Heterogeneous data integration methods for patient similarity networks.

Patient similarity networks (PSNs), where patients are represented as nodes and their similarities as weighted edges, are being increasingly used in clinical research. These networks provide an insightful summary of the relationships among patients and can be exploited by inductive or transductive learning algorithms for the prediction of patient outcome, phenotype and disease risk. PSNs can also be easily visualized, thus offering a natural way to inspect complex heterogeneous patient data and providing some level of explainability of the predictions obtained by machine learning algorithms. The advent of high-throughput technologies, enabling us to acquire high-dimensional views of the same patients (e.g. omics data, laboratory data, imaging data), calls for the development of data fusion techniques for PSNs in order to leverage this rich heterogeneous information. In this article, we review existing methods for integrating multiple biomedical data views to construct PSNs, together with the different patient similarity measures that have been proposed. We also review methods that have appeared in the machine learning literature but have not yet been applied to PSNs, thus providing a resource to navigate the vast machine learning literature existing on this topic. In particular, we focus on methods that could be used to integrate very heterogeneous datasets, including multi-omics data as well as data derived from clinical information and medical imaging.

State-Interaction Approach for Evaluating g-Tensors within EOM-CC and RAS-CI Frameworks: Theory and Benchmarks.

Among various techniques designed for studying open-shell species, electron paramagnetic resonance (EPR) spectroscopy plays an important role. The key quantity measured by EPR is the g-tensor, describing the coupling between an external magnetic field and molecular electronic spin. One theoretical framework for quantum chemistry calculations of g-tensors is based on response theory, which involves substantial developments that are specific to the underlying electronic structure models. A simplified and easier-to-implement approach is based on the state-interaction scheme, in which perturbation is included by considering a small number of states. We describe and benchmark the state-interaction approach using equation-of-motion coupled-cluster and restricted-active-space configuration interaction wave functions. The analysis confirms that this approach can deliver accurate results and highlights caveats of applying it, such as a choice of the reference state, convergence with respect to the number of states used in calculations, etc. The analysis also contributes toward a better understanding of challenges in calculations of higher-order properties using approximate wave functions.

Toxic effects of nanomaterials for health applications: How automation can support a systematic review of the literature?

Systematic reviews of the scientific literature can be an important source of information supporting the daily work of the regulators in their decision making, particularly in areas of innovative technologies where the regulatory experience is still limited. Significant research activities in the field of nanotechnology resulted in a huge number of publications in the last decades. However, even if the published data can provide relevant information, scientific articles are often of diverse quality, and it is nearly impossible to manually process and evaluate such amount of data in a systematic manner. In this feasibility study, we investigated to what extent open-access automation tools can support a systematic review of toxic effects of nanomaterials for health applications reported in the scientific literature. In this study, we used a battery of available tools to perform the initial steps of a systematic review such as targeted searches, data curation and abstract screening. This work was complemented with an in-house developed tool that allowed us to extract specific sections of the articles such as the materials and methods part or the results section where we could perform subsequent text analysis. We ranked the articles according to quality criteria based on the reported nanomaterial characterisation and extracted most frequently described toxic effects induced by different types of nanomaterials. Even if further demonstration of the reliability and applicability of automation tools is necessary, this study demonstrated the potential to leverage information from the scientific literature by using automation systems in a tiered strategy.

Changes in belowground biodiversity during ecosystem development.

