ABSTRACT

The use of microbial consortia as biofertilizers and biofungicides has received increasing attention in Indonesia as a sustainable alternative to improve agricultural productivity while reducing dependence on chemical inputs. Compared with single microbial inoculants, microbial consortia offer complementary biological functions that enhance nutrient availability, suppress plant pathogens, and improve plant resilience under diverse environmental conditions. This review summarizes the current development of microbial consortia for biofertilizer and biofungicide applications in Indonesia, emphasizing their concepts, microbial interactions, field applications, challenges, and future opportunities. The reviewed literature indicates that microbial consortia can improve plant growth, nutrient use efficiency, soil health, and tolerance to biotic and abiotic stresses through synergistic interactions among microorganisms. Nevertheless, several factors influence their effectiveness in the field, including formulation quality, microbial viability, strain compatibility, environmental variability, application methods, and product standardization. Indonesia has significant opportunities to develop microbial consortia based on indigenous strains, supported by high microbial biodiversity, advances in formulation technology, sustainable agricultural practices, and government policies promoting biofertilizer use. Future research should prioritize exploring indigenous microorganisms, developing stable formulations, establishing quality standards, and commercializing locally adapted microbial products to support sustainable agricultural development in Indonesia.

Keywords: formulation; indigenous microorganisms; plant growth-promoting rhizobacteria; rhizosphere; sustainability

INTRODUCTION

Indonesian agriculture faces significant challenges in maintaining productivity amid soil degradation, declining land quality, and heavy reliance on chemical fertilizers and pesticides. This has reduced soil fertility, disrupted soil microbial communities, and lowered nutrient use efficiency, affecting the long-term sustainability of crop production. Microorganism-based biofertilizers and biofungicides have emerged as a promising alternative because they can enhance nutrient availability, stimulate plant growth, suppress plant pathogens, and improve plant tolerance to environmental stresses (Backer et al., 2018). Studies in Indonesia have shown that biofertilizers based on plant growth-promoting rhizobacteria (PGPR) can enhance plant growth, nutrient uptake, and rice yield (Aryanto et al., 2015; Purwanto & Suharti, 2021). PGPR use has also been reported to improve rhizosphere quality and nutrient use efficiency, thereby contributing to sustainable agricultural productivity (Harahap et al., 2022).

The effectiveness of single-strain inoculants often becomes inconsistent under field conditions. Variations in soil physicochemical properties, microclimatic conditions, and interactions with indigenous microbial communities influence the ability of inoculated strains to survive, colonize, and perform their biological functions effectively. Several studies in Indonesia have reported that microbial consortia improve nutrient use efficiency, plant growth, and crop yield more consistently than single-strain inoculants under different cultivation conditions (Amanda et al. 2018; Purwanto & Suharti, 2021). These limitations have driven the development of microbial consortia, which combine multiple microorganisms with complementary functions to enhance the stability and effectiveness of bioinoculants across diverse agroecosystems (Negi et al., 2024). Synergistic interactions among bacteria and fungi promote nutrient availability, phytohormone production, pathogen suppression, and improved plant tolerance to both biotic and abiotic stresses (Rios-Ruiz et al., 2021).

Research on microbial consortia in Indonesia has expanded alongside growing exploration of indigenous microorganisms well adapted to tropical soil conditions. Local Trichoderma isolates have demonstrated considerable potential as both plant growth-promoting and biological control agents across a range of agroecosystems (Akbari et al., 2024). The development of bacterial–fungal consortia, such as Bacillus spp. and Trichoderma spp., has also been reported to enhance plant growth while suppressing bacterial leaf blight in rice more effectively than single-microbe inoculation (Permata et al., 2025). These findings suggest that microbial consortia represent a promising approach for supporting sustainable agriculture in Indonesia. However, information on the diversity, synergistic mechanisms, and field performance of consortia across Indonesian agroecosystems remains scattered. Therefore, this review summarizes the diversity of microbial consortia used as biofertilizers and biofungicides in Indonesia, discusses the synergistic mechanisms underlying their effectiveness, evaluates their performance across different Indonesian agroecosystems, and identifies future challenges and opportunities for their development to support the implementation of climate-smart agriculture.

METHODOLOGY

This review was conducted by systematically collecting literature on microbial consortia in biofertilizers and biofungicides, with a primary emphasis on studies conducted in Indonesia. Sources included Indonesian journals indexed in SINTA, Garuda, and Neliti, as well as proceedings, government reports, and relevant international publications. Inclusion criteria required studies conducted in Indonesia between 2010 and 2025 or international studies providing fundamental concepts focusing on microbial consortia (bacteria and fungi or multi-strain formulations) with applications in agriculture, forestry, peatlands, or post-mining lands. Studies unrelated to microbial consortia or to Indonesian agroecosystems were excluded. More than 45 publications were synthesized into thematic sections.

