Chilies thrive in tropical and subtropical regions up to 2000 m in altitude, excluding pungent varieties (Aashish et al., 2022). Optimal conditions include warm, humid climates that promote growth and fruit maturity, with an ideal annual rainfall of 850–1,200 mm. However, excessive rain and humidity can lead to poor fruit set and fruit rot. The ideal temperature for chilies ranges between 20°C and 25°C during the day and 15°C and 21°C at night (Arom, 2022). A day length of 9–10 h stimulates plant growth, boosting productivity by 21–24% and enhancing capsicum quality (Kramchote and Suwor, 2022).

Soil is the main substrate for chili in open field conditions, and various other solid substrates, such as grow bags, are used under greenhouse conditions. Chili prefers well-drained, aerated soils rich in organic matter. Ideal soils are light loamy or sandy loamy with lime and organic content, while light soils require irrigation and organic fertilization. The 6–7 pH range is ideal for optimum growth, and higher salinity hampers plant growth. Chili diseases have been a major reason for yield reductions in the world. Diseases caused by bacteria, viruses, fungi, and nematodes have badly affected chili crops worldwide (Su et al., 2023; Xie et al., 2023). Diseases associated with chili crops are summarized in Table 2. One such fatal disease is damping-off, which occurs by soil-borne fungi genera, whether occurring pre- or post-plant emergence, accounting for up to 90% plant death and 62% seedling viability loss in nurseries and fields, as originally documented by Majeed et al. (2018).

Pythium species are a group of soil-borne pathogens known for causing damping-off and root rot in a wide range of plants, including chili. They thrive in wet, poorly drained soils and attack seedlings, leading to stunted growth and plant death. Some Phytophthora species can cause damping-off in seedlings. For instance, Phytophthora capsici is known to cause damping-off in seedlings of various crops, including peppers and other vegetables. The pathogen attacks young seedlings, leading to poor germination, stem collapse, and death, similar to other damping-off pathogens such as Pythium and Rhizoctonia. Rhizoctonia solani is a soil-borne fungal pathogen that affects chili seedlings by attacking their roots and stems, leading to poor germination, wilting, and eventual death of the young plants. Rhizoctonia thrives in warm, moist conditions and can lead to significant crop losses if not managed effectively. Fusarium species are soil-borne fungi that attack chili seedlings’ roots and lower stems, leading to poor emergence, wilting, and seedling death. Fusarium thrives in warm, moist soils and can cause significant damage if conditions are favorable.

Environmental factors play a key role in spreading the disease (Ghorbani et al., 2024a). The susceptible host, the chili plant, and the virulent pathogen, Pythium spp., along with conducive environmental conditions, are key elements for disease establishment. Temperature, moisture, and organic matter (Hansen and Keinath, 2013) have been directly linked with the incidence and severity of the damping-off owing to better establishment of the Pythium spp. with respect to attachment, establishment, and penetration into host tissues. Other environmental factors such as soil type, clay soil with high moisture holding capacity, rainfall intensity and duration, irrigation, humidity, and seedling surface witness are key factors responsible for damping-off disease. The pre-emergence damping-off requires 12°C while post-emergence damping-off require18-30°C and the optimum range lies from 24 to 30°C for successful infection of Pythium spp. (Dubey et al., 2019). Furthermore, a high soil moisture (Martin and Loper, 1999; Majeed et al., 2019) supports the dissemination of propagules and increases the size of the spermosphere, while a pH of ˃5.8 supports successful infection. The relationship between environmental factors with inoculum and crop geometry spread also leads to the possible development of disease (Arora et al., 2021). The detection and diagnosis of Pythium spp. pathogenic to chili plants involves utilizing both morphological characteristics and the analysis of specific DNA marker regions from the isolated pathogen. Recent research on Pythium spp. has predominantly focused on advanced molecular techniques based on PCR, including real-time PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) (Sridapan and Krajaejun, 2023), and internal transcribed spacer (ITS) analysis (Gaikwad et al., 2023).

Pythium spp. are eukaryotic organisms composed of filamentous, non-septate hyphae. Cell walls are primarily composed of cellulose and glucan, with limited amounts of chitin (Kiselev, 2020). Pythium spp. in soil is attracted to the exudates released from germinating seeds and developing seedlings, leading to seed rot and seedling death (Wohor et al., 2022). There are two main stages of Pythium spp. When the environmental conditions are favorable in the first stage, pyrium produces sporangia that grow into hyphae and vesicles with motile zoospores asexually. They are attracted to plant roots or other organic matter in the soil. In the other stage, Pythium reproduces sexually by combining an antheridium and an oogonium to form oospores, mostly during unfavorable environments. Sporangia can be single-celled or multi-celled and can be motile or non-motile.

