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Forests are critical ecosystems to understand the global carbon budget, due to their carbon sequestration potential in both above- and belowground compartments, especially in species-rich forests. Soil carbon sequestration is strongly linked to soil microbial communities, and this link is mediated by the tree community, likely due to modifications of micro-environmental conditions (i.e., biotic conditions, soil properties, and microclimate). We studied soil carbon concentration and the soil microbial biomass of 180 local neighborhoods along a gradient of tree species richness ranging from 1 to 16 tree species per plot in a Chinese subtropical forest experiment (BEF-China). Tree productivity and different tree functional traits were measured at the neighborhood level. We tested the effects of tree productivity, functional trait identity and dissimilarity on soil carbon concentrations, and their mediation by the soil microbial biomass and micro-environmental conditions. Our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentrations. Besides, soil carbon concentration increased with tree productivity and tree root diameter while it decreased with litterfall C:N content. Moreover, tree productivity and tree functional traits (e.g. root fungal association and litterfall C:N ratio) modulated micro-environmental conditions with substantial consequences for soil microbial biomass. We also showed that soil history and topography should be considered in future experiments and tree plantations, as soil carbon concentrations were higher where historical (i.e., at the beginning of the experiment) carbon concentrations were high, themselves being strongly affected by the topography. Altogether, these results imply that the quantification of the different soil carbon pools is critical for understanding microbial community–soil carbon stock relationships and their dependence on tree diversity and micro-environmental conditions.

The gut microbiome plays an important role in bee health and disease. But it can be disrupted by pesticides and in-hive chemicals, putting honey bee health in danger. We used a controlled and fully crossed laboratory experimental design to test the effects of a 10-day period of chronic exposure to field-realistic sublethal concentrations of two nicotinic acetylcholine receptor agonist insecticides (nACHRs), namely flupyradifurone (FPF) and sulfoxaflor (Sulf), and a fungicide, azoxystrobin (Azoxy), individually and in combination, on the survival of individual honey bee workers and the composition of their gut microbiota (fungal and bacterial diversity). Metabarcoding was used to examine the gut microbiota on days 0, 5, and 10 of pesticide exposure to determine how the microbial response varies over time; to do so, the fungal ITS2 fragment and the V4 region of the bacterial 16S rRNA were targeted. We found that FPF has a negative impact on honey bee survival, but interactive (additive or synergistic) effects between either insecticide and the fungicide on honey bee survival were not statistically significant. Pesticide treatments significantly impacted the microbial community composition. The fungicide Azoxy substantially reduced the Shannon diversity of fungi after chronic exposure for 10 days. The relative abundance of the top 10 genera of the bee gut microbiota was also differentially affected by the fungicide, insecticides, and fungicide-insecticide combinations. Gut microbiota dysbiosis was associated with an increase in the relative abundance of opportunistic pathogens such as Serratia spp. (e.g. S. marcescens), which can have devastating consequences for host health such as increased susceptibility to infection and reduced lifespan. Our findings raise concerns about the long-term impact of novel nACHR insecticides, particularly FPF, on pollinator health and recommend a novel methodology for a refined risk assessment that includes the potential effects of agroc

Plant-soil feedbacks (PSFs) underlying grassland plant richness and productivity are typically coupled with nutrient availability; however, we lack understanding of how restoration measures to increase plant diversity might affect PSFs. We examined the roles of sward disturbance, seed addition and land-use intensity (LUI) on PSFs.We conducted a disturbance and seed addition experiment in ten grasslands along a LUI gradient and characterized plant biomass and richness, soil microbial biomass, community composition and enzyme activities.Greater plant biomass at high LUI was related to a decrease in the fungal to bacterial ratios, indicating highly productive grasslands to be dominated by bacteria. Lower enzyme activity per microbial biomass at high plant species richness indicated a slower C cycling. The relative abundance of fungal saprotrophs decreased, while pathogens increased with LUI and disturbance. Both fungal guilds were negatively associated with plant richness, indicating the mechanisms underlying PSFs depended on LUI.We show that LUI and disturbance affect fungal functional composition, which may feedback on plant species richness by impeding the establishment of pathogen-sensitive species. Therefore, we highlight the need to integrate LUI including its effects on PSFs when planning for practices that aim to optimize plant diversity and productivity.