Belowground organisms play critical roles in maintaining multiple ecosystem processes, including plant productivity, decomposition, and nutrient cycling. Despite their importance, however, we have a limited understanding of how and why belowground biodiversity (bacteria, fungi, protists, and invertebrates) may change as soils develop over centuries to millennia (pedogenesis). Moreover, it is unclear whether belowground biodiversity changes during pedogenesis are similar to the patterns observed for aboveground plant diversity. Here we evaluated the roles of resource availability, nutrient stoichiometry, and soil abiotic factors in driving belowground biodiversity across 16 soil chronosequences (from centuries to millennia) spanning a wide range of globally distributed ecosystem types. Changes in belowground biodiversity during pedogenesis followed two main patterns. In lower-productivity ecosystems (i.e., drier and colder), increases in belowground biodiversity tracked increases in plant cover. In more productive ecosystems (i.e., wetter and warmer), increased acidification during pedogenesis was associated with declines in belowground biodiversity. Changes in the diversity of bacteria, fungi, protists, and invertebrates with pedogenesis were strongly and positively correlated worldwide, highlighting that belowground biodiversity shares similar ecological drivers as soils and ecosystems develop. In general, temporal changes in aboveground plant diversity and belowground biodiversity were not correlated, challenging the common perception that belowground biodiversity should follow similar patterns to those of plant diversity during ecosystem development. Taken together, our findings provide evidence that ecological patterns in belowground biodiversity are predictable across major globally distributed ecosystem types and suggest that shifts in plant cover and soil acidification during ecosystem development are associated with changes in belowground biodiversity over centuries to millennia.

Climatic vulnerabilities and ecological preferences of soil invertebrates across biomes.

Unlike plants and vertebrates, the ecological preferences, and potential vulnerabilities of soil invertebrates to environmental change, remain poorly understood in terrestrial ecosystems globally. We conducted a cross-biome survey including 83 locations across six continents to advance our understanding of the ecological preferences and vulnerabilities of the diversity of dominant and functionally important soil invertebrate taxa, including nematodes, arachnids and rotifers. The diversity of invertebrates was analyzed through amplicon sequencing. Vegetation and climate drove the diversity and dominant taxa of soil invertebrates. Our results suggest that declines in forest cover and plant diversity, and reductions in plant production associated with increases in aridity, can result in reductions of the diversity of soil invertebrates in a drier and more managed world. We further developed global atlases of the diversity of these important soil invertebrates, which were cross-validated using an independent database. Our study advances the current knowledge of the ecological preferences and vulnerabilities of the diversity and presence of functionally important soil invertebrates in soils from across the globe. This information is fundamental for improving and prioritizing conservation efforts of soil genetic resources and management policies.

Decoupling of soil nutrient cycles as a function of aridity in global drylands.

The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems. It has been suggested that the C, N and P cycles could become uncoupled under rapid climate change because of the different degrees of control exerted on the supply of these elements by biological and geochemical processes. Climatic controls on biogeochemical cycles are particularly relevant in arid, semi-arid and dry sub-humid ecosystems (drylands) because their biological activity is mainly driven by water availability. The increase in aridity predicted for the twenty-first century in many drylands worldwide may therefore threaten the balance between these cycles, differentially affecting the availability of essential nutrients. Here we evaluate how aridity affects the balance between C, N and P in soils collected from 224 dryland sites from all continents except Antarctica. We find a negative effect of aridity on the concentration of soil organic C and total N, but a positive effect on the concentration of inorganic P. Aridity is negatively related to plant cover, which may favour the dominance of physical processes such as rock weathering, a major source of P to ecosystems, over biological processes that provide more C and N, such as litter decomposition. Our findings suggest that any predicted increase in aridity with climate change will probably reduce the concentrations of N and C in global drylands, but increase that of P. These changes would uncouple the C, N and P cycles in drylands and could negatively affect the provision of key services provided by these ecosystems.

Increasing aridity reduces soil microbial diversity and abundance in global drylands.

Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

Structure and functioning of dryland ecosystems in a changing world.

Understanding how drylands respond to ongoing environmental change is extremely important for global sustainability. Here we review how biotic attributes, climate, grazing pressure, land cover change and nitrogen deposition affect the functioning of drylands at multiple spatial scales. Our synthesis highlights the importance of biotic attributes (e.g. species richness) in maintaining fundamental ecosystem processes such as primary productivity, illustrate how N deposition and grazing pressure are impacting ecosystem functioning in drylands worldwide, and highlight the importance of the traits of woody species as drivers of their expansion in former grasslands. We also emphasize the role of attributes such as species richness and abundance in controlling the responses of ecosystem functioning to climate change. This knowledge is essential to guide conservation and restoration efforts in drylands, as biotic attributes can be actively managed at the local scale to increase ecosystem resilience to global change.

