Crop Molds and Mycotoxins: Alternative Management Using Biocontrol

Accepted Manuscript

Crop molds and mycotoxins: alternative management using biocontrol

Phuong-Anh Nguyen, Caroline Strub, Angélique Fontana, Sabine Schorr- Galindo

PII: S1049-9644(16)30199-2 DOI: http://dx.doi.org/10.1016/j.biocontrol.2016.10.004 Reference: YBCON 3497

To appear in: Biological Control

Received Date: 20 July 2016 Revised Date: 10 October 2016 Accepted Date: 18 October 2016

Please cite this article as: Nguyen, P-A., Strub, C., Fontana, A., Schorr-Galindo, S., Crop molds and mycotoxins: alternative management using biocontrol, Biological Control (2016), doi: http://dx.doi.org/10.1016/j.biocontrol. 2016.10.004

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Phuong-Anh Nguyen*, Caroline Strub, Angélique Fontana, Sabine Schorr-Galindo

UMR Qualisud (Université Montpellier), Place Eugene Bataillon, 34095 Montpellier Cedex 5, France

* Corresponding author:

Email: [email protected]

Phone number: +33 4 67 14 33 12

Fax number: +33 4 67 14 42 92

Abstract

Phytopathogenic and/or mycotoxigenic filamentous fungi are involved in a great number of plant diseases that cause yield and quality losses of crops. Besides the economic damages, these fungi produce mycotoxins that present health risks for humans and animals who consume contaminated foods. The most dangerous mycotoxins in the agriculture and the food industry that are regulated in European Union (trichothecenes especially deoxynivalenol, fumonisins, aflatoxins and ochratoxin A) are produced by three main fungal genera (Fusarium, Aspergillus and Penicillium). Many approaches have been applied to prevent and manage the phytopathogenic and/or mycotoxigenic fungi. However, these methods involve the use of chemical inputs that are harmful for humans, animals and environment. In a concern of sustainable development, the application of biocontrol has been considered for addressing this problem in a more environmentally friendly way. This review considered the incidence of the three fungal genera and their mycotoxins in crops and in foodstuff. The impacts of the fungal contamination and the toxin accumulation were reported. Besides, the biological control means against these pathogens were reviewed. Among them, organic amendments showed to be effective in both producing antifungal activities and reinforcing plant health.

Keywords: Filamentous fungi; mycotoxins; phytopathogenesis; biocontrol agents; organic amendments

Introduction

Fungi take an important part in the microorganism world. They might have benefices in sciences, industries and technology. Nevertheless, filamentous fungi appear to be a potential harm for humans, animals and crops. In fact, many of them are phytopathogenic and/or mycotoxigenic. Their occurrence leads to many soil-borne diseases for plants, thereby causing various food and feed- borne mycotoxicoses for humans and animals through the consumption of contaminated products. Thus, these filamentous fungi damaged not only human and animal health but also the international economy.

The main targets of molds are cereals, grains, fruits and vegetables. The major toxins that are associated with the contamination are deoxynivalenol (DON) (or nivalenol in some areas), fumonisins, zearalenone, aflatoxins and ochratoxin A (OTA) (Miller, 2008). These are the most important mycotoxins (Pitt, 2000) produced mainly by species of Aspergillus, Fusarium and Penicillium. Cereals constitute a staple food for all over the world as well as the main source of animal feed (Von Braun, 2007). So, research for protecting crops from molds and their mycotoxins has become indispensable.

For decades, various agricultural practices have been applied. However, the current approaches dealing with the fungal phytopathogens were based on the use of chemical agents that are reported to be acutely and chronically hazardous to humans, animals and ecosystems. Within the context of the “organic farming” and the sustainable development concern, alternative practices have to be developed, notably the biological solutions that maintain the quality and the abundance of crops with respecting the ecosystems and human and animal health.

In this context, this review describes: i) the main phytopathogenic and mycotoxigenic filamentous fungi and their mycotoxins, ii) the main strategies of biological control applied to these molds with emphasis to the application of organic amendments.

1. Phytopathogenic and mycotoxigenic fungi 1.1. The genus Fusarium 1.1.1. Phytopathogenesis

Fusarium is a large group of ascomycete fungi that belongs to the class of Sordariomycetes and to the family of Nectriaceae. Fusarium is one of the most important phytopathogenic group (Booth, 1971).

The occurrence of Fusarium can be found in all types of plant tissues, soil debris and soils in many cereal crops. The most affected cereal by the pathogenic Fusarium are corn (Aboul-Nasr and Obied- Allah, 2013; Sreenivasa et al., 2013; Becker et al., 2014; Liu et al., 2014), wheat (Cui et al., 2013; Lindblad et al., 2013; Tittlemier et al., 2013), barley (Oliveira et al., 2012; Běláková et al., 2014), sorghum (Sreenivasa et al., 2013; Divakara et al., 2014; Kange et al., 2015) and oat (Kiecana et al., 2012; Fredlund et al., 2013; Kiecana et al., 2014). The Fusarium species responsible for these contaminations are Fusarium graminearum, F. sporotrichioides, F. poae, F. avenaceum, F. culmorum, F. accuminatum, F. langsethiae, F. verticillioides, F. proliferatum, F. oxysporum, F. anthophilum and F. paranaense. Fusarium graminearum is the most common species in the infections.

The Fusarium pathogens were also found in various vegetables and fruits, i.e. soybeans (Arias et al., 2013; Chang et al., 2015; Costa et al., 2016), chili (Sundaramoorthy et al., 2012; Jalaluldeen et al., 2014) and tomato (Bharat and Sharma, 2014; Loganathan et al., 2014).

Fusarium spp. are the major soil-borne and seed-borne pathogens causing damage to a wide range of crops and they are responsible for various diseases. The most frequent diseases in cereal crops is Fusarium Head Blight – FHB that can lead to enormous loss of yield and low quality of crops (Zhang et al., 2013). Fusarium spp. are causative agents for rot disease in many plants: root rot in soybean (Arias et al., 2013; Chang et al., 2015), stalk rot in maize (Kaur et al., 2014), root and steam rots in cucumber (Pavlou and Vakalounakis, 2005). Fusarium oxysporum f. sp. cucumerum J.H.Owen caused the Fusarium wilt that has been reported as one of the most severe diseases in cucumber (Qiu et al., 2012). Fusarium oxysporum caused also the wilt in banana (Ploetz, 2006) and melon (Ma et al., 2014; Cohen et al., 2015). A newly soil-borne pathogen strain of F. oxysporum, which was identified as F. oxysporum f. sp. citri, caused diseases on seedling of citrus trees (Hannachi et al., 2015). The loss of yield and the severity of diseases is linked to the extent of the Fusarium infection (Chang et al., 2015). Fusarium infections are also reported in both humans and animals (Zhang et al., 2006; Antonissen et al., 2014).

1.1.2. Toxinogenesis

The majority of the Fusarium species are able to produce mycotoxins and are involved in the accumulation of toxins in food and feed which leads to human and animal intoxications. These mycotoxins produced by Fusarium sp. are called fusariotoxins and are characterized by their acute

3 and/or chronic toxicity. There are three groups of fusariotoxins: trichothecenes, zearalenone and fumonisins. Some species can produce several mycotoxins at the same time like F. graminearum which is considered as the most virulent among the Fusarium genus producing trichothecences. F. graminearum can produce also the zearalenone and some other secondary metabolites such as culmorin, sambucinol, dihydroxycalconectrin, butenolide and fusarin C which are more or less toxic (Farber and Sanders, 1986; Wang and Miller, 1988; Lysøe et al., 2006).

• Trichothecenes

Trichothecenes are a group of mycotoxins formed on the basis of their chemical structure and produced by various Fusarium spp. This group constitutes more than 200 chemical derivatives classed in 4 types A, B, C and D in which the 2 types A and B are mostly issued from Fusarium spp. and prevalent in the nature. The predominant trichothecenes in crops are DON and its derivatives, nivalenol, T-2 and HT-2 toxin and diacetoxy-scirpenol (DAS) produced mainly by Fusarium graminearum, F. sporotrichioides, F. poae, F. culmorum, F. asiaticum, F. crookwellense, F. equiseti, F. langsethiae and F. accuminatum (Golinski et al., 1988; Bottalico and Perrone, 2002; Zhang et al., 2010; Gale et al., 2011). Trichothecenes appear essentially in the food commodities based on maize and wheat such as flour, pasta and other cereals in which DON is the most found. DON was present in 85-90% of wheat samples with incidence of 500-15,000 µg/kg in China (Cui et al., 2013) and up to 4700 µg/kg in Canada (Tittlemier et al., 2013). In malting barley of Czech, DON was found at 2213.5 µg/kg with other trichothecenes as toxins T-2 and HT-2 (Běláková et al., 2014). Trichothecenes were also detected in oat, including T-2, HT-2, DAS and DON (127 µg/kg) with acetylated derivatives as 3- Acetyldeoxynivalenol (3-AcDON) and 15-Acetyldeoxynivalenol (15-AcDON) (Kiecana et al., 2012). The toxins contribute to the diseases in crops such as FHB and wilts (Bottalico and Perrone, 2002; Dedeurwaerder et al., 2014; Aoki et al., 2015; Touati-Hattab et al., 2016). They decrease the germination of grains in the water sensitivity and the accumulation of mycotoxins thus reduce the quality and the yield of crops productions (Oliveira et al., 2012). The toxin levels are positively correlated with the pathogen occurrence (Lindblad et al., 2013). Mycotoxins can easily transfer to humans and animals through the consumption of crops contaminated with these toxic molecules. Then, they cause exposure to both acute and chronical intoxication (Cortinovis et al., 2012). DON is responsible for impairment of weight gain, emesis, feed refusal and decreased nutritional efficiency in swine and poultry (Bryden, 2012). DON was reported to have several immunological effects in pigs (Tittlemier et al., 2013), chickens (Ren et al., 2015) and humans (Maresca et al., 2002). A historical outbreak of human toxicosis due to the DON was reported in large-scale in India (Bhat et al., 1989).

