Fungal and Bacterial Endophytes as Microbial Control Agents for...

[Full title: Fungal and Bacterial Endophytes as Microbial Control Agents for Plant-Parasitic Nematodes]

International Journal of Environmental Research and Public Health Review Fungal and Bacterial Endophytes as Microbial Control Agents for Plant-Parasitic Nematodes K. Kiran Kumar 1 and Surendra K. Dara 2, * Citation: Kumar, K.K.; Dara, S.K Fungal and Bacterial Endophytes as Microbial Control Agents for Plant-Parasitic Nematodes Int. J Environ. Res. Public Health 2021 , 18 , 4269. https://doi.org/10.3390/ ijerph 18084269 Academic Editors: David Nichols and Paul Tchounwou Received: 20 March 2021 Accepted: 15 April 2021 Published: 17 April 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations Copyright: © 2021 by the authors Licensee MDPI, Basel, Switzerland This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/) 1 ICAR-Central Citrus Research Institute, Nagpur 440033, Maharashtra, India; Kiran.Kommu@icar.gov.in 2 University of California Cooperative Extension, 2156 Sierra Way, Ste. C, San Luis Obispo, CA 93401, USA * Correspondence: skdara@ucdavis.edu Abstract: Endophytes are symbiotic microorganisms that colonize plant tissues and benefit plants in multiple ways including induced systemic resistance to biotic and abiotic stresses. Endophytes can be sustainable alternatives to chemical nematicides and enhance plant health in a variety of cropping and natural environments. Several in vitro and in vivo studies demonstrated the potential of multiple species of Fusarium and Bacillus against plant-parasitic nematodes in horticultural, agricultural, and fodder crops and in forestry. While there were efforts to commercialize some of the endophytes as bionematicides, a lack of good formulations with consistent field efficacy has been a major hurdle in commercializing endophytes for nematode control. Identification of efficacious and environmentally resilient strains, a thorough understanding of their modes of action, interactions with various biotic and abiotic factors, and developing strategies that improve their effectiveness are critical areas to advance the commercialization of bionematicides based on fungal and bacterial endophytes Keywords: endophyte; bacteria; fungi; plant-parasitic nematode; bionematicide 1. Introduction Plant-parasitic nematodes (PPN) such as root-knot nematodes ( Meloidogyne spp.), cyst nematodes ( Heterodera spp. and Globodera spp.), and root lesion nematodes ( Pratylenchus spp.) are important pests of many crops around the world causing significant yield losses. They primarily attack the root system by forming feeding sites such as, single giant cells, syncytia, non-hypertrophied nurse cells and coenocytes, which provide a protective feeding environment [ 1 ]. PPN feeding causes root deformity, stunting of plants, yellowing of leaves, and yield reduction. Additionally, PPN also act as entry ways for secondary pests and pathogens by causing wounds in the plant roots [ 2 ]. It is estimated that PPN cause an average yield loss of 12.6% equal to USD 215.8 billion in 20 major commercial crops including banana, coconut, peanut, potato, rice and sugarcane around the world [ 3 ]. While the root-knot and cyst nematodes are sedentary, root lesion nematodes, the burrowing nematode ( Radopholus similis ), the stem nematode ( Ditylenchus dipsaci ), and the reniform nematode ( Rotylenchulus reniformis ) are migratory [ 4 ]. Species of Longidorus , Xiphinema , Trichodorus , and Paratrichodorus are also vectors of plant viruses in addition to their feeding damage [ 5 ]. Fumigants and various classes of chemical nematicides are commonly used by growers for suppressing PPN, which have potential negative impacts on the environment including the detrimental effect on beneficial soil microbiota. Due to the higher cost of fumigation and the need for effective and safe non-chemical alternatives, bionematicides are gaining interest in the recent years [ 6 , 7 ]. There have been reports of nematode suppressive soils where PPN populations are suppressed due to the presence of bacteria and fungi. These beneficial microorganisms limit PPN proliferation by certain trapping structures or by producing toxins Trichoderma harzianum, Purpureocillium lilacinum, Pochonia chlamydosporia, Monacrosporium lysipagum, Pseudomonas fluorescens and Pasteuria penetrans are some of the microorganisms Int. J. Environ. Res. Public Health 2021 , 18 , 4269. https://doi.org/10.3390/ijerph 18084269 https://www.mdpi.com/journal/ijerph