Novel nuclear barcode regions for the identification of flatfish species.

The development of an efficient seafood traceability framework is crucial for the management of sustainable fisheries and the monitoring of potential substitution fraud across the food chain. Recent studies have shown the potential of DNA barcoding methods in this framework, with most of the efforts focusing on using mitochondrial targets such as the cytochrome oxidase 1 and cytochrome b genes. In this article, we show the identification of novel targets in the nuclear genome, and their associated primers, to be used for the efficient identification of flatfishes of the Pleuronectidae family. In addition, different in silico methods are described to generate a dataset of barcode reference sequences from the ever-growing wealth of publicly available sequence information, replacing, where possible, labour-intensive laboratory work. The short amplicon lengths render the analysis of these new barcode target regions ideally suited to next-generation sequencing techniques, allowing characterisation of multiple fish species in mixed and processed samples. Their location in the nucleus also improves currently used methods by allowing the identification of hybrid individuals.

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community.

Parasitic plants are important drivers of community and ecosystem properties. In this study, we identify different mechanisms by which mistletoe (Viscum album subsp. austriacum) can affect soil chemical and biological properties at different temporal stages of parasitism. We quantified the effect of parasitism on host growth and the number of frugivorous mutualists visiting the host canopy. Then we collected, identified, and weighed the organic matter input underneath tree canopies and analyzed its nutrient content. Simultaneously, we analyzed soil samples under tree canopies and examined the chemical properties, microbial abundance, and functional evenness of heterotrophic microbial communities. Mistletoe increased the amount, quality, and diversity of organic matter input beneath the host canopy, directly through its nutrient-rich litter and indirectly through a reduction in host litterfall and an increase in bird-derived debris. All these effects gave rise to enriched hotspots able to support larger and more functionally even soil microbial communities beneath parasitized hosts, the effects of which were accentuated after host death. We conclude that mistletoe, together with the biotic interactions it mediates, plays a key role in intensifying soil resource availability, regulating the functional evenness, abundance, and spatial distribution of soil microbial communities.

Intransitive competition is widespread in plant communities and maintains their species richness.

Intransitive competition networks, those in which there is no single best competitor, may ensure species coexistence. However, their frequency and importance in maintaining diversity in real-world ecosystems remain unclear. We used two large data sets from drylands and agricultural grasslands to assess: (1) the generality of intransitive competition, (2) intransitivity-richness relationships and (3) effects of two major drivers of biodiversity loss (aridity and land-use intensification) on intransitivity and species richness. Intransitive competition occurred in > 65% of sites and was associated with higher species richness. Intransitivity increased with aridity, partly buffering its negative effects on diversity, but was decreased by intensive land use, enhancing its negative effects on diversity. These contrasting responses likely arise because intransitivity is promoted by temporal heterogeneity, which is enhanced by aridity but may decline with land-use intensity. We show that intransitivity is widespread in nature and increases diversity, but it can be lost with environmental homogenisation.

Nitrogen supply modulates the effect of changes in drying-rewetting frequency on soil C and N cycling and greenhouse gas exchange.

Climate change and atmospheric nitrogen (N) deposition are two of the most important global change drivers. However, the interactions of these drivers have not been well studied. We aimed to assess how the combined effect of soil N additions and more frequent soil drying-rewetting events affects carbon (C) and N cycling, soil:atmosphere greenhouse gas (GHG) exchange, and functional microbial diversity. We manipulated the frequency of soil drying-rewetting events in soils from ambient and N-treated plots in a temperate forest and calculated the Orwin & Wardle Resistance index to compare the response of the different treatments. Increases in drying-rewetting cycles led to reductions in soil NO3- levels, potential net nitrification rate, and soil : atmosphere GHG exchange, and increases in NH4+ and total soil inorganic N levels. N-treated soils were more resistant to changes in the frequency of drying-rewetting cycles, and this resistance was stronger for C- than for N-related variables. Both the long-term N addition and the drying-rewetting treatment altered the functionality of the soil microbial population and its functional diversity. Our results suggest that increasing the frequency of drying-rewetting cycles can affect the ability of soil to cycle C and N and soil : atmosphere GHG exchange and that the response to this increase is modulated by soil N enrichment.

