Global hotspots for soil nature conservation

Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey

Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000-2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016-2027).

Global environmental dependences of soil biodiversity and functions are modified by water availability thresholds

Global soil biodiversity and functions are threatened by water availability thresholds. However, the role of these thresholds in modulating the environmental drivers of soil biodiversity and functions remains poorly understood. Analyzing a global dataset of 383 sites across major terrestrial biomes, we found that water availability threshold (measured by aridity index) reorganizes the relative importance of climate, vegetation, and soil properties in regulating soil biodiversity and functions. In less arid regions, vegetation and soil properties jointly explained the primary patterns of soil biodiversity and functions. Conversely, after crossing such water availability threshold toward more arid conditions, climate became the dominant controlling factor, outpacing other environmental variables. Notably, this water-induced shift in environmental dependence was more pronounced for soil multidiversity than for soil multifunctionality. Our findings highlight the critical role of water availability thresholds in shaping the environmental factors that govern soil biodiversity and ecosystem functions, providing valuable insights into potential ecosystem transformations in the context of on-going global aridification.

Spatiotemporal analysis of wildfires and their relationship with climate and land use in the Gran Chaco and Pantanal ecoregions

The Gran Chaco and Pantanal ecoregions are the largest remaining dry forest areas in South America. Supporting diverse savanna, woodland and wetland ecosystems, these ecoregions are experiencing rapid changes in land use and fire occurrence with implications for ecosystem integrity. Our study characterizes the spatiotemporal patterns of wildfires in the Gran Chaco and Pantanal, and then examines the relationship between patterns of fire occurrence and climatic and anthropogenic drivers. We evaluated fire data of the last two decades (2001-2020) using the MODIS Collection 6.1 and the Global Fire Atlas products. Results of the fire pattern characterization were then used to model the probability of fire occurrence across each ecoregion (Random Forest, Generalized Linear Model, and Generalized Additive Model). Our results indicated that most of the total burned area belonged to the Humid Chaco, while the largest individual burned areas were mainly observed in the Pantanal. Fires primarily occurred during the dry season, with the majority of burned areas recorded during this period. Findings from the three modelling approaches consistently illustrated the spatial distribution of fire occurrence, depicting a declining probability of fire occurrence from East to West. All models underscored the importance of three variables to predict fire occurrence: temperature, livestock abundance and forest cover. Fire occurrence increased with increasing maximum temperatures and livestock presence and decreased with tree cover. This research helps to clarify the potential consequences of changes in land use, rainfall regime and temperature, and uncontrolled burning practices on the current fire activity in the Gran Chaco and Pantanal ecoregions. Understanding the spatiotemporal patterns of fire occurrence and their relationship with climatic, environmental and anthropogenic drivers can help to design more effective management strategies to mitigate fire impacts and to preserve the ecological integrity of these highly diverse regions.

Quantitative sustainability assessment for in-situ electrical resistance heating coupled with steam enhanced extraction: An effective approach for the development of green remediation technologies

There is a lack of quantitative methodology for the sustainability assessment based on field data in the process of innovative technology development for groundwater remediation. This study developed a quantitative assessment framework, a model based on the life cycle assessment integrated with best management practices (LCA-BMPs), to evaluate the environmental, economic, and social sustainability of in-situ electrical resistance heating coupled with steam enhanced extraction (ERH-SEE), an innovative technology being demonstrated in the field. The results indicated that ERH-SEE offered better environmental sustainability performance compared to ERH only, with a reduction in carbon emissions by 52.6 %. ERH-SEE also significantly reduces human toxicity, resource consumption, and ecosystem impacts under the same remediation scenarios. The further assessment indicated that if taking the renewable energy share in energy structure in different countries into consideration, higher shares of renewable energy used in energy supplies can substantially reduce the environmental footprint of the studied scenarios. The economic sustainability assessment results showed that ERH-SEE was more sustainable than ERH only, as it reduces direct economic costs by 35.7 % and provides higher levels of worker employment. Regarding the social sustainability, ERH-SEE involved more complex operational procedures and presented more health risk exposure scenarios compared to ERH only, resulting in slightly more pronounced worker safety issues. Based on the final normalized results, the overall sustainability results of ERH-SEE and ERH only were 78.4 and 61.5, respectively, demonstrating that the sustainability performance of ERH-SEE was better than ERH only. It can be concluded that the application of ERH-SEE in groundwater remediation where significant heterogeneities occur in subsurface can increase the sustainability in developing countries, due to the lower percentage in renewable electricity in the energy supply. This study provided new insights into the technology development for the remediation of soil and groundwater contamination.

