi) or Cenococcum geophilum (Cg) under control conditions, drought stress and recovery. Both fungal isolates primed distinct local (root) and systemic (leaf) defences compared to non-inoculated (Ni) plants. Cg-colonised poplars exhibited constitutively elevated transcripts of heat shock proteins, galactinol synthase and aquaporins in roots and leaves, irrespective of drought. Pi colonisation enhanced growth and nitrogen-use-efficiency, along with transcriptional increases of the TOR/RAPTOR complex in leaves. Under severe soil moisture decline, Pi and Ni poplars showed reduced water potential, photosynthesis, growth and leaf shedding, whereas Cg-colonised plants maintained water status, sustained photosynthesis and retained foliage. These results reveal two contrasting mycorrhiza-mediated drought strategies in poplar: Pi fosters stress acclimation via drought-induced leaf abscission, enabling acclimation and recovery; Cg confers constitutive tolerance and suppresses growth. Ectomycorrhizal fungi thus occupy different positions on the growth-defence trade-off spectrum. Such genotypic effects have important ecological and applied implications, enabling targeted use of EM fungi in forestry and agriculture, depending on whether maximising productivity or enhancing stress resilience is the primary goal.

The relationship of fine root biomass (FRB) and fine root nutrient contents across large biogeographic scales is not well studied in European temperate conifer and deciduous forests. Here, we investigated the variation of FRB and their nutrient concentrations in the mineral topsoil in 150 plots in beech (Fagus sylvatica) and spruce (Picea abies) dominated forests in three regions, which are located along a climatic and edaphic gradient spanning a distance of approximately 800 km. We included ecological (climate, soil nutrients) and silvicultural drivers representing management intensity and determined their relationship with FRB and root nutrients and nonstructural carbohydrates. FRB did not differ between coniferous and deciduous forests, but increased with increasing soil moisture and soil fertility. FRB was negatively associated with forest management intensity mainly due to increases in spruce. In nutrient-poor dry soil, root concentrations of C, N, P, S and glucose were highest and in nutrient-rich, moist conditions lowest, whereas root cation and starch concentrations showed opposite behavior. The results support that water scarcity affected FRB more strongly than nutrient uptake and suggest carbohydrate tradeoff between biomass production and osmotic adjustment. Since longer and more severe periods of drought are expected, we recommend studies to explore the potential of basic cations, in particular potassium, to compensate for organic osmolytes.

We studied the effects of cover crop treatments (fallow or cover crop) and microbial grain inoculation (control, arbuscular mycorrhizal fungi (AMF), and AMF + bacteria) on soil microbial diversity, community composition, and maize yield across four field sites characterized by different farming systems over two consecutive years. Farming system emerged as the dominant factor driving variations in microbial community composition and diversity. The highest AMF and bacterial diversities were observed in the organic system, while the conventional systems exhibited the lowest diversity. Soil properties and management influenced the microbial community in each field site, whereas weather conditions were less important, due to the proximity of the field locations. Microbial grain inoculation significantly increased maize yield in the high-fertility conventional field, while cover cropping improved yield in the organic and transitional fields. Our study demonstrates that the effects of microbial inoculation and cover cropping are profoundly context-dependent, highlighting the complex interplay between these treatments and field site characteristics, and agricultural management practices. By identifying the specific contexts in which inoculation and cover cropping yield tangible benefits, our study promotes a more targeted, systems-based approach to sustainable agricultural intensification.

