Rice (Oryza sativa L.) is an economically important food crop in many developing countries, particularly, in the South Asian region. Approximately 50% of total agricultural land in South Asia is covered by rice-based cropping system. Rice is one of the most important staple food crops in India and many other countries in Asia. The yield potential of rice is severely affected by many biotic stresses, especially by diseases such as bakanae, rice blast, bacterial leaf blight (BLB), sheath blight, and brown spot are important diseases in rice-growing areas of the world (Imfeld and Vuilleumier, 2012; Tanwar et al., 2016). Yield loss due to diseases in rice can be 10–15% in tropical Asia (Savary et al., 2012b). Yield loss to individual disease may vary depending on geographic location and environmental conditions. For example, rice blast can cause yield loss of up to 50% (Asibi et al., 2019), bakanae diseases (13.8%) (Tanwar et al., 2016), sheath blight (50%) (Khoshkdaman et al., 2021) that depends on varietal susceptibility, the degree of infection, and the timing of fungicide application (Oerke, 2006).

Integrated pest management (IPM) is a holistic approach to disease management that emphasizes the use of multiple strategies to manage pest populations in an effective and environmentally sensitive manner (Chatterjee et al., 2021; Hajjar et al., 2023). Integrated management of rice diseases can improve yield by 10–20% of current harvested yield (Savary et al., 2012a). Unlike traditional pest control methods that may rely heavily on chemical pesticides, IPM incorporates a variety of techniques such as biological control, habitat manipulation, modification of cultural practices, and the use of resistant varieties (Veres et al., 2020; Zhang et al., 2022). The goal of IPM is to reduce or eliminate the use of chemical pesticides, thereby minimizing the potential negative impacts on human health, non-target organisms and the environment.

IPM operates on the principle of employing the least possible hazard to human health and the environment, focusing on the long-term prevention of pests or their damage through a combination of tactics (Singh, 2019). Monitoring and correct pest identification are the cornerstones of IPM, ensuring that any actions taken are based on the actual presence of pests and their potential threat to the crop or environment. Biological control, one of the key strategies in IPM, involves the use of bioagents and natural enemies of pests to control pest population (Babendreier et al., 2020; Veres et al., 2020; Chatterjee et al., 2021).

In India, farmers are mostly dependent on the advice of pesticide dealers and usually take 4–6 sprays of pesticides including a tank mix cocktail of pesticides (Tanwar et al., 2016). Excessive uses of pesticides have adverse effects on the environment which reduces the biodiversity of natural enemies and leads to environmental pollution, development of pesticide resistance, resurgence of pest population, and human health hazards (Avis et al., 2008; Imfeld and Vuilleumier, 2012). To get rid of this menace, some new avenues must be investigated. One of the effective ways is to develop eco-friendly, sustainable, and socio-economic acceptable IPM packages (Tanwar et al., 2016).

Biological control is the most important component of integrated pest management strategy (Khatoon et al., 2020; Somasundaram et al., 2020; Harman et al., 2021). Biological control aims to use natural enemies to regulate pest populations to a level where they do not cause yield loss (Ferreira and Musumeci, 2021; Ansari et al., 2023). However, there is a need for more optimal use of biological control at national and international levels. Technical knowledge and skills concerning the production and sustainable utilization of biocontrol or biopesticides in Asia are still inadequate to warrant its widespread adoption. However, the Indian Council of Agricultural Research (ICAR)-National Research Centre for Integrated Pest Management in New Delhi has already developed IPM packages against several destructive pests of various crops, including rice, with an emphasis on mass trapping with pheromones, the use of botanical and biopesticides, pest-resistant crop varieties, and modification of agronomic practices to reduce pest incidence (Tanwar et al., 2016; Sardana et al., 2020).

Normally, biological control tactics use single isolated microbes, such as Trichoderma, Pseudomonas, Bacillus, and Streptomyces (Kumar and Ashraf, 2017). However, the potential of microbial biological control always depends on significant knowledge of microbial ecology in the rhizosphere (Martínez-Viveros et al., 2010; Araujo et al., 2019). Microbials suppress pathogens in the rhizosphere through a variety mechanisms, including antibiosis, competition for nutrients, parasitism, and biosynthesis of microbial compounds that inhibit pathogens in the field and express beneficial traits (Compant et al., 2019; de Faria et al., 2021).

