Advances, Challenges and Perspectives in the Application of Novel Biocontrol Agents for Plant Disease Management

Advances, Challenges and Perspectives in the Application of Novel Biocontrol Agents for Plant Disease Management

Published: 2025.05.01
Accepted: 2025.04.30
30
Professor
Department of Plant Pathology, University of Agricultural Sciences, India
Junior Research Fellow
ICAR-IARI, Regional Research Centre, India

DOI: https://doi.org/10.56669/HYZL2696

ABSTRACT

The growing concerns among consumers and governments regarding the issues associated with synthetic chemicals in disease control and food safety have prompted growers to seek eco-friendly alternatives to traditional chemical-based practices. In response to increasing environmental awareness, the use of biocontrol agents for plant disease suppression is emerging as a viable alternative. Biological control relies on the complex interactions (agonistic and antagonistic)—between plants and microbes living in the rhizosphere and phyllosphere. Various organisms including fungi, bacteria, mycorrhiza, yeast, virus, algae, cyanobacteria and so on, were identified with biological control properties and thus can be applied in plant disease management. Research on the selection, evaluation, characterization and application of these agents has significantly increased over the past few decades. However, despite extensive global research, the adoption of biopesticides by farmers remains limited. To promote the development and effective use of bioformulations, it is essential to optimize the activity of biocontrol agents, share knowledge on formulation processes, and simplify registration procedures. This paper discusses the advancements, challenges and perspectives related to the application of novel biocontrol agents in plant disease management.   

Keywords:  Biocontrol, Modes of action, Research and development, Control    

INTRODUCTION

Plant diseases caused by infectious pathogens have significantly impacted human society and the natural environment, damaging food production, economic development, ecological resilience, and landscapes throughout human history. Plant diseases result from complex interactions among plants, pathogens, and the environment. Plant diseases can occur in the entire crop production chain and remain as one of the greatest threats to the sustainable development of society (Savary et al., 2019). According to the Food and Agriculture Organization (FAO), 14% of global crop production losses are caused by plant diseases each year, with fungal diseases accounting for 42% and bacteria for 27% (Roca-Couso et al., 2021). In the long history of agriculture, humans have developed a variety of approaches to manipulate the interaction to create a system in favor of the growth and development of host plants but suboptimum to the establishment, reproduction, and transmission of pathogens (Bisht et al., 2020). Depending on circumstances of crop, pathogen, geographic location, technology availability, regulation policy, and other factors, these control approaches can be agronomic (viz., crop diversification and field hygiene), regulative (viz., quarantine and eradication), genetic (viz., disease resistance and tolerance), physical (viz., soil solarization and flooding),  chemical (viz., pesticides and host-immunity inducer) and can be used individually or in combination (integrated disease management, IDM) to suppress causal pathogen, promote host immunity, or change the biotic and abiotic environment where host–pathogen interaction occurs (He et al., 2021). Over the past 50 years, the most common method for disease control has been the extensive use of chemical pesticides (Peshin et al., 2009; Peshin and Zhang, 2014; Zhang et al., 2011; Zhang, 2018). Chemical and synthetic pesticides are used in excessive amounts to control pests in crop fields and such excessive applications deteriorate soil fertility and ecosystem health (Zhang et al., 2011; Zhang, 2018). Concerns about the safety of chemical residues and possible emergence of pesticide resistance in some pest species have necessitated the development of substitutes for these synthetic agro-inputs. However, the high effectiveness and ease of utilization of these chemicals resulted in environmental contamination and the presence of pesticide residues in food, in addition to various social and economic problems. Today, in the light of growing concerns towards environmental safety, suppression of plant diseases through biocontrol agents (BCAs) is gaining ground as an alternative to traditional disease management strategies. Now it is essential to focus on the challenges involved in testing, formulating, and delivering newer potential biocontrol agents within the context of integrated disease management. The objective of this paper is to build-on recent detailed reviews on advances, challenges and perspectives in the application of novel biocontrol agents for plant disease management.

BIOCONTROL AGENTS

Organisms that originate from nature and are utilized to control pests, weeds and diseases are known as biocontrol agents. Biocontrol agents can be classified into four distinct types: i) Macrobials, which encompass insects, mites, and beneficial nematodes that target pests; ii) Microbials, which are microorganisms like bacteria, fungi, and viruses, along with their derivatives. Microbial products may include these microorganisms, their metabolites, or fragments of their cells, and they can combat pests through direct infection, competitive displacement, or by forming a physical barrier; iii) Semiochemicals, chemical compounds emitted by plants and animals that send signals capable of influencing pest behavior. These are employed as repellents, attractants, or to disrupt mating; iv) Natural substances sourced from plants, minerals, or animals, or artificially created to replicate these natural compounds. They serve to repel and control both microbes and insects (Kumar et al., 2019). Additionally, it encompasses modified organisms, genes or a gene product used to suppress the growth of the unwanted organism (pest/pathogen) and to enhance the growth and yield of the wanted organism (crops, microorganism, or insects). The use of biocontrol agents to control plant diseases and pests is called biocontrol. It is a method of plant disease management by inhibiting plant pathogens, improving plant immunity, and/or modifying the environment through the effects of beneficial microorganisms, compounds, or healthy cropping systems (Burketova et al., 2015). Biological control offers several advantages over other approaches of plant disease management (Figure 1).

