1 Introduction

Fungal diseases pose a serious threat to crop plant production and global food security. To meet the food requirements and avoid crop losses, agriculture is experiencing an abrupt rise in the use of chemical fungicides for the control of fungal phytopathogens in the last few decades (Mcloughlin et al. 2018). A number of chemical fungicides such as bavistin are now available on market at cheap prices and are being used both in agricultural fields at the growth and during the post-harvest stages (Rashid et al. 2013; Kumar et al. 2015). Chemical fungicides are made synthetically in industries out of various chemicals including heavy metals are extremely harmful to the natural ecosystem (Komárek et al. 2010). When chemical fungicides are sprayed over the plants, seeds and fruits, although they will kill the fungal pathogen, the traces of chemical is kept in the plant organs. Due to consumption of toxic and chemical-treated food products over a long period of time, serious diseases like cancer, food poisoning, paralysis occurs in humans (Gupta 2018). Similar toxic effects have also been observed in other organisms at different tropic levels of ecosystem like fishes and birds (Choudhury 2018; Ortiz-Santaliestra et al. 2020). Presently, the chemical fungicides are a serious threat to the environment and the scientific community across the world and are looking for alternatives to control fungal pathogens as well as safe for the environment.

The term “Biofungicides” implies biological source or formulations developed from consortia of living organisms that restrict the growth of fungal pathogens. Biofungicides are environment friendly, non-toxic and leaves no residues. Plant products treated with biofungicides are safe for consumption and better quality with improved shelf life (Kubheka et al. 2020). Furthermore, investigations have revealed that these biofungicides also function as growth promoter and also increase the stress tolerance ability of the crop plants (Madbouly and Abdelbacki 2017; Macena et al. 2020). With increasing awareness of the farmers and advancement in agricultural sector, biofungicides have now been widely adopted in fields during organic farming and has also been included in integrated pest management (IPM) strategy.

Biofungicides can be synthesized from different biological sources like microbes such as cyanobacteria, bacteria, fungi as well as from different group of plants like algae, lichens, bryophytes, pteridophytes, gymnosperms and angiosperms including monocots (Guha et al. 2005; Joshi and Sati 2012; Boulogne et al. 2012; Commisso et al. 2021). There are substantial reports in literature that depict the antifungal effects of these sources and presently number of biofungicides formulations is also available commercially in market. Spadaro and Gullino (2004) reviewed the role and mechanisms of various biological agents in management of various post-harvest disease causing pathogens. Otoguro and Suzuki (2018) reviewed the plausible biocontrol strategy of grapevine pathogen through application of different microorganisms like bacteria, fungi and various endophytes. Plant growth promoting rhizobacteria (PGPR) are known for their ability to assist plants for better growth and development through nutrient acquisition (Aquino et al. 2021). However, several reports indicate the biofungicidal role played by these PGPR against plant fungal pathogens (Sufyan et al. 2020; Sharf et al. 2021).

Among the microbial based a number of strains of genera Bacillus, Streptomyces, Pseudomonas and many more have been observed to play a vital role in biocontrol of phytopathogenic fungi (Law et al. 2017; Shafi et al. 2017; Chatterjee et al. 2020). Molecular studies have revealed the identification of key metabolites or antibiotics by these bacterial genera responsible for inhibiting fungal growth (Chen et al. 2018a, b; Myo et al. 2019; Singh et al. 2020a). Additionally, rhizobacteria exhibit potential antifungal effects along with growth promotion (Ali et al. 2020). With the advent of metagenomics, many novel species are currently underway that may have significant antimicrobial activity and huge prospects in management of severe fungal pathogens.

Fungi have also been classified as important biocontrol agents due to their antagonistic effects on growth of other fungi and proved to be valuable for production of biofungicides. Reports have shown the management of powdery mildew pathogens though fungal antagonists that proved to be an important biocontrol approach (Kiss 2003). Studies have demonstrated the hidden role of fungal endophytic partner in restricting the growth of phytopathogenic fungi under in vitro and in vivo conditions (Nandhini et al. 2018; Gholami et al. 2019; Pavithra et al. 2020). Fungal endophytes are a great reservoir of natural products with antimicrobial activity and can be used for plant disease control (Kumar and Kaushik 2012; Deshmukh et al. 2018). Gas chromatography mass spectrometry (GC–MS) and liquid chromatography mass spectrometry (LC–MS) assisted in separation and identification of such natural compounds that are signature of these fungal agents (Mane et al. 2018; Luh Suriani et al. 2020). An important fungus Trichoderma sp. is one of the important biological agents that engrossed the concept of biological control for management of pests and pathogens. Genomic and proteomic studies have ascertained the mechanism of Trichoderma sp. mediated biocontrol (Gajera et al. 2013).

Plant based biofungicides rely on application of various plant extracts prepared in different solvents like ethanol, methanol, ether etc. for the control of fungal pathogens (Aqil et al. 2010; Aiyaz et al. 2015). Studies have demonstrated the affirmative responses of algal and lichen extracts in limiting the growth of fungal pathogens (Halama and Haluwin 2004; Bajpai 2016). Similarly, extracts made from different medicinal plants have shown to be highly effective in cubing fungal growth (Vashist and Jindal 2012). Antifungal activity of these plant extracts may be attributed to the presence of various essential oils in the plant body and also in different parts like glandular trichomes and hairs. Previous studies have shown efficacy of various essential oils extracted from different plants in controlling growth of fungal pathogens and disease control (Soylu et al. 2010; Amri et al. 2013; Kordali et al. 2016). Similarly, plant extracts are also rich in secondary compounds such as phenols, glucosinolates that are antifungal in nature and provide resistance against pests and pathogens (Naboulsi et al. 2018). A number of plant based biofungicides has also shown to have biostimulatory activities i.e., they initiate production of various other compounds that may be involved in increasing growth, augment nutrient status as well improve the thickening of fruit and seed wall thereby promoting shelf life (Aiyaz et al. 2015; Nair et al. 2018).

Few reviews are available in the field of the biocontrol and most of them focus on microbe or on plant but no comprehensive articles present their scheme of action. Therefore, the present review focuses on the biocontrol approaches using various microbes and plant based biological agents and provide in depth details of their utilization as biofungicides. We will describe the various structural, physiological and molecular mechanism induced by these biofungicides for limiting the growth of fungal pathogens. Concomitantly, the review will also highlight on additional benefits of the biofungicides on crop plants besides fungicidal and will also remark upon the toxicity if any of these biofungicides on plant system.

2 Different categories of biofungicides

Biofungicides have been broadly categorised depending on the biological source, i.e. micro organisms (Jaber and Alananbeh 2018; Myo et al. 2019; Ferrigo et al. 2020; Nian et al. 2021); or plant based (Abbassy et al. 2014a; Karabulut and Ozturk 2015; Basile et al. 2015; Kekuda et al. 2018; Choudhury et al. 2018; O’Keeffe et al. 2019). Within the plants, biofungicide can be synthesized using different algal sources (Abbassy et al. 2014a, 2014b; Ambika and Sujatha 2014; Soliman et al. 2018; Vehapi et al. 2020); lichens (Tiwari et al. 2011; Shivanna and Garampalli 2014, 2015; Valadbeigi et al. 2014); and vascular plants (Singh and Srivastava 2012; Sun et al. 2017; Soylu and Incekara 2017; Liu et al. 2020) (Fig. 1). Biofungicides from all these sources are usually synthesized in the form of extracts (Kanwal et al. 2015; Falade et al. 2017), suspensions (Panwar et al. 2014; Rafi et al. 2016; Sujarit et al. 2020) and formulations (Eakjamnong et al. 2021) using various extraction processes. A number of investigations have validated utilization of water, ethanol, methanol, acetone, ethyl acetate, etc., as better solvents for enhanced extraction of biological components and further for the synthesis of biofungicides (Singh and Srivastava 2012; Valadbeigi et al. 2014; Wei et al. 2020).

Fig. 1
figure 1

source of origin like microbial based or plant based. Microbial based can be obtained from different microbial species such as bacteria and fungi while plant based have been obtained from lower plants like algae and lichen as well from higher plants like angiosperms. Factors that affect the application of biofungicides are the target plant, the source from where it is derived, the plant part to which it has to be applied, and the form in which it will be used like dry or liquid. Biofungicides have been used in three major forms like priming, foliar application and in soil based formulations in dry or liquid forms

Different categories of biofungicides and their mode of application. Biofungicides may be categorised depending upon their

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2.1 Microorganisms-derived biofungicides

Biofungicidal properties of different microorganisms towards phytopathogens have been extensively studied and several species of bacteria and fungi with potential antifungal activities has been reported so far (Eljounaidi et al. 2016; Shafi et al. 2017; Rojas et al. 2020; Eakjamnong et al. 2021). Microorganisms produce several antifungal metabolites which are of high importance and have been used for synthesis of biofungicides. Kumar and Kaushik (2012) reviewed the production of number of novel secondary metabolites like alkaloids, terpenoids, steroids, isocoumarins, chromones, phenolics and other volatiles by endophytic fungi that can be utilized for biofungicide synthesis. A comparable study was carried out by Leiter et al. (2017) that documented synthesis of varieties of antifungal proteins by different fungal species. Likewise, numerous other bacteria are also known to antagonise fungal growth through several modes of action like parasitism, competition, production of volatiles and biofilms (Carmona-Hernandez et al. 2019).