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 2 of 15 involved in nematode suppression [ 8 – 11 ]. Bionematicides based on the fungi P. chlamydosporia , P. lilacinum , Arthrobotrys oligospora , Trichoderma spp., and Verticillium spp., and bacteria P. fluorescens , P. penetrans , and Bacillus spp. have been used in many cropping systems including lettuce-tomato, tomato-carrot, potato, common bean, tomato, cucumber, snapdragon, wheat and sugarcane [ 12 – 19 ]. While these bacteria and fungi appear to be effective in PPN suppression, there is an increased interest to explore endophytes as bionematicides especially for sedentary PPN because both of them colonize the same plant tissues and the former have a better chance of suppressing the latter [ 20 ]. Since many endophytes produce secondary metabolites that have pesticidal properties, they could be excellent candidates as bionematicides [ 21 ]. This review provides an overview of bacterial and fungal endophytes as potential bionematicides, and the challenges and opportunities in associated with their commercialization 2. Endophytes Endophytes are microorganisms that colonize plant tissues and live between plant cells in a symbiotic relationship usually characterized by mutualism. Endophytes include members of bacteria, fungi, archaea, and protists, but bacteria and fungi are the most common and widely studied taxa. While the plants provide living space and nutrition to the endophytes, the latter trigger immune responses in plants that help them withstand various biotic and abiotic stresses. Since some of the endophytes are closely related to plant pathogens, but are avirulent, plants sense their presence and activate defense responses through the production of various proteins, secondary metabolites, and hormones imparting tolerance to pathogens, herbivores, and abiotic stresses such as salinity and drought. Endophytes are in rhizosphere and phylloplane and colonize plants at various stages through seeds, seedlings, or vegetative propagative materials. The species composition, population abundance, and colonization depend on the plant species and soil and environmental conditions. While the endophytism is a common phenomenon studied for a long time, the impact of endophytes on pests including PPN is a new area of scientific interest particularly due to the demand for environmentally sustainable agricultural practices Sikora et al. [ 20 ] discussed various laboratory, greenhouse, and field studies that explored endophytes for controlling PPN 2.1. Fungal Endophytes Among other endophytes, fungal endophytes are the most common, diverse, and well-studied group for their role in imparting stress resilience to plants [ 22 , 23 ]. Fungal endophytes are categorized into clavicipitaceous and non-clavicipitaceous groups based on their taxonomy, evolutionary relatedness, ecology, and host range [ 24 – 27 ]. Calvicipitaceous endophytes include the genera Balansia , Balansiopsis , Atkinsonella , Echinodothis , Epichloe , Myriogenospora , Neotyphodium , and Parepichloe , which are commonly associated with grasses and rely on their host throughout their life cycle as mutualists [ 24 , 26 , 28 , 29 ]. These endophytes grow in the intercellular spaces of the aboveground plant tissues and are transmitted both horizontally and vertically depending on the species [ 27 , 30 ]. Nonclavicipitaceous endophytes such as Fusarium , Colletotrichum , Phomopsis , and Xylaria are found in most terrestrial plants and do not rely on plants to complete their life cycle [ 29 , 31 ]. Among various species, Fusarium oxysporum is the most dominant endophyte isolated from different plants and is an antagonist of fungal pathogens, insects, and PPN [ 32 – 34 ]. Antagonism of F. oxysporum towards Helicotylenchus multicinctus , Meloidogyne incognita , Meloidogyne graminicola , Pratylenchus goodeyi , and R. similis , in banana, melons or tomato has been reported from different studies (Table 1 )[ 35 – 41 ]. Other examples include Epichloe coenophiala (= Acremonium coenophialum , Neotyphodium coenophialum ) against Pratylenchus scribneri , Meloidogyne marylandi , and Helicotylenchus pseudorobustus in tall fescue [ 42 – 44 ] and Chaetomium globosum towards M. incognita in cotton [ 45 ].

