M. phaseolina is characterized by hyaline hyphae with thin walls to light brown or dark brown hyphae with septa. Branches from the main hyphae are generally formed at right angle on parent hyphae with constriction at the point of origin. Microsclerotia, a compact mass of hardened fungal mycelium, are spherical, oval or oblong, light brown in the young stage becoming darker (brown to black) with ageing. Pycnidia, which are rarely observed under natural conditions, are larger than microsclerotia, dark brown to black, rough, globose, or irregular, beaked and ostiolated (Lakhran et al., 2018). The fungus can show a wide heterogeneity in mycelium colour, microsclerotia distribution, pycnidia formation and chlorate phenotypes between isolates on synthetic media. Nevertheless, the amplification of the internal transcribed spacers (ITS) has indicated that isolates belonged to one single species (Almomani et al., 2013). It has been suggested that the morphological heterogeneity could be attributed to the responses of the fungi to environmental factors or variation in their hosts species (Tok, 2019; Pandey et al., 2020).

Likewise, a high correlation between virulence and phenotype (i.e., morphological variations) has been reported by Tok (2019).

Microsclerotia is the primary infective source of M. phaseolina. This structure of resistance is able to survive up to 15 years in soil (Gupta et al., 2012). It can infect the roots of the host plant at the seedling stage via multiple germinating hyphae. Once in the roots, the fungus affects the vascular system, disrupting the water and nutrient transport to the upper parts of the plants (Figure 1). Typical symptoms are yellowing and senescence of leaves that remain attached to the stems by the petioles, sloughing of cortical tissues from the lower stem and taproot, and the grey appearance of these tissues due to the abundance of microsclerotia that can result in a premature death of the host plant (Short et al., 1978; Wyllie, 1988; Sinclair and Backman, 1989; Smith and Carvil, 1997; Figure 2).

Genetic diversity among M. phaseolina isolates has been widely studied using mostly molecular markers followed by cluster analysis. Genetic methods such as random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and rDNA sequencing have been successfully used for comparative genomics in M. phaseolina population from different countries (Mayék-Pérez et al., 2001; Almeida et al., 2003; Jana et al., 2005; Babu et al., 2010; Khan et al., 2017). Eventhough sexual reproduction in M. phaseolina is absent, results showed a high degree of genetic diversity among isolates of this pathogen. It is possible that parasexualism with fusion of cells from different hyphae could occur, and may form heterokaryons that contribute to the variability observed (Almeida et al., 2003).

In some studies (Jana et al., 2005; Babu et al., 2010; Mahdizadeh et al., 2012), genetic diversity has been associated with host plant origin and/or geographical locations, while in other studies (Mahdizadeh et al., 2011; Reznikov et al., 2018, 2019), clustering of data could not clearly differentiate isolates based on their pathogenicity, morphological characteristic, host or geographical origins. In numerous studies the distribution of M. phaseolina genotype has been found to be independent of sampling location and host (Khan et al., 2017; Tančić Živanov et al., 2019). Moreover, genetic variability among Brazilian isolates of M. phaseolina showed that one single root can harbor more than one haplotype (Almeida et al., 2003). M. phaseolina has a very heterogeneous nature. Variation in pathogenicity appeared to be associated with their ability to produce hydrolytic enzymes and to genetic diversity (Ramos et al., 2016; Khan et al., 2017). Thus, attempts to study genotype–genotype specific interactions between plant cultivars and M. phaseolina isolates as proposed by Reznikov et al. (2019) will help in the development of resistant cultivars.

Accurate diagnosis and early detection of pathogens is an essential step in plant disease management. Species-specific oligonucleotide primers and oligonucleotide probes can be used to rapidly detect and identify M. phaseolina by polymerase chain reaction (PCR) and hybridization (Babu et al., 2007). More recently, specific primers have been developed for the identification of M. phaseolina, M. pseudophaseolina, and M. euphorbiicola (Santos et al., 2020). This may contribute to broader studies conducted to evaluate the diversity and distribution of species of this genus.

Furthermore, a real-time qPCR assay has been developed to detect and quantify M. phaseolina abundance in rhizosphere soil and plant tissues. Sets of specific primers have been designed for SYBR green and TaqMan assay (Babu et al., 2011; Burkhardt et al., 2018). These are useful tools for the evaluation of a plant pathogen population in the soil, and it seems possible to estimate the vegetative population of M. phaseolina following direct extraction of soil DNA without culturing (Babu et al., 2011).

In the recent decade, Islam et al. (2012) edited the first whole genome of M. phaseolina which was characterized by a large number of enzymes involved in the degradation of cell wall polysaccharides and lignocellulose. This study opened the field to investigate the infection process at the cytological and molecular level via a diverse arsenal of enzymatic and toxin tools infecting a huge diversity of plants. To date and as far as we know, published genomes of M. phaseolina include strains isolated from jute, strawberry, alfalfa, and sorghum (Islam et al., 2012; Burkhardt et al., 2019; Quazi et al., 2019; Purushotham et al., 2020).