A large number of microbes with antifungal properties have been isolated from rhizospheric soil (Zou et al. 2007; Srivastava et al. 2016; Jakubiec-Krzesniak et al. 2018) as well as from plant tissues (Kumar et al. 2013; Mamangkey et al. 2022). Godebo et al. (2020) isolated 20 antagonistic bacteria from soil samples using crowded plate technique and three out of them K-Hf-L9 (Pseudomonas fluorescens), PSV1-7 (Pantoea agglomerans), and K-Hf-H2 (Lysobacter capsici) were highly effective in suppression of aphanomyces root rot caused by Aphanomyces euteiches. Similarly, in one of the study two potential endophytic bacteria with biocontrol properties has been isolated from different plant parts of Theobroma cacao and were identified as Pseudomonas aeruginosa and Chryseobacterium proteolyticum using sequencing of 16 s rDNA region (Alsultan et al. 2019). An interesting study by Tienda et al. (2020) deliberated use of semi solid formulation of Pseudomonas chlororaphis PCL1606 synthesized from standard fermentation procedure and fund to be highly efficient for the biocontrol of pathogen Rosellinia necatrix infecting avocado. Techniques like metagenomics has substantially helped in functional characterization of potential strains of disease suppressive microorganisms as evident from the review work of Lutz et al. (2020) that described integrated metagenomic approaches for studying of compost microbiome that may help in plant protection. Comparable work was carried out by Prasannakumar et al. (2020) that characterized endophytic diversity of two fingermillets on the basis of their susceptibility towards blast disease using metagenome approach. The work concluded that the two genera Bacillus cereus and Paenibacillus spp possess the maximum biocontrol activity in comparison to other microbes identified.

2.1.1 Bacteria as a potential source

Bacteria have been largely exploited for their antifungal activities towards plant pathogenic fungi (Dalié et al. 2010; Eljounaidi et al. 2016; Shafi et al. 2017; Carmona-Hernandez et al. 2019) which make them as suitable source of synthesis of biofungicides. Bacterial crude protein extracted from the broth culture of Bacillus siamensis LZ88 by Xie et al. (2021) has been shown to reduce both the occurrence and severity of fungal pathogen Alternaria alternata in tobacco plants. In a different study by Ahmadi et al. (2021) proteinaceous extract from fermenting sugarcane bagasse using Pichia membranifaciens exhibited antifungal activity against Aspergillus niger, Phytophthora capsica and Penicillium digitatum. Sujarit et al. (2020) prepared spore suspension and alginate beads using Streptomyces palmae CMU-AB204T. The spore suspension and beads were mixed with sterile soil prior to application as biofungicide against Ganoderma boninense. Independent studies using two different bacteria Pseudomonas aeruginosa (Irma et al. 2018) and Streptomyces palmae CMU-AB204T (Sujarit et al. 2020) demonstrated antifungal activity against pathogenic fungus Ganoderma boninense that affect oil palm. The antifungal activity of both the bacteria against the same pathogen provides a better picture on effectiveness of biofungicide obtained from different sources for controlling similar pathogens. Tadijan et al. (2014) reported biofungicide extracted from fermentation medium inoculated with Streptomyces hygroscopicus while an aqueous solution prepared using fluorescent Pseudomonas spp. was used in seed priming against Magnaporthe grisea (Patil et al. 2016).

Nian et al. (2021) used Lysobacter enzymogenes strain C3 (LeC3) for the management of several fungal pathogens of soybean (Macrophomina phaseolina, Sclerotinia sclerotiorum, Fusarium virguliforme, Septoria glycines, Cercospora sojina, Rhizoctonia solani, Phytophthora sojae and Pythium spp.). The study showed reduced mycelial growth and spore germination of all the above pathogens suggesting the diverse application of this strain in biocontrol strategy (Nian et al. 2021). In a similar study, Lysobacter enzymogenes have been shown to control infection of Valsa pyri in pear through significant degradation of mycelia that was attributed to increased protease production by L. enzymogenes (Yang et al. 2020). Bacillus subtilis RH5 and Lysinibacillus sphaericus have been reported to possess the ability to induce the production of defense related enzymes (Shabanamol et al. 2017) and hydrolytic enzymes (Jamali et al. 2020) respectively, which improved the resistance against Rhizoctonia solani affected rice plants. Chiquito-Contreras et al. (2019) documented the production of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT) and peroxidase (POX) in papaya fruit with the use of marine bacteria Stenotrophomonas rhizophila and Bacillus amyloliquefaciens that provided resistance towards Colletotrichum gloeosporioides. Lv et al. (2018) also reported the increased accumulation of defense enzymes such as phenylalanine ammonia lyase (PAL), peroxidase (POX) and polyphenol oxidase (PPO) with phenolics and flavonoids in Cucumis melo with the application of cell-free extracts obtained from Lactobacillus plantarum C10 against Trichothecium roseum. Sharma et al. (2018a) demonstrated that inoculation with Pseudomonas sp. and Bacillus sp. to Vigna radiata plants led to increased concentration of defense enzymes such as PPO, POX, and PAL. As a result, plants show better protection towards infection of Macrophomina phaseolina and Fusarium udum respectively.

Several members of genera Bacillus possess potent antifungal as well as growth promoting activity therefore, widely being used in agricultural sector as biofertilizers (Pérez-García et al. 2011). A study revealed that a bacterial strain Bacillus velezensis NKG-2 inhibited the growth of Fusarium graminearum, Ustilaginoidea virens, Alternaria alternata, Botrytis cinerea, Fulvia fulva and Fusarium oxysporum under in in vitro conditions. The study also demonstrated B. velezensis NKG-2 strain helped in lowering disease severity of wilt disease in tomato by inhibiting growth of F. oxysporum under in vivo conditions through production of hydrolytic enzymes like chitinase, cellulase, β-glucanase and amylase (Myo et al. 2019). Another strain of Bacillis i.e., B. stratosphericus (FW3) and Pseudomonas aeruginosa (D4) showed potential antifungal activity against phytopathogens causing root rot of ginseng (Ilyonectria, Cladosporium, Fusarium, Eutypella, Neurospora and Aschersonia) (Durairaj et al. 2018). Bacterial strains such as Bacillus subtilis EA-CB0015, B. subtilis BZR 336 g and Rhodopseudomonas palustris KTSSR54 are reported to synthesize lipopeptides such as iturin, fengycin and surfactin that showed effective antifungal action towards major fungal pathogens like Botrytis cinerea, Colletotrichum acutatum and Fusarium oxysporum var. Orthoceras (Arroyave-Toro et al. 2017; Sidorova et al. 2020; Nookongbut et al. 2020). Bacillus spp. (KFP-5, KFP-7, KFP-17) used against Pyricularia oryzae of rice by Rais et al. (2017) displayed significant induction of SOD, POX, PPO and PAL in both leaves and roots of the plant. Similarly, Jiang et al. (2019) showed upregulation of genes involved in both MAPK signaling pathway and phytohormone signaling pathway in response to Bacillus velezensis F21 inoculation in Citrullus lanatus which enhanced the resistance towards Fusarium oxysporum f. sp. niveum.

Apart from Bacillus various strains of Streptomyces have also been shown to reduce fungal growth and have been used as a biofungicide for management of plant diseases. Some of the reviews on Streptomyces sp. have highlighted their antifungal potential towards the fungal pathogens like Fusarium sp. and Magnaporthe oryzae (Law et al. 2017; Bubici 2018). A recent study by Streptomyces palmae CMU-AB204T have been shown to produce secondary metabolites like actinopyrone, anguinomycin and leptomycin that has significant inhibitory effects towards Ganoderma boninense that cause stem rot disease in oil palm (Sujarit et al. 2020). Manhas and Kaur (2016) have reported suppression of fungus Alternaria brassicola by the Streptomyces hydrogenans strain DH16 under in vivo and in vitro conditions. The S. hydrogenans strain DH16 strain led to production of both cellular extracellular metabolites that inhibit growth of fungus and at the same time increased vigour and germination of infected radish seeds infected with this strain. Similarly, metabolites produced from Streptomyces griseus H7602 strain demonstrated to have antifungal activity and arrested growth of Phytophthora capsici under in vitro conditions (Nguyen et al. 2015).

A number of rhizobacteria isolated by Sharma et al. (2018a) presented biocontrol activity against Alternaria brassicae in Brassica juncea. It was observed that the isolates HMR48, HMM21 and HMR25 were able to produce of indole acetic acid (IAA), δ-aminolevulinic acid (ALA) and hydrogen cyanide (HCN) respectively. Two endophytic bacterial isolates Pseudomonas aeruginosa and P. pseudoalcaligenes was able to induce the β-1,3-glucanase and catalase gene in paddy even in the absence of the pathogen making the plant more immune prior to infection (Jha 2019).

Isolated Pseudomonas putida CRN-09 and Bacillus subtilis CRN-16 as well as their consortium was able to induce systemic resistance (ISR) in Vigna radiata enhancing the concentration of β-1,3-glucanase, PPO, POX and PAL while resisting Macrophomina phaseolina (Sharma et al. 2018b). Furthermore, production of various lytic enzymes namely endochitinase, exochitinase, chitobiase, proteinase, cellulose, amylase, pectinase and lipase along with volatile ammonia and cyanide compounds were reported from two rhizobacteria Pseudomonas sp. NS 1 and Bacillus sp. NS 22 that inhibited the growth of Fusarium udum in Cajanus cajan (Dukare and Paul 2021). These studies support the idea for bacterial-derived biofungicide and the list of bacteria with potential antifungal activity towards pathogenic fungi have been listed in Table 1.