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 3 of 15 Table 1. Effect of fungal and bacterial endophytes against plant-parasitic nematodes (PPN) in different crops PPN Species Crop Endophytic Organism Effect on PPN References Vegetable crops Meloidogyne incognita Tomato Pantoe agglomerans (MK-29), Cedecea davisae (MK-30), Enterobacter intermedius (MK-42), Pseudomonas putida (MT-19), P putida (MT-04), Pseudomonas fluorescens (MK-35) Reduced the number of galls by 27–43% after soil drench application and reduced nematode infestation as a seed treatment [ 46 ] M. incognita Tomato F. oxysporum (strain 162) Reduced nematode penetration by 36–56% [ 35 ] M. incognita Tomato Agrobacterium radiobacter, Bacillus pumilus, B. brevis, B. megaterium, B mycoides, B. licheniformis, Chryseobacterium balustinum, Cedecea davisae, Cytophaga johnsonae, Lactobacillus paracasei, Micrococcus luteus, Micrcoccus halobius, Pseudomonas syringae and Stenotrophomonas maltophilia Reduced the number of galls and egg masses by 33 and 39% [ 47 ] M. incognita Bhendi Pseudomonas spp. (EB 3) Bacillus spp. (EB 16, EB 18), Methlobacterium spp. (EB 19) Reduced the number of adult females, egg masses, eggs per egg mass and lowered root gall index [ 48 ] M. incognita Cucumber Phyllosticta (Ph 5110), Chaetomium (Ch 1001), Acremonium (Ac 985), Paecilomyces (Pa 972) Reduced the number of galls by 24–58% in the first screening and 15.6–44.3% in the repeated test Chaetomium showed the highest potential for seed treatment against M. incognita [ 49 ] M. incognita Tomato Fusarium oxysporum (Fo 162); Rhizobium etli (G 12) Reduced the number of eggs per female 35 days after nematode inoculation [ 50 ] M. incognita Tomato P. agglomerans (MK-29), C. davisae (MK-30), Enterobacter spp (MK-42), P. putida (MT-19) Reduced early root penetration of J 2 s into roots up to 56% when applied as a root dip and soil drench; Reduced the number of galls by seed treatment with endophytic bacteria followed by soil drench application [ 51 ] Meloidogyne spp Tomato Gliocladium spp Significant decrease in damage intensity to 33% by inoculating conidial suspension at the rate of 10 6 mL − 1 [ 52 ] M. incognita Tomato Acremonium implicatum 96.0% of J 2 s were killed by a culture filtrate after 48 h; Formation of root galls was inhibited in potted plants and root gall index was reduced in the field [ 53 ]

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 4 of 15 Table 1. Cont PPN Species Crop Endophytic Organism Effect on PPN References M. incognita Tomato F. oxysporum ; F. solani; Trichoderma asperellum Reduced nematode penetration; T. asperellum and F. oxysporum isolates reduced nematode egg densities by 35–46% [ 36 ] M. incognita Tomato Bacillus cereus (BCM 2) Reduced gall and egg mass indexes [ 54 ] M. incognita Tomato Bacillus sp. (EB 16, EB 18) Methylobacterium sp. (EB 19) Pseudomonas sp. (EB 3) Reduced the number of adult females, egg masses, eggs per eggmass, soil and root population of M. incognita [ 55 ] Fruit crops Radopholus similis Banana Fusarium Reduced the number of J 2 s per gram root by >80% [ 56 ] R. similis Banana F. oxysporum Reduced nematode population density on tissue culture plantlets by 49–79% [ 37 ] R. similis Banana Fusarium spp. (V 5 w 2) Decreased nematode reproduction by 22.9 and 60.6% in cultivars, Enyeru and Kibuzi respectively [ 57 ] M. incognita, Pratylenchus coffeae , R. similis, Helicotylenchus multicinctus Banana Bacillus subtilis (EPB 5, 22, 31 and EPC 16) Talc based Reduced nematode population in the combined treatment of EPB 5+31 [ 58 ] R. similis Banana F. oxysporum (S 9, P 12) 63% reduction in R. similis population in root system [ 38 ] R. similis Banana F. oxysporum Pre-inoculation of banana plantlets on one half of the root system significantly reduced root penetration of J 2 s on the non-treated half of the root by 30–40% [ 59 ] R. similis Banana F. oxysporum (V 5 w 2) Disrupted nematode reproduction [ 60 ] R. similis Banana F. oxysporum (strain 162), Paecilomyces lilacinus (strain 251), Bacillus firmus Reduced nematode density by 68% after combined application of F. oxysporum and P. lilacinus ; Application of F. oxysporum and B. firmus resulted in reduced J 2 density by 86.2% [ 61 ] Pratylenchus goodeyi Banana F. oxysporum Increased paralysis and mortality of motile stages by 17–26% and 62–73% respectively [ 39 ] M. incognita Squash and melon F. oxysporum (strain 162) Reduced early root penetration of J 2 s in squash and melon up to 69 and 73%, respectively [ 40 ]

