ABSTRACT
Agricultural production in Indonesia has long relied on chemical fertilizer–based intensification to increase yields. However, rising fertilizer application rates have not been accompanied by proportional productivity gains, indicating declining fertilizer-use efficiency. This paper argues that the core constraint to sustainable productivity lies in soil degradation, particularly low soil organic carbon and weakened soil biological functions. Evidence from intensive paddy systems shows that soils with poor organic matter content exhibit reduced nutrient retention, lower microbial activity, and greater dependence on chemical inputs, further exacerbated by intensive pesticide use. The paper proposes soil fertility restoration based on organic fertilizers and functional soil microorganisms as a strategic foundation for improving nutrient-use efficiency and production system stability. This integrated approach positions organic and biofertilizers as complementary inputs that enhance soil system performance and support long-term agricultural sustainability.
Keywords: Soil fertility restoration; fertilizer use efficiency; soil organic carbon; soil microorganisms; sustainable agriculture
INTRODUCTION
Over the past several decades, increases in agricultural production in Indonesia have been managed primarily through an intensification strategy based on the use of chemical fertilizers, particularly nitrogen (N), phosphorus (P), and potassium (K). This approach represents a rational managerial choice in the context of short-term production growth, as it can rapidly and measurably boost crop yields. According to fertilizer use data compiled by StatBase (2025), fertilizer use in Indonesia has increased sharply over the last 30 years, from 127.81 kg/ha in 1993 to 311.01 kg/ha in 2023, representing a 2.4-fold increase. This strategy has contributed to a 1.2-fold increase in national rice productivity from approximately 4.3 tons/ha in the 1990s to 5.29 tons/ha in 2023.
Although the growth of rice production has supported national food supply, the trends in fertilizer use and rice output described above indicate that increases in fertilizer application per hectare have not been accompanied by proportional increases in production. Studies in various rice-growing areas in Indonesia show that increasing fertilizer application raises yields only up to a certain level, after which additional fertilizer has little effect on yield (Hartatik & Adiningsih, 2003; Kasno et al., 2022). This evidence suggests that chemical fertilizers alone cannot be relied upon as the sole factor for increasing crop production. Other contributing factors must be present alongside the use of chemical fertilizers.
When yield responses to additional inorganic fertilizer begin to show signs of saturation, attention should shift to soil quality as a key factor determining both fertilizer effectiveness and crop yields. In healthy soil ecosystems, soil organic matter plays a crucial role in improving soil structure, water retention, and nutrient availability. Conversely, soils with low organic matter content tend to exhibit lower fertilizer use efficiency, as the soil’s capacity to retain nutrients, support microbial activity, and reduce nutrient losses is limited (Brady & Weil, 2017).
Approximately more than 77% of paddy soils in Java have low levels of soil organic carbon (SOC), with average values ranging from 1.25% to 1.91% (Wibowo & Kasno, 2021). In the context of soil fertility, low SOC—which represents the soil organic carbon content causes soils to lose their capacity to retain water and nutrients, exhibit weak aggregate structure, and show low fertilizer effectiveness. Kasno et al. (2022) further demonstrate that in soils with organic carbon content below 2%, nitrogen fertilizer use efficiency may decline by 15–25% compared to soils with moderate organic matter levels.
From the perspective of farm management and food systems, soil degradation is not merely an agronomic issue but also a matter of efficiency and production system performance. Healthy soils function as natural capital that supports input-use efficiency and yield stability, whereas degraded soils tend to push farmers toward reactive managerial decisions, such as increasing fertilizer application rates to maintain yields. A panel study by Sumaryanto et al. (2023) shows that the technical efficiency of rice farming in several irrigated areas in Indonesia remains relatively high but has declined, reflecting underlying problems in management practices and the agricultural production base.
These findings indicate that the primary challenge in improving agricultural productivity in Indonesia no longer lies solely in the availability or increased application rates of chemical fertilizers, but rather in the management of the production system, particularly in maintaining and restoring soil quality as the foundation of crop production. Excessive reliance on chemical fertilizers, without adequate integration of organic matter management and soil biological functions, poses a risk of lower input-use efficiency while simultaneously undermining the long-term sustainability of farming systems. Therefore, an analytical framework is required that not only evaluates the limitations of conventional intensification approaches but also examines the strategic role of soil fertility and formulates more adaptive, efficient, and sustainable nutrient management pathways.
Based on the issues and discussions presented above, this paper aims to: (1) analyze the limitations of chemical fertilizer intensification in achieving sustainable agricultural productivity, particularly when increasing application rates no longer lead to proportional yield gains; (2) explain the role of soil fertility—especially organic matter and soil biological functions—as a key determinant of fertilizer-use efficiency and production system stability; and (3) formulate integrated soil fertility restoration strategies through strengthened use of organic fertilizers and soil microorganisms as the foundation for more efficient and sustainable nutrient management.
THE SOIL FERTILITY CRISIS BEHIND FERTILIZER INTENSIFICATION
Soil degradation in Indonesia involves not only physical and biological decline but also chemical degradation reflected in reduced soil fertility and nutrient status. Uniform fertilizer application that ignores site-specific soil conditions can accelerate this process, as nutrient accumulation, particularly of phosphorus (P) and potassium (K) in intensive paddy systems—does not necessarily increase nutrient availability or improve production performance (Wahyunto & Dariah, 2014).