MECHANISMS EMPLOYED BY BIOCONTROL AGENTS FOR MANAGEMENT OF PLANT DISEASES

Biological control agents protect crops from diseases caused by plant pathogens via different modes of action. The biocontrol activity is exerted either directly through antagonism of plant pathogens or indirectly by eliciting a plant-mediated resistance response. Direct antagonism results from physical contact and/or a high degree of selectivity for the pathogen, by different mechanism(s) expressed by the biocontrol agents. Indirect antagonism results from activities that do not involve sensing or targeting a pathogen by the biocontrol agent/s (Figure 2). Stimulation of plant host defence pathways by biocontrol agents is the most indirect form of antagonism (Köhl et al., 2019; Hegde et al., 2022).

Biological control is dependent on numerous agonistic and antagonistic interconnections between plants and microbes living in the rhizosphere and phyllosphere (Mishra et al., 2015) and their application to minimize disease and subdue pests. Organisms from the rhizosphere can be harnessed from the surrounding environment (the black box approach) or can be introduced into the field from external sources (the silver bullet approach). It is beneficial to apply a consortium of microbes with collaborative properties rather than relying on a single organism since microbial consortia make up a stable rhizosphere that offers more effective control against pathogens (Ram et al., 2018). Apart from microbial applications, the utilization of other plant products like extracts, biofertilizers, and biopesticides, natural enemies of pests and pathogens, and gene products also aid in carrying out biological control (Ab et al., 2018).

ADVANCES IN RESEARCH AND DEVELOPMENT OF NOVEL BIOCONTROL AGENTS IN MANAGEMENT OF PLANT DISEASES

There is an increasing preference for food produced in ways that impart as little environmental impact as possible. Biocontrol agents provide a natural and environmentally acceptable alternative to conventional pesticides, therefore lowering agriculture’s ecological imprint. Biocontrol agents play an important part in sustainable agriculture by promoting natural pest control processes and lowering the need for synthetic pesticides. Government rules and incentives aimed at improving sustainable agriculture increase the market for biocontrol chemicals. Therefore, the transition to more environment-friendly pest management corresponds with the usage of biocontrol agents, boosting market expansion as farmers seek effective and ecologically favorable solutions. Furthermore, customers’ growing desire for organic products fuels this trend, forcing farmers to invest in biocontrol methods to fulfil market needs while remaining organically certified. According to research, global biocontrol agent’s market was valued at US$5.8 billion in 2023 and is expected to reach US$10.6 billion by 2032, at a CAGR of 8.1% during the forecast period. Based on formulation, the liquid formulation segment dominated the market in 2022 with a market share of 40% and is expected to keep its dominance during the 2024-2032 forecast period. Based on the application method, the foliar spray segment dominated the market in 2022 with a market share of 55% and is expected to keep its dominance during the 2024-2032 forecast period. By region, Biocontrol agent’s market is segmented into North America, Europe, Asia-Pacific, Latin America, the Middle East & Africa. The Asia-Pacific dominated the global biocontrol agents market in 2022 with a market share of 45% and is expected to keep its dominance during the forecast 2024-2032 period (www.custommarketinsight.com). Overall, biocontrol agent’s registrations are increasing globally, the expansion of various technologies has increased the scope for more products and the change in the trend to develop biocontrol agents is definitely on the rise (Figure 3).

A group of novel biocontrol agents that effectively control diseases in economically important crop species are discussed (Table 1).

Table 1. Groups of successful biocontrol agents that effectively control diseases in economically important crop species

Groups

Biocontrol agent

Target pathogens

Crops

Diseases

References

Fungi

 

 

 

 

 

 

T. harzianum

Crinipellis perniciosa

Cocoa

Witches’ broom

Marco et al. (2003)

 

T. lignorum

R. solani

Bean

Damping off

Aziz et al. (1997)

 

T. viride,

T. pseudokoningii,

T. koningii

Sclerotium cepivorum

Onion

White rot

Clarkson et al. (2002)

 

 

T. harzianum

Penicillium expansum

Apple

Blue and grey mould

Batta (2004)

 

T. virens, T. harzianum

R. solani

Potato

Stem canker or black scurf

Brewer and Larkin (2005)

 

T. koningii, T. aureoviride,

T. longibrachiatum

Sclerotinia sclerotiorum

Sunflower

Head rot

Escande et al. (2002)

 

T. asperellum

F. oxysporum

Tomato

Wilt

Cotxarrera et al. (2002)

 

T. koningii

Gaeumannomyces graminis var. tritici

Wheat

Take-all disease

Simon (1989)

 

T. virens

 

Verticillium dahliae

Cotton

Wilt

Hanson (2000)

 

T.  afroharzianum

Uncinula necator

Grapes

Powdery mildew

Saxena et al. (2021)

 

Purpureocillium lilacinum (=Paecilomyces lilacinus) IIHR- Pl-2 (NAIMCC-SF-0034/ITCC 6887)

Meloidogyne incognita

Brinjal, tomato, carrot and okra

Root knot nematode

Saxena et al. (2021)

 

Pochonia chlamydosporia (=Verticillium chlamydosporium) IIHR- Vc-3(NAIMCC-SF-0035/ITCC 6898)

Meloidogyne incognita

 

Brinjal, tomato, carrot and okra

Root knot nematode

Saxena et al. (2021)

 

Trichoderma viride + Trichoderma harzianum

Pythium, Rhizoctonia,

Phytophthora and Fusarium

Many hosts

Saxena et al. (2021)

 

Pochonia chlamydosporia

Fusarium oxysporum f.sp. ciceris and F. udum, Meloidogyne incognita

Chickpea and redgram

Wilt disease complex

Saxena et al. (2021)

 

Gliocladium. spp.

