Soil health in agricultural systems

Ecotoxicity of bioinsecticide spinosad to soil organisms: Commercial formulation versus active ingredient

Spintor® (SPIT®) is a commercial formulation of a bioinsecticide with the active ingredient Spinosad (SPIN). Despite the efforts of regulatory agencies, there still is a lack of information regarding short- and long-term exposures to soil-dwellers, as well as effects at environmentally relevant concentrations. This work aimed to evaluate the effects of SPIT® and SPIN, on the oligochaete Eisenia fetida, and the arthropod Folsomia candida. For this, natural soil was spiked with environmentally relevant concentrations (0.00-1.49 mg of the active ingredient·kg-1 of dry soil) to assess avoidance behaviour in E. fetida and reproduction effects on both species. Further, in E. fetida adults exposed for 2- and 28-day biomarkers of oxidative stress, energetic reserves, neurotoxicity and genotoxicity were evaluated. A significant reduction in juvenile production for F. candida was observed for SPIT® at ≥0.66 mg kg-1 and SPIN at ≥0.13 mg kg-1, and although no effect was observed on E. fetida reproduction, the oligochaeta revealed a tendency to avoid soil spiked with SPIT® at 0.44, 0.66 and 1.49 mg kg-1. The sub-individual responses of E. fetida demonstrate genotoxicity upon exposure to SPIT® and SPIN for 2 days. The 2-day exposures of SPIT® and SPIN seem to induce defence mechanisms, and in general, SPIN exerted higher effects than SPIT® on the oligochaetes. Overall, the pro-oxidant performance and energy metabolism pathways were disrupted in both exposures to SPIT® and SPIN. The results suggest that spinosyns-based products can have an impact on soil arthropods F. candida and oligochaete's health, possibly affecting their essential functions in terrestrial ecosystems.

Soil health is associated with higher primary productivity across Europe

Soil health is expected to be of key importance for plant growth and ecosystem functioning. However, whether soil health is linked to primary productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity and plant disease control) in woodlands was 31.4% higher than in grasslands and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale, whereas climate best explained woodland productivity. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes and Proteobacteria and primary productivity. Among microbial functional groups, we found that primary productivity in croplands and grasslands was positively related to nitrogen-fixing bacteria and mycorrhizal fungi and negatively related to plant pathogens. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.

Index for refining soil health assessment through multivariate approach under diverse agro-climatic zones in the Indo-Gangetic basin of Bihar

A fundamental necessity in advancing sustainable crop production lies in the establishment of a reliable technique for assessing soil health. Soil health assessment is a challenge considering multiple interactions among dynamic indicators within various management strategies and agroecological contexts. Hence a study was conducted to determine the soil health variables, quantify the soil health index (SHI), and validate them with the productivity of rice (Oryza sativa L.)-wheat (Triticum aestivum L.) system for the Indo Gangetic basin of Bihar, India, under four contrasting agro-climatic zones (ACZ-I, II, IIIA & IIIB). For this study, 100 soil samples (0-15 cm) from each ACZ with a total of 400 soil samples were obtained for analyzing 20 soil health variables (soil physical, chemical, and biological properties). To identify SHI and important soil health variables, principal component analysis (PCA) was employed. Apart from specific variables, soil pH, soil organic carbon (SOC), available Zn and available water capacity (AWC) were identified as common indicators for the four ACZs. Results revealed that under the rice-wheat cropping system, ACZ-IIIB soils had a higher SHI (0.19-0.70) than other ACZs. SHI of ACZ-IIIB was significantly influenced by SOC (19.32 %), available P (10.52 %), clay (10.43 %), pH (10.80 %), and soil respiration (9.8 %). The strong relationship between SHI and system productivity of the rice-wheat (R2 = 0.79) system indicates that the selected soil health variables are representative of good soil health. It is concluded that ACZ-specific SHIs are a promising strategy for evaluating and monitoring soil health to achieve the United Nations' Sustainable Development Goal of 'zero hunger' by 2030.

Soil depth and physicochemical properties influence microbial dynamics in the rhizosphere of two Peruvian superfood trees, cherimoya and lucuma, as shown by PacBio-HiFi sequencing

The characterization of soil microbial communities at different depths is essential to understand their impact on nutrient availability, soil fertility, plant growth and stress tolerance. We analyzed the microbial community at three depths (3 cm, 12 cm, and 30 cm) in the native fruit trees Annona cherimola (cherimoya) and Pouteria lucuma (lucuma), which provide fruits in vitamins, minerals, and antioxidants. We used PacBio-HiFi, a long-read high-throughput sequencing to explore the composition, diversity and putative functionality of rhizosphere bacterial communities at different soil depths. Bacterial diversity, encompassing various phyla, families, and genera, changed with depth. Notable differences were observed in the alpha diversity indices, especially the Shannon index. Beta diversity also varied based on plant type and depth. In cherimoya soils, positive correlations with Total Organic Carbon (TOC) and Cation Exchange Capacity (CEC) were observed, but negative ones with certain cations. In lucuma soils, indices like the Shannon index exhibited negative correlations with several metals and specific soil properties. We proposed that differences between the plant rhizosphere environments may explain the variance in their microbial diversity. This study provides insights into the microbial communities present at different soil depths, highlighting the prevalence of decomposer bacteria. Further research is necessary to elucidate their specific metabolic features and overall impact on crop growth and quality.

A systematic benchmarking framework for future assessments of soil health: An example from Denmark

Based on current evidence and established critical thresholds for soil degradation indicators, it is concerning that over 60-70% of European soils are unhealthy due to unsustainable management and the impact of climate change. Despite European and national efforts to improve soil health, significant gaps remain. The proposal for a Soil Monitoring and Resilience Law, to be implemented by the European Union, seeks to establish a framework for soil monitoring and promote sustainable management practices to achieve healthy soils by 2050. This requires extensive data collection and soil monitoring systems to accurately estimate soil health across Europe, considering the diversity of soil types, climates, and land uses. To establish a framework for soil monitoring, we must understand the site-specific status of soil and the ranges of soil health indicators across specific pedoclimatic regions. In our study, we evaluated the soil status in agricultural areas in Denmark using soil health indicators and a site-specific benchmarking approach. We compiled nationally representative datasets, combining point and model-informed data of soil parameters such as organic carbon content, bulk density, pH, electrical conductivity, clay-to-soil organiccarbon ratio, water erosion, and nitrogen leaching. By categorizing Danish agricultural soils into monitoring units based on textural classes, landscape elements, and wetland types, we calculated benchmarks for these indicators, considering different cropping systems. Our approach provided detailed point-based results and a spatially explicit overview of the status of soil health indicators in Denmark. We identified areas where soil deviates from the benchmarks of different indicators. Such deviations might indicate soil functions operating outside the normal range, posing potential threats to soil health. This proposed framework could support the establishment of a baseline for assessing the directionality of future changes in soil health. Moreover, it is adaptable for implementation by other countries to support assessments of soil health.

A method for evaluating the effects of gentle remediation options (GRO) on soil health: Demonstration at a DDX-contaminated tree nursery in Sweden

Healthy soils provide valuable ecosystem services (ES), but soil contamination can inhibit essential soil functions (SF) and pose risks to human health and the environment. A key advantage of using gentle remediation options (GRO) is the potential for multifunctionality: to both manage risks and improve soil functionality. In this study, an accessible, scientific method for soil health assessment directed towards practitioners and decision-makers in contaminated land management was developed and demonstrated for a field experiment at a DDX-contaminated tree nursery site in Sweden to evaluate the relative effects of GRO on soil health (i.e., the 'current capacity' to provide ES). For the set of relevant soil quality indicators (SQI) selected using a simplified logical sieve, GRO treatment was observed to have highly significant effects on many SQI according to statistical analysis due to the strong influence of biochar amendment on the sandy soil and positive effects of nitrogen-fixing leguminous plants. The SQI were grouped within five SF and the relative effects on soil health were evaluated compared to a reference state (experimental control) by calculating quantitative treated-SF indices. Multiple GRO treatments are shown to have statistically significant positive effects on many SF, including pollutant attenuation and degradation, water cycling and storage, nutrient cycling and provisioning, and soil structure and maintenance. The SF were in turn linked to soil-based ES to calculate treated-ES indices and an overall soil health index (SHI), which can provide simplified yet valuable information to decision-makers regarding the effectiveness of GRO. The experimental GRO treatment of the legume mix with biochar amendment and grass mix with biochar amendment are shown to result in statistically significant improvements to soil health, with overall SHI values of 141 % and 128 %, respectively, compared to the reference state of the grass mix without biochar (set to 100 %).