Table 1 Different bacterial strains utilized for the control of various pathogenic fungi responsible for causing severe diseases in plants
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2.1.2 Fungi as a potential source

Several investigations on antifungal activities of different fungal isolates against various pathogenic fungi has highlighted their potential as a source for bio-fungicide production (Gholami et al. 2019; Roberti et al. 2019; Rojas et al. 2020; Eakjamnong et al. 2021; Yadav et al. 2021). Eakjamnong et al. (2021) synthesized dry powder formulation and crude ethyl acetate extract with potential antifungal activity from Talaromyces tratensis KUFA 0091 isolated from marine sponge Mycale sp. Kakvan et al. (2013) developed bioformulation using species of Trichoderma and Talaromyceres. Using peat, rice bran and talc as a carrier the formulation was then used as biofungicide against Rhizoctonia solani. Trichoderma harzianum suspension was used as seed bio-priming agent against fungal diseases (El-Mohamedy and Alla 2013; Ferrigo et al. 2020). Similarly, aqueous suspension of T. harzianum spore and mustard (Brassica campestris L.) cake was used as bio-priming agent against root infecting fungi namely Macrophomina phaseolina and Fusarium spp. (Rafi et al. 2016). Suspension of T. harzianum was used as biofungicide by Rusita and Sasongko (2020). Broth suspension of T. harzianum QTYC77 isolated from the guts of dragonfly showed chitinase and β-1,3-glucanase activity against Fusarium oxysporum f. sp. cucumerinum. Hyphal fragment suspension of hypo virulent isolate QT5-19 of Botrytis cinerea grown in potato dextrose broth (PDB) was applied as biofungicide against virulent isolates of B. cinerea and Sclerotinia sclerotiorum. Aqueous solution of Saccharomyces and other biocontrol yeasts containing metabolites, laminarinases and antifungal volatiles have been used as biofungicide against the fungal pathogens of grey and sour rot of grapes (Nally et al. 2015).

Endophytes are the endosymbiont micro-organisms that reside inside plant tissues without causing apparent disease. Reports of novel metabolites produced from endophytic fungus may have a vast potential in biocontrol approaches in disease management (Nandhini et al. 2018; Gholami et al. 2019). Endophytic fungi like Penicillium olsonii ML37, Anthracocystis flocculosa F63P, Sarocladium strictum C113L and Anthracocystis flocculosa P1P1 showed significant biocontrol potential against Fusarium graminearum which cause head blight in wheat (Rojas et al. 2020). Another study showed that endophytic fungi Trichoderma spp., Leotiomycete spp., Aureobasidium spp. and Aureobasidium pullulans isolated from Pinus halepensis presented reduction of necrotic length caused by Gremmeniella abietina in P. halepensis (Romeralo et al. 2015). Gholami et al. (2019) showed endophytic fungi (Fomes fomentarius M40, Rhizoctonia endophytica M9, Coprinopsis urticicola M2 and Rhizoctonia zeae M32) produces hydrolytic enzymes like protease, chitinase, pectinase, cellulase that probably caused dissolution of cell-wall thereby inhibition of Gaeumannomyces graminis var. tritici that causes take-all disease in wheat. Interestingly, two entomopathogens as endophyte (Metarhizium brunneum BIPESCO5 and Beauveria bassiana NATURALIS) were found to be antagonistic against Fusarium oxysporum, F. moniliforme and F. culmorum causing crown and root rot in Capsicum annuum L. (Jaber and Alananbeh 2018). Crude extract synthesized of endophytic fungi isolated from different plant parts of finger millet showed antifungal activity against Fusarium graminearum and can be used as biofungicide (Mousa et al. 2016). Another study reported metabolites extracted from endophytic fungus Diatrype palmicola MFLUCC 17–0313 had antifungal response against phytopathogenic fungus Athelia rolfsii isolated from infected tomato leaves under in vitro conditions (Tanapichatsakul et al. 2020). The study also confirmed that there are phytotoxic effects of these extracts on tomatoes although they can be used as potent biofungicide in future disease management programmes (Tanapichatsakul et al. 2020).

Several researches on Trichoderma sp. have provided enough evidences for their antifungal activities towards diverse class of fungal phytopathogens (Ghosh et al. 2018; Ferrigo et al. 2020; Rusita and Sasongko 2020). Above 60% of registered biofungicides formulations are based on Trichoderma spp. (Singh et al. 2018). Resistance to fungal pathogen Colletotrichum truncatum in chilli with bio-priming agents like T. harzianum, and T. asperellum was reported by Yadav et al. (2021). Similarly, T. asperellum inhibited the growth of Alternaria brassicae in Aloe vera (Ghosh et al. 2018). Furthermore, many strains of T. harzianum displayed antifungal properties against major disease-causing species of Fusarium like F. graminearum, F. verticillioides, F. oxysporum, F. oxysporum f. sp. cucumerinum (Ferrigo et al. 2020; Rusita and Sasongko 2020; Zhang et al. 2020a). Trichoderma deploys various biocontrol mechanisms towards phytopathogens that includes production of cell wall degrading hydrolytic enzymes, antibiotics, parasitism, and competition (Srivastava et al. 2016). A study depicted substantial increase in chitinase and β-1,3-glucanase activity in response to Fusarium oxysporum f. sp. cucumerinum in cucumber when inoculated with T. harzianum QTYC77 (Zhang et al. 2020a). Reports stated volatile and non-volatile metabolites produced by Trichoderma asperellum inhibiting the mycelial growth of Alternaria brassicae in Aloe vera (Ghosh et al. 2018). Such volatile and non-volatile metabolites were also reported from Aureobasidium pullulans that reduced the growth of pathogenic Trichoderma pleuroticola and T. pleuroti (green mould) of Pleurotus ostreatus (Roberti et al. 2019). Furthermore, Yadav et al. (2021) showed augmentation of ISR in pre-treated seeds of chilli with T. harzianum, and T. asperellum against fungal pathogen Colletotrichum truncatum. Increased activity of defense related enzymes such as PPO, PAL as well antioxidant enzymes like SOD, POD, APX, CAT, GPX along with accumulation of phenolics were observed (Yadav et al. 2021). Similar investigation carried out by Ferrigo et al. (2020) demonstrated T. harzianum INAT11 modulated expression patterns of ISR genes (LOX10, AOS, HPL and OPR8) as well as SAR genes (PAL and PR1) in tolerance against Fusarium graminearum and F. verticillioides causing Fusarium ear rot in maize. The study reported up regulation of ISR and SAR markers as a result decrease in disease incidence and severity. A list of fungi with potential antifungal activity towards pathogenic fungi has been shown in Table 2.

Table 2 Utilization of different fungi species for restricting the growth of various pathogenic fungi responsible for causing severe diseases in plants
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2.2 Plant-derived biofungicides

Several plants (Djahra et al. 2019; Saputri and Utami 2020; Shokouhi and Seifi 2020) including cyanobacteria (Usharani et al. 2015), algae (Esserti et al. 2017; Sarkar et al. 2018) and lichens (Oh et al. 2006; Ranković et al. 2007) has been investigated for the possibility of biofungicide production. Extracts of seaweeds, brown algae and cyanobacteria can also be used as a source of plant-based biofungicide because of their antifungal properties (Usharani et al. 2015; Esserti et al. 2017; Sarkar et al. 2018). Bryophytes also have been explored in the search of antifungals (Mekuria et al. 1999). In a study, methanolic extracts of Porella platyphylla, Cinclidotus fontinaloides and Anomodon viticulosus inhibited the growth of phytopathogenic Botrytis cinerea (Latinović et al. 2019). Subhisha and Subramoniam (2005) first time reported the antifungal activity of steroidal fraction of Pallavicinia lyellii against Aspergillus fumigatus Fres [MTCC 343]. Pteridophytes are equally explored for their bioactive properties towards fungal pathogens of plants (Aulakh et al. 2019). In vitro studies have shown potential in pteridophytes for the control of several important phytopathogenic fungi (Sahayaraj et al. 2009; Panda et al. 2014). For example, extracts from leaf and stem of Marsilea minuta showed high efficacy towards growth inhibition of several fungi namely Aspergillus niger, A. flavus, A. terreus, Trichoderma viride, and Fusarium solani under in vitro studies (Sabithira and Udayakumar 2018). In addition, He et al. (2011) isolated novel mannan-specific lectin from Ophioglossum pedunculosum that showed antifungal effects on Sclerotium rolfsii and Fusarium graminearum. Similarly, gymnosperms have been well studied for their antifungal properties. Antifungal potential of several genus like Pinus, Juniperus, Taxus, Ginkgo, Cupresses, Abies, Cedrus, Thuja and Araucaria have been well documented by Joshi and Sati (2012). Reports of several gymnosperms extracted using different solvents have shown efficient antifungal activities (Joshi et al. 2016, 2018). In a study done by Kwon et al. (2017), β-thujaplicin from Chamaecyparis obtuse showed significant growth inhibitory activity towards numerous economically important pathogenic fungi namely Sclerotinia sclerotiorum, Rhizoctonia solani AG-4, Phytophthora capsica, Colletotrichum coccodes, Stemphylium solani and Alternaria alternata. Furthermore, Kusumoto et al. (2014) also reported several antifungal terpenoids antifungal from Picea abies. The list of plant extract with potential antifungal activity towards pathogenic fungi have been listed in Table 3.