In tropical soils rich in iron (Fe) and aluminum (Al), phosphorus is readily fixed and forms poorly soluble compounds, leaving only a small fraction available for plant uptake (Dobermann & Fairhurst, 2000). Similar constraints occur for potassium, particularly in clay-textured soils that can retain potassium within soil fractions. Surveys of paddy soil nutrient status across several regions of Indonesia indicate that phosphorus (P) and potassium (K) levels in many irrigated rice fields have reached moderate to high levels due to long-term fertilization (Saidi, 2017). Under such conditions, the application of chemical fertilizers without considering existing soil nutrient status becomes inefficient and fails to generate proportional yield gains (Kasno et al., 2022).
Soil fertility problems are further exacerbated by low levels of soil organic matter and organic carbon. Agricultural intensification with minimal biomass returns such as crop residues, manure, and other organic waste has reduced soil organic carbon to below optimal thresholds. Soils with low organic matter lose their capacity to retain nutrients and water and tend to exhibit weak aggregate structure, leading to low fertilizer-use efficiency (Hardjowigeno, 2010). From a resource management perspective, soil has not yet been fully treated as production capital that requires long-term maintenance.
Declining soil organic matter directly weakens soil microbial activity. Microorganisms are key components in maintaining soil biogeochemical functions, including organic matter decomposition and nutrient cycling (Brady & Weil, 2017). Soil organic matter serves as the primary energy source for microorganisms; without adequate organic residue inputs, microbial biomass and activity decline due to limited carbon substrates for metabolism and soil aggregate formation (Subiksa, 2000). The weakening of this biological component reduces the soil’s capacity to support efficient nutrient utilization.
Stress on soil biological systems has increased with the intensification of pesticide use. Observations in the Karawang, West Java, rice-growing region indicate that pesticide application frequency has risen from 2–3 times per season in the early 1990s to 10–12 applications per cropping season at present. Ecotoxicological studies show that pesticide use can significantly reduce soil microbial biomass and activity (Lo, 2010). Research on vineyard systems similarly reports a 40–45% decline in microbial biomass, accompanied by shifts in microbial community composition and diversity (Steiner et al., 2024). These findings highlight the substantial chemical pressure exerted on soil health.
Persistent pesticide residues in soil affect not only target organisms but also disrupt soil microbial communities and biological processes. Declines in microbial biomass and diversity weaken key soil ecological functions, including nutrient cycling and ecosystem stability (Bardgett & van der Putten, 2014). Under conditions of low soil organic carbon and degraded microbial communities, the efficiency of chemical fertilizers further declines because soil biological processes do not function optimally (Paul, 2015). This situation creates a cycle of increasing dependence on chemical inputs that ultimately accelerates overall soil degradation (Lal, 2004).
POLICY FRAMEWORK FOR LAND REHABILITATION
The legal framework governing land rehabilitation and soil protection in Indonesia is well established by Law No. 37/2014 on Soil and Water Conservation. This law explicitly recognizes soil as a strategic natural resource whose functions must be protected, restored, and sustainably maintained to support long-term environmental and agricultural productivity. It mandates soil conservation measures across various land-use types, emphasizing the need to prevent further degradation while promoting the rehabilitation of degraded soils. Furthermore, the regulation defines land rehabilitation as a shared responsibility between the government and land users, underscoring the need for coordinated action and sustained commitment to soil conservation efforts.
Control of soil degradation for biomass production is regulated more technically under Government Regulation No. 150/2000, which establishes standard criteria for soil damage and the obligations for its control. This regulation provides a normative basis for assessing degraded soil conditions and requires the implementation of rehabilitation measures. In the agricultural context, this regulation is particularly relevant as a legal framework for identifying soil degradation resulting from intensive cultivation practices and uncontrolled use of chemical inputs.
From a broader environmental perspective, Law No. 32/2009 on Environmental Protection and Management serves as a cross-sectoral legal framework. This law emphasizes the precautionary principle and pollution prevention, including soil contamination by agricultural chemicals. These provisions are further reinforced by Government Regulation No. 22/2021, which governs the management of hazardous and toxic waste, including pesticide residues and other chemical substances with the potential to degrade soil quality.
The use of pesticides is specifically regulated under Government Regulation No. 7/1973, which serves as the legal basis for controlling the circulation, storage, and use of pesticides in Indonesia. This regulation has subsequently been strengthened by various ministerial regulations, particularly Minister of Agriculture Regulation No. 43/2019 on pesticide registration and Minister of Agriculture Regulation No. 107/2014 on pesticide supervision. These regulations aim to ensure that only pesticides meeting established safety standards are permitted for use and that their application does not cause adverse impacts on soil and the environment.
Control of pesticide active ingredients is also implemented through Minister of Agriculture Regulation No. 24/ of 2011, which specifies lists of permitted, restricted, and prohibited active substances. This regulation is particularly important in the context of soil rehabilitation, as it limits the use of highly toxic chemicals that can damage soil biological communities and leave long-term residues. Accordingly, soil protection is enforced from the earliest stage of pesticide selection for market circulation.