Sometimes the combination within trichothecenes or with other mycotoxins such as aflatoxin or zearalenone can produce a toxicity synergistic effect (Gerez et al., 2015; Sun et al., 2015).

• Zearalenone

Zearalenone is considered as mycooestrogenic toxin and can act as a sexual hormone since it is similar with a human ovarian hormone. Thus it can fit the oestrogenic receptor in human. This toxin is mainly produced by F. gramniearum, F. culmorum, F. crookwellense and F. equiseti (Caldwell et al., 1970; Golinski et al., 1988; Bottalico and Perrone, 2002). It is also synthetized by other species of Fusarium such as F. oxysporum, F. tricintum, F. sporotrichioides and F. laterum (El-Kady and El-

Maraghy, 1982). This toxin is frequently detected in maize, oat, wheat and barley at various concentrations. Moreover, zearalenone was usually found to co-occur with other mycotoxins like DON, aflatoxin B1 and ochratoxin (Ibáñez-Vea et al., 2012; Vidal et al., 2013; Ji et al., 2014). Thus, the consumption of cereals spoiled by zearalenone can cause genital and fecundity problems in aquatic and domestic animals such as pigs (Schoevers et al., 2012), horses (Minervini et al., 2006), bovines (Pizzo et al., 2016) and rainbow trouts (Woźny et al., 2015). The symptoms of infected cases are well defined, including: swelling of vagina, atrophy of ovaries (Mirocha et al., 2013) and, more serious, prolapse of vagina and rectum (Pitt, 2000). Zearalenone is also known to be hepatotoxic. It caused the histological changes in animal liver, associated with the decrease of hepatic function (Marin et al., 2013; Gerez et al., 2015; Woźny et al., 2015). In addition, zearalenone had effects on the hematological parameters and had genotoxic potential (Pietsch et al., 2015).

As animals, humans are also affected by consuming the food products containing this phytoestrogen. Zearalenone had been reported to be a possible causative agent in an outbreak of precocious pubertal changes in children in Puerto Rico (De Rodriguez et al., 1985).

• Fumonisins

Fumonisins are foodborne mycotoxins that were discovered and characterized in the late 1980s (Bezuidenhout et al., 1988; Marasas et al., 1988). This family of toxins consists of different molecules classified in 4 main groups A, B, C and P. The most widespread fumonisins in cereals are the fumonisins B, including fumonisin B1 (FB1), fumonisin B2 (FB2) and fumonisin B3 (FB3), in which the FB1 is the most abundant with the proportion of 70-80% of the total fumonisins (Rheeder et al., 2002). Fumonisins are frequently found in the corn-based foods. The fumonisin contamination level detected was sometimes quite high: up to 121,420 µg/kg in maize and 20,320 µg/kg in sorghum of India (Sreenivasa et al., 2013). Fumonisins were found in 29.4% of 68 processed products such as cornflakes and breakfast cereals in Morocco (Mahnine et al., 2012). The FB1 reached 5960 µg/kg in

5 corn in Morocco (Zinedine et al., 2006), 1304 µg/kg in just harvested wheat of Argentina (Cendoya et al., 2014) and 5400 µg/kg in wheat during storage in Serbia (Stanković et al., 2012). These studies also showed that fumonisin B1 had a co-occurrence with other fusariotoxins such as DON, zearalenone and ochratoxin A. Fumonisins are mainly produced by Fusarium verticillioides, F. proliferatum, F. nygamai, F. anthophilum and F. oxysporum. These strains of Fusarium are the most occurring pathogen causative of the ear rot, kernel rot and seedling blight in cereals. Even though fumonisins are not essential for pathogenicity of Fusarium (Covarelli et al., 2012), these toxins were often found simultaneously with the fusariosis symptoms and a correlation between the ear rot and the fumonisin concentration was established in maize (Balconi et al., 2014). In contrast, fumonisins have fatal effects on domestic animals. The most well-described pathology is the ELEM – Equine Leukoencephalomalacia – in horses whose brain is affected by the toxins (Pitt, 2000; Giannitti et al., 2011). Fumonisins were detected with a high level in feed samples associated with ELEM cases in the USA: 1,300-27,000 µg/kg of FB1 and 100-12,800 µg/kg of FB2 (Thiel et al., 1991) or in infected horses: 37,000-122,000 µg/kg and 2,000-23,000 µg/kg for FB1 and FB2 respectively (Wilson et al., 1990). In pigs, the consumption of contaminated feed can lead to the porcine pulmonary edema (PPE). FB1 was identified as causative agent for PPE for the first time in 1992. The symptoms of intoxication were a decrease in feed intake, followed by respiratory distress and cyanosis several days after and finally death because of a serious pulmonary edema (Osweiler et al., 1992). Lethal diseases due to corn contaminated by F. verticillioides, the first producer of fumonisins, caused death in thousands pigs in the USA (Haschek et al., 2001). Other domestic animals such as poultry can also be concerned. The fumonisins affected their intestinal microbiota composition and their sphingolipid metabolism, resulting in a diarrhea or worse, and poultry became even more susceptible for necrotic enteritis (Antonissen et al., 2015).

The most evident effect of fumonisins on humans was an oesophageal cancer associated with the corn reported in China and in areas of Southern Africa. The fumonisin levels in moldy corn of these regions were significantly high, up to 155,000 µg/kg of FB1 (Chu and Li, 1994; Yoshizawa et al., 1994; Isaacson, 2005). Fumonisins produced by F. verticillioides were reported to have cancer-promoting activity in rats (Gelderblom et al., 1988). Further studies showed that fumonisins had also hepatotoxic and nephrotoxic effect on rodents (Voss et al., 1989). Thus they were suspected to be a risk factor of cancer and other diseases in human.

1.2. The genus Aspergillus 1.2.1. Phytopathogenesis

The genus Aspergillus belongs to the ascomycete class with only asexual reproduction. The Aspergillus strains became among the most studied molds for their important roles in ecosystems and for their pathogenicity. They produce huge amount of spores that can spread in air and germinate when contacting with a substrate under favorable conditions (Bennett, 2010). Acting as saprophytes, they can be easily found in huge amount on decomposed material such as moldy hay, organic composts, leaves litter, plant litter, in degrading substrates like dung, human tissues, in the soil and in the air or dusts (Cvetnić and Pepeljnjak, 1997; Bennett, 2010). Aspergillus are also found in various food commodities and can spoil all type of foodstuffs. They are broadly dispersed in cereals and fruits. A wide range of cereals, grains and nuts is susceptible to be contaminated with Aspergillus spp., including rice, wheat, corn, barley, sorghum, soybean, peanut and black bean (Petchkongkaew et al., 2008; Tóth et al., 2012; Ruadrew et al., 2013; Kange et al., 2015). Some xerophilic species of Aspergillus can be found in spices and dried foods (Romero et al., 2005; Ruadrew et al., 2013). They can even grow in hostile environments like jams (Williams, 1990) or salted dried fish (Ahmed et al., 2005) where the pH and aw are low but the concentration of sugar or salt is quite important. The main species were identified as A. parasiticus, A. flavus, A. niger, A. ochraceus, A. oryzae and some of them could potentially produce mycotoxins in these products. The Aspergillus section Nigri, including A. carbonarius, are responsible for many diseases and accumulation of mycotoxins in grapes and wine (Serra et al., 2003; De Felice et al., 2008; Vitale et al., 2012). The Aspergillus are the most encountered species in different brands of cocoa-based beverage in Nigeria (Oyetunji, 2006) and in cocoa beans (Aspergillus section Flavi) (Sánchez-Hervás et al., 2008). Similarly in coffee, the black Aspergilli and some strains of Section Circumdati had high incidence on coffee beans and cherries (Taniwaki et al., 2003; Noonim et al., 2009). The main Aspergillus species of section Circumdati regarding potential ochratoxin A production in coffee, rice, beverages and other foodstuffs are A. ochraceus, A. westerdijkiae and A. steynii .

Despite of many favorable benefits in biotechnology and food technology, the genus Aspergillus is associated with critical diseases of humans and animals. A. niger, A. flavus, A. fumigatus, A. awamori and A. tubingensis were the common species that caused otomycosis in ear canal (Ozcan et al., 2003; Szigeti et al., 2012). A. fumigatus caused the pulmonary mycoses and hypersensitivity pneumonitis (Kosmidis and Denning, 2015). The spores of A. clavatus and A. fumigatus from contaminated barley and corn were present in a high concentration in the lungs of farmers and malt workers, the lungs of compost workers were also found to be colonized by Aspergillus spores (Patterson et al., 1974; Vincken and Roels, 1984; Moreno-Ancillol et al., 2004). The fungal conidia in the air can contaminate humans by inhalation or contact with the eyes and other body parts and thus, cause some airway diseases such as allergy and asthma. Besides, numerous species of

Aspergillus are known to be able to produce the toxic metabolites for humans, animals and plants. Among these mycotoxins, aflatoxins and OTA are the most problematic chemical compounds.

1.2.2. Toxinogenesis • Aflatoxins

Aflatoxins have been recognized as the most important and widely studied mycotoxins. There are 4 major aflatoxins (AFB1, AFB2, AFG1 and AFG2) produced particularly by Aspergillus flavus, A. parasiticus, A. nomius, A. bombycis, A. ochraceoroceus, A. pseudotamarii and A. tamarii (Pitt, 2000).