In Asia, large swathes of rainforest have been converted to rubber plantations, with major consequences for biodiversity and ecosystem services. However, the impact of this land use conversion on rhizosphere soil mycobiome has not yet been addressed. This study aims to investigate how rhizosphere soil fungal communities and their associated biological activity (soil respiration, soil methane (CH4) and potential soil enzyme production) are impacted by the conversion of rainforest to rubber plantations. Fungal richness and community composition in rhizosphere soils collected from natural rainforests, immature rubber, and mature rubber plantations were analyzed using paired-end Illumina sequencing. The conversion of natural rainforest to rubber plantations significantly altered fungal community composition of specific functional groups (saprotrophs, pathogens and mycorrhiza). We observed significant loss of saprotrophic and ectomycorrhizal fungi in natural rainforests, but enrichment of plant pathogenic fungi in immature rubber plantations. The mechanism underlying the effects of forest conversion on changes of fungal communities is related to reductions in soil pH, total nitrogen (N) and ammonium (NH4) in rubber plantations. Conversion to rubber plantation also resulted in decline of soil respiration rates and less potential for cellulase and chitinase productions. The significant negative correlations between fungal richness and soil respiration in mature rubber plantations indicated high competition among fungi and low nutrient availability in this system. We demonstrate the negative consequences of the conversion of rainforest to rubber plantations on soil biological activity and significant changes in fungal community composition that could threaten long-term ecosystem functions.

Opencast limestone mines or limestone quarries are considered challenging ecosystems for soil fungi as they are highly degraded land with specific conditions, including high temperature, prolonged sunlight exposure, and a lack of organic matter, moisture, and nutrients in soil. In such ecosystems, certain fungi can survive and have a crucial function in maintaining soil ecosystem functions. Unfortunately, we know very little about taxonomic diversity, potential functions, and the ecology of such fungi, especially for a limestone quarry in a tropical region. Here, we characterized and compared the living soil fungal communities in an opencast limestone mine, including mining site and its associated rehabilitation site (9 months post-rehabilitation), with the soil fungal community in a reference forest, using the amplicon sequencing of enrichment culture. Our results showed that living fungal richness in the quarry areas was significantly lower than that in the reference forest, and their community compositions were also significantly different. Living fungi in the mining sites mostly comprised of Ascomycota (Eurotiomycetes and Sordariomycetes) with strongly declined abundance or absence of Basidiomycota and Mucoromycota. After nine months of rehabilitation, certain taxa were introduced, such as Hypoxylon spp. and Phellinus noxius, though this change did not significantly differentiate fungal community composition between the mining and rehabilitation plots. The majority of fungi in these plots are classified as saprotrophs, which potentially produce all fifteen soil enzymes used as soil health indicators. Network analysis, which was analyzed to show insight into complex structures of living fungal community in the limestone quarry, showed a clear modular structure that was significantly impacted by different soil properties. Furthermore, this study suggests potential taxa that could be useful for future rehabilitation.

Forests are critical ecosystems to understand the global carbon budget, due to their carbon sequestration potential in both above- and belowground compartments, especially in species-rich forests. Soil carbon sequestration is strongly linked to soil microbial communities, and this link is mediated by the tree community, likely due to modifications of micro-environmental conditions (i.e., biotic conditions, soil properties, and microclimate). We studied soil carbon concentration and the soil microbial biomass of 180 local neighborhoods along a gradient of tree species richness ranging from 1 to 16 tree species per plot in a Chinese subtropical forest experiment (BEF-China). Tree productivity and different tree functional traits were measured at the neighborhood level. We tested the effects of tree productivity, functional trait identity and dissimilarity on soil carbon concentrations, and their mediation by the soil microbial biomass and micro-environmental conditions. Our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentrations. Besides, soil carbon concentration increased with tree productivity and tree root diameter while it decreased with litterfall C:N content. Moreover, tree productivity and tree functional traits (e.g. root fungal association and litterfall C:N ratio) modulated micro-environmental conditions with substantial consequences for soil microbial biomass. We also showed that soil history and topography should be considered in future experiments and tree plantations, as soil carbon concentrations were higher where historical (i.e., at the beginning of the experiment) carbon concentrations were high, themselves being strongly affected by the topography. Altogether, these results imply that the quantification of the different soil carbon pools is critical for understanding microbial community–soil carbon stock relationships and their dependence on tree diversity and micro-environmental conditions.