Potential health risk assessment of cyanobacteria across global lakes

Cyanobacterial blooms pose environmental and health risks due to their production of toxic secondary metabolites. While current methods for assessing these risks have focused primarily on bloom frequency and intensity, the lack of comprehensive and comparable data on cyanotoxins makes it challenging to rigorously evaluate these health risks. In this study, we examined 750 metagenomic data sets collected from 103 lakes worldwide. Our analysis unveiled the diverse distributions of cyanobacterial communities and the genes responsible for cyanotoxin production across the globe. Our approach involved the integration of cyanobacterial biomass, the biosynthetic potential of cyanotoxin, and the potential effects of these toxins to establish potential cyanobacterial health risks. Our findings revealed that nearly half of the lakes assessed posed medium to high health risks associated with cyanobacteria. The regions of greatest concern were East Asia and South Asia, particularly in developing countries experiencing rapid industrialization and urbanization. Using machine learning techniques, we mapped potential cyanobacterial health risks in lakes worldwide. The model results revealed a positive correlation between potential cyanobacterial health risks and factors such as temperature, N2O emissions, and the human influence index. These findings underscore the influence of these variables on the proliferation of cyanobacterial blooms and associated risks. By introducing a novel quantitative method for monitoring potential cyanobacterial health risks on a global scale, our study contributes to the assessment and management of one of the most pressing threats to both aquatic ecosystems and human health.

IMPORTANCE

Our research introduces a novel and comprehensive approach to potential cyanobacterial health risk assessment, offering insights into risk from a toxicity perspective. The distinct geographical variations in cyanobacterial communities coupled with the intricate interplay of environmental factors underscore the complexity of managing cyanobacterial blooms at a global scale. Our systematic and targeted cyanobacterial surveillance enables a worldwide assessment of cyanobacteria-based potential health risks, providing an early warning system.

Sensor Arrays for Electrochemical Detection of PCR-Amplified Genes Extracted from Cells Suspended in Environmental Waters

Ecological surveys of living things based on DNAs from environmental samples are attractive. However, despite simplicity of water sampling from the target environment, it is still necessary to transport the samples to the laboratory for DNA analysis based on skillful next-generation sequencers. To perform DNA-oriented surveys based on a simple protocol without any special training, we demonstrated, in this study, the detection of genes from cell-containing environmental waters using gene sensor arrays that require no DNA labeling and no external indicators. Cell-suspended PBS or river water were used as models of environmental waters containing living things, and DNA samples were prepared by PCR amplification. Ferrocene-terminated probes were synthesized and immobilized on an electrode array to develop a sensor array. The sensor array showed a large response to a target DNA complementary to the probe and no response to a mismatched DNA, indicating sequence-specific detection. For DNA samples prepared from the cells in PBS, they showed good responses similar to those for the target DNA. They also significantly detected DNA samples from the cells in river water at a general environmental concentration (38 cells mL-1) with 28-fold larger responses than those for 0 cells mL-1.

Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.

Effects of increasing soil moisture on Antarctic desert microbial ecosystems

Overgeneralization and a lack of baseline data for microorganisms in high-latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind-driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10-12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long-term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally.