Efforts to reduce chemical pressure on soils are also reflected in the regulations promoting sustainable agricultural practices, such as Minister of Agriculture Regulation No. 22/2021 and Minister of Agriculture Regulation No. 39/ 2015 on Integrated Pest Management (IPM). These regulations emphasize that pesticide use should be considered a last resort and applied strictly in accordance with IPM principles, prioritizing preventive and ecological control measures. By limiting routine and excessive pesticide application, this regulatory approach implicitly supports the recovery of soil biological functions and contributes to reducing long-term dependence on chemical inputs in agricultural systems.
In addition to chemical control measures, soil rehabilitation in Indonesia is also supported by regulations that explicitly promote improvements in soil fertility. These include Minister of Agriculture Regulation No. 15/2011 in conjunction with Minister of Agriculture Regulation No. 01/2019 on organic fertilizers and soil amendments, Minister of Agriculture Regulation No. 40/2007 on balanced fertilization, and Law No. 22/2019 on the Sustainable Agricultural Cultivation System. Collectively, these regulations demonstrate that, at the normative level, Indonesia has established a relatively comprehensive legal framework for soil rehabilitation that integrates fertility enhancement, nutrient management, and sustainability principles. Nevertheless, the primary challenge lies not in the absence of regulations but in ensuring consistent implementation, effective coordination, and policy integration at the field level.
An overview of the legal and regulatory framework for soil rehabilitation and protection in Indonesia is summarized in Table 1.
Table 1. Legal and Regulatory Framework for Soil Rehabilitation and Protection in Indonesia
|
Regulation
|
Relevance to Soil
|
|
Law No. 37/2014 on Soil and Water Conservation
|
Primary legal framework for soil rehabilitation, including degraded and critical land
|
|
Government Regulation No. 150/2000 on Control of Soil Degradation for Biomass Production
|
Legal basis for assessing degraded soils and mandating rehabilitation
|
|
Law No. 32/2009 on Environmental Protection and Management
|
Foundation for controlling soil contamination from chemical inputs
|
|
Government Regulation No. 7/1973 on Pesticide Supervision
|
Classical legal basis for pesticide control in Indonesia
|
|
Minister of Agriculture Regulation No. 43/2019
|
Screening pesticides to ensure safety for soil and the environment
|
|
Minister of Agriculture Regulation No. 107/2014
|
Control of application rates, methods, and environmental impacts
|
|
Minister of Agriculture Regulation No. 24/2011
|
Prevention of toxic substances that damage soil health
|
|
Minister of Agriculture Regulation No. 22/2021
|
Reduction of chemical pressure on soils
|
|
Minister of Agriculture Regulation No. 39/2015
|
Reduced dependence on chemical pesticides
|
|
Minister of Agriculture Regulation No. 15/2011 in conjunction with Minister of Agriculture Regulation No. 01/2019
|
Support for soil rehabilitation through organic matter inputs
|
|
Minister of Agriculture Regulation No. 40/2007 (Guidelines on Balanced Fertilization)
|
Technical foundation for restoring soil fertility
|
|
Law No. 22/2019 on the Sustainable Agricultural Cultivation System
|
Recognition of soil as long-term production capital
|
THE ROLE OF SOIL MICROORGANISMS IN SOIL FERTILITY RESTORATION
In soil fertility management, soil microorganisms are key components determining input-use efficiency and the sustainability of agricultural production systems. Microbes enable soil to function as a living system that recycles nutrients, reduces nutrient losses, and lowers dependence on chemical fertilizers and pesticides. Consequently, the role of soil microorganisms is not only biological but also strategic in soil resource management and farm-level efficiency.
Various microbial groups contribute directly to nutrient supply and mobilization. Nitrogen-fixing bacteria such as Rhizobium, Azotobacter, and Azospirillum provide nitrogen through biological fixation and serve as partial substitutes for chemical nitrogen fertilizers (Vessey, 2003). Phosphate- and potassium-solubilizing bacteria mobilize P and K reserves that are strongly fixed in iron- and aluminum-rich tropical soils, thereby increasing nutrient availability to plants (Richardson et al., 2009). This approach enables productivity gains through improved nutrient management efficiency rather than solely through increased application rates of chemical fertilizers (FAO, 2019).
Arbuscular mycorrhizal fungi play a key role in extending the effective root exploration area and enhancing the uptake of phosphorus, micronutrients, and water, particularly in soils with low organic matter. In addition to improving nutrient uptake efficiency, mycorrhizae enhance plant tolerance to drought stress and nutrient deficiencies, thereby helping to stabilize crop yields and support medium- to long-term soil fertility management (Smith & Read, 2008). Decomposer microorganisms, including fungi and actinomycetes, also contribute to organic matter decomposition, increases in soil organic carbon, and improvements in soil structure and water-holding capacity (Lal, 2004).
Plant growth–promoting rhizobacteria (PGPR) and antagonistic fungi such as Trichoderma enhance plant vigor while suppressing soil-borne pathogens through mechanisms including phytohormone production, competition, antibiosis, and the induction of systemic resistance (Harman et al., 2004). Nitrogen-fixing bacteria and cyanobacteria in paddy rice systems have been reported to contribute approximately 20–60 kg N/ha/season and 20–30 kg N/ ha/season, respectively, thereby functioning as partial substitutes for inorganic nitrogen fertilizers. The sustainability of these microbial functions is strongly influenced by the availability of organic matter, water management, and the intensity of chemical stress (Roger & Ladha, 1992; Brady & Weil, 2017; FAO, 2019).
