Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance

The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.

A Comprehensive Perception of Biological Control Potential of Endophytes and Quality Refinement of Lagenaria siceraria

Agriculture and livestock management practices known as organic farming rely more on internal processes than external inputs. Natural environments depend heavily on diversity, and organic farming incorporates both the stated purpose of fostering diversity as well as the use of diversity as a management tool. A more complete understanding of agriculture in terms of agro-ecology has begun to be questioned by the traditional reductionist approach to the study of agriculture. Therefore it is necessary to be aware more about the significance of microbes in processes including soil growth, plant nourishment, and the eradication of plant disease, pest, and weeds. In this study, fluorescent Pseudomonas strain (EFP56) and Trichoderma harzianum were studied for antifungal and antibacterial activity against four common root rot fungi and four common laboratory bacteria in vitro experiments. Furthermore, soil-borne disease surveillance and nutritional quality of Lagenaria siceraria, fluorescent Pseudomonas strain (EFP56) and Trichoderma harzianum were combined with neem cake and cotton cake to check their efficacy. Through the application of organic soil amendments in combination with biocontrol agents improved the quality of vegetables and their nutritional value by raising their polyphenol, carbohydrate, and protein content as well as enhancing antioxidant scavenging status. The experiments were conducted in pots and in fields to confirm their efficacy rate. The final outcomes also revealed greater induction of defense system, disease lessening and enriched fruit quality. Consortium of neem cake and cotton cake with bio-stimulants can regulate biotic as well as abiotic stress.

Biological remediation treatments improve the health of a mixed contaminated soil before significantly reducing contaminant levels

The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.

Cultivation of Melilotus officinalis as a source of bioactive compounds in association with soil recovery practices

Introduction

Melilotus officinalis is a Leguminosae with relevant applications in medicine and soil recovery. This study reports the application of Melilotus officinalis plants in soil recovery and as a source of bioactive compounds.

Methods

Plants were cultivated in semiarid soil under four different fertilizer treatments, urban waste compost at 10 t/ha and 20 t/ha, inorganic fertilizer and a control (no fertilizer). Agronomic properties of soil (pH, EC, soil respiration, C content, macro- and microelements) were analyzed before and after treatment. Also, germination, biomass, element contents, and physiological response were evaluated. Metabolite composition of plants was analyzed through Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS).

Results and discussion

Results showed a significant enhancement of the soil microbial activity in planted soils amended with compost, though there were no other clear effects on the soil physicochemical and chemical characteristics during the short experimental period. An improvement in M. officinalis germination and growth was observed in soils with compost amendment. Metabolite composition of plants was analyzed through Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Principal Component and Agglomerative Hierarchical Clustering models suggest that there is a clear separation of the metabolome of four groups of plants grown under different soil treatments. The five most important discriminative metabolites (annotated) were oleamide, palmitic acid, stearic acid, 3-hydroxy-cis-5-octenoylcarnitine, and 6-hydroxynon-7- enoylcarnitine. This study provides information on how the metabolome of Melilotus might be altered by fertilizer application in poor soil regions. These metabolome changes might have repercussions for the application of this plant in medicine and pharmacology. The results support the profitability of Melilotus officinalis cultivation for bioactive compounds production in association with soil recovery practices.

Mycoremediation with Agaricus bisporus and Pleurotus ostreatus growth substrates versus phytoremediation with Festuca rubra and Brassica sp. for the recovery of a Pb and γ-HCH contaminated soil

Mycoremediation with mushroom growth substrates can be used for the recovery of mixed contaminated soils due to the benefits derived from the physicochemical characteristics of the substrates, the activity of extracellular enzymes secreted by the fungi, and the presence of the fungal mycelia. The objective of this work was to assess the potential of Agaricus bisporus and Pleurotus ostreatus growth substrates (inoculated mushroom substrates vs. spent mushroom substrates) for the mycoremediation of soils co-contaminated with lead and lindane (γ-HCH). We compared the efficiency of these mycoremediation strategies with the phytoremediation with Brassica spp. Or Festuca rubra plants, in terms of both reduction in contaminant levels and enhancement of soil health. An enhanced soil health was achieved as a result of the application of mycoremediation treatments, compared to phytoremediation and control (untreated) treatments. The application of P. ostreatus inoculated substrate led to the most significant reduction in γ-HCH concentration (up to 88.9% compared to corresponding controls). In the presence of inoculated mushroom substrate, P. ostreatus fruiting bodies extracted more Pb than Brassica spp. Or F. rubra plants. Mycoremediation with P. ostreatus growth substrates appears a promising strategy for the recovery of the health of soils co-contaminated with Pb and γ-HCH.