The development of terrestrial ecosystems emerging after glacier retreat

The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes, with new ecosystems developing from apparently barren substrates1-4. The study of these emerging ecosystems is critical to understanding how climate change interacts with microhabitat and biotic communities and determines the future of ice-free terrains1,5. Here, using a comprehensive characterization of ecosystems (soil properties, microclimate, productivity and biodiversity by environmental DNA metabarcoding6) across 46 proglacial landscapes worldwide, we found that all the environmental properties change with time since glaciers retreated, and that temperature modulates the accumulation of soil nutrients. The richness of bacteria, fungi, plants and animals increases with time since deglaciation, but their temporal patterns differ. Microorganisms colonized most rapidly in the first decades after glacier retreat, whereas most macroorganisms took longer. Increased habitat suitability, growing complexity of biotic interactions and temporal colonization all contribute to the increase in biodiversity over time. These processes also modify community composition for all the groups of organisms. Plant communities show positive links with all other biodiversity components and have a key role in ecosystem development. These unifying patterns provide new insights into the early dynamics of deglaciated terrains and highlight the need for integrated surveillance of their multiple environmental properties5.

Aboveground and belowground biodiversity have complementary effects on ecosystem functions across global grasslands

Grasslands are integral to maintaining biodiversity and key ecosystem services and are under threat from climate change. Plant and soil microbial diversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, it remains virtually unknown whether plant and soil microbial diversity explain a unique portion of total variation or shared contributions to supporting multifunctionality across global grasslands. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that plant and soil microbial diversity independently predict a unique portion of total variation in above- and belowground functioning, suggesting that both types of biodiversity complement each other. Interactions between plant and soil microbial diversity positively impacted multifunctionality including primary production and nutrient storage. Our findings were also climate context dependent, since soil fungal diversity was positively associated with multifunctionality in less arid regions, while plant diversity was strongly and positively linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands.

Spatiotemporal drivers of Nature's contributions to people: A county-level study

Nature's contributions to people (NCP) encompass both the beneficial and detrimental effects of living nature on human quality of life, including regulatory, material, and non-material contributions. Globally, vital NCPs have been deteriorating, accelerated by changes in both natural and anthropogenic drivers over recent decades. Despite the often inevitable trade-offs between NCPs due to their spatially and temporally uneven distributions, few studies have quantitatively assessed the impacts of different drivers on the spatial and temporal changes in multiple NCPs and their interrelationships. Here we evaluate the effects of precipitation, temperature, population, gross domestic product, vegetation restoration, and urban expansion on four key regulatory NCPs-habitat maintenance, climate regulation, water quantity regulation, and soil protection-in Nei Mongol at the county level. We observe increasing trends in climate regulation and soil protection from 2000 to 2019, contrasted with declining trends in habitat maintenance and water quantity regulation. We have identified the dominant positive and negative drivers influencing each NCP across individual counties, finding that natural drivers predominantly overpowered anthropogenic drivers. Furthermore, we discover significant spatial disparities in the trade-off or synergy relationships between NCPs across the counties. Our findings illustrate how the impacts of various drivers on NCPs and their interrelationships can be quantitatively evaluated, offering significant potential for application in various spatial scales. With an understanding of trade-offs and scale effects, these insights are expected to support and inform policymaking at both county and provincial levels.

Deciphering the key factors affecting pesticide residue risk in vegetable ecosystem

