Extinction risk of soil biota

Competitive relationships due to similar nutrient preferences reshape soil bacterial metacommunities

Paddy soil, as an ecosystem with alternating drained and flooded conditions, microorganisms in it can maintain the stability of the ecosystem by regulating the composition and diversity of its species when disturbed by external biotic or abiotic factors, and the regulatory mechanism in this process is a controversial topic in ecological research. In this study, we investigate the effects of pigeon feces addition on bacterial communities in three textured soils, two conditions (drained and flooded) based on microcosm experiment using high-throughput sequencing techniques. Our results show that pigeon feces addition reduced environmental heterogeneity and community diversity, both under flooded and drained conditions and in all textured soils, thereby decreasing the effectiveness of environmental selection and increasing diffusion limitations among bacterial communities. Bacterial communities are altered by environmental factors including total organic carbon, available nitrogen, total phosphorus, available phosphorus and available potassium, resulting in the formation of new community structures and dominant genera. Bacteria from pigeon feces did not colonize the original soil in large numbers, and the soil bacterial community structure changed, with some species replaced the indigenous ones as new dominant genera. As nutrient diffusion increases the nutrient content of the soil, this does not lead to species extinction; however, nutrient diffusion creates new nutrient preferences of the bacterial community, which causes direct competition between species, and contributes to the extinction and immigration species. Our results suggest that species replacement is an adaptive strategy of soil bacterial community in response to dispersal of pigeon feces, and that bacterial community regulate diversity and abundance of the community by enhancing species extinction and immigration, thereby preventing bacteria in pigeon feces from colonizing paddy soils and maintaining ecosystem stability.

Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils

Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.

Seasonal Changes in the Soil Microbial Community Structure in Urban Forests

Urban forests play a crucial role in the overall health and stability of urban ecosystems. Soil microorganisms are vital to the functioning of urban forest ecosystems as they facilitate material cycling and contribute to environmental stability. This study utilized high-throughput sequencing technology to examine the structural characteristics of bacterial and fungal communities in the bulk soil of six different forest stands: Phyllostachys pubescens (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Soil samples were collected from each forest stand, including the corners, center, and edges of each plot, and a combined sample was created from the first five samples. The results revealed that among the bacterial communities, ZKG exhibited the highest alpha diversity in spring, while ZL demonstrated the highest alpha diversity in both summer and autumn. Proteobacteria was the most abundant bacterial phylum in all six forest stand soils. The dominant fungal phylum across the six forest stands was identified as Ascomycota. Notably, the microbial community diversity of SBL bulk soil exhibited significant seasonal changes. Although ZL exhibited lower bacterial community diversity in spring, its fungal community diversity was the highest. The bulk soil microbial diversity of ZL and SSL surpassed that of the other forest stands, suggesting their importance in maintaining the stability of the urban forest ecosystem in the Zhuyu Bay Scenic Area. Furthermore, the diversity of the bulk soil microbial communities was higher in all six stands during spring compared to summer and autumn. Overall, this study provides valuable insights into the seasonal variations of bulk soil microbial communities in urban forests and identifies dominant tree species, offering guidance for tree species' selection and preservation in urban forest management.

Native forests transformed into cash crops reduced soil multi-functionality by modifying the microbial community composition and keystone species' abundance in the Jianghuai Hilly Region

Conversion of native forest to cash crops is the predominant form of land use change in the Jianghuai Hilly Region. However, how plantations with different cash crops affect the soil multi-functionality is not well documented. In this study, we collected three kinds of cash crops soils (vegetable, orchard, and tea) and forest soil, to systematically review the relationship between soil microbial communities and soil multi-functionality. Soil multi-functionality had decreased in vegetable and orchard as compared to native forest, whereas tea plantation had no significant effects on soil multi-functionality. The results also showed that cash crop plantations decreased soil multi-functionality by shifting keystone species' abundance, for forest, vegetable, and orchard, the keystone species that were classified as module hubs in the bacterial co-occurrence network significantly negatively contributed to soil multi-functionality, but the keystone species categorized as module hubs in fungal co-occurrence network positively affected soil multi-functionality. Multiple soil properties were the drivers of the soil microbial community; thus, indicating that the altered soil properties under cash crop plantations were vital in determining microbial composition and biological processes. These results identified that sustainable management strategy in cash crop plantation needed to be developed for improving soil multi-functionality.

Time-dependent effects of microplastics on soil bacteriome

Microplastic threats to biodiversity, health and ecological safety are adding to concern worldwide, but the real impacts on the functioning of organisms and ecosystems are obscure owing to their inert characteristics. Here we investigated the long-lasting ecological effects of six prevalent microplastic types: polyethylene (PE), polypropylene (PP), polyamide (PA), polystyrene (PS), polyethylene terephthalate (PET), and polyvinyl chloride (PVC) on soil bacteria at a 2 % (w/w) level. Due to the inertia and lack of available nitrogen of these microplastics, their effects on bacteriome tended to converge after one year and were strongly different from their short-term effects. The soil volumes around microplastics were very specific, in which the microplastic-adapted bacteria (e.g., some genera in Actinobacteria) were enriched but the phyla Bacteroidetes and Gemmatimonadetes declined, resulting in higher microbial nitrogen requirements and reduced organic carbon mineralization. The reshaped bacteriome was specialized in the genetic potential of xenobiotic and lipid metabolism as well as related oxidation, esterification, and hydrolysis processes, but excessive oxidative damage resulted in severe weakness in community genetic information processing. According to model predictions, microplastic effects are indirectly derived from nutrients and oxidative stress, and the effects on bacterial functions are stronger than on structure, posing a heavy risk to soil ecosystems.

Seasonal fluctuations attenuate stimulatory or inhibitory impacts of colonial birds on abundance, structure and diversity of soil biota

Soil microorganisms and free-living nematodes were investigated in association with the nesting and roosting habitats of the following piscivorous and omnivorous colonial birds: black kite (Milvus migrans), great cormorant (Phalacrocorax carbo), black-crowned night heron (Nycticorax nycticorax) and little egret (Egretta garzetta), in Israel's Mediterranean region. Abiotic variables, abundance, trophic structure, sex ratio and genus diversity of soil free-living nematodes, and total abundance of bacteria and fungi, were measured during the wet season, following our previous study conducted during the dry season. The observed soil properties were important drivers of soil biota structure. Presence of the most efficient elements for soil organisms, such as phosphorus and nitrogen, was strongly dependent on the diet of the compared piscivorous and omnivorous bird colonies; levels of these nutrients were notably higher in the bird habitats than in their respective control sites during the study period. Ecological indices showed that the different species of colonial birds can have different (stimulatory or inhibitory) impacts on abundance and diversity of the soil biota, affecting the structure of the soil free-living nematode population at the generic, trophic and sexual levels during the wet season. A comparison with results from the dry season illustrated that seasonal fluctuations can change, and even attenuate the effect of bird activity on the abundance, structure and diversity of the soil communities.