The application of bioagents affects the survival and carry-over of microbial pathogens from one crop to another (Berendsen et al., 2012). To improve plant growth and soil health, it is important to know the microorganism present in the rhizosphere microbiome and as its function and purpose. Information on the interaction of soil microbial pathogens with Trichoderma/Pseudomonas and the appearance of diseases, nematodes, and insect pests in the plants is scanty. There is a need to understand the relationship between disease development and inoculum densities, their antagonistic activity and disease dynamics in the field or laboratory to achieve efficient crop protection in rice-based cropping systems.

Rice cultivation encompasses two primary methods: direct-seeded rice (DSR) and transplanted rice (TR). In DSR, rice seeds are directly sown into the field without prior germination in a nursery bed (Farooq et al., 2011). This method offers advantages such as water conservation, reduced labor, and time efficiency, making it particularly suitable for areas with water scarcity. However, direct-seeded rice is susceptible to diseases such as sheath blight, blast, bacterial leaf blight, and tungro disease (Hufnagel et al., 2020). On the other hand, transplanted rice involves raising rice seedlings in nurseries before transplanting them into the main field after a few weeks of growth. This method allows for better weed control, reduces competition among plants, and ensures uniform crop establishment (Rao et al., 2007; Khaliq et al., 2012). If unchecked, the loss due to weed infestation can be as high as 80% in DSR (Matloob et al., 2015). Despite these advantages, transplanted rice is also vulnerable to diseases such as sheath blight, blast, bacterial leaf blight, brown spot and sheath rot (Rao et al., 2007; Chaudhary et al., 2023).

Rice IPM studies are crucial to address the pressing need for sustainable agriculture practices that can enhance food security while minimizing environmental impacts. By focusing on the relationship between microbial populations, disease development, and soil physicochemical properties under IPM, researchers can identify strategies that promote crop health and yield without relying heavily on chemical inputs (Ganie et al., 2021; Ngalimat et al., 2021; Hajjar et al., 2023). IPM research contributes to the development of eco-friendly pest management practices, reduces the reliance on synthetic pesticides, and helps in maintaining or improving soil health. This, in turn, supports biodiversity, enhances the resilience of cropping systems to diseases, and can lead to more sustainable agricultural productivity (Siegel-Hertz et al., 2018). Through a better understanding of IPM’s effects, stakeholders can implement IPM practices that are not only economically viable but also environmentally safe, ensuring the long-term sustainability of agricultural ecosystems.

To explore the role of antagonist microbial populations in soil in relation to diseases in IPM, we conducted a study with the following objectives: (i) monitor the density of Trichoderma harzianum, Pseudomonas fluorescens, and Fusarium verticillioides in soil as influenced by IPM interventions in DSR and TR; (ii) determine relationships between microbes density and disease incidence; (iii) perform socio-economic studies, and (iv) investigate the effect of IPM and non-IPM practices on soil physiochemical properties in TR and DSR.

This is probably the first study that describes the relationships between the microbial inoculum density and disease incidence and the effect of IPM interventions on the soil population of T. harzianum, P. fluorescens, and F. verticillioides in DSR and TR at farmers’ fields at three locations in major rice-wheat growing region of India. Information on this is crucial for the assessment of disease risk and the development of an integrated disease management module.

Soil sample analysis of three locations, two in TR and one in DSR during 2017–2019 in rice crop, indicated significantly higher population of antagonistic fungi, T. harzianum, and antagonistic bacteria, P. fluorescence, in IPM compared to non-IPM fields. Maximum population density of T. harzianum and P. fluorescence was observed in mid-season in August–September months (2017–2019). At the time of sowing and transplanting of the rice seedlings, the count of T. harzianum was low in both TR and DSR locations, and the population of T. harzianum increased till the flowering stage (August–September). Higher population of T. harzianum was recorded in August–September during flowering coinciding with changes from vegetative to reproductive phase due to changes in exudation pattern. The present investigation recorded an increase in the population of T. harzianum and P. fluorescens with increasing plant age up to August–September which was possibly due to the creation of spermosphere at the initial growth period and subsequently changed the rhizosphere in the growing phase of the crop (Larkin et al., 2011; Larkin and Tavantzis, 2013).