Factors determining waste generation in Spanish towns and cities.

This paper analyzes the generation and composition of municipal solid waste in Spanish towns and cities with more than 5000 inhabitants, which altogether account for 87% of the Spanish population. To do so, the total composition and generation of municipal solid waste fractions were obtained from 135 towns and cities. Homogeneity tests revealed heterogeneity in the proportions of municipal solid waste fractions from one city to another. Statistical analyses identified significant differences in the generation of glass in cities of different sizes and in the generation of all fractions depending on the hydrographic area. Finally, linear regression models and residuals analysis were applied to analyze the effect of different demographic, geographic, and socioeconomic variables on the generation of waste fractions. The conclusions show that more densely populated towns, a hydrographic area, and cities with over 50,000 inhabitants have higher waste generation rates, while certain socioeconomic variables (people/car) decrease that generation. Other socioeconomic variables (foreigners and unemployment) show a positive and null influence on that waste generation, respectively.

Plant diversity and ecosystem multifunctionality peak at intermediate levels of woody cover in global drylands.

AIM: The global spread of woody plants into grasslands is predicted to increase over the coming century. While there is general agreement regarding the anthropogenic causes of this phenomenon, its ecological consequences are less certain. We analyzed how woody vegetation of differing cover affects plant diversity (richness and evenness) and multiple ecosystem functions (multifunctionality) in global drylands, and how this changes with aridity. LOCATION: 224 dryland sites from all continents except Antarctica widely differing in their environmental conditions (from arid to dry-subhumid sites) and woody covers (from 0 to 100%). METHODS: Using a standardized field survey, we measured the cover, richness and evenness of perennial vegetation. At each site, we measured 14 ecosystem functions related to soil fertility and the build-up of nutrient pools. These functions are critical for maintaining ecosystem function in drylands. RESULTS: Species richness and ecosystem multifunctionality were strongly influenced by woody vegetation, with both variables peaking at relative woody covers (RWC) of 41-60%. This relationship shifted with aridity. We observed linear positive effects of RWC in dry-subhumid sites. These positive trends shifted to hump-shaped RWC-diversity and multifunctionality relationships under semiarid environments. Finally, hump-shaped (richness, evenness) or linear negative (multifunctionality) effects of RWC were found under the most arid conditions. MAIN CONCLUSIONS: Plant diversity and multifunctionality peaked at intermediate levels of woody cover, although this relationship became increasingly positive under wetter environments. This comprehensive study accounts for multiple ecosystem attributes across a range of woody covers and environmental conditions. Our results help us to reconcile contrasting views of woody encroachment found in current literature and can be used to improve predictions of the likely effects of encroachment on biodiversity and ecosystem services.

Changes in biocrust cover drive carbon cycle responses to climate change in drylands.

Dryland ecosystems account for ca. 27% of global soil organic carbon (C) reserves, yet it is largely unknown how climate change will impact C cycling and storage in these areas. In drylands, soil C concentrates at the surface, making it particularly sensitive to the activity of organisms inhabiting the soil uppermost levels, such as communities dominated by lichens, mosses, bacteria and fungi (biocrusts). We conducted a full factorial warming and rainfall exclusion experiment at two semiarid sites in Spain to show how an average increase of air temperature of 2-3 °C promoted a drastic reduction in biocrust cover (ca. 44% in 4 years). Warming significantly increased soil CO2 efflux, and reduced soil net CO2 uptake, in biocrust-dominated microsites. Losses of biocrust cover with warming through time were paralleled by increases in recalcitrant C sources, such as aromatic compounds, and in the abundance of fungi relative to bacteria. The dramatic reduction in biocrust cover with warming will lessen the capacity of drylands to sequester atmospheric CO2 . This decrease may act synergistically with other warming-induced effects, such as the increase in soil CO2 efflux and the changes in microbial communities to alter C cycling in drylands, and to reduce soil C stocks in the mid to long term.

