RETRACTED: Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

Abstract

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

1. Introduction

The modern agricultural systems are characterized by intensive cropping systems, deep tillage, continuous monoculture and low organic matter content [1]. Inappropriate management practices have resulted in depletion of the topsoil (0–20 cm) with increased soil acidity and salinization, low soil nutrient content and hampered ecological services and functions [2,3]. Plant diseases caused by soil-borne pathogens such as take-all decline, damping-off, root rot and wilting can cause substantial economic yield loss in the major crops, increasing the soil decline [4,5,6]. Among the biotic factors of soil, soil-borne pathogens are among the major agents that can limit the productivity of the agro-ecosystems, being relatively difficult to control with resistant host cultivars [7]. Soil-borne pathogens include overall strains and isolates of filamentous fungi, oomycetes and bacteria Diseases such as damping-off, root rot, stem collar and crown rots and vascular wilting occurring in the pre- and post-emergence phases can be found in many cropping systems, being primarily caused by a wide spectrum of oomycetes (Pythium spp. and Phytophthora spp.) and fungi (Rhizoctonia spp., Sclerotium spp., Sclerotinia spp., Fusarium spp. and Verticillium spp.), and also by bacteria (Ralstonia spp., Pectobacterium carotovorum, Erwinia carotovora and Streptomyces scabies) [8,9,10,11]. Pathogens such as Fusarium graminearum and Rhizoctonia spp. can infect cereals, oilseed crops and pasture plants, being difficult to control due to their ability to persist in crop residues and litters for longer times through resistant propagules such as sclerotia of Sclerotinia and Sclerotium and microsclerotia of Verticillium [12,13,14,15]. Soil-borne diseases such as root rot of pea caused by Aphanomyces euteiches are difficult to control with fungicides, being able to develop plant resistance [16]. The synthetic fungicides and chemical fumigants are commonly applied to reduce inoculum abundance of pathogens [12,13,14,15], but their impacts on sustainable agriculture should be carefully assessed before being used for balancing benefits and hazards [17]. However, with the increasing awareness of sustainable agricultural practices, several fumigants such as 1,3-dichloropropene and chloropicrin have been restricted due to their negative impacts on the environment. Even methyl bromide was banned in 2004 by the Montreal Protocol for its ability to deplete the ozone layer and increase global warming [18]. More issues are raised by using pesticides that are not effective enough against a wider spectrum of diseases due to their negative effects on beneficial soil organisms [19] or that kill non-target organisms such as insects (bees), fishes, birds and other wildlife organisms [20] or have direct impact on humans and foods [21]. The only practical method to reduce yield loss is to avoid or reduce field infestation even in the presence of pathogens. In such cases, soil related to disease suppression could potentially act in reducing the productivity loss [16].

Disease-suppressive soil (DSS) can be one of the most effective tools in sustainable agriculture, whose indigenous microbial community effectively protects host plants against infection by pathogens by activating several biocontrol mechanisms [22,23]. Soil suppressiveness has already been related to a great number of pathogens [24]. The use of DSS does not refer to the complete eradication of the pathogen from the soil system [25], but it refers to those soils in which disease development can reach the minimum loading level, even in the presence of the virulent strain of the pathogen and the susceptible cultivar of the host plant under environmental conditions favorable to disease [26]. Although it is of primary importance to understand the functioning of the DSS [27], relatively few soils with suppressive property have been described well [28]. Disease suppression not only refers to healthy soil containing a stable microbial community, but also to advantageous physical and chemical soil properties that enhance crop protection. Disease suppression can be viewed as a biological property of a soil conferred by its own microbiome because soil sterilization destroys or reduces its own capacity in disease controlling [29]. Suppression can be transferred between different soils when a disease-conducive soil (DCS) receives a fixed amount (1–10% by volume) of a DSS [30,31]. The findings provided by Cook et al. (1995) [32] and Liu et al. (2020) [33] postulated that plant species tend to develop their defense strategies against soil-borne diseases through selective stimulation. The contribution of antagonistic microorganisms determines the suppressive potential of a soil [25,34,35]. DSS has the ability to suppress pathogens and diseases by integrated mechanisms such as improving plant fitness, inducing natural plant defense, producing antibiotics, competing against the pathogen and modulating the plant immunity systems or hyper-parasitizing the pathogen [25,33,35].

Comprehensive information on DSS is still lacking because soil is a complex dynamic ecosystem that provides nutrients to microbiota that can be defined as super-genomes in a specific habitat [36]. In fact, a teaspoonful of productive soil contains from 100 million to 1 billion organisms [37], where microorganisms are broadly classified into bacteria, archaea, fungi, algae, protozoa and nematodes that are the main drivers of fundamental ecological processes, ecosystem services and functions [37,38,39]. Advances describing the microbial communities have been accompanied by the use of specific terms such as “microbiota” and “microbiome,” whose definitions are still debated [40,41]. In the present review, the term “microbiota” refers to all microorganisms interacting in a specific environment, in this case the soil, while “microbiome” encompasses the structural elements and molecules (i.e., genes and their transcripts, proteins and metabolites, etc.). As well, the environmental conditions associated with the microbiota were initially described by Whipps et al. (1988) [42], then clarified by Berg et al. (2016) [43] and recently reviewed by Berg et al. (2020) [41]. Studies on the interactions between soil microbiota and plants have attracted worldwide interest due to the need for restoration and maintenance of wide biodiversity, which is the priority issue in every conservation policy. Soil microbiota have been studied since the 1990s for their critical role in maintaining the integrity, function and sustainability of a suppressive soil system [44]. Similarly, microbiota play a crucial role in soil functioning and maintaining soil health, with the capacity to control pathogens and diseases [45]. About 21% of carbon (C) fixed through photosynthesis is exuded at the root surface level [46] where the soil microbes feed on it, so influencing their activity and biodiversity. By understanding the interactions between plants and microbiota we can help the exploitation and recruitment of selective beneficial microorganisms to protect the plant against pathogens [32,33]. Although DSSs have been identified for almost 60 years [47], advancements in next-generation sequencing (NGS) have opened a new era in understanding their microbiomes [48]. The NGS technologies, such as metabarcoding (amplicon sequencing) and shotgun sequencing, have allowed to characterize in depth the soil microbiomes [29]. Amplicon sequencing has greater potentiality than culture-dependent techniques to enable the researcher to identify the fine microbiota with disease-suppressive properties in compost-amended soil [49]. In order to screen and identify how the beneficial microbiota can contribute to soil disease suppression, only by deciphering the rhizosphere microbiome can we know the direct and indirect mechanisms of action [22,23].

The current trends toward promising crop protection/production with eco-friendly practices, such as maintaining and promoting disease suppression by crop diversification and soil supplementation with organic amendments (OAs) and antagonistic bacteria (fluorescent pseudomonads), are the main challenges in soil microbiome studies [50,51,52]. Thus, a comprehensive literature has been the object of a very high number of exhaustive reviews since the 1980s. Nonetheless, critical comparison and improvement of the most recent findings based on the combined use of tailored OAs and bio-organic fertilizers, new co-products and organic formulates coming from the recycling in situ of agro-wastes in the light of microbiome-assisted strategies for improving the quality and efficiency of DSS for sustainable plant health management seem to be lacking or insufficiently considered in revision literature. This paper covers the major part of these issues, being mainly addressed to giving a comprehensive review describing, comparing and discussing the oldest concepts vs. the newest challenges based on the assumption that the use of DSS is still more viable and increasingly supported by NGS technology, which can help farmers to design new sustainable cropping systems from the perspective of a virtuous reuse in situ of agricultural wastes. The paper is therefore structured in the following five sections. The current knowledge on soil-borne pathogens and soil microbiota is summarized at the beginning of the paper. How microbiota determine soil quality and what NGS strategies are available to understand soil microbiomes in DSS are presented in the Section 3. Disturbance of the soil microbiota based on combined agricultural practices in the light of microbiome-assisted strategies supported by NGS is deeply considered in the Section 4. Sustainable soil microbiome management by recycling in situ agro-wastes is presented and critically discussed in the Section 5. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed at the end of the paper.

2. Soil-Borne Plant Pathogens and Microbiota Determine Disease Suppression

Disease suppression can be conceptually simplified with a triangle consisting of three major determinants: plant, pathogen and environment [53]. As soil microbes and pathogens share a common space in the rhizosphere, their interactions have a great influence on plant productivity [54]. Since plants are the main providers of soil C stocks and are an energy source, plant diversity affects the composition and structure of microbial communities. The soil physicochemical properties such as texture and clay content, pH, electrical conductivity, soil nutrient, soil organic carbon (SOC) and soil organic matter (SOM) determine microbial activities for the growth and development of the microbiota, giving them an optimum habitat [34]. In addition, crop management practices such as the continuous and rotational cropping systems, tillage, fertilization, amendment by compost, mulching, weeding and irrigation can significantly manipulate the soil, affecting its own microbiome [55,56,57]. It is nearly an impossible task to study the roles of all factors independent of the disease suppression, and thus researcher needs to address them simultaneously in an integrated approach [58]. Understanding the disease model based on the mutual interactions between the host plant, virulent pathogen and environmental conditions favorable for disease development, it can be possible to study the complex systems of DSS for a pathogen/host system [53]. The environmental component needs to be manipulated, being specifically addressed to developing tailored DSSs by reducing their conduciveness even in the presence of the pathogen-host system [34]. Unless the soil properties have been significantly modified to the maximum suppressiveness level or the virulent pathogens have mutated into non-pathogenic strains, the persistence of disease suppression usually lasts long, even with the repeated introduction of pathogens into the suppressive soil [32].

Compost, rice straw, animal manure, green-waste, etc., are OAs that have disease-suppressive attributes against a wide spectrum of pathogens through their influence on soil microbiota [59,60]. However, despite the amended soil showing satisfactory disease biocontrol properties either in the laboratory or under controlled conditions, there is still a major need to achieve the same results under field conditions [61,62]. Such a response is attributed to the complex and specific interactions between the three components of the disease triangle model by better mixing of the compost-enriched bio-inoculants with the soil. Previous authors have reported that the degree of suppressiveness is linked with soil features such as physical conditions, fertility level, biodiversity and abundance of the biota and soil management practices. The use of animal manure modifies the soil’s physical, chemical and biological parameters, affecting crop disease and survival of the pathogen, where Pythium spp. suppression was linked to volatilization of ammonia from manure amendments [61,62]. These authors also documented that application of liquid swine manure reduced the wilting occurrence of common scab in potato fields. Finally, they showed a more significant reduction in root disease of the red stele strawberry in the fields treated with steer/poultry and dairy manure compost than in the comparable unamended soil. DSS has been observed since the 1940s in suppressing Phytophthora root rot in avocado plants (Queensland, Australia), which remained healthy after more than 40 years despite the soil was exposed to an environment highly favorable for disease development. Afterwards, others examples reported are S. scabies [63], Pythium splendens [64], Pythium ultimum [65], Thielaviopsis basicola [66], Phytophthora cinnamomi [67], Phytophthora infestans [68], Fusarium oxysporum [69], Rhizoctonia solani [70], Gaeumannomyces graminis var. tritici [71], Ralstonia solanacearum [72], Aphanomyces euteiches [73] and Plasmodiophora brassicae [74]. The suppression of G. graminis var. tritici [75], which is responsible for the take-all decline of wheat, is one of the most cited examples of induced specific suppression by a monoculture system [22]. The main reason for the high incidence of soil-borne diseases in croplands is the deterioration of the micro-ecological environment that can destroy or alter the balance of the soil microbial communities [76]. Therefore, attempts have been made to differentiate the microbial community composition and structure in the DSS from the DCS [77]. Microbiota change in relation to a local decrease in conduciveness to damping-off and other diseases caused by R. solani [78]. Maintaining dynamic microbial balance among the species, high microbial biomass and high biodiversity are key factors that can facilitate the development of DSS [79,80,81]. High biodiversity allows fewer resident pathogens to survive for long times and may also prevent the invasion of the exogenous ones. Several soil microorganisms can confer benefits in nutrient availability [82,83] and can protect the host plant by preventing colonization and invasion of pathogen [23,84].