Table 3 A list of studies demonstrating application of lichens for the control of different pathogenic fungi
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In the present review, lichens and angiospermic plant-derived biofungicides has been discussed in great details as these have profoundly being used in synthesis of biofungicides.

2.2.1 Lichen based biofungicides

Ample of studies on lichens have demonstrated their antifungal properties (Wei et al. 2008; Jeon et al. 2009; Kowalski et al. 2011; Guo et al. 2017). These studies support the antifungal nature of several lichens towards many plant pathogenic fungi opening doors of lichen-based biofungicides (Ranković et al. 2007; Tiwari et al. 2011; Shivanna and Garampalli 2014, 2015; Babiah et al. 2015). Lichens are known to possess bioactive compounds like vulpinic acid, atranorin, usnic acid, fumarprotocetraric acid, lecanoric acid, protocetraric acid and stictic acid that have inhibitory effects against several fungal phytopathogens (Ranković and Mišić 2008; Kowalski et al. 2011; Guo et al. 2017).

Several solvents like water, methanol, ethanol, acetone and ethyl acetate are employed for the extraction of lichens (Ranković et al. 2007; Valadbeigi et al. 2014; Guo et al. 2017). Solvent extraction method using soxhlet extraction procedure from powdered lichens using methanol and ethyl acetate as solvents was used by Shivanna and Garampalli (2015) to extract biofungicide from lichens. Other studies have used soxhlet extraction method from powdered dried lichens using various solvents to obtain biofungicide (Ranković et al. 2007; Tiwari et al. 2011; Valadbeigi et al. 2014; Babiah et al. 2015; Shivanna and Garampalli 2015). Guo et al. (2017) used filtered extract obtained from powdered lichen dissolved in acetone was used against Saprolegnia parasitica, Achlya bisexualis and Pythium sp. Similarly, filtered solution of lichen powder soaked in acetone and methanol was used as biofungicide against Fusarium oxysporum of chilly (Shivanna and Garampalli 2014).

A study done by Jeon et al. (2009) showed that lichen-forming fungi (LFF) Evernia prunastri, Lecanora argentata and Lecania hyaline were able to inhibit mycelial growth whereas Cladonia furcate, Ramalina pollinaria, Hypogymnia physodes, Ramalina fastigiate and Lasallia pustulata displayed fungal lytic activity when evaluated against Colletotrichum acutatum, C. gloeosporioides and C. coccodes. Shivanna and Garampalli (2015) formulated organic extracts from Flavoparmelia caperata and Parmotrema tinctorium that have shown potential fungicidal activity at minimum inhibitory concentration 1.562 mg mL–1 against Fusarium solani causing rhizome rot of ginger. Similarly, another LFF Melanelia sp., Ramalina conduplican, Parmelia laevior, Ramalina sp., and Pertusaria sp. showed antifungal activity against several pathogenic fungi Botryosphaeria dothidea, Sclerotium longiseta, Botrytis cinerea, Rhizoctonia solani, Diaporthe actinidiae, Pythium sp. and Pestalotiopsis longiseta (Oh et al. 2006). Likewise, LFF Cetrelia japonica, Parmelia simplicior, Ramalina conduplicans, Nephromopsis pallescensn, Umbilicaria esculenta, Cetrelia braunsiana and Ramalina litoralis showed effective inhibition against Colletotrichum acutatum (Wei et al. 2008). The list of lichens with potential antifungal activity towards pathogenic fungi has been listed in Table 3.

2.2.2 Angiosperm-derived biofungicides

Plants contribute equally in the field of plant disease management and have been envisioned as a potential source of biofungicides. Plethora of studies has been done on plants in search of their antifungal properties (Eze and Eze 2010; Tascioglu et al. 2013; Gatan and David 2013; Šernaitė et al. 2020). Various biofungicide extracts are prepared using water, acetone, buffer, acid, etc., which are then applied using different methods (Dellavalle et al. 2011; Mahlo and Eloff, 2014). Extraction of biofungicide from the leaves of Ipomoea batatas L. was carried out by Saputri and Utami (2020). Ethanolic leaf extracts of I. batatas showed potential antifungal activity against Fusarium sp. In another study, Djahra et al. (2019) prepared methanolic solution using the powdered leaves of Datura stramonium and was used as biofungicide. Similarly, Singh and Srivastava (2012) used leaf extract of Lantana camara as a biofungicide. Extracts made from powdered leaves of L. camara using various solvents (methanol, ethanol, acetone, and water) showed antifungal activity against Alternaria alternata. Wei et al. (2020) extracted powdered phenolic acids from rice straw that exhibited fungicidal activity and can be used as potential biofungicide. According to Soylu et al. (2010), essential oils extracted from Origanum syriacum L. var. bevanii, Lavandula stoechas L. var. stoechas and Rosmarinus officinalis L. through steam distillation was used as a biofungicide against Botrytis cinerea. Biofungicide extraction from the seeds of Moringa peregrina was reported by Shokouhi and Seifi (2020). Extract of powdered seeds in different solvents (hexane, chloroform, and water) showed antifungal activity towards mycopathogenic fungus Mycogone perniciosa.

Leaf extracts prepared from number of plants like Ipomoea batatas, Datura stramonium and Lantana camara using various solvents like water, ethanol, methanol, etc. were found to be effective against several pathogenic fungi namely Fusarium sp., Aspergillus niger, Alternaria alternata, A. solani and Septoria nodurum (Singh and Srivastava 2012; Djahra et al. 2019; Saputri and Utami 2020). Concomitantly, seed extracts of Moringa peregrina and Cuminum cyminum showed positive antagonistic effect against Mycogone perniciosa and Fusarium oxysporum f. sp. niveum respectively (Sun et al. 2017; Shokouhi and Seifi 2020). Similarly, cuminic acid extracted from the seeds of Cuminum cyminum hindered gene regulation (Sun et al. 2017). According to their report, genes of bikaverin (Bike1, Bike2 and Bike3) and mycotoxin fusaric acid (FUB1, FUB2, FUB3 and FUB4) was downregulated after cuminic acid treatment. Further decrease in malondialdehyde (MDA) concentration and increase in SOD, POD and CAT hinted lower lipid peroxidation. Plant-based products contain antimicrobial compounds (Usharani et al. 2015; Shokouhi and Seifi 2020; Kumar et al. 2021a) that regulate gene expression (Sun et al. 2017; Ben Jabeur et al. 2017) which results in fungal hyphae degradation and further growth inhibition (Soylu and Incekara 2017). Recently Liu et al. (2020) reported the presence of novel chitinase (IbChiA) in Ipomoea batatas which showed remarkable fungicidal effects against both mycelium and conidia of Ceratocystis fimbriata. In one of the studies, plant phenolic acids extracted from rice straw provided resistance in tomato plant against Fusarium oxysporum (Wei et al. 2020). Interestingly, the phenolic acids derived from rice straw was able to disrupt membrane permeability thereby causing cytoplasmic leakage in pathogenic F. oxysporum of tomato inhibiting germination of spores and hyphal growth (Wei et al. 2020).

Investigations have revealed the potency of essential oils derived from number of plants like Curcuma longa, Eucalyptus globulus, Schleichera oleosa and Cymbopogon citratus in effectively inhibiting the growth of fungal pathogens (Hu et al. 2017; Ben Jabeur et al. 2017; Naveenkumar et al. 2017; Iqbal et al. 2020; Kumar et al. 2021a). Similarly, oils from Origanum onites L., Laurus nobilis L., Myrtus communis L., Foeniculum vulgare Mill., Lavandula stoechas L. subsp. stoechas exhibited strong detrimental effects towards Fusarium oxysporum f. sp. radicis-cucumerinum (Soylu and Incekara 2017). Plant oils contains volatile and non-volatile compounds (Kumar et al. 2021a, 2021b) that interferes with gene regulation (Ben Jabeur et al. 2017) resulting in detrimental degradation of fungal hyphae (Soylu and Incekara 2017). For example, essential oil isolated from Schleichera oleosa repressed gene expression encoding for MAPK (MgSlt2) and efflux pump (MgAtra4) along with PKA (MgBcy1) regulatory subunit in Mycosphaerella graminicola thereby exhibiting antifungal activity (Ben Jabeur et al. 2017).

Gene regulation in Citrus fruits after the application of clove essential oil was reported by Chen et al. (2019). With the help of real time quantitative polymerase chain reaction (qRT-PCR), they found upregulation of β-Glucanase, chitinase, PAL, POD and PPO genes while lipoxygenase (LOX) gene was down-regulated. Upregulation of β-1,3-glucanase gene was also observed in two cultivars of avocado (Persea americana Mill.) fruit after fumigation with thyme oil vapours which provided resistance towards anthracnose disease caused by Colletotrichum gloeosporioides (Bill et al. 2016). Similar study was done by Banani et al. (2018) in apple fruits, where they noticed that the thyme essential oil was able to efficiently increase the PR-8 gene expression which effectively inhibited the growth of Botrytis cinerea. Ocimum sanctum essential oil application downregulated zearalenone synthesizing PKS4 and PKS13 gene expression of Fusarium graminearum in maize grains (Kalagatur et al. 2015) while in another study, essential oil citral downregulated the biosynthetic genes of mycotoxin including pksI and omtI in Alternaria alternata (Wang et al. 2019). Table 4 summarizes list of studies that employed plant extracts for the management of fungal pathogens in different crop plants.