Fusarium, Rhizoctonia,

Sclerotium, and Pythium

Many hosts

Soil borne diseases

Saxena et al. (2021)

 

Trichoderma reesei CSR-T-3 (NAIMCC-SF-0030)

Fusarium oxysporum f. sp. cubense Tropical race 4 and race 1

Banana

Fusarium wilt

Saxena et al. (2021)

 

Aspergillus niger AN-27

Pythium, Fusarium,

Macrophomina,

Rhizoctonia and Sclerotinia

Prashant et al. (2016)

 

Trichoderma asperelloides 5R (NAIMCC-SF-0026)

Uncinula necator

Grapes

Powdery mildew

Saxena et al. (2021)

 

Trichoderma harzianum IARI P-4(MTCC 5371)

Fusarium oxysporum f. sp. ciceris, Sclerotium rolfsii, Sclerotinia sclerotiorum,

Rhizoctonia solani, R. bataticola, Fusarium

oxysporum f. sp. lycopersici, Pythium ultimum

Chickpea, tomato, mungbean French bean

Soil borne diseases

Saxena et al. (2021)

 

Trichoderma viride

Fusarium, R. solani,

Macrophomina phaseolina and Colletotrichum

Many hosts

Soil borne diseases

Prashant et al. (2016)

 

Trichoderma harzianum Th4d (NAIMCC-F-02188)

Phytophthora sp., Macrophomina phaseolina, Fusarium sp., Botrytis cinerea, Alternaria sp. and Golovinomyces cichoracearum

Safflower, castor, aster, sunflower

Seedling blight, root rot, wilt, grey mold, leaf blight, powdery mildew

Saxena et al. (2021)

 

Trichoderma erinaceum

Rhizoctonia solani, Sclerotium rolfsii, Helminthosporium oryzae and Sclerotium oryzae

Rice

Soil borne plant pathogens, brown leaf spot

Swain et al. (2018)

 

Bjerkandera adusta BK-1

Tomato

Grey mould, brown spot, and early blight

Chen et al. (2021)

Yeast groups

 

 

 

 

 

 

Cryptococcus albidus var. aerius, Pichia guilliermondii,

Debaryomyces hansenii

Botryodiplodia theobromae

Mango

Post-harvest rot

Sugiprihatini et al. (2011)

 

P. guilliermondii

Aspergillus flavus

Soybean

Post-harvest infection

Wisniewski et al. (1991)

 

P. membranefaciens, C. albidus

 

Monilinia fructicola, Penicillium

expansum, Rhizopus

stolonifer

Apple

Post-harvest

infection

 

Chan and Tian

(2005)

 

 

P. guilliermondii

P. digitatum

Citrus

Decay of citrus fruit

Droby et al. (1993)

 

C. laurentii

M. fructicola, P. expansum

Peach

Yao and Tian (2005)

 

Chaetomium globosum

Phoma betae, P. ultimum, R. solani

Sugar beet

Damping-off

Walther and

Gindrat (1988)

Oomycetes

 

 

 

 

 

 

Pythium oligandrum

Sclerotinia sclerotiorum

Wheat

White mould/stem rot

Madsen and de

Neergaard (1999)

 

 

Verticillium dahliae

Pepper

Wilt

Rekanovic et al. (2007)

 

 

Pythium dissotocum

Tomato

Root rot

Vallance et al. (2009)

 

 

P. parasitica

Tomato

Buckeye rot

Picard et al. (2000)

 

 

B. cinerea

Tomato

Grey mould

Lou et al. (2011)

 

 

R. solani

 

Potato

Black scurf

Ikeda et al. (2012)

 

 

Aphanomyces cochlioides

Sugar beet

Root rot

Takenaka and

Ishikawa (2013)

 

 

Cercospora beticola

Sugar beet

Leaf spot

Takenaka and

Tamagake (2009)

 

 

Phytoplasma

Tobacco

Lherminier et al. (2003)

Mycorrhiza

 

 

 

 

 

 

Glomus mosseae

Thielaviopsis basicola

Tobacco

Root infection

Baltruschat and

Schoenbeck (1975)

 

Vesicular arbuscular mycorrhiza

R. solani

Rape seed

Damping-off

Iqbal et al. (1977)

 

Glomus fasciculatus

 

S. rolfsii

Peanut

Southern blight

Krishna and

Bagyaraj (1983)

Bacteria

 

 

 

 

 

 

Pseudomonas chlororaphis

F. oxysporum f. sp. radicislycopersici

Tomato

 

Foot and root

rot

Bolwerk et al. (2003)

 

P. fluorescens

Phytophthora infestans

Potato

Late blight

Hunziker et al. (2015)

 

 

Sarocladium oryzae

Rice

Sheath rot

Saravanakumar et al. (2009)

 

 

Banana bunchy top virus

Banana

Bunchy top disease

Kavino et al. (2008)

 

 

Dematophora necatrix

Avocado

Root rot

Cazorla et al. (2006)

 

Pseudomonas fluorescens IIHR Pf-2 (NAIMCC-SB-0038/ITCC B0034) and Trichoderma harzianum IIHR Th-2 (NAIMCC-SF-0033/ITCC 6888)

Meloidogyne incognita, Ralstonia solanacearum, Erwinia carotovora, Fusarium oxysporum f. sp. vasinfectum, Fusarium solani

Tomato, cotton

Root knot nematode, bacterial wilt, vascular wilts

Saxena et al. (2021)

 

Pseudomonas fluorescens

(NAIMCC-SB-0053)

Wheat, rice tomato, chickpea

Spot blotch, sheath blight and wilt

Saxena et al. (2021)

 

P. putida

Fusarium sp.