Native microbiomes in danger: Could One Health help to cope with this threat to global health?

Planetary health faces an emergency associated with global change. Climate change, the increase in world population and urban concentration, the hyperintensification of productive systems, and the associated changes in land use, among other factors, are generating a risky substrate for global health deterioration. The emergence of the coronavirus disease 2019 pandemic is an example of the problems that this situation can provoke. Several researchers and health professionals have addressed the role of microorganisms, particularly bacteria, in promoting global health, mainly in the past decades. However, global changes have contributed to the extinction of a wide array of bacterial species and the disruption of microbial communities that support the homeostasis of humans, animals, and the environment. The need to protect the diversity and richness of native microbiomes in biotic and abiotic environments is crucial but has been frequently underestimated. The "One Health" approach, based on integrating traditionally unconnected fields such as human, animal, and environmental health, could provide a helpful framework to face this challenge. Anyway, drastic political decisions will be needed to tackle this global health crisis, in which the preservation of native microbial resources plays a critical role, even in preventing the risk of a new pandemic. This review aims to explain the importance of native microbiomes in biotic and abiotic ecosystems and the need to consider bacterial extinction as a crucial problem that could be addressed under a One Health approach.

Challenges of and opportunities for protecting European soil biodiversity

Soil biodiversity and related ecosystem functions are neglected in most biodiversity assessments and nature conservation actions. We examined how society, and particularly policy makers, have addressed these factors worldwide with a focus on Europe and explored the role of soils in nature conservation in Germany as an example. We reviewed past and current global and European policies, compared soil ecosystem functioning in- and outside protected areas, and examined the role of soils in nature conservation management via text analyses. Protection and conservation of soil biodiversity and soil ecosystem functioning have been insufficient. Soil-related policies are unenforceable and lack soil biodiversity conservation goals, focusing instead on other environmental objectives. We found no evidence of positive effects of current nature conservation measures in multiple soil ecosystem functions in Europe. In German conservation management, soils are considered only from a limited perspective (e.g., as physicochemical part of the environment and as habitat for aboveground organisms). By exploring policy, evidence, and management as it relates to soil ecosystems, we suggest an integrative perspective to move nature conservation toward targeting soil ecosystems directly (e.g., by setting baselines, monitoring soil threats, and establishing a soil indicator system).

A global review of microplastics in wastewater treatment plants: Understanding their occurrence, fate and impact

Microplastics (MPs) are emerging as a serious environmental concern, with wastewater treatment plants (WWTPs) acting as the main entry routes for MPs into aquatic and terrestrial ecosystems. On a global scale, our literature review found that MP research in WWTPs has only been conducted on 121 WWTPs in 17 countries, with the majority of the work being done in Europe (53%), followed by the United States of America and Canada (24%), Asia (18%), and Australia (5%) in recent years. MPs in WWTPs are primarily derived from Personal Care and Cosmetic Products (PCCPs), which are primarily composed of polyethylene (PE) derivatives. Based on the studies, microfibers (57%) and fragments (47%) are observed to be the most common MP forms in influents and effluents of WWTPs. The chemical characterization of MPs detected in WWTPs, showed the occurrence of polyethylene (PE) (22%), polystyrene (PS) (21%), and polypropylene (13%). Although MP retention/removal efficiencies of different treatment technologies vary from medium to high, deliberations on sludge disposal on agricultural soils containing MPs and MP intrusion into groundwater are required to sustainably regulate MP contaminant transport. Thus, the development of efficient detection methods and understanding their fate are of immense significance for the management of MPs. Despite the fact that ongoing research in MPs and WWTPs has unquestionably improved our understanding, many questions and concerns remain unanswered. In this review, the current status of the detection, occurrence, and impact of MPs in WWTPs across the world are systematically reviewed to prioritize policy-making to recognize the WWTPs as global conduits of MPs.

Illuminating biodiversity changes in the ‘Black Box’

Soil is often described as a ‘black box’, as surprisingly little is known about the high levels of biodiversity that reside there. For aboveground organisms, we have good knowledge of the distribution of the species and how they might change under future human impacts. Yet despite the fact that soil organisms provide a wide variety of ecosystem functions, we have very limited knowledge of their distribution and how their diversity might change in the future. In order to create accurate and generalisable models of biodiversity, the underlying data need to be representative of the entire globe. Yet even with our recently compiled global earthworm dataset of over 11000 sites, there are gaps across large regions. These gaps are consistent across many other datasets of both above- and belowground diversity. In order to fill the gaps we propose a sampling network (SoilFaUNa), to create a comprehensive database of soil macrofauna diversity and soil functions (e.g. decomposition rates). Building on the existing dataset of earthworm diversity and early data from the SoilFaUNa project, we will investigate changes in earthworm diversity. From our current work, we know that both climate and land use are main drivers in predicting earthworm diversity, but both will change under future scenarios and may alter ecosystem functions. We will, using space-for-time substitution models, estimate how earthworm diversity and their functions might change in the future, modelling earthworm diversity as a function of climate, land use and soil properties and predicting based on future scenarios. Previous studies of aboveground diversity changes over time using time-series analysis have found no-net-loss in richness, but analyses have criticisms. We aim to use time-series data on earthworms to move this debate forward, by using data and statistical methods that would address the criticisms, whilst increasing our knowledge on this understudied soil group. Field experiments and micro-/mesocosm experiments have been used to investigate the link between a number of soil organisms and ecosystem functions under few environmental conditions. Meta-analyses, which can produce generalisable results can only answer questions for which there are data. Thus, we have been lacking on information on the link between the entire community of soil fauna and ecosystem functions and impact of changes to the soil fauna community across environmental contexts. Using data collected from the SoilFaUNa project, we will, for the first time, synthesise globally distributed specifically-sampled data to model how changes in the community composition of soil macrofauna (due to changes in land use, climate or soil properties) impact the ecosystem functions in the soil.