Environmental risk of multi-year polythene film mulching and its green solution in arid irrigation region

Environmental risk of multi-year polythene film mulching (PM) was evaluated and investigated. The location observation following 19-year (2000-2018) PM in irrigated region indicated that the cumulative accumulation of soil microplastics was as high as 2900 ± 19.5 n kg^-1. Microplastic accumulation was tightly associated with soil plasticizer concentration (Pearson's r = 0.728, p <0.05), and the concentration of dominant phthalic acid esters (PAEs) was up to 117.5-705 μg kg^-1. As such, we conducted organic mulching substitute experiment (2019-2020) with non-mulching (CK), maize straw mulching (SM), living clover mulching (CM), PM, PM+SM and PM+CM respectively. The data showed that organic mulching (SM, CM) achieved similar productivity benefit as PM-involved treatments (p > 0.05). Critically, total concentration of PAEs decreased by 6.43% in SM relative to CK, and by 9.61% in PM+SM relative to PM respectively. High throughput sequencing indicated that the proportions of predominant bacteria and fungi were totally lower in PM than those of organic mulching, particularly Sphingomonadaceae and Stachybotryaceae. KEGG analyses indicated that organic mulching promoted the metabolisms of polycyclic aromatic hydrocarbons, benzoic acid (probability>75%) and heterologous organism metabolism (p<0.001), due to improved microbial community assembly. Therefore, organic mulching efficiently accelerated microbial mineralization of PM pollutants, and may act as a green solution to displace PM.

Advanced Collagen-Based Composites as Fertilizers Obtained by Recycling Lime Pelts Waste Resulted during Leather Manufacture

Recent trends in ecological agriculture practices are focused on finding optimal solutions for reuse and recycling of pelt waste from tannery industry. In this context, new collagen-based hydrogels with NPK nutrients encapsulated have been functionalized with synthetic and natural additives, including starch and dolomite, to be used as composite fertilizers. Possible interaction mechanisms are presented in case of each synthetic or natural additive, ranging from strong linkages as a result of esterification reactions until hydrogen bonds and ionic valences. Such interactions are responsible for nutrient release towards soil and plants. These fertilizers have been adequately characterized for their physical chemical and biochemical properties, including nutrient content, and tested on three Greek poor soils and one Romanian normal soil samples. A series of agrochemical tests have been developed by evaluation of uptake and leaching of nutrients on mixtures of sand and soils. It was observed that the clay soil exhibits a higher adsorption capacity than the loam soil for most of nutrients leached from the composite fertilizers tested, with this being correlated with a slower control release towards cultivated plants, thus assuring efficiency of these collagen-based composite fertilizers. The most significant effect was obtained in the case of collagen-based fertilizer functionalized with starch.

How does partial substitution of chemical fertiliser with organic forms increase sustainability of agricultural production?

To ensure global food security, agriculture must increase productivity while reducing environmental impacts associated with chemical nitrogen (N) fertilisation. This necessitates towards more sustainable practices such as recycling organic waste to substitute chemical fertiliser N inputs. However, hitherto how such strategy controls the succession of microbial communities and their relationship with crop yields and environmental impacts have not been comprehensively investigated. We conducted a field experiment with vegetable production in China examining partial substitution (25-50%) of chemical fertiliser with organic forms (pig manure or municipal sludge compost) considering key sustainability metrics: productivity, soil health, environmental impacts and microbial communities. We demonstrate that partial organic substitution improved crop yields, prevented soil acidification and improved soil fertility. Treatments also reduced detrimental environmental impacts with lower N₂O emission, N leaching and runoff, likely due to reduced inorganic nitrogen surplus. Microbial communities, including key genes involved in the N cycle, were dynamic and time-dependent in response to partial organic substitution, and were also important in regulating crop yields and environmental impacts. Partial organic substitution increased bacterial diversity and the relative abundance of several specific microbial groups (e.g. Sphingomonadales, Myxococcales, Planctomycetes, and Rhizobiales) involved in N cycling. Additionally, partial organic substitution reduced the number of bacterial ammonia oxidizers and increased the number of denitrifiers, with the proportion of N₂O-reducers being more pronounced, suggesting a mechanism for reducing N₂O emissions. Comprehensive economic cost-benefit evaluation showed that partial organic substitution increased economic benefit per unit area by 37-46%, and reduced agricultural inputs and environmental impacts per unit product by 22-44%. Among them, 50% substitution of pig manure was the most profitable strategy. The study is crucial to policy-making as it highlights the potential advantages of shifting towards systems balancing chemical and organic fertilisers with economic benefits for farmers, reduced environmental damage and an efficient way for organic waste disposal.