OVERVIEW OF MICROBIAL CONSORTIA

Definition and concept of microbial consortia

Microbial consortia are combinations of two or more microorganisms designed to function synergistically to promote plant growth and suppress plant pathogens (Santoyo et al., 2021). They commonly consist of PGPR, nitrogen-fixing bacteria, phosphate-solubilizing bacteria, nutrient-solubilizing fungi, and antagonistic fungi with complementary mechanisms of action (Singh et al. 2023). Their success depends not only on the diversity of constituent microorganisms but also on strain compatibility, the ability to colonize the rhizosphere, and formulation stability during storage and field application. In Indonesia, genera such as Bacillus, Pseudomonas, Trichoderma, and Aspergillus have been widely incorporated into microbial consortia to enhance plant growth while strengthening the functions of biofertilizers and biofungicides (Tyasmoro et al. 2024). Trichoderma has particularly gained increasing attention because, in addition to its role as a biological control agent, it improves nutrient uptake efficiency and stimulates root system development (Doo et al., 2023).

Advantages of microbial consortia over single-strain inoculants

Single-strain inoculants often perform well under controlled conditions, but their performance may decline in the field because of competition with indigenous soil microorganisms and environmental variability (Nunes et al., 2024). Microbial consortia have been developed to overcome these limitations through synergistic interactions among consortium members (Singh et al., 2023). Combining multiple microorganisms enables nitrogen fixation, phosphate solubilization, phytohormone production, and pathogen suppression accur simultaneously (Sahlan et al., 2023). Their diverse physiological characteristics also contribute to greater ecological stability, enabling them to better withstand environmental fluctuations than single-strain inoculants (Nunes et al., 2024). These benefits may be further enhanced by using indigenous strains, which are considered well adapted to the tropical soil conditions of Indonesian agroecosystems (Doo et al., 2023). Through these complementary functions, microbial consortia can serve as both biofertilizers, by improving nutrient availability, and biofungicides, by suppressing pathogen development and enhancing plant tolerance to environmental stresses (Singh et al., 2023).

Common types of microbial consortia used in Indonesia

Studies on microbial consortia in Indonesia indicate that consortium composition is generally designed according to the desired biological functions. One common approach combines PGPR with antagonistic fungi, particularly Trichoderma spp., to promote plant growth and suppress diseases, as demonstrated by reduced downy mildew severity in sweet corn (Purwanti et al., 2023). Other formulations combine bacteria with phosphate-solubilizing fungi or integrate nitrogen fixation, phosphate solubilization, phytohormone production, and organic matter decomposition into multifunctional consortia (Tyasmoro et al., 2024). The use of indigenous isolates is also gaining attention because of their potential to adapt better to Indonesian agroecosystems (Doo et al., 2023).

Trends in microbial consortium development in Indonesia

Research on microbial consortia in Indonesia has shifted from exploring single microbial isolates to developing multifunctional formulations better adapted to field conditions (Nunes et al., 2024). Consortia are now effectively mainstream in the Indonesian product market because most registered biofertilizer and biofungicide products are consortium-based (Ministry of Agriculture 2026), although their uptake in routine farm practice remains limited by adoption barriers (Rafiudin et al., 2022). Current research increasingly addresses strain compatibility, formulation stability (Singh et al., 2023), and function-based consortium design (Doo et al., 2023).

MICROBIAL DIVERSITY

The microorganisms used in Indonesian biofertilizers and biofungicides reflect the rich biodiversity of tropical soils across irrigated rice fields, drylands, horticultural systems, plantations, peatlands, and post-mining areas. The distinct environmental characteristics of these agroecosystems support diverse microbial communities with different functional traits, making them valuable sources for developing biological agents adapted to local conditions (Harahap et al., 2022). Studies have shown that biofertilizer and biofungicide products in Indonesia are predominantly composed of PGPR and biocontrol fungi, particularly Bacillus, Pseudomonas, Azotobacter, Rhizobium, Burkholderia, Trichoderma, Penicillium, Aspergillus, and Beauveria which promote plant growth, improve soil fertility, and suppress pathogens (Pratiwi et al., 2020).

Dominant bacterial genera in indonesian products and research

Bacillus spp.

The genus Bacillus is the most widely used bacterial group in biofertilizer formulations in Indonesia because it can form endospores, allowing greater tolerance to environmental stress and prolonged storage. Species such as Bacillus subtilis, B. amyloliquefaciens, and B. megaterium promote plant growth through phytohormone production, phosphate solubilization, nitrogen fixation, and the synthesis of antimicrobial compounds that promote plant growth and suppress soil-borne pathogens (Backer et al., 2018). Pratiwi et al. (2020) reported that Bacillus isolates from Jambi’s peatlands could produce indole-3-acetic acid (IAA) and solubilize phosphate, indicating their potential for locally adapted biofertilizers.

Pseudomonas spp.

Pseudomonas, particularly P. fluorescens, is among the most extensively studied PGPR in horticultural and food crops. These bacteria produce siderophores, phytohormones, and antimicrobial metabolites that enhance nutrient uptake and suppress rhizosphere pathogens (Backer et al. 2018). Harahap et al. (2022) demonstrated that Indonesian Pseudomonas isolates have considerable potential to improve plant growth and increase rice productivity through plant growth promotion and improved rhizosphere health.

Azotobacter spp.

Azotobacter is a free-living nitrogen-fixing bacterium commonly found in Indonesian agricultural soils and plays an important role in increasing nitrogen availability for plants. It also produces exopolysaccharides and phytohormones that stimulate root development and plant growth. Hindersah et al. (2019) reported that Azotobacter inoculation enhanced soybean nodulation and biomass production, while Hindersah et al. (2017) found that exopolysaccharide-producing isolates improved nitrogen uptake and soybean growth across different soil types.