In the context of soil fertility restoration, organic and biofertilizers serve as a biological foundation that enhances the efficiency of chemical fertilizers rather than acting as their complete substitutes. The effectiveness of organic fertilizers is highly dependent on their biological quality and the presence of living microorganisms, requiring production practices and quality standards to explicitly accommodate the role of functional microbes (Vessey, 2003; FAO, 2019). This approach calls for integrated management encompassing organic matter, crops, water, and chemical inputs in a balanced manner, along with policy support for local organic fertilizer production and its integration into fertilizer recommendation and subsidy systems (Lal, 2004; Hardjowigeno, 2010; Cassman et al., 2002).
A MODEL FOR AGRICULTURAL SOIL RESTORATION BASED ON ORGANIC FERTILIZERS AND MICROORGANISMS
In response to the increasingly evident of soil fertility crisis, restoring soil functions through the addition of organic matter and the strengthening of soil microbial activity has been scientifically demonstrated as an effective approach to improving the physical, chemical, and biological properties of soils and enhancing their capacity to support sustainable crop production (Haque et al., 2021). Organic fertilizers play a dual role as nutrient sources and soil amendments, improving soil structure and water-holding capacity and providing carbon substrates for soil microorganisms. From a fertility management perspective, increasing soil organic matter and organic carbon represents a medium- to long-term investment that has been shown to improve fertilizer-use efficiency, enhance crop nutrient responses, and stabilize agricultural productivity (Lal, 2004; Hardjowigeno, 2010).
Nevertheless, the effectiveness of organic fertilizers is not determined solely by their nutrient content but also by their biological quality and the presence of living microorganisms. In fertilizer production and management practices, quality standards that overly emphasize sterilization—particularly through high-temperature processing—may reduce pathogen risks but can also eliminate functional microorganisms that play critical roles in nutrient solubilization, nitrogen fixation, and plant growth stimulation. Numerous studies indicate that organic and biofertilizers that retain active microbial communities, such as phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and mycorrhizal fungi, provide greater nutrient-use efficiency and more consistent yield improvements than organic fertilizers that function merely as passive sources of organic matter (Vessey, 2003; FAO, 2019).
In the context of local resource management, village-level production of organic fertilizers represents a highly strategic approach. Indonesia has abundant raw materials in the form of livestock waste, rice straw, rice husks, corn cobs, and some other agricultural biomass that have not yet been optimally utilized. The processing of biomass into organic and biofertilizers through microbially mediated decomposition processes—such as composting and controlled fermentation—allows beneficial microorganisms to remain alive and functional in the final product. During composting, various groups of bacteria and fungi gradually break down organic matter, whereas in fermentation processes, fermentative microbes help preserve nutrients and active microbial populations that contribute to the quality of organic biofertilizers (Aguilar-Paredes et al., 2023).
Furthermore, the production of microbe-friendly, locally produced organic fertilizers supports sustainable and efficient agricultural systems. Increases in soil organic matter content and microbial activity contribute to more efficient nutrient cycling and plant nutrient uptake, thereby allowing the gradual reduction of inorganic fertilizer use without yield penalties (Vessey, 2003). Biologically restored soils have a greater capacity to mobilize nutrients, reduce nutrient losses, and enhance crop resilience through the active role of soil microbial communities in nutrient cycling and soil–plant interactions (FAO, 2019). Within an input management framework, organic fertilizers and soil microorganisms are not positioned as complete substitutes for inorganic fertilizers, but rather as a biological foundation that enables inorganic fertilizers to be applied more precisely, adaptively, and efficiently by improving the internal efficiency of soil systems (Cassman et al., 2002).
From a policy and governance perspective, soil restoration initiatives based on organic fertilizers and local microbial resources require integrated support. Simplifying licensing procedures for small-scale organic fertilizer production, developing quality standards that recognize the role of living microorganisms, and providing incentives for cooperatives and village-based enterprises are essential prerequisites for encouraging adoption. Integrating organic and biofertilizers into extension services, site-specific fertilizer recommendations, and fertilizer subsidy policies would accelerate implementation at the farm level. Accordingly, soil fertility restoration should be understood not merely as a technical agronomic agenda, but also as an integrated strategy closely linked to rural development, job creation, and long-term food security.
CONCLUSION
The restoration of agricultural soil fertility in Indonesia should be understood as a systemic effort to address the physical, chemical, and—most critically—biological degradation of soils resulting from long-term agricultural intensification. Declining levels of soil organic matter and beneficial microbial activity have reduced fertilizer use efficiency and driven increasing dependence on chemical fertilizers and pesticides. Therefore, strengthening the role of organic matter and soil microorganisms constitutes a fundamental foundation for restoring soil functions as a living ecosystem capable of supplying nutrients more efficiently, enhancing crop resilience, and stabilizing agricultural productivity.
The integration of soil restoration based on organic fertilizers and local microbial resources provides a strategic direction for more precise and sustainable nutrient management. The production of microbe-friendly organic fertilizers at the village level not only accelerates improvements in soil quality but also creates business opportunities and strengthens local economies. To strengthen food security and sustainably improving farmers’ welfare, an integrated policy support is needed which include: (a) soil testing consist of testing period, test for pre or post fertilizer application, required microorganism level for specific crop; (b) organic fertilizer standards that recognize the role of living microorganisms, mixing ratios of existing components; and (c) adjusting fertilizer subsidy policies to include production cost support and offer price discount through matching fund system.