Recently, proteome data of M. phaseolina was provided by Zaman et al. (2020). A total of 2204 proteins were identified, of which 137 were found to be differentially regulated in presence of the biocontrol microorganism Bacillus contaminans NZ. Interestingly, most of these proteins with altered expression were related to defense, virulence, cell proliferation, and cell wall composition, together with the proteins of redox and metabolic pathways (Zaman et al., 2020). Interestingly, the metabolites profile of M. phaseolina has been compared in the presence and absence of Eucalyptus globulus stem tissue (Salvatore et al., 2020). The presence of host tissue during M. phaseolina growth induced the production of azelaic acid, suggesting that this secondary metabolite may play a role in disease establishment.

To the best of our knowledge, there is no known vertical resistance (R-gene based) to M. phaseolina inhibiting or limiting infection but rather, a partial resistance which do not limit infection but reduce or compensate the damages, and therefore the consequences on the fitness of plants.

Cultivars of soybean and strawberry with varying degrees of resistance to M. phaseolina have been identified (Reznikov et al., 2018; Gomez et al., 2020). Differences in fungal behaviour close to the roots and during infection of roots have been observed between resistant vs. susceptible varieties of sesame. The rhizosphere around the resistant variety had a reduced growth of M. phaseolina as compared to the susceptible variety (Chowdhury et al., 2014). Similarly, Hemmati et al. (2018) reported the formation of adventitious roots around the crown of soybean and inability of the pathogen to complete its life cycle in resistant cultivars, while pre-penetration steps within the roots were not linked to resistance, as they did not observe differences in microsclerotia germination and hyphae development.

Notably, the identification and mapping of QTLs associated with resistance to M. phaseolina, revealed candidate genes with potential for further functional genomics analysis and it may facilitate breeding and molecular engineering progress against this pathogen (Srinivasa Reddy et al., 2007; Muchero et al., 2011; Tomar et al., 2017; Mahmoud et al., 2018; da Silva et al., 2019).

The chemical control of M. phaseolina is difficult, since there are no systemic fungicides that move towards the root. As far as we know, no fungicides have been registered to control this pathogen. However, systemic and non-systemic fungicides (i.e., carbendazim, difenoconazole, benomyl, azoxystrobin, dazome) at different concentration were evaluated in vitro and in vivo against M. phaseolina (Cohen et al., 2012; Tonin et al., 2013; Chamorro et al., 2015a; Parmar et al., 2017; Lokesh et al., 2020).

Results indicates that the mycelial growth and formation of sclerotia are highly sensitive to carbendazim (50 ppm), an impact that increases with the increase in concentration of this systemic fungicide (Lokesh et al., 2020). Carbendazim inactivates tubulin function, the building block of microtubules, necessary for the fungal growth (Davidse and Flach, 1978). In addition, in another set of experiments, carbendazim application reduced disease incidence and increased the rate of plant survival (Iqbal and Mukhtar, 2020). Interestingly, the nanoformulation (particle size < 100 nm) of the commercial fungicide Trifloxystrobin 25% + Tebuconazole 50% (75 WG), was better in comparison to the conventional one (micro sized). The nanoform was effective at 10 ppm and it exerted hyphal abnormality, hyphal lysis and abnormality of sclerotial formation on M. phaseolina when tested under in vitro conditions (Kumar et al., 2016).

Disease management combining cultural practices with chemicals have been reported, but no conclusive results could be drawn, requiring further investigations (Cohen et al., 2012). Although the efficacy of certain chemical fumigants has been demonstrated (Iqbal and Mukhtar, 2020; Lokesh et al., 2020), agro-environmental policies and the increasing negative perception of the public on the agrochemicals have led to the evaluation and comparison of chemicals agents with more sustainable alternatives to control plant diseases caused by M. phaseolina (Reznikov et al., 2016; Swamy et al., 2018; Adhikary et al., 2019).

There is a relationship between pathogen inoculum density in soil and disease intensity, and between disease intensity and yield loss. Hence, some agricultural practices have intended to reduce the inoculum density. Biosolarization, a technique that combines biofumigation and solarization, has been shown effective in the reduction or stabilization of M. phaseolina microsclerotia population in soil, reducing the incidence of strawberry charcoal rot (Chamorro et al., 2015b). Conversely, irrigation maintained densities of microsclerotia relatively constant and did not prevent infection by M. phaseolina. However, high soil moisture (above 60%) reduced disease severity (Kendig et al., 2000; Jordaan et al., 2019). The wide host range and high persistence of M. phaseolina microsclerotia make crop rotation, intercropping and lay period strategies less considered. Although crop rotation has not been effective in controlling this pathogen, reduced densities of inoculum occurred when soybean was less frequently used in rotations (Francl et al., 1988). For the particular case of sesame, grown as mixed or inter cropped with green gram, less incidence of Macrophomina stem and root rot and higher seed yield equivalent as compared to sole sesame was observed (Rajpurohit, 2002).

Approaches intended to modify the soil environment, favouring antagonistic organisms interfering with the pathogen, have also been attempted. For example, the adoption of conservation strategies as direct seeding, showed a suppression of M. phaseolina favoured by the higher microbial abundance and activity, and the subsequent development of plants with healthier root systems (Perez-Brandán et al., 2012). Similarly, combining irrigation with soil amendment, increased the population of lytic bacteria against M. phaseolina (Lodha et al., 1997). Finally, fertilization has shown different effects on the severity of M. phaseolina. Phosphorus fertilization have shown a reduction, while nitrogen increased disease severity (Spagnoletti et al., 2018, 2020).