Rhizobium spp.

The genus Rhizobium forms symbiotic association with legumes through root nodule formation that facilitates biological nitrogen fixation. Its application in soybean and other leguminous crops has been widely adopted in Indonesia because it reduces the need for nitrogen fertilizers while improving crop productivity. Febriati and Rahayu (2019) demonstrated that Rhizobium inoculation combined with biochar enhanced soybean growth in calcareous soils, whereas Putri and Rahayu (2019) reported that the combination of Rhizobium, Azotobacter, and rice straw compost produced greater growth responses than single inoculation.

Burkholderia spp.

Burkholderia is another promising PGPR genus because it can solubilize phosphate, produce siderophores and phytohormones, and help suppress soil-borne pathogens (Backer et al., 2018). Although its use in commercial products remains more limited than that of Bacillus or Pseudomonas, PGPR possessing these functional traits can enhance plant growth by improving nutrient uptake and physiological performance. Cavite et al. (2021) reported that PGPR isolates capable of producing IAA, solubilizing phosphate, synthesizing siderophores, and expressing ACC deaminase activity significantly improved upland rice growth and yield, supporting the potential inclusion of Burkholderia in microbial consortium formulations.

Dominant fungal genera in Indonesian biofertilizers and biofungicides

Trichoderma spp.

Trichoderma is one of the most extensively used fungal genera in Indonesian biofungicides and biofertilizers. Its antagonistic activity against plant pathogens is mediated through mycoparasitism, competition for space and nutrients, and the production of hydrolytic enzymes and antimicrobial compounds. Several species also promote plant growth by stimulating root development and improving nutrient uptake efficiency. Purwantisari et al. (2021) demonstrated that indigenous Trichoderma harzianum isolates as biological control agents, while Doo et al. (2023) highlighted the broad potential of Trichoderma as components of biofertilizers and biofungicides due to their adaptability across diverse agroecosystems.

Aspergillus spp.

The genus Aspergillus can produce extracellular enzymes, accelerate organic matter decomposition, and enhance nutrient availability through phosphate solubilization. These characteristics make Aspergillus a promising component of multifunctional microbial consortia aimed at improving nutrient use efficiency. Hasanah and Sutarman (2023) reported that Aspergillus flavus isolates from marginal show potential as biofertilizer agents because of their plant growth-promoting properties. Furthermore, combining beneficial fungi such as Aspergillus and Trichoderma have shown potential for developing multifunctional microbial consortia to improve crop productivity (Sutarman et al., 2023).

Penicillium spp.

Penicillium is a rhizosphere-associated genus widely investigated for phospate solubilization, which achieves by secreting organic acids and phosphatase enzymes. Phosphate-solubilizing fungi, including Penicillium and Aspergillus, effectively convert insoluble phosphorus into plant-available forms, highlighting their potential for biofertilizer development (Alori et al., 2017; Surtiningsih et al., 2020). Its potential as a microbial input is supported by P. bilaii, the active ingredient of a commercial phosphate inoculant that produced modest maize yield gains of approximately 1.8% in replicated multi-site trials (Leggett et al., 2015). However, some Penicillium species produce mycotoxins, and introduced strains may affect non-target soil communities. Therefore, isolates should be identified to species level and screened for toxic metabolites, as demonstrated for P. bilaii (Savard et al., 1994), with preference given to indigenous, well-characterized strains that are registered before release.

Beauveria bassiana

Beauveria bassiana is widely recognized as an entomopathogenic fungus used as a biological insecticide for controlling insect pests. It has also been identified as an endophytic fungus that can colonize plant tissues and provide additional benefits to host plants. Hendra et al. (2023) reported that endophytic colonization of rice plants by B. bassiana reduced brown planthopper (Nilaparvata lugens) populations by increasing insect mortality and reducing fecundity. In addition, endophytic colonization by B. bassiana has also been shown to enhance the growth of common bean (Phaseolus vulgaris L.), suggesting its potential in multifunctional microbial consortia (Afandhi et al., 2019).

Indigenous Indonesian microorganisms: potential and adaptation

Indonesia possesses abundant indigenous microbial resources originating from diverse agroecosystems. Differences in soil properties, nutrient availability, and environmental pressures have resulted in microbial communities with habitat-specific adaptive traits (Singh et al., 2023). Irrigated rice fields harbor PGPR, including Bacillus, Azospirillum, Azotobacter, and Burkholderia, which contribute to nitrogen fixation, phosphate solubilization, and phytohormone production, thereby enhancing rice growth and yield (Cavite et al., 2021). In peatlands with acidic conditions and limited nutrient availability also support indigenous microorganisms with biofertilizer potential. For example, bacterial isolates from Jambi peatlands have demonstrated IAA production and phosphate solubilization (Pratiwi et al., 2020). Agroforestry systems support diverse microbial communities involved in organic matter decomposition, nutrient cycling, and nutrient mobilization (Alori et al., 2017). Post-mining lands harbor stress-tolerant microorganisms, including Pseudomonas and Bacillus with potential applications in land rehabilitation and ecological restoration (Singh et al., 2023). These habitat-specific adaptations make indigenous microorganisms valuable resources for developing biofertilizer and biofungicide consortia suited to tropical conditions.