Table 4 Application of different angiospermic plant in different forms as a potential biofungicide
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3 Defense priming

3.1 Bio-priming

Bio-priming is one of the seed priming techniques in which seeds are pre-soaked (physiological soaking) along with the beneficial microorganisms (Waqas et al. 2019) before being sown in soil. Bio-priming is one of the best approaches to manage those pathogens that affects plant growth in early stages of the development as this method induces resistance to plant against such pathogens (El-Mohamedy and Alla 2013; Rafi et al. 2016; Mona et al. 2017; Rajaput et al. 2019; Amruta et al. 2019) (Fig. 1). Simultaneously, bio-priming promotes germination, increases yield, stimulates higher root-shoot length, enhanced metabolic activity as well as nutritional value in plants (Kanwal et al. 2015; Anitha and Jahagirdar 2015; Singh et al. 2016a).

Bacteria and fungi show enormous potential in the field of biofungicide and therefore they can be used as a bio-priming agent against fungal diseases. The ability to induce defence related pathways (Ferrigo et al. 2020; Xie et al. 2021; Yadav et al. 2021) and production of hydrolytic enzymes (Nandhini et al. 2018; Durairaj et al. 2018; Gholami et al. 2019; Myo et al. 2019) makes them a potent biofungicide. Number of studies has been done using bacteria like, Bacillus sp. (El-Mohamedy and Alla 2013; Anitha and Jahagirdar 2015; Tumpa et al. 2016), Pseudomonas sp. (Patil and Kumudini 2019; Rajaput et al. 2019; Jayamohan et al. 2020; Sufyan et al. 2020), Serratia marcescens strain UASBR4 (Amruta et al. 2019), etc., as bio-priming agents against fungal pathogens (Fig. 1). Similarly, number of fungi like Trichoderma sp. (El-Mohamedy and Alla 2013; Anitha and Jahagirdar 2015; Singh et al. 2016a; Mona et al. 2017; Yadav et al. 2021), Rhizobium melilotii (Rafi et al. 2016), Paenibacillus dendritiformis (Yadav et al. 2021) are used for bio-priming of seeds against fungal pathogens (Fig. 1).

Bio-priming with Trichoderma pseudokoningii BHUR2 to tomato seeds conferred resistance through the activity of anti-oxidative enzymes like SOD, POX, PAL and phenolics against Sclerotium rolfsii (Rajput et al. 2019). Similar results of increased activity of SOD and CAT in Solanum lycopersicum was observed when T. erinaceum used as bio-priming agent against Fusarium oxysporum f. sp. lycopersici (Aamir et al. 2019). Separate combination of T. asperellum BHU P-1 and Ochrobactrum sp. BHU PB-1 with ascorbic acid when applied as bio-priming agent resulted in increase of defense enzymes like PAL, POX and PPO (Singh et al. 2020b). Similarly, Bacillus sp. BSp.3/aM bio-priming induced resistance in Capsicum annuum through increased activity of PAL, POX, PPO and LOX along with higher accumulation of phenolics (Jayapala et al. 2019).

Seed priming is a popular, cost-effective and commercially used technique for accelerating seed germination (Nawaz et al. 2013) (Fig. 1). Plant extracts are known to contain many antifungal compounds that inhibits fungal growth and development (Shuping and Eloff 2017; Abdelkhalek et al. 2020) and are used as seed priming agents against plant pathogenic fungi (Rafi et al. 2015; Ali et al. 2019). Kanwal et al. (2015) used extracts of papaya as seed priming agent against the fungal pathogens of beans Rhizoctonia solani, Fusarium spp. and Macrophomina phaseolina. The extract of Carica papaya contains proteolytic enzymes like papain and chymopapain that inhibit fungal growth. Similarly, Acacia nilotica and Sapindus mukorossi extract primed seeds were effective against root rot fungi like Rhizoctonia solani, Fusarium spp. and Macrophomina phaseolina (Rafi et al. 2015). Improved germination with enhanced antioxidative enzymes like SOD and POD resulting in ROS modulation was observed in Solanum melongena after the seeds were primed with aqueous extracts of garlic (Ali et al. 2019). Methanolic extracts of Ammi visnaga was able to up-regulate genes responsible for pathogen related proteins like chitinase and thaumatin like proteins in primed seeds of maize lowering root rot incidence caused by R. solani (Rashad et al. 2018). Leaf extract of Aegle marmelos primed tomato seeds displayed better growth parameters in presence of pathogenic Fusarium oxysporum (Prabha et al. 2016). Similarly, primed sorghum seeds with aqueous extracts of Eclipta alba and Balanites aegyptiaca exhibited higher yield and antifungal activity towards Curvularia lunata (Zida et al. 2018). Seed priming with extracts of Toddalia asiatica revealed its antifungal activity towards Fusarium verticillioides and Aspergillus flavus while seed germination and vigour was increased significantly in Zea mays (Aiyaz et al. 2015). Lignin protects the cell by strengthening the cell wall and are synthesised through phenylpropanoid pathway. In case of finger millet, plants grown after bio-priming of seeds with rhizospheric Pseudomonas isolates JUPC113 and JUPW121, increased production of enzymes like PAL and Tyrosine ammonia lyase (TAL) that are involved in lignin biosynthesis pathway (Patil and Kumudini 2019).

3.2 Foliar application

Spraying is one of the conventional and easiest methods for application of biofungicides (Fig. 1). Large number of microbial and plant extracts are sprayed on leaves, seeds, and fruits to control many fungal diseases (Yu et al. 2017; Pertot et al. 2017; Jiang et al. 2018) (Fig. 1). Spraying of biofungicides induces resistance in the plant through the production of various antifungal compounds like isocladosporin, 5′-hydroxyasperentin, and cladosporin-8-methyl ether (Wang et al. 2013), lipopeptides (Ji et al. 2013), phenazine-1-carboxamide (Chen et al. 2018a, b), secondary metabolites and volatile organic compounds (Jiang et al. 2018; Hassan et al. 2021) (Fig. 2). Furthermore, bacterial spray interferes with gene regulation mechanisms (Narusaka et al. 2015; Jiang et al. 2018) thereby producing pathogen related (PR) proteins (Khalaf and Raizada 2018; Xie et al. 2021) and defense related enzymes (Jiang et al. 2018). The study was undertaken by Panwar et al. (2014) in which foliar spray containing spore suspension of Trichoderma harzianum and T. viride led to reduced disease severity caused by Fusarium graminearum. Interestingly, seed treatment followed by spraying with Pseudomonas fluorescens and T. harzianum not only supressed Rhizoctonia solani f.sp. sasakii but also resulted in increase in yield in maize plants (Rajput and Harlapur 2015; Venkateswarlu and Beura 2020). Similarly, seed treatment followed by foliar spray using P. fluorescens and T. viride showed effective results in terms of both disease control and yield against Rhizoctonia solani of rice (Pal et al. 2015). Extract of Datura stramonium when sprayed against Colletotrichum lindemuthianum, reduced the disease incidence in cowpea (Falade et al. 2017). Likewise, aqueous extract of Syzygium aromaticum L. displayed positive effect towards Alternaria alternata when applied as a foliar spray (Hassan et al. 2021).

Fig. 2
figure 2

Mechanism of action of biofungicides in strengthing plant resistance against phytopathogens. Pathogen attack different plant parts and diseased plants show necrotic lesions, chlorosis, reduced growth of shoots and altered root growth. Plant primed with biofungicides tolerate pathogen attack more firmly and shows healthier growth than without primed plants. Biofungicides derived from various plant sources may be applied on leaves or it may be applied in the soil as a consortium of different benefical microbes. Biofungicides suitably enhance induced systemic responses (ISR) of plants and brings about various structural, physiological and molecular changes that protect the plants from pathogen attack. Concomitantly, in soil based formulations the consortial of beneficial microbes acts directly and prevent growth of pathogens through competition, antibiotic production, and siderophores as well as modulate composition of root exudates that affect growth of harmful microbial partners

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3.3 Soil application

Soil application is another widely used traditional methods for delivering biofungicides used for plant protection against phytopathogens. Soil treatments with biofungicides not only aid in disease suppression but also stimulate growth and yield of host plant (Narasimhan and Shivakumar 2015). A study showed that soil application with Lysobacter enzymogenes LE16 autolysates provided effective results against blight caused by Phytophthora capsici in pepper (Chen et al. 2020). Several years of research have shown tremendous potential of Trichoderma as a biocontrol agent and it is now one of the most effective potent contenders for its application in biofungicide industry (Vinale et al. 2008; Srivastava et al. 2016) and is sold under different trade names worldwide (Woo et al. 2014). Biofungicide formulation containing Trichoderma viride mixed with pre-sterilized talc when applied to soil comprising pathogenic Rhizoctonia solani, reduced plant mortality and increased yield of plants like cotton, okra and sunflower (Mathivanan et al. 2000). In the same way, soil application of antifungal compound 6-pentyl-α-pyrone isolated from Trichoderma harzianum SQR-T037 reduced disease severity of Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum by 78.1–89.6% in cucumber (Chen et al. 2012).

Similarly, quite a number of species belonging to the genera Bacillus have been well known for their growth promoting (Bavaresco et al. 2020), antibiotic producing and pathogen antagonizing properties in plant system (Shafi et al. 2017). Antifungal activities of several members of the genera are well documented by Khan et al. (2021) making them worthy biofungicide candidate. About 90% of reduction in growth of pathogenic Plasmodiophora brassicae in Brassica napus was observed after soil drenching with biofungicide Serenade® containing Bacillus subtilis QST713 (Lahlali et al. 2011). The application of biofungicide Serenade® modulated the growth of pathogen by inhibition of spore germination and viability. Likewise, soil application of talc/lignite-based formulations of Bacillus subtilis (JN032305) biofungicides, used by Narasimhan and Shivakumar (2015) increased plant growth as well as suppressed the anthracnose disease in chilli caused by Colletotrichum gloeosporioides.