There are two distinct models of disease suppressiveness differentiated by general and/or specific mechanisms. General suppression (GS) is a multi-trophic interaction that can be associated with the total microbial biomass in soil, affecting more than one pathogen simultaneously. GS exhibits non-specific mechanisms, such as offering basal protection against a broader spectrum of pathogens [85,86] or biological buffering [87]. GS is defined as the capacity of a soil to suppress the growth and activity of the pathogen up to certain level due to the antagonistic activity of the microbiomes fighting with the pathogens [22]. GS refers to disease suppression through competition between the resident soil microbiota and the pathogens for a common resource such as nutrient and space, and release of antibiotics and toxins from an active microbial consortium that hampers the growth and development of the pathogens [34]. Specific suppression (SS) is another type of disease suppression [88], which refers to the effects of an individual microorganism or a restricted group of microorganisms (or during specific stages of the pathogen life cycle) on suppression [89]. The main distinctive characteristic of SS is due to its transferability [90] from a suppressive soil into a conducive soil (from 1 to 10% by volume) that can be eliminated or reduced by sterilization or pasteurization at 55–60 °C for 30 min or irradiation with gamma rays [22,76,77]. It is important to recall that suppressiveness must be seen as a continuum from GS to SS [91]. However, GS includes antibiosis, competition, parasitism and predation, while SS includes parasitism and predation of the pathogen by the dwelling microbes [92]. Authors have recently provided an interesting new perspective to explain both general and specific suppressiveness by using NGS of the microbiomes. Three soil suppressive models were proposed: “take-all decline” of wheat caused by G. graminis var. tritici, “damping-off” by Rhizoctonia bare patch of wheat and “Streptomyces” in suppression [25]. These authors proposed a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils.

Though authors have argued for limiting the term “disease suppressiveness” to situations involving only a clear biological component [93], there is plentiful evidence for the role of abiotic factors of soil involved in disease suppression [35,53,58]. The chemical and physical attributes can operate in suppression, either directly or indirectly, through their impacts on soil microbial activity. These attributes are largely influenced by different management practices, and thereby they can control the microbial population and diversity in the rhizosphere [94]. On basis of the durability of disease suppression, soils can be grouped into two further categories: “induced suppression” and “long-standing suppression” [71]. The induced suppression is initiated and sustained only when a crop covers the soil, becoming available for the pathogen and stimulating beneficial microbiota to target the pathogen [22]. The induced suppression is well reported with the take-all decline in consecutive monoculture of wheat or barley, where the suppression involves the enrichment of antagonistic bacteria [95]. In contrast, long-standing suppression is a natural process in developing suppressive soils without covering crops, but its origin is still unknown [23].

Developing and studying DSS means understanding the microbiological basis of suppressiveness and identifying the role of each microbial group involved in disease suppression. The first step is to check whether the DSS is microbiota-dependent in nature or not, and if it can be easily verified through sterilization, soil fumigation, steaming, autoclaving, gamma radiation or using selective biocides [96]. Autoclaving and gamma irradiation can eliminate or reduce specific suppression [22]; while soil fumigation can reduce general suppression [89]. The effects of these treatments may vary according to the suppression mechanism.

Figure 1 summarizes the main steps usually followed for studying GS, SS and the continuum between them to isolate and characterize new microbial biological control agents (BCAs) suitable to be used as bio-inoculants to improve soil suppression.

3. Microbiological Basis in Soil Suppression

3.1. Case Studies of Soil-Borne Pathogens and Diseases

Degraded soils may show a relatively lower diversity of beneficial microorganisms when compared to the healthy soils [97]. For instance, continuous cropping (CC) systems of such industrial crops as wheat, corn, sorghum, soybean, tobacco, tomato, banana, cotton, ramie, sesame, peanut, vanilla and ginseng in open fields can potentially contribute to soil degradation and reduction of own biodiversity [98]. Thus, fungal and bacterial diseases can significantly disturb the soil-root interactions, leading to soil depletion and yield loss [99]. The following sections generally focus on the impact of pathogens affecting crops in long-term monoculture systems.

3.1.1. Contribution of Pathogenic Fungi and Oomycetes

Nowadays, most of the soil-borne fungal diseases are well documented in both the intensive and CC systems as being generally caused by filamentous fungi and oomycetes. Ramie [100], soybean [101] and ginseng [102] monocultures showed a substantial reduction of the beneficial microbiota abundance under disease pressure against pathogenic fungi and oomycetes [103]. The beneficial microbiota diversity was also significantly reduced by ginseng monoculture during three years of cultivation. Evidences showed a negative correlation between the diseased plant rate and fungal diversity due to higher abundance, richness and biodiversity as key indicators of soil health, where the relative abundance of F. oxysporum and Phaeosphaeria rousseliana was positively correlated with the incidence and severity of ginseng monoculture [104]. Soybean monoculture was affected by root rot disease and associated with an increased level of F. oxysporum load in soil and reduction in fungal diversity where the CC may alter the fungal community composition [105]. This topic can be explained by some examples of the take-all decline of wheat by G. graminis var. tritici [71], where long-term wheat monoculture increased fluorescent pseudomonad populations associated with biocontrol by production of toxic metabolites for the pathogen [106] and in reducing crop yield [107]. Other evidences confirmed an increased abundance of fungal pathogens that was positively correlated with the simplification of the biodiversity and a reduction of beneficial fungal microbiota, causing decreased growth and yield of continuous peanut crop [108]. Similarly, a large-scale study reported that soybean root rot disease increased dramatically after fewer than three years of CC in field condition in comparison to control soil under crop rotation condition [109]. Moreover, vanilla stem wilt disease outbreak was positively correlated to the increased and decreased abundance of pathogenic strains of F. oxysporum and beneficial microbes in CC of vanilla, respectively [110]. Authors investigated the evolution of the bacterial and fungal communities in soils of banana crops where CC was significantly related to fusarium wilt outbreaks in China [111]. The same authors noticed that fungal microbiome abundance was more related to wilt suppression than the bacterial ones in banana monocultures. Unexpectedly, high fungal species richness was positively correlated with the highest incidence and severity of fusarium wilt on banana, F. oxysporum f. sp. cubense abundance and crop yield reduction, suggesting a weak antagonistic effect of the fungal community of the banana rhizosphere. In fact, the Fusarium spp. and Phyllosticta spp. abundances showed a significant correlation with the reduction of the banana yield [111]. Similarly, authors investigated the impacts of sweet potato monoculture on soil mycobiota, demonstrating that both fungal diversity and richness significantly increased in CC systems, while the ascomycota fungi and oomycetes abundance decreased over time [112]. These authors observed that abundance of the beneficial fungi belonging to the species of Chaetomium decreased overall; but, at the same time, more pathogenic fungi and oomycetes belonging to species of Verticillium, Fusarium, Colletotrichum, Pythium and Phytophthora increased in monocultured soil. The findings of [111] and [112] contrast partly with other studies that showed instead a positive trend of the relatively large richness and diversity of the microbiota in suppressing F. oxysporum f. sp. lycopersici in a mono-cultured Italian area with cherry tomato for at least five consecutive years showing severe fusarium wilt outbreaks [113]. Though this study suggested that abundance, richness and diversity of the fungal and bacterial communities may be strongly determinant for soil suppression, further research is needed to elucidate the role of some fungal community parameters in the emergence and development of disease suppression in a broader range of soils and crops.

3.1.2. Contribution of Pathogenic Bacteria

Continuous monoculture affects composition and taxonomic structure of soil microbiota. Disturbance of the bacterial community may also be determined by the CC systems, where microbiota are often related to the occurrence outbreaks of bacterial wilt disease that may cause damages to plant health and yield [114,115]. For instance, bacterial wilt disease can reduce potato yield drastically [116]. Some studies confirmed that the microbial communities in the healthy rhizosphere were more rich and diverse in term of species than in the diseased rhizosphere, suggesting that microbiome-rich soil may exclude pathogens from the infection sites by restricting their ecological niches [117,118]. In this regard, authors investigated microbial communities of the healthy and diseased cotton fields at the different plant growth stages during consecutive monoculture [119]. These authors reported that microbial communities in the healthy rhizosphere were more rich and diverse than in the diseased cotton field. In fact, the highest evenness of the microbial communities in diseased cotton plants was often observed, so suggesting the existence of relationships between microbial community composition and soil sickness. In particular, diseased cotton plants grown in the mono-cultured soil showed a higher abundance of the genera Deinococcus, Thermus and Bacillus. Other authors showed that diseased soil showed more of a reduction of the alpha-diversity of the microbial communities in ginseng monoculture than in healthy soil [120] and investigated the bacterial communities in tobacco monoculture [121]. They found that in the bacterial alpha-diversity as the observed operational taxonomic units (OTUs), Chao1 richness, Shannon and Simpson diversity were reduced, the evenness was increased. However, abundance of the Ralstonia spp. was positively correlated with bacterial wilt disease in tobacco monoculture. In another study, authors investigated the relationship of nitrogen (N) application and bacterial wilt on the bacterial community in CC of sesame, showing that both N-addition and wilt disease altered the bacterial composition and its structure [122]. This was likely due to fungi, although CC may promote soil-borne bacterial diseases with time, and more research to elucidate the impact on soil-borne bacterial diseases is needed.

3.2. Soil Microbiome Influences Disease Suppression

Microbiota disturbance can limit detrimental effects due to severe diseases in the field, preserving the natural soil microbial biodiversity. For example, deciphering wheat endosphere-rhizosphere microbiomes in R. solani-infested soils is a challenge in developing new Streptomyces strains employed as BCAs [123] and in reducing the incidence and severity of plant diseases [124,125]. In this regard, the main functions, dynamics and roles of the rhizosphere microbiome in plant disease protection were reviewed by Rabelo de Faria et al. (2020) [126]. A multitude of studies revealed that the enrichment of specific microbial populations is related to the composition and amount of root exudates released from the crop into the rhizosphere [127,128,129,130]. On the other hand, microbiota disturbances have consequences for macro- and micronutrients and SOC, pH, origin and localization of the topsoil, and microbial diversity and functions [131]. The microbial interactions caused by disturbance of the microbiomes are the main drivers to shape bacterial abundance, alpha-diversity, richness, and functional diversity in the rhizosphere from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystems [132,133,134,135,136,137,138,139].