Aflatoxins can be detected in many cereals and their derived products. After a severe infestation of Aspergillus spp. in corn, that reduced food quality in the USA in 1998, measurements of aflatoxin levels in harvested corn from 1998 to 2001 were conducted. Results showed that almost samples contained aflatoxins. The contamination level reached 653 µg/kg, in which aflatoxin B1 concentration was 641 µg/kg (Abbas et al., 2006). The 4 major types of aflatoxins were detected in sorghum grains in Kenya (freshly harvested and in store) (Kange et al., 2015). Wheat derived products such as spaghetti, noodles, macaroni, lasagna and bucatini appeared to be contaminated with aflatoxins at concentration above EU legal limit. Results led to a strict attention to quality control of foods (Iqbal et al., 2014). The contamination of aflatoxins may also concern animals. Aflatoxigenic Aspergillus section Flavi including A. flavus, A. parasiticus and A. tamarii were isolated from poultry feed and they were able to produce aflatoxins with level up to 440,521 µg/kg in maize grains (Ezekiel et al., 2014). The incidence of aflatoxins in nuts and dried fruits like dried raisins, dried figs, walnut and pistachio was also quite high (Arrus et al., 2005; Juan et al., 2008). Despite of a low occurrence, A. flavus, A. parasiticus and A. nomius can synthesize aflatoxin B1, B2, G1 and G2 in cocoa beans. Thereby these toxins were highly present in cocoa sub-products that are widely consumed, notably by children (Sánchez-Hervás et al., 2008; Copetti et al., 2011; Copetti et al., 2012b). Furthermore, aflatoxins can be found in dairy products through the consumption of contaminated feed with aflatoxin B1 by lactating animals, followed by transformation of aflatoxin B1 into M1 by the animal metabolism and digestion (Bognanno et al., 2006). The toxin can resist to the technological process and the aflatoxin M1 can be found in pasteurized and Ultra-high temperature processed (UHT) milk (Zheng et al., 2013; Bilandžić et al., 2014), in milk powder (Kim et al., 2000; García Londoño et al., 2013), in yogurt (Issazadeh et al., 2012; Mason et al., 2015) and cheeses (Fallah et al., 2009; Elkak et al., 2012).

Feed and food that were previously contaminated by aflatoxins are threat for human and animal health by both acute and chronic intoxication, notably for the immunocompromised. Goldblatt (2012) described in his review a hysterical epidemic and a massive death of turkeys in 1960 in

England that was termed “turkey X disease”. The same disease affected and led to death of 14,000 ducklings. At the same period, an outburst of trout hepatoma was reported in the USA. Later results showed that aflatoxins were the common cause of all. In birds, the consumption of these mycotoxins resulted in a refusal to eat, lethargy and a weakness of wings. Then the birds could die within a week (Goldblatt, 2012). For humans, aflatoxins were considered as hepatotoxic. The toxin attacked liver and induced tumors and teratogenic effects or even death of patients. Symptoms of aflatoxicosis were described as an edema, a hemorrhagic necrosis of liver and deep coma (Williams et al., 2004). Aflatoxins were also considered as carcinogenic, notably the aflatoxin B1. The aflatoxins were associated with a high incidence of human liver cancer in Central Africa and Southeast Asia (Shank et al., 1972a; Shank et al., 1972b; Kirk et al., 2006).

• Ochratoxin A

OTA is one of the most occurring mycotoxins and appears to be nephrotoxic, carcinogenic, immunosuppressive and teratogenic in both humans and animals (Al-Anati and Petzinger, 2006; Wangikar et al., 2010; Khan et al., 2013; Qi et al., 2014). This toxin is a toxic secondary metabolite produced by filamentous fungi of Aspergillus and Penicillium genera. Different species of Aspergillus genus are able to produce OTA such as A. ochraceus, A. carbonarius, A. steynii, A. niger and A. westerdijkiae. Ochratoxin A was detected in a large spectrum of food commodities like wheat, corn, barley, oat, rice, fruits, nuts and spices and derived products such as breakfast cereals, bread, coffee beverage, chocolate, wine and beer (Molinié et al., 2005; Zinedine et al., 2006; Vidal et al., 2013; Lai et al., 2015). Sometimes the toxin incidence was sometimes quite high and exceeded the legal limit. The contamination results in a loss of nutritive and sanitary quality in seeds and a decreased germination level, thus a problematic loss of yield. A broad spectrum of fruits and dried fruits can be contaminated by OTA, i.e. grapes, dried grapes, black and white sultanas, dates, dried plums and dried figs. In these types of products, OTA was produced by black aspergilli species (section Nigri) especially A. carbonarius and contamination occurs at field (Iamanaka et al., 2005; Zinedine et al., 2007; Lucchetta et al., 2010). OTA level in grapes, dried grapes and derived-grape products were sometime found to be particularly high (4.95 µg/kg and more than 2µg/L which is the OTA limit concentration in grape juice, must, wine and dried food in the European Community). In tropical zone, OTA is mainly produced in coffee beans by A. ochraceus and A. westerdijkiae (section Circumdati). OTA had been found in both green coffee, roasted coffee and instant coffee. OTA in green coffee samples was found with concentrations ranging between 0.2 and 62 µg/kg (Heilmann et al., 1999; Romani et al., 2000; Gopinandhan et al., 2008). The presence of ochratoxin A in roasted coffee and in coffee brews was reported by Tsubouchi et al. (1987). Before this date, it was generally accepted that OTA was decomposed during roasting, nevertheless concentrations superior to the 20

µg/kg have been reported in commercial roasted coffee (Mounjouenpou et al., 2007). The concentration of OTA was reported to be 2.7 µg/kg in green coffee and 0.24 µg/kg in roasted coffee, suggesting that a heat treatment might reduce OTA level in coffee bean although the complete degradation of OTA was rarely reached during roasting (Castellanos-Onorio et al., 2011; Vanesa and Ana, 2013). The OTA contamination in soluble coffee was variable 45e could reach up to 6.40 µg/kg and occurred in almost all of coffee samples. This occurrence urged to an effective control of this kind of product (Vecchio et al., 2012). Similarly, the raw cocoa and the cocoa byproducts, such as nibs, cocoa butter, cocoa powder, cakes and chocolate, can be associated with OTA contamination (Copetti et al., 2013). OTA had been found to co-occur with aflatoxins in cocoa products (Copetti et al., 2012a). Despite their antimicrobial properties due to some essential oils, aniseed and anise fruits can be susceptible to contamination of OTA produced by A. carbonarius and A. steynii (Espejo et al., 2010). Humans can be exposed to OTA not only by consumption of contaminated foods but also by inhaling airborne OTA. OTA was detected in blood of consumers and workers in transformation units of coffee, cocoa beans and spices (Iavicoli et al., 2002; Sangare-Tigori et al., 2006). Besides the vegetal products, OTA can be found in meat. Numerous studies showed that OTA was present in hams both on surface and inside (Wang et al., 2006; Rodríguez et al., 2012a; Rodríguez et al., 2012b).

1.3. The genus Penicillium 1.3.1. Phytopathogenesis

Penicillium is a genus of ascomycetous fungi that is ubiquitous, opportunistic phythopathogenic, this genus can reproduce by asexual and sexual means. They produce a huge number of conidiospores which are abundantly detected in air and in the habitations. The Penicillium spp. can develop in almost any conditions within a wide range of aw, temperature and pH. Majority of species are soil fungi whose natural habitats are decaying vegetables (Pitt, 2002).

Penicillium spp. are one of the most prevalent fungi isolated from cereals such as wheat, maize, barley, rye and sorghum. The main isolated species are P. chrysogenum, P. expansum, P. verrucosum, P. viridicatum, P. oxalcum, P. brevicompactum, P. cyclopium, P. roqueforti and P. velutinum. They can occur in cereal grains at field and during processing and storage, in cereal- derived products and in the air of the production chain (Domijan et al., 2005; Lugauskas et al., 2006; Cabañas et al., 2008; Kange et al., 2015). Penicillium strains commonly contaminate grains, nuts and their byproducts. They are frequently found in peanuts, soybean, almonds, chestnuts and rice (Adjou et al., 2012; Al-Seeni, 2012; Rodrigues et al., 2013; Yassin et al., 2013; Ok et al., 2014). Penicillium spp. can produce several mycotoxins. P. citreonigrum whose presence is ubiquitous is the main source of citreoviridin. This mycotoxin is the causing agent of “yellow rice” that can lead to the acute

10 cardiac beriberi (Kushiro, 2015). An outbreak of deaths linked to beriberi associated with citreoviridin was reported in Brazil (Rosa et al., 2010). Concerning the beverage products, Penicillium was one of the most abundant taxa isolated from coffee plant tissues (Vega et al., 2010), coffee and cocoa beans (Moulia et al., 2014) and cocoa powder (Oyetunji, 2006). Some species of Penicillium, such as P. expansum, P. digitatum, P. italicum, P. solitum and P. ulaiense are devastating pathogens on fruits. They are responsible for the rot, the blue and green molds along with the mycotoxins they produce within a wide range of fruits and vegetables including cabbages, carrots and onions (Lugauskas et al., 2004). Several Penicillium such as P. cyclopium, P. viridicatum, P. verrucosum and P. funiculosum caused rot on apples, pears, pineapples and melons, as reported in a review by Barkai (Barkai-Golan and Paster, 2011). According to this study, grapes are susceptible to host Penicillium spp. and their mycotoxins. The isolates found from grape samples were P. chrysogenum, P. citrinum, P. brevicompactum, P. aurantiogriseum and P. crustosum. Blue mold and green mold caused important diseases in citrus because of the contamination by P. italicum, P. expansum and P. digitatum (Errampalli, 2014). Besides the contamination potential of vegetables, Penicillium spp. were also found in many processed animal origin products (Hocking and Faedo, 1992; Tabuc et al., 2004; Ahmed et al., 2005; Hayaloglu and Kirbag, 2007; Asefa et al., 2009; Wigmann et al., 2016).

This genus contaminates various types of food commodities and products but only some species are known to involve human and animal diseases. The penicilliosis is associated with the mycotoxins secreted by Penicillium. Penicillium strains are able to produce a wide range of chemical compounds in which many are considered as highly toxic such as cyclopiazonic acid, penicillic acid, patulin, citrinin and especially ochratoxin A. Most species produce only one mycotoxin but some species can potentially synthetize several toxins at the same time.