Furthermore, Pythium spp. can be heterothallic or homothallic depending on the type of reproduction (Figure 1). When spores come into contact with a susceptible host, they can adsorb onto the root surface, forming a germ tube. The germ tube then penetrates the host’s cells via wounds, root tips, or direct penetration, grows to branch mycelium through intracellular and intercellular spaces, and absorbs nutrients while exhibiting pathogenic symptoms externally (Kushwaha, 2020). Sexual spores can thrive dormant in the soil in harsh environmental conditions as saprophytes and become active again when conditions become favorable (Parveen et al., 2020).

Chemical control via fungicides is often considered a quick and effective way to prevent pathogens from infecting plant systems, particularly when applied to young, growing tissues like leaves, fruits, and flowers. This method is widely adopted due to the immediate results it yields compared to the lengthy process of developing resistant cultivars (Sawant et al., 2022). Farmers have resorted to various chemical alternatives to methyl bromide for soil fumigation, as non-chemical methods can sometimes be labor-intensive and less effective against soilborne diseases (Duniway, 2002). However, the use of chemical fungicides is constrained by a limited number of products registered for use on various crops and the high costs associated with these products, limiting chemical management of damping-off to a few active ingredients (Garzón et al., 2011). Fungicides from groups such as captan, benzimidazole, triazole, and dicarboximide have been recognized for their efficacy in controlling damping-off diseases (Lamichhane et al., 2016). Specifically, metalaxyl, tridiazole, and captan are effective against Pythium and Phytophthora species, while maneb and mancozeb work against Pythium and Fusarium species, and these are commonly used by growers (Lamichhane et al., 2016). Using systemic fungicides like metalaxyl before sowing can reduce Phytophthora and Pythium populations in the soil (Russell et al., 1990). For seed treatments, Satija and Hooda found that benlate (0.1%) and dithane M-45 were the most effective against Pythium aphanidermatum and Fusarium solani (Ansari et al., 1990). Soil drench applications of captan (Khrieba, 2020), as well as soil treatments with methyl bromide, solarization, and metalaxyl soil drench, have been successful in preventing P. aphanidermatum infection (Hickman and Michailides, 1998).

Cultural practices are vital in ensuring disease-free chili production with optimum yield. In detail, proper site selection, avoiding areas with a history of damping-off infection, ensuring good drainage, applying organic amendments to enhance soil quality, adopting the best cropping systems, and using healthy seeds are best cultural practices to avoid damping-off disease (Magnee et al., 2022). Further measures include infected plant parts being removed as soon as possible from the fields (Manjunatha et al., 2022), timely and adequate fertilizing, irrigation, mulching to regulate soil temperature and suppress weeds, implementation strategies to protect crops from pests and diseases, sterilization through solarization or seed treatment (Arora et al., 2022), cover cropping, green manuring, crop rotation, tillage, and managing proper space between crops (Moura et al., 2022). Soil physiochemical properties management, such as pH, CEC, and moisture, is also important. Combining these practices is the most effective approach to managing damping-off disease in chili crops (Cook and Haglund, 1991; Cook, 2001). Furthermore, enhancing seed vigor is crucial for controlling damping-off, even in high pathogen density (Lamichhane et al., 2017).

The utilization of botanical extracts presents a highly promising approach for managing chili damping-off disease caused by Pythium spp. Plant extracts, including neem, garlic, ginger, turmeric, lemon, and pepper, have been shown to possess inherent antifungal properties. Consequently, these botanical extracts can be a viable and eco-friendly substitute (Postma et al., 2003) for conventional chemical fungicides (Islam and Faruq, 2012; Hyder et al., 2021; Arora et al., 2022). However, it is essential to recognize that the effectiveness of botanicals can show variability dependent upon the particular plant species, the specific plant part used, and the method that was used for extraction (Arora et al., 2022). Moreover, the utilization of plant growth-promoting rhizobacteria (PGPR) in disease management endeavors shows promising results in the biocontrol of Pythium spp., as well as their positive impact on promoting the growth of solanaceous crops (Kenawy et al., 2019), and many other major crop varieties. In many cases, it has been properly noted that imported bioformulations occasionally exhibit suboptimal performance owing to the influence of climate change (Compant et al., 2010) and limitations in nutrient availability (Kandeler et al., 2006). Therefore, the detection and characterization of PGPR endemic to chili rhizospheres capable of suppressing the inoculum of P. myriotylum and enhancing the growth of chilies in nurseries is in need.

Trichoderma, a prominent genus of filamentous fungi within the phylum Ascomycota, demonstrates remarkable potential as a biocontrol agent (BCA) against Pythium pathogens (Thambugala et al., 2020; Yao et al., 2023). These beneficial fungi, particularly the avirulent strains, have proven effective in plant protection, biostimulation, and biofertilization. Their effectiveness in agricultural applications depends on their metabolic activity and interactions with plants and other microorganisms.