Earthworms are considered ecosystem engineers due to their fundamental impact on soil structure, soil processes and on other soil biota. An invasion of non-native earthworm species has altered soils of North America since European settlement, a process currently expanding into still earthworm-free forest ecosystems due to continuous spread and increasing soil temperatures owing to climate change. Although earthworms are known to modify soil microbial diversity and activity, it is as yet unclear how eukaryote consumers in soil microbial food webs will be affected. Here, we investigated how earthworm invasion affects the diversity of Cercozoa, one of the most dominant protist taxa in soils. Although the composition of the native cercozoan community clearly shifted in response to earthworm invasion, the communities of the different forests showed distinct responses. We identified 39 operational taxonomic units (OTUs) exclusively indicating earthworm invasion, hinting at an earthworm-associated community of Cercozoa. In particular, Woronina pythii, a hyper-parasite of plant-parasitic Oomycota in American forests, increased strongly in the presence of invasive earthworms, indicating an influence of invasive earthworms on oomycete communities and potentially on forest health, which requires further research.

Leaf fungal pathogens alter their host species’ performance and, thus, changes in fungal species composition can translate into effects at the tree community scale. Conversely, the functional diversity of tree species in a host tree’s local neighbourhood can affect the host’s foliar fungal infestation. Therefore, understanding the factors that affect fungal infestations is important to advance our understanding of biodiversity-ecosystem functioning (BEF) relationships. Here we make use of the largest BEF tree experiment worldwide, the BEF-China experiment, where we selected tree host species with different neighbour species. Identifying fungal taxa by microscopy and by high-throughput DNA sequencing techniques based on the internal transcribed spacer (ITS) rDNA region, we analysed the fungal richness and infestation rates of our target trees as a function of local species richness. Based on the visual microscopic assessment, we found that a higher tree diversity reduced fungal richness and host-specific fungal infestation in the host’s local neighbourhood, while molecular fungal richness was unaffected. This diversity effect was mainly explained by the decrease in host proportion. Thus, the dilution of host species in the local neighbourhood was the primary mechanism in reducing the fungal disease severity. Overall, our study suggests that diverse forests will suffer less from foliar fungal diseases compared to those with lower diversity.

Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar‐associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions.

Forests perform various important ecosystem functions that contribute to ecosystem services. In many parts of the world, forest management has shifted from a focus on timber production to multi-purpose forestry, combining timber production with the supply of other forest ecosystem services. However, it is unclear which forest types provide which ecosystem services and to what extent forests primarily managed for timber already supply multiple ecosystem services. Based on a comprehensive dataset collected across 150 forest plots in three regions differing in management intensity and species composition, we develop models to predict the potential supply of 13 ecosystem services. We use those models to assess the level of multifunctionality of managed forests at the national level using national forest inventory data.

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommen

Little is known about microbial communities of aquatic plants despite their crucial ecosystem function in aquatic ecosystems. Here, we analyzed the microbiota of an aquatic rheophyte Hanseniella heterophylla growing at three areas differing in their degree of anthropogenic disturbance in Thailand employing metabarcoding approach. Our results show that diverse taxonomic and functional groups of microbes colonize H. heterophylla. Proteobacteria, Actinobacteria, Dothideomycetes, and Sordariomycetes form the backbone of the microbiota. Surprisingly, the beneficial microbes reported from plant microbiomes in terrestrial habitats, such as N fixing bacteria and ectomycorrhizal fungi were also frequently detected. We showed that biofilms for attachment of H. heterophylla plants to rocks may associate with diverse cyanobacteria (distributed in eight families, including Chroococcidiopsaceae, Coleofasciculaceae, Leptolyngbyaceae, Microcystaceae, Nostocaceae, Phormidiaceae, Synechococcaceae and Xenococcaceae) and other rock biofilm forming bacteria (mainly Acinetobacter, Pseudomonas and Flavobacterium). We found distinct community compositions of both bacteria and fungi at high and low anthropogenic disturbance levels regardless of the study areas. In the highly disturbed area, we found strong enrichment of Gammaproteobacteria and Tremellomycetes coupled with significant decline of total bacterial OTU richness. Bacterium involved with Sulfamethoxazole (antibiotic) degradation and human pathogenic fungi (Candida, Cryptococcus, Trichosporon, Rhodotorula) were exclusively detected as indicator microorganisms in H. heterophylla microbiota growing in highly disturbed area, which can pose a major threat to human health. We conclude that aquatic plant microbiota are sensitive to anthropogenic disturbance. Our results also unravel the potential use of these plants as biological indicators in remediation or treatment of such disturbed ecosystems.