Authors have reported that the beneficial microbiota act as a protective defense layer generally in the rhizosphere and endophyte root microbiome [140]. How specific bacterial taxa are enriched in the rhizosphere, giving important plant defense mechanisms operating as a true “second microbial barrier of plant defense” has been reported in literature. The perception of the complexity and structure of the rhizosphere microbiota has been highlighted in the last 10 years [141]. Plant protection against pathogens by bacterial and fungal communities related to beneficial taxa inhabiting the rhizosphere is generally displayed for DSS [82,142]. Modification and selection of the rhizosphere microbiome represent a suitable strategy to improve crop health, thanks to the rhizosphere and endophyte root microbiomes that act in synergy as “the first and second lines of defense against pathogens,” respectively [143,144,145]. From this perspective, the use and exploration of beneficial microbial consortia provide a challenge for farmers to significantly increase productivity in agricultural production systems in a sustainable way [146].

3.2.1. Contribution of Bacterial and Archaeal Communities

Most of the assessment studies have been focused on soil bacteria because the composition of the bacterial and archaeal microbiomes is one of the major factors that drive suppression [147]. In DNA microarray studies for the DSS, conclusions have been drawn by higher signals from non-pathogenic strains of the genera Streptomyces, Bradyrhizobium, Burkholderia [148,149] and Nitrospira [150], whereas the DCS exhibited higher signals from Acidobacterium spp., Pseudomonas spp., Agrobacterium tumefaciens and Janithobacterium spp. [151,152]. Bacteria are known for their inherent ability to produce large numbers of such bioactive secondary metabolites as 2,4-diacetylphloroglucinol (2,4-DAPG) released by fluorescent Pseudomonas spp., which inhibits development of take-all decline in wheat and barley by defense plant roots [153]. Similarly, the archaeal community is also neglected in biocontrol and disease suppression, though it is only a part of the rhizosphere microbiome [48]. These authors differentiated the DCS from the DSS by the lower abundance of Actinobacteria (Streptomyces spp.) specific archaea and micro-eukaryotes in the conducive soils than in the suppressive ones. In a PhyloChip-based metagenomics study of the rhizosphere microbiome, authors detected strong suppressive characteristics in soils containing more abundances of the phylotypes Proteobacteria, Firmicutes and Actinobacteria [48]. Beneficial microbiota for suppressing pathogens in the land management generally belong to the families Xylariaceae and Lactobacillaceae, and to the genus Bacillus [54,154]; while, Enterobacter spp., Flavobacterium balustinum, Pseudomonas fluorescens, Pseudomonas putida and Streptomyces griseus were sourced by compost [155].

3.2.2. Contribution of Fungal Community

Although fungi and micro-eukaryotes are closely associated with the suppressiveness, being crucial for crop protection, most of them are often neglected [112]. Microfauna and mesofauna can feed on pathogens, can help in nutrients’ recycling and their turnover, and can maintain specific biodiversity with dominant bacterial taxa [156]. Soils with higher disease suppressiveness rates are also associated with higher fungal diversity [157]. Since there exists a large diversity of uncultured fungi, culture-independent approaches such as amplicon sequencing must be developed to completely describe the whole fungal community and screen the mycobiota with high suppressiveness along the soil health gradient [158]. Authors have assessed the fungal composition differences between suppressive, weakly suppressive, and conducive soils using the terminal restriction fragments length polymorphisms (T-RFLPs) method as a culture-independent technique [54]. In this regard, arbuscular mycorrhizal (AM) fungi can contribute to disease suppression in several ways [159]. Mycorrhizal plants can recruit more pathogen-antagonistic Actinomycetes than the non-mycorrhizal ones [160]. AM fungi does not compete with other bacteria as do, for instance, plant growth-promoting rhizobacteria (PGPR). Rather, PGPR interact for mutual establishment in order to increase plant disease resistance [161]. AM fungi are often known to increase the nutritional status of the host plant and to help indirectly the suppression of plant diseases. AM fungi increase availability of phosphorus (P) by increasing the tolerance of the plant to pathogen damage [159]. Other non-nutritional mechanisms of AM fungi such as change in exudation patterns, activation of plant defense systems, increased lignification of cell walls, and competition for colonization space and infection sites were documented [162]. AM fungi such as Glomus fasciculatum releases a large variety of antibiotics and toxins acting against pathogens [163]. Besides AM fungi, the feeding preference of the main fungal BCAs like Aspergillus spp., Penicillium spp., Gliocladium spp. and Trichoderma spp. is one of the major determinants in developing a specific rhizosphere microbiome [112]. The interactions between the different trophic levels can modify the nutrient cycling in the soil, influencing the soil nutrient status and plant vigor [164] and affecting suppression against, for instance, the common scab disease by accumulation of mineral elements in the tuber periderm of different potato cultivars [165].

3.3. Omics Approach for Studying Soil Microbiome

The issues related to the complexity and structure of microbial communities in the rhizosphere have been studied in the last 10 years [29]. From this perspective, the use and exploration of beneficial microorganisms in agricultural production systems provide new opportunities to increase crop productivity in a sustainable way by microbiome disturbance [82]. Although a lot of progress has been made in understanding interactions between plants and microorganisms, there is a need to increase the current knowledge of the microbiome ecology and functions. Thus, a detailed understanding of the soil microbiomes in order to limit inconsistencies, drawbacks and failures related to microbiota disturbance is needed. Two major approaches have been used to describe the soil microbiota diversity in combination with numerous identification strategies allowing to identify and quantify microorganisms at the various taxonomic levels, from the highest (kingdom and phylum) to the lowest (genus, species and strains) [41].

The first approach is “culture-dependent.” It involves isolation and purification of the microorganisms from soil or similar substrates as compost, biochar, digestate, etc. [49]. In this approach some basic morphological identifications using staining and microscopy techniques have been frequently employed to identify, for example, AM and other filamentous fungi. The morphological analyses have often been combined with the standard biochemical tests, such as those analyzing carbon source utilization and enzymatic assays in determining the microbial community-level physiological profiles of soil using Biolog EcoPlates™ (Biolog, Inc., Lyon, France) to identify bacteria, fungi and yeasts. Some more complex biochemical tests have sometimes been applied to confirm the microorganism’s identity, such as the multi-locus enzyme electrophoresis for nitrogen-fixing bacteria, the fatty acid methyl esters gas chromatography for some bacterial isolates, and the matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacteria and yeasts.

The second approach is “culture-independent.” It regards the molecular-based methods, with DNA-DNA reassembling study as one of the first molecular methods employed by bacterial taxonomists since the 1960s to describe the relationships among bacterial species [166]. Up to now, it is still the “gold standard method” to identify new species as well as to discriminate bacterial isolates at the lowest taxonomic levels. These approaches were first studied generally in nosocomial microbiology for human illness in gut microbiota [167,168,169,170]. With the development of the first-generation sequencing technologies (Roche 454-pyrosequencing), DNA sequences comparison contributed to identify a number of microbial species in an unprecedented manner [171,172]. Amplification and sequencing of simple genetic markers such as the rDNA gene repeats, the 16S rDNA of prokarya and bacteria, as well as the 18S or 26S/28S rDNA of eukarya and fungi and, more recently, the fungal nuclear ribosomal internal transcribed spacer (ITS) gene regions (ITS1, ITS2, ITS4, ITS5 and more) have been extensively used in soil metagenomics study [173]. Some housekeeping genes, like those coding the β-tubulin and TEF-1α factors, were sequenced for specific fungal identifications as Aspergillus spp. and Penicillium spp. [174,175]. More recently, the combination of several sequences in the multi-locus sequence typing was used to increase the reliability of the identification, as well as the NGS technology being employed to sequence the whole genome of soil microbiota [29]. This methodology does not require cultivation of the microorganisms. During its early development, it consisted in pooling DNA extraction, PCR-amplifying with DNA marker regions by universal/specific primer pairs, and then sequencing them after amplicon separation by the denaturing gradient gel electrophoresis or the cloning of single sequences. Nowadays, the culture-independent strategy is increasingly used. The development of NGS allows to perform metabarcoding analyses involving the amplification and sequencing of specific marker genes to identify a whole community in a DNA sample without the need of cloning or separation steps. Finally, NGS involving the random sequencing of the fragmented DNA extract (shotgun metagenomics approach) and allowing the study of the microbial diversity and the prediction of associated gene functions, was used to perform metagenomics soil analyses. It is important to underline that each approach displays its own strengths and weaknesses [29]. On the one hand, the culture-dependent strategy allows isolating the microorganisms and further characterization of their biochemical and functional traits. However, this way is very laborious, time-consuming, and has a limited capacity to cover the whole diversity of microorganisms because it is dependent on many parameters, such as the culture media employed. Indeed, the concept of “un-culturable microorganism” was highlighted for the first time in the early 20th century, where there were far fewer colonies able to grow on the medium than the number of cells observed by microscopy [176,177]. Nevertheless, this limit can now be bypassed with the use of various culture media leading to the development of the “culturomics” approach. On the other hand, the culture-independent strategy is more labor/cost-effective in studying the abundance, richness and diversity of the microorganisms’ community, as well as in identifying the uncultivable ones. This strategy can highlight the relative abundance of the observed OTUs in metabarcoding and the potential functions of associated genes in metagenomics study. Despite a bias that can be introduced by the DNA extraction step when studying the microbial relative abundance, soil amendment with an exogenous microbial community and the improvement of the DNA extraction protocols can help to standardize the results [41]. Another constraint is the difficulty to reach the lowest taxonomic levels due to the limited amplicon length when using the first-generation sequencers (Roche 454-pyrosequencer), which was discontinued in 2016 [29,178,179]. Indeed, most of the metabarcoding studies related to soil microbiome diversity in coffee plantations under organic and conventional production in tropical agro-ecosystems were performed with the second-generation sequencers (Illumina MiSeq and Illumina HiSeq) that allowed sequencing of the hypervariable regions V3–V4 of bigger markers such as the 16S rDNA gene for bacteria and prokarya, and the 18S rDNA gene for eukarya, or smaller markers such as the ITS gene region for fungi, oomycetes and yeasts [180,181]. Moreover, it has already been demonstrated that smaller sequences do not achieve the highest taxonomic resolution levels for fungi, which are obtained instead with the full length 16S rDNA for bacteria [178]. By contrast, the latest technologies of third (Ion Torrent) and fourth generations (PacBio and Oxford Nanopore) allowed to generate longer sequences if compared to the others’ NGS, but this is done at the expense of the quality due to higher sequencing error rate [29]. However, the full capacity of the platforms remained unexploited as they sequenced only the ITS1-5.8S-ITS2 region of rDNA (<1 kb). The latest technologies of the third generation allow overcoming this problem by generating longer high-quality sequences if compared to the advent of the high-throughput sequencing [178]. Finally, it is important to remind that the data generated by Illumina and Ion Torrent need laborious and advanced statistical analyses for sequence processing by using algorithms implemented by bioinformatics analyses that still need to be improved [182,183,184].