Effects of aftercrop tomato and maize on the soil microenvironment and microbial diversity in a long-term cotton continuous cropping field

Long-term continuous cropping affects the soil microecological community and leads to nutrient imbalances, which reduces crop yields, and crop rotation can increase soil productivity. To study the effects of the cultivation of tomato (Solanum lycopersicum) and corn (Zea mays) on the microbial community, physical and chemical factors and the structure of aggregates in cotton (Gossypium hirsutum) long-term continuous cropping soils were examined. Four cropping patterns were established, including one continuous cropping pattern and three crop rotation patterns, and the diversity of the soil microecological community was measured using high-throughput sequencing. The physical and chemical properties of different models of soil were measured, and the soil aggregate structure was determined by dry and wet sieving. Planting of aftercrop tomato and corn altered the bacterial community of the cotton continuous soil to a lesser extent and the fungal community to a greater extent. In addition, continuous cropping reduced the diversity and richness of the soil fungal community. Different aftercrop planting patterns showed that there were very high contents of soil organic carbon and organic matter in the cotton-maize rotation model, while the soil aggregate structure was the most stable in the corn-cotton rotation model. Planting tomato in continuous cropping cotton fields has a greater effect on the soil microbial community than planting maize. Therefore, according to the characteristics of different succeeding crop planting patterns, the damage of continuous cropping of cotton to the soil microenvironment can be alleviated directionally, which will enable the sustainable development of cotton production.

Organic fertilizer application promotes the soil nitrogen cycle and plant starch and sucrose metabolism to improve the yield of Pinellia ternata

Pinellia ternata (Thunb.) Breit is a traditional Chinese medicine with important pharmacological effects. However, its cultivation is challenged by soil degradation following excessive use of chemical fertilizer. We conducted an experiment exploring the effects of replacing chemical fertilizers with organic fertilizers (OF) on the growth and yield of P. ternata, as well as on the soil physicochemical properties and microbial community composition using containerized plants. Six fertilization treatments were evaluated, including control (CK), chemical fertilizer (CF), different proportions of replacing chemical fertilizer with organic fertilizer (OM1-4). Containerized P. ternata plants in each OF treatment had greater growth and yield than the CK and CF treatments while maintaining alkaloid content. The OM3 treatment had the greatest yield among all treatments, with an increase of 42.35% and 44.93% compared to the CK and CF treatments, respectively. OF treatments improved soil quality and fertility by enhancing the activities of soil urease (S-UE) and sucrase (S-SC) enzymes while increasing soil organic matter and trace mineral elements. OF treatments increased bacterial abundance and changed soil community structure. In comparison to the CK microbial groups enriched in OM3 were OLB13, Vicinamibacteraceae, and Blrii41. There were also changes in the abundance of gene transcripts among treatments. The abundance of genes involved in the nitrogen cycle in the OM3 has increased, specifically promoting the transformation of N-NO3- into N-NH4+, a type of nitrogen more easily absorbed by P. ternata. Also, genes involved in "starch and sucrose metabolism" and "plant hormone signal transduction" pathways were positively correlated to P. ternata yield and were upregulated in the OM3 treatment. Overall, OF in P. ternata cultivation is a feasible practice in advancing sustainable agriculture and is potentially profitable in commercial production.

Bacillus tequilensis influences metabolite production in tomato and restores soil microbial diversity during Fusarium oxysporum infection

This study evaluates cellular damage, metabolite profiling, and defence-related gene expression in tomato plants and soil microflora during Fusarium wilt disease after treatment with B. tequilensis PBE-1. Histochemical analysis showed that PBE-1 was the primary line of defence through lignin deposition and reduced cell damage. GC-MS revealed that PBE-1 treatment ameliorated stress caused by F. oxysporum infection. PBE-1 also improved transpiration, photosynthesis, and stomatal conductance in tomato. qRT-PCR suggested that the defence-related genes FLS2, SERK, NOS, WRKYT, NHO, SAUR, and MYC2, which spread infection, were highly upregulated during F. oxysporum infection, but either downregulated or expressed normally in PBE-1 + P treated plants. This indicates that the plant not only perceives the bio-control agent as a non-pathogen entity but its presence in normal metabolism and gene expression within the host plant is maintained. The study further corroborated findings that application of PBE-1 does not cause ecological disturbances in the rhizosphere. Activity of soil microflora across four treatments, measured by Average Well Colour Development (AWCD), showed continuous increases from weeks 1 to 4 post-pathogen infection, with distinct substrate usage patterns like tannic and fumaric acids impacting microbial energy source utilization and diversity. Principal Component Analysis (PCA) and diversity indices like McIntosh, Shannon, and Simpson further illustrated significant microbial community shifts over the study period. In conclusion, our findings demonstrate that B. tequilensis PBE-1 is an ideal bio-agent for field application during Fusarium wilt disease management in tomato.

Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence

BACKGROUND

Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing.

RESULTS

Fungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion.

CONCLUSIONS

Microbial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.

Endophyte Inoculation and Elevated Potassium Supply on Productivity, Growth and Physiological Parameters of Spring Barley (Hordeum vulgare L.) Genotypes over Contrasting Seasons

In recent years, recurrent droughts have significantly affected spring barley production, reducing the quantity and quality of grain. This study aims to identify genotype-specific traits and the drought resilience of six different Hordeum vulgare L. (spring barley) genotypes, while also examining the potential of potassium application and fungal endophyte Serendipita indica inoculation to mitigate the negative effects of dry periods during the growing season. Field experiments were conducted over a three-year period from 2020 to 2022, measuring physiological, growth, and yield parameters. To get insight into the physiological state of the plants, we measured the soluble sugars content and the ratio of stable carbon isotopes in the flag leaf tissue, which reflects conditions during its formation. The dominant factors that influenced the measured parameters were the genotypes and seasons, as well as their interaction, rather than other experimental factors. The results showed that the Spitfire and Accordine varieties were the best performing in both the 2020 and 2021 seasons, as indicated by their yield. However, in the drier 2022 season, the yield of these two varieties decreased significantly (to 55% for Spitfire and to 69% for Accordine of their yield in 2021), while for the arid-region genotypes, it remained at the same level as the previous year. This study sheds light on the potential of various genotypes to withstand periods of drought and the effectiveness of using potassium application and S. indica inoculation as mitigation approaches.

Soil health reduction following the conversion of primary vegetation covers in a semi-arid environment

A degraded forest is the outcome of a degradation process that has adverse effects on ecosystem functions and services. This phenomenon results in alterations of soil physicochemical and biological properties, which serve as valuable indicators for assessing soil health that has been recognized as a crucial component of soil quality. For several decades, the conversion of forested areas into rangeland has been documented in specific regions of the world. There is a widespread lack of global understanding regarding the lasting consequences of land degradation on soil health indicators. The present study aims to investigate the impact of forest degradation on soil health indicators in a mountainous semi-arid region located in northern Iran. The study area was predominantly forested, but due to human activities over the past 30 years, it has been transformed into three distinct land uses: forest, forest-rangeland ecotones and rangeland. In each of these land covers, a total of 20 litter (O-horizon) and 20 soil (from two depths of 0-15 and 15-30 cm) samples were collected in the summer (August 2022) season. According to our results, the highest litter thickness, P and Mg were in forest ecosystem, the lowest in rangeland ecosystem. The findings indicated that following the conversion of forest to rangeland, there was a decrease in soil aggregate stability, porosity, soil organic matter, POC, PON, NH4+, NO3- and nutrient levels, while soil bulk density increased. The forest ecosystem showed notably higher C and N stocks (45 and 5.21 Mg ha-1) in comparison to the rangeland (38 and 3.32 Mg ha-1) ecosystem. In addition, P, K, Ca, and Mg exhibited elevated levels within the total root of the forest ecosystem (2.12, 1.23, 0.71, and 0.38 %, respectively), whereas the lower values (1.29, 1.01, 0.43, and 0.23 %, respectively) were found in the rangeland ecosystem. Following the shift of land cover from forest to rangeland, soil fauna, microflora populations, soil enzymes and microbial activities decreased (about 1-2 times higher in the forestland). This research emphasizes the urgent need to advance sustainable management practices to prevent further degradation and promote the implementation of restoration or rehabilitation techniques in degraded forests. Despite being conducted in a semi-arid region situated in northern Iran, the findings of this study have considerable value for the sustainable management of soil and land conservation in various other semi-arid regions around the world.