Radish

Wilt

de Boer et al. (2003)

 

Bacillus pumilus, B. amyloliquefaciens, B. subtilis

Cucumber mosaic virus

Tomato

Mosaic disease

 

Zehnder et al. (2000)

 

B. amyloliquefaciens, B. subtilis, B. pumilus

Tomato mottle virus

Tomato

Tomato mottle

Murphy et al. (2000)

 

B. pumilus

Erwinia tracheiphila

Cucumber

Bacterial wilt

Zehnder et al. (2001)

 

 

Peronospora tabacina

Tobacco

Blue mould

Zhang et al. (2002)

 

B. subtilis, B. pumilus

Sclerospora graminicola

Pearl millet

Downy mildew

Niranjan Raj et al. (2003)

 

B. cereus

Corynespora cassiicola

Tomato

Foliar diseases

Silva et al. (2004)

 

Bacillus sp.

Phytophthora capsici

Bell pepper

Blight

Jiang et al. (2006)

 

 

Magnaporthe grisea

Rice

Blast

Naureen et al. (2009)

 

 

P. capsici

Squash

Blight

Zhang et al. (2010)

 

B. amyloliquefaciens

F. oxysporum

Maize

Wilt

Koumoutsi et al. (2004)

 

Brevibacillus brevis

B. cinerea

Cucumber

Grey mould

Konstantinidou-Doltsinis et al. (2002)

 

Enterobacter agglomerans

R. solani

Cotton

Root rot

Chernin et al. (1995, 1997)

 

Paenibacillus sp.

F. oxysporum

Sorghum

Wilt

Budi et al. (2000)

 

Lysobacter enzymogenes

F. graminearum

Wheat

Wilt

Li et al. (2008)

 

Stenotrophomonas maltophilia

P. ultimum

Sugar beet

Damping-off

Dunne et al. (2000)

 

Agrobacterium radiobacter

Agrobacterium tumefaciens

Many hosts

Vicedo et al. (1993)

 

Collimonas fungivorans

F. oxysporum

Tomato

Wilt

Kamilova et al. (2007)

 

L. enzymogenes

Pythium aphanidermatum

Cucumber

Root and crown rot

Folman et al. (2003)

 

Burkholderia cepacia

 

Pythium sp. and

Aphanomyces sp.

Peas

Damping off,

root rot

Heungens and

Parke (2000)

 

Bacillus velezensis K01

Botrytis cinerea

Tomato and pepper

Xue et al. (2023)

Actinobacteria

 

 

 

 

 

 

S. janthimts,

S. cinerochromogenes

Pythium coloration

Carrot

Cavity spot

El-Tarabily et al. (1997)

 

Streptomyces species

Phytophthora medicaginis and Phytophthora sojae

Alfalfa and soybean

Root rot

Xiao et al. (2002)

 

 

Plectosporium tabacinum

Lupin

Root rot

El-Tarabily (2003)

 

 

Pythium aphanidermatum

Cucumber

Damping-off

El-Tarabily (2006)

 

Actinomadura sp.

Phytophthora cinnamomi

Snapdragon

Root rot

You et al. (1996)

 

Micromonospora sp.

Gaeumannomyces graminis var. tritici

Wheat

Take all

Coombs et al. (2004)

 

 

Fusarium oxysporum f. sp. lycopersici

Tomato

Wilt

Smith (1957)

 

M. carbonacea

P. coloratum

Carrots

Cavity spot

El-Tarabily et al. (1997)

 

 

Sclerotinia minor

Lettuce

Basal drop

El-Tarabily et al. (2000)

 

M. chalcea

P. aphanidermatum

Cucumber

Damping-off

El-Tarabily (2006)

 

Microbispora rosea

P. aphanidermatum

 

Cucumber

Damping-off

El-Tarabily (2006)

 

 

G. graminis var. tritici

Wheat

Take all

Coombs et al. (2004)

 

Streptosporangium albidum,

Streptoverticillium netropsis

 

P. coloratum

Carrots

Cavity spot

El-Tarabily et al. (1997)

 

Arthrobacter sp.

Fusarium moniliforme var. subglutinans

Pine

Pitch canker

Barrows-Broaddus and

Kerr (1981)

Virus

 

 

 

 

 

 

Zucchini yellow mosaic virus (mild strain)

Severe strains of same

Cucurbits

Mosaic

Lecoq and Lemaire (1991)

 

Papaya ringspot virus (mild strain)

Severe strains of same

Papaya

Ring spot disease

Tennant et al. (1994)

 

Mild strain of Citrus tristeza virus (mild strain)

Severe strains of same

Citrus

Tristeza

Folimonova  (2013)