In concluding this issue, it must be recalled that the phylogenetic characterization of microbiota based on DNA analyses does not reflect the real biological activity of the microbial community. It is worth noting that both culture-dependent and culture-independent approaches should remain complementary. In other words, it is of a great interest to decipher the microbial diversity through metabarcoding and metagenomic analyses for a better understanding of the interactions between plant and microorganism. Furthermore, microbial diversity is a relevant indicator of soil changes. However, it is necessary to isolate the microorganisms, to screen their beneficial capacities, and to develop biotechnological applications since more efforts will be certainly required to develop the culturomics approaches for soil microbiota.

4. Microbiota Disturbance Influences the Suppressive Properties

4.1. Microbiome Induces Defense Response

The interactions among pathogen, plant and microbiota are fundamental to modulate a protective phytobiome to fungal invasion [185]. Plant pathogenic fungi and bacteria can induce differential responses to the stress that lead to variation in the microbiome composition of soil and activation of general and/or specific antagonisms restraining the infection through direct/indirect actions of the microbiome or through responses of the host plant. The rhizosphere microbiome can create a barrier against the root infection that can exclude the pathogenic invader activating competition [186]. For instance, PGPR act as a dynamic microbial network that affects the invasion, infection and severity of the disease [186]. Ribosomal RNA-based analyses revealed that the most abundant taxa in the sugar beet seedlings rhizosphere after invasion of R. solani belonged to the families Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae and Sphingomonadaceae [185]. In this study, the authors observed that bacterial taxa identified at a family level upregulated the stress-related genes (ppGpp) in response to pathogen invasion and colonization.

Maintaining the higher soil functionality, the microbial biodiversity increased the ecosystem resilience by making the soil less vulnerable to the biotic stress [187]. Soil biodiversity can significantly contribute to disease suppressiveness by supporting higher trophic level organisms that feed on pathogens and improving plant health and resistance [188]. In general, the mechanisms by which DSS can control disease development are different [189]: (a) parasitism against pathogens by beneficial microbes/microbial communities; (b) production of metabolites, toxins and antibiotics [190,191]; (c) competition for nutrients/resources/substrates; (d) activation of disease-resistance genes in the host plant by beneficial microbes; and (e) improvement of plant nutrition and soil health. Disease suppressiveness can be attributed to the combination of different mechanisms that support each other by forming a true microbial consortium acting as a “super-organism” against specific pathogens. For example, the combined action of mutually compatible non-pathogenic F. oxysporum Fo47 and several strains of fluorescent Pseudomonas spp. can stimulate soil suppressiveness [192]. Relative abundance of disease-suppressive functional genes can be assessed targeting the prnD gene [193] that is responsible for the production of antifungal compounds such as pyrrolnitrin (PRN) [77]. The natural development of DSS is a very slow process that can take up to several years, during which disease outbreaks may occur at a higher rate [48,194]. The process of natural disease suppression is a time-consuming phenomenon since microorganisms need to stabilize the soil with a multitude of physical and chemical processes, so that diverse microorganisms are likely to dominate in the soil [195]. For these reasons, farmers might be reluctant to promote the naturally occurring suppression. Therefore, the speed of developing DSS can be accelerated with the adoption of suitable agronomical management strategies in the mainstream practices [48].

Interaction between the beneficial microbiome and plant pathogenic microorganisms can reduce pathogen invasion and virulence in planta [196]. Interactions among the rhizosphere microbes and the plant roots improve the plant health by defense mechanisms under the disturbance of the microbiome [82]. Microbial BCAs are an important strategy against pathogen invasion in the tissue of the host plant [197,198,199]. Microbial antagonism considered here generally includes competition for nutrients and space and biosynthesis of microbial compounds such as volatiles, enzymes, antibiotics and siderophores that inhibit the pathogens’ development [196]. A cocktail of cell-degrading enzymes such as chitinases and β-1,3-glucanase can be produced by Trichoderma spp. during mycoparasitism of R. solani. In order to be more effective, antagonistic BCAs should grow quickly, proliferate, and survive in the rhizosphere to reach high enough propagules density during pathogen infection. Traditionally, the most common biocontrol strategy uses either single isolates of Trichoderma [200], Pseudomonas [201], Bacillus [202] and Streptomyces [203] or combinations of selected strains. Recently, combining BCA-based purified cell culture with on-farm green composts in proper commercial formulations achieved the main goals in controlling phytopathogens [60,204].

4.1.1. Microbiostasis (Fungistasis)

Manipulation of the soil nutrient content that stimulates stress to the soil-borne pathogenic community, inhibits spore and conidia germination, and suppresses mycelia growth is named “microbiostasis” or “fungistasis” [205]. It results from the loss of energy of the pathogen, which dies or is inactivated [206]. For example, the insufficient N and P content in soil inhibit the germination of conidia and chlamydospores (thick-walled spores produced asexually from mycelia) of Fusarium spp. [205]. Using NGS, it was found that the Streptomyces isolates modulate the endosphere–rhizosphere microbiomes during fungistasis [123].

4.1.2. Production of Antibiotics and Toxins

Streptomyces spp. accounts for 80% of the currently available antibiotics [207]. The common scab of potato caused by S. scabies releases phytotoxins (Thaxtomin A) that induce the disease on potato field [208]. Control is performed through the biological interaction between antibiotics and enzymes among the beneficial microbiota and pathogens [209]. Another example is the production of PRN and 2,4-DAPG by fluorescent pseudomonads that are known to suppress fungal pathogens [50]. Abundance of 2,4-DAPG–producing bacteria such as Burkholderia cepacia and Peanibacillus azotofixans largely depends on the age of the host plant [210]. In maize, the abundance of 2,4-DAPG bacterial producers was relatively lower at the first stage of plant growth than at the advanced stages [211]. Other studies confirmed that young and immature roots recruited more microbes typically living in unstable environments (r-strategists) [212], while mature roots stimulated more abundance of microbes typically occupying more stable environments (k-strategists) [213,214]. Therefore, disease suppression also depends on the plant species and their growth stages.

4.1.3. Production of Volatile Organic Compounds (VOCs)

Besides antibiotics, Streptomyces spp. produce VOCs reducing the severity of plant diseases, causing morphological abnormalities in different fungal pathogens [215,216]. Species of Streptomyces that were found to be antagonistic to R. solani can produce more than 10,000 secondary metabolites, including antibiotics and VOCs [217]. The chemical composition of VOCs is highly diverse, complex, and unique for each microorganism [218]. VOCs can exhibit versatile functions such as inhibition of pathogen growth, enhancement of plant growth, and stimulation of plant resistance [219]. Chemical composition of VOCs is the main driver for their specificity to the targeted pathogens. Streptomyces spp. can produce butanone (methyl vinyl ketone) and dimethyl disulphide, which inhibit the spore germination of Cladosporium cladosporioides [216]. Streptomyces albus can produce anisole that acts against Sclerotinia sclerotiorum and F. oxysporum [220]. Pseudomonas spp. can produce cyclohexanal, decanal, 2-ethyl 1-hexanol, nonanal, benzothiazole, and dimethyl trisulfide, which suppress the fungal growth and germination of S. sclerotiorum [221]. VOCs display strong bioactivity in plant growth promotion such as the production of indole, 1-hexanol, pentadecane, 1,3-tetradecadien-1-ol, 2-butanone, and 2-methyl-n-1-tridecene, which indirectly influence disease suppression [222]. In addition, VOCs act as signaling molecules in intra-specific interactions that indirectly help in disease suppression, although their primary modes of action are still not fully known [219]. Further studies must be implemented to provide conclusive evidence of the role of the VOCs in suppression using specific soil bioassays where the VOC producers and the pathogens are physically separated [223].

4.1.4. Adherence and Colonization of the Pathogen

The pathogen propagules are typically colonized by higher populations of bacteria, fungi and protozoa as well as chlamydospores of F. oxysporum f. sp. raphani by soil bacteria, having an effect on radish germination [224]. The colonized chlamydospores are difficult to germinate and to lyse readily than the non-colonized spores [225]. Another example, the bacterial colonization of Cochliobolus sativus, the causal agent of root rots of grasses, can decrease the virulence of the pathogen by its effects on matric potential, pH, temperature, and clay minerals [226].

4.1.5. Pathogen Destroying

The microbial antagonists can stimulate lysis of pathogens and degradation of chlamydospores, conidia and zoospores [205]. For example, Trichoderma spp. act against Phytophthora root rot of avocado in organic mulching systems by stimulating hyphal lysis of the pathogen [227].

4.1.6. Competition for the Nutritional Sources

As most of the plant pathogens are weak saprophytes, there exists a strong competition for organic substrates between the pathogens and beneficial microbiota [80]. For example, Pythium nunn wins over P. ultimum for colonization of organic compounds, resulting in the suppression of P. ultimum [228]. In addition, the association between P. nunn and Trichoderma harzianum T-95 reduces Pythium damping-off of cucumber in greenhouse conditions, demonstrating that two compatible BCAs can be combined in potting soil to give an additional control of pathogens [229].

4.1.7. Competition for the Infection Sites

As the rhizosphere is a rich source of SOM for the microbes, the pathogens and the BCAs can compete for root colonization and lead to disease suppression [205]. For example, the non-pathogenic strains of Fusarium equiseti from manures suppressed verticillium wilt of potato by competition with the pathogen for the root sites [230].

4.1.8. Activation of Induced Systemic Resistance (ISR)

One indirect way to suppress disease incidence is to increase plant resistance to soil-borne infections by activating the ISR mechanism [205]. For example, the non-pathogenic isolates of F. oxysporum from the soil can stimulate ISR to fusarium wilt of watermelon [231]. This resistance is increased with better plant health by modification of certain organs of the plant (root, leaves and stem) to reduce infections. In some cases, suppression is associated with the production of pre-infection physical barriers in callus-rich plant root. Callus is a multi-layered wall that opposes pathogen invasion and colonization into the vascular tissue [232].

4.2. Sustainable Agronomical Practices Re-Shape the Soil Microbiome

In order to improve soil health and crop yield, the understanding of how microorganisms can interact with their hosts and among themselves in the natural soil environment through their phytobiomes and rhizosphere microbiomes can be used to directly or indirectly address the correct manipulation of the microbiota [233,234,235,236,237]. In this framework, the proper management of the biotic and abiotic soil indicators that promote the activity of beneficial microbiota is a challenge for the sustainable agriculture [238]. If the microbial community and the root system are closely connected, they can be manipulated by agronomic practices. Microbiome disturbance through the sustainable management of the agricultural resources that minimize the negative impact of pathogens can develop novel organic farming systems [236]. Authors have performed comparative microbiome analyses between a fusarium wilt-suppressive soil and a fusarium wilt-conducive soil in a French region (Chateaurenard), showing clear microbiome shifts after manipulation [24].

