Microbial diversity creates a global firewall against pathogens in soil.

This chapter focuses on the concept of “One Health,” a global, collaborative, multidisciplinary effort to attain optimal health for plants, animals, people, and the environment. In this relationship, the fungi benefit from carbon resources provided by the plants, and in most cases, arbuscular mycorrhizal fungi enhance plant health through different mechanisms. The efficiency at which soil minerals are absorbed by plants is critical to human and animal health. Healthy and diverse soil organism populations reduce the impact of plant and soil pathogens that can negatively affect the growth of forage and grains needed to feed humans and animals. Healthy soil contains an optimal balance of macro- and micronutrients to support the health of plants, animals, and humans. Exposure to pesticides generally reduces the number of neutral or beneficial organisms and facilitates the overgrowth of pathogenic organisms in soil, whereas the addition of biochar can increase the soil's microbial diversity and plant health.

The soil is a reservoir for various clostridial pathogens, with agricultural soils representing a major source of contamination for overlying crops and grazing livestock. Understanding the prevalence and behaviour of pathogens in these soils is fundamental to ascertaining and mitigating the risk of disease from agroecosystems. This article reviews research pertaining to the overall distribution and abundance of clostridial pathogens in the soil while identifying possible environmental and soil factors influencing their behaviour. Large‐scale soil screens have identified pathogens across the globe, although some Clostridium botulinum toxinotypes are more prevalent in certain geographic regions. Faecal inputs and organic waste amendments to the soil can elevate the levels of enteric clostridial pathogens in the soil and the subsequent disease risk, as highlighted by case–control studies. The ability of Clostridia to sporulate results in their long‐term persistence post‐introduction, increasing the time period for disease transmission. Regularly or permanently saturated soils may also enhance survival, or potentially facilitate the regrowth of some indigenous or introduced Clostridia. This is supported by the high prevalence of Clostridia in paddy soils, greater detection of pathogens in flooded soils, and the higher onset of some clostridial diseases in regions with poorly drained soils. Future research should elucidate soil types and environmental conditions which can enhance pathogen survival/regrowth. The adoption of molecular and sequencing technologies for future diagnostics can facilitate more sensitive detection and a higher resolution of pathogen typing, allowing a better understanding of pathogen population dynamics in farm soils and disease epidemiology. Highlights Understanding the behaviour of soil‐borne clostridial pathogens is key for disease management. Soil, environmental and management factors affecting pathogen survival/introduction are discussed. Soil waterlogging and application of organic soil amendments may increase the number of soil pathogens. More pathogen surveillance and standardisation of diagnostics to better understand behaviour is needed.

One Health - Cycling of diverse microbial communities as a connecting force for soil, plant, animal, human and ecosystem health

Background: The veterinarian Calvin Schwabe described as One Medicine linkages of veterinary medicine and human health that strengthen cooperation between human and animal health professionals and improve provision of health services. The terms One Health and EcoHealth were coined for the interplay of human, animal and ecosystem health. Healthy plants are essential for healthy animals and humans, but plant health and its linkages to human and animal health have rarely been described or trialed. Plantwise, an initiative led by CABI, helps establish community-based plant clinics to improve food security and reduce crop losses. Harmonization of the three health services might increase performance and health status of humans, animals and plants, with positive socioeconomic consequences particularly in remote rural areas. Aims: To describe the human, animal and plant health systems in rural Uganda and identify synergies and benefits of their closer cooperation. Methods: A systematic review on the structure and mandates of the human, animal and plant health systems to conceptualize a framework between them. The main linkages are described qualitatively by stakeholders (smallholder farmers, NGOs, researchers, health workers, administrative staff) in a rural context of Africa within a transdisciplinary approach. The selection of districts is based on agricultural livelihoods and an active network of plant health clinics. Identified synergies are evaluated and quantified by a questionnaire survey. A trial to test the most prominent joint intervention will be outlined. Expected results: An evaluation of synergies between human, animal and plant health systems that can be tested to describe benefits of closer cooperation. An established shared framework on these that facilitates the identification of further practical linkages. This approach should be valid for Uganda and any environment where smallholders depend on extension services for the health of household, livestock and crops. The framework and survey results will be presented.

This study examined the long-term effects of the landfill disposal of untreated urban waste for soil fertilization on the prevalence and antibiotic resistance profiles of various human opportunistic pathogens in soils from Burkina Faso. Samples were collected at three sites in the periphery of Ouagadougou during two campaigns in 2008 and 2011. At each site, amendment led to changes in physico-chemical characteristics as shown by the increase in pH, CEC, total C, total N, and metal contents. Similarly, the numbers of total heterotrophic bacteria were higher in the amended fields than in the control ones. No sanitation indicators, i.e., coliforms, Staphylococci, and Enterococci, were detected. Pseudomonas aeruginosa and Burkholderia cepacia complex (Bcc) were detected at a low level in one amended field. Stenotrophomonas maltophilia was detected from both campaigns at the three sites in the amended fields and only once in an unamended field. Diversity analysis showed some opportunistic pathogen isolates to be closely related to reference clinical strains responsible for nosocomial- or community-acquired infections in Northern countries. Antibiotic resistance tests showed that P. aeruginosa and Bcc isolates had a wild-type phenotype and that most S. maltophilia isolates had a multi-drug resistance profile with resistance to 7 to 15 antibiotics. Then we were able to show that amendment led to an increase of some human opportunistic pathogens including multi-drug resistant isolates. Although the application of untreated urban waste increases both soil organic matter content and therefore soil fertility, the consequences of this practice on human health should be considered.