1.3.2. Toxinogenesis • Ochratoxin A

Ochratoxin A is considered as the most dangerous mycotoxin produced by the genus Penicillium. The main OTA-producing species of Penicillium genus are Penicillium verrucosum and P. nordicum. As described in the previous part, OTA from Penicillium can occur in a wide range of raw materials and foods. Concerning the nuts and seeds which appeared to be a main target for Penicillium spp., OTA was detected with a high incidence in walnuts and peanuts (Zinedine et al., 2007). The toxin occurred in stored cereals such as maize and wheat (Shah et al., 2010; Adetunji et al., 2014; Kuruc et al., 2015). The presence of OTA was also reported in meats and meat products where a significant amount of OTA was due to the prevalence of toxigenic fungi, notably Penicillium spp., during the

11 ripening or the fermentation of meats. The meats can also be contaminated by OTA via the ingestion of contaminated feed by domestic animals (Dall’Asta et al., 2010; Markov et al., 2013).

• Patulin

Although patulin has antimicrobial properties (Ciegler et al., 1971), it is considered acutely toxic for humans at high concentrations (Donmez-Altuntas et al., 2013). Thus, its occurrence in agricultural products remains a worldwide concern in food safety. This toxin is reported to be toxic for animals, it affected animals by causing loss weight and inflammation in several organs such as intestines, lungs, larynx, liver and kidney tissue. Patulin is responsible for mutation, cancer and teratogenicity in several laboratory animals (Ciegler et al., 1976; McKinley and Carlton, 1980; Becci et al., 1981; Shafiq, 2015). Recently, studies in-vitro showed that patulin induced the oxidative stress in mammalian cells (Liu et al., 2007; Boussabbeh et al., 2015).

Patulin is produced by different species of Aspergiullus spp., Byssochlamys spp. and Penicillium spp., particularly by Penicillium expansum. As its producers are ubiquitous, patulin is considered as natural contaminant of many cereals and fruits in which pome fruits are the most important. In Spain, patulin was found in both organic and conventional apple-based foods (Piqué et al., 2013), and previously in pear and apple concentrates with level up to 126 µg/kg (Marín et al., 2011). However, the patulin incidence didn’t exceed the maximum level regulated by the EU. It was not the case for apple-based products largely consumed in Tunisia including infant foods where the concentration of patulin exceeded these tolerable limits (Zaied et al., 2013). Patulin can appear in other fruits, cereals and vegetables such as tomatoes and their derived products, sweet bell peppers and soft red fruits. The occurrence of contamination depended on the origin of products and was linked to the presence of Penicillium (Cunha et al., 2014; Sarubbi et al., 2016). Patulin was also detected in cheeses (inner part and rind) where this toxin was found occurring simultaneously with ochratoxin A (Pattono et al., 2013). Patulin was found in cured-meat (Rodríguez et al., 2012b) and in seafood (Vansteelandt et al., 2012) as well as in processed food. The contamination can be avoided by screening raw materials but patulin control measures need to be applied.

1.4. Conclusion

Among the fungi that contaminate food and are sources of regulated mycotoxins only those from the genus Fusarium are real phytopathogens. The species of Aspergillus and Penicillium genera are saprophytes which become opportunistic pathogens and contaminate productions sometimes without associated diseases. Fusarium genus is the one that produces the most different toxins but essentially contaminates cereal productions with main regulations for trichothecenes and

12 fumonisins. The Aspergillus species contaminate various foodstuffs such as cereals, fruits or nuts with a major production of highly regulated toxins like AFB1 and OTA. Penicillium genus is recognized as major producer of patulin including regulations concerning fruits, especially apples. Given the toxigenic potential, plant pathogenic fungi have adverse impacts in terms of health, economy and environment via chemical inputs used to control them. That urges to investigate into more respectful biocontrol measures.

2. Biological control of the phythopathogenic and/or toxigenic fungi 2.1. Biocompetition

This is a mechanism of biocontrol involving a competition between one or several microorganisms, used as antagonist agents, and the negative strains. They compete for nutritive resources (such as carbon, azote and iron), for ecological niche occupation and for water or air. This competition may happen at different levels. The antagonist or biocontrol agent and the pathogen may compete for one or several resources, thus lead to an inhibition of growth, of the pathogenic activity and/or the proliferation ability of pathogen population.

The actinomycetes are a group of filamentous microorganisms with interesting features for the biocontrol. Among them, the Streptomyces spp. are known to have a strong antifungal activity against various pathogens from soil and crops including Curvularia sp., Aspergillus niger, Helminthosporium sp., Fusarium sp., Alternaria sp., Phythophthora capsici, Collectotrichum sp., Rhizoctonia sp., Penicillium sp., Cercospora canescece, Diaporthe citri, Magnaporthe grisea and Sclerotinia soleroforum (Oskay, 2009; Lee et al., 2011; Evangelista-Martínez, 2014). Besides the actinomycetes, the Trichoderma spp. have been reported to be effective biocontrol agents. Studies demonstrated the inhibitory ability of various Trichoderma towards pathogenic and/or mycotoxigenic fungi including F. graminearum, F. culmorum (Matarese et al., 2012), F. oxysporum (Perveen and Bokhari, 2012) and A. niger (Gajera and Vakharia, 2010). Sometimes, the antagonist activity is associated with the decrease of mycotoxin accumulation. Two Bacillus isolates from Thailand fermented soybean, which are identified as B. licheniformis and B. subtilis, appeared to strongly inhibit the growth of A. flavus and A. westerdijkiae and significantly decrease the levels of aflatoxin B1 and ochratoxin A on both solid and liquid synthetic media. The detoxification was found to be linked to the carboxypeptidase A activity that degraded ochratoxin A in ochratoxin α which is much less toxic. Concerning the aflatoxin B1, its hydrolysis into products exhibiting greatly decreased toxicity could be due to the presence of ammonia during fermentation (Petchkongkaew et al., 2008). Bacillus amyloliquefaciens and Microbacterium oleovorans were able to reduce both the F.

13 vericillioides population and the fumonisin B1 and B2 levels in maize (Pereira et al., 2007). Thus, the reduction of mycotoxin production may also due to the decrease of pathogen populations.

Many yeast have been studied for the bio-treatment. For example, the development and patulin accumulation of P. expansum in apple was significantly reduced with the presence of Rhodotorula glutinis LS11. These decreases were apparently related to the delay of the pathogen growth and perhaps to the metabolization of patulin by the yeast (Castoria et al., 2005). Some strains of Saccharomyces cerevisiae reduced significantly the growth rate of F. graminearum and A. carbonarius and even their ochratoxin A, DON and zearalenone production. On the one hand, the biocontrol agents have been previously reported to be able to adsorb aflatoxin B1, ochratoxin A and zearalenone in-vitro. On the other hand, the presence of yeast, that caused the growth reduction of the toxigenic fungi may induce some stresses and influence their mycotoxin production (Armando et al., 2013)

2.2. Antibiosis

In this case, the antagonists produce molecules or secondary metabolites which possesses antimicrobial activity towards the targeted microorganisms. The antagonist agent inhibits or kills the pathogenic/toxigenic agent. Various bacterial and fungal strains are able to produce antibiotics and secondary metabolites that appears to have antiphytopathogen potential. The more compounds that the biocontrol agent produces, the stronger the biocontrol efficiency is (Pal et al., 2000).

Important antifungal activities observed in Streptomyces sp. were due to the production of antibiotic compounds such as polyene antimycotics belong to the macrolide group. Those produced by S. rimosus disturbed fungal cell membranes and thus led to the cell death of 14 phytopathogen fungi including F. oxysporum (Liu et al., 2009). A polyene antibiotic produced by S. lydicus and identified as natamycin, which has been largely used in food preservation, contributed effectively to the suppression of grey mold in tomato caused by F. oxysporum, B, cinerea and Monilinia laxa (Lu et al., 2008).

Although less studied, peptaibols are reported as an important group of antimicrobial agents. The Trichoderma spp. are well-known producers of peptaibols. These antibiotics proved their ability to protect and to stimulate the self-defense in plants against microbial and fungal infections (Viterbo et al., 2007). Peptaibols were also found to cause the apoptosis in phythopathogenic fungi. Trichokonins, a peptaibol type from T. pseudokoningii, caused a high occurrence of DNA fragmentation (the cytological marker of programmed cell death) and the translocation of phosphatidylserine (an important phospholipid membrane component) in cells of fungal hyphae,

14 thus leading to apoptotic cell death. This is the mechanism of the strong antifungal activity of T. pseudokoningii against a wide range of plant pathogens: A. citrullina, B. cinerea, F. oxysporum, P. parasitica and V. dahlia (Shi et al., 2012).

Besides peptaibols, 6-pentyl-α-pyrone can be mentioned as a potential antimicrobial compound. Studies ascertained the correlation between 6-pentyl-α-pyrone production and antimicrobial ability of producing strains (Reithner et al., 2007).

Production of siderophores can be a strategy for biocontrol of pathogenic fungi. Siderophores are produced under low iron conditions by bacteria, fungi or plants. These small peptide molecules play an important role in the competition for Fe between biocontrol agent or plants with the phytopathogens (Beneduzi et al., 2012). Treatment with siderophore producing strains on plants reduce effectively the disease severity caused by pathogenic fungi (Tortora et al., 2011; Verma et al., 2011; Yu et al., 2011) and reduced the phytopathogen invading (Laslo et al., 2012; Shobha and Kumudini, 2012; Sulochana et al., 2014).

Recently, lactic acid bacteria (LAB) were investigated for bio-preservation in food industry for their abilities to produce various bioactive molecules such as organic acids, hydrogen peroxide and bacteriocins. Besides, studies documented the antifungal capacity of LAB towards mycotoxigenic strains of Fusarium, Aspergillus, Penicillium and other fungi (Rouse et al., 2008; Gerez et al., 2009; Hamed et al., 2011; Belkacem-Hanfi et al., 2014). The antifungal compounds discovered were acetic acid, phenyllactic acid, lactic acid and possibly proteinaceous molecules.