Fungal agents for biocontrol

The well-known fungal biocontrol agents include the Trichoderma species, ectomycorrhizas, arbuscular mycorrhizas (AMF), yeasts and endophytes. Even the nonvirulent strains of certain pathogens can utilize hypovirulence-associated mycoviruses in order to function as biocontrol fungi (Ghorbanpour et al., 2018). There are 300 fungal antagonists belonging to 13 classes and 113 genera that were used against fungal plant pathogens. Trichoderma is identified as the genus (comprising 25 species) with greatest potential of biocontrol and  is used as a biocontrol agent against a number of plant fungal diseases. Trichoderma species namely T. atroviride, T. hamatum, T. harzianum and T. viride are effective in the control of soil borne fungal pathogens (Hegde and Vijaykumar, 2023). In addition, some more antagonistic species, Alternaria, Aspergillus, Candida, Fusarium, Gliocladium, Penicillium, Pichia, Pythium, Talaromyces and Verticillium play important roles in the management of plant diseases (Hegde and Jahagirdar, 2020; Kasun et al., 2020). Microbial communities can inhabit both external surfaces (epiphytes) or internal plant tissues (endophytes), and these communities play an important role in protecting plants from diseases (Parasuraman et al., 2019). Numerous metabolites with various chemical structures, including terpenoids, alkaloids, steroids, peptides, isocoumarins, benzopyranones, and quinones, have been identified in endophytic fungi. The identification of these metabolites provided a solid chemical basis for the development of agrochemicals that may have antibacterial, antifungal, herbicidal, nematicidal, insecticidal and other agricultural uses (Risoli et al., 2022). Biocontrol agents Chaetomium sp. and Athelia bombacina were successful in suppression of Venturia inaequalis; Rhodotorula kratochvilovae strain LS11 controlled Monilinia spp., while Tuberculina maxima parasitizes the white pine blister rust fungus Cronartium ribicola; Darluca filum and Verticillium lecanii parasitize several rusts, Tilletiopsis sp. parasitizes the cucumber powdery mildew fungus Sphaerotheca fuliginea, and Nectria inventa and Gonatobotrys simplex parasitize two pathogenic species of Alternaria (Agrios, 2005). A novel isolate, Trichoderma erinaceum isolated from above-ground habitats effectively controlled three soil borne plant pathogens of rice i.e., Rhizoctonia solani, Sclerotium rolfsii and Sclerotium oryzae under controlled conditions and R. solani and Helminthosporium oryzae under field conditions while  improving the germination rate and vigor of rice plant (Swain et al., 2018). The fungal strain, Bjerkandera adusta BK-1, is a novel promising broad-spectrum biocontrol agent against multiple plant fungal diseases (Chen et al., 2021).

Mycorrhizal fungi as biocontrol agents

Several studies lay emphasis on the biocontrol abilities of Arbuscular mycorrhizal fungi (AMF) as they have been shown to reduce the incidence of fungal diseases and nematode attacks on host plants by 30 to 42% and 44–57%, respectively (Veresoglou and Rillig, 2012; Mishra et al., 2018). AMF offers defence against several fungal pathogens belonging to the genera Colletotrichum, Alternaria, Erysiphe, Gaeumannomyces, Macrophomina, Botrytis, Rhizoctonia, Fusarium, Cylindrocladium, Sclerotium and Verticillium (Singh, 2017). Notable ectomycorrhizal species such as Amanita spp., Boletinus spp., Cenococcum spp., Lactarius spp., Laccaria laccata, Pisolithus tinctorius, Suillus luteus and Thelephora terrestris are known to generate metabolites that safeguard plant root systems from diseases (Trappe, 1962). Suillus luteus has been identified as an effective bio control agent against damping-off disease caused by Fusarium verticillioides and Fusarium oxysporum in Scots and Stone pine trees (Mateos et al. 2017).

Biocontrol by yeasts

Yeasts such as Aureobasidium pullulans, Cryptococcus albidus, Candida oleophila, Saccharomyces cerevisiae, and Metschnikowia fructicola are currently being employed as biocontrol agents as they are effective adversaries of various plant pathogens (Pandit et al. 2022). Biofungicides based on Aureobasidium pullulans strains indicated for biocontrol applications against fungal pathogens of fruit (e.g., Boni protect®) are available in the market (Weiss et al., 2006). The BCA Papiliotrema terrestris strain LS28 was isolated from apple epiphytic microflora and selected for its ability to counteract fungal pathogens of plants and fruits, both in the field and in postharvest stages (Palmieri et al., 2021). Low temperature-adapted yeasts Leucosporidium scottii and Cryptococcus laurentii were highly effective in their biocontrol activity on apple and tomatoes inoculated with Botrytis cinerea in cold storage conditions (Hu et al., 2017).

Bacteria for biocontrol

A wide variety of bacterial genera, including Agrobacterium, Alcaligenes, Arthrobacter, Bacillus, Enterobacter, Erwinia, Pseudomonas, Rhizobium, Serratia, Stenotrophomonas, Streptomyces, Xanthomonas have been described to have plant disease protection activity against fungal and bacterial pathogens (Bonaterra et al., 2022). The activity of P. fluorescens EPS62e and P. pseudoalcaligenes AVO110 in the reduction of Erwinia amylovora or Rosellinia necatrix infections, respectively, is based on their strong fitness in colonizing plant tissues as they have higher growth potential and nutrient use efficiency than the target pathogens (Cabrefiga et al., 2007; Pliego et al., 2008, Dobhal and Hegde, 2021). In Vitis, P. fluorescens PTA-CT2 induces ISR to Plasmopara viticola and Botrytis cinerea that depends on the activation of SA or JA and ABA defensive pathways (Lakkis et al., 2019). Species of Bacillus including B. subtilis, B. amyloliquefaciens, B. methylotrophicus, B. polymyxa, B. cereus, B. coagulans, B. subterraneous, B. licheniformis, B. pumilus, B. circulans, B. velezensis, B. megaterium, B. firmus, B. aquimaris, B. vietnamensis, and B. aerophilus have been reported to be suitable for biological control of plant disease and plant growth promotion (Fan et al., 2017; Saxena et al., 2020; Hegde and Malligawad, 2020). Bacillus spp. produce several bacteriocins with antimicrobial activity such as amylolysin, amylocyclicin, amysin, subtilin, subtilosin A, subtilosin B, thuricin. Bac-GM17 produced by B. clausii GM17 have activity against Agrobacterium tumefaciens (Mouloud et al., 2013) or thuricin Bn1 from B. thuringiensis subsp. kurstaki Bn1 against Pseudomonas savastanoi and Pseudomonas syringae (Ugras et al., 2013). B. amyloliquefaciens FZB42 produced secondary metabolites (surfactin, fengycin, and bacillomycin D) that trigger plant defense gene expression and contribute to lettuce bottom rot reduction (Chowdhury et al., 2015). A novel biocontrol agent Bacillus velezensis K01 has a broad-spectrum antagonistic activity and demonstrated a biocontrol efficiency of over 78% against preharvest and postharvest grey mold diseases in tomato and pepper (Xue et al., 2023). Streptomyces CBQ-EA-2 and CBQ-B-8 have chitinolytic, cellulolytic, and proteolytic activity and result in reduced Macrophomina phaseolina and Rhizoctonia solani infections in Phaseolus vulgaris (Díaz-Díaz et al., 2022). Pantoea species were shown to target a wide spectrum of plant pathogens including bacteria, fungi, and oomycetes via secretion of antimicrobial compounds such as pantocins, herbicolins, microcins, and phenazines (Walterson and Stavrinides, 2015). Lactobacillus plantarum PM411 and TC92 are effective in preventing bacterial plant diseases (Daranas et al., 2019).

