Rather than a human-centric, the basic strategy of achieving Sustainable Development Goals must be focused on restoring and sustaining planetary processes. The urgency of meeting the demands of the humanity must be reconciled with the necessity of enhancing the environment. Increasing and restoring soil organic matter content of the degraded and depleted soils is critical to strengthening planetary processes.

Developments in soil biology and in methods to characterize soil organic carbon can potentially deliver novel soil quality indicators that can help identify management practices able to sustain soil productivity and environmental resilience. This work aimed at synthesizing results regarding the suitability of a range of soil biological and biochemical properties as novel soil quality indicators for agricultural management. The soil properties, selected through a published literature review, comprised different labile organic carbon fractions [hydrophilic dissolved organic carbon, dissolved organic carbon, permanganate oxidizable carbon (POXC), hot water extractable carbon and particulate organic matter carbon], soil disease suppressiveness measured using a Pythium-Lepidium bioassay, nematode communities characterized by amplicon sequencing and qPCR, and microbial community level physiological profiling measured with MicroResp^TM. Prior studies tested the sensitivity of each of the novel indicators to tillage and organic matter addition in ten European long-term field experiments (LTEs) and assessed their relationships with pre-existing soil quality indicators of soil functioning. Here, the results of these previous studies are brought together and interpreted relative to each other and to the broader body of literature on soil quality assessment. Reduced tillage increased carbon availability, disease suppressiveness, nematode richness and diversity, the stability and maturity of the food web, and microbial activity and functional diversity. Organic matter addition played a weaker role in enhancing soil quality, possibly due to the range of composition of the organic matter inputs used in the LTEs. POXC was the indicator that discriminated best between soil management practices, followed by nematode indices based on functional characteristics. Structural equation modeling shows that POXC has a central role in nutrient retention/supply, carbon sequestration, biodiversity conservation, erosion control and disease regulation/suppression. The novel indicators proposed here have great potential to improve existing soil quality assessment schemes. Their feasibility of application is discussed and needs for future research are outlined.

Healthy soils are essential for sustainable agricultural development and soil health requires careful assessment with increasing societal concern over environmentally friendly agricultural development. Soil health is the capacity of soil to function within ecological boundaries to sustain productivity, maintain environmental quality, and promote plant and animal health. Physical, chemical and biological indicators are used to evaluate soil health; the biological indicators include microbes, protozoa and metazoa. Nematodes are the most abundant metazoa and they vary in their sensitivity to pollutants and environmental disturbance. Soil nematode communities are useful biological indicators of soil health, with community characteristics such as abundance, diversity, community structure and metabolic footprint all closely correlated with the soil environment. The community size, complexity and structure reflect the condition of the soil. Both free-living and plant-parasitic nematodes are effective ecological indicators, contributing to nutrient cycling and having important roles as primary, secondary and tertiary consumers in food webs. Tillage inversion, cropping patterns and nutrient management may have strong effects on soil nematodes, with changes in soil nematode communities reflecting soil disturbance. Some free-living nematodes serve as biological models to test soil condition in the laboratory and because of these advantages soil nematodes are increasingly being used as biological indicators of soil health.

Assessment of soil health requires complex evaluation of properties and functions responsible for a broad range of ecosystem services. Numerous soil quality indices (SQI) have been suggested for the evaluation of specific groups of soil functions, but comparison of various SQI is impossible because they are based on a combination of specific soil properties. To avoid this problem, we suggest an SQI-area approach based on the comparison of the areas on a radar diagram of a combination of chemical, biological and physical properties. The new approach is independent of the SQI principle and allows rapid and simple comparison of parameter groups and soils. Another approach analyzing the resistance and sensitivity of properties to degradation is suggested for a detailed evaluation of soil health. The resistance and sensitivity of soil properties are determined through comparison with the decrease of soil organic carbon (SOC) as a universal parameter responsible for many functions. The SQI-area and resistance/sensitivity approaches were tested based on the recovery of Phaeozems and Chernozems chronosequences after the abandonment of agricultural soils. Both the SQI-area and the resistance/sensitivity approaches are useful for basic and applied research, and for decision-makers to evaluate land-use practices and measure the degree of soil degradation.