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 5 of 15 Table 1. Cont PPN Species Crop Endophytic Organism Effect on PPN References R. similis , P. goodeyi , H. multicinctus Banana F. oxysporum Higher nematode mortality after 24 h exposure to culture filtrates; H. multicinctus was less sensitive to culture filtrates than R. similis and P. goodeyi [ 41 ] P. goodeyi Banana F. oxysporum (4 MOC 321, 11 SR 23) Significant reduction of P. goodeyi population by >50% and percentage root necrosis was reduced by >30% [ 62 ] M. javanica Banana Streptomyces sp Inhibition rate of >50% in vitro and biocontrol efficiency of 70.7% in sterile soil against J 2 s [ 63 ] Tuber crops M. incognita Potato R. etli (G 12) The no. of galls on roots was 34% lower than control [ 64 ] Globodera rostochiensis Potato P. fluorescens , P. putida 3 , P. syxantha , P. aurantiacea 13 Reduced nematode multiplication by 40.7–42.2% over the control with P. putida 3 and P. aurantiacea 13 respectively [ 65 ] G. rostochiensis Potato Bacillus carotarum , B. cereus , and Pseudomonas pseudoalcaligenes Increased the mortality of J 2 s by 67–97%; No effect on eggs; suppressed the number of cysts by 51–65% and J 2 s by 48–76% in greenhouse experiment [ 66 ] Ornamental crops M. incognita Ornamentals P. agglomerans (MN 34); P. putida 9 MN 12) Decreased galling index [ 67 ] Plantation crops R. similis Black pepper Bacillus megaterium (BP 17) and Curtobacterium luteum (TC 10) Higher nematode suppression with C. luteum followed by B. megaterium [ 68 ] Meloidogyne sp Black pepper B. megaterium (DS 9) Reduced nematode population with great inhibition values of 81 and 73% [ 69 ] Meloidogyne spp ; Pratylenchus spp ; Apratylenchus spp ; Criconemella spp.; Xiphinema spp ; Rotylenchulus spp Coffee Bacillus spp., Serratia spp., Paenibacillus spp., Enterobacter spp and Streptomyces spp. (CBG 9) Streptomyces sp. showed inhibited egg hatching by 85% and mortality of M. incognita J 2 s by 85% [ 70 ] M. incognita; R. similis Black pepper AA 2, MER 7, ANIC, TT 2, MER 9, HEN 1, EH 11, TT 2 Reduced the number of root galls by 30–91%; reduced nematode population in the soil by 15–99% [ 7 ] Agricultural crops M. incognita Cotton Reduced 30–50% of root galls by seed treatment application [ 71 ]

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 6 of 15 Table 1. Cont PPN Species Crop Endophytic Organism Effect on PPN References Meloidogyne graminicola Rice Bacillus megaterium Reduced nematode penetration and gall formation by >40% [ 72 ] M. graminicola Rice Fusarium spp Reduced root-galling by 29–42% and increased root weight by 33% [ 73 ] M. incognita Cotton Chaetomium globosum TAMU 520 Inhibited nematode infection and reduced female production [ 45 ] M. graminicola Rice Fusarium moniliforme Fe 14 Reduced J 2 penetration into roots by 55% and increased male to female ratio by nine times [ 74 ] Fodder crops Pratylenchus scribneri Tall fescue Epichloe coenophiala Reduced nematode population [ 42 ] Meloidogyne marylandi Tall fescue E. coenophiala Reduced the emergence of J 2 s, number of egg masses per pot and the number of eggs per egg mass [ 43 , 44 ] P. scribneri; Helicotylenchus pseudorobustus; M marylandi Tall fescue E. coenophiala Hinderance in reproduction of the nematodes [ 43 ] Pratylenchus spp Tall fescue E. coenophiala Non-ergot strain AR 584 confer resistance in cv. Georgia 5 [ 75 ] Tylenchorhynchus spp., Criconemella spp., Helicotylenchus spp ; Pratylenchus spp Tall fescue E. coenophiala (AR 584; AR 542; AR 502) No effect on nematode population densities [ 76 ] Forest trees Bursaphelenchus xylophilus Pine trees Escherichia coli (M 131, M 132) Serratia marcescens (M 44) E. coli and S. marcescens showed significant nematicidal activity (67 and 60% mortality) respectively [ 77 ] M. incognita Shorea sp.; Swietenia sp.; Albizia falcataria ; Anthocephalus cadamba ; Juglans nigra Bacterial isolates Inhibited egg hatching up to 81% and mortality up to 85% [ 78 ] B. xylophilus Pine trees Stenotrophomonas and Bacillus sp Significant inhibitory activity against PWN during their developmental stages [ 79 ] 2.2. Bacterial Endophytes Bacterial endophytes are the second most common endophytes and colonize most plant species locally or systemically living within the cells, in the intercellular spaces or vascular system [ 71 , 80 ]. Their antagonism towards PPN has been reported since mid- 1990 s [ 71 , 81 ]. Most of the Gram-negative endophytes and some species of Gram-positive endophytes are antagonists of plant pathogens [ 82 ]. Agrobacterium radiobacter , Burkholderia cepacian , and P. fluorescens are examples of Gram-negative endophytes and Bacillus spp.