In the complex soil systems framework it is possible to reconsider diversified approaches with a potential improvement of the optimized microbial inoculants and a microbiome engineering in situ for enhancing crop yield and environmental sustainability in the field [239]. The management of the resident bacterial and fungal communities to induce disease suppression emerges as a primary possibility for farmers since the microbial communities stand out as an important inducer of suppressiveness [26]. In this context, Rabelo de Faria et al. (2020) [126] reviewed the main manipulation strategies and related drivers in assembling beneficial communities. Soil management by combined agricultural practices in reducing the pathogen inoculum potential or in increasing the level of suppression have been proposed [240]. For instance, the dynamics and changes of beneficial microbial communities can be strongly influenced by the interactions among the agricultural practices and soil moisture [241]. The increase of plant diversity in the space (intercropping) or over time (crop rotation or cover cropping) can result in beneficial shifts of the rhizosphere microbiome [81,159].

The common application of bio-organic fertilizers is an old strategy to suppress soil-borne pathogens and to promote plant growth such as for fusarium wilt of lentil and cucumber by antagonistic strains of Bacillus subtilis [242,243]. For instance, the incorporation of composts fortified with microbial inoculants into the soil can trigger suppressiveness by growth and diversification of the native microbiota that can release antifungal compounds during the SOM breakdown [244]. Many reports resulting in incorporation of OAs and compost [245], biochar and pre-conditioned biochar [246,247], brassica green manure [248] and paper mill processing wastes [249] were reported [60]. The targeted pathogens included such fungi as Verticillium spp., Fusarium spp., Sclerotinia spp., Sclerotium spp. and R. solani; or bacteria such as R. solanacearum; or oomycetes like Pythium spp. and Phytophthora spp. [60]. Introduction of organic matter combined with soil solarization manipulates the soil biological structure, becoming an efficient tool in pathogen prevention. Solarization is old practice that uses solar energy to raise the soil temperature to those levels by which the structures of the pathogens are strongly weakened or inactivated in the presence or absence of the host plant. This practice can achieve a significant disease control without eliminating all soil microorganisms, by just modifying the microbiota balance in favor of the beneficial communities [250,251]. Authors found no significant difference in the disease suppression levels between the conventional and organic farms in Sweden [252]. Similar distribution to Pythium aphanidermatum by short-term cover crop decomposition in conventional and organic farming systems was also reported [253]. In contrast, other studies reported higher suppressiveness levels in the conventional farming systems than in the organic ones to Pythium damping-off of sugar beet [254]. In general, organic farming systems showed higher suppression than the conventional ones due to supplementation of organic matter that can increase the soil biological health and suppressive attributes to fusarium wilts [45]. Crop management can significantly affect the microbial diversity and enhance Rhizoctonia disease suppression [190]. Thus, the combined approaches to reduce crop yield loss that include diversified practices such as domestication, breeding and selection of suitable crop varieties; crop rotation, intercropping and cover cropping; soil treatment with eco-friendly bio-fumigation and soil application with OAs, compost, bio-organic fertilizers and BCAs; soil drainage and avoidance of soil compaction; and choice of the more appropriate sowing and harvesting times can induce a significant rhizosphere microbiome disturbance [255,256]. However, long-term adoption of crop management practices that supply higher levels of biologically-available inputs of C, N and P, as well as of magnesium, calcium, copper and iron, either through crop residues or addition of composts and organic manures, can lead to higher levels of suppression. This occur through changes in the abundance, richness, diversity and bioactivity of the soil microbial community that compete with the pathogen [62,157,257].

Agricultural management plays a complex role in developing disease suppression, and the outcome may vary and the results are often indirect. More agricultural practices have been reviewed in literature [29,126] in order to choose the best strategies to reshape the soil microbiome in promoting suppression without the use of hazardous synthetic chemicals. In addition, the key roles of SOM, soil microbial biomass, and biodiversity in supporting the natural suppressiveness during the microbiome reshaping were featured in a recent survey [49].

4.2.1. Land Use and Conservative Agriculture

Natural soil ecosystems are generally more disease-suppressive than arable lands, and such differential response is attributed mainly to differences in the microbial community structure [190]. The type of crop in arable lands and the plants grown in wild ecosystems differ in their impacts on the characteristics of the resident microbiota, which can play different roles in suppression. Higher aboveground biodiversity richness can maintain higher microbial diversity. Land-use changes are often associated with the shift in microbiota. The concept of grassland as a “preserver of microbial diversity” can be explored in order to identify more microbial taxa inducing suppression. Abundance of 2,4-DAPG and PRN producers has been reported to increase with the plant diversity, and also with greater spatial diversity in grassland soil than in the cultivable ones [77,84]. Grasses tend to increase the prnD gene abundance, whereas legumes tend to decrease the 2,4-DAPG and PRN producers.

The effects of long-term agricultural management practices such as the adoption of minimum tillage [258], bio-fumigation with volatile [259], crop rotation [260], crop residue retention [261], and organic farming systems [262] have been beneficially assessed on disease suppression. Conventional intensive farming is associated with the increased destroying of soil structure, which leads to the decreased biodiversity [263]. Therefore, it is expected that suppression is higher in conservative agriculture (CA) and no-tillage (NT) than in conventional farming systems [261]. CA and NT displayed positive effects on soil properties (i.e., improvement in water stable aggregates, increase in the SOC stock, higher pore space and lower soil bulk density) that make it a suitable substrate in order to reproduce and grow the promoting antagonists [264]. The models of suppression may vary with the type of crop residues incorporated into the soil. For example, lignocellulosic substrates increased the abundance of specific antagonists such as Trichoderma spp., whereas more readily decomposable substrates increased the general microbial activity [261]. Although there was wide variability in the suppression response to the inputs of exogenous organic matter, most of the studies reported encouragement results [255]. This variability can be attributed to the differences in chemical composition of the organic matter added to the soil toward a most unified framework for disease suppression [265]. Finally, the decomposition rate of SOM determines the efficiency of the amendment in suppression because the suppressive capacity of the OAs can disappear with time from their first application into the soil, unless they OAs have been continuously applied [266].

4.2.2. Crop and Cultivar Choice

Among the several ways to manage soil microbiome, crop selection is one of the main strategies that can alter the physical, chemical and biological properties of the rhizosphere [193]. Resistance to disease differs from one cultivar to another due to their differences in the eco-physiological properties that influence the type and diversity of microbial activity [267]. The resistant cultivars differ from the susceptible ones by their higher microbial diversity, higher number of putative bacterial interactions, and specific microbial community. Composition of the microbial community changes with the growth stages of the host plant due to the presence of different types of rhizodeposition. However, the dominant modes of biocontrol might not differ significantly along the growth stages [54]. Plants can attract specific antagonists [193]. Depending on the most dominant and active pathogens infecting the host species, new beneficial Pseudomonads spp. at the strain levels are a promising option in suppression of Rhizoctonia and Pythium root rot of wheat [268]. Plants can manipulate microbiota through production of specific root exudates such as malic acid [269,270]. The chemical structure of the exudates addresses the type and nature of the colonization. Cotton monoculture exudes more amino acids and less sugars and phenolic acids in own rhizosphere than in the fallow soil (control), increasing the growth phases of the crop. The physiological shift in root exudation systematically affects the plant–microbial interactions. An increase of some amino acids (i.e., Glu, Ala and Gly) in the cotton rhizosphere leads to a decrease in some beneficial bacterial families as Xanthomonadaceae, Comamonadaceae and Oxalobacteraceae [271], thereby reducing the suppressive level of the soil in cotton monoculture [48].

4.2.3. Rotation, Crop Diversification, Intercropping and Cover Cropping

By reviewing the most recent findings, authors have concluded that monoculture based on the most important horticultural and industrial crops has a significant relevance to the soil health-related concerns [99]. Monoculture may negatively impact on the multiple biotic and abiotic indicators of soil health, fertility, and crop yield. Long-term monoculture potentially can alter abundance, composition, richness, and diversity of the microbial consortia and enzyme activities. Monoculture can accelerate soil depletion by increasing the accumulation of toxic metabolites, salts and acids; reducing soil aggregation; altering the composition of soil aggregate-size classes; and decreasing mineralization, SOM, active carbon and nutrient contents.

In contrast to monoculture, crop rotation can develop suppressive property, having a long history in the agronomical research [272]. It has been proved that crop rotation can increase yield [273] and support some of the essential ecosystem functions [81] such as SOC addition and its storage, nutrient cycling, and disease control [274,275]. The types of crop used in rotation have strong implications in developing soil microbial structure. For example, maize is considered as a source of root exudation where 30% of the total photosynthate is released in the rhizosphere in supporting soil microbe groups [190]. However, in order to elucidate the specific microorganisms from complex soil microbiota that predominantly contribute to suppression is difficult task. The increase in yield for crop rotation might be due to diversity that decreases soil pathogen abundance and virulence, although there are contrasting evidences as to the effect of crop rotation on disease control [193]. Another reason might be attributed to inclusion of non-host crops in the rotation cycle [276]. Crop rotation can enrich the soil of specific faunal communities that increase suppression [277]. For example, the increase of protozoan predation on bacterial communities can lead to enhanced 2,4-DAPG production, activating the disease suppression ability by the expression of biocontrol genes of rhizosphere-associated P. fluorescens [278,279]. Crop rotation can also decrease microbial diversity with increasing crop diversity [193]. Some studies reported better disease control in monoculture than in crop rotation. For example, control of the take-all decline is better in wheat monoculture than in wheat rotation due to increased abundances of siderophore-producing fluorescent pseudomonads [280]. The benefits of crop rotation on disease control can be related to the diversification of the agronomical practices associated with the rotated crops, which could have selected specific microbiomes for pathogen suppression, as observed in an Italian area where long-term tomato monoculture was replaced by triannual rotation between durum wheat and cherry tomato in controlling fusarium wilt on tomato [113] by means of a specific group of microbiota positively correlated to wilt suppression.

In contrast to monoculture, large-scale field experiments highlighted the importance of intercropping in increasing crop yield and reducing disease [281]. Intercropping can be a beneficial practice against the bacterial wilt of tomato [282] and fungal damping-off and root rot of lentil [283]. For example, pepper monoculture can lead to Phytophthora blight outbreaks, but a maize–pepper intercropping system can reduce the spread of Phytophthora blight on pepper, which is attributed to the formation of “root wall” in maize root that acts as a physical barrier against the oomycete [284]. Moreover, maize exudes a significant quantity of antimicrobial compounds that inhibit the growth and spread of Phytophthora capsici. Authors have studied the suppressive effects of peanut intercropped with the medicinal herb Atractylodes lancea against fusarium wilt of peanut in China [285]. They concluded that suppression is triggered by the production of toxic volatile from the root and rhizome of A. lancea into the soil microbiota capable of shifting the native microbiome toward a reshaped microbiome acting as a BCA to Fusarium wilt. Finally, inclusion of cover crops into the cropping system can be a promising option that improves soil properties [286,287].