Soil contamination, particularly from pesticide residues, presents a significant challenge to the sustainable development of agricultural ecosystems. Identifying the key factors influencing soil pesticide residue risk and implementing effective measures to mitigate their risks at the source are essential. Here, we collected soil samples and conducted a comprehensive survey among local farmers in the Three Gorges Reserve Area, a major agricultural production region in Southwest China. Subsequently, employing a dual analytical approach combining structural equation modeling (SEM) and random forest modeling (RFM), we examined the effects of various factors on pesticide residue accumulation in vegetable ecosystems. Our SEM analysis revealed that soil characteristics (path coefficient 0.85) and cultivation factor (path coefficient 0.84) had the most significant effect on pesticide residue risk, while the farmer factors indirectly influenced pesticide residues by impacting both cultivation factors and soil characteristics. Further exploration using RFM identified the three most influential factors contributing to pesticide residue risk as cation exchange capacity (CEC) (account for 18.84%), cultivation area (account for 14.12%), and clay content (account for 13.01%). Based on these findings, we carried out experimental trials utilizing Integrated Pest Management (IPM) technology, resulting in a significant reduction in soil pesticide residues and notable improvements in crop yields. Therefore, it is recommended that governmental efforts should prioritize enhanced training for vegetable farmers, promotion of eco-friendly plant protection methods, and regulation of agricultural environments to ensure sustainable development.

Dissimilar forests along the Rio Doce watershed call for multiple restoration references to avoid biotic homogenization

An environmental disaster caused by the rupture of a mining tailings dam has impacted a large area of the Rio Doce watershed in the Brazilian Atlantic Forest, resulting in unprecedented damage at spatial and temporal scales. The Atlantic Forest is one of the world's most important biodiversity hotspots. A long history of land use conversion has resulted in a highly fragmented landscape. Despite numerous restoration initiatives, these efforts have often biased criteria and use limited species assemblages. We conducted a comprehensive synthesis of the plant community in riparian forests along the Rio Doce watershed. Our work detailed vegetation composition (tree and sapling strata) and examined its relationship with edaphic and landscape factors, aiming to inform restoration projects with scientifically robust knowledge. A total of 4906 individuals from the tree strata and 4565 individuals from the sapling strata were recorded, representing a total of 1192 species from 75 families. Only 0.8% of the tree species and 0.5% of the sapling species occurred in all sampled sectors, with over 84% of the species occurring in a single watershed sector for both strata. We observed a high species heterogeneity modulated by turnover (92.3% in the tree, and 92.7% in the sapling strata) among sites. Overall, our research revealed a gradient of soil fertility influencing species composition across different strata. Additionally, we discovered that preserved landscapes had a positive impact on species diversity within both strata. The species exclusivity in the sampled sites and the high turnover rate imply the need to consider multiple reference ecosystems when restoring the watershed to reduce the risk of biotic homogenization. Finally, the reference ecosystems defined here serve as a basis for the selection of locally particular species in the implementation of restoration projects that aim to improve biodiversity, ecosystem services, and water security.

Climate mismatches with ectomycorrhizal fungi contribute to migration lag in North American tree range shifts

Climate change will likely shift plant and microbial distributions, creating geographic mismatches between plant hosts and essential microbial symbionts (e.g., ectomycorrhizal fungi, EMF). The loss of historical interactions, or the gain of novel associations, can have important consequences for biodiversity, ecosystem processes, and plant migration potential, yet few analyses exist that measure where mycorrhizal symbioses could be lost or gained across landscapes. Here, we examine climate change impacts on tree-EMF codistributions at the continent scale. We built species distribution models for 400 EMF species and 50 tree species, integrating fungal sequencing data from North American forest ecosystems with tree species occurrence records and long-term forest inventory data. Our results show the following: 1) tree and EMF climate suitability to shift toward higher latitudes; 2) climate shifts increase the size of shared tree-EMF habitat overall, but 35% of tree-EMF pairs are at risk of declining habitat overlap; 3) climate mismatches between trees and EMF are projected to be greater at northern vs. southern boundaries; and 4) tree migration lag is correlated with lower richness of climatically suitable EMF partners. This work represents a concentrated effort to quantify the spatial extent and location of tree-EMF climate envelope mismatches. Our findings also support a biotic mechanism partially explaining the failure of northward tree species migrations with climate change: reduced diversity of co-occurring and climate-compatible EMF symbionts at higher latitudes. We highlight the conservation implications for identifying areas where tree and EMF responses to climate change may be highly divergent.

