Sustainable soil management in East, South and Southeast Asia

ABSTRACT

The 2030 Agenda was promulgated for the Sustainable Develop Goals (SDGs), which consist of 17 goals created to eradicate poverty and realize a more sustainable world. Among the goals, soil science can contribute significantly toward achieving zero hunger (#2), implementing climate action (#13), bettering life on land (#15), among others. Paddy fields are important sustainable agro-ecosystems for rice (Oryza sativa) production, and rice is the staple food for more than 2 billion people worldwide. Paddy rice is produced mainly in East, South, and Southeast Asia, in region with a monsoon climate. Paddy soils are unique, as they are mostly managed under waterlogged conditions during the rice-growing season. Nitrogen (N) is one of the most important nutrients for many crops, including rice. Some potential sustainable soil management methods are suggested to meet the SDGs, especially in paddy fields and wetlands in East, South, and Southeast Asia, based on current achievements, including N mineralization analysis, soil microbial analysis, and greenhouse gas measurements, to predict soil fertility and effective environmental management practices in the future. One such example of sustainable soil management practice is the amendment of silicate fertilizer produced from steel-making sludge that reduced methane emission from paddy fields (3%–50%) and increased the rice yield in Vietnam.

KEY WORDS:

• Soil microbial biomass
• paddy soil
• greenhouse gases
• nitrogen

The United Nations Sustainable Development Summit was held in September 2015 to promulgate the 2030 Agenda for Sustainable Development (the 2030 Agenda), a set of international development goals from 2016 to 2030 (‘Sustainable Development Goals’; SDGs). The 2030 Agenda listed the SDGs, which consist of 17 goals and 169 targets that need to be met to eradicate poverty and realize a more sustainable world (UN 2015). Across several goals and targets, soil science can contribute widely to achieving many of them, including achieving zero hunger (#2), implementing climate action (#13), bettering life on land (#15), among others. In this review, potential sustainable soil management methods to achieve SDGs, especially in the paddy fields and wetlands of East, South, and Southeast Asia, are suggested based on current knowledge and future prospects.

1. Nitrogen mineralization and soil fertility

Paddy fields are important sustainable agro-ecosystems used for rice production, and rice is the staple food for more than 2 billion people worldwide. Paddy rice production is practiced mainly in East, South, and Southeast Asia in regions with a monsoon climate. Paddy soils are unique in that they are mostly managed under waterlogged conditions during the rice-growing season. Nitrogen (N) is one of the most important bio-elements for many crops, including rice. N mineralization from soil organic nitrogen is fundamentally important, and works in harmony with an adequate application of nitrogen fertilizer and environmental soil, water, and air quality. For this reason, it has been studied for many decades, but further integrations of quantitative and qualitative research is still needed to improve the basic understanding and inform practical soil managements. For example, some of the traditional indices used for paddy soil fertility in Japan include mineralizable N, mineralized N after waterlogged incubation of air-dried soil, and rate of N mineralization (percentage of mineralizable N in total N), which all vary across different soils and fertilization management practices. However, in several long-term experiments on paddy soils in Japan that had a continuous application of manure, the ratio of the increase in mineralizable N to the total N increased by manure application was nearly constant, indicating that soil N fertility shows a shared an upward trend when manure is applied in the long-term. The extent of these increases was proportional to the amount of total manure applied over the long-term experiments until they reach a certain level. Interestingly, when a standard level of manure was applied, it took approximately 50 years to plateau in Japan, while in the UK, the level of soil organic matter took about 100 years to plateau after the long-term application of manure. This indicates that there is a difference in organic matter stabilization under different climate conditions (Wada et al. 1981; Jenkinson and Ladd 1981). Later, the dynamics of soil organic matter accumulation was described in a mathematical model for soil in the UK (Roth C model; Coleman and Jenkinson 1996), and then modified to fit paddy soil with some modifications to the decomposition rate and other parameters (Shirato and Yokozawa 2005).

N mineralization in the paddy soils of Japan and the Philippines were first investigated using mathematical first-order kinetics models (Inubushi, Wada, and Takai 1985). It was discovered that N mineralization was regulated by two parameters: namely, the total organic nitrogen content and the clay content. The former parameter regulates mineralization potentials, and the second parameter regulates the mineralization rate constant. Mineralization potentials were positively correlated with the total amount of soil N, while mineralization rate constants were negatively correlated with clay content. Interestingly, the slope of the linear regression showing a negative correlation between mineralization rate and clay content was different for Japanese and Philippine soil, the former slope being about half of the later slope. N mineralization is affected by in situ soil temperature, but it has been suggested that, even under the same incubation temperature, the rate constants remain some influences of the soil origins, either temperate or tropical conditions.