Cross‐kingdom associations play a fundamental role in ecological processes. Yet our understanding of plant–fungal co‐occurrences in tropical rainforests and the potential impacts of land‐use change shaping species connections remain limited. By using amplicon sequencing on DNA from roots and their associated fungal communities, we aim to understand the impact of rainforest transformation on the composition and structure of root–fungal ecological networks in human‐modified landscapes in Sumatra, Indonesia. Each land‐use type supports a distinctive set of indicator species, which are organisms that reflect specific environmental conditions and can signal changes in ecosystem health. We observed a decline in the richness of indicator plant taxa and plant–fungal associations with increasing land‐use intensification. Additionally, there is a turnover in root communities, shifting from native and endemic species in rainforests to non‐native, generalist herbaceous species in rubber and oil palm plantations. Plant–fungal connectivity significantly declined with increasing land‐use intensification, suggesting that managed ecosystems may have weakened root‐fungal interactions. Network analysis highlights the distinct responses of various fungal groups. For instance, arbuscular mycorrhizal fungi (AMF) showed fewer connections with modules linked to oil palm and rubber roots, indicating weakened root–fungal associations in monocultures. This aligns with the observed reduction in AMF diversity in converted land‐use areas compared to forests, further reinforcing the negative impact of land‐use practices in oil palm and rubber monocultures on AMF diversity. Synthesis . Dimensioning the impacts of rainforest transformations below‐ground is constrained by our understanding of fungal functional guilds. Highly modified systems exhibited fewer connections, suggesting a dynamic restructuring of root–fungal relationships in response to land‐use changes. Understanding the intricate interplay between plants and fungi in the face of land‐use change can provide valuable information for conservation efforts, agricultural practices, and ecosystem management strategies aimed at promoting biodiversity, soil health and ecosystem resilience in the context of changing environmental conditions. Moreover, it underscores the importance of communities' networks in land‐use planning and management decisions to support plant and fungal diversity in terrestrial ecosystems.

Isoprene, the most abundant hydrocarbon emitted by vegetation, protects photosynthesis against oxidative and thermal stress and significantly impacts atmospheric chemistry. While laboratory studies suggest a role for isoprene in plant defense, its function in plant-plant communication under natural conditions remains unclear. Here, we demonstrate that isoprene acts as a signaling molecule, triggering systemic immune responses in neighboring plants against bacterial pathogens under field conditions. We established an experimental system using wild-type and transgenic silver birch (Betula pendula) lines engineered to emit varying levels of isoprene. Over two growing seasons, we examined the effects of birch-emitted volatile organic compounds on neighboring Arabidopsis thaliana, including wild-type and immune signaling mutants (llp1: legume lectin-like protein 1; jar1: jasmonate resistant 1). Isoprene emission rates positively correlated with systemic resistance in receiver plants, with higher emissions enhancing inhibition of Pseudomonas syringae growth. This immune response occurred independently of jasmonate signaling but required functional LLP1, suggesting a specific recognition pathway. By combining Arabidopsis mutant responses with birch volatile profiles, we confirmed that isoprene, rather than other terpenoids, mediates this effect. These findings reveal an unrecognized ecological function of isoprene as an airborne immune signal, establishing transgenic birch as a robust model for studying volatile-mediated plant defense networks in natural environments. Our results provide new insights into the molecular mechanisms underlying plant volatile perception and expand our understanding of chemical communication in terrestrial ecosystems. ### Competing Interest Statement The authors have declared no competing interest.

Mycorrhizal symbiosis shapes plant growth and stress resilience. Here, we compared physiological and molecular responses of poplars colonized by Paxillus involutus (Pi) or Cenococcum geophilum (Cg) under control conditions, drought stress, and recovery. Both fungal species primed distinct local (root) and systemic (leaf) defenses compared to non-inoculated (Ni) plants. Cg-colonized poplars exhibited constitutively elevated transcripts of heat shock proteins ( HSP s), galactinol synthase, and aquaporins in roots and leaves, irrespective of drought. Pi colonization enhanced growth and nitrogen-use-efficiency along with transcriptional increases of TOR/RAPTOR complex. Under severe soil moisture decline, Pi and Ni poplars showed reduced water potential, photosynthesis, growth, and leaf shedding, whereas Cg-colonized plants maintained water status, sustained photosynthesis, and retained foliage. These results reveal two contrasting mycorrhiza-mediated drought strategies in poplar: Pi fosters stress acclimation via drought-induced leaf abscission, enabling rapid recovery; Cg suppresses growth even without stress, conferring constitutive tolerance. Ectomycorrhizal species thus occupy different positions on the growth– defense trade-off spectrum. Such species-specific effects have important ecological and applied implications, enabling targeted use of EM fungi in forestry and agriculture depending on whether maximizing productivity or enhancing stress resilience is the primary goal. ### Competing Interest Statement The authors have declared no competing interest. China Scholarship Council, https://ror.org/04atp4p48 German Academic Exchange Service, https://ror.org/039djdh30 University of Göttingen, https://ror.org/01y9bpm73, Open Access Publication Funds