4 Mechanism of action of biofungicides

4.1 Structural

4.1.1 Inhibition of fungal growth

Inhibition of fungal growth is achieved through antagonism (Khalaf and Raizada 2018), hyper parasitism (Ghosh et al. 2018), rapid colonisation (Surono and Narisawa 2018; Gholami et al. 2019) or through the competition for resources (Nally et al 2015). Several antifungal volatile compounds like S-methyl ethanethioate, 1,2-dimethyldisulfane, acetic acid, 2-methyl propanoic acid, 3-methyl-butanoic acid, nonan-2-one, undecan-2-one and 2-isopropyl-5-methylcyclohexan-1-ol has been reported from the actinobacteria Nocardiopsis sp. that inhibit fungal growth (Widada et al. 2021). Likewise, Trichoderma-derived volatile organic compounds like 6-pentyl-2H-pyran-2-one and 2-pentylfuran inhibited the growth of Plasmopara viticola in grapevine through increased callose accumulation (Lazazzara et al. 2021) thereby limiting the entry and nutrient acquisition of the pathogen. On the other hand, essential oils of plants contain various antifungal components that explain their inhibitory effect towards the pathogenic fungi. As reported by Ali et al. (2021), essential oil of Mentha longifolia containing menthone and eucalyptol, while Citrus reticulata essential oil containing β-caryophyllene, β-caryophyllene oxide, and β-elemene as the major compounds found to be effective in growth inhibition of Aspergillus flavus and A. fumigatus.

Application of biofungicide controls mycelial growth and spore germination of pathogenic fungi (Xie et al. 2021) as well as conidia production (Xu et al. 2021). Biofungicide decreases germinal tube length of fungal spores (Ji et al. 2013; Nally et al. 2015), increases cell membrane permeability (Sun et al. 2017) causing cytoplasmic leakage (Wei et al. 2020) resulting in wilting, abnormal swelling (Ji et al. 2013) with thick, depressed, irregular branching or curved hyphal morphology (Arroyave-Toro et al. 2017; Gholami et al. 2019). For example, essential oils used by Soylu and Incekara (2017) were able to completely inhibit Fusarium oxysporum f. sp. radicis-cucumerinum conidial germination along with hyphal degradation while retarded hyphae displayed enlarged vacuoles and coagulations. Similarly, LFF extract treated fungi showed disentangled pulpy lytic pattern hyphae suggesting cell wall degradation (Jeon et al. 2009).

4.1.2 Strengthen plant structural features

Structural defense mechanism is the primary line of defense in plants towards any pathogen attack. Pathogens can gain entry from various plant surfaces like leaf, stem, roots, etc., through openings like wound, cuts, hydathodes, stomata, etc. It is evident from earlier studies that deposition of lignin on plant cell walls prior and after pathogen attack restricts the growth and proliferation of pathogen (Vance et al. 1980; De Alwis et al. 2009). Zhang et al. (2020b) reported Pichia membranefaciens induced lignin accumulation in peach tissues that additionally contributed resistance towards Rhizopus stolonifer. Likewise, Fusarium oxysporum F2 increased lignin concentration in grapevines affected with tracheomycotic fungus Phaeomoniella chlamydospore (Gkikas et al. 2021). Increased lignin concentration attribute towards cell wall thickening providing resistance towards phytopathogens as evident from the work of Cantoro et al. (2021) that showed increased lignin deposition in Triticum aestivum plants infected by Fusarium graminearum in response to Bacillus velezensis RC 218 inoculation that prevent further proliferation. Increment in thickness of mid vein and lamina was also observed in Vitis vinifera treated with Streptomyces violatus for controlling Plasmopara viticola (El-Sharkawy et al. 2018).

Lignin accumulation occurs through the activation of phenylpropanoid pathway by microbial consortium (Sarma et al. 2015). It was reported that exogenous application of Trichoderma harzianum UBSTH-501- and methyl jasmonate induced PAL dependent lignin biosynthesis through phenylpropanoid pathway in Triticum aestivum (Singh et al. 2019). Eliciting defense responses through application of purified hairpin protein from Erwinia amylovora in strawberries showed disease reduction caused by Botrytis cinerea (Scariotto et al. 2021). The study further showed the application hairpin induced PAL synthesis in strawberries which contributed towards the disease resistance. Likewise, elicitor prepared from Penicillium chrysogenum by Lu et al. (2021) was able to increase PAL production in broccoli cells via nitric oxide signalling pathway. Zhang et al. (2019) observed the ability of Pichia membranaefaciens and Kloeckera apiculate to activate phenylpropanoid pathway in ‘Qingcui’ plum against Monilinia fructicola invasion. Upregulation of lignin metabolic pathway genes in Fusarium solani CEF559 pretreated roots of cotton was observed by Wei et al. (2019) that provided additional resistance towards Verticillium dahliae. Similar report of lignin accumulation was reported by Gkizi et al. (2021) in Paenibacillus alvei K165 treated Arabidopsis thaliana that contributed in resisting V. dahliae infection. Furthermore, histochemical studies of vascular bundles showed maximum and uniform lignin deposition in Cicer arietinum treated with consortium containing Pseudomonas (PHU094), Trichoderma (THU0816) and Rhizobium (RL091) strain under Sclerotium rolfsii stress (Singh et al. 2013).

4.2 Physiological

Biofungicides confer resistance against several phytopathogens through the production of various antifungal compounds (Usharani et al. 2015; Leiter et al. 2017; Shokouhi and Seifi 2020; Kumar et al. 2021b), secondary metabolites like cladosporin, isocladosporin, 5′-hydroxyasperentin and cladosporin-8-methyl ether (Wang et al. 2013), phenolic compounds (Fernandes et al. 2014), volatile organic compounds (Jiang et al. 2018; Myo et al. 2019; Kumar et al. 2021b), hydrolytic enzymes (Nandhini et al. 2018; Durairaj et al. 2018; Yang et al. 2020; Zhang et al. 2020b) and also through gene regulation mechanism (Ferrigo et al. 2020; Yadav et al. 2021). In addition, biofungicide also primes the host through the production of volatile organic compounds, lipopeptides (surfactin, fengycin and iturin) (Ji et al. 2013; Arroyave-Toro et al. 2017; Sidorova et al. 2020; Nookongbut et al. 2020) and H2O2 (Jiang et al. 2018) which can elicit plant defense system. Concomitantly, there are reports that states competition for resources (Nally et al 2015), antagonism (Khalaf and Raizada 2018), rapid colonisation (Surono and Narisawa 2018; Gholami et al. 2019) and hyper parasitism (Ghosh et al. 2018; Zhang et al. 2020a) when biofungicides are utilized for biocontrol of pathogens.

Biofungicide triggers the production of defense related enzymes like POX, POD, PPO, LOX and PAL (Nandhini et al. 2018; Amruta et al. 2019; Yadav et al. 2021; Xie et al. 2021). For example, cuminic acid extracted from seed of Cuminum cyminum significantly enhanced defense related enzymes like SOD, POD, CAT and MDA in the leaves of watermelon (Sun et al. 2017). Likewise, biocontrol agent Trichoderma atroviride induced increased concentration of POX and CAT activities along with higher concentration of protein and phenol in wheat (Benyahia et al. 2021). Similarly, two PGPR strains Bacillus megaterium OSR3 and Pseudomonas fluorescence PF-097 provided resistance to chilli plants against Sclerotium rolfsii and plants showed enhanced activity of antioxidative enzymes including CAT, POD and PPO (Sharf et al. 2021). In the same way, application of Jacaranda mimosifolia leaf formulations on maize seeds also induces activities of POD, PPO and PAL as reported by Naz et al. (2021). Apart from antioxidative enzymes like SOD, CAT and POD, increase in other parameters like chlorophyll concentration and fresh mass of rice seedlings was reported from the application of Bacillus tequilensis JN-369 under Magnaporthe oryzae infection (Zhou et al. 2021).

Pre-treatment of seeds shows infliction of ISR by augmenting phenolic, defence and antioxidative enzymes biosynthesis (Yadav et al. 2021). Mechanism for antifungal activity through ISR induction is also supported by the study done by Esserti et al. (2017) where they observed higher concentration of defence enzymes activities in Solanum lycopersicum plants after the application of aqueous extracts of brown algae. Likewise, increasing concentration of salicylic acids (SA) in finger millets while using biofungicide activated the SAR pathway enhancing metabolites of phenylpropanoid pathway which resulted in lignin deposition on the cell walls minimizing pathogen entry in finger millets (Patil and Kumudini, 2019). Accumulation of pathogenesis related (PR) proteins occur through the regulation of systemic resistance by biofungicides (Patil et al. 2016; Jayamohan et al. 2020). Increase in concentration of cell wall degrading enzymes like protease, pectinase (Gholami et al. 2019), chitinases, β-1,3-glucanase, amylase and cellulase (Myo et al. 2019) was observed after biofungicide application (Fig. 2). For example, Liu et al. (2020) isolated novel chitinase (IbChiA) from sweet potatoes roots that exhibited fungicidal effects on conidia and mycelia of Ceratocystis fimbriata. Rhizospheric Pseudomonas sp. NS 1 and Bacillus sp. NS 22 induced resistance towards Fusarium udum by producing several antifungal metabolites including endochitinase, exochitinase, chitobiase, proteinase, cellulase, amylase, pectinase, lipase, etc. (Dukare and Paul 2021). Detailed mechanism of biocontrol of fungal pathogens through application of different categories of biofungicides has been very well illustrated in Fig. 2.