A red seaweed Kappaphycus alvarezii-based biostimulant (AgroGain®) improves the growth of Zea mays and impacts agricultural sustainability by beneficially priming rhizosphere soil microbial community

The overuse of chemical-based agricultural inputs has led to the degradation of soil with associated adverse effects on soil attributes and microbial population. This scenario leads to poor soil health and is reportedly on the rise globally. Additionally, chemical fertilizers pose serious risks to the ecosystem and human health. In this study, foliar sprays of biostimulant (AgroGain/LBS6) prepared from the cultivated, tropical red seaweed Kappaphycus alvarezii increased the phenotypic growth of Zea mays in terms of greater leaf area, total plant height, and shoot fresh and dry weights. In addition, LBS6 improved the accumulation of chlorophyll a and b, total carotenoids, total soluble sugars, amino acids, flavonoids, and phenolics in the treated plants. LBS6 applications also improved the total bacterial and fungal count in rhizospheric soil. The V3-V4 region of 16S rRNA gene from the soil metagenome was analyzed to study the abundance of bacterial communities which were increased in the rhizosphere of LBS6-treated plants. Treatments were found to enrich beneficial soil bacteria, i.e., Proteobacteria, especially the classes Alphaproteobacteria, Cyanobacteria, Firmicutes, Actinobacteriota, Verrucomicrobiota, Chloroflexi, and Acidobacteriota and several other phyla related to plant growth promotion. A metagenomic study of those soil samples from LBS6-sprayed plants was correlated with functional potential of soil microbiota. Enrichment of metabolisms such as nitrogen, sulfur, phosphorous, plant defense, amino acid, co-factors, and vitamins was observed in soils grown with LBS6-sprayed plants. These results were further confirmed by a significant increase in the activity of soil enzymes such as urease, acid phosphatase, FDAse, dehydrogenase, catalase, and biological index of fertility in the rhizosphere of LBS6-treated corn plant. These findings conclude that the foliar application of LBS6 on Z. mays improves and recruits beneficial microbes and alters soil ecology in a sustainable manner.

Runoff and soil loss are drastically decreased in a rubber plantation combining the spreading of logging residues with a legume cover

Soil erosion on agricultural land is a major threat for food and raw materials production. It has become a major concern in rubber (Hevea brasiliensis) plantations introduced on sloping ground. Alternative agroecological crop management practices must be investigated. One aim of our study was to assess the ability of logging residues (i.e., trunks, branches, leaves and stumps of a clearcut plantation) and of legume cover (Pueraria phaseoloides) to mitigate N, P and K losses through runoff and soil detachment in a young rubber plantation. The other aim was to investigate the relationships of these nutrient losses with soil structure and soil macrofauna diversity. Runoff and soil loss were monitored for 3 years using 1-m2 plots under different practices as regards the management of logging residues and the use or not of a legume. The monitoring started when rubber trees were one-year-old. The planting row, where soil was bare, was the hotspot of soil erosion, with an average runoff of 832 mm y-1 and soil loss of 3.2 kg m-2 y-1. Sowing a legume in the inter-row reduced runoff and soil loss by 88 % and 98 % respectively, compared to bare soil. Spreading logging residues as well as growing a legume cover almost eliminated runoff and soil detachment (19 mm y-1 and 4 g m-2 y-1 respectively). Nutrient losses were negligible as long as the soil surface was covered by a legume crop, with or without logging residues. Total N loss from soil detachment ranged from 0.02 to 0.2 g m-2 y-1, for example. Spreading logging residues in the inter-rows significantly improved soil structure and soil macrofauna diversity compared to bare soil. Nutrient losses from runoff and soil detachment were negatively correlated with improved soil structure and soil macrofauna diversity. We recommend investigating alternative ways to manage planting rows.

The role of edaphic variables and management practices in regulating soil microbial resilience to drought - A meta-analysis

Environmental disturbances such as drought can impact soil health and the resistance (ability to withstand environmental stress) and resilience (ability to recover functional and structural integrity after stress) of soil microbial functional activities. A paucity of information exists on the impact of drought on soil microbiome and how soil biological systems respond to and demonstrate resilience to drought stress. To address this, we conducted a systematic review and meta-analysis (using only laboratory studies) to assess the response of soil microbial biomass and respiration to drought stress across agriculture, forest, and grassland ecosystems. The meta-analysis revealed an overall negative response of microbial biomass in resistance (-31.6 %) and resilience (-0.3 %) to drought, suggesting a decrease in soil microbial biomass content. Soil microbial respiration also showed a negative response in resistance to drought stress indicating a decrease in soil microbial respiration in agriculture (-17.5 %), forest (-64.0 %), and grassland (-65.5 %) ecosystems. However, it showed a positive response in resilience to drought, suggesting an effective recovery in microbial respiration post-drought. Soil organic carbon (SOC), clay content, and pH were the main regulating factors of the responses of soil microbial biomass and respiration to drought. In agriculture ecosystem, soil pH was primarily correlated with soil microbial respiration resistance and resilience to drought, potentially influenced by frequent land preparation and fertilizer applications, while in forest ecosystem SOC, clay content, and pH significantly impacted microbial biomass and respiration resistance and resilience. In grassland ecosystem, SOC was strongly associated with biomass resilience to drought. The impact of drought stress on soil microbiome showed different patterns in natural and agriculture ecosystems, and the magnitude of microbial functional responses regulated by soil intrinsic properties. This study highlighted the importance of understanding the role of soil properties in shaping microbial responses to drought stress for better ecosystem management.

Soils in distress: The impacts and ecological risks of (micro)plastic pollution in the terrestrial environment

Plastics have revolutionised human industries, thanks to their versatility and durability. However, their extensive use, coupled with inadequate waste disposal, has resulted in plastic becoming ubiquitous in every environmental compartment, posing potential risks to the economy, human health and the environment. Additionally, under natural conditions, plastic waste breaks down into microplastics (MPs<5 mm). The increasing quantity of MPs exerts a significant burden on the soil environment, particularly in agroecosystems, presenting a new stressor for soil-dwelling organisms. In this review, we delve into the effects of MP pollution on soil ecosystems, with a specific attention to (a) MP transport to soils, (b) potential changes of MPs under environmental conditions, (c) and their interaction with the physical, chemical and biological components of the soil. We aim to shed light on the alterations in the distribution, activity, physiology and growth of soil flora, fauna and microorganisms in response to MPs, offering an ecotoxicological perspective for environmental risk assessment of plastics. The effects of MPs are strongly influenced by their intrinsic traits, including polymer type, shape, size and abundance. By exploring the multifaceted interactions between MPs and the soil environment, we provide critical insights into the consequences of plastic contamination. Despite the growing body of research, there remain substantial knowledge gaps regarding the long-term impact of MPs on the soil. Our work underscores the importance of continued research efforts and the adoption of standardised approaches to address plastic pollution and ensure a sustainable future for our planet.