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Restoring Soil Fertility to Enhance the Efficiency and Sustainability of Agricultural Production Systems in Indonesia
ABSTRACT
Agricultural production in Indonesia has long relied on chemical fertilizer–based intensification to increase yields. However, rising fertilizer application rates have not been accompanied by proportional productivity gains, indicating declining fertilizer-use efficiency. This paper argues that the core constraint to sustainable productivity lies in soil degradation, particularly low soil organic carbon and weakened soil biological functions. Evidence from intensive paddy systems shows that soils with poor organic matter content exhibit reduced nutrient retention, lower microbial activity, and greater dependence on chemical inputs, further exacerbated by intensive pesticide use. The paper proposes soil fertility restoration based on organic fertilizers and functional soil microorganisms as a strategic foundation for improving nutrient-use efficiency and production system stability. This integrated approach positions organic and biofertilizers as complementary inputs that enhance soil system performance and support long-term agricultural sustainability.
Keywords: Soil fertility restoration; fertilizer use efficiency; soil organic carbon; soil microorganisms; sustainable agriculture
INTRODUCTION
Over the past several decades, increases in agricultural production in Indonesia have been managed primarily through an intensification strategy based on the use of chemical fertilizers, particularly nitrogen (N), phosphorus (P), and potassium (K). This approach represents a rational managerial choice in the context of short-term production growth, as it can rapidly and measurably boost crop yields. According to fertilizer use data compiled by StatBase (2025), fertilizer use in Indonesia has increased sharply over the last 30 years, from 127.81 kg/ha in 1993 to 311.01 kg/ha in 2023, representing a 2.4-fold increase. This strategy has contributed to a 1.2-fold increase in national rice productivity from approximately 4.3 tons/ha in the 1990s to 5.29 tons/ha in 2023.
Although the growth of rice production has supported national food supply, the trends in fertilizer use and rice output described above indicate that increases in fertilizer application per hectare have not been accompanied by proportional increases in production. Studies in various rice-growing areas in Indonesia show that increasing fertilizer application raises yields only up to a certain level, after which additional fertilizer has little effect on yield (Hartatik & Adiningsih, 2003; Kasno et al., 2022). This evidence suggests that chemical fertilizers alone cannot be relied upon as the sole factor for increasing crop production. Other contributing factors must be present alongside the use of chemical fertilizers.
When yield responses to additional inorganic fertilizer begin to show signs of saturation, attention should shift to soil quality as a key factor determining both fertilizer effectiveness and crop yields. In healthy soil ecosystems, soil organic matter plays a crucial role in improving soil structure, water retention, and nutrient availability. Conversely, soils with low organic matter content tend to exhibit lower fertilizer use efficiency, as the soil’s capacity to retain nutrients, support microbial activity, and reduce nutrient losses is limited (Brady & Weil, 2017).
Approximately more than 77% of paddy soils in Java have low levels of soil organic carbon (SOC), with average values ranging from 1.25% to 1.91% (Wibowo & Kasno, 2021). In the context of soil fertility, low SOC—which represents the soil organic carbon content causes soils to lose their capacity to retain water and nutrients, exhibit weak aggregate structure, and show low fertilizer effectiveness. Kasno et al. (2022) further demonstrate that in soils with organic carbon content below 2%, nitrogen fertilizer use efficiency may decline by 15–25% compared to soils with moderate organic matter levels.
From the perspective of farm management and food systems, soil degradation is not merely an agronomic issue but also a matter of efficiency and production system performance. Healthy soils function as natural capital that supports input-use efficiency and yield stability, whereas degraded soils tend to push farmers toward reactive managerial decisions, such as increasing fertilizer application rates to maintain yields. A panel study by Sumaryanto et al. (2023) shows that the technical efficiency of rice farming in several irrigated areas in Indonesia remains relatively high but has declined, reflecting underlying problems in management practices and the agricultural production base.
These findings indicate that the primary challenge in improving agricultural productivity in Indonesia no longer lies solely in the availability or increased application rates of chemical fertilizers, but rather in the management of the production system, particularly in maintaining and restoring soil quality as the foundation of crop production. Excessive reliance on chemical fertilizers, without adequate integration of organic matter management and soil biological functions, poses a risk of lower input-use efficiency while simultaneously undermining the long-term sustainability of farming systems. Therefore, an analytical framework is required that not only evaluates the limitations of conventional intensification approaches but also examines the strategic role of soil fertility and formulates more adaptive, efficient, and sustainable nutrient management pathways.
Based on the issues and discussions presented above, this paper aims to: (1) analyze the limitations of chemical fertilizer intensification in achieving sustainable agricultural productivity, particularly when increasing application rates no longer lead to proportional yield gains; (2) explain the role of soil fertility—especially organic matter and soil biological functions—as a key determinant of fertilizer-use efficiency and production system stability; and (3) formulate integrated soil fertility restoration strategies through strengthened use of organic fertilizers and soil microorganisms as the foundation for more efficient and sustainable nutrient management.
THE SOIL FERTILITY CRISIS BEHIND FERTILIZER INTENSIFICATION
Soil degradation in Indonesia involves not only physical and biological decline but also chemical degradation reflected in reduced soil fertility and nutrient status. Uniform fertilizer application that ignores site-specific soil conditions can accelerate this process, as nutrient accumulation, particularly of phosphorus (P) and potassium (K) in intensive paddy systems—does not necessarily increase nutrient availability or improve production performance (Wahyunto & Dariah, 2014).