Soils provide the structural support, water and nutrients for plants in nature and are considered to be the foundation of agriculture production. Improving soil quality and soil health has been advocated as the goal of soil management toward sustainable agricultural intensification. There have been renewed efforts to define and quantify soil quality and soil health but establishing a consensus on the key indicators remains difficult. It is argued that such difficulties are due to the former ways of thinking in soil management which largely focus on soil properties alone. A systems approach that treats soils as a key component of agricultural production systems is promoted. It is argued that soil quality must be quantified in terms of crop productivity and impacts on ecosystems services that are also strongly driven by climate and management interventions. A systems modeling approach captures the interactions among climate, soil, crops and management, and their impacts on system performance, thus helping to quantify the value and quality of soils. Here, three examples are presented to demonstrate this. In this systems context, soil management must be an integral part of systems management practices that also include managing the crops and cropping systems under specific climatic conditions, with cognizance of future climate change.

Plants growing in natural soils encounter diverse biotic and abiotic stresses and have adapted with sophisticated strategies to deal with complex environments such as changing root system structure, evoking biochemical responses and recruiting microbial partners. Under selection pressure, plants and their associated microorganisms assemble into a functional entity known as a holobiont. The commonest cooperative interaction is between plant roots and arbuscular mycorrhizal (AM) fungi. About 80% of terrestrial plants can form AM symbiosis with the ancient phylum Glomeromycota. A very large network of extraradical and intraradical mycelium of AM fungi connects the underground biota and the nearby carbon and nutrient fluxes. Here, we discuss recent progress on the regulators of AM associations with plants, AM fungi and their surrounding environments, and explore further mechanistic insights.

Harnessing disease-suppressive microbiomes constitutes a promising strategy for optimizing plant growth. However, relatively little information is available about the relationship between bulk and rhizosphere soil microbiomes. Here, the assembly of banana bulk soil and rhizosphere microbiomes was investigated in a monoculture system consisting of bio-organic (BIO) and organic management practices. Applying BIO practice in newly reclaimed fields resulted in a high-efficiency biocontrol rate, thus providing a promising strategy for pre-control of Fusarium wilt disease. The soil microbiota was further characterized by MiSeq sequencing and quantitative PCR. The results indicate that disease suppression was mediated by the structure of a suppressive rhizosphere microbiome with respect to distinct community composition, diversity and abundance. Overall microbiome suppressiveness was primarily related to a particular set of enriched bacterial taxa affiliated with Pseudomonas, Terrimonas, Cupriavidus, Gp6, Ohtaekwangia and Duganella. Finally, structural equation modeling was used to show that the changes in bulk soil bacterial community determined its induced rhizosphere bacterial community, which serves as an important and direct factor in restraining the pathogen. Collectively, this study provides an integrative approach to disentangle the biological basis of disease-suppressive microbiomes in the context of agricultural practice and soil management.

Managing plant health is a great challenge for modern food production and is further complicated by the lack of common ground between the many disciplines involved in disease control. Here we present the concept of rhizosphere immunity, in which plant health is considered as an ecosystem level property emerging from networks of interactions between plants, microbiota and the surrounding soil matrix. These interactions can potentially extend the innate plant immune system to a point where the rhizosphere immunity can fulfil all four core functions of a full immune system: pathogen prevention, recognition, response and homeostasis. We suggest that considering plant health from a meta-organism perspective will help in developing multidisciplinary pathogen management strategies that focus on steering the whole plant-microbe-soil networks instead of individual components. This might be achieved by bringing together the latest discoveries in phytopathology, microbiome research, soil science and agronomy to pave the way toward more sustainable and productive agriculture.

The use of antibiotics in human medicine and animal husbandry has resulted in the continuous release of antibiotics into the environment, which imposes high selection pressure on bacteria to develop antibiotic resistance. The spread and aggregation of antibiotic resistance genes (ARGs) in multidrug-resistant pathogens is one of the most intractable clinical challenges. Numerous studies have been conducted to profile the patterns of ARGs in agricultural ecosystems, as this is closely related to human health and wellbeing. This paper provides an overview of the transmission of ARGs in agricultural ecosystems resulting from the application of animal manures and other organic amendments. The future need to control and mitigate the spread of antibiotic resistance in agricultural ecosystems is also discussed, particularly from a holistic perspective, and requires multiple sector efforts to translate fundamental knowledge into effective strategies.