Effects of plastic residues and microplastics on soil ecosystems: A global meta-analysis

Plastic pollution is one of the global pressing environmental problems, threatening the health of aquatic and terrestrial ecosystems. However, the influence of plastic residues and microplastics (MPs) in soil ecosystems remains unclear. We conducted a global meta-analysis to quantify the effect of plastic residues and MPs on indicators of global soil ecosystem functioning (i.e. soil physicochemical properties, plant and soil animal health, abundance and diversity of soil microorganisms). Concentrations of plastic residues and MPs were 1-2700 kg ha^-1 and 0.01-600,000 mg kg^-1, respectively, based on 6223 observations. Results show that plastic residues and MPs can decrease soil wetting front vertical and horizontal movement, dissolved organic carbon, and total nitrogen content of soil by 14%, 10%, 9%, and 7%, respectively. Plant height and root biomass were decreased by 13% and 14% in the presence of plastic residues and MPs, while the body mass and reproduction rate of soil animals decreased by 5% and 11%, respectively. However, soil enzyme activity increased by 7%441% in the presence of plastic residues and MPs. For soil microorganisms, plastic residues and MPs can change the abundance of several bacteria phyla and families, but the effects vary between different bacteria.

The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification

Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.

The biodiversity effect of reduced tillage on soil microbiota

The conversion of natural habitats into farmland has been a leading cause of species loss worldwide. Here, we investigated to what extent less intensive soil disturbance can mitigate this loss. Specifically, we examined whether reduced soil disturbance by tillage in agricultural fields could contribute to soil microbial biodiversity by providing a habitat for species that are limited by conventional tillage. To do so, we studied the diversity of soil biotas from three agricultural practices representing conventional tillage, reduced tillage and no tillage. Study fields were sampled by taking a bulk soil sample at the centre and edge of each field. The soil communities were recorded with environmental DNA metabarcoding using three molecular markers targeting bacteria, fungi and eukaryotes. While these three markers represent the vast majority of biotic variation in the soil, they will inevitably be dominated by the megadiverse microbiota of bacteria, microfungi and protists. We found a significant differentiation in community composition related to the intensity of tillage. Richness was weakly correlated to tillage, and more influenced by whether the sample was taken in the center or the edge of the field. Despite the significant effect of tillage on composition, comparisons with natural ecosystems revealed that all 30 study fields were much more similar in composition to other rotational fields than to more natural habitats, oldfields and leys. Despite a slightly higher similarity to oldfields and semi-natural grasslands, the contribution of no-till soil communities to biodiversity conservation is negligible, and our results indicate that restoration on set aside land may contribute more to conservation.

Inconsistent Patterns of Soil Fauna Biodiversity and Soil Physicochemical Characteristic Along an Urbanization Gradient

Urbanization has induced substantial changes in soil physicochemical characteristic, which plays an important role in regulating soil fauna biodiversity in forests and grasslands. However, less is known about the urbanization effect on soil fauna biodiversity and how soil physicochemical changes mediate this effect. Along an urbanization gradient in the city of Guangzhou, we established four sites with different urbanization intensities, including an urban site, two suburban sites, and a rural site, and then studied their soil physicochemical characteristic and soil fauna biodiversity. The soil physicochemical characteristic dramatically changed along the urbanization gradient. In contrast, the soil fauna biodiversity exhibited a very different pattern. Soil fauna abundance was highest in the suburban sites. Moreover, there were significant changes of Pielou’s evenness and community structure in the suburban sites. Soil fauna biodiversity property in the urban site was similar to that in the rural site, except that the rural site was characterized by Enchytraeidae while the urban site was not characterized by any taxa. Our linear and canonical correspondence analysis models suggested that soil physicochemical characteristic only contributed a little to the variance of soil fauna abundance (19%), taxa number (27%), and community structure (12%). In contrast, soil physicochemical characteristic explained about half of the variance in Shannon’s diversity and Pielou’s evenness. However, with urbanization intensity increasing, soil physicochemical changes could both increase and decrease the diversity and evenness. Thus, our results revealed an inconsistent pattern between soil fauna biodiversity and soil physicochemical characteristic along an urbanization gradient. This study suggested that soil physicochemical change was less important as expected in regulating soil fauna biodiversity pattern under an urbanization context. To elucidate the effect of urbanization on soil fauna biodiversity, further studies should take other urbanization agents into account.

Microplastics and environmental pollutants: Key interaction and toxicology in aquatic and soil environments

Nowadays, a growing number of microplastics are released into the environment due to the extensive use and inappropriate management of plastic products. With the increasing body of evidence about the pollution and hazards of microplastics, microplastics have drawn major attention from governments and the scientific community. As a kind of emerging and persistent environmental pollutants, microplastics have recently been detected on a variety of substrates in the world. Therefore, this paper reviews the recent progress in identifying the sources of microplastics in soil, water, and atmosphere and describing the transport and fate of microplastics in the terrestrial, aquatic and atmospheric ecosystems for revealing the circulation of microplastics in the ecosystem. In addition, considering the persistence of microplastics, this study elucidates the interactions of microplastics with other pollutants in the environment (i.e., organic pollutants, heavy metals) with emphasis on toxicity and accumulation, providing a novel insight into the ecological risks of microplastics in the environment. The negative impacts of microplastics on organisms and environmental health are also reviewed to reveal the environmental hazards of microplastics. The knowledge gaps and key research priorities of microplastics are identified to better understand and mitigate the environmental risks of microplastics.

Artefactual depiction of predator-prey trophic linkages in global soils

Soil invertebrates contribute to multiple ecosystem services, including pest control, nutrient cycling, and soil structural regulation, yet trophic interactions that determine their diversity and activity in soils remain critically understudied. Here, we systematically review literature (1966-2020) on feeding habits of soil arthropods and macrofauna and summarize empirically studied predator-prey linkages across ecosystem types, geographies and taxa. Out of 522 unique predators and 372 prey organisms (constituting 1947 predator-prey linkages), the vast majority (> 75%) are only covered in a single study. We report a mean of just 3.0 ± 4.7 documented linkages per organism, with pronounced taxonomic biases. In general, model organisms and crop pests (generally Insecta) are well-studied, while important soil-dwelling predators, fungivores and detritivores (e.g., Collembola, Chilopoda and Malacostraca) remain largely ignored. We argue that broader food-web based research approaches, considering multiple linkages per organism and targeting neglected taxa, are needed to inform science-driven management of soil communities and associated ecosystem services.

