Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide

Synergistic removal of total petroleum hydrocarbons and antibiotic resistance genes in Yellow River Delta wetlands contaminated soil composting regulated by biogas slurry addition

The interactive effects between the emerging contaminant antibiotic resistance genes (ARGs) and the traditional pollutant total petroleum hydrocarbons (TPHs) in contaminated soils remain unclear. The synergistic removal of TPHs and ARGs from composted contaminated soil, along with the microbial mechanisms driven by the addition of biogas slurry, have not yet been investigated. This study explored the impact of biogas slurry on the synergistic degradation mechanisms and bacterial community dynamics of ARGs and TPHs in compost derived from contaminated soil. The addition of biogas slurry resulted in a reduction of targeted ARGs and mobile genetic elements (MGEs) by 9.96%-95.70% and 13.32%-97.66%, respectively. Biogas slurry changed the succession of bacterial communities during composting, thereby reducing the transmission risk of ARGs. Pseudomonas, Cellvibrio, and Devosia were identified as core microorganisms in the synergistic degradation of ARGs and TPHs. According to the partial least squares path model, temperature and NO3- indirectly influenced the removal of ARGs and TPHs by directly regulating the abundance and composition of host microbes and MGEs. In summary, the results of this study contribute to the high-value utilization of biogas slurry and provide methodological support for the low-cost remediation of contaminated soils.

Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome

Antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) coexist in organic fertilized agroecosystems based on their correlations in abundance, yet evidence for the genetic linkage of ARG-MRGs co-selected by organic fertilization remains elusive. Here, an analysis of 511 global agricultural soil metagenomes reveals that organic fertilization correlates with a threefold increase in the number of diverse types of ARG-MRG-carrying contigs (AMCCs) in the microbiome (63 types) compared to non-organic fertilized soils (22 types). Metatranscriptomic data indicates increased expression of AMCCs under higher arsenic stress, with co-regulation of the ARG-MRG pairs. Organic fertilization heightens the coexistence of ARG-MRG in genomic elements through impacting soil properties and ARG and MRG abundances. Accordingly, a comprehensive global map was constructed to delineate the distribution of coexistent ARG-MRGs with virulence factors and mobile genes in metagenome-assembled genomes from agricultural lands. The map unveils a heightened relative abundance and potential pathogenicity risks (range of 4-6) for the spread of coexistent ARG-MRGs in Central North America, Eastern Europe, Western Asia, and Northeast China compared to other regions, which acquire a risk range of 1-3. Our findings highlight that organic fertilization co-selects genetically linked ARGs and MRGs in the global soil microbiome, and underscore the need to mitigate the spread of these co-resistant genes to safeguard public health.

A multivariate analysis of microplastics in soils along the headwaters of Yangtze river on the Tibetan Plateau

Microplastics (MPs) are among the most widespread anthropogenic pollutants of natural environments, while limited research has focused on the fate of MPs in soils along the Plateau rivers. In this study, we investigated MPs in soils along the source areas of the Yangtze River on the Qinghai-Tibet Plateau. The results showed mean MP abundance values of (89.4 ± 51.0) and (64.4 ± 24.5) items/kg of dry soils around the tributary and mainstream areas, respectively. Film, transparent colors, and polyethylene were common shape, color, and compositions, respectively. The correlation analysis and PCA revealed that MP abundance was related to soil heavy metals (Cr and Ni) and nutrients (TOC and TP) (p < 0.05). Structural equation modeling also revealed that population density was the dominant driving factor contributing to MPs, with a total effect coefficient of 0.45. In addition, the conditional fragmentation model further distinguished the differences in MP sources from upstream to downstream along the Jinsha River. The significant sources of MPs in the bare land and grasslands from the upper reaches of the Jinsha River included traffic, tourism, and atmospheric transport. In contrast, MP transport during farming activities mainly contributed to MPs in the agricultural soil in the lower reaches.

A Deep Learning Approach for Chromium Detection and Characterization from Soil Hyperspectral Data

High levels of chromium (Cr) in soil pose a significant threat to both humans and the environment. Laboratory-based chemical analysis methods for Cr are time consuming and expensive; thus, there is an urgent need for a more efficient method for detecting Cr in soil. In this study, a deep neural network (DNN) approach was applied to the Land Use and Cover Area frame Survey (LUCAS) dataset to develop a hyperspectral soil Cr content prediction model with good generalizability and accuracy. The optimal DNN model was constructed by optimizing the spectral preprocessing methods and DNN hyperparameters, which achieved good predictive performance for Cr detection, with a correlation coefficient value of 0.79 on the testing set. Four important hyperspectral bands with strong Cr sensitivity (400-439, 1364-1422, 1862-1934, and 2158-2499 nm) were identified by permutation importance and local interpretable model-agnostic explanations. Soil iron oxide and clay mineral content were found to be important factors influencing soil Cr content. The findings of this study provide a feasible method for rapidly determining soil Cr content from hyperspectral data, which can be further refined and applied to large-scale Cr detection in the future.