Global biogeography of microbes driving ocean ecological status under climate change

Microbial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, and how these factors respond to climate change remains a significant challenge. Here, we propose seven distinct ecological statuses by systematically considering the diversity, structure, and biogeochemical potential of the ocean microbiome to delineate their biogeography. Anthropogenic climate change is expected to alter the ecological status of the surface ocean by influencing environmental conditions, particularly nutrient and oxygen contents. Our predictive model, which utilizes machine learning, indicates that the ecological status of approximately 32.44% of the surface ocean may undergo changes from the present to the end of this century, assuming no policy interventions. These changes mainly include poleward shifts in the main taxa, increases in photosynthetic carbon fixation and decreases in nutrient metabolism. However, this proportion can decrease significantly with effective control of greenhouse gas emissions. Our study underscores the urgent necessity for implementing policies to mitigate climate change, particularly from an ecological perspective.

Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing

The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.

Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils

In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.

Effects of climate on the distribution and conservation of commonly observed European earthworms

Belowground biodiversity distribution does not necessarily reflect aboveground biodiversity patterns, but maps of soil biodiversity remain scarce because of limited data availability. Earthworms belong to the most thoroughly studied soil organisms and-in their role as ecosystem engineers-have a significant impact on ecosystem functioning. We used species distribution modeling (SDMs) and available data sets to map the spatial distribution of commonly observed (i.e., frequently recorded) earthworm species (Annelida, Oligochaeta) across Europe under current and future climate conditions. First, we predicted potential species distributions with commonly used models (i.e., MaxEnt and Biomod) and estimated total species richness (i.e., number of species in a 5 × 5 km grid cell). Second, we determined how much the different types of protected areas covered predicted earthworm richness and species ranges (i.e., distributions) by estimating the respective proportion of the range area. Earthworm species richness was high in central western Europe and low in northeastern Europe. This pattern was mainly associated with annual mean temperature and precipitation seasonality, but the importance of predictor variables to species occurrences varied among species. The geographical ranges of the majority of the earthworm species were predicted to shift to eastern Europe and partly decrease under future climate scenarios. Predicted current and future ranges were only poorly covered by protected areas, such as national parks. More than 80% of future earthworm ranges were on average not protected at all (mean [SD] = 82.6% [0.04]). Overall, our results emphasize the urgency of considering especially vulnerable earthworm species, as well as other soil organisms, in the design of nature conservation measures.

Deforestation impacts soil biodiversity and ecosystem services worldwide

Deforestation poses a global threat to biodiversity and its capacity to deliver ecosystem services. Yet, the impacts of deforestation on soil biodiversity and its associated ecosystem services remain virtually unknown. We generated a global dataset including 696 paired-site observations to investigate how native forest conversion to other land uses affects soil properties, biodiversity, and functions associated with the delivery of multiple ecosystem services. The conversion of native forests to plantations, grasslands, and croplands resulted in higher bacterial diversity and more homogeneous fungal communities dominated by pathogens and with a lower abundance of symbionts. Such conversions also resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Responses of the microbial community to deforestation, including bacterial and fungal diversity and fungal guilds, were predominantly regulated by changes in soil pH and total phosphorus. Moreover, we found that soil fungal diversity and functioning in warmer and wetter native forests is especially vulnerable to deforestation. Our work highlights that the loss of native forests to managed ecosystems poses a major global threat to the biodiversity and functioning of soils and their capacity to deliver ecosystem services.

Bioavailability (BA)-based risk assessment of soil heavy metals in provinces of China through the predictive BA-models