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 7 of 15 are examples of Gram-positive endophytes. It has also been found that species of Acrhomobacter , Acinetobacter , Agrobacterium , Bacillus , Brevibacterium , Microbacterium , Pseudomonas , Xanthomonas , and others have the potential for controlling PPN [ 83 ]. 2.3. Mode of Action of Endophytes Endophytes suppress the growth and development of various stages of PPN through various mechanisms and thus contribute to the improvement of plant health. These can be categorized into direct and indirect mechanisms as described below: 2.3.1. Direct Mechanisms Endophytes can directly attack, kill, immobilize or repel PPN as they find their host, compete for space and produce secondary metabolites and other compounds that are detrimental to PPN. Endophytes produce metabolites such as flavonoids, peptides, quinones, alkaloids, steroids, phenols, terpenoids, and polyketones or lytic enzymes such as chitinases, cellulases, hemicellulases, and 1,3-glucanases [ 84 – 86 ]. These compounds inhibit the growth and development of PPN and other biotic stressors through antibiosis. Additionally, endophytes occupy plant tissues and inhibit PPN through niche competition or competitive displacement [ 85 ]. For example, F. oxysporum isolated from banana, paralyzes and kills P. goodeyi [ 39 ], while C. globosum produce secondary metabolites viz., chaetoglobosin A, chaetoglobosin B, flavipin, 3-methoxyepicoccone and 4,5,6-trihydroxy-7-methylphthalide against M. incognita [ 87 ]. 2.3.2. Indirect Mechanisms Endophytes induce systemic resistance by upregulating genes that produce various phytohormones, phytoalexins, volatile organic compounds, pathogenesis-related proteins, and trigger salicylic acid, jasmonic acid, and ethylene pathways that protect plants from stressors. Some of these defenses antagonize stressors such as PPN while others such as phytohormones promote plant growth and compensate for the damage by stressors Additionally, endophytes can also influence root exudate composition and production that further inhibit stressors. For example, Bacillus sphaericus B 43 and Rhizobium etli G 12 application induced systemic resistance to Globodera pallida in potato [ 88 ] and to M. incognita in tomato [ 89 ]. Meloidogyne incognita showed a preference to root exudates extracted from tomato roots than those extracted from roots colonized by endophytic F. oxysporum strain Fo 162 [ 35 ]. Such an interaction was also observed in M. graminicola with respect to rice in the presence or absence of F. moniliforme strain Fe 14 [ 74 ]. 3. Endophytes as Bionematicides While regulatory guidelines might place certain endophytes as biostimulants or soil amendments and others as biopesticides, for this review, we present various examples of endophytes as microbial control agents of PPN in a variety of crops and forestry 3.1. Vegetable Crops Researchers around the world evaluated the culture filtrates of bacterial and fungal endophytes against root-knot nematodes in cucumber, okra, and tomato with a majority of the studies in tomato (Table 1 ) [ 35 , 46 , 47 , 50 – 55 ]. Tian et al. [ 53 ] reported that Acremonium implicatum inhibited the formation of root galls caused by M. incognita in potted tomato plants to 41 per plant compared to 122 in untreated plants. Under field conditions, root gall index was significantly reduced to 25 from the endophyte treatment compared to 96 in untreated plants. In a greenhouse study, Hu et al. [ 54 ] found that various isolates of Bacillus cereus caused 53–76% reduction in M. incognita egg masses, 70–81% reduction in gall formation while repelling second stage juveniles (J 2 s). Similarly, isolates of Bacillus sp., Methylobacterium sp., and Pseudomonas sp. significantly reduced the egg masses, number of eggs per egg mass, number of adult females, and overall M. incognita numbers in both soil and roots of tomato growing in pots [ 55 ]. The two isolates of Bacillus sp. resulted in the

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 8 of 15 lowest gall index of 1.33 compared to 4.67 in control plants. Zhao et al. [ 90 ] reported 88–93% mortality in M. incognita J 2 s and 88–83% reduction in egg-hatch from Pseudomonas protegens and Serratia plymuthica in greenhouse tomato. Metabolites of both bacteria reduced the number of egg masses and root galls, while P. protegens also promoted seed germination and plant growth. In another study, Munif et al. [ 78 ] obtained 81% mortality of J 2 s and 81% reduction in egg-hatch of M. incognita with a consortium of bacterial endophytes isolated from trees. Details of these endophytic species were not revealed, however Seed treatment with endophytes has been explored as an option for controlling PPN Yan et al. [ 49 ] found that Acremonium sp., Chaetomium sp., Fusarium spp., Paecilomyces sp., Phyllosticta sp., and Trichoderma sp. reduced the number of galls by M. incognita in cucumber after treating the seeds. Metabolites from some of these endophytes negatively impacted the motility of J 2 s. Among these fungi, Chaetomium