2. Quantification of microbial biomass in Japanese and Philippine paddy soils

The soil microbial biomass is the active nutrient pools of nitrogen and phosphorus among other elements, and it is also an engine for nutrient turnover (Jenkinson and Ladd 1981). It was first examined via the chloroform-fumigation incubation method that was originally developed for aerobic upland soils, and later adapted for paddy soil under water-logged conditions in Japan and the Philippines after some modifications (Inubushi, Wada, and Takai 1984; Inubushi and Watanabe 1986). In the incubation experiment, ¹⁵N from both labeled ammonium sulfate and ¹⁵N₂ gas was incorporated into microbial biomass for a short period (−1 week), and then re-mineralized at the end of the incubation period (−4 weeks) (Inubushi and Watanabe 1987). In field experiments using the ¹⁵N tracer technique, it was discovered that the soil microbial biomass supplied nitrogen to rice plants, especially during the active rice growth stage. N supplied by the microbial biomass was proportional to the N uptake by rice plant. However, the ratio of N uptake to biomass N varied depending on soil type, and decreased with the application of organic matter (Inubushi et al. 1997a). The turn-over rate of nitrogen in microbial biomass in paddy soil was much faster in Japan and the Philippines (Inubushi and Watanabe 1986; Shibahara, Yamamuro, and Inubushi 1998) than it was in upland soils in Japan (Sakamoto and Hodono 2000) and the UK (Jenkinson and Ladd 1981) during the growing season.

The chloroform-fumigation extraction method was also modified to suit submerged paddy soil. It was used to compare the microbial biomass in a long-term paddy experimental station in Kounosu, Japan, with the microbial biomass in upland soil at the Rothamsted Experimental Station in Harpenden, UK. The results showed that the amount of microbial biomass decreased rapidly during anaerobic incubation, more rapidly in the Harpenden soils, but it recovered quickly after a short aeration period. This was especially so in the Konosu soils, as was confirmed by ATP measurements, all of which indicate that the unique characteristics of the soil microbial biomass in paddy soil are adapted to regular flooding-drying cycles (Inubushi, Brookes, and Jenkinson 1989a, 1991). Microbial biomass C and N contents were closely related each other, but the ratio of C to N in microbial biomass depended on paddy soil type and drainage condition during the winter fallow season in Japan (Shibahara and Inubushi 1995) and in the Philippines (Witt et al. 2000). In long-term rice-wheat experiments in Kyushu, Japan; Ludhiana, India; and Bhairahawa, Nepal, organic amendments affected soil parameters including microbial biomass (Tirol-Padre et al. 2005, 2007). Even in Uganda, located in sub-Saharan Africa, fertilizer managements in the long-term experiment affected the biochemical and microbiological properties of the soil, including its microbial biomass, in NERICA (New Rice for Africa) cultivated upland (Inubushi et al. 2020), where available P was another important factor. On the basis of these studies, organic manure has been recognized as essential for sustainably maintaining soil quality. Furthermore, the amount of organic manure needed to supplement inorganic fertilizers must be optimized to increase C, N and P accumulation in the soil without negatively affecting the crop yield.

3. Dynamics of elements in soil microbial biomass and its community

In Japan, heavy metal (such as cadmium, mercury and arsenicum) contamination of paddy soils became a serious problem starting from the 1880s, mostly due to mining activities (Arao et al. 2010). However, some soil parent materials in some area already contained heavy metals substantially. When heavy metal-contaminated paddy fields were reclaimed by covering with uncontaminated low-fertile mountain soil, the microbial biomass proved to be a good indicator for evaluating how soil fertility recovered in the reclaimed fields and how it was stabilized with the amendment of organic matter (Yoshikawa and Inubushi 1995).

As significant linear relationship was observed between the microbial biomass C content and the total amount of phospholipid fatty acid (PFLA) in the surface (0–1 cm) and sub-surface (1–10 cm) soils of paddy fields (Acquaye et al. 2000; Inubushi et al. 2002a; Acquaye and Inubushi 2004a, 2004b). The effect of different fertilizer types on the microbial biomass N content was small, even with a 20% reduction in coated urea application compared to uncoated urea (Inubushi and Acquaye 2004). The difference was also small across different soil types, but was clearer between different soil layers (surface or subsurface). A similar result was also obtained for microbial diversity; fertilizer type and soil type did not have much of an effect on PFLA, but soil layers and timing (flooding or pre-flooding) significantly affected diversity, indicating that these factors are more determinant than soil types or fertilizer type (Inubushi and Nagano 2017). This is likely because subsurface soil is more anaerobic than surface soil during rice cultivation, and the oxygenated surface soil is more hospitable for phototrophic microorganisms. These features of soil biodiversity may be common characteristics in various paddy soil ecosystems, although much more diversity was found in flooded water, plant debris and compost (Kimura and Asakawa 2006). The microbial diversity in paddy soil has also been studied using DNA and RNA techniques, with work done on denitrifiers (Yoshida et al. 2009), methanogens (Watanabe, Kimura, and Asakawa 2006) and microbial biomass K in paddy soil (Yamashita et al. 2014). The results suggested that better soil management is required to reduce N loss via denitrification and C loss via methane emission, and also that better K fertilizer management is important for the sustainability of the environment. The diversity of methanogens in paddy soil was also reviewed (Dubey 2005), and examined in Indian paddy soils with Japanese group to find some similarities with Japanese paddy soils (Dubey et al. 2014).