Cover cropping, alone or in combination with rotation and/or intercropping, can enhance the abundance of the prnD gene, influencing the suppressive potential of the soil [193]. Thus, it is not surprising that cover cropping can modify the physical and chemical properties of the soil, having an indirect impact on the microbial community. Previous studies reported the immediate effects of cover crops [288], which can enhance plant water availability, improving soil structure, reducing soil bulk density, and increasing soil aeration [274]. Several studies correlated the expression of antimicrobial genes with the soil texture and nutrient availability [289]. Cover crops can enhance the SOC content through decomposition of residues and release of exudates from plant roots [290]. Microbial activity is stimulated as a result of increased C recruitment from the root exudates released from the cover crops into the soil. Therefore, significant shifts in the microbial community structure related to the differences in the quantity and quality of the root exudates from cover crops were reported [291].

4.2.4. Organic Amendments Application

Soil supplementation with exogenous organic matter such as compost and bio-organic fertilizer, alone or in combination, has represented a suitable agronomical practice since the 2000s for increasing the natural disease suppressiveness of conducive soil [292]. Application of OAs manipulates the soil’s biological factors and influences the physical and chemical features creating pathways for suppression. OAs enhance growth and development of antagonistic microbes such as Lysobacter antibioticus and Lysobacter gummosus, which can inhibit R. solani [293]. Highly suppressive soil can gradually lose its own property under fluctuation of the environmental conditions [294]. Such fluctuations are expected in a system that is highly dependent on the experimental issues. In fact, the analysis procedures and the protocols used for studying microbiota, such as the sampling and collecting time and the humidity degree of the sample, are stronger concerns for the researcher because a sufficient time period and proper humidity of the sample are needed to develop enough abundance of antagonistic microorganisms after the application of organic materials.

By amending the soil with organic material of different origin and provenance can increase the efficiency of the suppression. Higher SOM content due to frequent supplementation with composted biomass from agro-industrial co-products and plant green-wastes (green composts) is associated with lower incidence and severity of diseases than the soil amended with composted biomass from municipal solid organic waste, household waste, and animal manure [295,296,297,298,299]. Many reports have focused on the beneficial effect of compost addition on suppressiveness to elucidate the diverse mechanisms of action [49]. Addition of suppressive compost can enhance the plant defense system through the ISR mechanisms more than application of a single bio-inoculant [300]. Further, matured and stabilized compost contains multifaceted microbial consortia inducing suppression [301]. In addition, the efficiency of compost in suppression can be enhanced with the inoculation of specific biocontrol agents such as Trichoderma hamatum or B. subtilis [34] or by recruiting beneficial microbial consortia from the highly suppressive compost (green composts) into the conducive ones by using compost water extract [302]. In order to understand the mechanisms of disease suppression by a combination of compost and BCA, sterilization and pasteurization [303,304,305] or heat treatment of the soil–compost mixture should be included [306]. Such treatments lead to reduction or elimination of the suppressive capacity, indicating the biological nature of the suppressiveness in compost. Water extract recruited from several compost types is reported to be suppressive although no significant amount of antibiotics and siderophores were detected [307]. This observation provides more hints on the contribution of the biotic factors than the physical and chemical features in disease suppression. Another mechanism of biocontrol by using composts and un-composted vegetable residues is the release of toxic or stimulatory volatile compounds that lead to changes in the physical and chemical properties of soil, affecting the development of the pathogens [308,309]. Compost-mediated suppression takes place through the competition of nutrient and space between the BCAs and pathogens [205]. For example, cotton produces long-chain fatty acids such as the linoleic acid, which is an important microbial stimulant for zoospore germination of the oomycete P. ultimum that causes Pythium damping-off of cotton [310]. The biocontrol agent Enterobacter cloacae inoculated in compost metabolizes fatty acids and prevents the zoospore germination of P. ultimum, thus reducing the disease incidence level. This is the most probable mode of action of E. cloacae because it does not produce any inhibitory compounds for the propagules or possess any predatory activity [311]. In addition, higher populations of bacteria metabolizing the linoleic acid are commonly found in suppressive compost than in the conducive ones, as such suggesting that the linoleic acid is strongly determinant in suppressing Pythium damping-off of cotton. The composting process has a strong impact on suppression [205] because immature and unstabilized compost from animal manure mixed with Trichoderma spp. does not exert any biological control against Pythium spp. and F. oxysporum. In fact, immature compost represses the biosynthesis of lytic enzymes secreted by the Trichoderma genus due to high glucose concentrations [312]. The soil ecosystem is usually at the state of oligotrophication during decomposition of the exogenous organic matter that it thus changes the soil bacteria ratio from the oligotrophics state into the copiotrophics state during the microbial succession [312]. This ratio change is closely associated with the general suppression mechanism.

Authors have critically evaluated the disease-suppressive capacity of several types of OAs [206]. They observed that OAs were suppressive in 45% of the case studies, 35% non-significantly suppressive, and the remaining 20% even increased the disease incidence. Supplementation with OAs can develop DSS with reduction more than 80%, but it was limited to only 12% of all case studies. Moreover, the suppressive ability of the OAs varied significantly with the targeted pathogens. The same authors who employed BCAs, OAs, and compost fortified with bio-inoculants to plant seeds and/or roots showed that beneficial microorganisms do not last in the rhizosphere for longer times (months or even years), only lasting for some weeks, at the most. However, failures and inconsistencies related to use of OAs and BCAs often make farmers more skeptical of using them for disease suppression in the field.

Concluding this issue, it is also essential to evaluate the economic aspects of compost application. The compost application is currently still too expensive for farmers for controlling Rhizoctonia damping-off in sugar beet under field conditions [294]. In addition to that, the following issues, such as the complex European regulations and national laws, animal manure surplus, variability in availability and transporting of compost, variability in compost quality and feedstock composition, greenhouse gas emissions, and energy requirement are very hard barriers to implementing on-farm composting and compost application in the field [204]. Nonetheless, some recommendations, novelties, innovations, and directions of future researches that might help farmers to solve a number of these issues in the light of a sustainability system were presented and discussed in a recent survey [204]. Therefore, the development of inexpensive agricultural bio-based formulates and tailored on-farm green compost with reliable effects on suppression and soil quality is a greater challenge for implementing new strategies based on the external input of organic matter.

4.2.5. Chitosan Application

Biopolymers based on chitin and chitosan have been suggested to have the potential to enhance disease suppressiveness in soil [313]. Application of chitin and/or chitosan extracted from animal wastes can temporarily increase root growth and reduce the incidence of diseases in cropping systems. Though most of the underlying mechanisms explaining the disease suppression related to biopolymer treatment are still unknown, one of them could be the change in the biodiversity and/or bioactivity of the microbiota that confer the known benefits on suppression. Application of chitin stimulates chitinolytic microorganisms in the soil, which are capable of hydrolyzing chitin of fungal hyphae of the pathogens; afterward, the hydrolyzed chitin attracts secondary responders in enhancing suppression. In this context, studies have postulated that the addition of chitosan can stimulate members of the genus Streptomyces [314] more than the fungal community [315,316]. The ubiquitous Actinobacteria were studied for their primary ability in degrading chitin-like complex organic molecules [317], while their secondary role in suppression was reported. Application of chitosan can be recommended for the pathogens that are currently controlled by chemicals, such as, for example, for Verticillium dahliae of tomato [313]. Although application of green manure and chitin have been reported to increase disease suppression against V. dahliae in a tomato cropping system in greenhouse and field, it does not follow that every OA must stimulate suppressiveness in every crop. Chitin application could not stimulate the antagonistic bacteria Lysobacter spp. for controlling R. solani in sugar beet [294], but it was successfully employed for controlling Rhizoctonia disease in radish and common bean [318,319]. Despite these encouraging findings, there are still more unexplored fields in disease suppression through application of biopolymers. In fact, the effects of chitin and chitosan in relation to crop rotation, soil properties, and nutrient management must be still studied to understand their behaviors in suppression.

4.2.6. Reductive Soil Disinfestation (RSD)

Another way to manage soil is RSD, a pre-planting practice of anaerobic soil disinfestation (ASD) whereby organic matter is incorporated into the soil before planting; then, it is irrigated up to the maximum field capacity and covered with mulches and plastic films [320,321]. RSD has been reported to increase disease tolerance in upland paddy rotation. RSD treatment enhances accumulation of antimicrobial compounds, micronutrients (manganese and ferrous cations), and ammonia that contribute in suppressing a wide range of pathogens. RSD indirectly influences suppression by improving the soil pH, electrical conductivity, microbial population, SOC content, etc. RSD combined or not with the Trichoderma spp. strains for the treatment of degraded and Rhizoctonia-infested greenhouse soils through microbial community changes by RSD in cucumber seedling were reported [322,323,324]. Instead, the effect of ASD on the bacterial community and key-pathogens in a walnut tree crop nursery was documented [325]. ASD combined with soil solarization for improving vegetable crop performances and nutrient dynamics was a suitable alternative to fumigation with methyl bromide in several countries, including Japan, USA and China [326,327].

4.2.7. Soil Pre-Fumigation Combined with Supplementation of OAs and Bio-Organic Fertilizers

There are agricultural practices that can directly control the pathogens without necessarily influencing the soil suppressiveness. For example, bio-fumigation with brassicaceous seed meal, one co-product of the biodiesel chain based on Brassicaceae oleaginous crops as Camelina sativa, Brassica juncea and Sinapis alba, is generally used to control Rhizoctonia damping-off in horticultural nursery due to emission of VOCs (i.e., isothiocyanates and an array of secondary metabolites) derived from the glucosinolate breakdown and mediated by the myrosinase–hydrolysis enzymatic complex in soil. Although such VOCs were toxic for the pathogen, any influence on the suppressive property was found [328]. However, the original chemical state of the soil amended with brassicaceous seed meal was altered by the microbiota [329].

Soil management based on the combined use of pre-fumigation with eco-friendly nitrogen-based substances (i.e., ammonium bicarbonate) and bio-organic fertilizers (composts fortified with tailored bio-inoculants) is an innovative strategy that can trigger the microbiota change for reducing disease incidence and the severity of Ralstonia wilt on tomato [330]. The authors questioned that any efficient method was widely recognized for controlling and/or preventing bacteria wilt of tomato by R. solanacearum. Treating the soil in tomato fields naturally affected by Ralstonia wilt using four types of treatment, and evaluating the outcomes of disease incidence and severity in response to the treatments, the bacterial wilt disease can be effectively controlled without the use of synthetic fumigants or systemic fungicides. All treatments had one of the two tested compost-fortified applications, each with or without soil pre-fumigation. These authors found that soil pre-fumigation resulted in a very strong reduction of the disease. Afterwards, they determined the amplicon sequencing patterns of the soil microbiota to evaluate the soil microbial community structure, either before or after the treatments. Based on their findings, these authors presented an interesting hypothesis on how soil pre-fumigation combined with compost-fortified application resulted in microbiota restructuring by two main steps. In the first one, pre-fumigation destroys the wild microbiota; afterwards, compost-fortified application sets up the further stages of soil colonization. In this way, more benefits from supplying beneficial soil microbiota consortia to suppress bacteria wilt can be achieved. This combined strategy effectively controlled the disease despite the high abundance of R. solanacearum in soil that was found, leading to significant changes in the bacterial and fungal communities. Thus, the shift of the bacterial community in the rhizosphere at the end of the treatments acts as a key factor for controlling Ralstonia wilt of tomato by the increased abundance of bacteria of the genera Rhodanobacter, Terrimonas and Chitinophaga, which are associated to new potential key biomarkers related to suppression of fusarium and verticillium wilt by short-term application of sewage sludge anaerobic digestates into a cherry tomato monoculture of southern Italy (personal communication).