Human-induced disturbances to ecosystems cause a direct loss of biodiversity, and also alter the inherent processes that shape ecosystems even after the main disturbance has ceased. Therefore, is it important to understand the ongoing consequences of past and present land use practices on both above- and belowground components of agroecosystems. Our study takes a detailed investigation of what shapes communities in semi-natural grasslands under long-term management as either pastures or meadows. We investigated the relative importance of land use (land management (LM) and land use intensity (LUI)) and abiotic conditions (soil, topographic, climatic) across five grassland sites in central Germany in explaining species occurrence patterns of vascular plants and soil fungi. Analyses included a hierarchical joint-species distribution modeling approach to uncover the role of possible drivers shaping the local communities. Our results show that abiotic factors are of particularly high importance compared to LM and LUI for both vascular plant and soil fungal communities. In general, the relative importance of explanatory variables was similar across both taxon groups, however, for plant communities, local climate conditions were more important, while for fungal communities the soil variables (e.g., soil acidity and fertility including soil carbon and potassium concentrations) played a more prominent role. Species-specific responses to the respective variables showed some similarity across the taxon groups, however less so than expected given the long legacy of past LM. Here we found that approximately 50% of the plant and fungi species had clear LM preferences and responses to LUI. More plant species were positively related to pasture than meadow management, while the opposite was found for fungal species. Our findings advance the understanding of how abiotic conditions and human land use impact local species communities in managed semi-natural grasslands, aiding further r

Global change exposes forest ecosystems to many risks including novel climatic conditions, increased frequency of climatic extremes and sudden emergence and spread of pests and pathogens. At the same time, forest landscape restoration has regained global attention as an integral strategy for climate change mitigation. Owing to unpredictable future risks and the need for new forests that provide multiple ecosystem services, mixed-species forests have been advocated for this purpose. However, the successful establishment of mixed forests requires intrinsic knowledge of biodiversity's role for forest ecosystem functioning. In this respect, a better understanding of tree-tree interactions and how they contribute to observed positive tree species richness effects on key ecosystem functions is critical. Here, we review the current knowledge of the underlying mechanisms of tree-tree interactions and argue that positive net biodiversity effects at the community scale may emerge from the dominance of positive over negative interactions at the local neighbourhood scale. In a second step, we demonstrate how tree-tree interactions and the immediate tree neighbourhood's role can be systematically assessed in a tree diversity experiment. The expected results will improve predictions about the effects of tree interactions on ecosystem functioning based on general principles. We argue that this knowledge is urgently required to guide the design of tree species mixtures for the successful establishment of newly planted forests.

Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.

Experiments showed that biodiversity increases grassland productivity and nutrient exploitation, potentially reducing fertiliser needs. Enhancing biodiversity could improve P-use efficiency of grasslands, which is beneficial given that rock-derived P fertilisers are expected to become scarce in the future. Here, we show in a biodiversity experiment that more diverse plant communities were able to exploit P resources more completely than less diverse ones. In the agricultural grasslands that we studied, management effects either overruled or modified the driving role of plant diversity observed in the biodiversity experiment. Nevertheless, we show that greater above- (plants) and belowground (mycorrhizal fungi) biodiversity contributed to tightening the P cycle in agricultural grasslands, as reduced management intensity and the associated increased biodiversity fostered the exploitation of P resources. Our results demonstrate that promoting a high above- and belowground biodiversity has ecological (biodiversity protection) and economical (fertiliser savings) benefits. Such win-win situations for farmers and biodiversity are crucial to convince farmers of the benefits of biodiversity and thus counteract global biodiversity loss.

There is limited knowledge on how the association of trees with different mycorrhizal types shapes soil microbial communities in the context of changing tree diversity levels. We used arbuscular (AM) and ectomycorrhizal (EcM) tree species as con- and heterospecific tree species pairs (TSPs), which were established in plots of three tree diversity levels including monocultures, two-species mixtures, and multi-tree species mixtures in a tree diversity experiment in subtropical China. We found that the tree mycorrhizal type had a significant effect on fungal but not bacterial alpha diversity. Furthermore, only EcM but not AM TSPs fungal alpha diversity increased with tree diversity, and the differences between AM and EcM TSPs disappeared in multi-species mixtures. Tree mycorrhizal type, tree diversity and their interaction had significant effects on fungal community composition. Neither fungi nor bacteria showed any significant compositional variation in TSPs located in multi-species mixtures. Accordingly, the most influential taxa driving the tree mycorrhizal differences at low tree diversity were not significant in multi-tree species mixtures. Collectively, our results indicate that tree mycorrhizal type is an important factor determining the diversity and community composition of soil microbes, and higher tree diversity levels promote convergence of the soil microbial communities.