The strains which produce cell wall degrading enzymes (CWDE) such as chitinase and β-1,3- glucanase are considered as promising biocontrol of fungal plant pathogens. Indeed, these enzymes can lyse chitin, a characteristic component of fungal cell walls. CWDE can be produced by various microorganisms: actinomycetes (Tahtamouni et al., 2006), bacterial communities (Hjort et al., 2014; Kim et al., 2014), yeasts (Yan et al., 2008) and molds (Gajera and Vakharia, 2010). The CWDE contributed strongly in the inhibition of phytopathogenic fungi including S. sclerotiorum, B. squamosal, R. stolonifera, C. gloeosporivides, F. oxysporum, F. graminearum and A. niger. Studies on chitinases from plants and bacteria have shown that the enzyme activities differ and that chitinases act selectively depending on their origin (endo or exochitinases) (Roberts and Selitrennikoff, 1988). Plant chitinases can thus protect the plant against fungal phytopathogens. Similarities have been noticed between the plant and fungal chitinases (Hamid et al., 2013). Targeted action of the chitinases appeared to be linked to the chitin content and microstructure of the cell wall of targeted fungi (Yan et al., 2008). These characteristics help to ensure a specific activity against pathogens. In term of enhancing the effectiveness of these enzymes, genetic engineering might be used. However,

15 the use of Genetically Modified Organisms doesn’t match with the concept of organic farming. Kowsari et al., (2014a) conjugated a chitin-binding domain (ChBD) to chitinase Chit42 excreted from Trichoderma in order to improve its antifungal potential. ChBD facilitated the binding of the chitinase to insoluble chitin, thus the combination displayed accurate higher inhibitory activity on R. solani, F. graminearum, F. oxysporum, S. sclerotiorum, A. brassicicola and V. dahlia (Kowsari et al., 2014a). The chitinase can be also overexpressed using genetics. Chitinase producing strains were co- transformed to contain the acetamidase gene amdS. Pyruvate constitutive promotor has been found to improve successfully chitinase activity in comparison with the wild type (Limon et al., 1999; Kowsari et al., 2014b). 2.3. Parasitism

Many examples of mycoparasitism can be found in the literature. They described the phenomena in which one fungus parasitized other fungus. In term of biological control, they resulted in the control of the pathogens either by direct confrontation between the 2 organisms or by the production of antifungal compounds.

Acting as a mycoparasite, some Trichoderma gamsii and T. velutinum strains inhibited the growth of 2 DON producing strains, F. graminearum and F. culmorum, by coiling around their hyphae and invading the Fusarium colonies. Interestingly, the mycoparasitic condition stimulated the expression of the genes encoding for chitinase and N-acetylglucosaminidase (Matarese et al., 2012). Similarly, the expression of the CWDEs, including β-1,3-glucanase, β-1,4-glucanase, chitinase and β-1,4-N- acetylglucosaminidase, was high during mycoparasitism of T. harzianum on F. solani. Along with the mycoparasitism using CWDEs, there were a synergic effect by nutrient competition and an antagonism by secondary metabolites (Steindorff et al., 2012). On the other hand, the parasitism caused morphological changes resulting in the destruction of the host. The hyphae of F. oxysporum f. sp. lycopersici, causative agent of Fusarium wilt in tomato, have been described as abnormal: the mycelium cells were lysed close to the interaction areas with T. asperellum. During the confrontation, T. asperellum overgrew and widely sporulated on the pathogen colonies (El-Komy et al., 2015). The mycoparasitic potential of Aspergillus section Nigri on Sclerotinia sclerotiorum from oilseed rape has also been studied. In this study, 90.7% of pathogen sclerotia were parasitized by Aspergillus. In planta, this strain inhibited the germination of S. sclerotiorum and the number of apothecia from sclerotia germination decreased through the time with the treatment of soil with Aspergillus (Hu et al., 2013).

2.4. ISR

ISR, Induced Systemic Resistance, is the term describing the reaction induced in plants by some non- pathogenic microorganisms. The induced resistance improves self-defense capacity of plants by an appropriate stimulus. Concerning the biocontrol, the inducers of resistance are usually the rhizobacteria and recently some fungi were also described. The plants benefits a resistance improvement either through the antagonist interactions between the rhizosphere microflora and the soil-borne pathogens or though metabolic reactions due to the colonization of plant roots by rhizobacteria or fungi.

The combination of biocontrol agents has been assessed for a synergistic effect on the ISR in plants. In the case of the combination of a T. harzianum and a Pseudomonas sp., the resistance of cucumber against Fusarium stem and root rot caused by F. oxysporum sp. radicis cucumerinim was demonstrated when treated with these strains. The combination helped to control disease in stimulating the expression of genes CHIT1 and β-1,3-glucanase that encode for chitinase and glucanase in cucumber (Alizadeh et al., 2013).

Although they are generally considered as pathogens, Fusarium spp. sometimes can act as activator for responses in plants against diseases. The treatment with Fusarium led to the stimulation of several defense-related genes such as chitianse, β-1,3-glucanase and peroxidase, thereby repelling effectively the pathogen invading and the disease incidence (Elsharkawy et al., 2012b; Martinuz et al., 2012). Penicillium spp. can contribute to the ISR in plants too. Penicillium simplicissimum elicited the ISR against the cucumber mosaic virus in Arabidopsis thaliana and tobacco by multiple defense pathways including the SA (salicylic acid) signaling pathway (Elsharkawy et al., 2012a).

2.5. PGPR and PGPF

PGPR and PGPF are the Plant Growth-Promoting Rhizobacteria/Fungi. These microorganisms live in the rhizosphere zone of plants. Generally, the rhizosphere should be defined as the soil part surrounding the root systems. This zone is influenced by plant roots and their secreted compounds (Ahemad and Kibret, 2014). The compounds synthesized by plants and their roots are called root exudates. Theses exudates influence soil physical and chemical properties. Moreover, exudates promote also interactions between plant and the microorganisms which are attracted to the root secretions. They use these exuded substances for their growth and reproduction on the surface of root and in the adjacent root soil. The exudates have an important impact on the rhizosphere microbial communities and vice versa. These rhizosphere microflora are associated with the beneficial effect on plant development and tolerance against abiotic stresses.

Rhizomicroorganisms are diverse but practically they are characterized by following traits: they live in the rhizosphere and colonize plant roots in competing with other microbiota by one or several activities. They can act as biofertilizer, phytostimulator, phytoprotector, biopesticides or rhizoremediator (Ahemad and Kibret, 2014). These microorganisms of the rhizosphere are more flexible than others in soil regarding transforming, mobilizing and solubilizing nutrients. The PGPR/PGPF may interact on plants through direct and indirect mechanisms.

2.5.1. Direct mechanisms

The PGPR and PGPF directly elicit the multiplication of plants and facilitate the plant growth through fixing atmospheric nitrogen, helping plant to solubilize nutritive compounds and stimulating the production of plant growth regulators (Table1).

• Nitrogen binding

As an essential element in plant growth, nitrogen amounts to about 2% of plant dry matter. Despite of the huge presence of nitrogen in the atmosphere, plants are not able to use directly dinitrogen gas. Plants can absorb nitrogen in the form of ammonium and nitrates from soil through the root systems. Only some bacteria have the ability to fix biologically the atmospheric nitrogen for the plant uses (Pundhir and Kharayat, 2013; Santi et al., 2013). These bacteria are called diazotrophs, they possess the genes encoding nitrogenase that transfers nitrogen gas to ammonia. The diazotrophs are specific for numerous legumes (such as Rhizobium, Bradyrhizobium, Azorhizobium, Sinorhizobium and Mesorhizobium) and non-legume bacterial species.

• Phosphate solubilizing

After nitrogen, phosphorus is the second important nutrient for plants. Phosphorus exists in soil in both organic and inorganic forms but soil phosphorus is found primarily in insoluble form such as inorganic mineral (apatite) or some organic compounds like inositol phosphate, phosphomonesters and phosphotriesters (Glick, 2012). Meanwhile plants can only use two forms of soluble phosphorus:

- 2- the monobasic (H2PO4 ) and the diabasic (HPO4 ). To a result, the availability of phosphorus for plants is very low despite the quite high quantity of phosphorus in soil. In order to overcome the phosphorus deficiency for plant uptake, the phosphatic fertilizers are usually applied at the field. However, the measure is costly and undesirable for environment because of the huge amount of phosphate residue that the treatment generates (Ahemad and Kibret, 2014). The use of phosphate fertilizers can worsen the metal(loid)s contamination in croplands and agriculture system. They are a significant contributor of residue of arsenic, lead and notably cadmium. The cadmium has become an international concern because of the rise of its long-term accumulation in the food chain and its

18 chronic toxicity which results in kidney tubule dysfunction and reduced bone density (Jiao et al., 2012; Grant, 2015).

In this case, the use of phosphate solubilizing microorganisms (PSM) may be an ecological and economical alternative for crops grown on soils with low P content. The PSM of the rhizosphere may transform the phosphorus in soluble forms and thus provide a source of phosphorus for plants, other than chemical phosphatic fertilizers. Thus, the PGPR possessing a phosphate solubilizing activity appear as a promising tool to be added into biofertilizers to promote the plant growth.

• Siderophore production

Iron is one of the most abundant element on the earth and is indispensable for all forms of life. Excluding certain lactobacilli, microorganisms and plants required high amounts of iron. However, in the aerobic soils, the major form of iron is the ferric ion Fe+3 which is only slightly soluble and thus less available to plants and microorganisms. Therefore, the competition for iron uptake between plants, bacteria and pathogenic fungi, especially those living in the rhizosphere zone, become significant (Rajkumar et al., 2010). To overcome this competition, some bacteria may produce siderophores, low-molecular mass iron chelators.