5. Recycling Agricultural Biomass for Sustainable Soil Microbiome Management

5.1. Background of a Circular Economy System

Circular economy constitutes a suitable option to establish new production models by combined strategies to achieve a sustainable development based on optimization of the natural and renewable resources [331]. The circular economy is currently defined as “an economic system that replaces the end-of-life concept with reducing, alternatively reusing, recycling and recovering materials in production/distribution and consumption processes” [332]. Three main drivers address the circular economy background [333]: (a) the preservation and improvement of the natural capital, (b) the optimization of the resource efficiency, and (c) the promotion of the efficiency of the system. The application of a circular economy strategy in agriculture leads to reducing the use of hazardous chemicals from fossil sources in the agricultural production cycles in field and greenhouse to close the nutrient cycles, minimize wastes and recover agro-food co-products [334,335]. Recently, the European Commission also endorsed this objective re-establishing its commitment to climate and the environment through the recommendations of the “European Green Deal”.

A model of circular economy based on these three pillars either optimizes the use of renewable resources or minimizes the generation of agricultural and agro-industrial wastes. In order to obtain long-term sustainability, the opportunities that the circular economy can offer to farmers are truly wider, overall, than those derived from the intensive cropping systems under greenhouse and plastic tunnel [336]. Agricultural activity generates a significant amount of biomass waste in the forms of animal manure and slurries; unsold residual biomass from cultivated green residues, plant wastes, non-marketable products; agro-wastes coming from the crop cultivation fields and minimally-processed fruit and vegetable industries; food waste and agro-industrial by/co-products from the olives, grapes and milk processing [337]. Thus, the most recent research focuses on valorization of fruit and vegetable wastes as the main challenge to solve the logistic-related problems as well as the management of the perishability and heterogeneity of such waste. Furthermore, the increasing amount of disposable biomass waste from various agricultural activities, including agro-bioenergy co-products from the biofuel and biogas chains, should be reduced or even avoided rather than wasted, especially those coming from the greenhouse cultivation and warehouse processing [338].

By recovering and recycling such biomass into new production cycles, the objectives of a virtuous reuse of such organic agricultural and agro-industrial wastes and co-products into many cropping systems can be reached [204]. However, designing and adopting a circular agriculture model should require preliminary analysis by which the specific features of the area of study are first defined to identify all the aspects that can be improved by assessment of the different alternatives in accordance with the preferences and interests of players and stakeholders [336].

There are many agricultural practices that can contribute to improve the circularity models of a sustainable agriculture [338]. Among them, the production of tailored composts and bio-organic fertilizers from agro-wastes, agricultural residues and agro-bioenergy co/by-products for controlling pathogens can be an interesting change of perspective by transforming agricultural wastes into quality composts and bio-organic fertilizers to increase the soil’s natural suppressiveness whenever the SOM content in soil is very low (less than 1%) or scarcely humified [339,340,341].

5.2. Application of On-Farm Green Compost and Bio-Organic Fertilizer

Considering the previous scenario, on-farm green composts and bio-organic fertilizers application in soil can play a key role in the circular economy toward the best environmental sustainability of organic cropping systems by transforming residual biomass into profitable resources. Production of high-quality composts and their derivative products such as compost teas and humic substances represents one possibility for exploiting richer and marketable sources of eco-friendly organic molecules and beneficial microorganisms from agricultural wastes where their co/by-products can become available over time [204]. These authors lead on how such biomass waste, recycled into tailored compost, can be a formidable tool either to reduce organic residuals or to guarantee the supply of humified C, N, P, minerals, and beneficial microbial consortia associated to suppression. On-farm composting has more environmental benefits than the industrial ones, from the lowest greenhouse gas emissions to the lowest leachate generation when compared to landfilling and anaerobic digestion. Soil supplementation with on-farm green compost and bio-organic fertilizer represents one of the best agronomical practices because of their benefits to soil health and disease suppression [49,204]. Recently, authors have focused on the improvement of the soil fertility once compost is applied, on the suppressor effects of compost, and on the concerns due to massive compost application when it exceeds the recommended application rate in mixed soil [342].

The production in situ of a collection of disease-suppressive composts from different feedstocks of agro-wastes represents a concrete and marketable possibility for exploiting a source of microbiota and nutrients for enhancing suppressiveness of conducive or weakly suppressive soils [295,297,302] for a long-term period (at least five years) in several horticultural cropping systems placed in the Italian regions. Pane et al. (2015) [343] tested a set of four types of composted tomato-based residues in a real on-farm composting system against Fusarium wilt disease of tomato caused by F. oxysporum f. sp. lycopersici. Blaya et al. (2016) [344] evaluated the microbial structure of a set of four disease-suppressive composts from vineyard pruning wastes mixed with pepper sludge, pepper wastes, and other vegetable wastes showing different suppressiveness degrees against Phytophthora diseases (damping-off and root rot) by Phytophthora nicotianae in pepper. Chilosi et al. (2017) [345] produced and tested several on-farm green composts from residues of pruning of woody plants and grass clippings in a lavender nursery system against Rhizoctonia damping-off by R. solani, Phytophthora root diseases by P. nicotianae and Sclerotinia root rot by S. sclerotiorum in lavender, obtaining a significant suppression in potting soil for all pathogens. Besides, further research on this topic has been conducted by authors who produced in situ and tested different collections of on-farm green compost. Scotti et al. (2020) [299] and Pane et al. (2020) [346] tested sets of 13 and 2 composts, respectively, from vegetable wastes against Rhizoctonia damping-off by R. solani and Sclerotinia root rot by Sclerotinia minor in cress. Pane et al. (2020) [346] concluded that all tested composts significantly suppressed pathogen populations two weeks after soil application, with greater effects using green compost than the composted dairy and horse manure, but, the suppressive effect disappeared within eight weeks (for dairy and horse manure) and 14 weeks (for green composts) from the application. They correlated the differences of the suppressive composts with the alpha- and beta-diversity of the microbiota associated with the suppression. The differential patterns of suppressiveness can be better predicted by the alpha-diversity targeting the 16S rRNA gene rather than the T-RFLPs technique. Scotti et al. (2020) [299] showed the potential role of the bacterial genera Nocardiopsis and Pseudomonas in disease suppression, and Flavobacterium and Streptomyces in plant biostimulation. Bellini et al. (2020) [347] studied four different waste-based composts by omics procedures, targeting the 16S rRNA and 18S rRNA genes by real-time PCR amplification and the 26S gene by amplicon-based sequencing. They concluded that the composts possessed suppressive property against Phytophthora diseases (root, fruit, foliar and crown rot) by P. capsici in summer squash. Total abundance of the bacterial and fungal communities was found to be higher when compared to the literature data, thus confirming that compost is good inoculum for increasing the suppressive property of conducive soils. Lutz et al. (2020) [298] reviewed the opportunities to increasingly harness compost microbiomes for plant protection through an integrated approach that combined the power of the functional assays to isolate BCAs and PGPR by amplicon and shotgun sequencing to achieve a better understanding of the compost complex system for identifying what taxa were enriched in suppressive composts.

Combined application of OAs supplemented with BCAs, commonly named bio-organic fertilizers (or compost-fortified), were proven to enhance plant resistance against pathogens that is partly due to the impact of the resident soil microbiome on the structure and function of the pathogen-infected plant. Although this topic has been extensively studied since the 2000s and then reviewed by Meghvansi and Varma, (2015) [60], nonetheless, it remains still unclear whether such improvements were driven by the specific action of exogenous bio-inoculants and resident microbial population in the bio-organic fertilizer or by the physicochemical properties of the substrate. Chilosi et al. (2020) [348] investigated the composted spent espresso coffee ground property as a high-value organic fertilizer for soil amendment if fortified with selected fungal inoculants in suppressing damping-off of cress by S. sclerotiorum and P. nicotianae in greenhouse potting soil. These authors explained the suppressive action through multiple antagonistic effects related to the bioactivity of antimicrobial compounds, toxic volatile and non-volatile metabolites produced by Trichoderma atroviride, Trichoderma citrinoviride and Aspergillus spp. Tao et al. (2020) [349] conducted an experimental trial tracking the fusarium wilt disease of banana by F. oxysporum f. sp. cubense and the changes in microbial communities over three growth seasons in response to the following treatments: (a) bio-organic fertilizer supplemented with Bacillus amyloliquefaciens W19, (b) organic fertilizer alone, (c) sterilized organic fertilizer, and (d) sterilized organic fertilizer supplemented with the strain W19. They concluded that suppression was linked to the impact on the resident soil microbial communities, specifically leading to the increase in specific strains of Pseudomonas spp. They further observed correlation between the Bacillus spp. amendment and the indigenous Pseudomonas spp. that might underlie pathogen suppression. These studies revealed that specific bacterial taxa can synergistically increase the biofilm formation around roots, acting as a plant-beneficial consortium against the pathogen.

Table 1. Most recent and promising green composts and bio-organic fertilizers obtained through a circular economy system and mostly studied for their suppressive properties on soil-borne plant pathogens and diseases from the perspective of a microbiome-assisted strategy supported by omics-based approaches for increasing soil suppression.