Trichoderma species can colonize the rhizoplane and plant roots (Poveda and Eugui, 2022). They produce an array of metabolites with antimicrobial properties, including cell wall-degrading enzymes, both volatile and non-volatile antibiotics (Jayaraj et al., 2006), as well as phytohormones and phytoregulators such as Indole Acetic Acid (IAA), cytokinin and ethylene that stimulate plant growth indirectly (Rahman et al., 2012). They also secrete chitinase, which enhances plant defense mechanisms (Subash et al., 2013) against fungal pathogens, and 1–3 glucanase, a protease contributing to fungal pathogen defense and improved nutrient supply (Mannai and Boughalleb-M’Hamdi, 2023). Conversely, Trichoderma stimulates plant resistance locally or systemically by releasing products known as elicitors (Majeed et al., 2019). These elicitors originate from the cell walls of both the host plant (endoelicitors) and the invading microorganism (exoelicitors). Pythium acidifies soil by secreting organic acids that can solubilize phosphate and other micronutrients supporting plant nutrition (Rahman et al., 2012).

Notably, Trichoderma can control Pythium spp. through mechanisms such as necrotrophic mycoparasitism, competition for nutrients and space, and the synthesis of antifungal metabolites (Tyśkiewicz et al., 2022). These fungi exhibit rapid growth, metabolic versatility, and resistance to various toxic chemicals, including fungicides and herbicides, as adaptations (El Enshasy et al., 2020; Jia et al., 2024; Yang et al., 2024).

Among Trichoderma species, T. harzianum strains stand out for their ability to protect plants by antagonizing Pythium pathogens in damping-off (Muthukumar et al., 2011b), showing more promising performance than T. viridae, B. subtilis, and T. asperellum, which exhibit synergistic effects against P. aphanidermatum in solanaceous crops (Kipngeno et al., 2015). Peroxidase activity was significantly higher in the roots of sugar beet seedlings treated with T. virens as biocontrol agents (Hanson and Howell, 2004).

Pseudomonas fluorescens is a beneficial bacterium widely used as a biocontrol agent against damping-off disease in chili via antibiosis, siderophore production, competition, induced systemic resistance, and enzyme production against damping-off disease in chili (Mehmood et al., 2023). Bacterial species such as Bacillus have been proven to control fungal diseases. B. subtilis showed high antagonistic activity against Colletotrichum gloeosporioides, which caused anthracnose disease of chili (Ashwini and Srividya, 2014). Bacillus has chitinolytic activity to control different fungal pathogens. Chitinolytic is a pathogenesis-related protein that increases the plant’s defense mechanism against fungal pathogens (Mabuchi et al., 2000; Huang et al., 2005). Bacillus species were found to colonize the root surface, increase plant growth, and cause the lysis of fungal mycelia (El-Bendary et al., 2016). As shown in previous reports, Bacillus spp. significantly control the damping-off chili caused by P. myriotylum (Jimtha et al., 2016). Similar results from Hyder et al. (2021) showed that B. cereus and B. megaterium significantly control damping off disease (Hyder et al., 2021).

Recent advances in plant breeding have significantly improved efforts to develop resistant chili cultivars to combat biotic and abiotic stresses. Marker-assisted selection (MAS) has accelerated the identification and incorporation of resistance genes into new cultivars, allowing breeders to develop varieties resistant to diseases such as powdery mildew, anthracnose, bacterial wilt, and viral diseases. Quantitative trait loci (QTL) mapping has been crucial in identifying resistance traits linked to these pathogens. Additionally, genomic selection and CRISPR-Cas9 gene editing technologies are revolutionizing breeding by enabling the precise modification of specific genes responsible for resistance. Traditional methods like germplasm screening and hybridization remain integral, but these are now supplemented with advanced genomic tools to improve efficiency and precision.

Host plants have evolved complex defense mechanisms that can either activate or suppress a range of genes when under attack by pathogens (Kumar et al., 2022). These induced resistance responses include various physiological processes such as the generation of reactive oxygen species, synthesis of phytohormones, and production of pathogenesis-related (PR) proteins. The utilization of host plant resistance as a management strategy encompasses two distinct approaches: (i) the utilization of plant varieties that possess resistance to pathogens, resulting in reduced pathogen populations or enhanced ability to resist pathogen-induced damage, and (ii) the integration of these resistant varieties with other management tactics as part of an integrated pest management (IPM) framework. However, a significant number of plant diseases, especially those responsible for damping-off diseases, lack any plant cultivar that exhibits quantifiable resistance (Babadoost and Islam, 2003). As a result, the optimal utilization of crop varieties possessing pathogen resistance can only be achieved by effectively integrating them with other strategies for disease management. However, there has been a lack of emphasis on incorporating plant resistance into other IPM strategies and a lack of research on quantifying the benefits of plant resistance within IPM programs that utilize various approaches (Davis, 2009).