Microbial profiles of registered products in the indonesian database

Database of registered biofertilizer and biofungicide products indicate that commercial formulations are predominantly composed of PGPR, particularly Bacillus, Pseudomonas, Azotobacter, Azospirillum, and Rhizobium. Most registered products employ consortium-based formulations that combine microorganisms with complementary biological functions. Bacillus is the most frequently recorded bacterial genus, including B. subtilis, B. megaterium, B. amyloliquefaciens, B. pumilus, and B. licheniformis, while Trichoderma is the dominant fungal genus, with Aspergillus and Penicillium appearing less frequently. Since 2018, multifunctional consortia containing three or more microbial species have become increasingly common, often combining bacteria and fungi, such as Bacillus-Trichoderma, Pseudomonas-Trichoderma, and Azotobacter-Aspergillus. Many products also incorporate indigenous strains isolated from Indonesian agroecosystems, including rice fields, horticultural systems, plantations, and marginal tropical lands, to improve adaptation to local conditions. However, viable microbial populations vary considerably, ranging from approximately 10⁴ to 10¹¹ CFU g⁻¹ or CFU mL⁻¹, highlighting the need for stronger standardization and quality control to ensure microbial viability and consistent field performance  (Ministry of Agriculture 2026).

MECHANISMS OF SYNERGY

The principal advantage of microbial consortia over single-isolate inoculants lies in synergistic interactions that allow nitrogen fixation, phosphate solubilization, phytohormone production, antimicrobial metabolite synthesis, and organic matter decomposition. These complementary interactions improve nutrient acquisition, plant growth, and tolerance to biotic and abiotic stresses (Singh et al. 2023). In Indonesia, microbial consortia development has increasingly focused on combining PGPR with beneficial fungi, particularly Trichoderma for dual functions as biofertilizers and biofungicides (Tyasmoro et al. 2024).

Nutrient acquisition mechanisms: N-fixation, P-solubilization, and K-mobilization

Nitrogen fixation

Nitrogen is a primary macronutrient limiting plant growth because plants cannot directly use atmospheric nitrogen (N₂). Within microbial consortia, nitrogen-fixing bacteria such as Azotobacter., Azospirillum, and Rhizobium. convert atmospheric nitrogen into ammonia through the nitrogenase enzyme, making it available for plant uptake (Backer et al. 2018). Husna et al. (2019) demonstrated that a Bacillus-based consortium also solubilized phosphate and produced IAA, promoting plant growth through multiple mechanisms.

Phosphate solubilization

Most phosphorus in tropical soils exists in insoluble forms bound to iron (Fe), aluminum (Al), or calcium (Ca). Phosphate-solubilizing microorganisms, including Bacillus, Pseudomonas, Aspergillus, and Penicillium, increase phosphorus availability by producing organic acids, protons, and phosphatase enzymes that release phosphorus into plant-available forms (Alori et al. 2017). Hutagaol et al. (2017) reported that indigenous phosphate-solubilizing fungi significantly increased phosphorus availability and uptake in rice, highlighting their potential as biofertilizer components. Within microbial consortia, bacteria and fungi with complementary phosphate-solubilizing mechanisms can act synergistically, resulting in more efficient phosphorus mobilization than single-microbe inoculants.

Potassium mobilization

Potassium is an essential macronutrient involved in enzyme activation, osmotic regulation, stomatal function, and plant tolerance to environmental stresses. Although tropical soils often contain abundant total potassium, much of it remains trapped within silicate minerals and is unavailable to plants. Several bacterial genera, particularly Bacillus, Paenibacillus, and Pseudomonas, mobilize potassium by producing organic acids, chelating compounds, and weathering minerals, thereby increasing potassium availability (Etesami et al. 2017). In microbial consortia, potassium mobilization complements nitrogen fixation and phosphate solubilization, collectively improving nutrient acquisition under diverse soil conditions.

Biocontrol mechanisms: antibiotics, lytic enzymes, and siderophores

Antibiotic and antimicrobial metabolite production

Bacteria such as Bacillus and Pseudomonas produce bioactive compounds including iturin, surfactin, fengycin, and pyoluteorin, which inhibit spore germination, mycelial growth, and the activity of soil-borne pathogens (Backer et al. 2018). Within microbial consortia, multiple antimicrobial-producing microorganisms broaden the spectrum of pathogen suppression and improve the stability of biological control. In addition, several Trichoderma strains function as mycoparasites and induce plant defense responses, thereby enhancing disease suppression (Maknunin et al. 2024).

Lytic enzyme production

Biocontrol activity is also mediated by hydrolytic enzymes, particularly chitinases, β-1,3-glucanases, and cellulases, which degrade fungal cell walls. Trichoderma is one of the most widely utilized antagonistic fungi because it produces diverse lytic enzymes while simultaneously exhibiting mycoparasitic activity against plant pathogens (Woo & Pepe 2018). In Indonesia, Trichoderma has been extensively developed as a biofungicide that also stimulates root growth and induces plants' systemic resistance (Doo et al. 2023).