sp. had the highest colonization of roots (70.5%) and aboveground parts (73.5%) with 42–47% reduction in root galls. In another study, bacterial isolates of Pantoe aagglomerans , Cedecea davisae , Enterobacter spp., and Pseudomonas putida reduced early root penetration of M. incognita in tomato by up to 56% when applied as seed treatment, root dip, or soil drench [ 51 ]. Seed treatment followed by soil drenching appeared to be more effective than single application in reducing gall formation Some consider that a consortium of beneficial microorganisms is better than using a single microorganism and several commercial products based on microbial consortia have been developed in the recent years [ 78 , 91 ]. However, consortia may not always provide better control than a single endophyte due to potential negative interactions among the members. For example, the fungal endopyte Piriformospora indica alone suppressed M. incognita infestations in tomato better than as a member of a consortium with Bacillus pumilus and P. fluorescens [ 92 ]. While all of them promoted the plant growth, nematode control of P. indica decreased in the presence of bacterial endophytes 3.2. Fruit Crops In pineapple, application of Bacillus sp. isolated from its roots suppressed R. reniformis infestations by 54–60% in two cultivars [ 93 ]. Crop rotation with sunn hemp ( Crotalaria juncea ) and application of the endophyte were found to be effective non-chemical alternatives for PPN control in pineapple. Effective use of F. oxysporum for controlling PPN in banana has been reported from several studies Fusarium isolates induced systemic resistance and caused up to 41% of reduction in R. similis J 2 s penetration 15 days after treatment in a greenhouse study [ 59 ]. Three strains of F. oxysporum caused >85% mortality of R. similis , P. goodeyi and H. multicinctus mixed stages (J 2 s, males and females) after 24 h of exposure [ 41 ]. A strain of Streptomyces sp. isolated from banana roots showed >50% inhibiting rate of Meloidogyne javanica J 2 s in vitro and 71% of biocontrol efficiency in sterile soil [ 63 ]. However, in the presence of Streprtomyces sp., populations of bacterivorous nematode genera Mesorhabditis and Cephalobus also increased. In another study, Mendoza and Sikora [ 61 ] found that the combination of the strains of F. oxysporum and the egg parasitic fungus P. lilacinum (= Paecilomyces lilacinus ) reduced R. similis populations by 68.5% while the combination of F. oxysporum and Bacillus firmus reduced PPN populations by 86% in banana under greenhouse conditions 3.3. Tuber Crops In potato, A. radiobacter and B. sphaericus induced systemic resistance against the potato cyst nematode, G. pallida [ 94 ]. Another study demonstrated significant control of M. incognita in potato from R. etli G 12 application with 34% fewer galls than in control [ 64 ]. Bacillus carotarum , B. cereus , and Pseudomonas pseudoalcaligenes isolated from the roots and tubers of potato caused ≥ 80% mortality of Globodera rostochiensis J 2 s in vitro but did not limit the egg-hatch [ 66 ].

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 9 of 15 3.4. Ornamental Crops There was only one example of using endophytes for PPN control in ornamental crops Application of the endophytic bacteria P. agglomerans (MN 34) and P. putida (MN 12) reduced the gall index from M. incognita and promoted plant growth in natal plum ( Carissa macrocarpa ), dwarf lilyturf ( Ophopogan japonicas ), and other ornamental plants [ 67 ]. 3.5. Plantation Crops Endophytes for PPN control have been explored in black pepper, coffee, and other crops. In an Indian study, B. megaterium and Curtobacterium leteum , isolated from black pepper, provided the highest suppression of R. similis J 2 s among other isolates tested [ 68 ]. Similarly, a Vietnamese isolate of B. megaterium reduced numbers of Meloidogyne sp. by 82 and 73% in soil and pepper roots, respectively [ 69 ]. In Indonesia, 52% suppression in root galls and 75% suppression in M. incognita numbers was observed from the application of endophytic bacteria isolated from pepper plants [ 7 ]. When organic matter, in the form of cow manure, was applied along with endophytic bacteria, there was a 93% decrease in root galls and 97% decrease in nematode populations while a commercial organic fertilizer applied with endophytes caused 86 and 79% reduction in root galls and nematode numbers, respectively. In Vietnam, Streptomyces sp. (CBG 9) isolated from robusta coffee in Central Highland inhibited M. incognita egg-hatch by 86% and caused 85% of mortality in J 2 s [ 70 ]. 