Biological control agents (BCAs) has well as plant metabolites and elicitors of plant defenses have received increasing attention in the last few decades. Some BCAs impact the pathogens directly, inhibiting their growth, while others affect the pathogen indirectly by eliciting defense pathways in the host plant.

Most plants exhibit inhibitory and stimulatory biochemical interactions with other plants and microorganisms, referred to as “allelopathy.” Especially, through root exudates, higher plants are able to prevent phytopathogens from infecting crops (Ushiki et al., 1996). Plant extracts and their volatile oils have been reported as natural phytosanitary products aiming the substitution or reduction in the application of conventional fungicides.

In plant defense systems, secondary metabolites can be divided into distinct chemical groups: terpenes, phenolics, nitrogen and sulfur containing compounds. A high number of secondary metabolites possesses antifungal characteristics (Zaynab et al., 2018).

Whole plant or leaf extracts of medicinal plants viz: Prosopis africana, Anacardium occidentale and Nigella sativa have been assayed against M. phaseolina, observing an inhibition of its growth. Analysis of the extracts showed the presence of alkaloids, saponins, tannins, flavonoids, anthraquinones, octadecadienoic acid, pentadecanoic acid, 1,2,3,4, butaneteterol, octadecanoic acid and linoleic acid. The antifugal activity of these extracts have been confirmed in several studies (Elaigwu et al., 2018; Aftab et al., 2019). Moreover, some extracts were able to induce the activity of defense enzymes in soybean plants inoculated with M. phaseolina (Lorenzetti et al., 2018). Additionally, Lippia gracilis oil extract showed an important inhibitory effect on the mycelial growth of M. phaseolina, becoming a promising alternative as control method (Ugulino et al., 2018). Furthermore, exogenous application of the synthetic strigolactone (SL) GR24 suppressed M. phaseolina hyphal branching. These results suggests that SLs released by plant roots, not only affect AMF and parasitic plants, but they also may play other important roles by affecting other organisms in the plant environment (Dor et al., 2011).

Elicitors are natural or synthetic compounds, which sprayed on the plants have been shown to induce systemic acquired resistance (SAR) and deter infection from bacterial, fungal, and viral pathogens. In order to control M. phaseolina and two other soybean pathogens (Phytophtora sojae and Sclerotinia sclerotiorum), the elicitors benzothiadiazole (BTH), chitosan (CHT), phenylalanine (PHE), and salicylic acid (SA), have been applied to soybean foliage. Results showed that the elicitor effectiveness varied based on soybean genotypes, pathogens, and environmental conditions (Pawlowski et al., 2016).

Chitosan has shown a potential dual role by inducing defense response in jute seedlings and directly inhibiting M. phaseolina during infection. Changes in enzyme profiles of jute after treatment with water-soluble chitosan (s-chitosan) helped to understand the mode of action of this antifungal compound. In this sense, the activity of defense related enzymes like chitosanase and peroxidase in infected seedlings was observed to be enhanced after treatment with s-chitosan in jute seedlings during infection by M. phaseolina (Chatterjee et al., 2014).

A better understanding of the immune responses triggered by elicitors is necessary. The use of elicitors in plant resistance may be detrimental to other physiological processes impacting negatively other plant traits, such as biomass and seed production. Therefore, it is important to make distinction between elicitors that directly activate plant defenses and those which acts as priming compounds. Priming condition, whereby plants that have been subjected to prior stimulus will respond more quickly or more strongly to a subsequent attack, is thought to be a relatively low-cost mechanism of advancing plant defense (Paré et al., 2005; Conrath, 2011; Denancé et al., 2013).

Small interfering RNA (siRNA) molecules have been used as a tool for the management of many plant pathogens (i.e., Fusarium, Aspergillus, Verticillium, Sclerotinia) (Mcloughlin et al., 2018). RNAi-mediated suppression of selected target genes, chosen based on their importance in growth and/or pathogenicity, can negatively affect the pathogen’s ability to infect the host or minimizing host symptoms.

Exogenous siRNAs were applied to target genes, β-1,3-glucan synthase and chitin synthase, in M. phaseolina. These targeting genes are important for the fungal cell wall synthesis. Interestingly, growth of siRNA-treated fungi has been suppressed, as indicated by smaller growth area and less dense mycelium. The siRNA treatments have also been reported to delay the maturation of the fungus since microsclerotia developed and melanized at a slower pace under multiple treatment conditions. Moreover, M. phaseolina growth suppression was correlated with a significant decreases in transcript abundances of target genes (Forster and Shuai, 2020a, b). Selection of siRNAs, where undesirable results due to off-target binding in a host plant or other organisms are minimized, is very important as they can be used for application in other innovative technologies. For example, Host-Delivered RNA interference (HD-RNAi), where plants contain genes encoding siRNA targeting toward pathogens (Hu et al., 2015).