Siderophore production

Siderophores are iron-chelating compounds produced by rhizosphere bacteria, particularly Pseudomonas and Bacillus, to improve iron acquisition. By sequestering Fe³⁺, siderophores reduce iron availability for pathogens, thereby limiting their growth and virulence (Backer et al. 2018). Siderophore production also facilitates the establishment of beneficial microbes in the rhizosphere and contributes to the plant health. Within microbial consortia, siderophore-mediated competition complements antibiotic production and lytic enzyme activity, resulting in more stable biological control than single-agent applications (Singh et al. 2023).

Mechanisms enhancing plant stress tolerance

Drought tolerance

Drought stress impairs plant growth by reducing water uptake, photosynthesis, and hormonal balance. Many PGPR enhance drought tolerance by producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which lowers stress-induced ethylene levels and promotes root development (Vurukonda et al. 2016). Some microorganisms within microbial consortia also produce extracellular polymeric substances (EPS), which help retain moisture around the root zone. Together, these complementary mechanisms enable microbial consortia to provide more stable drought tolerance than single-strain inoculants (Singh et al. 2023).

Salinity tolerance

Salinity imposes osmotic stress and ion toxicity that severely restrict plant growth and productivity. Beneficial microorganisms improve plant tolerance through phytohormone production, enhanced antioxidant enzyme activity, osmoprotectant synthesis, and regulation of ionic balance (Etesami & Beattie 2018). In microbial consortia, these complementary mechanisms can improve root growth and water uptake efficiency while mitigating salt stress. Consequently, consortium-based inoculants are generally considered more effective than individual strains (Nunes et al. 2024).

Heavy metal stress

Heavy metal contamination in degraded and post-mining soils inhibits plant growth by disrupting metabolism and increasing reactive oxygen species (ROS) production. Rhizosphere bacteria, particularly Pseudomonas, Bacillus, and Azotobacter, alleviate heavy metal toxicity through biosorption, bioaccumulation, siderophore production, extracellular polymeric substance (EPS) formation, and transformation of toxic metals into less harmful forms (Ma et al. 2016). In microbial consortia, these mechanisms complement nutrient acquisition and phytohormone production, supporting plant establishment and growth under metal-stressed conditions, and make such consortia promising candidates for the restoration of degraded lands.

Microbe-microbe interactions within microbial consortia

Functional complementarity

The effectiveness of microbial consortia depends on the functional complementarity among community members enable multiple biological processes to occur simultaneously. Nitrogen-fixing bacteria supply bioavailable nitrogen, phosphate-solubilizing bacteria and fungi increase phosphorus availability, whereas Trichoderma act as biocontrol agents through mycoparasitism and induction of plant defense responses (Doo et al. 2023). This division of labour results in a more efficient and stable biological system than single-microbe inoculants (Nunes et al. 2024).

Cross-feeding (metabolite exchange)

Microorganisms within a consortium exchange metabolites through cross-feeding, allowing products from one species to serve as nutrients or substrates for others. This interaction enhances resource use efficiency, supports microbial growth, and improves the stability of microbial communities in the rhizosphere under varying environmental conditions (Singh et al. 2023; Nunes et al. 2024).

Beneficial competition

Competition for space and nutrients in microbial consortia is not necessarily detrimental. Beneficial competition limits pathogen colonization by efficiently utilizing ecological niches and available resources. The production of antibiotics, siderophores, and other antimicrobial compounds further strengthens the competitive advantage of beneficial microorganisms in the rhizosphere, promoting microbial community stability and plant health (Backer et al. 2018).

Multi-level colonization

PGPR typically colonize the rhizosphere and root surface, whereas fungi such as Trichoderma colonize both root surfaces and internal tissues, providing more comprehensive biological protection. This multi-level colonization enhances nutrient uptake, suppresses pathogens, and promotes more stable plant–microbe associations (Woo & Pepe 2018; Doo et al. 2023). These interactions explain why microbial consortia generally exhibit more consistent field performance than single-strain inoculants.

FIELD APPLICATION

Field application is the most critical for developing microbial consortium-based biofertilizers and biofungicides as their success depends not only on its effectiveness under laboratory conditions but also on its ability to adapt to complex field environments. The field performance of microbial consortia is often influenced by agroecosystem characteristics, soil properties, microclimatic conditions, and crop management practices (Nunes et al. 2024). Several studies have demonstrated the successful application of microbial consortia across a wide range of agricultural and plantation crops, including rice, chili pepper, tomato, shallot, oil palm, cocoa, and coffee, as well as in marginal lands such as peatlands and post-mining areas. In general, microbial consortia enhance plant growth, improve nutrient use efficiency, suppress plant diseases, and increase crop productivity through complementary interactions among consortium members (Singh et al. 2023).