In tropical soils rich in iron (Fe) and aluminum (Al), phosphorus is readily fixed and forms poorly soluble compounds, leaving only a small fraction available for plant uptake (Dobermann & Fairhurst, 2000). Similar constraints occur for potassium, particularly in clay-textured soils that can retain potassium within soil fractions. Surveys of paddy soil nutrient status across several regions of Indonesia indicate that phosphorus (P) and potassium (K) levels in many irrigated rice fields have reached moderate to high levels due to long-term fertilization (Saidi, 2017). Under such conditions, the application of chemical fertilizers without considering existing soil nutrient status becomes inefficient and fails to generate proportional yield gains (Kasno et al., 2022).
Soil fertility problems are further exacerbated by low levels of soil organic matter and organic carbon. Agricultural intensification with minimal biomass returns such as crop residues, manure, and other organic waste has reduced soil organic carbon to below optimal thresholds. Soils with low organic matter lose their capacity to retain nutrients and water and tend to exhibit weak aggregate structure, leading to low fertilizer-use efficiency (Hardjowigeno, 2010). From a resource management perspective, soil has not yet been fully treated as production capital that requires long-term maintenance.
Declining soil organic matter directly weakens soil microbial activity. Microorganisms are key components in maintaining soil biogeochemical functions, including organic matter decomposition and nutrient cycling (Brady & Weil, 2017). Soil organic matter serves as the primary energy source for microorganisms; without adequate organic residue inputs, microbial biomass and activity decline due to limited carbon substrates for metabolism and soil aggregate formation (Subiksa, 2000). The weakening of this biological component reduces the soil’s capacity to support efficient nutrient utilization.
Stress on soil biological systems has increased with the intensification of pesticide use. Observations in the Karawang, West Java, rice-growing region indicate that pesticide application frequency has risen from 2–3 times per season in the early 1990s to 10–12 applications per cropping season at present. Ecotoxicological studies show that pesticide use can significantly reduce soil microbial biomass and activity (Lo, 2010). Research on vineyard systems similarly reports a 40–45% decline in microbial biomass, accompanied by shifts in microbial community composition and diversity (Steiner et al., 2024). These findings highlight the substantial chemical pressure exerted on soil health.
Persistent pesticide residues in soil affect not only target organisms but also disrupt soil microbial communities and biological processes. Declines in microbial biomass and diversity weaken key soil ecological functions, including nutrient cycling and ecosystem stability (Bardgett & van der Putten, 2014). Under conditions of low soil organic carbon and degraded microbial communities, the efficiency of chemical fertilizers further declines because soil biological processes do not function optimally (Paul, 2015). This situation creates a cycle of increasing dependence on chemical inputs that ultimately accelerates overall soil degradation (Lal, 2004).
POLICY FRAMEWORK FOR LAND REHABILITATION
The legal framework governing land rehabilitation and soil protection in Indonesia is well established by Law No. 37/2014 on Soil and Water Conservation. This law explicitly recognizes soil as a strategic natural resource whose functions must be protected, restored, and sustainably maintained to support long-term environmental and agricultural productivity. It mandates soil conservation measures across various land-use types, emphasizing the need to prevent further degradation while promoting the rehabilitation of degraded soils. Furthermore, the regulation defines land rehabilitation as a shared responsibility between the government and land users, underscoring the need for coordinated action and sustained commitment to soil conservation efforts.
Control of soil degradation for biomass production is regulated more technically under Government Regulation No. 150/2000, which establishes standard criteria for soil damage and the obligations for its control. This regulation provides a normative basis for assessing degraded soil conditions and requires the implementation of rehabilitation measures. In the agricultural context, this regulation is particularly relevant as a legal framework for identifying soil degradation resulting from intensive cultivation practices and uncontrolled use of chemical inputs.
From a broader environmental perspective, Law No. 32/2009 on Environmental Protection and Management serves as a cross-sectoral legal framework. This law emphasizes the precautionary principle and pollution prevention, including soil contamination by agricultural chemicals. These provisions are further reinforced by Government Regulation No. 22/2021, which governs the management of hazardous and toxic waste, including pesticide residues and other chemical substances with the potential to degrade soil quality.
The use of pesticides is specifically regulated under Government Regulation No. 7/1973, which serves as the legal basis for controlling the circulation, storage, and use of pesticides in Indonesia. This regulation has subsequently been strengthened by various ministerial regulations, particularly Minister of Agriculture Regulation No. 43/2019 on pesticide registration and Minister of Agriculture Regulation No. 107/2014 on pesticide supervision. These regulations aim to ensure that only pesticides meeting established safety standards are permitted for use and that their application does not cause adverse impacts on soil and the environment.
Control of pesticide active ingredients is also implemented through Minister of Agriculture Regulation No. 24/ of 2011, which specifies lists of permitted, restricted, and prohibited active substances. This regulation is particularly important in the context of soil rehabilitation, as it limits the use of highly toxic chemicals that can damage soil biological communities and leave long-term residues. Accordingly, soil protection is enforced from the earliest stage of pesticide selection for market circulation.