Recent advances on ecological effects of microplastics on soil environment

The mass production and wide application of plastics and their derivatives have led to the release of a large number of discarded plastic products into the natural environment, where they continue to accumulate due to their low recycling rate and long durability. These large pieces of plastic will gradually break into microplastics (<5 mm), which are highly persistent organic pollutants and attract worldwide attention due to their small particle size and potential threats to the ecosystem. Compared with the aquatic system, terrestrial systems such as soils, as sinks for microplastics, are more susceptible to plastic pollution. In this article, we comprehensively summarized the occurrence and sources of microplastics in terrestrial soil, and reviewed the eco-toxicological effects of microplastics in soil ecosystems, in terms of physical and chemical properties of soil, soil nutrient cycling, soil flora and fauna. The influence of microplastics on soil microbial community, and particularly the microbial community on the surface of microplastics, were examined in detail. The compound effects of microplastics and other pollutants, e.g., heavy metals and antibiotics, were addressed. Future challenges of research on microplastics include development of new techniques and standardization for the extraction and qualitative and quantitative analysis of microplastics in soils, toxic effects of microplastics at microbial or even molecular levels, the contribution of microplastics to antibiotic resistance genes migration, and unraveling microorganisms for the degradation of microplastics. This work provides as a better understanding of the occurrence, distribution and potential ecological risks of microplastics in terrestrial soil ecosystems.

Trophic level drives the host microbiome of soil invertebrates at a continental scale

BACKGROUND

Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.

RESULTS

Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.

CONCLUSIONS

Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates. Video abstract.

Impacts of Plastic Pollution on Ecosystem Services, Sustainable Development Goals, and Need to Focus on Circular Economy and Policy Interventions

Plastic pollution is ubiquitous in terrestrial and aquatic ecosystems. Plastic waste exposed to the environment creates problems and is of significant concern for all life forms. Plastic production and accumulation in the natural environment are occurring at an unprecedented rate due to indiscriminate use, inadequate recycling, and deposits in landfills. In 2019, the global production of plastic was at 370 million tons, with only 9% of it being recycled, 12% being incinerated, and the remaining left in the environment or landfills. The leakage of plastic wastes into terrestrial and aquatic ecosystems is occurring at an unprecedented rate. The management of plastic waste is a challenging problem for researchers, policymakers, citizens, and other stakeholders. Therefore, here, we summarize the current understanding and concerns of plastics pollution (microplastics or nanoplastics) on natural ecosystems. The overall goal of this review is to provide background assessment on the adverse effects of plastic pollution on natural ecosystems; interlink the management of plastic pollution with sustainable development goals; address the policy initiatives under transdisciplinary approaches through life cycle assessment, circular economy, and sustainability; identify the knowledge gaps; and provide current policy recommendations. Plastic waste management through community involvement and socio-economic inputs in different countries are presented and discussed. Plastic ban policies and public awareness are likely the major mitigation interventions. The need for life cycle assessment and circularity to assess the potential environmental impacts and resources used throughout a plastic product’s life span is emphasized. Innovations are needed to reduce, reuse, recycle, and recover plastics and find eco-friendly replacements for plastics. Empowering and educating communities and citizens to act collectively to minimize plastic pollution and use alternative options for plastics must be promoted and enforced. Plastic pollution is a global concern that must be addressed collectively with the utmost priority.

The Future of (Soil) Microbiome Studies: Current Limitations, Integration, and Perspectives

Microbes dominate the planet's biodiversity in terms of species number and by driving essential Earth system functions such as the carbon cycle. Soils contain most of this microbial biodiversity. Only recently, we have started to better understand the diversity of bacteria and fungi at the global scale. Here, I list my views on some shortcomings of contemporary soil microbiome studies and potential solutions to overcome them. In particular, I highlight that (soil) microbiome studies should become more holistic in terms of (i) taxa and resolution targeted, (ii) by adding functional to taxonomic information, and (iii) by integrating temporal analysis into spatial analyses. Considering those elements with the methodology that is now available will advance our understanding on (soil) microbiomes to reliably address major ecological hypotheses and to advance insights into the importance for life on Earth.

Potential Impacts of Climate Change on the Toxicity of Pesticides towards Earthworms

This review examined one of the effects of climate change that has only recently received attention, i.e., climate change impacts on the distribution and toxicity of chemical contaminants in the environment. As ecosystem engineers, earthworms are potentially threatened by the increasing use of pesticides. Increases in temperature, precipitation regime changes, and related extreme climate events can potentially affect pesticide toxicity. This review of original research articles, reviews, and governmental and intergovernmental reports focused on the interactions between toxicants and environmental parameters. The latter included temperature, moisture, acidification, hypoxia, soil carbon cycle, and soil dynamics, as altered by climate change. Dynamic interactions between climate change and contaminants can be particularly problematic for organisms since organisms have an upper and lower physiological range, resulting in impacts on their acclimatization capacity. Climate change variables such as temperature and soil moisture also have an impact on acidification. An increase in temperature will impact precipitation which might impact soil pH. Also, an increase in precipitation can result in flooding which can reduce the population of earthworms by not giving juvenile earthworms enough time to develop into reproductive adults. As an independent stressor, hypoxia can affect soil organisms, alter bioavailability, and increase the toxicity of chemicals in some cases. Climate change variables, especially temperature and soil moisture, significantly affect the bioavailability of pesticides in the soil and the growth and reproduction of earthworm species.

The role of soils in provision of genetic, medicinal and biochemical resources

Intact, 'healthy' soils provide indispensable ecosystem services that largely depend on the biotic activity. Soil health is connected with human health, yet, knowledge of the underlying soil functioning remains incomplete. This review highlights selected services, i.e. (i) soil as a genetic resource and hotspot of biodiversity, forming the basis for providing (ii) biochemical resources and (iii) medicinal services and goods. Soils harbour an unrivalled biodiversity of organisms, especially microorganisms. Some of the abilities of autochthonous microorganisms and their relevant enzymes serve (i) to improve natural soil functions and in particular plant growth, e.g. through beneficial plant growth-promoting, symbiotic and mycorrhizal microorganisms, (ii) to act as biopesticides, (iii) to facilitate biodegradation of pollutants for soil bioremediation and (iv) to yield enzymes or chemicals for industrial use. Soils also exert direct effects on human health. Contact with soil enriches the human microbiome, affords protection against allergies and promotes emotional well-being. Medicinally relevant are soil substrates such as loams, clays and various minerals with curative effects as well as pharmaceutically active organic chemicals like antibiotics that are formed by soil microorganisms. By contrast, irritating minerals, soil dust inhalation and misguided soil ingestion may adversely affect humans. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People.