Application of microbial consortia in rice field

Rice (Oryza sativa L.) is Indonesia’s primary staple crop and one of the most extensively studied crops for microbial consortium-based biofertilizers and biofungicides. Combinations of plant growth-promoting rhizobacteria (PGPR) and antagonistic fungi improve plant growth and suppress major rice diseases. Microbial consortia generally provide greater effectiveness because each consortium member performs complementary functions, including enhancing nutrient uptake, stimulating root development, and suppressing pathogen growth. Permata et al. (2025) reported that a consortium consisting of Bacillus sp. BTH22 and Trichoderma sp. effectively suppressed bacterial leaf blight, reducing disease severity to 30.02%, and achieving nearly 70% disease suppression. Similarly, indigenous Trichoderma isolates from organic rice field in West Java improved seed germination, root length, seedling height, and seedling vigor, indicating their potential as bioinoculants for sustainable rice cultivation (Akbari et al. 2024). These findings highlight the benefits of applying microbial inoculants during seed treatment or the nursery stage, particularly when using indigenous strains adapted to local agroecosystems. Beyond improving plant growth and disease suppression, microbial consortia can also enhance fertilizer use efficiency by increasing nutrient availability and uptake. Setiawati et al. (2020) reported that applying biofertilizer combined with 50% of the recommended NPK dose resulted in higher rice productivity than applying 100% NPK without biofertilizer. These findings indicate that microbial consortia may reduce dependence on chemical fertilizers in rice production.

Application in horticultural crops

Horticultural crops represent another major group of commodities in which microbial consortium-based biofertilizers and biofungicides have been widely investigated. Beneficial microorganisms applied to crops such as chili pepper, tomato, and shallot can enhance plant growth and productivity while suppressing diseases through improved nutrient availability, plant growth promotion, and biological control (Agustina et al. 2024; Taruna et al. 2024; Syarifudin et al. 2021). Rokhminarsi et al. (2019) reported that the application of the Mikotricho biofertilizer (mycorrhiza–Trichoderma) combined with a 25% reduction in synthetic fertilizer increased chili yield by 22.2% compared with the full synthetic fertilizer treatment. In addition, Agustina et al. (2024) found that a consortium of Bacillus spp. (Ba9) and Pseudomonas fluorescens inhibited the growth of Fusarium sp. by 31.5%, outperforming either bacterial strain applied individually.

Microbial consortia have also shown promising results in tomato (Solanum lycopersicum L.) cultivation by simultaneously promoting plant growth and suppressing soil-borne diseases. Taruna et al. (2024) reported that a consortium of Bacillus subtilis and Pseudomonas fluorescens increased plant height to 42.29 cm compared with 32.69 cm in the control. The bacterial consortium also reduced Fusarium wilt incidence to 27.50%, demonstrating its considerable potential as both a biofertilizer and a biofungicide for tomato production. In shallot (Allium ascalonicum L.), the KIBRT biofertilizer increased bulb weight to 85.98 g compared with 41.28 g in the control, while the Azoto-Tricho formulation reduced Fusarium oxysporum wilt incidence to 8.00%, substantially lower than the 25.33% observed in the control (Syarifudin et al., 2021).

Application in plantation crops

Oil palm (Elaeis guineensis Jacq.) is one of Indonesia’s most important plantation commodities, yet its productivity is often constrained by basal stem rot caused by Ganoderma boninense. Muniroh et al. (2019) reported that a consortium of Pseudomonas aeruginosa and Trichoderma asperellum increased seedling height to 140.45 cm and reduced disease severity to 50% under greenhouse conditions. Both microorganisms exhibited plant growth-promoting traits through phosphate solubilization and IAA production, while also functioning as biological control agents by producing hydrolytic enzymes and inhibiting G. boninense.

Cocoa (Theobroma cacao L.) and coffee (Coffea spp.) have also shown positive responses to beneficial microbial inoculation for improving seedling growth and root health. In cocoa, applying Trichoderma spp. has been shown to increase plant height, stimulate root development, and suppress pathogen infection during seed germination and seedling establishment, resulting in more vigorous seedlings (de Sousa et al. 2021). Similarly, in Arabica coffee seedlings, bacterial consortia increased plant height by approximately 9.5%, enhanced root length by 6.8%, and reduced populations of the root-knot nematode Meloidogyne incognita by 60.6%, demonstrating that microbial consortia also improve resistance to root-associated pests (Pradana et al. 2022).

Application in marginal lands

Peatlands are characterized by acidic pH, high organic matter content, and limited availability of essential nutrients, particularly phosphorus, making them challenging environments for crop production. Microbial consortia have therefore emerged as a promising strategy for sustainably improving peat soil fertility. Ichriani et al. (2022) reported that the application of Biocom enriched with phosphate-solubilizing fungi increased soil phosphorus availability by up to 406.18% at a peatland site in Kalimantan and improved nutrient use efficiency.

Post-mining lands are generally characterized by poor soil fertility, degraded soil structure, and elevated heavy metal concentrations that restrict plant establishment and growth. Aulia et al. (2026) reported that a consortium of PGPR and arbuscular mycorrhizal fungi (AMF) applied to former gold-mining soils significantly increased plant biomass and root colonization, improved soil chemical properties, including soil pH, cation exchange capacity, and nutrient availability. In addition, the consortium reduced the accumulation of heavy metals such as mercury (Hg), arsenic (As), and zinc (Zn) in plant tissues supporting the sustainable rehabilitation of post-mining lands.