3.6. Agricultural Crops Meloidogyne graminicola is an important pest of rice in South Asia and South East Asia. Rice is a staple food of billions around the world and M. graminicola is one of the pests that cause significant losses, if left uncontrolled. Various studies demonstrated the potential of endophytes in controlling M. graminicola . In Taiwan, B. megaterium , isolated from rice growing regions, provided more than 40% reduction in J 2 penetration and gall formation by M. graminicola and 60% reduction of J 2 migration [ 72 ]. In a German study, Fusarium isolates from rice producing areas in Vietnam reduced gall formation by 29–42% and improved the root weight by 33% [ 73 ]. Trichoderma spp. evaluated in this study also had a similar impact with up to 38% reduction in root galling. Similarly, in another German study F. moniliforme (Fe 14) suppressed J 2 s penetration by 55% and increased the male to female ratio by 9 times [ 74 ]. Additionally, root exudates from endophyte treated plants were also less attractive to J 2 s In the US, C. globosum (TAMU 520), isolated from upland cotton used as a seed treatment, negatively impacted M. incognita , the cotton aphid ( Aphis gossypii ), and the beet armyworm ( Spodoptera exigua ) [ 45 ]. Endophyte reduced nematode infection and female reproduction as well as the fecundity of both insect species. In a different study in the USA, hundreds of nematophagous fungal endophytes were isolated from the roots of corn and soybean where the majority was Fusarium spp. along with less common Hirsutella rhossiliensis , Metacordyceps chlamydosporia , and Arthrobotrys iridis [ 95 ]. It was also observed that PPN population density influences the endophyte diversity as the fungal diversity in soybean roots was higher when Heterodera glycines density was higher 3.7. Fodder Crops Species of Epichloë (= Neotyphoidium and Acremonium ) are endophytes of Gramineae family that contains tall fescue, perennial rye grass and others used for fodder. Although some endophytes release metabolites that are toxic to cattle, there are several examples of PPN reduction from the presence of various species of endophytes (Table 1 ). An earlier report indicated that the presence of the fungal endophyte E. coenophiala significantly reduced populations of P. scribneri and Tylenchorhynchus acutus in tall fescue and improved the yields [ 42 ]. However, endophyte colonized grass appeared to be toxic to cattle because of the ergot alkaloids they release. Inoculating tall fescue with non-ergotic strain of E. coenophiala offered resistance to Pratylenchus zeae and P. scribneri , however, to a lesser extent than ergotic strains [ 75 ]. In another study, 100% mortality of M. marylandi was

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 10 of 15 observed when PPN-infested soil in pots was inoculated with E. coenophiala and with water deficit stress [ 44 ]. 3.8. Forestry The pine wilt nematode, Bursaphelenchus xylophilus , is a serious problem in Korea, Canada, USA, China, Japan and other South Eastern countries causing pine wilt of coniferous trees of the genus Pinus . Ponpandian et al. [ 79 ] isolated and investigated hundreds of bacterial endophytes for controlling B. xylophilus . Among them, Stenotrophomonas spp. and Bacillus spp. were very effective, causing ≥ 70% mortality of adult nematodes. Liu et al. [ 77 ] isolated 48 genera of Gamma-proteobacteria and others from four species of pine trees in Korea. Among those isolates, Escherichia coli and Serratia marcescens produced nematicidal metabolites causing 67 and 60% mortality in B. xylophilus , respectively, in laboratory assays 4. Metabolites from Endophytes Endophytes produce an array of secondary metabolites, which have biopesticide potential against plant pathogens and PPN. These metabolites categories include alkaloids, flavonoids, peptides, phenols, polyketones, quinols, terpenoids, and steroids [ 96 ], which induce systemic resistance in plants against various biotic and abiotic stresses.Several of these secondary metabolites have nematicidal properties and can be important IPM options (Table 2 ). For example, F. oxysporum isolated from the roots of the tomato cultivar Moneymaker produces several bioactive compounds including 4-hydroxybenzoic acid, indole-3-acetic acid, and gibepyrone D, which are nematicidal with LC 50 values of 104, 117, and 134 µ g/mL, respectively [ 97 ]. In another study, five metabolites—chaetoglobosin A, chaetoglobosin B, flavipin, 3-methoxyepicoccone, and 4, 5, 6-trihydroxy-7-methylphthalide—derived from C. globosum caused moderate to high levels of mortality in M. javanica J 2 s [ 87 ]. With LC 50 values of 200 µ g/mL, chaetoglobosin A and B significantly suppressed nematode reproduction and promoted plant growth in a potted plant study Table 2. Secondary metabolites identified in endophytes and their effect on PPN Metabolite Bacteria/Fungi Nematode References Pregaliellalactone Galiella rufa Meloidogyne incognita [ 98 ] 3-Hydroxypropionic acid Endophytic fungi M. incognita [ 99 ] Chlorinated oxazinane derivate (1-[(2 R*,4 S*,5 S*)- 2-chloro-4-methyl-1,3-oxazinan-5-yl] ethenone) and an epimer of the former (1-[(2 R*,4 S*,5 R*)-2- chloro-4-methyl-1,3-oxazinan-5-yl] ethanone) Geotrichum sp. (AL 4) Bursaphelenchus xylophilus; Panagrellus redivivus [ 100 ] Fusaric acid and Bikaverin Fusarium oxysporum (EF 119) B. xylophilus [ 101 ] (R)-( − )-2-ethylhexan-1-ol Brevundimonas diminuta (LCB-3) B. xylophilus [ 102 ] Chaetoglobosin A Chaetomium globosum (NK 102) M. incognita [ 103 ] 3-methyl-1-butanol, ( ± )-2-methyl-1-butanol, 4-heptanone, and isoamyl acetate Daldinia cf concentrica Meloidogyne javanica [ 104 ] 4-hydroxybenzoic acid, indole- 3-acetic acid and gibepyrone D F. oxysporum (162) M. incognita [ 97 ] Chaetoglobosin A, chaetoglobosin B and flavipin C. globosum (YSC 5) M. javanica [ 87 ] 5. Commercialization Identification, mass-production, and commercialization of nematicidal endophytes have a great potential for PPN control in many systems in a sustainable manner. Since some of these endophytes induce systemic resistance against multiple stressors or antagonize multiple categories of pests, endophytes can be comprehensive tools for improving