Plant viruses and their biocontrol nature

Viruses are not regarded as living organisms, but certainly as valid agents of biological control, and hence they are included (with these caveats) within our definition of living agents (Stenberg et al., 2021). Viruses have been increasingly used to combat pests both directly (by pathogenic pest infection) and indirectly (by cross-protection, i.e., ‘vaccinating’ crops with mild virus strains), and placed in the canon of biological control with no conceptual opposition from the scientific community (Di Giallonardo and Holmes, 2015). Qu et al. (2021) have elucidated the effects of a single-stranded DNA virus, Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) that infects the fungus Sclerotinia sclerotiorum, a disease causative agent of many crops and they have further elucidated the altered expression of phenotype related genes upon SsHADV-1 infection by using digital RNA sequencing.

Phage-based biocontrol

Phages have been in use as biocontrol agents against bacterial pathogens for a long time. Peptidoglycan hydrolases, lysins from phages Atu_ph02 and Atu_ph03 are capable of blocking cell division in Agrobacterium tumefaciens (causes crown gall disease) resulting in its lysis (Attai et al., 2017). Other lysins from CMP1 and CN77 phages have also shown lytic capacity against Clavibacter michiganensis subsp. michiganensis, that cause bacterial wilt and canker of tomato (Wittmann et al., 2016). Mostly, the application of phages and phage lysins in plant disease management is a progressive step and has shown positive outcomes in a number of instances. Focus now needs to be on developing better delivery methods and guaranteeing a longer shelf life for the phage and its enzymes on the host plant (Dy et al., 2018) to facilitate effective biocontrol.

Algal and cyanobacterial biocontrol activities

Algal and cyanobacterial extracts are a rich source of bioactive elicitors (Jimenez et al., 2011) with antifungal, antiviral and antibacterial properties (Arunkumar et al., 2010).  Activity of polyphenol oxidase and peroxidase enzymes improved when extracts from Cystoseira myriophylloides, Laminaria digitata and Fucus spiralis were utilized against Verticillium dahliae wilt of tomato (Esserti et al., 2017). Employing Nostoc entophytum and Nostoc muscorum in the soil against Rhizoctonia solani greatly enhance seedling endurance along with improving root and shoot dry weight and plant length (Osman et al., 2011). Usage of Cyanobacteria, Anabaena sp. on zucchini cotyledons infected with powdery mildew (Podosphaera xanthii) resulted in enhanced enzymatic activity of peroxidases, endochitinase, chitin 1,4-β-chitotriosidase, β-N-acetylhexosaminidase, and β-1,3-glucanase (Roberti et al., 2015).

ADVANCED BIOCONTROL STRATEGIES

FOR THE MANAGEMENT OF PLANT DISEASES

Microbial volatilome and its role in the biological control

Among the several microbiological strategies used by BCAs, the production of volatile organic compounds (VOCs) is a method that is helpful in situations where the straightforward association between the pathogen and its competitor is not possible. All living forms synthesize VOCs, and these can be exploited for usage in biocontrol of plant pathogens like bacteria, oomycetes, and fungi. VOCs are a sustainable preference for synthetic fungicides due to their ease of application, low residue deposition in the environment and on crops, and their biocontrol efficacy (Tilocca et al., 2020). In vitro studies indicated that Bacillus volatile compounds reduced Ralstonia growth and viability and caused significant problems in cell integrity and motility in addition to considerable alterations in Ralstonia genes expression that controls tobacco wilt disease progression (Tahir et al., 2017). It’s possible that bacterial volatiles have a role in Bacillus reported biocontrol properties both directly and indirectly, and that bacterial VOC bouquets function as multifactorial, sequential, or simultaneous signals on pathogens and hosts (Bailly and Weisskopf, 2017).

Microbiome-based solutions for plant protection

A wide range of microorganisms effectively interact with plants in the rhizosphere region. Microbial invasion can affect the network of microorganisms that are linked with plants. These network models of soil and plant microbiomes can be interpreted for biocontrol and present new prospects for disease management. While single organisms were commonly utilized in the past, their effects were often uneven, microbiome-based biocontrol techniques are now possible (Berg et al., 2017; Jahagirdar et al., 2021). Microbial consortia offer numerous benefits for managing plant diseases compared to the application of a single strain such as i) Consortia of bio-control agents targets wide range of phytopathogens, ii) Enhancement of soil suppressiveness through increased microbial diversity within the soil rhizosphere, iii) Diverse species occupy different ecological niches in rhizosphere and thereby restricts competition between them, iv) Improved rhizosphere colonization due to interactions among microbes within the consortium,  v) Utilization of multiple strains with varied modes of action, which boosts the bio-control efficiency of the consortia. Mixture of four bacterial isolates comprising of Serratia marcescens, Pseudomonas fluorescens, Rahnella aquatilis and Bacills amyloliquefaciens improved soil suppressiveness against Fusarium oxysporum f.sp. ciceris race 0 and Fusarium solani f.sp. pisi causing Fusarium decline in chickpea by increasing microbial diversity in rhizosphere (Palmieri et al., 2017). In the future, microbial consortia and biocontrol agents can be employed to improve biodiversity associated with crops via microbiome engineering to achieve definitive microbiome outcomes as desired (Erlacher et al., 2014; Jadav et al., 2022).