Schall et al. (2020) assessed how a combination of different forest management systems in managed forest landscapes dominated by European beech may affect the biodiversity (alpha, beta and gamma) of 14 taxonomic groups. Current forest policy and nature conservation often demand for combining uneven-aged managed and unmanaged, set-aside for nature conservation, beech forests in order to promote biodiversity. In contrast to this, Schall et al. (2020) found even-aged shelterwood forests, represented by different developmental phases, to support highest regional (gamma) diversity.By pointing out that unmanaged forests included in our study are not old-growth forests, Bruun and Heilmann-Clausen (2021) challenge our conclusion as not providing sound scientific advice to societies. It is true that the studied unmanaged forests are not representing old-growth forests as defined in the literature. However, we demonstrate the representativeness of our unmanaged forests for current beech forest landscapes of Central Europe, where managed forests were more or less recently set-aside in order to develop old-growth structures. We also show that the managed and recently unmanaged forests in our study already differ distinctively in their forest structures.We use this response to stress the role of forest reserves for promoting certain species groups, and to emphasise their importance as valuable research sites today and in the future.Synthesis and applications. We see two main conclusions from our study. First, unmanaged forests still matter. We agree with Bruun and Heilmann-Clausen (2021) on the general importance of unmanaged, old-growth or long-untouched forests, and we do not question the importance of set-aside forests for biodiversity conservation. However, a complete complementarity to managed systems may only reveal after many decades of natural development. Second, safeguarding biodiversity in largely managed forest landscapes should focus on providing a landscape matrix

Plant diversity begets diversity at other trophic levels. While species richness is the most commonly used measure for plant diversity, the number of evolutionary lineages (i.e. phylogenetic diversity) could theoretically have a stronger influence on the community structure of co-occurring organisms. However, this prediction has only rarely been tested in complex real-world ecosystems. Using a comprehensive multitrophic dataset of arthropods and fungi from a species-rich subtropical forest, we tested whether tree species richness or tree phylogenetic diversity relates to the diversity and composition of organisms. We show that tree phylogenetic diversity but not tree species richness determines arthropod and fungi community composition across trophic levels and increases the diversity of predatory arthropods but decreases herbivorous arthropod diversity. The effect of tree phylogenetic diversity was not mediated by changed abundances of associated organisms, indicating that evolutionarily more diverse plant communities increase niche opportunities (resource diversity) but not necessarily niche amplitudes (resource amount). Our findings suggest that plant evolutionary relatedness structures multitrophic communities in the studied species-rich forests and possibly other ecosystems at large. As global change non-randomly threatens phylogenetically distinct plant species, far-reaching consequences on associated communities are expected.

Land-use intensification can increase provisioning ecosystem services, such as food and timber production, but it also drives changes in ecosystem functioning and biodiversity loss, which may ultimately compromise human wellbeing. To understand how changes in land-use intensity affect the relationships between biodiversity, ecosystem functions, and services, we built networks from correlations between the species richness of 16 trophic groups, 10 ecosystem functions, and 15 ecosystem services. We evaluated how the properties of these networks varied across land-use intensity gradients for 150 forests and 150 grasslands. Land-use intensity significantly affected network structure in both habitats. Changes in connectance were larger in forests, while changes in modularity and evenness were more evident in grasslands. Our results show that increasing land-use intensity leads to more homogeneous networks with less integration within modules in both habitats, driven by the belowground compartment in grasslands, while forest responses to land management were more complex. Land-use intensity strongly altered hub identity and module composition in both habitats, showing that the positive correlations of provisioning services with biodiversity and ecosystem functions found at low land-use intensity levels, decline at higher intensity levels. Our approach provides a comprehensive view of the relationships between multiple components of biodiversity, ecosystem functions, and ecosystem services and how they respond to land use. This can be used to identify overall changes in the ecosystem, to derive mechanistic hypotheses, and it can be readily applied to further global change drivers.