The current breeding methodology employed thus far for the development of crop varieties that exhibit resistance should be reevaluated if the intent is to prioritize sustainable crop protection strategies based on IPM. This is especially valid because the majority of cultivated plant varieties developed thus far have been rooted in a market-oriented strategy emphasizing the cultivation of high-yielding and economically advantageous crop varieties. The current tendency has resulted in increased utilization of short rotations or monoculture methods while neglecting the potential benefits that minor crops may offer for IPM (Messéan et al., 2016). Crop diversification is hindered by the limited range of minor crop types, which limits beneficial activities like multiple cropping and intercropping (Benvenuto et al., 2020). Hence, in light of the pivotal role of breeding in enhancing crop competitiveness and facilitating adaptation to diverse cropping systems, it is imperative to use a distinct approach for breeding in IPM compared to conventional methods (Benvenuto et al., 2020). Detailed information about management strategies is described in Table 4.

Even though chemical fungicides are effective in rapidly controlling damping-off, they lead to human and ecotoxicity, particularly in developing nations (Voorrips et al., 2004). Human toxicity includes irritant dermal injuries, mucus membranes, and dermal sensitization. For animals, livestock poisoning and aquatic organisms, particularly fish, experience adverse impacts from fungicides. Furthermore, fungicides reduce the fungal and total microbial biomass in soil (Verdenelli et al., 2023), influencing the imbalance in soil microbiota, and another detrimental effect is phytotoxicity by fungicide residues (Kovačič et al., 2013). Different fungicides have different modes of action and differ in how long they last to suppress disease. At the same time, fungicide resistance occurs with the longer usage of the same fungicide type. For a greater chance of enhanced disease protection in the fields, it is strongly advised to rotate two or more distinct classes of fungicides to prevent the development of fungicide-resistant pathogens (Förster et al., 2007). It is hard to achieve sustainable disease management by using fungicides alone. Hence, the need for integrated disease management is discussed.

Recent advances in the molecular understanding of damping-off diseases have significantly enhanced detection and management strategies. Molecular diagnostics, such as polymerase chain reaction (PCR) and quantitative PCR (qPCR), now allow for rapid and precise identification of soil-borne pathogens like Pythium, Fusarium, and Rhizoctonia at early stages of infection. These techniques enable species-level identification and quantification of pathogen load in soil and plant tissues, which can help predict disease outbreaks. The advent of metagenomics and next-generation sequencing (NGS) has further revolutionized detection by allowing a comprehensive analysis of microbial communities, identifying emerging pathogens, and understanding the microbial shifts that occur during disease progression (Fu et al., 2024).

On the management side, molecular advances have improved the use of biological control agents and the development of resistant cultivars. Functional genomics, through tools like RNA interference (RNAi) and CRISPR-Cas9, is used to knock out or modify plant susceptibility genes, providing a novel method for increasing disease resistance. Furthermore, insights into the molecular interactions between pathogens and biocontrol agents, such as Trichoderma and Pseudomonas fluorescens, have led to enhanced formulations that can better suppress pathogen activity through targeted modes of action, such as mycoparasitism and antibiosis. These advances highlight the critical role of molecular tools in both early detection and integrated management approaches, offering a promising future for sustainable control of damping-off diseases.

The challenge of damping off disease remains as critical as ever, especially with its large-scale spread exacerbated by flooding and climate change. Despite extensive research on the epidemic nature of the disease, gaps still persist in our understanding of host–pathogen interactions, disease proliferation, and effective management strategies.

There is an urgent need to devise efficient integrated management strategies that consider the increasing incidence of flooding, environmental factors, and the variability of pathogenic races. Developing resistant varieties of chili appears to be one of the most promising approaches for the long-term management of damping-off disease. By breeding for resistance, we can reduce the vulnerability of crops to this disease under various environmental conditions.

In addition to developing resistant varieties, integrating cultural practices tailored to specific climatic changes is crucial for more effective disease management. As the climate continues to change, previously effective strategies may need to be adapted to remain effective under new conditions. Furthermore, there is a growing need for more molecular studies to deepen our understanding of plant–microbe interactions. Insights into the infection mechanisms of pathogens will be invaluable for creating targeted management strategies that can interrupt the infection process and mitigate the disease’s impact.

Additionally, our laboratory is exploring the potential of nanoparticles as a novel approach to combat Pythium spp. Nanoparticles represent an innovative frontier in managing damping-off disease in chili. These microscopic particles could offer new mechanisms of action against the pathogen, potentially enhancing the effectiveness of existing treatments or providing alternative management solutions. As this research advances, it could open new pathways for controlling this persistent and damaging disease.