Earthworms mediate the influence of polyethylene (PE) and polylactic acid (PLA) microplastics on soil bacterial communities

There is a growing body of evidence that suggests that both biodegradable and conventional (non-degradable) microplastics (MP) are hazardous to soil health by affecting the delivery of key ecological functions such as litter decomposition, nutrient cycling and water retention. Specifically, soil fauna may be harmed by the presence of MPs while also being involved in their disintegration, degradation, migration and transfer in soil. Therefore, a comprehensive understanding of the interactions between MPs and soil fauna is essential. Here, we conducted a 120-day soil microcosm experiment applying polyethylene (PE) and polylactic acid (PLA), in the absence/presence of the earthworm Eisenia nordenskioldi to estimate the relative singular and combined impact of MPs and earthworms on the soil bacterial community. Our findings revealed contrasting effects of PE and PLA on the composition and diversity of soil bacteria. All treatments affected the community and network structure of the soil bacterial community. Compared to the control (no MPs or earthworms), PE decreased bacterial alpha diversity, while PLA increased it. Patescibacteria were found to be significantly abundant in the PE group whereas Actinobacteria and Gemmatimonadetes were more abundant in PE, and PLA and earthworms groups. The presence of earthworms appeared to mediate the impact of PE/PLA on soil bacteria, potentially through bacterial consumption or by altering soil properties (e.g., pH, aeration, C availability). Earthworm presence also appeared to promote the chemical aging of PLA. Collectively, our results provide novel insights into the soil-fauna-driven impact of degradable/nondegradable MPs exposure on the long-term environmental risks associated with soil microorganisms.

Impact of long-term resource conservation techniques on biogeochemical characteristics and biological soil quality indicators in a rice green-gram farming system

Nutrient management in resource conservation practices influence the structural and functional microbial diversities and thereby affect biological processes and biochemical properties in soil. We studied the long-term effects of resource conservation technologies on functional microbial diversity and their interactions with soil biochemical properties and enzymatic activities in tropical rice-green gram cropping system. The experiment includes seven treatments viz., conventional practice (CC), brown manuring (BM), green manuring (GM), wet direct drum sowing, zero tillage, green manuring-customized leaf colour chart based-N application (GM-CLCC-N) and biochar (BC) application. The result of the present study revealed that microbial biomass nitrogen (N), carbon (C) and phosphorus (P) in GM practice were increased by 23.3, 37.7 and 35.1%, respectively than CC. GM, BM and GM-CLCC-N treatments provide higher yields than conventional practice. The average well color development value, Shannon index and McIntosh index were significantly higher by 26.6%, 86.9% and 29.2% in GM as compared to control treatment. So, from this study we can conclude that resource conservation practices like GM, GM-CLCC N and BM in combination with chemical fertilizers provide easily decomposable carbon source to support the microbial growth. Moreover, dominance of microbial activity in biomass amended treatments (GM, GM-CLCC N and BM) indicated that these treatments could supply good amount of labile C sources on real time basis for microbial growth that may protect the stable C fraction in soil, hence could support higher yield and soil organic carbon build-up in long run under rice-green gram soil.

Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India

Introduction

Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied.

Methods

Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods.

Results and Discussion

Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50-23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2-13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.

Environmental impacts of microplastic and role of plastisphere microbes in the biodegradation and upcycling of microplastic

Increasing usage of plastic has led to the deposition of plastic in the environment which later become microplastic, a pollutant of global concern. These polymeric particles affect the ecosystem bestowing toxicity and impede the biogeochemical cycles. Besides, microplastic particles have been known for their role in aggravating the effect of various other environmental pollutants including organic pollutants and heavy metals. These microplastic surfaces are often colonized by the microbial communities also known as "plastisphere microbes" forming biofilms. These microbes include cyanobacteria like Nostoc, Scytonema, etc., and diatoms like Navicula, Cyclotella, etc. Which become the primary colonizer. In addition to the autotrophic microbes, Gammaproteobacteria and Alphaproteobacteria dominate the plastisphere microbial community. These biofilm-forming microbes can efficiently degrade the microplastic in the environment by secreting various catabolic enzymes such as lipase, esterase, hydroxylase, etc. Besides, these microbes have shown great potential for the bioconversion of microplastic to polyhydroxyalkanoates (PHA), an energy efficient and sustainable alternative to the petroleum based plastics. Thus, these microbes can be used for the creation of a circular economy using waste to wealth strategy. This review provides a deeper insight into the distribution, transportation, transformation, and biodegradation of microplastic in the ecosystem. The formation of plastisphere by the biofilm-forming microbes has been described in the article. In addition, the microbial metabolic pathways and genetic regulations involved in the biodegradation have been discussed in detail. The article suggests the microbial bioremediation and upcycling of microplastic along with various other strategies for effectively mitigate the microplastic pollution.

Influence of manure application method on veterinary medicine losses to water

Veterinary medicines are routinely used within modern animal husbandry, which results in frequent detections within animal manures and slurries. The application of manures to land as a form of organic fertiliser presents a pathway by which these bioactive chemicals can enter the environment. However, to date, there is limited understanding regarding the influence of commonly used manure application methods on veterinary medicine fate in soil systems. To bridge this knowledge gap, a semi-field study was conducted to assess the influence of commonly used application methods such as, broadcast, chisel sweep, and incorporation on veterinary medicine losses to waters. A range of veterinary medicines were selected and applied as a mixture; these were enrofloxacin, florfenicol, lincomycin, meloxicam, oxytetracycline, sulfadiazine, trimethoprim and tylosin. All the assessed veterinary medicines were detected within surface runoff and leachates, and the concentrations generally decreased throughout the irrigation period. The surface runoff concentrations ranged from 0.49 to 183.47 μg/L and 2.26-236.83 μg/L for the bare soil and grass assessments respectively. The leachate concentrations ranged from 0.04 to 309.66 μg/L and 0.33-37.79 μg/L for the bare soil and grass assessments respectively. More advanced application methods (chisel sweep) were found to significantly reduce the mass loads of veterinary medicines transported to surface runoff and leachate by 13-56% and 49-88% over that of broadcast. Incorporating pig slurries reduced the losses further with surface runoff and leachate losses being 13-56% and 49-88% lower than broadcast. Our results show that manure application techniques have a significant effect on veterinary medicine fate in the environment and as such these effects should be considered in the decision-making processes for the management of manures as well as from a risk mitigation perspective for aquatic compartments.

Connecting soil characteristics to edge-of-field water quality in Ohio

Soil health and water quality improvement are major goals of sustainable agricultural management systems, yet the connections between soil health and water quality impacts remain unclear. In this study we conducted an initial exploratory assessment of the relationships between soil chemical, physical, and biological properties and edge-of-field water quality across a network of 40 fields in Ohio, USA. Discharge, dissolved reactive P (DRP), total P (TP), and nitrate (NO₃ ) losses associated with precipitation events via surface runoff and tile drainage were monitored. Agronomic soil tests and a suite of soil health indicators were measured, then predictive relationships between the field average soil properties and tile drainage and surface runoff discharge and DRP, TP, and nitrate loads were explored with random forest and multiple linear regression approaches. Among the soil health indicators, water extractable C and N were consistently found to be positively related to tile nitrate loads, but other soil health indicators had little or inconsistent importance for water quality impacts. Several other soil properties were important predictors, particularly soil P pools for surface and tile DRP and TP losses as well as Mehlich-3 (M3) extractable Fe and Al for surface and tile discharge. Thus, we did not observe strong evidence that soil health was associated with improved edge-of-field water quality across the edge-of-field monitoring network. However, additional studies are needed to definitively test the relationships between a broader array of soil health metrics and water quality outcomes.

Status of Ecosystem Services in Abandoned Mining Areas in the Iberian Peninsula: Management Proposal

An abandoned sphalerite mining area in the southwest (SW) of the Iberian Peninsula was studied to evaluate the impact that the presence of metal(loid)s has on soil and ecosystem health. Five zones were delimited: sludge, dump, scrubland, riparian zone, and dehesa. Critical total levels of lead (Pb), zinc (Zn), thallium (Tl), and chromium (Cr), well above the limit indicative of toxicity problems, were found in the areas close to the sources of contamination. Pb-Zn concentrations were very high in the riparian zone, reaching values of 5875 mg/kg Pb and 4570 mg/kg Zn. The whole area is classifiable as extremely contaminated with Tl, with concentrations above 370 mg/kg in the scrubland. Cr accumulation mainly occurred in areas away from the dump, with levels up to 240 mg/kg in the dehesa. In the study area, several plants were found growing luxuriantly despite the contamination. The measured metal(loid)s content is the cause of a significant decrease in ecosystem services, resulting in unsafe soils for food and water production, so the implementation of a decontamination program is advisable. The plant species Retama sphaerocarpa, present in the sludge, scrubland, riparian zone, and dehesa, is postulated as suitable for use in phytoremediation.