Variability in field performance

Microbial consortium effectiveness under field conditions is not always consistent because agroecosystem characteristics strongly influence their performance. Differences in soil properties, environmental conditions, and crop management practices affect microorganisms' ability to survive, colonize the rhizosphere, and perform their intended functions. Soil characteristics are among the primary factors determining the success of microbial consortium application. Ultisols are generally acidic pH and low organic matter and available nutrients, requiring microorganisms that improve nutrient availability, particularly through phosphate solubilization and enhanced soil biological activity. In contrast, peatlands require acid-tolerant strains, whereas post-mining lands require microorganisms that can tolerate heavy metal stress during land rehabilitation (Permata et al. 2025).

Environmental factors such as temperature, soil moisture, rainfall, and water availability influence microbial viability and metabolic activity after application. Indonesia’s diverse tropical environments can therefore lead to varying consortium performance across regions, highlighting the importance of selecting strains and formulations adapted to local environmental conditions (Irwandhi et al. 2024). Crop management practices further affect to the success of microbial consortium application. Intensive pesticide use, excessive tillage, and unbalanced fertilization may reduce populations of beneficial microorganisms in the rhizosphere. Conversely, practices that maintain soil quality and support balanced soil microbial communities can enhance microbial colonization and improve biofertilizer and biofungicide effectiveness (Irwandhi et al. 2024).

Product formulation also contributes to variations in field performance by influencing microbial survival after application. The choice of carrier material affects microbial stability and viability during storage and distribution. Liquid carriers generally provide a faster response after application but have a relatively shorter shelf life. In contrast, solid carriers such as peat and compost better maintain microbial viability, making them more suitable for long-term storage and distribution (Ariani & Simarmata 2023; Bashan et al. 2014).

Factors influencing the successful application of microbial consortia

Formulation is one of the most critical factors determining the success of microbial consortia application because it influences inoculant viability, stability, and shelf life. Selecting an appropriate carrier protects microorganisms during storage and after field application. Solid carriers, such as peat and compost, generally provide greater storage stability, whereas liquid formulations offer a faster initial response but have a relatively shorter shelf life (Ariani & Simarmata 2023; Bashan et al. 2014). Inoculum dosage is another important factor as the amount applied should be optimized to ensure effective rhizosphere colonization and microbial activity. Shahwar et al. (2023) reported that biofertilizers can provide substantial benefits at relatively low application rates compared with chemical fertilizers because microorganisms can proliferate after application, and their activity is further influenced by plant roots and indigenous microbial communities.

The application method and timing should be selected according to crop species, growth stage, and cultivation system to maximize rhizosphere colonization. Microbial consortia can be applied through seed treatment, nursery inoculation, or direct soil application, depending on the intended purpose. For example, Taruna et al. (2024) applied bacterial consortia through seed treatment, Muniroh et al. (2019) inoculated oil palm seedlings during the nursery stage, and Permata et al. (2025) directly applied microbial consortia to peat soil. Application timing also influences the opportunity for microorganisms to colonize the rhizosphere during early plant development. Kong et al. (2025) demonstrated that inoculation timing significantly affects microbial colonization and subsequent plant growth responses, suggesting that early-stage inoculation can help maximize bioinoculant performance.

CHALLENGES

Variability in the quality of commercial products

Registration data from the Ministry of Agriculture indicate that some commercial products still vary in the number of viable microorganisms (CFU), strain compatibility, potential cross-contamination, and microbial viability during storage (Ministry of Agriculture 2026). Such variation may lead to inconsistent field performance and reduce farmers' confidence in microbial-based technologies.

Microbial viability during storage and transportation

A decline in microbial viability during storage reduces consortium members' ability to survive, colonize the rhizosphere, and perform their intended biological functions. Ariani and Simarmata (2023) reported that biofertilizers generally have a relatively limited shelf life, highlighting the importance of carrier formulations that preserve microbial viability and effectiveness throughout storage and distribution.

Strain incompatibility within microbial consortia

The success of a microbial consortium depends not only on the number of microorganisms included but also on their compatibility. Selecting microorganisms with complementary biological functions helps minimize competition and promote synergistic interactions. Tyasmoro et al. (2024) emphasized the importance of considering these roles when designing biofertilizers and biofungicides. Compatibility screening is essential because antagonistic interactions can reduce microbial viability and function (Hao et al., 2022). Strains may be produced separately before formulation or applied sequentially to account for differences in colonization timing (Bashan et al. 2014; Kong et al. 2025). Consortia typically contain two to six members, but more strains do not necessarily improve performance; the optimal combination and ratio should be determined empirically (Hao et al., 2022).

Variability of field conditions

Field variability remains a major challenge for applying microbial consortia in Indonesia as soil type, microclimate, and crop management affect microbial survival and rhizosphere colonization. Ultisols and inceptisols generally require phosphate-solubilizing consortia, peatlands require acid-tolerant strains, and post-mining lands require microorganisms that can tolerate heavy metal stress. Environmental conditions and cultivation systems may influence consortium performance across different agricultural commodities (Permata et al. 2025; Taruna et al. 2024; Muniroh et al. 2019).

Lack of national standardization

The Indonesian government has established technical requirements through the Minister of Agriculture Regulation No. 1 of 2019 and the Minister of Agriculture Decree No. 261/KPTS/SR.310/M/4/2019, which specify quality standards for biofertilizers, including minimum viable microbial counts (CFU), formulation specifications, and methods for quality and efficacy testing. However, stronger implementation and enforcement of these standards are still needed to ensure consistent product quality and more reliable field performance.