Forest ecosystem management requires the conservation of associated biodiversity. Enriching native forests with economically valuable conifer species provides economic gains and meets the increasing societal demand for timber but may threaten biodiversity. Soil sustains most of forest biodiversity, but the impact of changes in tree species composition, including native and non-native species, on soil invertebrates remains little studied. We investigated the impact of different forest types on the taxonomic and functional composition of springtail communities (Collembola, Insecta), an abundant and diverse microarthropod group inhabiting litter and soil. Using native Fagus sylvatica (European beech) as reference, we compared Collembola communities with native but range-expanding Picea abies (Norway spruce) and non-native Pseudotsuga menziesii (Douglas fir) as well as beech-conifer mixtures. The abundance of Collembola was higher in Norway spruce than in European beech, with little difference among the other forest types. Further, the taxonomic and functional composition of Collembola was shifted to more parthenogenetic species at sandy sites, stressing the importance of regional factors such as soil type and climate in structuring Collembola communities. Collembola communities in Douglas fir were more pigmented and distributed to the surface, resulting in a lower proportion of euedaphic Collembola compared to European beech forests. In mixed forests, the impacts of Douglas fir on euedaphic Collembola were reduced, suggesting that negative effects of introduced tree species on soil animal communities might be alleviated by limiting Douglas fir to enrichment plantings only. Overall, the results indicate that vertical distribution in soil and morphological traits of Collembola help to better understand the changes in decomposer communities due to planting non-native tree species.

Climate change-enforced drought stress conditions and diseases caused by pathogens often co-occur and represent one of the greatest challenges in plant science. Wilt pathogens that colonize water-conducting plant tissues can aggravate the problem and affect a wide range of agricultural crops. However, whilst fungal infections with the vascular pathogen Verticillium dahliae are typically associated with wilt symptoms due to occlusion of xylem tissues, the related V. longisporum induces de novo formation of tracheary elements. This promotes not only its virulence but also enables elevated water storage capacity of the infected host plant and resilience against drought stress conditions. Here, we identified a secreted Verticillium protein, TRANSDIFFERENTIATION EFFECTOR (TRADE), which triggers cell identity switches of bundle sheath cells into tracheary elements. We show that TRADE interacts with the intracellular plant protein VARICOSE (VCS), a conserved component of the mRNA turnover machinery and ortholog of the metazoan protein ENHANCER OF DECAPPING 4 (EDC4/HEDLS/Ge-1). The TRADE-VCS interaction induces SUCROSE NON-FERMENTING 1 (SNF1)-related protein kinase (SRK)-dependent phosphorylation and thus dysfunction of VCS. This affects the abundance of mRNAs encoding master regulators of xylem differentiation and demonstrates how a single pathogen effector protein triggers complex tissue-specific developmental reprogramming and thus promotes abiotic stress resilience. ### Competing Interest Statement The authors have declared no competing interest.

Many industrial applications of wood and woody biomass require harsh physicochemical pretreatments to improve the hydrophobicity and durability of the products. Environmentally friendly wood biorefineries necessitate the replacement of chemicals and energy-consuming wood processing. Here, our goal was to increase wood hydrophobicity via the ectopic expression of Jojoba (Simmondsia chinensis) wax ester synthase (ScWS) in poplar (Populus × canescens). We expressed ScWS under a wood-specific promoter (DX15), which naturally controls the expression of FASCICLIN-like ARABINOGALACTAN PROTEIN 15 (FLA15) in the xylem. In the DX15::ScWS lines, ScWS was highly expressed in wood but not in leaves. The transgenic lines exhibited normal photosynthesis and growth similar to the wild-type poplars. Compared with the wild-type poplars, the DX15::ScWS lines accumulated greater amounts of triacylglycerol in wood and a greater number of lipid droplets in ray parenchyma cells. The composition of the bark cuticle wax esters was unaffected. The wood of the DX15::ScWS lines showed greater water repellency and less swelling than that of the wild-type poplars. Furthermore, the DX15::ScWS lines had an increased expression of FLA15 and increased cell wall deposition in fibers, resulting in increased wood density. Our results highlight the potential of combining the wood-specific DX15 promoter with ScWS to enhance the technological properties of poplar wood. Reduced wood hydrophilicity represents a significant improvement in wood quality. In addition, our results suggest that the overexpression of the DX15 promoter could be a promising strategy for improving lignocellulose biomass in plants. Since poplars are highly productive species that can be cultivated in short-rotation plantations, our results have high translational potential for advancing sustainable wood utilization for a wider range of applications.