These siderophores act in solubilizing and complexing the iron from mineral or organic compounds in low-iron conditions. Moreover, siderophores are able to complex stably with other metals such as Al, Cd, Cu, Ga, In, Pb and Zn (Rajkumar et al., 2010). The siderophore binding ability increases with the metal concentration in soils. Thus they help to the metal uptake by microorganisms and plants. Besides, siderophores help to relieve the stress on plants in soils with high level of heavy metals. Siderophores are mainly produced by the PGPR. Hence, the PGPR with a siderophore production ability might be practically useful for bioremediation purposes (Gadd, 2004; Zhuang et al., 2007).

• Phytohormone production

Hormones or plant-growth regulators are produced within plants at extremely low concentration. Hormones play an important role in plant growth through regulating and affecting the development of all plant parts. Hormones determine the formation of branches, stems, flowers, leaves and fruits. So they are considered as vital factors for plants. There are five major groups of phytohormones: auxins, gibberellins, abscisic acid, cytokinins and ethylene. These hormones, like indole acetic acid (IAA), the most important hormone for root development, are naturally produced by plants but also produced and modulated by diverse bacteria and fungi. Thus, the PGPR can modulate the phytohormone levels in plants and affect the plant growth and its response to stress in negative environmental conditions (Glick et al., 2007).

2.5.2. Indirect mechanism

The PGPR can be used as biocontrol agents for soil-borne diseases of plants. The PGPR suppress the pathogenic strains (notably the fungal pathogens) by antagonism or by reinforcing the resistance system in plants. In fact, the competition for nutrients or for habitat, the antifungal metabolite production and induced systemic resistant (IRS) are the main modes of biocontrol activity in PGPR (Lugtenberg and Kamilova, 2009).

Numerous PGPR have been reported to control the phytopathogenic fungi and the diseases they caused in plants. Fusarium wilt is a vascular wilt disease that affects a wide range of host plants and is due to Fusarium species. The PGPR induced the plant resistance against Fusarium wilt in chill (Sundaramoorthy et al., 2012), in winter wheat (Wachowska et al., 2013) and in tomato where the nutritional quality and the texture of fruits was improved (Loganathan et al., 2014). It was demonstrated that two Bacillus strains (B. amyloliquefaciens and B. subtilis) induced the production of several defense enzymes in plant (phenyl alanine ammonia lyase, chitinase and polyphenol oxidase), thereby decreased significantly the wilt incidence in treated plants. Similarly, Bacillus strains (B. megaterium) isolated from the rhizosphere of plants such as bean, tomato, paddy, etc. were found to be producers of IAA, ammonia, HCN and siderophores. These PGPR traits led to an important antagonism towards F. oxysporum (Shobha and Kumudini, 2012). Along with HCN and ammonia, the diffusible and volatile antifungal metabolites (produced by Streptomyces idiaensis strains) can be involved in the inhibition of F. oxysporum in chili (Jalaluldeen et al., 2014). Production of siderophores is the mechanism that contributes to the antifungal activity of various PGPR against phytopathogens like F. oxysporum radicis-lycopersici and F. graminearum (Laslo et al., 2012). The antimicrobial agent 2,4-diacetylphloroglucinol (DAPG) was found in the crude extract of PGPR antagonistic to Fusarium spp. (comprising F. verticillioides) causative agents of Fusarium wilt. Furthermore, the PGPR led to an increase of seed germination and seedling vigor in cucurbit (Shanthi and Vittal, 2013). The inoculation of barley roots with Pseudomonas fluorescens promoted the defense system in plants under the infection of Fusarium graminearum. The activation resulted in a prevention of the plant biomass loss (Henkes et al., 2011). Applying a mixture of Lactobacillus plantarum and Bacillus amyloliquefaciens to durum wheat from heading until anthesis helped to reduce the FHB incidence caused by Fusarium culmorum and F. graminearum (Baffoni et al., 2015). The PGPR showed in-vitro an adherence on the hyphae surface of the pathogenic fungi that led to a hyphae hypotrophy.

The inhibition of the pathogen Aspergillus spp. by PGPR was also recorded. Using root colonization, the PGPR strains Bacillus megaterium, B. subtilis and Pseudomonas sp. showed their antagonistic

20 ability against A. niger that caused root rot diseases in peanut. The mechanism of this antifungal activity was found to be the production of the proteinase K by the PGPR isolates. More interestingly, the isolates were able to produce IAA (Yuttavanichakul et al., 2012). The PGPF Trichoderma viride significantly suppressed the collar rot disease due to A. niger in peanut. The treatment with T. viride induced in plants the production of defense enzymes (polyphenol oxidase and phenyl alanine ammonia lyase) and pathogenesis related enzymes (1,3-β-glucanase and chitinase), thereby improving the tolerance of plants to diseases (Gajera et al., 2015). The Trichoderma spp. that produced IAA, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase and siderophores and had ability of phosphate solubilization were successful in suppressing seed-borne and rhizospheric population of A. flavus in groundnut seeds. However, these strains were not able to reduce aflatoxin level in seed under greenhouse conditions (Navya et al., 2015). The PGPR Bacillus strains also showed a high inhibition rate against A. parasiticus, the main pathogen responsible for aflatoxins in peanuts. The inoculation of the peanut seeds with these strains promoted the germination rate and increased the bud weight. The strains could also produce the phytohormone 6-chaff (6-KT) (Wei et al., 2014). The liquid culture and the supernatant of Bacillus subtilis cultures inhibited the hyphal extension of Aspergillus carbonarius in-vitro and the rot extension in grape fruits. The liquid culture of B. subtilis also appeared to limit the fungal contamination by Aspergillus spp., Penicillium spp. and yeasts in the fruits during cold storage. After 80 days storage, the grape berries treated with B. subtilis liquid culture remained intact and the contamination concentration was much lower than in untreated samples. Nevertheless, the volatile compounds produced by the strain didn’t show strong effect on the pathogen (Jiang et al., 2014).

Except Pseudomonas spp., the examples of PGPR potential biocontrol agents against the Penicillium spp. pathogens are scarce. Pseudomonas fluorescens reduced the incidence and the severity of blue mold caused by P. expansum and P. solitum in apples (Etebarian et al., 2005). Along with Pseudomonas syringae pv. syringae, three strains of Trichoderma (including T. atroviride and T. reesi) reduced significantly the damage caused by P. expansum. Furthermore, the treatment with P. syringae pv. syringae and acibeanzolar-S-methyl (a chemical inducer of resistance) led to an important increase of pathogenesis-related proteins in apple peels (Quaglia et al., 2011). The Penicillium digitatum strain isolated from decaying citrus fruits was strongly inhibited by various Bacillus sp. (including B. subtilis, B. megaterium, B. anthracis and B. pumilus) and even more strongly by the cell-free culture supernatant of these strains which contained antifungal substances. Several strains were also able to produce volatile organic compounds that limited the mycelial growth of P. digitatum. The simultaneous use of bacterial strains and secondary metabolites onto wounded citrus fruits decreased the lesion level and delay the decay symptoms (Leelasuphakul et al., 2008).

Nevertheless, several Penicillium spp. have been reported as a potential PGPR against other fungal pathogens. Penicillium spp. enhanced the growth and induced the self-defense of cucumber against the damping-off and anthracnose (Shimizu et al., 2013; Hossain et al., 2014) and these strains helped Arabidopsis and tobacco resist towards mosaic virus (Elsharkawy et al., 2012a; Zhong et al., 2015). On the other hand, Penicillium spp. can produce numerous antifungal compounds. The strain Penicillium oxalicum was reported to produce antifungal substances that suppressed the growth of many phytopathogenic fungi. At least two active compounds have been found. Both the spores and the filtrated culture of P. oxalicum inhibited strongly the phytopathogens (including Sclerotinia seclerotiorum, S. minor, Alternaria alternate, Botrytis cinerea, Fusarium oxysporum f. sp. vasinfectum and Gibberella zeae). The sclerotioum infection of oilseed leaves was significantly suppressed and the lesion was reduced (Yang et al., 2008). The IAA-producing strains of Penicillium spp. increased the growth of sesame plants (augmentation of the shoot length and fresh weight of seedling). The strains demonstrated a biocontrol activity against Fusarium spp. In-vitro, Penicillium spp. inhibited Fusarium mycelial growth and injured the fungal hyphae. In-vivo, Penicillium spp. suppressed the stress induced by Fusarium on the plants (such as damaging lipid membranes and reducing protein contents) (Radhakrishnan et al., 2013). Penicillium chrysogenum which produces the Penicillium antifungal proteins (PAF) can also repress a wide range of phytopathogenic fungi (Hegedűs et al., 2011). The PAF caused the apoptotic cell death in Aspergillus nidulans (Leiter et al., 2005) and inhibited the growth of Aspergillus fumigatus (Marx et al., 2008). These substances inhibited efficiently the growth of various pathogenic fungi: Aspergillus carbonarius, A. niger, A. flavus, A. ochraceus, A. parasiticus, A. versicolor, Penicillium restrictum, P. expansum and P. griseofulvum (Delgado et al., 2015). The chitinase released by a highly chitinolytic strain of Penicillium ochrochloron contributed to the biocontrol of two phytopathogens, Fusarium oxysporum and Aspergillus niger (Patil et al., 2013). Thus, various strains of Penicillium spp. appear as promising biocontrol agents.