The microbial population of P. fluorescence before transplanting was high in IPM at Bambawad and Haridwar compared to non-IPM fields. However, during the mid-crop season, the trend reversed, with CFU recorded higher in non-IPM compared to IPM at Bambawad and Haridwar in TR, while the microbial density of P. fluorescens was higher in DSR at the time of sowing at Karnal. The present study indicated that host plant, soil type, agroecology, microclimate, and soil microbial communities had a combined effect on the diversity of fluorescent pseudomonads which induced population build-up. In future studies, use of a dual consortium of bioagents may be used for better disease management in agroecosystems (Sarkar and Rakshit, 2021, 2023).

In the present study, the abundance of inoculum density of T. harzianum and P. fluorescens was affected by crop management practices in all 3 years. Earlier researchers showed that indigenous T. harzianum species were known to have a greater tolerance for pesticides than other soil microorganisms (Bonanomi et al., 2010). In our study, the inoculum density of T. harzianum and P. fluorescens was found higher in fields under IPM than non-IPM during 2017–2019, which might be due to the different management practices in conventional farms due to the application of fungicides and synthetic fertilizers. In this perspective, the dynamics of beneficial microbial communities can be strongly influenced by soil interactions, agricultural management practices, and moisture (Mavrodi et al., 2018).

In the present study, the population density of F. verticillioides was higher in non-IPM fields compared to IPM in all three locations. Present findings are in line with the earlier findings in various cropping systems (Pullman, 1982; Harris et al., 1993; Mendes et al., 2011; Bhatt et al., 2012). For disease management, it is desirable to reduce pathogen inoculum density to a desired low level. The information generated from this study would help to decide on the nature of disease management strategies for rice crops in both TR and DSR systems. In general, an increase in CFU counts of both tested bioagents T. harzianum and P. fluorescens was recorded over the years. DSR recorded a 9.2% reduction in F. verticillioides population in IPM over the years. Interestingly in non-IPM, the F. verticillioides population also decreased significantly, which may be due to the high number of pesticide applications in non-IPM fields compared to IPM fields.

During the 3 years of this study, the disease spectrum was not uniform and did not follow a specific trend. Bakanae and BLB in Bambawad, BLB, sheath blight, and bakanae in Haridwar, and brown spot in Karnal were the major diseases recorded during the period. In general, lower disease incidence was reported in IPM in comparison with non-IPM fields. Increased disease severity in non-IPM fields may be associated with increased nitrogen fertilization and dense canopy, while regular addition of organic amendments and biocontrol agents might have led to induced disease suppression in IPM fields (Bulluck and Ristaino, 2002; Davis et al., 2010). Trichoderma and Pseudomonas not only promote plant growth and development (Wintermans et al., 2016) but also prevent the colonization of plant pathogens and induce plant defense resistance to biotic and abiotic stresses (Rais et al., 2016; de Faria et al., 2021; Kaur et al., 2022).

Our study demonstrated that the incidence of rice diseases in DSR and TR decreased, whereas the population of antagonistic T. harzianum and P. fluorescens increased in IPM fields. However, the population of T. harzianum and P. fluorescens was not directly correlated with disease suppressiveness in all diseases. As previously reported, the incidence of southern blight in maize has decreased (Longa et al., 2009; Larkin et al., 2011). A strong and weak correlation between inoculum density and disease incidence in our study under field conditions reflects combined effect of hosts, cultural practices, soil type, environmental conditions, host resistance, and virulence variation of pathogenic isolates prevailing in the soil. A similar type of results was also reported earlier (Joaquim, 1991; Harris et al., 1993; Weller et al., 2002). In the present study, linear regression analysis between inoculum density and disease development gave both positive and negative correlations in TR and DSR.