Removal of mercury bonded in residual glass from spent fluorescent lamps.

The current technologies available for recycling fluorescent lamps do not completely remove the phosphor powder attached to the surface of the glass. Consequently, the glass contains the mercury diffused through the glass matrix and the mercury deposited in the phosphor powder that has not been removed during treatment at the recycling plant. A low-cost process, with just one stage, which can be used to remove the layer of phosphor powder attached to the surface of the glass and its mercury was studied. Several stirring tests were performed with different extraction mixtures, different liquid-solid ratios, and different agitation times. The value of the initial mercury concentration of the residual glass was 2.37 ± 0.50 µg/g. The maximum extraction percentage was 68.38%, obtained by stirring for 24 h with a liquid-solid ratio of 10 and using an extraction solution with 5% of an acid mixture prepared with HCl and HNO(3) at a ratio of 3:1 by volume. On an industrial scale the contact time could be reduced to 8 h without significantly lowering the percentage of mercury extracted. In fact, 64% of the mercury was extracted.

Influence of organic matter transformations on the bioavailability of heavy metals in a sludge based compost.

The agricultural use of anaerobically digested sewage sludge (ADSS) as stable, mature compost implies knowing its total content in heavy metals and their bioavailability. This depends not only on the initial characteristics of the composted substrates but also on the organic matter transformations during composting which may influence the chemical form of the metals and their bioavailability. The objective of this work was to examine the relationships between the changes in the organic matter content and humus fractions, and the bioavailability of heavy metals. A detailed sampling at 0, 14, 84, and 140 days of the composting process was performed to measure C contents in humic acids (HAs), fulvic acids, (FAs) and humin, the total content of Zn, Pb, Cu, Ni, and Cd, and also their distribution into mobile and mobilisable (MB), and low bioavailability (LB) forms. Significant changes of C contents in HA, FA, and Humin, and in the FA/HA, HA/Humin and C(humus)/TOC ratios were observed during composting. The MB and LB fractions of each metal also varied significantly during composting. The MB fraction increased for Zn, Cu, Ni, and Cd, and the LB fraction increased for Pb. Stepwise linear regressions and quadratic curve estimation conducted on the MB and LB fractions of each metal as dependent on the measured organic variables suggested that Zn bioavailability was mainly associated to percentage of C in FAs. Bioavailability of Cu, Ni and Cd during composting was associated to humin and HAs. Pb concentration increased in the LB form, and its variations followed a quadratic function with the C(humus)/TOC ratio. Our results suggest that the composting process renders the metals in more available forms. The main forms of metal binding in the sludge and their availability in the final compost may be better described when metal fractionation obtained in sequential extraction and humus fractionation during composting are considered together.

Evolution of sorted waste collection: a case study of Spanish cities.

This work analyses how selective collection evolved over the period 1998-2007 in Spanish towns and cities with more than 50 000 inhabitants. To do so, both the legislation in force during the years included in the study and logistic factors, such as the radius of action of the pick-up points, were taken into account. Information about the towns and cities was obtained from a survey sent out in 1998 and 2007 to the councils of the municipalities included in the study. The results obtained in the two years show that the most widely implemented separate collection system in 1998 no longer existed in 2007 but, in order to comply with the law, had been transformed by adding new fractions, above all that of lightweight packaging. To determine whether the targets set by law as regards recovery and recycling were met in the two years, an efficiency indicator was used to evaluate the effectiveness of the collection systems. Results show how separation increased in the paper/board and glass fractions.