Earthworm-Driven Changes in Soil Chemico-Physical Properties, Soil Bacterial Microbiota, Tree/Tea Litter Decomposition, and Plant Growth in a Mesocosm Experiment with Two Plant Species

Earthworms and soil microorganisms contribute to soil health, quality, and fertility, but their importance in agricultural soils is often underestimated. This study aims at examining whether and to what extent the presence of earthworms (Eisenia sp.) affected the (a) soil bacterial community composition, (b) litter decomposition, and (c) plant growth (Brassica oleracea L., broccoli; Vicia faba L., faba bean). We performed a mesocosm experiment in which plants were grown outdoors for four months with or without earthworms. Soil bacterial community structure was evaluated by a 16S rRNA-based metabarcoding approach. Litter decomposition rates were determined by using the tea bag index (TBI) and litter bags (olive residues). Earthworm numbers almost doubled throughout the experimental period. Independently of the plant species, earthworm presence had a significant impact on the structure of soil bacterial community, in terms of enhanced α- and β-diversity (especially that of Proteobacteria, Bacteroidota, Myxococcota, and Verrucomicrobia) and increased 16S rRNA gene abundance (+89% in broccoli and +223% in faba bean). Microbial decomposition (TBI) was enhanced in the treatments with earthworms, and showed a significantly higher decomposition rate constant (k_TBI) and a lower stabilization factor (S_TBI), whereas decomposition in the litter bags (d_litter) increased by about 6% in broccoli and 5% in faba bean. Earthworms significantly enhanced root growth (in terms of total length and fresh weight) of both plant species. Our results show the strong influence of earthworms and crop identity in shaping soil chemico-physical properties, soil bacterial community, litter decomposition and plant growth. These findings could be used for developing nature-based solutions that ensure the long-term biological sustainability of soil agro- and natural ecosystems.

Impact of plastic mulching as a major source of microplastics in agroecosystems

The contamination of agroecosystems by microplastics (MPs) has raised great concerns recently. Plastic mulching has contributed a lot in the building of MP pollution in farmlands. This technique has been in use for decades worldwide because of its immense advantages, preferably in drier and colder regions. The physical extraction of plastic mulches at the end of the growing season is very laborious and ineffective, and thus small pieces of mulches are left in the field which later convert into MP particles after aging, weathering, or on exposure to solar radiation. MPs not only influence physical, chemical, or biological properties of soils but also reduce crop productivity which could be a threat to our food security. They also interact with and accumulate other environmental contaminants such as microbial pathogens, heavy metals, and persistent organic pollutants on their surfaces which increase their risk of toxicity in the environment. MPs also transfer from one trophic level to the other in the food chain and ultimately may impact human health. Because of the ineffectiveness of the recovery of plastic film fragments from fields, researchers are now mainly focusing on alternative solutions to conventional plastic mulch films such as the use of biodegradable mulches. In this review, we have discussed the issue of plastic mulch films in agroecosystems and tried to link already existing knowledge to the current limitations in research on this topic from cropland soils and future prospects have been identified and proposed.

Soil physicochemical and biological properties in soybean areas under no-till Systems in the Brazilian Cerrado

No-till (NT) as a conservation practice aims to minimize soil disturbance and enhance soil sustainability. However, how NT practice affects soil physicochemical and biological properties in soybean areas remains unclear. This study selected 65 high-yielding soybean farms under a long-term NT system in the Brazilian Cerrado and collected soil samples at 0.0-0.10 m (L1), 0.10-0.20 m (L2) and 0.20-0.40 m (L3) depths. The effect of NT on soil properties and interactions with soybean productivities were assessed. Results showed that the average soybean yield of the study areas in the last three years was 4.13 Mg ha^-1, with 26 areas presenting yields over 4.20 Mg ha^-1. Most studied soil properties showed a depth stratification and were strongly concentrated in L1, except for S, Al³⁺ and aluminum saturation, which displayed lower surface and higher subsurface concentrations. Moreover, a high proportion of SOM is composed of light SOM fraction in areas of high soybean yield, with the average SOM values of 39.9, 27.8 and 19.6 g kg^-1 in L1, L2 and L3, respectively. Soils under long-term NT present moderate values of enzyme activity compared with the relatively low values under conventional tillage system, especially 94 % of the plots have moderate values of activity of arylsulfatase enzymes. The data presented support the conclusion that NT system can enhance soil fertility and biological quality in soybean cultivation. Our results suggest that it is necessary to adopt NT practice because it allows increasing soybean productivity in Brazil without the need to increase the sown area, in addition to increasing productivity associated with an improvement in the agroecosystem quality, thus moving toward a more sustainable agriculture.

Awaking the dormant virome in the rhizosphere

The rhizosphere is a vital soil compartment providing key plant-beneficial functions. However, little is known about the mechanisms driving viral diversity in the rhizosphere. Viruses can establish lytic or lysogenic interactions with their bacterial hosts. In the latter, they assume a dormant state integrated in the host genome and can be awakened by different perturbations that impact host cell physiology, triggering a viral bloom, which is potentially a fundamental mechanism driving soil viral diversity, as 22%-68% of soil bacteria are predicted to harbour dormant viruses. Here we assessed the viral bloom response in rhizospheric viromes by exposing them to three contrasting soil perturbation agents: earthworms, herbicide and antibiotic pollutant. The viromes were next screened for rhizosphere-relevant genes and also used as inoculant on microcosms incubations to test their impacts on pristine microbiomes. Our results show that while post-perturbation viromes diverged from control conditions, viral communities exposed to both herbicide and antibiotic pollutant were more similar to each other than those influenced by earthworms. The latter also favoured an increase in viral populations harbouring genes involved in plant-beneficial functions. Post-perturbation viromes inoculated on soil microcosms changed the diversity of pristine microbiomes, suggesting that viromes are important components of the soil ecological memory driving eco-evolutionary processes that determine future microbiome trajectories according to past events. Our findings demonstrate that viromes are active players in the rhizosphere and need to be considered in efforts to understand and control the microbial processes towards sustainable crop production.

Linking Rhizosphere Soil Aggregates with Belowground and Aboveground Plant Traits

Rhizosphere soil ecosystems are represented by the diversity of different soil aggregate-size classes, such as large macroaggregates, small macroaggregates, mesoaggregates, and microaggregates. Though these aggregate-size classes represent distinct biological, chemical, and physical properties, little is known about their dynamics and relationships with belowground and aboveground plant traits. In this study, we examined the relationships of various soil aggregate-size classes and their organic carbon contents with many aboveground and belowground soybean plant traits. Our study revealed several novel and interesting relationships between soil structural properties and plant traits. Notably, small macroaggregates represented a major portion of the rhizosphere soil ecosystem of soybean plants while organic carbon contents decreased with decreasing size of soil aggregates. Only microaggregates showed a significant relationship with root architectural traits, such as length and surface area. Among all soil aggregate size classes, the abundance of small macroaggregates and the organic carbon contents of microaggregates were better correlated with plant traits. In general, organic carbon contents of different soil aggregate-size classes showed positive correlations with leaf trichome density (defense traits) and major macronutrients, such as root P, K, and S contents; while there were mostly negative correlations with some micronutrient (Ca, Mn, Zn, Cu, B, and Mg) contents of roots and shoots. However, the abundance of small macroaggregates mostly positively correlated with the mineral contents of plant roots and shoots. Collectively, the positive and negative correlations of organic carbon contents of different soil aggregate-size classes with trichomes (defense) and physiological traits (micro-mineral contents) suggest their significance in plant nutrition and defense. Though our results suggest the relationships of soil aggregate properties with aboveground and belowground traits, further research is needed to discern the role of soil structural traits in mediating plant growth, development, defense, and physiology.

Detecting the research trends and evolution of energy resilience: a bibliometric analysis

The concept of resilience is widely used in many specific fields, such as energy. Energy resilience is receiving increasing scientific attention. In the long-term sustainable development of society, energy and resilience policies are the key strategies to achieve international development goals. This paper analyzes the existing energy resilience literature and presents the research hot spots and trends. After extracting 4887 articles from the Science Citation Index Expanded and Social Sciences Citation Index databases, this paper takes the literature data during 1985-2021 through topic search using the keywords of energy resilience and applies bibliometrics to study the development traits of the field. The primary research purposes are to discover the knowledge framework of energy resilience, together with a review of integral development trends, elementary publication characteristics, and an analysis of related leading journals. Aside from analyzing the number of publications, citations, and cooperation types, this study identifies the most prolific researchers from the country-level, institution-level, and author-level in this area, thus providing a longitudinal overview of the dynamic research evolution of energy resilience and the knowledge spread locus in this domain.