Limited farmer adoption

Farmers' knowledge and perceptions of biofertilizer benefits influence adoption, including the perception that their effects are slower than those of chemical fertilizers. Dependence on inorganic fertilizers, limited extension services and field demonstrations, and previous experiences with inconsistent-quality products may also reduce farmers' confidence in microbial technologies. Rafiudin et al. (2022) demonstrated that improving farmers' access to information and technical assistance important to increase biofertilizer adoption.

Limited development of indigenous strains

Indonesia possesses a rich diversity of beneficial microorganisms, but the exploration, characterization, and large-scale production remain limited. Consequently, locally adapted microorganisms have not yet been fully utilized, despite their generally superior adaptation to local agroecosystem conditions. Tyasmoro et al. (2024) suggested that developing microbial consortia from indigenous microorganisms could improve biofertilizers and biofungicides effectiveness while supporting sustainable agricultural practices.

OPPORTUNITIES

Development of indigenous strain-based consortia

Native strains offer the opportunity to produce biofertilizers and biofungicides better adapted to local agroecosystems, including acidic soils, peatlands, and degraded lands. Tyasmoro et al. (2024) demonstrated that indigenous microbial consortia can improve bioinoculant effectiveness, while Permata et al. (2025) highlighted the potential application in peat-based growing media as an alternative strategy for managing marginal lands.

Innovations in formulation and carrier technology

Developing carrier materials from locally available resources, such as compost, peat, and biochar, can enhance microbial viability during storage while maintaining effectiveness after field application. Ariani and Simarmata (2023) reported that appropriate carrier formulations play an essential role in maintaining the stability and shelf life of biofertilizers, whereas Bashan et al. (2014) emphasized that carrier selection is a key factor in the successful delivery of microorganisms to the target environment.

Integration with agroecological and organic farming practices

Microbial consortia have considerable potential for integration into sustainable farming systems through organic fertilizers, reduced chemical inputs, and cultivation practices that promote soil health. Such integration can improve nutrient use efficiency while enhancing long-term soil quality. Microbial consortia can also be applied across a wide range of cropping systems and growing media, depending on crop characteristics and local environmental conditions (Taruna et al. 2024; Muniroh et al. 2019; Permata et al. 2025).

Application of genomics, metagenomics, and bioinformatics

Genomics, metagenomics, and bioinformatics enable the identification of superior microbial strains, characterization of microbial community structures, mapping of rhizosphere interactions, and the design of function-based microbial consortia with greater precision. Rajguru et al. (2024) reported that metagenomic approaches provide a more comprehensive understanding of microbial diversity and function, thereby supporting the development of more adaptive and efficient bioinoculants.

Development of microbial consortia for climate-smart agriculture

Beneficial microorganisms have been shown to improve plant tolerance to drought, salinity, and other environmental stresses through mechanisms such as ACC deaminase production, osmoprotectant synthesis, enhanced antioxidant activity, and improved soil quality. Shahwar et al. (2023) reported that microbial biofertilizers can improve plant resilience under various environmental stresses, while Chem et al. (2025) demonstrated that multifunctional microbial consortia can enhance crop growth stability under unfavorable environmental conditions.

Policy opportunities and government support

The Indonesian government has established technical regulations through the Minister of Agriculture Regulation No. 1 of 2019 and the Minister of Agriculture Decree No. 261/KPTS/SR.310/M/4/2019, which govern the technical requirements, quality standards, and registration procedures for biofertilizers. In addition, national programs promoting reduced chemical fertilizer use, sustainable agriculture, land rehabilitation, and ecosystem restoration provide broader opportunities for the adoption of microbial consortia.

Commercialization opportunities and the national microbial industry

The commercialization potential of microbial consortia in Indonesia continues to grow with increasing demand for environmentally friendly agricultural inputs. Marlina et al. (2018) highlighted opportunities to develop microbial-based products through marketing strategies that address users' needs. Further research, formulation innovation, use of indigenous strains, and collaboration among universities, industry, and government could accelerate the commercialization of biofertilizers and biofungicides for large-scale application.

CONCLUSION

Microbial consortia have considerable potential for developing biofertilizers and biofungicides in Indonesia by integrating complementary microbial functions within a single formulation. This approach can enhance plant growth, improve nutrient use efficiency, promote soil health, and increase plant tolerance to both biotic and abiotic stresses. However, field performance depends on formulation quality, strain compatibility, microbial viability, agroecosystem conditions, application methods, regulatory support, and user adoption. Indonesia's rich indigenous microbial diversity, advances in formulation technology, and the growing emphasis on sustainable agriculture, offers promising opportunities to develop microbial consortia better adapted to local conditions. Further research on exploring indigenous microbial strains, developing more stable formulations, standardizing quality, and commercializing research outcomes is expected to facilitate the broader application of microbial consortia in sustainable agricultural systems across Indonesia.

ACKNOWLEDGEMENTS

The author would like to thank colleagues at IPB University for discussions and insights during the preparation of this manuscript. Appreciation is also extended to Indonesian researchers whose work on microbial consortia provided the foundation for this review. Special thanks to the Ministry of Agriculture for providing access to national data on biofertilizer and biofungicide registration.

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