The real biological effect is not generated by the total content of heavy metals (HMs), but rather by bioavailable content. A new bioavailability-based ecological risk assessment (BA-based ERA) framework was developed for deriving bioavailability-based soil quality criteria (BA-based SQC) and accurately assessing the ecological risk of soil HMs at a multi-regional scale in this study. Through the random forest (RF) models and BA-based ERA framework, the 217 BA-based SQC for HMs in 31 Chinese provinces were derived and the BA-based ERA was comprehensively assessed. This study found that bioavailable HMs extraction methods (BHEMs) and total HMs content play the predominant role in affecting HMs (As, Cd, Cr, Cu, Ni, Pb, and Zn) bioavailability by explaining 27.55-56.11% and 9.20-62.09% of the variation, respectively. The RF model had accurate and stable prediction ability for the bioavailability of soil HMs with the mean R2 and RMSE of 0.83 and 0.43 for the test set, respectively. The results of BA-based ERA showed that bioavailability could avoid the overestimation of ecological risks to some extent after reducing the uncertainty of soil differences. This study confirmed the feasibility of using bioavailability for ERA and will utilised to revise the soil environmental standards based on bioavailability for HMs.

Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia

Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine-learning models, we generated high-resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes.

Multiple invasion routes have led to the pervasive introduction of earthworms in North America

Soil-dwelling organisms play a key role in ecosystem functioning and the delivery of ecosystem services. As a consequence, soil taxa such as earthworms are iconic in good land management practices. However, their introduction in places where species did not co-evolve with them can trigger catastrophic changes. This issue has been largely ignored so far in nature management policies because of the positive image of soil taxa and the lack of knowledge of the magnitude of soil fauna introductions outside their native range. Here we address this gap with a large spatio-temporal database of introduced alien earthworms. We show that 70 alien earthworm species have colonized the North American continent. They have larger geographical ranges than native species and novel ecological functions, representing a serious threat to the biodiversity and functioning of native ecosystems. The probably continuous introduction of alien earthworms, from a variety of sources and introduction pathways, into many distant and often empty niches, contrasts with the classical patterns of invasions in most aboveground taxa. This suggests that earthworms, and probably other soil organisms, constitute a major but overlooked pool of invasive species that are not adequately managed by existing control and mitigation strategies.

Widespread cooling of topsoil under nitrogen enrichment and implication for soil carbon flux

Increasing reactive nitrogen (N) to terrestrial ecosystems is considered to enhance ecosystem carbon sink, which plays a critical role in ameliorating global warming. Besides this indirect buffering of temperature rise, the N-induced enhancement of vegetation growth may exert a biophysical cooling effect on soils. However, the magnitude and drivers of this cooling effect have rarely been evaluated. Here, using a global meta-analysis with 321 paired measurements, we demonstrated a widespread topsoil cooling (-0.30 °C in average) under anthropogenic N enrichment, which was primarily associated with the increase in aboveground biomass. This biophysical cooling could also buffer topsoil temperature rise by an average of 0.39 °C under experimental warming. Further, the reduced soil temperature was found to contribute to a reduction of soil respiration rate as temperature declines gradually. Overall, our results underpin a previously overlooked function of global N enrichment-the lowering of topsoil temperature, which suggests that the warming of topsoil may not be as fast as previously predicted under future global change scenarios. This biophysical cooling effect will also slow down soil carbon emissions and further mitigate climate warming.

Positive associations fuel soil biodiversity and ecological networks worldwide

Microbial interactions are key to maintaining soil biodiversity. However, whether negative or positive associations govern the soil microbial system at a global scale remains virtually unknown, limiting our understanding of how microbes interact to support soil biodiversity and functions. Here, we explored ecological networks among multitrophic soil organisms involving bacteria, protists, fungi, and invertebrates in a global soil survey across 20 regions of the planet and found that positive associations among both pairs and triads of soil taxa governed global soil microbial networks. We further revealed that soil networks with greater levels of positive associations supported larger soil biodiversity and resulted in lower network fragility to withstand potential perturbations of species losses. Our study provides unique evidence of the widespread positive associations between soil organisms and their crucial role in maintaining the multitrophic structure of soil biodiversity worldwide.