Amendment	Feedstock	Pathogen	Crop	Disease	Next-Generation Sequencing	Reference
On-farm green compost	Tomato residues (17.5%), escarole residues (15.5%), woodchips (65%). Tomato residues (25%), escarole residues (13%), woodchips (60%). Tomato residues (37%), escarole residues (11%), woodchips (50%). Tomato residues (50%), woodchips (48%).	Fusarium oxysporum f. sp. lycopersici	Tomato	Fusarium wilt	Amplicon sequencing of the bacterial 16S rDNA gene and the fungal ITS1 and ITS2 regions of the ITS rDNA gene using Illumina MiSeq platform.	[343]
On-farm green compost	Vineyard pruning wastes with pepper sludge and wastes. Vineyard pruning wastes with pepper and artichoke wastes. Vineyard pruning wastes with pepper sludge and pepper waste, garlic waste, carrot waste and almond shells. Vineyard pruning wastes with compost, artichoke sludge and artichoke waste.	Phytophthora nicotianae	Pepper	Phytophthora blight	Amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS1 and ITS2 regions of the ITS rRNA gene using Ion Torrent PGM platform.	[344]
On-farm green compost	Composted agro-industrial residues of spent coffee ground, defatted olive marc and woodchips. Composted green-wastes of artichoke, fennel and tomato mixed with agro-bioenergy liquid wastes derived from steam explosion of lignocellulosic biomass for producing 2nd-generation bioethanol.	Sclerotinia sclerotiorum	Lettuce	Sclerotinia root rot	Amplicon sequencing of the ITS1 and ITS2 gene regions adjacent to 5.8 S rDNA gene for fungi Aspergillus, Penicillium and Trichoderma using real-time qPCR assay.	[295]
On-farm green compost	Green nursery compost from residues of pruning of woody plants and grass clippings during the nursery activities.	Rhizoctonia solani	Lavender	Rhizoctonia damping-off	- Amplicon sequencing the ITS1-5.8S-ITS2 region of the rDNA amplified with the universal primers pair ITS1 and ITS4 using real-time qPCR assay. - For Trichoderma: amplification of the chitinase ech42 gene region with the primer pair Chit42-1a and Chit42-2a by qPCR.	[345]
		Phytophthora nicotianae	Lavender	Phytophthora, damping-off
		Sclerotinia sclerotiorum	Lavender	Sclerotinia root rot
Green compost	Composted olive mill.	Verticillium dahliae	Cotton	Verticillium wilt	Procedure not published.	[350]
Green compost	Composted tomato waste.	Verticillium dahliae	Eggplant	Verticillium wilt	Procedure not published.	[351]
Tailoring green compost	Rhizosphere microbiome recruited from a suppressive compost improves plant fitness and increases protection.	Fusarium oxysporum f. sp. Lycopersici	Tomato	Fusarium wilt	Targeting the fungal rDNA ITS gene region and the bacterial 16S rDNA gene by terminal restriction fragments length polymorphisms.	[352]
		Verticillium dahliae	Tomato	Verticillium wilt
On-farm green compost	Composted defatted olive marc and fennel green-waste. Composted un-defatted olive marc and artichoke waste. Composted spent coffee grounds with green-wastes of celery and carrot. Composted spent tea bags with green-wastes of tomato and lettuce. Composted wood chips with green-wastes of tomato and escarole. Composted aspen chips with green-wastes of artichoke and fennel. Composted vineyard pruning wastes, vinery residues and wheat straw with green-wastes of potato and pepper.	Verticillium dahliae	Eggplant	Verticillium wilt	- Amplicon sequencing of the bacterial 16S rDNA gene and the fungal ITS1 and ITS2 regions of the ITS rDNA gene using real-time qPCR assay. - Trichoderma is identified by sequencing the ITS1-5.8S-ITS2 gene regions of the rDNA gene using real-time qPCR assay.	[297]
		Rhizoctonia solani	Bean	Rhizoctonia damping-off
		Phytophthora cinnamomi	Azalea	Phytophthora damping-off
		Phytophthora nicotianae	Tomato	Phytophthora damping-off
		Pythium ultimum	Cucumber	Pythium damping-off
		Pythium irregulare	Zucchini	Pythium damping-off
Industrial/On-farm green compost	Green composted differentiated municipal solid organic wastes. Wet composted differentiated municipal solid organic wastes. Composted cow manure and household waste.	Fusarium oxysporum f. sp. lycopersici	Tomato	Fusarium wilt	Amplicon sequencing of the bacterial 16S rDNA gene and the fungal ITS1 and ITS2 regions of the ITS rDNA gene using real-time qPCR assay.	[297]
		Fusarium oxysporum f. sp. melonis	Melon	Fusarium wilt
		Fusarium oxysporum f. sp. basilici	Basil	Fusarium wilt
On-farm green compost	Dairy and horse manure-based mixed compost. Grape pomace compost. Olive pomace–dairy manure mixed compost. Mixed crop residue compost.	Verticillium dahliae	Bell pepper	Verticillium wilt	Procedure not published.	[353]
On-farm green compost	Leafy vegetables of fennel and woodchips. Maize, livestock waste and woodchips. Leafy vegetables, basil, tomato, watermelon and woodchips. Leafy vegetables of basil, watermelon and woodchips. Leafy vegetables of basil, pumpkin and woodchips. Leafy vegetables of basil and woodchips. Leafy vegetables of basil, watermelon and woodchips. Leafy vegetables of basil and woodchips. Leafy vegetables of basil and woodchips. Leafy vegetables of basil, pumpkin and woodchips. Leafy vegetables of artichoke and woodchips. Leafy vegetables of cabbage, walnut husk and woodchips. Leafy vegetables of basil, sorghum, tomato, pumpkin and woodchips.	Rhizoctonia solani	Cress	Rhizoctonia damping-off	Targeting the 16S rRNA gene for bacteria by terminal restriction fragments length polymorphisms.	[346]
		Sclerotinia minor	Cress	Sclerotinia root rot
On-farm green compost	Vegetable wastes of rocket, endivia, lettuce, fennel, broccoli, pumpkin and basil. Citrus wastes of mandarin orange. Wood scraps.	Rhizoctonia solani	Cress	Rhizoctonia damping-off	Amplicon sequencing of the bacterial hypervariable V3-V4 regions of the 16S rRNA gene and the fungal NS1 and NS2 region of the 18S rRNA gene using Illumina MiSeq platform.	[299]
		Sclerotinia minor	Cress	Sclerotinia root rot
On-farm green compost	Green-waste compost produced in a dynamic composting system for 6 months. Green compost enriched with experimental BCA (Trichoderma sp. TW2). Municipal bio-waste compost produced using green and urban organic fraction bio-wastes in a dynamic composting system for 4 months. Green compost produced in a dynamic composting system for 4 months.	Phytophthora capsici	Summer squash	Root, fruit, foliar and crown rot	Mycobiota evaluated amplifying the D1 domain of the 26S gene using Illumina MiSeq platform.	[347]
Bio-organic fertilizer	Composted spent espresso coffee grounds inoculated with bio-inoculant of Trichoderma atroviridae, Trichoderma citrinoviride and Aspergillus spp.	Sclerotinia sclerotiorum	Cress	Sclerotinia root rot	Procedure not published.	[348]
		Phytophthora nicotianae	Cress	Phytophthora damping-off
Bio-organic fertilizer	Organic fertilizer inoculated with bio-inoculant of Bacillus amyloliquefaciens W19.	Fusarium oxysporum f. sp. cubense	Banana	Fusarium wilt	Amplicon sequencing of the hypervariable V4 region of the 16S rRNA gene and the ITS gene region of fungal ribosomal DNA with the universal primer pairs (520F/802R for bacteria and ITS1F/ITS2R for fungi) using Illumina MiSeq PE 250 platform.	[349]
Bio-organic fertilizer	Effects of biocontrol agents and compost against the Phytophthora capsici of zucchini and their impact on the rhizosphere microbiota.	Phytophthora capsici	Zucchini	Phytophthora blight	Amplicon sequencing of the V3–V4 region of the 16S rRNA gene (for bacteria) and the D1 domain of the 26S gene (for fungi) using Illumina Metagenomic sequencing library.	[354]
Seed meal from oleaginous crop	Change of the soil bacterial community by Brassicaceae seed meal application from Camelina sativa, Brassica juncea and Sinapis alba for suppression of fusarium wilt on pepper.	Fusarium oxysporum f. sp. capsici	Pepper	Fusarium wilt	Amplicon sequencing of the 16S rRNA gene using Roche 454-pyrosequencing with the universal primer pair 27F and 519R.	[355]

summarizes the most recent and promising green composts and bio-organic fertilizers obtained through a circular economy system for increasing soil suppression. Such biomass was studied in the last five years for its suppressive effects on soil-borne pathogens and diseases in relation to characterization of its microbiomes by high-throughput amplicon sequencing.

Table 2. Most promising agricultural practices assisted by omics-based technologies for increasing soil suppression.

Practice	Topic of the Research	Pathogen	Crop	Disease	Next-Generation Sequencing	Reference
Intercropping peanut with medicinal herbs	Peanut intercropped with Atractylodes lancea induces suppression against soil-borne Fusarium pathogens.	Fusarium oxysporum	Peanut	Fusarium wilt	Amplicon sequencing of the hypervariable V4 region of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Roche 454-pyrosequencing.	[285]
Long-term application of organic waste	Long-term organic farming manipulates rhizospheric microbiome and Bacillus antagonism in organic farming system.	Phytophthora capsici	Pepper	Phytophthora blight	Amplicon sequencing of the bacterial 16S rRNA gene using Illumina HiSeq 2500 platform.	[356]
Soil bio-fumigation combined with compost-fortified application	Rhizosphere bacteria assembles molecules derived from fumigation and organic amendment triggers suppression to Ralstonia bacterial wilt.	Ralstonia solanacearum	Tomato	Bacterial wilt	Amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Illumina MiSeq platform.	[330]
Crop rotation cherry tomato with durum wheat	Soil management under tomato–wheat rotation increases the suppressive response against fusarium wilt and tomato shoot growth by changing the microbial composition and chemical parameters.	Fusarium oxysporum f. sp. lycopersici	Tomato	Fusarium wilt	Amplicon sequencing targeting the bacterial 16S rRNA gene and the ITS1 gene region, respectively, with universal primer pairs (27F/907R for bacteria and ITS1F/ITS4R for fungi) using Illumina MiSeq platform.	[113]

overviews the most promising combined agricultural practices supported by the omics-based technologies for increasing soil suppression.

6. Concluding Remarks and Potential Directions of Future Researches

A primary goal is develop high-yielding resistant cultivars and selective microbial inoculants in the rhizosphere to overcome the issues related to the indiscriminate use of hazardous chemicals in controlling soil-borne plant pathogens. This review paper has highlighted some innovative aspects of the soil microbiome manipulation by combined agricultural practices for sustainable plant health management from the perspective of a circular economy. Earlier research was focused on the identification of factors responsible for disease suppressiveness, but now there is an increasing trend of studies based on the omics procedures and culture-independent approaches that make it possible to decipher the underlying mechanisms of soil suppressiveness for harnessing the greater benefits of the reshaped microbiomes. DSS is a promising option that still requires further understanding of the biochemical and ecological interactions between microbiota, plant, pathogen and environment to develop durable and efficient disease suppressiveness. There is an urgent need to identify specific patterns in the relationships between the microbial diversity and ecosystem services adopting the virtuous recycling of agro-wastes into the farm to produce tailored green compost, selected bio-inoculants, and a combination of them for bio-organic fertilizer.

Several questions need to be answered for further studies: (a) What are the differences between the 2,4-DAPG producers in improving the disease-suppressive capacity? (b) Since suppressiveness is closely associated with the microbial community, what are the biggest concerns and issues that should be overcome with respect to the compatibility among the soil microbes and associated effects on disease suppression? (c) Why can certain monoculture systems enrich the soil of 2,4-DAPG producers? Future studies will generate insights that will serve as new pillars for the development of cost-effective and eco-friendly strategies to manage disease suppression. It is still a challenge to develop metagenomics studies to unravel the antagonistic behaviors of the microbiomes toward the pathogens. As well, researches on uncultured microorganisms for the production of antibiotics (Texiobactin) and specific growth factors (siderophores) are also promising options. In addition, the complex interaction between the abiotic and biotic factors and their fluctuation in different soil systems should be further studied. This intricate framework can be broadened with the promotion of integrated competences by a trans-disciplinary approach that is needed to understand the complexity of the soil system for identifying and decoding the suppressive mechanisms and expanding the practical applications of DSS overall in the field.