Inventory of the benthic eukaryotic diversity in the oldest European lake

We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth's systems with eukaryotes in freshwater sediments being among the least known. In this study, we used high-throughput sequencing of the 18S rRNA gene to investigate the entire diversity of benthic eukaryotes in three distinct habitats (littoral sediment and hard substrate, profundal sediment) of Lake Ohrid, the oldest European lake. Eukaryotic sequences were dominated by annelid and arthropod animals (54% of all eukaryotic reads) and protists (Ochrophyta and Ciliophora; together 40% of all reads). Eukaryotic diversity was 15% higher in the deep profundal than on either near-surface hard substrates or littoral sediments. The three habitats differed in their taxonomic and functional community composition. Specifically, heterotrophic organisms accounted for 92% of the reads in the profundal, whereas phototrophs accounted for 43% on the littoral hard substrate. The profundal community was the most homogeneous, and its network was the most complex, suggesting its highest stability among the sampled habitats.

Soil biota shift with land use change from pristine rainforest and Savannah (Cerrado) to agriculture in southern Amazonia

Southern Amazonia is currently experiencing extensive land use change from forests to agriculture caused by increased local and global demand for agricultural products. However, little is known about the impacts of deforestation and land use change on soil biota. We investigated two regions in southern Amazonia (rainforest and Savannah/Cerrado biomes), analysing soil biota community turnover based on 16S (Archaea and Bacteria) and 18S rRNA genes (Eukaryotes, including Fungi, Protists and Animalia) and correlating them with soil chemistry and land use intensity. We found that soil biota community structure is driven by land use change in both Cerrado and rainforest. Crop fields approximatively doubled the richness of soil Archaea, Bacteria and Protists. We propose that crop systems not only increase soil pH and fertility, but also create continued disturbance (crop seasons) that stimulates soil diversity, as predicted by the dynamic equilibrium model (DEM) and the intermediate disturbance hypothesis (IDH). Even though agricultural fields had higher soil biota richness, some taxa were suppressed by agriculture (6/31 operational taxonomic units of Archaea, 245/1790 of Bacteria, 12/74 of Animalia, 20/144 of Fungi and 25/310 of Protists). Consequently, land use change in this region should proceed with caution. In the southern Amazonia region of Brazil, current laws require farmers to keep 20%-80% pristine vegetation areas on their property. Our data support the relevance of this law: since there are unique soil taxa under native vegetation, keeping these pristine areas adjacent to the agricultural fields should maximize soil biodiversity protection in these regions.

Comparing the long-term responses of soil microbial structures and diversities to polyethylene microplastics in different aggregate fractions

Microplastics (MPs) alter soil aggregation stability. However, studies have yet to determine whether these alterations further affect microbial community structures and diversities within different soil aggregates and whether they influence the responses of soil microbial structures and diversities to MPs in different aggregate fractions. In this study, long-term soil incubation experiments and soil fractionation were combined to investigate the effects of polyethylene microplastics (PE-MPs) on soil aggregate properties and microbial communities in soil aggregates with different particle sizes. Results showed that the existence of PE-MPs significantly reduced the physicochemical properties of soil aggregates, inhibited the activities of soil enzymes, and changed the richness and diversity of bacterial and fungal communities. Such variations exerted notable differences in soil aggregate levels. The response sensitivity of bacteria in the silt and clay fraction was higher than that in the macroaggregate fraction, but the response sensitivity of fungi in the macroaggregate fraction was higher than that in the silt and clay fraction. Relationships and path analysis between soil aggregate properties and microbial communities after PE-MPs addition were proposed. PE-MPs affected microbial community structures by directly and indirectly influencing soil microenvironmental conditions. The relative abundances of Acidobacteria, Gemmatimonadetes, Bacteroides, Basidiomycota, Chtridiomyota, and Glomeromycota were significantly correlated with physicochemical properties and soil enzyme activities. Enzyme activities were direct factors influencing soil microbial community structures, and physicochemical properties (i.e., dissolved organic carbon, soil available phosphorus) could indirectly affect these structures by acting on soil enzyme activities. Our findings helped improve our understanding of the responses of soil microbial structures and diversities to MPs through the perspective of different soil aggregates.

Genomic Features of Parthenogenetic Animals

Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.

Soil biodiversity enhances the persistence of legumes under climate change

Global environmental change poses threats to plant and soil biodiversity. Yet, whether soil biodiversity loss can further influence plant community's response to global change is still poorly understood. We created a gradient of soil biodiversity using the dilution-to-extinction approach, and investigated the effects of soil biodiversity loss on plant communities during and following manipulations simulating global change disturbances in experimental grassland microcosms. Grass and herb biomass was decreased by drought and promoted by nitrogen deposition, and a fast recovery was observed following disturbances, independently of soil biodiversity loss. Warming promoted herb biomass during and following disturbance only when soil biodiversity was not reduced. However, legumes biomass was suppressed by these disturbances, and there were more detrimental effects with reduced soil biodiversity. Moreover, soil biodiversity loss suppressed the recovery of legumes following these disturbances. Similar patterns were found for the response of plant diversity. The changes in legumes might be partly attributed to the loss of mycorrhizal soil mutualists. Our study shows that soil biodiversity is crucial for legume persistence and plant diversity maintenance when faced with environmental change, highlighting the importance of soil biodiversity as a potential buffering mechanism for plant diversity and community composition in grasslands.

An invasive plant rapidly increased the similarity of soil fungal pathogen communities

BACKGROUND AND AIMS

Plant invasions can change soil microbial communities and affect subsequent invasions directly or indirectly via foliar herbivory. It has been proposed that invaders promote uniform biotic communities that displace diverse, spatially variable communities (the biotic homogenization hypothesis), but this has not been experimentally tested for soil microbial communities, so the underlying mechanisms and dynamics are unclear. Here, we compared density-dependent impacts of the invasive plant Alternanthera philoxeroides and its native congener A. sessilis on soil fungal communities, and their feedback effects on plants and a foliar beetle.

METHODS

We conducted a plant-soil feedback (PSF) experiment and a laboratory bioassay to examine PSFs associated with the native and invasive plants and a beetle feeding on them. We also characterized the soil fungal community using high-throughput sequencing.