Int. J. Environ. Res. Public Health 2021 , 18 , 4269 11 of 15 overall crop health, yields, and optimize the cost of crop care. Although numerous studies demonstrated the potential of bacterial and fungal endophytes for controlling PPN, there are noncommercial nematicides based on these endophytes. However, some strains are available as biostimulants or biofungicides 6. Constraints and Future Opportunities Major constraints of biopesticides are their high cost of production and relatively fewer efficacy data compared to synthetic pesticides. As a result, there is some hesitation in the farming community to use biopesticides as their primary choice. Some of the reasons for low, slow, or inconsistent field performance of some endophytes are adverse soil conditions, competition with other soil microorganisms, the presence of mycophagous or bacteriophagous nematodes [ 105 , 106 ]. In some cases, endophytes might release toxic metabolites that are harmful to herbivorous mammals or alter the microbial community in the rhizosphere or phylloplane with negative consequences [ 107 ]. Some strategies to improve the prospects of bionematicides based on endophytic bacteria and fungi are investing in applied research that generates field efficacy data, developing formulation technologies that optimize production costs and improve product efficacy, and educating the farming community with IPM practices that make the best use of bionematicides and other such products. Research, outreach, communication at various levels, employing various control options, and exploiting modern technologies for monitoring crop health and delivering agricultural inputs are various elements of IPM [ 108 ]. When bionematicides are integrated with other management practices, they provide effective and long-term suppression of PPN Author Contributions: Conceptualization, K.K.K. and S.K.D.; methodology, K.K.K. and S.K.D.; writing—original draft preparation, K.K.K. and S.K.D.; writing—review and editing, S.K.D. All authors have read and agreed to the published version of the manuscript Funding: This research received no external funding Institutional Review Board Statement: Not applicable Informed Consent Statement: Not applicable Data Availability Statement: Not applicable Conflicts of Interest: The authors declare no conflict of interest References 1 Palomares-Rius, J.E.; Escobar, C.; Cabrera, J.; Vovlas, A.; Castillo, P. Anatomical alterations in plant tissues induced by plantparasitic nematodes Front. Plant Sci 2017 , 8 , 1987. [ CrossRef ] [ PubMed ] 2 Caboni, P.; Aissani, N.; Demurtas, M.; Ntalli, N.; Onnis, V. Nematicidal activity of acetophenones and chalcones against Meloidogyne incognita , and structure–activity considerations Pest Manag. Sci 2016 , 72 , 125–130. [ CrossRef ] 3 Abd-Elgawad, M.M.M.; Askary, T.H. Impact of phytonematodes on agriculture economy. In Biocontrol Agents of Phytonematodes ; Askary, T.H., Martinelli, P.R.P., Eds.; CAB International: Wallingford, UK, 2015; pp. 3–49 4 Jones, J.T.; Haegeman, A.; Danchin, E.G.; Gaur, H.S.; Helder, J.; Jones, M.G.; Kikuchi, T.; Manzanilla-L ó pez, R.; Palomares-Rius, J.E.; Wesemael, W.M.; et al. Top 10 plant-parasitic nematodes in molecular plant pathology Mol. Plant Pathol 2013 , 14 , 946–961 [ CrossRef ] 5 Dijkstra, J.; de Jager, C.P. Virus transmission by nematodes. In Practical Plant Virology: Protocols and Excercises ; Dijkstra, J., de Jager, C.P., Eds.; Springer: Berlin, Germany, 1998; pp. 128–142 6 Kumar, K.K.; Sridhar, J.; Murali-Baskaran, R.K.; Senthil-Nathan, S.; Kaushal, P.; Dara, S.K.; Arthurs, S. Microbial biopesticides for insect pest management in India: Current status and future prospects J. Invertebr. Pathol 2019 , 165 , 74–81. [ CrossRef ] 7 Munif, A.; Harni, R. Management of endophytic bacteria and organic material for the biological control of yellowing disease on pepper IOP Conf. Ser. Earth Environ. Sci 2020 , 418 , 012052. [ CrossRef ] 8 Davies, K.G.; Srivastava, A.; Kumar, K.K.; Mohan, S. Understanding nematode suppressive soils: Molecular interactions between Pasteuria endospores and the nematode surface coat. In Proceedings of the 4 th Symposium of Potato Cyst Nematode Management (including Other Nematode Parasites of Potatoes), Newport, UK, 7–8 September 2015; Association of Applied Biologists: Wellesbourne, UK, 2015.

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