Microbiome engineering

Plant microbiome engineering can be achieved in two ways: bottoms-up methods involve isolating, altering, and reviving certain microbes, whereas top-down approaches involve synthetic ecology, which includes horizontal gene transfer to a variety of hosts in situ and then phenotyping the microbiome (Ab Rahman et al., 2018). The root microbiome can be engineered by soil conditioning techniques such as incorporating legumes to enrich native diazotrophic microorganisms. Additionally, the use of substrates/non-microbial biostimulants, including innovative organic soil amendments and root exudates, can help attract beneficial microbiota. Introducing external microbial inoculations, whether through soil application or as endophytes, can effectively manage Xanthomonas blight in rice (Saikia et al. 2020). Another strategy is to alter indigenous microbial strains through genetic engineering techniques, including CRISPR/Cas9 and RNA interference. This modification seeks to enhance the microbes' ability to withstand stress and optimize their nutrient utilization (Joshi et al. 2025). It would be extremely helpful to develop microbiomes that are long-lasting, stress-resistant, and capable of increasing agricultural output. Microbiome bioengineering is a fascinating choice for improving plant health and will provide enormous benefits to biocontrol methods in the future (Orozco-Mosqueda et al., 2018). Plant microbiome bioengineering is an intriguing option for improving a plant’s biological capabilities, an approach that, while still in its infancy, has the potential to be of immense agricultural value (del Carmen et al., 2018).

Genetically modified biocontrol agents

The recent advancements in genome engineering tools, genome-wide functional tools and meta-omic tools can improve our ability to design microbes for biocontrol and biofertilization, as well as increase agricultural productivity and yield. Rhizoctonia solani infection in beans can be brought under control by transferring a gene coding for the enzyme chitinase from Serratia to a Pseudomonas endophyte (Downing and Thomson, 2000). Clermont et al. (2011) employed genome shuffling to create superior Streptomyces melanosporofaciens EF76 biocontrol strains. Four strains with improved antagonistic activity against the potato diseases Streptomyces scabies and Phytophthora infestans were isolated after two rounds of genome shuffling. Biological control ability can also be improved by employing chemical mutagenesis. Examples include the use of nitrosoguanidine mutagenesis in Pseudomonas aurantiaca B-162 to produce a strain with better phenazine synthesis leading to improved biocontrol activity (Feklistova and Maksimova, 2008) and Trichoderma harzianum strains that exhibited enhanced biocontrol ability after UV mutagenesis (Marzano et al., 2013). A recombinant strain of Pseudomonas synxantha, designated ZHW 15 and ZHW 25, demonstrated enhanced biocontrol efficacy against soil-borne pathogens affecting wheat (Zhang et al. 2020). The addition of the required mutation can at times produce altered gene expression in non-targeted genes resulting in undesired effects. These constraints can be overcome using more recently established genome editing approaches. We can insert mutations into specific regions in the genome with high precision and efficiency using techniques like Crispr/Cas (Barrangou and van Pijkeren, 2016). The gene editing approach could also help in commercialization of BCA’s through ease of regulatory clearances.

Mycoviruses as biocontrol agents

Mycoviruses having capability to infect fungal pathogens are known to have the potential to be used as biological control agents against plant diseases. The mycoviruses were recognized to induce hypovirulence (reduced virulence) in their hosts and this notion elicited great interest in characterization of viruses from phytopathogenic fungi and to utilize them as biocontrol agents (García-Pedrajas et al., 2019). Surprisingly, numerous plant pathogenic fungi are found to harbor mycoviruses, which reduce the virulence of their fungal host (Kumar and Chandel, 2016). Hypovirulence-associated mycoviruses are those mycoviruses that reduce the pathogenicity of their inhabiting fungal hosts. However, it is difficult to transmit these mycoviruses easily between vegetatively incompatible groups and hence it has been difficult to develop commercial mycovirus biocontrol strategies for phytopathogenic fungi (Khalifa and MacDiarmid, 2021).

MAJOR CHALLENGES FOR BIOCONTROL RESEARCH IN THE PLANT DISEASE MANAGEMENT

Biological control strategy was initially employed at the end of the 19th century. Displaying an array of advantages, the literature has also mentioned many limitations of this biocontrol strategy for controlling plant diseases (Stenberg et al., 2021). Though these methods offer effective alternatives to chemical pesticides for controlling pests and plant diseases, there are still various challenges to overcome. These challenges are briefly discussed in the subsequent paragraphs.

The journey of biocontrol agents from lab to field

Researchers are screening potential microbes as part of their work to create biological pesticide remedies that are very effective for controlling plant diseases in agriculture. These strains are usually chosen based on factors such as disease resistance, host range, availability, formulation, mass production, and farmer practice (Farrar et al., 2014). Bioagents can be assessed by considering geographical locations, host crop species, soil types, and environmental factors. The growth of BCAs is typically easier to observe in controlled environments such as greenhouses. The preference of most researchers at this stage might be associated with the reliability of the environment (Spadaro and Gullino, 2004). The performance of BCAs in greenhouse trials can provide important theoretical and practical support for field utilization. The stability of BCAs is affected by the method of formulation, shipment, and storage environment. To achieve high levels of BCA strategy success, it is important to improve the formulation technology, extend the storage duration of the BCA product, optimize the production of selected microbial strains, and achieve large-scale application through low-cost manufacturing companies (Barratt et al., 2018). During the formulation and field efficacy trials, private sector partners and licensed laboratories conduct the essential environmental and human health assessments, as well as quality assurance for the ultimate commercialization of biopesticides. Before utilizing biopesticides on a large scale in the field, government authorities must grant permission. Typically, the biopesticide registration and regulation portfolio includes modified versions of synthetic pesticides as well as risk evaluation. This includes ecotoxicological and toxicological tests, as well as studies into their mechanism of action and host spectrum. Most of these requirements are difficult for authorities to achieve because producing effective bioagents while maintaining acceptable safety and consistency standards for commercialization might be a difficult task (Chandler et al., 2011).