Isoprene, the most abundant biogenic hydrocarbon in the atmosphere, is known to protect photosynthesis from abiotic stress and significantly impact atmospheric chemistry. While laboratory studies show that isoprene can enhance plant immunity, its role in plant-plant communication under natural field conditions remains unclear. In a 2-year field experiment, we used wild-type and transgenic silver birch (Betula pendula) lines with enhanced isoprene emission levels to examine their impact on neighboring Arabidopsis thaliana, including wild-type and immune signaling mutants (llp1: legume lectin-like protein 1; jar1: jasmonate resistant 1). Receiver plants exposed to higher isoprene levels showed increased resistance to Pseudomonas syringae, independent of jasmonate signaling but dependent on LLP1, a protein essential for systemic acquired resistance. Volatile analysis indicated isoprene as an airborne molecule that can also trigger an immune response in neighboring plants along with other terpenoids. Our study using transgenic birches in a complex environment provides new insights into the molecular mechanisms underlying plant volatile perception and expands our understanding of plant chemical communication in terrestrial ecosystems.

Climate warming promotes the expansion of insect pests. Among the inducible defense responses activated by attacked plants, Kunitz trypsin protease inhibitors (KTIs) play an outstanding role. KTIs affect food digestion and thereby control the fitness of herbivorous insects. Poplars contain an expanded family of KTIs, whose distinct intrinsic functions are under investigation. Here, we set out to identify KTIs with anti-herbivore activity and assessed the potential growth trade-off incurred by high KTI expression levels. Using in-silico database searches, we identified 28 KTIs in the haploid genome of Populus x canescens; 21 of them were responsive to herbivory. The greatest induction by herbivory was observed for KTI_400, KTI_600 and KTI_0882 (P. trichocarpa orthologues Potri.019G124400, Potri.019G124600, Potri.019G088200), whereas a moderate response was found for KTI_53200 (Potri.017G153200 orthologue). Mechanical wounding and methyl-jasmonate treatments resulted in fast and strong induction of KTI_400 and KTI_600 and moderate or lacking responses in KTI_0882 and KTI_53200. Increased KTI expression levels were associated with upregulation of ALLENE OXIDE SYNTHASE, a key enzyme involved in jasmonate biosynthesis. On the contrary, exposure to compounds eliciting ethylene or salicylic acid signaling did not affect KTIs. We generated stable CRISPR-Cas12a-mediated knock-out and p35S-mediated overexpression lines of KTI_400, KTI_600 and KTI_53200 in Populus x canescens. Among the wildtype and transgenic lines, only kti_400 + kti_600 double knock-out lines produced greater biomass. Larvae of Helicoverpa armigera, a pest expanding in Europe due to a warmer climate, were allowed to feed on wildtype and transgenic poplar lines. Transgenic poplars overexpressing KTI_400 or KTI_600 resulted in reduced, and their double knockout lines in increased weight gain of the larvae. In contrast, overexpressing or knockout lines of KTI_53200 had no effect on larval weight gain compared with controls. KTI_400 and KTI_600 are potent, natural in-planta anti-herbivorous agents. Their expression is associated with larval growth reductions. Modulation of KTI_53200 levels had no direct effects on the fitness of leaf-feeding H. armigera or on plant growth. This study sheds light on the potential application of KTI in plant defenses and biocontrol against H. armigera in trees and presents new options to investigate growth-defense theories.