Soil macrofauna communities in Brazilian land-use systems

Background

Soil animal communities include more than 40 higher-order taxa, representing over 23% of all described species. These animals have a wide range of feeding sources and contribute to several important soil functions and ecosystem services. Although many studies have assessed macroinvertebrate communities in Brazil, few of them have been published in journals and even fewer have made the data openly available for consultation and further use. As part of ongoing efforts to synthesise the global soil macrofauna communities and to increase the amount of openly-accessible data in GBIF and other repositories related to soil biodiversity, the present paper provides links to 29 soil macroinvertebrate datasets covering 42 soil fauna taxa, collected in various land-use systems in Brazil. A total of 83,085 georeferenced occurrences of these taxa are presented, based on quantitative estimates performed using a standardised sampling method commonly adopted worldwide to collect soil macrofauna populations, i.e. the TSBF (Tropical Soil Biology and Fertility Programme) protocol. This consists of digging soil monoliths of 25 x 25 cm area, with handsorting of the macroinvertebrates visible to the naked eye from the surface litter and from within the soil, typically in the upper 0-20 cm layer (but sometimes shallower, i.e. top 0-10 cm or deeper to 0-40 cm, depending on the site). The land-use systems included anthropogenic sites managed with agricultural systems (e.g. pastures, annual and perennial crops, agroforestry), as well as planted forests and native vegetation located mostly in the southern Brazilian State of Paraná (96 sites), with a few additional sites in the neighbouring states of São Paulo (21 sites) and Santa Catarina (five sites). Important metadata on soil properties, particularly soil chemical parameters (mainly pH, C, P, Ca, K, Mg, Al contents, exchangeable acidity, Cation Exchange Capacity, Base Saturation and, infrequently, total N), particle size distribution (mainly % sand, silt and clay) and, infrequently, soil moisture and bulk density, as well as on human management practices (land use and vegetation cover) are provided. These data will be particularly useful for those interested in estimating land-use change impacts on soil biodiversity and its implications for below-ground foodwebs, ecosystem functioning and ecosystem service delivery.

New information

Quantitative estimates are provided for 42 soil animal taxa, for two biodiversity hotspots: the Brazilian Atlantic Forest and Cerrado biomes. Data are provided at the individual monolith level, representing sampling events ranging from February 2001 up to September 2016 in 122 sampling sites and over 1800 samples, for a total of 83,085 ocurrences.

Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Litter and soil biodiversity jointly drive ecosystem functions

The decomposition of litter and the supply of nutrients into and from the soil are two fundamental processes through which the above- and belowground world interact. Microbial biodiversity, and especially that of decomposers, plays a key role in these processes by helping litter decomposition. Yet the relative contribution of litter diversity and soil biodiversity in supporting multiple ecosystem services remains virtually unknown. Here we conducted a mesocosm experiment where leaf litter and soil biodiversity were manipulated to investigate their influence on plant productivity, litter decomposition, soil respiration, and enzymatic activity in the littersphere. We showed that both leaf litter diversity and soil microbial diversity (richness and community composition) independently contributed to explain multiple ecosystem functions. Fungal saprobes community composition was especially important for supporting ecosystem multifunctionality (EMF), plant production, litter decomposition, and activity of soil phosphatase when compared with bacteria or other fungal functional groups and litter species richness. Moreover, leaf litter diversity and soil microbial diversity exerted previously undescribed and significantly interactive effects on EMF and multiple individual ecosystem functions, such as litter decomposition and plant production. Together, our work provides experimental evidence supporting the independent and interactive roles of litter and belowground soil biodiversity to maintain ecosystem functions and multiple services.

Climate change impacts on plant pathogens, food security and paths forward

Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.

Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections

Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.