4.3 Molecular

Investigations have shown the gene regulatory properties of biofungicides as evident by work of Ben Jabeur et al. (2017) that reported use of thyme oil and thymol initially up-regulated MgMfs1, MgAtr4, MgBcy1 and MgHog1 genes encoding for efflux pump, protein kinase A and MAPK while later it repressed the expression MgAtr4, MgBcy1, and MgSlt2. Downregulation of bikaverin (Bike1, Bike2 and Bike3) and fusaric acid (FUB1, FUB2, FUB3 and FUB4) genes was observed with the application of cuminic acid (Sun et al. 2017). qRT-PCR analysis of defence gene (WRKY) in tomato done by Aamir et al. (2019) displayed upregulation of SlWRKY31 and SlWRKY37 while SlWRKY4 was downregulated after bio-priming with Trichoderma erinaceum against Fusarium oxysporum f. sp. lycopersici (Fig. 2). Similarly, qRT-PCR revealed PR-1 and PR-2 genes were significantly upregulated in Zea mays with the application of Pseudomonas aeruginosa strain MF-30 as biofungicide against Rhizoctonia solani (Singh et al. 2020a). Interestingly, bacterial compound phenazine-1-carboxamide was able to directly interact with the Fusarium graminearum protein FgGcn5 (histone acetyltransferase) causing deregulated acetylation of histone (H2BK11, H3K14, H3K18, and H3K27) resulting in suppression of growth, virulence and mycotoxin production (Chen et al. 2018a, b). Surfactin produced by the bacteria Brevibacillus brevis KN8(2) imparted damage to DNA and proteins of Fusarium moniliforme (Krishnan et al. 2019). Upregulation of SA signal markers and plant defence related genes was observed in pepper after the application of Botrytis cinerea (Jiang et al. 2018). Similarly, resistance through SA dependent pathway against Colletotrichum higginsianum was reported in Arabidopsis thaliana (Narusaka et al. 2015). Moreover, rapid upregulation of lipoxygenase C [SlLoxC], allene oxide synthase 1 [SlAOS1] and allene oxide cyclase [SlAOC] genes involved in jasmonic acid (JA) biosynthetic pathway along with protease inhibitor I [SlPI-I], protease inhibitor II [SlPI-II] and ethylene response factor 2 [SlERF2] involved in JA responsive signalling was also reported from tomato fruits inoculated with Bacillus velezensis QSE-21 that aided in resistance against Botrytis cinerea (Xu et al. 2021).

Metabolites derived from microorganisms or plants as well as other cellular components like flagellin protein, peptidoglycans, b-glucans, chitin, extracellular lipopolysaccharides derived from various sources elicits defense responses (Yamaguchi and Huffaker 2011). Concomitantly, with application of biofungicide to host plant signal transduction events at molecular level gets switched on and bring about increased expression of several transcription factors and genes involved in immune responses. Plant immune system is broadly divided into two categories, microbe/pathogen-associated molecular patterns (PAMPs) triggered immunity (PTI) which regulated transcriptional factors and effector-triggered immunity (ETI) which is associated with hypersensitive reactions (Malinovsky et al. 2014). Receptors on plasma membrane recognize the incoming signals and triggers the defense responses in plants through activation of kinases like mitogen-activated protein kinases (MAPKs) and calcium dependent protein kinases (CDPKs). Cumulatively, these signalling results in synthesis of various defense related transcriptional factors. Upon elicitation, PTI and ETI triggers the activation of systemic acquired resistance (SAR) and induced systemic resistance (ISR) in plants (Lahlali et al. 2013). Concomitantly, SAR and ISR is coupled with increased concentration of phytohormones like salicylic acid, jasmonic acid, ethylene, etc. that is followed by the production of various pathogenesis related proteins (Persello-Cartieaux et al. 2003). Furthermore, the activation of SAR and ISR also activates several defence related enzymes like POX, PAL, PPO, POD, etc. (Nandhini et al. 2018; Amruta et al. 2019; Xie et al. 2021).

5 Advantages and disadvantages of biofungicides

5.1 Advantages

Biofungicides have been shown to be advantageous for promoting growth and yield in crop plants besides to plant protection also. Numerous studies have provided substantial evidences for increased plant growth and yield with biofungicide application (Rajput and Harlapur 2015; Rafi et al. 2015). Biofungicides comparatively provide better results in seed germination of several plants like Vigna radiate (Sarkar et al. 2018), Oryza sativa (Naveenkumar et al. 2017; Amruta et al. 2019), Solanum lycopersicum (Rajaput et al. 2019), Cicer arietinum L. (Sufyan et al. 2020), etc. Reports state bio-priming of seeds with antifungal suspension of micro-organisms (Anitha and Jahagirdar 2015; Myo et al. 2019; Rajaput et al. 2019), plant extracts (Rafi et al. 2015; Sarkar et al. 2018) as well as plant-based oils (Naveenkumar et al. 2017) aids in seed germination. Along with enhancement of seed germination and growth biofungicides also aids in the increase in yield of crops.

Bio-primed seeds with Bacillus amyloliquefaciens UA SBR9 (Amruta et al. 2019), B. subtilis (Anitha and Jahagirdar 2015; Mona et al. 2017) and Pseudomonas fluorescens (Rajput and Harlapur 2015) increased the grain yield of rice, soybean and maize respectively. Similar results were obtained using Trichoderma harzianum and Pseudomonas fluroscens in maize (Venkateswarlu and Beura 2020). Seed treatment followed by spray using Trichoderma viride at 1% resulted in higher yield and grain mass of rice as reported by Pal et al. (2015). Liquid consortial formulation used by Upamanya et al. (2020) resulted in increase in fruit yield of brinjal (Solanum melongena L.). In another study, both crude and dry formulation of Talaromyces tratensis KUFA 0091 showed increase in rice yield when used as a biofungicide (Eakjamnong et al. 2021). Interestingly, application of biofungicide along with intercropping promoted higher yield of cowpea comparatively than the sole crop grown (Falade et al. 2017).

With the use of biofungicides there is increased production of IAA, gibberellins and siderophores that stimulates plant growth parameters (Nandhini et al. 2018; Gholami et al. 2019). Furthermore, enhancement of nutrient status of the soil by increasing the P and K s in the soil by biofungicide application is another characteristic that points towards plant growth promotion (Upamanya et al. 2020). Higher seedling length and dry mass was reported in bio-primed seeds of Oryza sativa with the use of different bacterial isolates (Amruta et al. 2019). Similar results were observed with the fungus Trichoderma sp. which improved shoot and seedling length in Glycine max JS 335 (Anitha and Jahagirdar 2015) and increased the number of leaves and fresh-dry mass in Pisum sativum cv. NBR- Ruchi (Singh et al. 2016a). Lower concentration of Talaromyces tratensis KUFA0091 formulations stimulated shoot–root growth and vigour in rice (Eakjamnong et al. 2021). Combined seed and seed bed treatment with fungal biofungicide seems to be beneficial over their independent use in terms of germination percentage, shoot–root length and plant vigour (Upamanya et al. 2020). Likewise, the use of microbial antagonist and soil amended with different oil cakes showed effective results in enhancing growth and disease resistance (Rafi et al. 2016). PGPR primed seeds of Cicer arietinum suppressed the disease caused by Fusarium oxysporum f. sp. Ciceris concurrently promoting root length, fresh-dry mass and total biomass (Sufyan et al. 2020). Coat priming of seeds also showed good results in terms of plant height, branches, fresh and dry mass in soybean (Mona et al. 2017).

Aqueous extracts of plants like Acacia nilotica and Sapindus mukorossi when used in seed priming enhanced the growth parameters of multiple plants like peanut, chickpea, okra and sunflower (Rafi et al. 2015). Algal extracts with antifungal activity also displayed increment in root and shoot length along with higher accumulation of chlorophyll, carbohydrates and proteins in Vigna radiata (Sarkar et al. 2018). Seed priming with oil of Cymbopogon citratus improved seed germination, root-shoot length and seedling vigour in Oryza sativa (Naveenkumar et al. 2017). It is reported that the antifungal extract from Toddalia asiatica seems to posses growth promoting ability as it increased the germination and seedling vigour of maize plants (Aiyaz et al. 2015). Besides fungicidal activity, growth stimulating ability of Cinnamomum zeylanicum powder suspension was also observed in tomatoes as the treated plants showed increments in number leaves and branches (Kowalska et al. 2020). In a study done by Luh Suriani et al. (2020), combined mixture of Piper caninum and P. betle var. Nigra leaves extracts and rhizobacteria (Enterobacter cloacae, Bacillus subtilis and Stenotrophomonas maltophilia) apart from Pyricularia oryzae inhibition, promoted the growth, yield and quality of Bali rice. Furthermore, compost materials with varying composition have also been studied for antifungal and plant growth promoting abilities in peach seedlings (Mannai et al. 2018).