KEY RESULTS

We found locally differentiated soil fungal pathogen assemblages associated with high densities of the native plant A. sessilis but little variation in those associated with the invasive congener A. philoxeroides, regardless of plant density. In contrast, arbuscular mycorrhizal fungal assemblages associated with high densities of the invasive plant were more variable. Soil biota decreased plant shoot mass but their effect was weak for the invasive plant growing in native plant-conditioned soils. PSFs increased the larval biomass of a beetle reared on leaves of the native plant only. Moreover, PSFs on plant shoot and root mass and beetle mass were predicted by different pathogen taxa in a plant species-specific manner.

CONCLUSION

Our results suggest that plant invasions can rapidly increase the similarity of soil pathogen assemblages even at low plant densities, leading to taxonomically and functionally homogeneous soil communities that may limit negative soil effects on invasive plants.

Functional Diversity of Soil Nematodes in Relation to the Impact of Agriculture—A Review

The analysis of the functional diversity of soil nematodes requires detailed knowledge on theoretical aspects of the biodiversity–ecosystem functioning relationship in natural and managed terrestrial ecosystems. Basic approaches applied are reviewed, focusing on the impact and value of soil nematode diversity in crop production and on the most consistent external drivers affecting their stability. The role of nematode trophic guilds in two intensively cultivated crops are examined in more detail, as representative of agriculture from tropical/subtropical (banana) and temperate (apple) climates. The multiple facets of nematode network analysis, for management of multitrophic interactions and restoration purposes, represent complex tasks that require the integration of different interdisciplinary expertise. Understanding the evolutionary basis of nematode diversity at the field level, and its response to current changes, will help to explain the observed community shifts. Integrating approaches based on evolutionary biology, population genetics and ecology can quantify the contribution of nematode fauna to fundamental soil functions. These include carbon transformation, nutrient cycling, pest control and disease transmission. In conclusion, different facets of nematode diversity such as trophic groups, life history traits, variability in body size and/or taxa identities in combination with DNA-based techniques are needed in order to disclose nematode–soil–ecosystem functioning relationships. Further experimental studies are required to define locally adapted and sustainable management practices, through ecosystem-based approaches and nature-based solutions.

The role of soil in defining planetary boundaries and the safe operating space for humanity

We use soils to provide 98.8% of our food, but we must ensure that the pressure we place on soils to provide this food in the short-term does not inadvertently push the Earth into a less hospitable state in the long-term. Using the planetary boundaries framework, we show that soils are a master variable for regulating critical Earth-system processes. Indeed, of the seven Earth-systems that have been quantified, soils play a critical and substantial role in changing the Earth-systems in at least two, either directly or indirectly, as well as smaller contributions for a further three. For the biogeochemical flows Earth-system process, soils contribute 66% of the total anthropogenic change for nitrogen and 38% for phosphorus, whilst for the land-system change Earth-system process, soils indirectly contribute 80% of global anthropogenic change. Furthermore, perturbations of soils contribute directly to 21% of climate change, 25% to ocean acidification, and 25% to stratospheric ozone depletion. We argue that urgent interventions are required to greatly improve soil management, especially for those Earth-system processes where the planetary boundary has already been exceeded and where soils make an important contribution, with this being for biogeochemical flows (both nitrogen and phosphorus), for climate change, and for land-system change. Of particular importance, it is noted that the highly inefficient use of N fertilizers results in release of excess N into the broader environment, contributes to climate change, and results in release of ozone-depleting substances. Furthermore, the use of soils for agricultural production results not only in land-system change, but also in the loss (mineralization) of organic matter with a concomitant release of CO₂ contributing to both climate change and ocean acidification. Thus, there is a need to markedly improve the efficiency of fertilizer applications and to intensify usage of our most fertile soils in order to allow the restoration of degraded soils and limit further areal expansion of agriculture. Understanding, and acting upon, the role of soils is critical in ensuring that planetary boundaries are not transgressed, with no other single variable playing such a strategic role across all of the planetary boundaries.

Microplastics in soils: A review of methods, occurrence, fate, transport, ecological and environmental risks

The global prevalence of microplastics (MPs) poses a potential threat and unpredictable risk to the function and health of environmental systems. However, the research progress of soil MPs is restricted by the inherent technical inconformity and difficulties in analyzing particles in complex matrices. Here, we reviewed a selection of papers and then extrapolated a tentative standardized method for such analyses. The multiple sources of soil MPs in soil need to be quantified. Global monitoring data of soil MPs is far from sufficient. The interaction between MPs and different properties and environmental factors controls the migration and retention of MPs in soil. The migration behavior and key mechanisms of MPs in real-world environments remain to be determined. The presence of MPs threatens soil microbial-plant-animal ecosystem function and health, and may enter the human body through the food chain, although the extent of these hazards is currently debated. In particular, attention should be paid to the potential transport and ecotoxicological mechanisms of contaminants derived and adsorptive from MPs and of harmful microorganisms (such as pathogens) attached as biofilms. Although there exist preliminary studies on soil MPs, it is urgent to consider the diversity of MPs as a suite of contaminants and to systematically understand the sources, flux and effects of these artificial pollutants in time and space from the perspective of plastic environmental cycle. More comprehensive quantification of their environmental fate is undertaken to identify risks to global human and ecological systems. From the perspective of controlling soil MP pollution, the responsibility assignment of government manage-producer-consumer system and the strategy of remediation should be implemented. This review is helpful for providing an important roadmap and inspiration for the research methods and framework of soil MPs and facilitates the development of waste management and remediation strategies for regional soil MP contamination.

Effects of microplastics and nanoplastics on marine environment and human health

Microplastics (MPs) with an average size of less than 5 mm, along with nanoplastics (NPs) of an average size of fewer than 0.1 μm are the result of huge plastic waste fragmentation or straight environmental emissions. Pollution from micro- and nanoplastics is a worldwide paradigm that raises environmental and human health concerns. They may also comprise very harmful chemicals that are implemented in plants and animals when MPs/NPs are used that may lead to higher accumulation of these compounds in food chains. In addition, higher surface area-to-volume ratio, characteristic of MPs/NPs can contribute to their potentially harmful impact as other pollutants, like continuous organic contaminants, can also be bio-accumulated and adsorbed. A complex issue correlated with MPs/NPs is their ability to absorb and interact with other common pollutants in the environment, such as metals, pharmaceuticals, and other contaminants. Thus, MPs/NPs can directly influence on destiny and toxicity of these substances to the environment and organisms. In this review, first, we introduce possible sources and formation, their destinies, and environmental impact of MPs/NPs and then explain feasible paths of all these particles entering the human body. Then, the review highlights the effect of MPs/NPs on human health. Finally, it provides a brief summary of the potential as well as the neurological toxicity of MPs/NPs.

Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari

High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.

The concept and future prospects of soil health

Soil health is the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals and humans, and connects agricultural and soil science to policy, stakeholder needs and sustainable supply chain management. Historically, soil assessments focused on crop production, but today soil health also includes the role of soil in water quality, climate change and human health. However, quantifying soil health is still dominated by chemical indicators, despite growing appreciation of the importance of soil biodiversity, due to limited functional knowledge and lack of effective methods. In this Perspective, the definition and history of soil health are described and compared to other soil concepts. We outline ecosystem services provided by soils, the indicators used to measure soil functionality, and their integration into informative soil health indices. Scientists should embrace soil health as an overarching principle that contributes to sustainability goals, rather than only a property to measure.

TOC BLURB

Soil health is essential to crop production, but is also key to many ecosystem services. In this Perspective, the definition, impact and quantification of soil health are examined, and the needs in soil health research are outlined.

Microplastics in waters and soils: Occurrence, analytical methods and ecotoxicological effects

Microplastics (MPs) are ubiquitous in the environment and more abundant in the marine environment. Consequently, increasing focus has been put on MPs in oceans and seas, while little importance has been attached to their presence in freshwaters and soils. Therefore, this paper aimed to provide a comprehensive review of the occurrence, analysis and ecotoxicology of MPs. The abundance and distribution of MPs in several typical freshwater systems of China were summarized. It suggested that the surface water of Poyang Lake contained the highest concentration of 34 items/L MPs among all the 8 freshwater systems, and the content of MPs in sediments were higher than that of the surface water. Net-based zooplankton sampling methods are the most frequently utilized sampling methods for MPs, and density separation, elutriation and digestion are three major pretreatment methods. Fourier transform infrared spectroscopy, Raman spectroscopy and pyrolysis-gas chromatography coupled to mass spectrometry are often used to identify the polymer types of MPs. Besides, MPs might damage the digestive tract of various organisms and negatively inhibit their growth, feeding and reproduction. The ways of human exposure to MPs are by ingestion, inhalation and dermal exposure, digestive and respiratory system might be adversely influenced. However, potential health risks of MPs to humans are remained insufficiently researched. Overall, by showing the presence of MPs in freshwaters and soils as well as possible ecotoxicological effects on the environment and humans, this paper provided a framework for future research in this field.

Challenges and Opportunities for Soil Biodiversity in the Anthropocene

Biodiversity on Earth is strongly affected by human alterations to the environment. The majority of studies have considered aboveground biodiversity, yet little is known about whether biodiversity changes belowground follow the same patterns as those observed aboveground. It is now established that communities of soil biota have been substantially altered by direct human activities such as soil sealing, agricultural land-use intensification, and biological invasions resulting from the introduction of non-native species. In addition, altered abiotic conditions resulting from climate change have also impacted soil biodiversity. These changes in soil biodiversity can alter ecosystem functions performed by the soil biota, and therefore, human-induced global changes have a feedback effect on ecosystem services via altered soil biodiversity. Here, we highlight the major phenomena that threaten soil biodiversity, and we propose options to reverse the decline in soil biodiversity. We argue that it is essential to protect soil biodiversity as a rich reservoir that provides insurance against the changes wrought by the Anthropocene. Overall, we need to better understand the determinants of soil biodiversity and how they function, plan to avoid further losses, and restore soil biodiversity where possible. Safeguarding this rich biotic reservoir is essential for soil sustainability and, ultimately, the sustainability of human society.

Altered rhizoctonia assemblages in grasslands on ex-arable land support germination of mycorrhizal generalist, not specialist orchids

Species-rich seminatural grasslands in Central Europe have suffered a dramatic loss of biodiversity due to conversion to arable land, but vast areas are being restored. Population recovery of orchids, which depend on mycorrhizal fungi for germination, is however limited. We hypothesised that ploughing and fertilisation caused shifts in orchid mycorrhizal communities in soil and restricted orchid germination. We examined edaphic conditions in 60 restored and seminatural grasslands, and germination success in 10 restored grasslands. Using a newly designed primer, we screened the composition of rhizoctonias in soil, seedlings and roots of seven orchid species. Seminatural and restored grasslands differed significantly in nutrient amounts and rhizoctonia assemblages in soil. While Serendipitaceae prevailed in seminatural grasslands with a higher organic matter content, Ceratobasidiaceae were more frequent in phosphorus-rich restored grasslands with increased abundance on younger restored sites. Tulasnellaceae displayed no preference. Germination success in restored grasslands differed significantly between orchid species; two mycorrhizal generalist species germinated with a broad range of rhizoctonias at most restored grasslands, while germination success of specialists was low. Past agricultural practices have a long-lasting effect on soil conditions and orchid mycorrhizal communities. Altered mycorrhizal availability may be the main reason for low germination success of specialist orchid species.

Identifying potential threats to soil biodiversity

A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils' ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* "soil biodiversity"), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified emerging threats, particularly microplastics, in the 10 years following these knowledge based rankings. We found that many soil biodiversity studies do not focus on biodiversity sensu stricto, rather these studies examined either changes in abundance and/or diversity of individual groups of soil biota, instead of soil biodiversity as a whole, encompassing all levels of the soil food web. This highlights the complexity of soil biodiversity which is often impractical to assess in all but the largest studies. Published global scientific activity was only partially related to the threats identified by the expert panel assessment. The number of threats and the priority given to the threats (by number of publications) were quite different, indicating a disparity between research actions versus perceived threats. The lack of research effort in key areas of high priority in the threats to soil biodiversity are a concerning finding and requires some consideration and debate in the research community.

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

Source, migration and toxicology of microplastics in soil

Microplastics are emerging contaminants and their presence in water and soil ecosystems has recently drawn considerable attention because they pose a great threat to entire ecosystems. Recent researches have focused on the detection, occurrence, characterization, and toxicology of microplastics in marine and freshwater ecosystems; however, our understanding of the ecological effects of microplastics in soil ecosystems is still limited compared with that in aquatic ecosystems. Here, we have compiled literature, studying the sources, migration of microplastics in soil, negative impacts on soil health and function, trophic transfer in food chains, and the corresponding adverse effects on soil organisms in order to address the potential ecological and human health risks caused by microplastics in soil. This review aims to address gaps in knowledge, shed light on the ecological effects of microplastics in soil, and propose future studies on microplastic pollution and the resultant soil ecotoxicity. Furthermore, this review is focused on limiting microplastics in soil and establishing management and remediation measures to mitigate the risks posed by microplastic pollution.