Potential reduction of greenhouse gas emissions from pig production in China on the basis of households' pork consumption

In the past decades, the greenhouse gas (GHG) emissions from pig production in China have been increasing rapidly, which has become a huge challenge in fulfilling China's "carbon neutral" commitment. However, few studies have focused on reducing the GHG emissions from pig production in view of households' pork consumption. This study analyzed the temporal and spatial pattern of the GHG emissions from pig production in China in 2001-2020 through geographical information system, optimized the pig production in China, and estimated thepotentialGHG emissions reduction from pig production in China in 2020 through spatial analysis based on pork surplus or deficit. Results show that the temporal and spatial pattern of the GHG emissions from pig production and its proportion in the total GHG emissions from livestock production in China in 2001-2020 varied differently at the province level and conformed to the "Hu Huanyong Line" mode. The largest and smallest GHG emissions from pig production were 108.93 million tons (MT) in 2014 and 78.10 MT in 2020, respectively. The largest and smallest proportions of GHG emissions from pig production in the total GHG emissions from livestock production were 77.52% in Zhejiang in 2013 and 0.13% in Tibet in 2009, respectively. Moreover, a potential optimization scheme of pig production in China in 2020 was provided and a method of GHG emissions reduction from pig production is proposed. The results indicate that the total potentialGHG emissions reduction from pig production on the basis of households' pork consumption could reach 35.21 MT, accounting for 45.09% of the total GHG emissions from pig production and 10.27% of the total GHG emissions from livestock production in China in 2020. These findings areusefulin the spatial layout planning of pig production, agricultural GHG reduction, and global warming mitigation.

Soil microbial responses to simultaneous contamination of antimony and arsenic in the surrounding area of an abandoned antimony smelter in Southwest China

Soil contamination with heavy metal(loid)s may influence microbial activities in the soil, and consequently jeopardize soil health. Microbial responses to soil contamination play an important role in ecological risk assessment. This study investigated the effect of heavy metal(loid)s contamination on microbial community structure and abundance in the surrounding soil of an abandoned antimony (Sb) smelter in Qinglong county, Guizhou province, Southwest China. A total of 46 soil samples were collected from ten sampling sites (labelled as A-I, and CK) across the study area at depths of 0-2, 2-10, 10-20, 20-30, 30-40, and 40-50 cm. The soil samples were analyzed for total and bioavailable heavy metal(loid) concentrations, bacterial, fungal, and archaeal community structures, diversities, and functions, together with soil basic physicochemical properties. Much greater ecological risk of Sb and arsenic (As) was present in the surface soil (0-2 cm) compared to that in the subsoils. The activities of dominant microorganisms tended to be associated with soil pH and heavy metal(loid)s (i.e., Sb, As, lead (Pb), cadmium (Cd), and chromium (Cr)). Bacteria associated with IMCC26256, Rhizobiales, Burkholderiales, and Gaiellales, and archaea associated with Methanocellales were estimated to be tolerant to high concentrations of Sb and As in the soil. In addition, the magnitude of soil microbial responses to Sb and As contamination was in the order of archaea > bacteria > fungi. In contrast to the negligible response of fungi and negative response of bacteria to Sb and As contamination, there was a strongly positive correlation between archaeal activity and total Sb and As concentrations in the soil. Our findings provide a theoretical basis for the remediation of Sb smelter-affected soil.

Diamonds in the rough: Dryland microorganisms are ecological engineers to restore degraded land and mitigate desertification

Our planet teeters on the brink of massive ecosystem collapses, and arid regions experience manifold environmental and climatic challenges that increase the magnitude of selective pressures on already stressed ecosystems. Ultimately, this leads to their aridification and desertification, that is, to simplified and barren ecosystems (with proportionally less microbial load and diversity) with altered functions and food webs and modification of microbial community network. Thus, preserving and restoring soil health in such a fragile biome could help buffer climate change's effects. We argue that microorganisms and the protection of their functional properties and networks are key to fight desertification. Specifically, we claim that it is rational, possible and certainly practical to rely on native dryland edaphic microorganisms and microbial communities as well as dryland plants and their associated microbiota to conserve and restore soil health and mitigate soil depletion in newly aridified lands. Furthermore, this will meet the objective of protecting/stabilizing (and even enhancing) soil biodiversity globally. Without urgent conservation and restoration actions that take into account microbial diversity, we will ultimately, and simply, not have anything to protect anymore.