2.6. Conclusion

There are many possibilities of action of biocontrol agents that have proven effective against the phytopathogenic fungi. The latest advances in scientific research highlight different microbial interest groups such as actinomycetes in the case of biocompetition (Evangelista-Martínez, 2014) or LAB in the case of antibiosis (Belkacem-Hanfi et al., 2014). And all these promising abilities, like stimulating and protecting the plant growth, described in the previous paragraph, point out the PGPR as efficient biocontrol agents. For years, the PGPR have been investigated as biofertilizers which are defined as preparation containing live or latent cells of PGP strains. Just a small dose of biofertilizers can produce the desirable results in crops and plant yields because of the huge amount

22 of viable cells of specific strains. These strains enhance the nutrient uptake, the plant growth, induce the tolerance and defense system against abiotic stresses and diseases and moreover they control the phytopathogens and their epidemics (Nehra and Choudhary, 2015).

3. Organic amendments in biocontrol

The agricultural practices and the use of chemical products have led to the modification of the soil properties and thus the loss of crop productivity and the increase of soil-borne diseases. In the context of the biological control, the application of organic amendments (OA) has been reported as an interesting strategy for managing soil and controlling diseases caused by soil-borne pathogens.

The nutrient availability in soils for plants and the liberation of several bioactive substances by plants or PGPR has been shown to be improved using OA. The pathogen viability and their diffusion in soils was also reduced (Bailey and Lazarovits, 2003; Bonanomi et al., 2010; Larney and Angers, 2012).

3.1. Impact on physical and chemical properties of soils

OA are usually added to crop soils in order to improve the soil fertility by reinforcing their physical and chemical properties.

OA contribute in improving the soils through promoting the physical factors such as the bulk density, the capacity to retain water, to exchange cations, the aeration, etc. Beneficial effects were observed in sandy, infertile soil (Zebarth et al., 1999), in loamy soil, in clay soil (Aggelides and Londra, 2000), in saline soil (Tejada et al., 2006), in urban soil (De Lucia et al., 2013) and in vegetable farm soil (Bulluck et al., 2002) during and after application of OA. The treated soils showed a decreased soil bulk density, thereby improved physical properties through structural stability, water retention capacity, infiltration rate and soil moisture. Along with increasing infiltration rate and reducing bulk density, OA had positive effect on mean weight diameter and geometric mean diameter – the important indices to characterize the soil aggregate stability (Karami et al., 2012).

OA are rich in nutrients and represent a valuable source of N, P, K and other organic compounds, the most important property affecting quality and functioning of soil (Larney and Angers, 2012). They have been associated with desirable changes in soil chemical properties such as the ratio C/N and the electrical conductivity. With applying OA, the concentration of soil nutrients (Ca, K, Mg, Mn, P, K and Fe) was increased along with organic matter content, the total C amount and the total organic N, so that the plant growth was improved and a higher yield was obtained (Hue and Silva, 2000; Bulluck et al., 2002; Tejada et al., 2006; Karami et al., 2012; De Lucia et al., 2013; Shen et al., 2013; Blaya et al., 2015).

The metals and metalloids can mainly get into the food chain through the plant uptake and the transfer to the animals. However, the OA have been reported to reduce the bioavailability of metal(loid)s through adsorption, complexation and volatilization of these compounds. Many metal(loid)s have been eliminated through these processes: Cd, Zn, Pb, Cu, Ni, Se, Hg and As (Park et al., 2011).

3.2. Impact on biological properties of plants and soils

OA influence the biological properties of soils and plants through the impact on the soil microbial communities and the plant resistance systems.

Firstly, OA, as a source of plant nutrients, contributed to improve the plant growth and the production yield. The growth parameters promoted in the presence of OA were the length, the height and the fresh/dry weight of shoots and roots (Yadav, 2012; Sabet et al., 2013; Lin et al., 2014).

The literatures suggested that OA or composts can modify the resistance of plants towards diseases or phytopathogens. Zhang et al. (1998) showed that the use of compost and compost water extracts reduced the population of pathogens and the symptoms of diseases they caused in plants. This was the case for P. syringae pv. maculicola, responsible for bacterial speck in Arabidopsis. The β-D- glucuronidase activity was enhanced in presence of compost. Similarly, the β-1,3-glucanase activity in cucumber was significantly induced towards the infection of Collectotrichum orbiculare that caused anthracnose (Zhang et al., 1998).

In recent researches, the composts showed their positive effect against damping-off due to Pythium ultimum, Rhizoctonia solani and Sclerotinia minor. The parameters involved in the composts were the contents of nitrogen and organic nitro, extractable carbon, O-arylC, C/N ratio, alkyl/O-alkyl ratio and the enzymatic activites of N-acetyl-glucosaminidase and chitobiosidase (Pane et al., 2011). The compost water extracts (CWE) were reported to inhibit the germination and the development of Phytophthora capsici, to suppress the disease incidence in seedling and to reduce the population of the phytopathogen and hence to reduce the disease severity in pepper. The inhibition was the same using either autoclaved or non-autoclaved CWE, which support the existence of heat-stable inhibiting compounds. The mechanism involved in reducing the lesion in pepper leaves was ISR in the plant through enhancing the expression of pathogenesis-related genes which encoded for β-1,3- glucanase, chitinase and peroxidase activities. Through ISR, the CWE could also repress Collectotrichum coccodes in pepper leaves and Collectotrichum orbiculare in cucumber leaves (Sang et al., 2010). In the same way, a compost made of tomato residues and cattle manure reduced the wilt disease caused by Fusarium oxysporum f. sp. melonis in melon and Botrytis cinerea in cucumber

(Yogev et al., 2010). 60% suppression of the disease caused by Botrytis cinerea was observed in tomato plants grown with compost which stimulated ISR through the salicylic acid (SA)/abscisic acid (ABA) pathway (Fernández et al., 2014).

Application of OA has positive effects on the soil microbiota. The organic nutrients in soil can affect the population and activities of biocontrol agents (BCA). Composts represent a favorable environment for BCAs, thereby incite their development and their antifungal activities in soils. By this way, the BCAs prevent the pathogens, by declining their population, thus controlling their propagation and the diseases (Borrero et al., 2004; Khan and Sinha, 2006; Shen et al., 2013).

The soil of a farm was treated with an OA and a synthetic amendment. The beneficial soil fungi of the genus Trichoderma increased in the complemented fields but the propagule density of the fungi of interest was higher in the organic soil. The propagule densities of the phytopathogens Phytophthora and Pythium were found lower in soil with organic amendment than in those with synthetic amendment and in control soil (Bulluck et al., 2002). The culturable microorganism analysis and the estimation of microbial populations by real-time PCR revealed that the soil amended with bio-fertilizer contains the highest abundance of bacteria and actinomycetes. The use of the biofertilizer stimulated the beneficial microorganisms (for example the Bacillus species) and the decrease of Fusarium oxysporum f. sp. cubense responsible for Fusarium wilt (Shen et al., 2013). The effect of OA on the microbial communities could be evaluated by the quantification of the soil microbial biomass and the measurement of the microbial enzyme activities (Bossio et al., 1998; Larney and Angers, 2012). The increase of the soil microbial biomass and the soil respiration during the treatment with OAs were noticed. Similarly, soil enzymatic activities (dehydrogenase, urease, N- α-benzoyl-L-argininamide (BBA) protease, β-glucosidase, arylsulfatase and alkaline phosphatase) were higher after amending soils with poultry manure or crushed cotton gin compost (Tejada et al., 2006). Enzyme activities were found also in three types of composts applied to muskmelon and pepper seedlings. All of the amendments modified positively the plant growth (plant length and plant weight) as well as the inhibition of the disease severity caused by F. oxysporum f. sp. melanois and Phytophthora capsici. The inhibition levels were different and depended on the microbial community structures but all the three composts showed protease, N-acetyl-β-D-glucosaminidase, chitinase, dehydrogenase and β-glucosidase activities significantly higher than the control (Blaya et al., 2015).

The composts applied to melon plants demonstrated their ability of reducing efficiently the mycelial growth of the pathogenic fungi Fusarium oxysporum. The composts provided antagonistic strains of bacteria and fungi with biocontrol effect against F. oxysporum. Moreover, the compost showed a

25 phytohormone effect (including auxin and cytokinin) that explained the improved plant growth and the decrease of the pathogen incidence in treated samples (Bernal-Vicente et al., 2008). Compared to an organic fertilizer, a bio-organic fertilizer (including OAs and antagonistic microorganisms) showed thoroughly higher inhibition on disease incidence of Fusarium wilt caused by Fusarium spp. in cucumber, so that the yield lost due to Fusarium wilt was significantly reduced. The biomolecular analysis showed an increased abundance of beneficial bacteria and fungi such as Trichoderma, Hypoxylon, Tritirachum, Paenibacillus, Bacillus, Haliangium and Streptomyces, meanwhile the quantity of Fusarium pathogen was clearly decreased. The study showed that the application of antagonistic strains into fertilizers was an effective measure to suppress pathogenic fungi (Qiu et al., 2012). The two antagonistic strains Trichoderma harzianum and Pseudomonas fluorescens that showed a strong biocontrol potential against F. oxysporum f. sp. Lycopersici were added to OA. The treatments showed their effective performance in increasing the yield of tomatoes as well as decreasing the incidence of tomato wilt (Yadav, 2012). The presence of OA may enhance the production and the antifungal ability of some active compounds produced by antagonistic strains in term of biocontrol. Seven volatile organic compounds (benzothiazole, benzaldehyde, undecanal, dodecanal, hexadecanal, 2-tridecanone and phenol) produced by Paenibacillus polymyxa were found to inhibit the growth and also completely inhibit the germination of F. oxysporum f. sp. niveum. The inhibitory effect was strongly increased in the presence of organic fertilizer in both agar medium, sterilized soil and natural soil (Raza et al., 2015).