Limited number of registered bioagents and lack of awareness

Despite their well-documented efficacy, BCAs now account for less than 5% of the crop protection sector’s commercial value (He et al., 2021). The identification, characterization, and registration of potential microbes takes more time and requires academic-industry collaborations (Stenberg et al., 2021). Furthermore, using natural resources to manage diseases (i.e., BCAs) raises several ethical and legal issues that might affect the biodiversity of an area (Sundh and Eilenberg, 2020). In this situation, new BCA species and populations have been restricted from entering specified countries. At present, every country has its own regulatory system, which varies widely. For example, high development costs for new commercial BCAs have been recognized as an obstacle to the BCA industry’s development in Australia (Hidayah, 2022). The standards for data submission for temporary registration in India are less demanding than those for standard registration. It is imperative to meet the quality standards set forth by the Central Insecticides Board, which encompass content, the virulence of the organism in terms of LC50, moisture content, shelf life, and secondary non-pathogenic microbial load. Biopesticides are exempted from the fees for pesticide registration and for the right to sell the product in Canada, except for the cost charged for reviewing the product label. Like Canada, the US does not require registration of indigenous beneficial insects or entomopathogenic nematodes or similar types of microbial inoculants as long as they do not make a pest control claim. In the U.S. and EU, biopesticide registration can take over 3 years as compared to 6-12 months for synthetic products. The timeline for obtaining approval and registration of a microbial pest control product, starting from the pre-consultation with the Pest Control Products Board, Kenya is influenced by the complexity of the product and generally ranges from 2 to 4 years (Hoeschle-Zeledon et al., 2013). To facilitate the registration and commercialization of novel BCAs and their products, BCA registration requires extensive cooperation among governmental institutes, universities, and industry sectors. The number of programs that provide financial and ecological benefits plays a vital role in bioagents registration (Stenberg et al., 2021). Hence, local usage and global marketing commercialization must fulfil international legislation. The International Biological Control Organization (IOBC) was established to bring together scholars, scientists, and professionals from a wide range of industries and fields to identify barriers and offer recommendations to overcome those (Brodeur et al., 2018). Biocontrol management has a direct impact on farmers’ expenses and income, but it also has an indirect impact on their financial benefits due to its effect on farmland biodiversity and environmental sustainability (Barratt et al., 2018). However, farmers have not fully utilized commercial bioagents due to a lack of information and awareness. Therefore, there is a need to strengthen the idea of biological management in the farming community to restore their trust in the use of bioagents (Ayaz et al., 2023; Hegde et al., 2023).

Bioagents commercialization and legislative procedure

Despite their growing popularity in crop disease management, biocontrol agents currently represent only 1% of agricultural control techniques, whereas synthetic-based pesticides account for 15% in the agriculture sector (Fravel, 2005). The commercialization of bioagents is a multi-step procedure that faces numerous challenges. Before being licensed for commercialization, similar to synthetic pesticides, BCAs are subjected to risk evaluations (Wilson and Jackson, 2013). The current trend of reducing the use of synthetic pesticides and simplifying the regulatory process for low-risk products may allow BCAs to be commercialized worldwide (Chandler et al., 2011; Hegde and Vijaykumar, 2022).

CONCLUSION AND PERSPECTIVES

Synthetic pesticides, due to their eco-toxicological risks, are facing increasing restrictions on their use worldwide. Biocontrol products based on microbial antagonists offer safer alternatives to replace or complement chemical pesticides. As a result, research on the selection, characterization and commercial development of BCAs is   steadily increasing over the last few decades. Among the most studied biocontrol agents are fungi, bacteria and yeasts. Despite the large number of studies on biocontrol agents, the commercial formulations of BCA are still too limited and insufficient to meet the growing demand for sustainable agricultural systems. The main challenges hindering the development of new microbe-based formulation are (i) the sometimes lower efficacy of BCAs compared to synthetic pesticides, (ii) the lack of information available on the microbial formulation protocols, due to industrial secrecy and (iii) the complex registration and patent procedures in various countries. The use of molecular and omics tools could significantly improve the selection of biocontrol agents by providing a deeper understanding of their mechanisms of action, which is critical for optimizing BCAs activity and streamlining the registration processes. Future research should also investigate the economic feasibility and societal impact of expanding the use of biocontrol technologies. Analyzing the cost effectiveness and potential benefits for farmers and the agriculture sector would be valuable. For the widespread adoption of biocontrol strategies, it is essential to enhance dissemination among farmers, extension services, and policymakers. Efforts should focus on developing educational programs and outreach initiatives to raise awareness and make biocontrol solutions more accessible. Despite the technical and bureaucratic challenges associated with developing microbial BCAs, there is a growing shift towards plant disease control methods with lower environmental impact and fewer risks for human health. Additionally, political support for research into new technologies, particularly those addressing climate change and biodiversity conservation, is increasing. Consequently, research into the design and development of more efficient bioproducts, including microbial formulations to be used against plant diseases, will attract more and more attention in the near future.

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