Efforts to reduce chemical pressure on soils are also reflected in the regulations promoting sustainable agricultural practices, such as Minister of Agriculture Regulation No. 22/2021 and Minister of Agriculture Regulation No. 39/ 2015 on Integrated Pest Management (IPM). These regulations emphasize that pesticide use should be considered a last resort and applied strictly in accordance with IPM principles, prioritizing preventive and ecological control measures. By limiting routine and excessive pesticide application, this regulatory approach implicitly supports the recovery of soil biological functions and contributes to reducing long-term dependence on chemical inputs in agricultural systems.
In addition to chemical control measures, soil rehabilitation in Indonesia is also supported by regulations that explicitly promote improvements in soil fertility. These include Minister of Agriculture Regulation No. 15/2011 in conjunction with Minister of Agriculture Regulation No. 01/2019 on organic fertilizers and soil amendments, Minister of Agriculture Regulation No. 40/2007 on balanced fertilization, and Law No. 22/2019 on the Sustainable Agricultural Cultivation System. Collectively, these regulations demonstrate that, at the normative level, Indonesia has established a relatively comprehensive legal framework for soil rehabilitation that integrates fertility enhancement, nutrient management, and sustainability principles. Nevertheless, the primary challenge lies not in the absence of regulations but in ensuring consistent implementation, effective coordination, and policy integration at the field level.
An overview of the legal and regulatory framework for soil rehabilitation and protection in Indonesia is summarized in Table 1.
Table 1. Legal and Regulatory Framework for Soil Rehabilitation and Protection in Indonesia
Regulation
Relevance to Soil
Law No. 37/2014 on Soil and Water Conservation
Primary legal framework for soil rehabilitation, including degraded and critical land
Government Regulation No. 150/2000 on Control of Soil Degradation for Biomass Production
Legal basis for assessing degraded soils and mandating rehabilitation
Law No. 32/2009 on Environmental Protection and Management
Foundation for controlling soil contamination from chemical inputs
Government Regulation No. 7/1973 on Pesticide Supervision
Classical legal basis for pesticide control in Indonesia
Minister of Agriculture Regulation No. 43/2019
Screening pesticides to ensure safety for soil and the environment
Minister of Agriculture Regulation No. 107/2014
Control of application rates, methods, and environmental impacts
Minister of Agriculture Regulation No. 24/2011
Prevention of toxic substances that damage soil health
Minister of Agriculture Regulation No. 22/2021
Reduction of chemical pressure on soils
Minister of Agriculture Regulation No. 39/2015
Reduced dependence on chemical pesticides
Minister of Agriculture Regulation No. 15/2011 in conjunction with Minister of Agriculture Regulation No. 01/2019
Support for soil rehabilitation through organic matter inputs
Minister of Agriculture Regulation No. 40/2007 (Guidelines on Balanced Fertilization)
Technical foundation for restoring soil fertility
Law No. 22/2019 on the Sustainable Agricultural Cultivation System
Recognition of soil as long-term production capital
THE ROLE OF SOIL MICROORGANISMS IN SOIL FERTILITY RESTORATION
In soil fertility management, soil microorganisms are key components determining input-use efficiency and the sustainability of agricultural production systems. Microbes enable soil to function as a living system that recycles nutrients, reduces nutrient losses, and lowers dependence on chemical fertilizers and pesticides. Consequently, the role of soil microorganisms is not only biological but also strategic in soil resource management and farm-level efficiency.
Various microbial groups contribute directly to nutrient supply and mobilization. Nitrogen-fixing bacteria such as Rhizobium, Azotobacter, and Azospirillum provide nitrogen through biological fixation and serve as partial substitutes for chemical nitrogen fertilizers (Vessey, 2003). Phosphate- and potassium-solubilizing bacteria mobilize P and K reserves that are strongly fixed in iron- and aluminum-rich tropical soils, thereby increasing nutrient availability to plants (Richardson et al., 2009). This approach enables productivity gains through improved nutrient management efficiency rather than solely through increased application rates of chemical fertilizers (FAO, 2019).
Arbuscular mycorrhizal fungi play a key role in extending the effective root exploration area and enhancing the uptake of phosphorus, micronutrients, and water, particularly in soils with low organic matter. In addition to improving nutrient uptake efficiency, mycorrhizae enhance plant tolerance to drought stress and nutrient deficiencies, thereby helping to stabilize crop yields and support medium- to long-term soil fertility management (Smith & Read, 2008). Decomposer microorganisms, including fungi and actinomycetes, also contribute to organic matter decomposition, increases in soil organic carbon, and improvements in soil structure and water-holding capacity (Lal, 2004).
Plant growth–promoting rhizobacteria (PGPR) and antagonistic fungi such as Trichoderma enhance plant vigor while suppressing soil-borne pathogens through mechanisms including phytohormone production, competition, antibiosis, and the induction of systemic resistance (Harman et al., 2004). Nitrogen-fixing bacteria and cyanobacteria in paddy rice systems have been reported to contribute approximately 20–60 kg N/ha/season and 20–30 kg N/ ha/season, respectively, thereby functioning as partial substitutes for inorganic nitrogen fertilizers. The sustainability of these microbial functions is strongly influenced by the availability of organic matter, water management, and the intensity of chemical stress (Roger & Ladha, 1992; Brady & Weil, 2017; FAO, 2019).