Robotics-assisted, organic agricultural-biotechnology based environment-friendly healthy food option: Beyond the binary of GM versus Organic crops

Human society cannot afford the luxury of the business-as-usual approach when dealing with the emerging challenges of the 21st century. The challenges of food production to meet the pace of population growth in an environmentally-sustainable manner have increased considerably, emphasizing the need to explore newer approaches to agriculture. Agrochemical-based agricultural practices are known to have serious environmental and health implications. Even conventional organic farming is not sustainable in the long run. Although some "age-old" practices are useful, these will not help feed more people on the same or less land more sustainably. Sustainable intensification is the way forward. There is a need to incorporate a customer-centric outlook and make the organic system sustainable. Here, we bring forth the necessity to enhance the efficiency of organic agriculture by the inclusion of robotics and agrochemical-free GM seeds. Such an organic-GM hybrid agriculture system integrated with the use of artificial intelligence (AI) based technologies will have better energy efficiency. The produce from such a system will offer consumers a 'third' choice and create a new food label, 'organically-grown GM produce'.

Barriers and opportunities of soil knowledge to address soil challenges: Stakeholders' perspectives across Europe

Climate-smart sustainable management of agricultural soil is critical to improve soil health, enhance food and water security, contribute to climate change mitigation and adaptation, biodiversity preservation, and improve human health and wellbeing. The European Joint Programme for Soil (EJP SOIL) started in 2020 with the aim to significantly improve soil management knowledge and create a sustainable and integrated European soil research system. EJP SOIL involves more than 350 scientists across 24 Countries and has been addressing multiple aspects associated with soil management across different European agroecosystems. This study summarizes the key findings of stakeholder consultations conducted at the national level across 20 countries with the aim to identify important barriers and challenges currently affecting soil knowledge but also assess opportunities to overcome these obstacles. Our findings demonstrate that there is significant room for improvement in terms of knowledge production, dissemination and adoption. Among the most important barriers identified by consulted stakeholders are technical, political, social and economic obstacles, which strongly limit the development and full exploitation of the outcomes of soil research. The main soil challenge across consulted member states remains to improve soil organic matter and peat soil conservation while soil water storage capacity is a key challenge in Southern Europe. Findings from this study clearly suggest that going forward climate-smart sustainable soil management will benefit from (1) increases in research funding, (2) the maintenance and valorisation of long-term (field) experiments, (3) the creation of knowledge sharing networks and interlinked national and European infrastructures, and (4) the development of regionally-tailored soil management strategies. All the above-mentioned interventions can contribute to the creation of healthy, resilient and sustainable soil ecosystems across Europe.

On the importance of longer-term exposure to stressors - A critical review and proposal for multigenerational testing in standard soil invertebrates

Standard laboratory tests to describe the impact of stressors (most notably: chemicals) on organisms offer a good compromise between feasibility and outcome, i.e., they should be reproducible and provide robust results. However, these tests may underestimate the potential effects of prolonged exposures, particularly for persistent contaminants. Within the last years, we have observed an increase in studies aiming to target prolonged exposure, e.g., via an extended test duration or by multigenerational (MG) exposure. Seemingly, both reduced and increased impacts have been observed in these studies, but it is also clear that no unique test setup was used, and test designs vary widely among studies. To better describe long term effects, MG is a highly relevant aspect which deserves more consideration at various testing and assessment levels. Therefore, we conducted a literature review focusing on available studies performed with soil invertebrates, exposed to stressors for periods longer than in standard laboratory tests, i.e., full life cycle tests, as well as extensions to standard and MG tests. So far, it has been recommended that such studies should cover more than one generation, but this statement is probably too vague. In this contribution, we summarize and critically discuss the information provided in the literature, and we provide suggestions for future research. The currently available test results from long-term studies have produced clear evidence to recommend the implementation of long-term tests in existing regulatory testing requirements (e.g., for pesticides), in particular for persistent substances and also for delayed effects. Consequently, we recommend the inclusion of such longer exposure test designs (e.g., as annexes) in current OECD and ISO guidelines. However, when doing so, the long-term test designs proposed so far have to be critically adapted for a selected set of representative soil invertebrate test species.

An Open Soil Health Assessment Framework Facilitating Sustainable Soil Management

The crucial role of healthy soil in achieving sustainable food production and environment is increasingly recognized, as is the importance of proper assessment of soil quality. We introduce a new framework, open soil index (OSI), which integrally evaluates soil health of agricultural fields and provides recommendation for farming practices. The OSI is an open-source modular framework in which soil properties, functions, indicators and scores, and management advice are linked hierarchically. Soil health is evaluated with respect to sustainable crop production but can be extended to other ecosystem functions. The OSI leverages the existing knowledge base of agronomic research and routine laboratory data, enabling its application with limited cost. The OSI is a generic framework that can be adopted for specific regions with specific objectives. As a proof of concept, the OSI is implemented for all (>700,000) Dutch agricultural fields and illustrated with 11 pairs ("good" and "poor") of local fields and 32 fields where soil quality and crop yield have been monitored. The OSI produced reasonable evaluation for most pairs when soil physical functions were refined with on-site soil visual assessment. The soil functions are sufficiently independent and yet together reflect complex multidimensionality of soil quality. The framework can facilitate designing sustainable soil management programs by bridging regional targets to field-level actions.

Higher-Quality Pumpkin Cultivars Need to Recruit More Abundant Soil Microbes in Rhizospheres

Two different qualities of pumpkin, cultivars G1519 and G1511, were grown in the same environment under identical management. However, their qualities, such as the contents of total soluble solids, starch, protein, and vitamin C, were significantly different. Do rhizospheric microbes contribute to pumpkin quality? To answer this question, this study investigated the soil microbial compositions in the rhizospheres of different quality pumpkin cultivars to determine the differences in these soil microbial compositions and thus determine how soil microbes may affect pumpkin quality. Firstly, a randomized complete block design with two pumpkin cultivars and three replications was performed in this study. The soil microbial compositions and structures in the rhizospheres of the two pumpkin cultivars were analyzed using a high-throughput sequencing technique. In comparison with the low-quality pumpkin cultivar (G1519), higher microbial diversity and richness could be found in the rhizospheres of the high-quality pumpkin cultivar (G1511). The results showed that there were significant differences in the soil bacterial and fungal community compositions in the rhizospheres of the high- and low-quality pumpkin cultivars. Although the compositions and proportions of microorganisms were similar in the rhizospheres of the two pumpkin cultivars, the proportions of Basidiomycota and Micropsalliota in the G1519 rhizosphere were much higher than those in the G1511 rhizosphere. Furthermore, the fungal phylum and genus Rozellomycota and Unclassified_p__Rozellomycota were unique in the rhizosphere of the high-quality pumpkin cultivar (G1511). All the above results indicate that soil microbes were enriched differentially in the rhizospheres of the low- and high-quality pumpkin cultivars. In other words, more abundant soil microbes were recruited in the rhizosphere of the high-quality pumpkin cultivar as compared to that of the low-quality cultivar. Rozellomycota and Unclassified_p__Rozellomycota may be functional microorganisms relating to pumpkin quality.