Biocrusts increase the resistance to warming-induced increases in topsoil P pools.

Ongoing global warming and alterations in rainfall patterns driven by climate change are known to have large impacts on biogeochemical cycles, particularly on drylands. In addition, the global increase in atmospheric nitrogen (N) deposition can destabilize primary productivity in terrestrial ecosystems, and phosphorus (P) may become the most limiting nutrient in many terrestrial ecosystems. However, the impacts of climate change on soil P pools in drylands remain poorly understood. Furthermore, it is unknown whether biocrusts, a major biotic component of drylands worldwide, modulate such impacts.Here we used two long-term (8-10 years) experiments conducted in Central (Aranjuez) and SE (Sorbas) Spain to test how a ~2.5°C warming, a ~30% rainfall reduction and biocrust cover affected topsoil (0-1 cm) P pools (non-occluded P, organic P, calcium bound P, occluded P and total P).Warming significantly increased most P pools-except occluded P-in Aranjuez, whereas only augmented non-occluded P in Sorbas. The rainfall reduction treatment had no effect on the soil P pools at any experimental site. Biocrusts increased most soil P pools and conferred resistance to simulated warming for major P pools at both sites, and to rainfall reduction for non-occluded and occluded P in Aranjuez. Synthesis. Our findings provide novel insights on the responses of soil P pools to warming and rainfall reduction, and highlight the importance of biocrusts as modulators of these responses in dryland ecosystems. Our results suggest that the observed negative impacts of warming on dryland biocrust communities will decrease their capacity to buffer changes in topsoil P driven by climate change.

Tanto el calentamiento global en curso como las alteraciones en los patrones de precipitaciones provocados por el cambio climático tienen grandes impactos en los ciclos biogeoquímicos, particularmente en los ecosistemas áridos y semiáridos. Además, el aumento global de la deposición de nitrógeno (N) atmosférico puede desestabilizar la productividad primaria en los ecosistemas terrestres, y el fósforo (P) puede convertirse en el nutriente más limitante en muchos de estos ecosistemas. Sin embargo, los impactos del cambio climático en las reservas de P del suelo en los ecosistemas áridos y semiáridos siguen sin comprenderse totalmente. Además, se desconoce si la costra biológica del suelo, un componente biótico importante de los ecosistemas áridos y semiáridos en todo el mundo, modulan tales impactos.Utilizamos dos experimentos a largo plazo (8­10 años) ubicados en el centro (Aranjuez) y el sureste (Sorbas) de España para probar cómo el calentamiento de ~2,5°C, la reducción de las precipitaciones de ~30 % y la cobertura de costra biológica afectaron los pools de P (P no ocluido, P orgánico, P ligado al calcio, P ocluido y P total) de la capa superior del suelo (0­1 cm).El calentamiento aumentó significativamente la mayoría de los pools de P ­excepto el P ocluido­ en Aranjuez, mientras que solo aumentó el P no ocluido en Sorbas. El tratamiento de reducción de las precipitaciones no tuvo efecto en los pools de P del suelo en ningún sitio experimental. La costra biológica aumentó la mayoría de los depósitos de P del suelo y confirieron resistencia al calentamiento simulado para los principales pools de P en ambos sitios, y a la reducción de las precipitaciones para el P no ocluido y ocluido en Aranjuez. Síntesis. Nuestros hallazgos brindan información novedosa sobre las respuestas de los pools de P del suelo al calentamiento y la reducción de las precipitaciones, y resaltan la importancia de la costra biológica como moduladora de estas respuestas en los ecosistemas áridos y semiáridos. Nuestros resultados sugieren que los impactos negativos observados del calentamiento en las comunidades de costra biológica de los ecosistemas áridos y semiáridos disminuirán su capacidad para amortiguar los cambios en el P del suelo provocados por el cambio climático.

The global distribution and environmental drivers of the soil antibiotic resistome.

BACKGROUND: Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. RESULTS: We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. CONCLUSIONS: Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.