Soil pH was reduced in both IPM and non-IPM fields studied at three locations (0.71 in Bambawad, 0.50 at Haridwar, and 0.04 in Karnal). EC of the soil suggested that in all three locations, soil was non-saline and was suited for rice cultivation. It was observed that organic carbon increased in IPM and non-IPM fields at all the locations. Improvement of macronutrients (K) and micronutrient Zn was observed over the years in IPM fields at Bambawad and Haridwar. Available N in soil improved significantly in both IPM and non-IPM fields which might have increased the incidence of foliar diseases such as BLB, brown spot, and sheath blight. In IPM, Sesbania rostrata was applied as green manure leading to increased microbial activity and organic “C” content and decreased pH and EC of soil which also might have favored increase in propagules of T. harzianum and P. fluorescens in IPM fields and possibly responsible for the low incidence of diseases in IPM fields. Availability of macronutrients such as N, P, and K were significantly influenced by agriculture practices (Jat et al., 2018; Zhang et al., 2018; Sithole and Magwaza, 2019), which corroborates higher N, P, and K observed during the present study under both IPM and non-IPM fields. Soil properties such as soil organic carbon, macronutrients (N and K), and micronutrients (Zn and Mn) were the important variables that significantly influenced the structure and distribution of microbes. The use of green manuring, organic amendments, biocontrol agents, and need-based application of pesticides in IPM fields influenced the availability of several plant nutrients that improved the physical and chemical conditions of the soil in wetland rice (Tilak, 2004). Our results also corroborate with the findings of Singh (2019), who suggested application of IPM inputs over the years not only improves the soil health and fertility but also helps to manage the rice root-knot nematode, M. graminicola.

In our study, socio-economic studies conducted at Bambawad indicated higher yield as well as benefit–cost ratio in IPM compared to non-IPM in TR and DSR. It is mainly due to good agriculture practices and reduction in number of pesticides in IPM. A similar trend of higher yield and B-C ratio in IPM as compared to non-IPM was also observed at Haridwar and Karnal. In all the IPM trials conducted from 2017 to 2019, net return remained higher as compared to non-IPM at all three locations. It is evident from the economic point of view that the application of bioagents along with the adoption of the IPM package resulted in a significant reduction in the disease incidence in IPM fields compared to non-IPM. Green manuring in IPM has favored the availability of nutrients along with N to the crop, which helped in reducing the application of additional N, which could be one of the factors responsible for the low incidence of diseases in IPM fields. This principle could be useful in integrated disease management strategies of many soil-borne pathogens, the incidence of which is dependent on the initial inoculum density.

This study highlighted the benefits of IPM interventions on soil physicochemical properties and microbial communities. Density of T. harzianum and P. fluorescens was higher in IPM during 2017–2019, while the inoculum density of F. verticillioides was higher in non-IPM fields. Both significant positive and negative correlations were observed between disease incidence and pathogen inoculum density of T. harzianum, P. fluorescens, and F. verticillioides. Increased levels of soil organic carbon in IPM fields contributed toward good soil health. Socio-economic studies indicated higher yield and benefit–cost ratio in IPM compared to non-IPM. The present study would provide a better understanding of both beneficial microbes and pathogens that could provide a basis for disease risk assessment and the development of biological control strategies for the management of rice diseases. In future, there should be IPM experiments with single bioagent and consortium applications of diseases suppressing agents to explore their effect in disease management.

The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

MK: Writing – review & editing, Writing – original draft, Visualization, Validation, Supervision, Software, Resources, Project administration, Methodology, Investigation, Funding acquisition, Formal analysis, Data curation, Conceptualization. RK: Writing – review & editing, Visualization, Validation, Supervision, Software, Resources, Project administration, Methodology, Investigation, Funding acquisition, Formal analysis, Data curation, Conceptualization. AK: Writing – original draft, Visualization, Validation, Supervision, Software, Resources, Project administration, Methodology, Funding acquisition, Formal analysis, Data curation, Conceptualization. MS: Writing – review & editing, Supervision, Investigation. SS: Writing – original draft, Conceptualization. PM: Writing – original draft, Funding acquisition, Formal analysis, Data curation, Conceptualization. NS: Writing – original draft, Project administration, Methodology, Investigation. LA: Writing – review & editing, Writing – original draft, Investigation. AB: Writing – review & editing, Writing – original draft. KS: Writing – review & editing. RB: Writing – review & editing. MG: Writing – review & editing. SC: Writing – review & editing. MC: Writing – original draft, Visualization, Validation, Supervision, Software, Resources, Project administration, Methodology, Investigation, Funding acquisition, Formal analysis, Data curation, Conceptualization, Writing – review & editing.