Bio-Based Waste’ Substrates for Degraded Soil Improvement—Advantages and Challenges in European Context

The area of degraded sites in the world is constantly expanding and has been a serious environmental problem for years. Such terrains are not only polluted, but also due to erosion, devoid of plant cover and organic matter. The degradation trends can be reversed by supporting remediation/reclamation processes. One of the possibilities is the introduction of biodegradable waste/biowaste substrates into the soil. The additives can be the waste itself or preformed substrates, such composts, mineral-organic fertilizers or biochar. In EU countries average value of compost used for land restoration and landfill cover was equal 4.9%. The transformation of waste in valuable products require the fulfillment of a number of conditions (waste quality, process conditions, law, local circumstances). Application on degraded land surface bio-based waste substrates has several advantages: increase soil organic matter (SOM) and nutrient content, biodiversity and activity of microbial soil communities and change of several others physical and chemical factors including degradation/immobilization of contaminants. The additives improve the water ratio and availability to plants and restore aboveground ecosystem. Due to organic additives degraded terrains are able to sequestrate carbon and climate mitigate. However, we identified some challenges. The application of waste to soil must comply with the legal requirements and meet the end of use criteria. Moreover, shorter or long-term use of bio-waste based substrate lead to even greater soil chemical or microbial contamination. Among pollutants, “emerging contaminants” appear more frequently, such microplastics, nanoparticles or active compounds of pharmaceuticals. That is why a holistic approach is necessary for use the bio-waste based substrate for rehabilitation of soil degraded ecosystems.

Mitigation of petroleum-hydrocarbon-contaminated hazardous soils using organic amendments: A review

The term "Total petroleum hydrocarbons" (TPH) is used to describe a complex mixture of petroleum-based hydrocarbons primarily derived from crude oil. Those compounds are considered as persistent organic pollutants in the terrestrial environment. A wide array of organic amendments is increasingly used for the remediation of TPH-contaminated soils. Organic amendments not only supply a source of carbon and nutrients but also add exogenous beneficial microorganisms to enhance the TPH degradation rate, thereby improving the soil health. Two fundamental approaches can be contemplated within the context of remediation of TPH-contaminated soils using organic amendments: (i) enhanced TPH sorption to the exogenous organic matter (immobilization) as it reduces the bioavailability of the contaminants, and (ii) increasing the solubility of the contaminants by supplying desorbing agents (mobilization) for enhancing the subsequent biodegradation. Net immobilization and mobilization of TPH have both been observed following the application of organic amendments to contaminated soils. This review examines the mechanisms for the enhanced remediation of TPH-contaminated soils by organic amendments and discusses the influencing factors in relation to sequestration, bioavailability, and subsequent biodegradation of TPH in soils. The uncertainty of mechanisms for various organic amendments in TPH remediation processes remains a critical area of future research.

Mycorrhizal-Assisted Phytoremediation and Intercropping Strategies Improved the Health of Contaminated Soil in a Peri-Urban Area

Soils of abandoned and vacant lands in the periphery of cities are frequently subjected to illegal dumping and can undergo degradation processes such as depletion of organic matter and nutrients, reduced biodiversity, and the presence of contaminants, which may exert an intense abiotic stress on biological communities. Mycorrhizal-assisted phytoremediation and intercropping strategies are highly suitable options for remediation of these sites. A two-year field experiment was conducted at a peri-urban site contaminated with petroleum hydrocarbons and polychlorinated biphenyls, to assess the effects of plant growth (spontaneous plant species, Medicago sativa, and Populus × canadensis, alone vs. intercropped) and inoculation of a commercial arbuscular mycorrhizal and ectomycorrhizal inoculum. Contaminant degradation, plant performance, and biodiversity, as well as a variety of microbial indicators of soil health (microbial biomass, activity, and diversity parameters) were determined. The rhizosphere bacterial and fungal microbiomes were assessed by measuring the structural diversity and composition via amplicon sequencing. Establishment of spontaneous vegetation led to greater plant and soil microbial diversity. Intercropping enhanced the activity of soil enzymes involved in nutrient cycling. The mycorrhizal treatment was a key contributor to the establishment of intercropping with poplar and alfalfa. Inoculated and poplar-alfalfa intercropped soils had a higher microbial abundance than soils colonized by spontaneous vegetation. Our study provided evidence of the potential of mycorrhizal-assisted phytoremediation and intercropping strategies to improve soil health in degraded peri-urban areas.

Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review

Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil.

Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture

Dynamic consortium of microbial communities (bacteria, fungi, protists, viruses, and nematodes) colonizing multiple tissue types and coevolving conclusively with the host plant is designated as a plant microbiome. The interplay between plant and its microbial mutualists supports several agronomic functions, establishing its crucial role in plant beneficial activities. Deeper functional and mechanistic understanding of plant-microbial ecosystems will render many "ecosystem services" by emulating symbiotic interactions between plants, soil, and microbes for enhanced productivity and sustainability. Therefore, microbiome engineering represents an emerging biotechnological tool to directly add, remove, or modify properties of microbial communities for higher specificity and efficacy. The main goal of microbiome engineering is enhancement of plant functions such as biotic/abiotic stresses, plant fitness and productivities, etc. Various ecological-, biochemical-, and molecular-based approaches have come up as a new paradigm for disentangling many microbiome-based agromanagement hurdles. Furthermore, multidisciplinary approaches provide a predictive framework in achieving a reliable and sustainably engineered plant-microbiome for stress physiology, nutrient recycling, and high-yielding disease-resistant genotypes.