The availability of different organic substrates influences the assembly and functionality of hyphosphere microbial communities; however, the underlying processes are poorly understood, particularly under natural field conditions. To fill this knowledge gap, we constructed so-called 'hyphoboxes' separating (mycor)rhizosphere, hyphosphere, and substrate compartments using different mesh sizes. The substrate compartments were amended with 13C-15N-labeled organic substrates that differed in quality; i.e., the amino acid arginine and root litter. Hyphoboxes were buried in a temperate grassland soil for 20 weeks, allowing us to investigate effects of the substrates on hyphosphere microbial community assembly and on the transport of substrate-derived 15N into plant roots. The different substrates had pronounced effects on the assembly of fungal and bacterial communities in the hyphosphere: compared to arginine, root litter fostered a higher fungal biomass and greater relative abundances of specific saprotrophic fungi (e.g., Pleosporales, Helotiales, and Sordariales) and bacteria (Actinobacteria) involved in organic matter degradation. Accordingly, root litter-derived C was quickly incorporated into the fungal phospholipid fatty acid C18:2 omega 6,9, highlighting the involvement of saprotrophic fungi in root litter degradation. In addition, we observed less pronounced N transport from root litter to plant roots compared to the more easily available arginine. Our results indicate that distinct substrate qualities not only shape microbial community assembly but also influence nutrient transport via the hyphosphere, with implications for plant nutrition in grassland ecosystems. Importantly, we highlight a potential key role of fungal-fungal interactions, particularly between AM fungi and saprotrophs, in modifying organic N availability to plants, warranting greater attention in future studies.

Industrial oil palm plantation management degrades tropical soils and disrupts ecosystem functions. Applying oil palm leaf litter can help restore soil fertility, but the underlying fungal-driven decomposition and nitrogen recycling remain understudied. This study examines fungal succession in degrading oil palm leaf litter, the fate of litter-derived nitrogen in soil and roots, and the potential for the restoration of fungal biodiversity. We produced 15N-labelled oil palms and exposed dry leaf litter in 2-mm and 37-µm mesh bags within a plantation. The finer mesh allowed microbial access but restricted roots and most detritivores. We measured litter mass loss, carbon and nitrogen dynamics, and fungal communities via ITS barcoding over six months. Root ingrowth and soil chemistry were also analyzed. Litter mass decreased by 70

In monoculture-dominated landscapes, recovering biodiversity is a priority, but effective restoration strategies have yet to be identified. In this study, we experimentally tested passive and active restoration strategies to recover taxonomic, phylogenetic, and functional diversity of woody plants within 52 tree islands established in an oil palm landscape. Large tree islands and higher initial planted diversity catalyzed diversity recovery, particularly functional diversity at the landscape level. At the local scale, results demonstrated that greater initial planting diversity begets greater diversity of native recruits, overcoming limitations of natural recruitment in highly modified landscapes. Establishing large and diverse tree islands is crucial for safeguarding rare, endemic, and forest-associated species in oil palm landscapes.

IntroductionHigh-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data, providing a very powerful tool to analyze biodiversity of soil organisms. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databases, controversial sequence similarity thresholds for delimitating taxa, and downstream compositional data analysis. MethodsHere, we use HTS data from a soil nematode biodiversity experiment to explore standardized HTS data processing procedures. We compared the taxonomic assignment performance of two main rDNA reference databases (SILVA and PR2). We tested whether the same ecological patterns are detected with Amplicon Sequence Variants (ASV; 100% similarity) versus classical Operational Taxonomic Units (OTU; 97% similarity). Further, we tested how different HTS data normalization methods affect the recovery of beta diversity patterns and the identification of differentially abundant taxa.ResultsAt this time, the SILVA 138 eukaryotic database performed better than the PR2 4.12 database, assigning more reads to family level and providing higher phylogenetic resolution. ASV- and OTU-based alpha and beta diversity of nematodes correlated closely, indicating that OTU-based studies represent useful reference points. For downstream data analyses, our results indicate that loss of data during subsampling under rarefaction-based methods might reduce the sensitivity of the method, e.g. underestimate the differences between nematode communities under different treatments, while the clr-transformation-based methods may overestimate effects. The Analysis of Compositions of Microbiome with Bias Correction approach (ANCOM-BC) retains all data and accounts for uneven sampling fractions for each sample, suggesting that this is currently the optimal method to analyze compositional data.DiscussionOverall, our study highlights the importance of comparing and selecting taxonomic reference databases before data analyses, and provides solid evidence for the similarity and comparability between OTU- and ASV-based nematode studies. Further, the results highlight the potential weakness of rarefaction-based and clr-transformation-based methods. We recommend future studies use ASV and that both the taxonomic reference databases and normalization strategies are carefully tested and selected before analyzing the data.