In the context of soil fertility restoration, organic and biofertilizers serve as a biological foundation that enhances the efficiency of chemical fertilizers rather than acting as their complete substitutes. The effectiveness of organic fertilizers is highly dependent on their biological quality and the presence of living microorganisms, requiring production practices and quality standards to explicitly accommodate the role of functional microbes (Vessey, 2003; FAO, 2019). This approach calls for integrated management encompassing organic matter, crops, water, and chemical inputs in a balanced manner, along with policy support for local organic fertilizer production and its integration into fertilizer recommendation and subsidy systems (Lal, 2004; Hardjowigeno, 2010; Cassman et al., 2002).
A MODEL FOR AGRICULTURAL SOIL RESTORATION BASED ON ORGANIC FERTILIZERS AND MICROORGANISMS
In response to the increasingly evident of soil fertility crisis, restoring soil functions through the addition of organic matter and the strengthening of soil microbial activity has been scientifically demonstrated as an effective approach to improving the physical, chemical, and biological properties of soils and enhancing their capacity to support sustainable crop production (Haque et al., 2021). Organic fertilizers play a dual role as nutrient sources and soil amendments, improving soil structure and water-holding capacity and providing carbon substrates for soil microorganisms. From a fertility management perspective, increasing soil organic matter and organic carbon represents a medium- to long-term investment that has been shown to improve fertilizer-use efficiency, enhance crop nutrient responses, and stabilize agricultural productivity (Lal, 2004; Hardjowigeno, 2010).
Nevertheless, the effectiveness of organic fertilizers is not determined solely by their nutrient content but also by their biological quality and the presence of living microorganisms. In fertilizer production and management practices, quality standards that overly emphasize sterilization—particularly through high-temperature processing—may reduce pathogen risks but can also eliminate functional microorganisms that play critical roles in nutrient solubilization, nitrogen fixation, and plant growth stimulation. Numerous studies indicate that organic and biofertilizers that retain active microbial communities, such as phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and mycorrhizal fungi, provide greater nutrient-use efficiency and more consistent yield improvements than organic fertilizers that function merely as passive sources of organic matter (Vessey, 2003; FAO, 2019).
In the context of local resource management, village-level production of organic fertilizers represents a highly strategic approach. Indonesia has abundant raw materials in the form of livestock waste, rice straw, rice husks, corn cobs, and some other agricultural biomass that have not yet been optimally utilized. The processing of biomass into organic and biofertilizers through microbially mediated decomposition processes—such as composting and controlled fermentation—allows beneficial microorganisms to remain alive and functional in the final product. During composting, various groups of bacteria and fungi gradually break down organic matter, whereas in fermentation processes, fermentative microbes help preserve nutrients and active microbial populations that contribute to the quality of organic biofertilizers (Aguilar-Paredes et al., 2023).
Furthermore, the production of microbe-friendly, locally produced organic fertilizers supports sustainable and efficient agricultural systems. Increases in soil organic matter content and microbial activity contribute to more efficient nutrient cycling and plant nutrient uptake, thereby allowing the gradual reduction of inorganic fertilizer use without yield penalties (Vessey, 2003). Biologically restored soils have a greater capacity to mobilize nutrients, reduce nutrient losses, and enhance crop resilience through the active role of soil microbial communities in nutrient cycling and soil–plant interactions (FAO, 2019). Within an input management framework, organic fertilizers and soil microorganisms are not positioned as complete substitutes for inorganic fertilizers, but rather as a biological foundation that enables inorganic fertilizers to be applied more precisely, adaptively, and efficiently by improving the internal efficiency of soil systems (Cassman et al., 2002).
From a policy and governance perspective, soil restoration initiatives based on organic fertilizers and local microbial resources require integrated support. Simplifying licensing procedures for small-scale organic fertilizer production, developing quality standards that recognize the role of living microorganisms, and providing incentives for cooperatives and village-based enterprises are essential prerequisites for encouraging adoption. Integrating organic and biofertilizers into extension services, site-specific fertilizer recommendations, and fertilizer subsidy policies would accelerate implementation at the farm level. Accordingly, soil fertility restoration should be understood not merely as a technical agronomic agenda, but also as an integrated strategy closely linked to rural development, job creation, and long-term food security.
CONCLUSION
The restoration of agricultural soil fertility in Indonesia should be understood as a systemic effort to address the physical, chemical, and—most critically—biological degradation of soils resulting from long-term agricultural intensification. Declining levels of soil organic matter and beneficial microbial activity have reduced fertilizer use efficiency and driven increasing dependence on chemical fertilizers and pesticides. Therefore, strengthening the role of organic matter and soil microorganisms constitutes a fundamental foundation for restoring soil functions as a living ecosystem capable of supplying nutrients more efficiently, enhancing crop resilience, and stabilizing agricultural productivity.
The integration of soil restoration based on organic fertilizers and local microbial resources provides a strategic direction for more precise and sustainable nutrient management. The production of microbe-friendly organic fertilizers at the village level not only accelerates improvements in soil quality but also creates business opportunities and strengthens local economies. To strengthen food security and sustainably improving farmers’ welfare, an integrated policy support is needed which include: (a) soil testing consist of testing period, test for pre or post fertilizer application, required microorganism level for specific crop; (b) organic fertilizer standards that recognize the role of living microorganisms, mixing ratios of existing components; and (c) adjusting fertilizer subsidy policies to include production cost support and offer price discount through matching fund system.
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