As a nutritive medium, OA are an abundant source of useful antimicrobial strains. The inhibiting capacity of OA is due to the antagonistic activity of their own microbial community. These strains could display an antifungal activity as well as promoting the plant growth. In a study concerning agro-industrial composts, 135 strains comprising bacteria, actinobacteria and fungi were isolated (Suárez-Estrella et al., 2013) . Half of them had antifungal activity against F. oxysporum f. sp. melonis, and more than 10% was effective against Xanthomonas campestris. Several of them suppressed both pathogens. The best effective strains were identified as Acetobacter indonesiensis, Bacillus pumilus, Paecilomyces variotii, Streptomyces griseus and Acremonium chrysogenum. In-vivo tests showed that the selected strains improved the plant health status through reducing the infection of pathogens and the disease incidence in cucumber and melon plants. In the study of Lin, Du et al. (2014), the bacterial strains isolated from vinegar waste compost were identified as Bacillus spp. the strains exhibited a large antagonism spectrum against numerous fungal pathogens including Fusarium oxysporum f. sp. cucumerinum, F. oxysporum f. sp. melon, F. oxysporum f. sp. cubense, F. oxysporum f. sp. niveum, F. graminearum, Glomerella cingulate and R. solani. Furthermore, the antifungal strains possessed many plant growth-promoting traits such as nitrogen-fixing ability, IAA

26 and siderophores productions and besides, exhibited enzymatic activities like chitinase, cellulose and protease. Therefore, they were found to control effectively the wilt and damping-off caused by F. oxysporum f. sp. cucumerinum in cucumber (Lin et al., 2014). A strain of Bacilllus subtilis isolated from an Agaricus bisporus mushroom compost inhibited successfully the red bread mold Neurospora sitophila. This strain exhibited also an antifungal activity towards other mushroom pathogens and phytopathogens (Trichoderma harzianum, Fusarium incarnatum, Fusarium solani, Fusarium graminearum and Botrytis cinerea). A substance involved in the biocontrol mechanism was purified and identified as a new type lipopeptide fengycin (Liu et al., 2015).

There are few reports on controlling the phytopathogens of Aspergillus and Penicillium genus acting into OA. However, several strains of these two genus can be found as antagonistic agents isolated from composts. 5 isolates of Penicillium spp. and 6 isolates of Aspergillus spp. isolated from commercial composts had inhibitory effect towards the root-rot phytopathogenic fungi of cucumber plants (Fusarium solani, Pythium ultimum, Rhizoctonia solani and Sclerotium rolfsii). The inhibiting strains contributed also in the reduction of pathogen population and the disease occurrence in cucumber plants (Sabet et al., 2013).

3.3. Conclusion

Thus, the use of organic amendments can be considered as a useful and effective measure for bio- controlling soil-borne diseases. The organic amendments act in supplying nutrient resources for plants, in improving soil fertility and in protecting biologically plants from pathogens and diseases. All of these points contribute to point out organic amendments as promising tools for sustainable agriculture.

4. General conclusion

To summarize, the phytopathogenic and/or mycotoxigenic fungi remains always one of the most preoccupations for agriculture and food safety in all over the world. Besides the cultural practices including good sanitation, preparation of soil and water, rotation of crops and improvement of plant varieties, other protective measures are required for a more sufficiently effective control of plant diseases and mycotoxin accumulation. As a long-term strategy, the use of biological control has been seriously developed and supported by both scientists and industrials. Along with the development of sciences and technologies where agricultural and environmental conditions are more managed and predictable, numerous bio-practices have been applied and achieved as described above. However, there is still left much to learn. The new biocontrol technologies are always in progress in order to facilitate their applications on fields.

Since most phytopathogenic and/or mycotoxigenic fungi are soil-borne pathogens, soil treatment and plant care are essential in biocontrol strategies. The use of bio-fertilizers supplemented with plan-growth-promoting and/or biocontrol agents can be focused. Thus the exploration and the exploitation of promising strains for a pertinent biological control are in progress.

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Tables

Table 1: Direct beneficial interactions between PGPR/PGPF and plants

PGPR/PGPF Plants/Crops Results References Pseudomonas, Sugarcane Increase N uptake by biological nitrogen (Taulé et al., Stenotrophomonas, (Saccharum fixation (BNF) 2012) Xanthomonas, officinarum L.) Acinetobacter, Rhanella, Enterobacter, Pantoea, Shinella, Agrobacterium, Achromobacter Bacteria isolated from Chlorophytum Increase N fixation, solubilize phosphate (Gupta et al., rhizosphere borivilianum and produce indole acetic acid (IAA) 2014)

Herbaspirillum spp. Maize (Zea mays Increase maize yield, BNF (Alves et al., L.) 2014) Pseudomonas putida, Artichoke Improve significantly radicle, shoot and (Jahanian et al., Azotobacter, Azotospirilium (Cynara seedling length. Increase seedling dry 2012) scolymus) matter, germination percentage Pseudomonas sp. PS1 Mung bean Significantly increase plant dry weight, (Ahemad and (Vigna radiate) nodulation, root N, shoot N, root P, shoot Khan, 2012) P, seed yield Alcaligenes, Staphylococcus, Strawberry Cv Increase fruit yield, rise N, P, K, Ca, Fe, Cu, (Ipek et al., Agrobacterium, Pantoea, ‘Aromas’ Mn, B concentration of all plant tissues 2014) Bacillus (under high calcium level soils) Pseudomonas aeruginosa, Rice (Oryza In combination, make greater grain yield, (Lavakush et al., Pseudomonas putida, sativa) higher plant growth and nutrient content 2014) Pseudomonas fluorescens, of grain and straw. Increase N, P, K Azotobacter chroococum, availability in soil Azotospirillum brasilense Bacillus subtilis, Bacillus Tomato-spinach Enhance soil microbial biomass C and N. (Song et al., mucilaginosus in synergistic rotation Improve yield, decrease nitrate 2015) activity with vermicompost concentration in soil meanwhile increase vitamin C content in tomato and soluble protein in spinach Bacillus sphaericus, Rice (Oryza Increase significantly seedling emergence, (Mia et al., Rhizobium strains sativa L.) seedling vigor, root growth (including root 2014) length, root surface area and volume) Bacillus, Pseudomonas, Pigeon pea Express PGPR traits (excellent IAA (Rani et al., Aeromonas (Cajanus cajan) production, phosphate solubilisation, HCN 2014) production, enzyme (chitinase, 1,3-β- glucanase) production. Increase seed germination percentage, seedling height, root length and dry weight Kosakonia radicincitans, Yerba mate (Ilex Express BNF, produce IAA and (Bergottini et Rhizobium pusense, paraguariensis siderophores. Affected significantly al., 2015)

Pseudomonas putida St. Hill) positively to seedling growth: shoot and root dry mass, shoot N content in poor substrate (normal soil). Increase macronutrient (N, P, K, Ca) content in shoot in riche substrate (compost) Bradyrhizobium spp., Peanut (Arachis Increase nodulation status, BNF. Improve (Badawi et al., Serratia marcescens hypogaea L.) number and weight of root nodules 2011) Promicromonospora sp. Tomato Produce gibberellins, salicylic acid. Have (Kang et al., (Solanum phosphate solubilizing potential. Stimulate 2012) lycopersicum) plant growth: higher shoot length and biomass Serratia nematodiphila Pepper Produce gibberellin. Regulate the stress (Kang et al., (Capsicum hormones in plant for an adaptation 2015) annuum L.) exposed to low temperature stress Bacillus sp. Cotton Enhance P availability. Produce higher seed (Qureshi et al., yield, higher plant height and number of 2012) bolls per plant Bacillus subtilis Wheat (Triticum Produce cytokininsm thus increase amino (Kudoyarova et durum) acid rhizodeposition. Increase also the al., 2014) chlorophyll and nitrogen contents in leaves Bacillus licheniformis, Grapevine (Vitis Produce abscisic acid (ABA), IAA, (Salomon et al., Pseudomonas fluorescens vinifera) gibberellins. Colonize roots. Induce ABA 2014) and terpenes in plant, thereby diminish the plant water losses Penicillium sp. Sesame Produce IAA. Trigger plant growth (shoot (Radhakrishnan (Sesamum length, fresh weight of seedling). Suppress et al., 2013) indicum L.) Fusarium sp.-induced oxidative stress Trichoderma harzianum, Rice (Oryza Enhance shoot and root dry weight. (Gusain et al., Fusarium pallidoroseum sativa L.) Increase activity of stress related enzymes 2014) Penicillium spp. GP15 Cucumber Enhance root and shoot growth and (Hossain et al., biomass. Colonize root. Reduce damping- 2014) off and anthracnose Piriformospora indica Barley seedlings Enhance root dry weight. Colonize root. (Varma et al., 2012) Piriformospora indica Zea mays Colonize root. Enhance phosphate uptake (Yadav et al., in plant 2010) Phoma sp. GS8-1 Arabidopsis Reduce disease severity and proliferation (Hossain et al., thaliana of pathogen 2008) Cladosporium sp., Tobacco Enhance plant growth. Increase plant fresh (Naznin et al., Ampelomyces sp., Phoma (Nicotiana weight 2013) sp., Mortierella sp. tabacum L. cv. Xanthi-nc) Fusarium spp. PPF1 Indian spinach Enhance germination percentage and vigor (Islam et al., seedlings index in spinach. Increase shoot length, 2014) (Basella alba), shoot fresh and dry weight, root length, Cucumber root fresh and dry weight, leaf area and leaf chlorophyll content of cucumber. Penicillium oxalicum Pearl millet Enhance plant growth. Reduce disease. (Murali and Enhance NPK uptake. Increase activity of Amruthesh, peroxidase and chitinase in seedlings 2015) Glomus mosseae, Lactuca sativa Increase shoot biomass, root biomass. (Kohler et al., Pseudomonas mendocina Stimulate root colonization. Decrease 2010) saline stress Penicillium notatum, Ground nut Increase dry matter and yield. Increase N, (Malviya et al., Aspergillus niger (Arachis P, protein and oil contents in plant. 2011) hypogaea)

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Research Highlights

Fungi take an important part in the microorganism world. Mycotoxins are mainly associated to 3 fungal genus. Biocontrol of these strains involves multiple mechanisms. Organic amendments are promising tools for sustainable agriculture.

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