Global vulnerability of soil ecosystems to erosion

CONTEXT

Soil erosion is one of the main threats driving soil degradation across the globe with important impacts on crop yields, soil biota, biogeochemical cycles, and ultimately human nutrition.

OBJECTIVES

Here, using an empirical model, we present a global and temporally explicit assessment of soil erosion risk according to recent (2001-2013) dynamics of rainfall and vegetation cover change to identify vulnerable areas for soils and soil biodiversity.

METHODS

We used an adaptation of the Universal Soil Loss Equation together with state of the art remote sensing models to create a spatially and temporally explicit global model of soil erosion and soil protection. Finally, we overlaid global maps of soil biodiversity to assess the potential vulnerability of these soil communities to soil erosion.

RESULTS

We show a consistent decline in soil erosion protection over time across terrestrial biomes, which resulted in a global increase of 11.7% in soil erosion rates. Notably, soil erosion risk systematically increased between 2006 and 2013 in relation to the baseline year (2001). Although vegetation cover is central to soil protection, this increase was mostly driven by changes in rainfall erosivity. Globally, soil erosion is expected not only to have an impact on the vulnerability of soil conditions but also on soil biodiversity with 6.4% (for soil macrofauna) and 7.6% (for soil fungi) of these vulnerable areas coinciding with regions with high soil biodiversity.

CONCLUSIONS

Our results indicate that an increasing proportion of soils are degraded globally, affecting not only livelihoods but also potentially degrading local and regional landscapes. Similarly, many degraded regions coincide with and may have impacted high levels of soil biodiversity.

A framework to bridge scales in distribution modeling of soil microbiota

Creating accurate habitat suitability and distribution models (HSDMs) for soil microbiota is far more challenging than for aboveground organism groups. In this perspective paper, we propose a conceptual framework that addresses several of the critical issues holding back further applications. Most importantly, we tackle the mismatch between the broadscale, long-term averages of environmental variables traditionally used, and the environment as experienced by soil microbiota themselves. We suggest using nested sampling designs across environmental gradients and objectively integrating spatially hierarchic heterogeneity as covariates in HSDMs. Second, to incorporate the crucial role of taxa co-occurrence as driver of soil microbial distributions, we promote the use of joint species distribution models, a class of models that jointly analyze multiple species’ distributions, quantifying both species-specific environmental responses (i.e. the environmental niche) and covariance among species (i.e. biotic interactions). Our approach allows incorporating the environmental niche and its associated distribution across multiple spatial scales. The proposed framework facilitates the inclusion of the true relationships between soil organisms and their abiotic and biotic environments in distribution models, which is crucial to improve predictions of soil microbial redistributions as a result of global change.

Mixing effect of polylactic acid microplastic and straw residue on soil property and ecological function

Microplastics have become a contaminant of increasing concern in soils. Although biodegradable plastics were considered as alternatives of traditional plastics, some evidence showed that biodegradable plastics might produce more microplastics. Until now, the effect of biodegradable microplastics on soil functions and processes, as well as microbial communities is uncertain. Based on high throughput sequencing, enzymatic activity assay and dynamic analysis of soil carbon and nitrogen, we investigated the effects of biodegradable polylactic acid microplastics (PLA MPs) on soil microbiota and related ecological processes under conditions of high or low carbon content. The results showed that PLA MPs had no significant effect on the overall diversity and composition of bacterial communities or related ecosystem functions and processes. However, co-occurrence network analysis revealed that PLA MPs impacted the interactions between constituent species, which might have legacy effect on soil bacterial communities and functions. Our data also revealed that PLA MPs could trade off the priming effect of carbon source. Our results provided an integrated picture in understanding the effects of PLA MPs on soil microbes, properties and ecological functions, which will help to further understand the effects of MPs on terrestrial ecosystems.

Extinction debt in local habitats: quantifying the roles of random drift, immigration and emigration

We developed a time-dependent stochastic neutral model for predicting diverse temporal trajectories of biodiversity change in response to ecological disturbance (i.e. habitat destruction) and dispersal dynamic (i.e. emigration and immigration). The model is general and predicts how transition behaviours of extinction may accumulate according to a different combination of random drift, immigration rate, emigration rate and the degree of habitat destruction. We show that immigration, emigration, the areal size of the destroyed habitat and initial species abundance distribution (SAD) can impact the total biodiversity loss in an intact local area. Among these, the SAD plays the most deterministic role, as it directly determines the initial species richness in the local target area. By contrast, immigration was found to slow down total biodiversity loss and can drive the emergence of species credits (i.e. a gain of species) over time. However, the emigration process would increase the extinction risk of species and accelerate biodiversity loss. Finally but notably, we found that a shift in the emigration rate after a habitat destruction event may be a new mechanism to generate species credits.

Climate change effects on earthworms - a review

Climate change can have a plethora of effects on organisms above and below the ground in terrestrial ecosystems. Given the tremendous biodiversity in the soil and the many ecosystem functions governed by soil organisms, the drivers of soil biodiversity have received increasing attention. Various climatic factors like temperature, precipitation, soil moisture, as well as extreme climate events like drought and flood have been shown to alter the composition and functioning of communities in the soil. Earthworms are important ecosystem engineers in the soils of temperate and tropical climates and play crucial roles for many ecosystem services, including decomposition, nutrient cycling, and crop yield. Here, we review the published literature on climate change effects on earthworm communities and activity. In general, we find highly species- and ecological group-specific responses to climate change, which are likely to result in altered earthworm community composition in future ecosystems. Earthworm activity, abundance, and biomass tend to increase with increasing temperature at sufficiently high soil water content, while climate extremes like drought and flooding have deleterious effects. Changing climate conditions may facilitate the invasion of earthworms at higher latitudes and altitudes, while dryer and warmer conditions may limit earthworm performance in other regions of the world. The present summary of available information provides a first baseline for predictions of future earthworm distribution. It also reveals the shortage of studies on interacting effects of multiple global change effects on earthworms, such as potential context-dependent effects of climate change at different soil pollution levels and across ecosystem types.