Temporal Dynamics of Rare and Abundant Soil Bacterial Taxa from Different Fertilization Regimes Under Various Environmental Disturbances

Global climate change has emerged as a critical environmental problem. Different types of climate extremes drive soil microbial communities to alternative states, leading to a series of consequences for soil microbial ecosystems and related functions. An effective method is urgently needed for buffering microbial communities to tackle environmental disturbances. Here, we conducted a series of mesocosm experiments in which the organic (NOF) and chemical fertilizer (NCF) long-term-amended soil microbiotas were subjected to environmental disturbances that included drought, flooding, freeze-thaw cycles, and heat. We subsequently tracked the temporal dynamics of rare and abundant bacterial taxa in NOF and NCF treatment soils to assess the efficiencies of organic amendments in recovery of soil microbiome. Our results revealed that freeze-thaw cycles and drought treatments showed weaker effects on bacterial communities than flooding and heat. The turnover between rare and abundant taxa occurred in postdisturbance succession of flooding and heat treatments, indicating that new equilibria were tightly related to the rare taxa in both NCF and NOF treatment soils. The Bayesian fits of modeling for the microbiome recovery process revealed that the stability of abundant taxa in NOF was higher than that in NCF soil. In particular, the NOF treatment soil reduced the divergence from the initial bacterial community after weak perturbations occurred. Together, we demonstrated that long-term organic input is an effective strategy to enhance the thresholds for transition to alternative states via enhancing the stability of abundant bacterial species. These findings provide a basis for the sustainable development of agricultural ecosystems in response to changing climates. IMPORTANCE Different climate extremes are expected to be a major threat to crop production, and the soil microbiome has been known to play a crucial role in agricultural ecosystems. In recent years, we have known that organic amendments are an effective method for optimizing the composition and functioning of the soil microbial community and maintaining the health of the soil ecosystem. However, the effects of organic fertilization on buffering bacterial communities against environmental disturbances and the underlying mechanisms are still unclear. We conducted a series of mesocosm experiments and showed that organic fertilizers had additional capacities in promoting the soil microbiome to withstand climate change effects. Our study provides both mechanistic insights as well as a direct guide for the sustainable development of agricultural ecosystems in response to climate change.

Indictors of wetland health improve following small-scale ecological restoration on private land

Globally wetlands are imperilled and restoring these highly productive and biodiverse ecosystems is key to regaining their lost function and health. Much of the fertile, low-lying land that was historically wetland is now farmed, so privately-owned locations play critical roles in regaining space for wetlands. However, wetland restoration on private property is often small-scale and supported by minimal funding and expertise. Little is known about what these efforts achieve, and what contexts facilitate the greatest gains in wetland health. Using a paired plot design for 18 restored and 18 unrestored wetlands, we aimed to understand changes in wetland health following restoration on private property. We characterised plant and microbial communities and soil characteristics following wetland restoration and explored how environmental settings of restored wetlands related to the clustering of wetland health indicators. We found that all indicators of wetland health significantly increased following restoration except for the ratio of Gram negative to Gram positive bacteria. Restoration enhanced plant alpha and beta diversity, adding ~13 native plant species per plot. Soils in restored wetlands contained 20% more organic matter, and 25% more microbial biomass, which was driven by an increased abundance of fungi. Restoration reduced soil bulk density by 0.19 g^-1 cm³ and Olsen Phosphorus by 23%. These effects on soil physical characteristics and microbial communities were strongest in the wettest locations. Restored wetlands clustered into three main groups based on indicators of wetland health. Hydrological flow explained the clustering of wetlands, with riverine wetlands exhibiting greater indicators of recovery than depressional wetlands, suggesting that hydrological flow may influence post-restoration recovery. Overall, this study shows that small-scale wetland restoration on private land improved wetland health, providing evidence that it can be an effective use of marginal agricultural land.

Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties

Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

Low-disturbance farming regenerates healthy deep soil toward sustainable agriculture - Evidence from long-term no-tillage with stover mulching in Mollisols

Currently, global agricultural development is in a critical period, as it contends with a growing population, degraded farmland, and serious environmental issues. Although low-disturbance practices are recommended to improve soil health, it is unclear whether such practices benefit critical deep soil functioning. Here, we compared the soil bacterial communities and physicochemical parameters across 3-m deep soil profiles in a Mollisol of Northeast China at the end of the dormant season after 10 years of farming under conventional tillage without stover mulching (CT), no-tillage without stover mulching (NTNS), and no-tillage with stover mulching (NTSM). We found that low-disturbance practices (NTNS and NTSM), compared with CT, evidently promoted soil bacterial species richness and diversity and enriched potential metabolic diversity. When compared to the bacterial communities in CT, the vertical dissimilarity of bacterial communities in NTNS decreased, while that in NTSM increased, indicating that no-tillage alone homogenized the composition of the bacterial community through soil depth profiles, but straw mulching enhanced the uniqueness of community composition at each layer. In comparison to CT, no-tillage with stover mulching significantly increased the soil water content and root-associated organic carbon (SEOC), and decreased soil pH. Mineral nitrogen declined with depth to 60 cm and then increased to its maximum at 250-300 cm under CT and at 120-150 cm under NTNS and NTSM. More mineral nitrogen at 0-150 cm under low-disturbance practices would provide more available nitrogen for crops in the coming growing season, while the accumulated nitrogen at 150-300 cm under CT may leach into the groundwater. Taken together, our results show that low-disturbance practices can regenerate whole-soil bacterial diversity and potential function, and promote water retention and nitrogen holding capacity within the root zone, thus reducing the dose of nitrogen fertilizer and mitigating nitrogen contamination to deep groundwater, ultimately contributing to agricultural sustainability in Mollisol regions.

Soil Disinfestation: From Soil Treatment to Soil and Plant Health

This feature article tracks 100 years of soil disinfestation, from the goal of eradicating soilborne pathogens and pests to much milder approaches, aimed at establishing a healthier soil, by favoring or enhancing the beneficial soil microflora and introducing biological control agents. Restrictions on the use of many chemical fumigants is favoring the adoption of nonchemical strategies, from soilless cultivation to the use of physical or biological control measures, with more focus on maintaining soil microbial diversity, thus enhancing soil and plant health. Such approaches are described and discussed, with special focus on their integrated use.

Tillage, green manure and residue retention improves aggregate-associated phosphorus fractions under rice-wheat cropping

The sustainability of the rice–wheat system is threatened due to the deterioration of soil health and emergence of new challenges of climate change caused by low nutrient use efficiency and large scale burning of crop residues. The conservation agriculture based on tillage intensity, crop residue retention and raising green manuring (GM) crops during the intervening period between wheat harvest and rice establishment offers opportunities for restoration of phosphorus (P) dynamics and stimulate phosphatase activities within the macro-and micro-aggregates. Phosphorus and phosphatase activities in the soil aggregates affected by different residue management practices remain poorly understood. Thus, soil samples were obtained after a five-year field experiment to identify the effect of tillage, green manure and residue management on aggregate-associated phosphorus fractions. Four main plot treatments in rice included combination of wheat straw and GM were conventional till puddled transplanted rice (PTR) with no wheat straw (PTR_W0), PTR with 25% wheat stubbles retained (PTR_W25), PTR without wheat straw and GM (PTR_W0 + GM), and PTR with wheat stubbles and GM (PTR_W25 + GM). Three sub-plots treatments in the successive wheat crop were conventional tillage (CT) with rice straw removed (CTW_R0), zero tillage (ZT) with rice straw removed (ZTW_R0) and ZT with rice straw retained as surface mulch (ZTW_R100). Results of the present study revealed significantly higher phosphorus fractions (HCl-P, NaHCO₃-P_i and NaOH-P_o) in treatment PTRW₂₅ + GM and ZTW_R100 compared with PTRW₀/CTW_R0 within both macro- and micro-aggregates. The total phosphorus (P), available P, alkaline phosphatase and phytin-P were significantly higher under ZTW_R100 than CTW_R0. The principal component analysis identified NaOH-P_o, NaHCO₃-P_i and HCl-P as the dominant and reliable indicators for evaluating P transformation within aggregates under conservation agriculture-based practices.

Absence of a home-field advantage within a short-rotation arable cropping system

Aims

The home-field advantage (HFA) hypothesis predicts faster decomposition of plant residues in home soil compared to soils with different plants (away), and has been demonstrated in forest and grassland ecosystems. It remains unclear if this legacy effect applies to crop residue decomposition in arable crop rotations. Such knowledge could improve our understanding of decomposition dynamics in arable soils and may allow optimisation of crop residue amendments in arable systems by cleverly combining crop-residue rotations with crop rotations to increase the amount of residue-derived C persisting in soil.