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

Systemic stomatal responses in plants: Coordinating development, stress, and pathogen defense under a changing climate

To successfully survive, develop, grow and reproduce, multicellular organisms must coordinate their molecular, physiological, developmental and metabolic responses among their different cells and tissues. This process is mediated by cell-to-cell, vascular and/or volatile communication, and involves electric, chemical and/or hydraulic signals. Within this context, stomata serve a dual role by coordinating their responses to the environment with their neighbouring cells at the epidermis, but also with other stomata present on other parts of the plant. As stomata represent one of the most important conduits between the plant and its above-ground environment, as well as directly affect photosynthesis, respiration and the hydraulic status of the plant by controlling its gas and vapour exchange with the atmosphere, coordinating the overall response of stomata within and between different leaves and tissues plays a cardinal role in plant growth, development and reproduction. Here, we discuss different examples of local and systemic stomatal coordination, the different signalling pathways that mediate them, and the importance of systemic stomatal coordination to our food supply, ecosystems and weather patterns, under our changing climate. We further discuss the potential biotechnological implications of regulating systemic stomatal responses for enhancing agricultural productivity in a warmer and CO2 -rich environment.

Interaction of microplastics with heavy metals in soil: Mechanisms, influencing factors and biological effects

Microplastics (MPs) and heavy metals (HMs) in soil contamination are considered an emerging global problem that poses environmental and health risks. However, their interaction and potential biological effects remain unclear. Here, we reviewed the interaction of MPs with HMs in soil, including its mechanisms, influencing factors and biological effects. Specifically, the interactions between HMs and MPs mainly involve sorption and desorption. The type, aging, concentration, size of MPs, and the physicochemical properties of HMs and soil have significant impacts on the interaction. In particular, MP aging affects specific surface areas and functional groups. Due to the small size and resistance to decomposition characteristics of MPs, they are easily transported through the food chain and exhibit combined biological effects with HMs on soil organisms, thus accumulating in the human body. To comprehensively understand the effect of MPs and HMs in soil, we propose combining traditional experiments with emerging technologies and encouraging more coordinated efforts.

The impact of multifactorial stress combination on plants, crops, and ecosystems: how should we prepare for what comes next?

The complexity of environmental conditions encountered by plants in the field, or in nature, is gradually increasing due to anthropogenic activities that promote global warming, climate change, and increased levels of pollutants. While in the past it seemed sufficient to study how plants acclimate to one or even two different stresses affecting them simultaneously, the complex conditions developing on our planet necessitate a new approach of studying stress in plants: Acclimation to multiple stress conditions occurring concurrently or consecutively (termed, multifactorial stress combination [MFSC]). In an initial study of the plant response to MFSC, conducted with Arabidopsis thaliana seedlings subjected to an MFSC of six different abiotic stresses, it was found that with the increase in the number and complexity of different stresses simultaneously impacting a plant, plant growth and survival declined, even if the effects of each stress involved in such MFSC on the plant was minimal or insignificant. In three recent studies, conducted with different crop plants, MFSC was found to have similar effects on a commercial rice cultivar, a maize hybrid, tomato, and soybean, causing significant reductions in growth, biomass, physiological parameters, and/or yield traits. As the environmental conditions on our planet are gradually worsening, as well as becoming more complex, addressing MFSC and its effects on agriculture and ecosystems worldwide becomes a high priority. In this review, we address the effects of MFSC on plants, crops, agriculture, and different ecosystems worldwide, and highlight potential avenues to enhance the resilience of crops to MFSC.

Manure application maintained the CO2 fixation activity of soil autotrophic bacteria but changed its ecological characteristics in an entisol of China

The response of soil autotrophs to anthropogenic activities has attracted increasing attention against the background of global change. Here, three entisol plots under different fertilizing regimes, including no fertilization (CK), manure (M), and a combined application of chemical fertilizer and manure (NPKM) were selected, and then the soil RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity and cbbl (gene encoding the large subunit of RubisCO) composition were measured to indicate the activity and community of autotrophic bacteria, respectively. The results revealed that the RubisCO activity of CK showed no difference from that of M but was significantly higher than that of NPKM. The CK and M had the lowest and highest soil cbbl abundance, respectively. The α-diversity of soil cbbl-carrying bacteria showed no significant difference among these treatments, whereas they showed significantly different community structures of cbbl-carrying bacteria. Meanwhile, compared with CK, M had significantly lower abundances of bacterial species with the functions of nitrogen fixation (Azoarcus sp.KH32C) or detoxification (Methylibium petroleiphilum), indicating that manure application might have an inhibiting potential to some beneficial autotrophic bacterial species in this entisol.