5.2 Disadvantages

Biofungicides, although being an eco-friendly approach for eradicating fungal diseases but have some disadvantages. As biofungicides utilizes living microorganisms or their formulations, one of the major problems is the long term storage of these products (Sabaratnam and Traquair 2002) and it has been observed that these biofungicides present the shelf life of few months and preservation of their viability as well as their competitiveness necessitate food base for their survival. Advancements has been made for extending the shelf life of biofungicides with the use of different culturing techniques (Kolombet et al. 2008). On the contrary, chemical fungicides can last for much longer period of time during their storage with no or less changes in their efficacy. Previous, investigations also have shown phytotoxic effects of some biofungicides when applied to the host plant. Reduced germination and root-shoot are some of the changes that are observed in plants after biofungicide applications (Meepagala et al. 2019). Biofungicidal toxicity is not limited to plants but there are reports for their toxic effects on animal systems like Artemia salina (Kordali et al. 2008; Li et al. 2014). For example, antifungal essential oils from Thymus kotschyanus containing thymol as the major compound was able to inhibit germination of Amaranthus retroflexus and Panicum miliaceum, as well as showed insecticidal effect towards Oryzaephilus surinamensis and Sitophilus oryzae (Ghasemi et al. 2020). Furthermore, production of biofungicides at mass industrial scale is another important limiting factor that must also be considered.

6 Toxic effects of biofungicides

6.1 Toxicity of microorganism-derived biofungicides

A toxic side effect of biofungicide is another important issue that needs to be understood. The negative effects of biofungicides on germination, growth and development of plants as well as to another non-target organism should be evaluated prior to application. Higher application of such biological products might create disbalance in the non-target communities. Apart from antifungal metabolites produced by microorganisms, studies suggest that other phytotoxic compounds interfere with the germination, growth and development of plants (Song et al. 2015; Meepagala et al. 2019) as well as animals (). Metabolites like 6,8-di-O-methylnidurufin, 6,8-di-O-methyl versiconol and (S)-ornidazole isolated from the extracts of Penicillium purpurogenum were toxic towards radish seedlings at low concentrations (Li et al. 2014). While the other two compounds (6,8-di-O-methyl averufnin and 5-methyoxysterigmatocystin) isolated were toxic towards Artemia salina with 100% lethality rate at 10 µm.

Similar results for the production of phytotoxic metabolites have been reported from fungal communities too. An antifungal compound dihydrosterigmatocystin, isolated from algal endophytic fungus Aspergillus versicolor D5 not only inhibited Botrytis cinerea but displayed phytotoxic activity towards Amaranthus retroflexus (Zhao et al. 2020b). A fungitoxic metabolite pyrichalasin H, isolated from Pyricularia grisea affected plant growth by interfering with root and shoot development of barley and lettuce (Meepagala et al. 2019). In the same way, volatile organic compounds basically the 2-methyl-1-propanol and 2-methyl-1-butanol, produced by antifungal endophyte Xylaria sp. PB3f3 of Haematoxylon brasiletto exhibited significant reduction in germination and root growth of Amaranthus hypochondriacus and Solanum lycopersicum as reported by Sánchez-Ortiz et al. (2016). Another antifungal endophytic fungus Epichloë bromicola isolated from Elymus tangutorum showed interference in root and shoot development of Lolium perenne and Poa crymophila seedlings (Song et al. 2015). Furthermore, high volume spraying of biofungicides like Plant Guard (Trichoderma harzianum) and Polyversum (Pythium oligandrum) showed decrement in species diversity and community equitability of non-targeted organisms (Al-Assiuty et al. 2014).

6.2 Toxicity of plant-derived biofungicides

Plant essential oils (EO) have been found to be highly efficient in controlling fungal pathogens owing to their huge antifungal potential. However, there are several reports of phytotoxicity with the use of such essential oils (Amri et al. 2013; Hamrouni et al. 2015). Ghnaya et al. (2013) reports the phytotoxic nature of antifungal Eucalyptus erythrocorys leaf EO in Sinapis arvensis and Phalaris canariensis, effecting both the seed germination and seedling growth. Fungicidal EO extracted from the leaves of Tetraclinis articulata also displayed similar herbicidal effects towards Sinapis arvensis and Phalaris canariensis (Ghnaya et al. 2016). Germination and growth inhibitory effects on plants like Amaranthus retroflexus, Chenopodium album, Cirsiumarvense, Lactuca serriola and Rumex crispus was also observed with the application of fungitoxic Myrtus communis EO by Kordali et al. (2016). Similarly, apart from antifungal properties, essential oil extracted from the roots of Senecio amplexicaulis at higher concentrations reduced germination percentage Phalaris minor and Triticum aestivum (Singh et al. 2016b). Antifungal EO from Origanum sp. with carvacrol and terpinen-4-ol as their main constituents showed inhibitory effects towards both seed germination and radicle elongation of Lactuca sativa, Lepidium sativum and Solanum lycopersicum (Della Pepa et al. 2019).

According to Aiyaz et al. (2015), the extract derived from Psoralea corylifolia displayed antifungal activity towards Fusarium verticillioides and Aspergillus flavus but on the other hand, reduced seed germination and vigour of Zea mays. Moreover, growth reduction of lettuce root and shoot after the application of fungicidal Zingiber montanum EO was observed by Verma et al. (2018). Similarly, antifungal and root inhibitory potential of Fraxinus hupehensis extract in Echinochloa crus-galli was reported by Zhao et al. (2020a). The genus Rumex is well studied for their antifungal constituents (Shafiq et al. 2017). However, Rumex maritimus has been reported to possess a phytotoxic compound 2-Methoxystypandrone (Islam et al. 2017). In another study, the volatile organic compounds released from the leaves of Pulicaria sp. that were previously found to possess antifungal properties, effectively reduced the growth of lettuce by 83–85% as reported by Amini et al. (2014). Likewise, trans-ferulaldehyde a bioactive antifungal compound isolated from the leaves and stems of Eleocharis atropurpurea was first reported to exhibit allelopathic effects towards Lepidium sativum, Medicago sativa, Lolium multiflorum, and Phleum pratense seedling growth (Zaman et al. 2018).

7 Effectiveness of biofungicides

Biofungicides has been reported to control of plant fungal diseases where some are comparatively effective as the synthetic ones. Application of Clonostachys rosea strain ACM941 at a concentration of 106 cfu mL−1 was able to significantly suppress Fusarium head blight of wheat to the levels of registered fungicide Folicur® (tebuconazole) (Xue et al. 2014). Similarly, corn starch based formulation of Bacillus licheniformis N1 resulted in 90.5% disease control of Botrytis cinerea, while the chemical fungicide (carbendazim and diethofencarb; 1:1) only showed 77% control of disease in tomato plants (Lee et al. 2006). Seed treatments followed by soil application of talc based biofungicide containing Trichoderma viride as the main biocontrol agent, reported significant reduction in mortality of eggplant and sunflower infected with Rhizoctonia solani in comparison to fungicides like captan, carbendazim and copper oxychloride (Mathivanan et al. 2000). According to Chen et al. (2018a, b), soil application of biofungicide Bacillus subtilis NCD-2 positively regulated soil biota and thereby chrysanthemum growth from Fusarium wilt infection in comparison to the chemical fungicide dazomet. Interestingly, high disease control efficacy of about 86.2–93.1% was depicted by unheated self-digestive solutions (autolysates) prepared from Lysobacter enzymogenes LE16 against blight causing Phytophthora capsica in pepper (Chen et al. 2020). Effectiveness of biofungicides depends upon various factors like temperature (Puopolo et al. 2015), shelf life, nutrient and oxygen availability (Kolombet et al. 2008). In order to increase the efficacy of biofungicides various means of techniques have been adopted. Applying biofungicides in combination with pesticides, soil disinfestation, other antagonists as well as genetic engineering seems to increase the effectiveness as reviewed by Spadaro and Gullino (2005).

8 Future perspectives

Biological control has gained momentum with the increasing public concerns about the toxicity of chemical fungicides. Production of biofungicides at industrial scales is very important in the present scenarios as due to increased food demand and threat to environment. Potentiality of biofungicides as the replacement over the chemical fungicides have been supported by several studies till date. With the availability of large number of sources, screening of low cost biofungicides with higher efficiency would be easier. Biofungicides not only show potential towards disease management but can also act a plant growth promoting agents paving its way towards the production of biofungicide based biofertilizers in future. Very few studies have been done on the toxicity of biofungicides towards non-target organisms therefore proper studies on biofungicides prior to application in coming days. In addition, increased shelf life of biofungicides is of utmost importance for the viability and efficacy for longer period of time. Most of the studies on biofungicide have shown positive results under in vitro conditions, very few have assessed their potential benefits under natural field conditions. Therefore, it is recommended that application of biofungicide should be carried out in large scale in agricultural fields. Moreover, most of the biofungicides are quite specific towards fungal pathogens. To overcome as such use of some studies have suggested use of biocontrol agents in combinations. Therefore, development of universal biofungicides is important from that perspective. Also, the toxicity of biofungicides is very serious issue. Proper studies and trials must be involved with biofungicides prior to their release. From the study, we found that the concentration of biofungicide plays an important role as higher concentration seems to affect plant growth and development. Such issues must be resolve before the release of biofungicides in order to avoid negative consequences. Furthermore, involvement of various molecular pathways induced through the application of biofungicide are vaguely understood therefore, molecular studies including transcriptomics, proteomics can help in understanding the underlying mechanism of biofungicides in fungal disease management in the near future. Simultaneously, due to advancement in genomics and fungal genomes sequences are available for the number of pathogenic fungi; target approach based methods for loss of virulence can be utilized through these biofungicides.