Methods

We tested the HFA hypothesis in a reciprocal transplant experiment with mesh bags containing wheat and oilseed rape residues in soils at three stages of a short-rotation cropping system. Subsets of mesh bags were retrieved monthly for six months to determine residue decomposition rates, concomitantly measuring soil available N, microbial community structure (phospholipid fatty acid analysis), and microbial activity (Tea Bag Index protocol) to assess how plants may influence litter decomposition rates via alterations to soil biochemical properties and microbial communities.

Results

The residues decomposed at similar rates at all rotational stages. Thorough data investigation using several statistical approaches revealed no HFA within the crop rotation. Soil microbial community structures were similar at all rotational stages.

Conclusions

We attribute the absence of an HFA to the shortness of the rotation and soil disturbance involved in intensive agricultural practices. It is therefore unlikely that appreciable benefits could be obtained in short conventionally managed arable rotations by introducing a crop-residue rotation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11104-022-05419-z.

Logging residues promote rapid restoration of soil health after clear-cutting of rubber plantations at two sites with contrasting soils in Africa

Soil health is defined as the soil's capacity to deliver ecosystem functions within environmental constraints. On tree plantations, clear-cutting and land preparation between two crop cycles cause severe physical disturbances to the soil and seriously deplete soil organic carbon and biodiversity. Rubber, one of the main tropical perennial crops worldwide, has a plantation life cycle of 25 to 40 years, with successive replanting cycles on the same plot. The aim of this study was to assess the effects of clear-cutting disturbance on three soil functions (carbon transformation, nutrient cycling and structure maintenance) and their restoration after the planting of the new rubber crop, in two contrasting soil situations (Arenosol and Ferralsol) in Côte d'Ivoire. In this 18-month diachronic study, we intensively measured soil functions under different scenarios as regards the management of logging residues and the use or not of a legume cover crop. We investigated the relationship between soil macrofauna diversity and soil heath. At both sites, clear-cutting and land preparation disturbed carbon transformation and nutrient cycling significantly and, to a lesser extent, structure maintenance function. When logging residues were applied, carbon transformation and structure maintenance functions were fully restored within 12 to 18 months after disturbance. By contrast, no restoration of nutrient cycling was observed over the study period. A legume cover crop mainly improved the restoration of carbon transformation. We found a strong relationship (P ≤ 0.001; R² = 0.62-0.66) between soil macrofauna diversity and soil health. Our overall results were very similar at the two sites, despite their contrasting soil conditions. Keeping logging residues in the plots and sowing a legume in the inter-row at replanting accelerated the restoration of soil functions after major disturbance caused by clear-cutting and land preparation. Our results confirm the necessity of taking soil macrofauna diversity into account in the management of tropical perennial crops.

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.

Integrated Soil Health Management for Plant Health and One Health: Lessons From Histories of Soil-borne Disease Management in California Strawberries and Arthropod Pest Management

Many soil health assessment methods are being developed. However, they often lack assessment of soil-borne diseases. To better address management strategies for soil-borne disease and overall soil and plant health, the concept of Integrated Soil Health Management (ISHM) is explored. Applying the concept of Integrated Pest Management and an agroecological transdisciplinary approach, ISHM offers a framework under which a structure for developing and implementing biointensive soil health management strategies for a particular agroecosystem is defined. As a case study, a history of soil-borne disease management in California strawberries is reviewed and contrasted with a history of arthropod pest management to illustrate challenges associated with soil-borne disease management and the future directions of soil health research and soil-borne disease management. ISHM system consists of comprehensive soil health diagnostics, farmers' location-specific knowledge and adaptability, a suite of soil health management practices, and decision support tools. As we better understand plant-soil-microorganism interactions, including the mechanisms of soil suppressiveness, a range of diagnostic methodologies and indicators and their action thresholds may be developed. These knowledge-intensive and location-specific management systems require transdisciplinary approaches and social learning to be co-developed with stakeholders. The ISHM framework supports research into the broader implications of soil health such as the “One health” concept, which connects soil health to the health of plants, animals, humans, and ecosystems and research on microbiome and nutrient cycling that may better explain these interdependencies.

Edaphic Response and Behavior of Agricultural Soils to Mechanical Perturbation in Tillage

Mechanical perturbation constrains edaphic functionality of arable soils in tillage. Seasonal soil tool interactions disrupt the pristine bio-physio-mechanical characteristics of agricultural soils and crop-oriented ecological functions. They interfere with the natural balancing of nutrient cycles, soil carbon, and diverse organic matter that supports soil ecosystem interactions with crop rooting. We review soil working in tillage, associated mechanistic perturbations, and the edaphic response of affected soil properties towards cropping characteristics and behavior as soil working tools evolve. This is to further credit or discredit the global transition to minimum and no-till systems with a more specific characterization to soil properties and edaphic crop-oriented goals of soil tooling. Research has shown that improvement in adoption of conservation tillage is trying to characterize tilled soils with edaphic states of native soil agroecosystems rendering promising strategies to revive overworked soils under the changing climate. Soil can proliferate without disturbance whilst generation of new ecologically rich soil structures develops under more natural conditions. Researchers have argued that crops adapted to the altered physio-mechanical properties of cultivated soils can be developed and domesticated, especially under already impedance induced, mechanically risked, degraded soils. Interestingly edaphic response of soils under no-till soil working appeared less favorable in humid climates and more significant under arid regions. We recommend further studies to elucidate the association between soil health state, soil disturbance, cropping performance, and yield under evolving soil working tools, a perspective that will be useful in guiding the establishment of future soils for future crops.

UK Government Policy and the Transition to a Circular Nutrient Economy

The “circular economy” is an increasingly influential concept linking economic and environmental policy to enable sustainable use of resources. A crucial although often overlooked element of this concept is a circular nutrient economy, which is an economy that achieves the minimization of nutrient losses during the production, processing, distribution, and consumption of food and other products, as well as the comprehensive recovery of nutrients from organic residuals at each of these stages for reuse in agricultural production. There are multiple interconnecting barriers to transitioning from the current linear economic system to a more circular one, requiring strongly directional government policy. This paper uses interpretive policy analysis to review six UK government strategies to assess their strengths and weaknesses in embracing nutrient circularisation. Our analysis highlights the acute underrepresentation of the circular nutrient economy concept in these strategies as well as the potential to reorient the current policy towards its development. We find significant barriers to transition presented by ambiguity in key policy terms and proposals, the use of inappropriate indicators, the lack of a systematic approach to key sustainability objectives, and the presence of a “techno-optimist imaginary” throughout the strategies. We develop these findings to make recommendations to help integrate definitions, objectives, and activities across the policy domains necessary for the operational development of a circular nutrient economy.

Future roots for future soils

Mechanical impedance constrains root growth in most soils. Crop cultivation changed the impedance characteristics of native soils, through topsoil erosion, loss of organic matter, disruption of soil structure and loss of biopores. Increasing adoption of Conservation Agriculture in high-input agroecosystems is returning cultivated soils to the soil impedance characteristics of native soils, but in the low-input agroecosystems characteristic of developing nations, ongoing soil degradation is generating more challenging environments for root growth. We propose that root phenotypes have evolved to adapt to the altered impedance characteristics of cultivated soil during crop domestication. The diverging trajectories of soils under Conservation Agriculture and low-input agroecosystems have implications for strategies to develop crops to meet global needs under climate change. We present several root ideotypes as breeding targets under the impedance regimes of both high-input and low-input agroecosystems, as well as a set of root phenotypes that should be useful in both scenarios. We argue that a 'whole plant in whole soil' perspective will be useful in guiding the development of future crops for future soils.

How Much Margin Is Left for Degrading Agricultural Soils? The Coming Soil Crises

Agricultural soils are in peril. Multiple lines of observational and empirical evidence suggest that we are losing the world’s fertile soils at an alarming rate, worsening the on-going global food crisis. It is increasingly clear that the risk of soil crises driven by erratic precipitation, warming air, and farming mismanagement is coming sooner rather than later. At this critical time, society cannot avoid looking for ways to curb soil crises. We argue that now is the right time for science-based mitigation strategies and new insights to protect soils. We offer four research priority areas that society needs to address. Arresting and reversing the ongoing soil degradation are tantamount to safeguarding humanity and the environment. To the extent that we continue to treat soil crises as a problem for farmers only—not as a global challenge—we only escalate the scale to which the problem will grow in time and complexity.