A global review on the abundance and threats of microplastics in soils to terrestrial ecosystem and human health

Soil is the source and sink of microplastics (MPs), which is more polluted than water and air. In this paper, the pollution levels of MPs in the agriculture, roadside, urban and landfill soils were reviewed, and the influence of MPs on soil ecosystem, including soil properties, microorganisms, animals and plants, was discussed. According to the results of in vivo and in vitro experiments, the possible risks of MPs to soil ecosystem and human health were predicted. Finally, in light of the current status of MPs research, several prospects are provided for future research directions to better evaluate the ecological risk and human health risk of MPs. MPs concentrations in global agricultural soils, roadside soils, urban soils and landfill soils had a great variance in different studies and locations. The participation of MPs has an impact on all aspects of terrestrial ecosystems. For soil properties, pH value, bulk density, pore space and evapotranspiration can be changed by MPs. For microorganisms, MPs can alter the diversity and abundance of microbiome, and different MPs have different effects on bacteria and fungi differently. For plants, MPs may interfere with their biochemical and physiological conditions and produce a wide range of toxic effects, such as inhibiting plant growth, delaying or reducing seed germination, reducing biological and fruit yield, and interfering with photosynthesis. For soil animals, MPs can affect their mobility, growth rate and reproductive capacity. At present epidemiological evidences regarding MPs exposure and negative human health effects are unavailable, but in vitro and in vivo data suggest that they pose various threats to human health, including respiratory system, digestive system, urinary system, endocrine system, nervous system, and circulation system. In conclusion, the existence and danger of MPs cannot be ignored and requires a global effort.

Magnetic biochar enhanced copper immobilization in agricultural lands: Insights from adsorption precipitation and redox

Biochar has exceeded expectations for heavy metal immobilization and has been prepared from widely available sources and inexpensive materials. In this research, coconut shell biochar (CSB), bamboo biochar (BC), magnetic coconut shell charcoal (MCSB), and magnetic bamboo biochar (MBC) were manufactured via co-pyrolysis, and their adsorption properties were tested. The pseudo-secondary (R2 = 0.980-0.985) adsorption kinetic fittings for the four biochas were superior to the pseudo-primary kinetics (R2 = 0.969-0.982). Unmodified biochar adsorption isotherms were more consistent with the Freundlich model, while magnetic biochar fitted Langmuir models better. The maximum adsorption capacity of MCSB for Cu(Ⅱ) reached 371.50 mg g-1. The adsorption mechanisms quantitatively analysis of the biochar indicated that chemical precipitation and ion exchange contributed to the adsorption, in which the magnetic biochar metal-π complexation also enhanced the adsorption. The pot experiment revealed that MCSB (2.0 %DW) significantly enhanced the biomass of lettuce, and facilitated the immobilization of DTPA-Cu (p < 0.05). SEM-EDS, XPS, and FTIR were utilized for morphological characterization and functional group identification, and the increased active adsorption sites (-OH, -COOH, CO, and Fe-O) of MCSB enhanced chemisorption and π-π EDA complexation with Cu(Ⅱ). EEM-PARAFAC and RDA analysis further elucidated that magnetic biochar immobilized copper and reduced biotoxicity (efficiency: 76.12%) by adjusting soil pH, phosphate, and SOM release (negative correlation). The presence of iron oxides (FeOx) promoted in situ adsorption of metallic copper and offered new insights into soil remediation.

Evaluating YOLO architectures for detecting road killed endangered Brazilian animals

Wildlife roadkill is a recurring, dangerous problem that affects both humans and animals and has received increasing attention from environmentalists worldwide. Addressing this problem is difficult due to the high investments required in road infrastructure to effectively reduce wildlife vehicle collisions. Despite recent applications of machine learning techniques in low-cost and economically viable detection systems, e.g., for alerting drivers about the presence of animals and collecting statistics on endangered animal species, the success and wide adoption of these systems depend heavily on the availability of data for system training. The lack of training data negatively impacts the feature extraction of machine learning models, which is crucial for successful animal detection and classification. In this paper, we evaluate the performance of several state-of-the-art object detection models on limited data for model training. The selected models are based on the YOLO architecture, which is well-suited for and commonly used in real-time object detection. These include the YoloV4, Scaled-YoloV4, YoloV5, YoloR, YoloX, and YoloV7 models. We focus on Brazilian endangered animal species and use the BRA-Dataset for model training. We also assess the effectiveness of data augmentation and transfer learning techniques in our evaluation. The models are compared using summary metrics such as precision, recall, mAP, and FPS and are qualitatively analyzed considering classic computer vision problems. The results show that the architecture with the best results against false negatives is Scaled-YoloV4, while the best FPS detection score is the nano version of YoloV5.

Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China

Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R2 = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.

Soil contamination and carrying capacity across the Tibetan plateau using structural equation models

Soil contamination is a major environmental issue worldwide. Compared with Arctic, European Alps and Rocky Mountains, the soil contamination and soil environment carrying capacity (SECC) of the Tibetan Plateau (TP) is not systematic and multidimensional. In this study, the levels, influencing factors including climate factors [(i.e., mean annual precipitation (MAP) and mean annual temperature (MAT)], socio-economic factors [(i.e., population, population density and gross domestic product (GDP)], vegetation coverage factor, soil factors [(i.e., pH, soil organic carbon (SOC), total phosphorus and total nitrogen] and topographic factors [(i.e., longitude, latitude and digital elevation model (DEM)] and carrying capacity of multiple soil contaminants [persistent organic pollutants (POPs), heavy metals (HMs) and microplastics (MPs)] was systematically studied. Results show that the spatial distribution of POPs in the eastern was higher than that in the western region, and the structural equation model (SEM) demonstrate that SOC and MAT were the key factors influencing distribution. Regarding HMs, except As, moderate and heavy pollution of the remaining elements were found in the northern and eastern TP regions, and pH and MAP were the main influencing factors. The MPs showed that the distribution of the patches was influenced by GDP and MAP. Furthermore, a higher SECC in the eastern region that gradually decreased from east to west. pH is the primary factors affecting SECC, followed by normalized difference vegetation index (NDVI). An increase of pH and NDVI by one unit is likely to make SECC scores decrease by 0.8 and increase by 0.32, respectively. Taken together, these studies provide a system, cost-effective, and quantitative framework for soil contamination and carrying capacity in the TP.

Soil core microbiota drive community resistance to mercury stress and maintain functional stability

Soil microbial communities have resistance to environmental stresses and thus can maintain ecosystem functions such as decomposition, nutrient provisioning, and plant pathogen control. However, predominant factors driving community resistance of soil microbiome to heavy metal pollution stresses and ecosystem functional stability are still unclear, limiting our ability to forecast how soil pollution might affect ecosystem sustainability. Here, we conducted microcosm experiments to estimate the importance of soil microbiome in predicting community resistance to heavy metal mercury (Hg) stress in paired paddy and upland fields. We found that community resistance of soil microbiome was strongly correlated with ecosystem functional stability, so were the individual groups of organisms such as bacteria, saprotrophic fungi, and phototrophic protists. The core phylotypes within soil microbiome had a major contribution to community resistance, which was essential for the maintenance of functional stability. Co-occurrence network further confirmed that community resistances of main ecological clusters were positively correlated with ecosystem functional stability. Together, our results provide new insights into the link between community resistance and functional stability, and highlight the importance of core microbiota in driving community resistance to environmental stresses and maintain functional stability.

Effects of land use on soil microplastic distribution adjacent to Danjiangkou reservoir, China

As a new type of pollutant, microplastics (MPs) are an increasingly prominent threat to terrestrial ecosystems. However, the distribution, sources and influencing factors of MPs need to be further studied, especially in reservoir surrounding soil, a hot zone for MPs accumulation and a source of MPs in the watershed. Here, we detected MPs in 120 soil samples collected around Danjiangkou reservoir, with their amount ranging from 645 to 15,161 items/kg. The topsoil layer at 0-20 cm had lower levels of MPs (mean 3989 items/kg) than subsoils at 20-40 cm (mean 5620 items/kg). The most commonly detected types of MPs were polypropylene (26.4%) and polyamide (20.2%), with sizes ranging from 0.05 to 0.5 mm. With regard to shape, most MPs (67.7%) were fragmented, while fibers make up 25.3% of the MPs. Further analysis revealed that the number of villages had the highest driving force for the abundance of MPs with 51%, followed by pH 25% and land use types 10%. The water and sediment of reservoirs are important sources of agricultural soil microplastics. Paddy lands showed higher microplastics levels than orchards and dry croplands. The polymer risk index indicated that the agricultural soil near Danjiangkou reservoir had the highest MPs risk. This study highlights the importance of assessing MPs contamination in the agroecosystems surrounding reservoirs and provides valuable insight into clarify the ecological risks of MPs in the reservoir area.