Effect of Organic Residues on Pesticide Behavior in Soils: A Review of Laboratory Research

The management of large volumes of organic residues generated in different livestock, urban, agricultural and industrial activities is a topic of environmental and social interest. The high organic matter content of these residues means that their application as soil organic amendments in agriculture is considered one of the more sustainable options, as it could solve the problem of the accumulation of uncontrolled wastes while improving soil quality and avoiding its irreversible degradation. However, the behavior of pesticides applied to increase crop yields could be modified in the presence of these amendments in the soil. This review article addresses how the adsorption–desorption, dissipation and leaching of pesticides in soils is affected by different organic residues usually applied as organic amendments. Based on the results reported from laboratory studies, the influence on these processes has been evaluated of multiple factors related to organic residues (e.g., origin, nature, composition, rates, and incubation time of the amended soils), pesticides (e.g., with different use, structure, characteristics, and application method), and soils with different physicochemical properties. Future perspectives on this topic are also included for highlighting the need to extend these laboratory studies to field and modelling scale to better assess and predict pesticide fate in amended soil scenarios.

Recent Trends in Sustainable Remediation of Pb-Contaminated Shooting Range Soils: Rethinking Waste Management within a Circular Economy

Soil metal contamination in recreational shooting ranges represents a widespread environmental problem. Lead (Pb) is the primary component of traditional ammunition, followed by metalloids such as antimony (Sb) and arsenic (As). Lead-based bullets and pellets deposited on the soil surface are subject to steady weathering; hence, metal(loid)s are released and accumulated in the underlying soil, with potential adverse consequences for ecosystem function and human health. Amongst the currently available environmentally-safe technologies for the remediation of metal-contaminated soils, chemical immobilization is recognized as the most practical and cost-effective one. This technology often uses inorganic and organic amendments to reduce metal mobility, bioavailability and toxicity (environmental benefits). Likewise, amendments may also promote and speed up the re-establishment of vegetation on metal-affected soils, thus facilitating the conversion of abandoned shooting ranges into public green spaces (social benefit). In line with this, the circular economy paradigm calls for a more sustainable waste management, for instance, by recycling and reusing by-products and wastes in an attempt to reduce the demand for raw materials (economic benefit). The objective of this manuscript is to present a state-of-the-art review of the different industrial and agro-food by-products and wastes used for the remediation of metal-contaminated shooting range soils.

Carbon Amendments Influence Composition and Functional Capacities of Indigenous Soil Microbiomes

Soil nutrient amendments are recognized for their potential to improve microbial activity and biomass in the soil. However, the specific selective impacts of carbon amendments on indigenous microbiomes and their metabolic functions in agricultural soils remain poorly understood. We investigated the changes in soil chemical characteristics and phenotypes of Streptomyces communities following carbon amendments to soil. Mesocosms were established with soil from two field sites varying in soil organic matter content (low organic matter, LOM; high organic matter, HOM), that were amended at intervals over nine months with low or high dose solutions of glucose, fructose, malic acid, a mixture of these compounds, or water only (non-amended control). Significant shifts in soil chemical characteristics and antibiotic inhibitory capacities of indigenous Streptomyces were observed in response to carbon additions. All high dose carbon amendments consistently increased soil total carbon, while amendments with malic acid decreased soil pH. In LOM soils, higher frequencies of Streptomyces inhibitory phenotypes of the two plant pathogens, Streptomyces scabies and Fusarium oxysporum, were observed in response to soil carbon additions. Additionally, to determine if shifts in Streptomyces functional characteristics correlated with microbiome composition, we investigated whether shifts in functional characteristics of soil Streptomyces correlated with composition of soil bacterial communities, analyzed using 16S rRNA gene sequencing. Regardless of dose, community composition differed significantly among carbon-amended and non-amended soils from both sites. Carbon type and dose had significant effects on bacterial community composition in both LOM and HOM soils. Relationships among microbial community richness (observed species number), diversity, and soil characteristics varied among soils from different sites. These results suggest that manipulation of soil resource availability has the potential to selectively modify the functional capacities of soil microbiomes, and specifically to enhance pathogen inhibitory populations of high value to agricultural systems.

Potential Benefits and Risks for Soil Health Derived From the Use of Organic Amendments in Agriculture

The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.