Soil contamination with heavy metal(loid)s threatens soil ecological functions, water quality and food safety; the latter is the focus of this review. Cadmium (Cd) and arsenic (As) are the toxic elements of most concern for food safety because they are relatively easily taken up by food crops. Rice is a major contributor of both Cd and As intakes to the Chinese population. Contamination and soil acidification are the main causes of high Cd levels in rice grains produced in some areas of southern China. The risk of Cd and As accumulation in food crops can be mitigated through agronomic practices and crop breeding. Liming is effective and economical at reducing Cd uptake by rice in acid soils. Paddy water management can produce opposite effects on Cd and As accumulation. Many genes controlling Cd and As uptake and translocation have been characterized, paving the way to breeding low accumulating crop cultivars through marker-assisted molecular breeding or genetic engineering. It is important to protect agricultural soils from future contamination. Long-term monitoring of anthropogenic additions and accumulation of heavy metal(loid)s in agricultural soils should be undertaken. Mass-balance models should be constructed to evaluate future trends of metal(loid)s in agricultural soils at a regional scale.

Irrigation consumes three quarters of global water withdrawals each year. Strategies are needed to reduce irrigation water use, including increasing the efficiency of transfer methods and field application. Comprehensive restoration of soil health, specifically through organic matter amendments, can substantially reduce irrigation demand and increase crop yield. A program to restore severely degraded and desertified soils by incorporating coarse woodchips into the soil successfully increased rainfall capture and elevated soil moisture for several weeks between rainfall events at both Ningxia, north-west China and North Dakota, USA. With addition of fertilizer, woodchip incorporation further increased growth of wheat and alfalfa. Comprehensive soil health assessment of remnant grasslands was used to develop target reference soil profiles by which to guide restoration efforts. Given that most agricultural soils are degraded to some degree, soil health restoration can provide a powerful strategy toward achieving global food and water security.

Soil is the foundation for sustainable food production and environmental protection. Created by unsustainable land management practices and a range of social, economic and environmental drivers, soil degradation and pollution have been an ongoing threat to international food security and environmental quality. Soil degradation and pollution assessments are, however, often focused on the soil itself with little scope to devise new soil management approaches that match food production systems and/or environmental protection. This study draws lessons from an Australia-China Joint Research Center Program, Healthy Soils for Sustainable Food Production and Environmental Quality: a research platform that has brought together multi-disciplinary approaches from world-renowned universities and research organizations in Australia and China. To this end, a framework is presented for future soil management in a new way that combines excellence in research, industry and policymakers in a partnership that will ensure not only the right focus of the research but also that high-quality outputs will be transferable to industry and end-users.

Population growth, increasing drought, and natural resources degradation are significant global issues. Fortunately, management practices to improve soil health can address many of these issues in ways that are both good for the farmer and the environment. In 2012, the United States Department of Agriculture (USDA) Natural Resources Conservation Service initiated its “Unlock the Secrets in the Soil” campaign to assist farmers and ranchers with adopting soil health systems. Other notable efforts at the federal level include research and education projects by USDA Agricultural Research Service, National Institute of Food and Agriculture, and Sustainable Agriculture Research and Education program. The importance of improving soil health is also recognized far beyond federal government programs. The Soil Health Institute, a nonprofit charity, was established to safeguard and enhance the vitality and productivity of soil through scientific research and adoption. Crop commodity organizations are promoting soil health, such as the Soil Health Partnership. The Nature Conservancy is helping companies and private landowners incorporate soil health into their sustainability efforts. Such efforts are supported by the Foundation for Food and Agriculture Research, as well as by some of the leading global food companies such as General Mills. These are just a few of the many efforts to improve soil health in the USA. The significance of the expanding global population, natural resource challenges, and responsibilities to current and future generations truly make enhancing soil health a global imperative.