Pathogen Decontamination of Food Crop Soil: A Review

Effective biosecurity policies are essential to address several major sociological and environmental challenges facing humankind including existential pandemic risks, threats to food security, loss of ecosystem services and public resistance to pesticides and vaccines. Yet biosecurity is subject to multiple interpretations that include dealing with the threats from bioterrorism, managing laboratory biosafety to prevent the escape of pathogenic organisms, handling food and agricultural production systems to prevent disease introduction and addressing the threat of introduced organisms to flora, fauna and humans. The absence of a shared vision of what biosecurity encompasses means that decision-makers are often challenged to design appropriate biosecurity policies at national and global scales. The design of effective policy strategies requires an understanding of the methodological and conceptual barriers that constrain attempts to build an interdisciplinary approach to biosecurity. Here, the first thematic map of the biosecurity research landscape is undertaken to assess just how diverse the interpretation of biosecurity is amongst the global research community and the extent to which the articles published since 2000 represent a common conceptual foundation or are largely clustered within sectors. Co-citation, bibliographic coupling and co-word analyses highlighted that the field of biosecurity encompasses a wide range of domains from biochemistry through to political science, but the research supporting different sectors largely draws from a distinct literature base. While ecosystem and plant health were clustered together within the broad grouping of biological invasions, there was a clear separation from both human and animal health. Yet, there is considerable scope for the management of biological invasions to benefit from insights derived from social perspectives in human and animal health. Biosecurity remains divided by conceptual differences and specialised vocabularies that limit the effectiveness of biosecurity policies addressing biodiversity conservation, public health and food security. To overcome these constraints requires the building of a global biosecurity community that accepts a broader definition of biosecurity, avoids sectorial jargon and establishes mechanisms to cultivate interdisciplinarity through specialised collaborative centres, cross-sectorial research programmes and conceptually rich training programmes.

The ecohealth approach is a core concept integrating environmental aspects with human and animal health (domestic and wild animals). Zoonotic and emerging diseases affect human health and impact negatively on food security. Although both the risk of contracting a disease and the subsequent impacts vary between different genders, age groups, cultures and social conditions, very little research has been done on this and few guidelines or interventions focus adequately on these aspects. This paper is based on a conceptual framework identifying the relationship between gender inequalities and the risk of contracting a disease in an ecohealth perspective. It looks at the varying impacts of plant, animal and human diseases and identifies four contributing factors. This paper first discusses the socially defined roles including social, economic, cultural, legal and political factors that often determine which place men and women occupy in society, which animals and plants men or women have accumulated knowledge of, which they have control of and which they benefit from and consequently the impact men and women have on the environment due to these specific roles. Secondly, it analyses the gender differences in risk of infection. It also analyses cultural differences that influence practices connected to animal, plant and human diseases and discusses respective preventions and treatments. Thirdly, it also identifies the ways men and women are impacted by the diseases of human, plants and animals in different ways. Lastly, this paper assesses the biological factors that influence the differences in exposure, infection rates and mortality rates between men and women during their life cycle. These four factors contribute to gender variations in relation to animal, human, plant and ecological health.

Human pathogens in the soil ecosystem: Occurrence, dispersal, and study method

Effects of solarisation combined with compost on soil pathogens and the microbial community in a spinach cropping system

Fungi constitute a diverse group with highly positive and negative impacts in different environments, having several natural roles and beneficial applications in human life, but also causing several concerns. Fungi can affect human health directly, but also indirectly by being detrimental for animal and plant health, influencing food safety and security. Climate changes are also affecting fungal distribution, prevalence, and their impact on different settings. Searching for sustainable solutions to deal with these issues is challenging due to the complex interactions among fungi and agricultural and forestry plants, animal production, environment, and human and animal health. In this way, the “One Health” approach may be useful to obtain some answers since it recognizes that human health is closely connected to animal and plant health, as well as to the shared environment. This review aims to explore and correlate each of those factors influencing human health in this “One Health” perspective. Thus, the impact of fungi on plants, human, and animal health, and the role of the environment as an influencing factor on these elements are discussed.

Exploring the reservoir of potential fungal plant pathogens in agricultural soil

Municipal-treated wastewater as a practical alternative to conventional rice irrigation: Effects on antibiotic resistance genes, virulence factors and human bacterial pathogens in soil, and responses of rice grain quality

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Background and aims Plant-associated microbiomes play a critical role in host health, yet the effects of belowground pathogens on aboveground microbiomes remain poorly understood. Since systemic plant responses can alter microbial recruitment across organs, we hypothesized that plant-pathogen interactions belowground can trigger specific shifts in the phyllosphere microbiome. Methods Here, we used a tomato microcosm system to test whether the presence of three pathogens in soil — Pseudomonas syringae pv. tomato , Fusarium oxysporum f.sp. lycopersici , and Alternaria alternata — alter the plant phyllosphere bacterial community. We characterized the phyllosphere bacterial community using 16S rRNA amplicon sequencing and inferred the effect of pathogens on microbial diversity, community structure, ecological strategies, co-occurrence network robustness, and assembly processes. Results While overall diversity remained unchanged, we observed pathogen-specific signatures in community structure, ecological strategies, and assembly processes. In addition, exposure to belowground pathogens led to a reduction in microbial network robustness, a shift from specialist to generalist and competitor taxa, and pathogen-specific taxa enriched through selection. Conclusions Our findings suggest that plants are able to modulate their leaf microbiome in response to different belowground pathogens, even in the absence of visible symptoms. While this helps us to better understand the interactions within the holobiont, our results contribute to the development of microbiome-based diagnostic tools, and the targeted design of beneficial microbial consortia for plant protection.