4. Organic matter decomposition and methane production in paddy soil

Organic matter decomposition in paddy soil occurs anaerobically under submerged conditions via a series of reduction reactions, until methane (CH₄), a greenhouse gas, is produced as the end product in the final stage of the reduction process. Based on a quantitative analysis of these reactions (Inubushi, Wada, and Takai 1984), the rapid decomposition of organic matter in the early stage of submergence is mainly associated with Fe (II) formation, while the gradual decomposition of organic matter in the later stages of submergence is associated with the formation of volatile fatty acids (VFA) and CH₄. Paddy fields are regarded as one of the most important sources of CH₄, a gas that has about 30 times stronger global warming potential (GWP) than CO₂ in molar basis that could enhance climate change (IPCC 2013). The total amounts of CH₄, CO₂ and accumulated VFA produced were set into a mathematical model based on first-order kinetics, similar to the nitrogen mineralization model (Inubushi et al. 1997b), which showed that organic matter decomposition is parallelly proceeding in carbon and nitrogen. Their decomposition rates were influenced by temperature and other soil condition, such as air-drying and amendment, among others. In these studies, it was also found that CH₄ production decreased when Fe and fertilizers containing S were added (Inubushi, Umebayashi, and Wada 1990a; Inubushi et al. 1997b; Furukawa, Tsuji, and Inubushi 2001). The balance and relationship between oxidizing agents, especially soil Fe, and reducing agents, namely soil organic matter, on methane production was investigated in Southeast Asian paddy, and results showed a similar relationship between oxidizing and reducing agents as has been observed in Japanese paddy soils (Inubushi et al. 2018).

5. Methane emission from paddy field and mitigation strategies

The handy potable chamber method was established to measure the methane gas flux of paddy soil, and results confirmed that the rice plant itself is a major passage of methane flux from soil to the atmosphere, while gas buddle is a minor passage (Inubushi et al. 1989b). It has also been demonstrated that mid-summer draining of the fields significantly reduced the methane flux in sites in Japan (Inubushi et al. 1990b; Yagi et al. 1996) and Indonesia (Hadi, Inubushi, and Yagi 2010), and this practice has been widely disseminated in Japan through regional and governmental supports. The alternate wetting and drying (AWD) management system has also been tested in Indonesia, the Philippines, Thailand, Vietnam (Setyanto et al. 2018; Sibayan et al. 2018; Tirol-Padre et al. 2018; Chidthaisong et al. 2018; Tran et al. 2018) and India (Oo et al. 2017). Another strategy to reduce methane emission from paddy fields is the amendment of silicate fertilizer with iron sourced from steel slag, which has been shown to reduce methane emission in Japan (Furukawa and Inubushi 2002; Singla and Inubushi 2015) as well as in Vietnam (a reduction ratio of 3%₋50%; Figure 1), while also increasing rice yield (Figure 2), as seen in other Asian countries. Steel-making slag began being used as a silicate fertilizer in Japan in 1956 because steel-making slag contains a significant amount of available silica, which is an important element for rice growth (Ma and Takahashi 2002; Darmawani et al. 2006). The effect of steel-making slag on rice yield was seen in some field experiments in Vietnam, especially in soils with low available silicate, measured using the incubation method (JSSSPN 1986) (Figure 3). Silicon elution from steel-making slag fertilizers into a paddy field has also been visualized using an electron probe micro-analyzer (EPMA) (Ito, Shiratori, and Inubushi 2015). To mitigate methane emissions from paddy fields, measuring the rate of methane oxidation and methanotrophs activity are also important, particularly in rice plant-soil systems that have different rice cultivars and growth stages (Inubushi et al. 2002b). Another mitigation strategy to reduce CH₄ emission from paddy fields is via organic farming using aquatic weeds, especially those that have a high methane-oxidation capability (Inubushi et al. 2001), as well as microbes such as photosynthetic bacteria (Kato, Iwaishi, and Inubushi 2008). Further investigations are needed to test these strategies, such as root-associated soil methanotrophic bacteria as shown by Bao et al. (2014).

Figure 1. Effect of steel making slag on methane emissions in paddy fields in Vietnam. The yield scale total CH₄ emission (amount of total CH₄ emission divided by rice yield) was calculated for each treatment, and the ratio (the yield scale CH₄ emission from steel slag treated plot)/(the yield scale CH₄ emission from control) was plotted in the Y-axis. Open bar □ indicates summer season, closed bar ■ indicates spring season

Figure 2. Effect of steel making slag on rice grain yield in Vietnam. The ratio (the yield in steel slag treated plot)/(the yield in control plot)

Figure 3. Available SiO₂ in paddy soil samples

6. Effect of elevated CO₂ on methane and soil microbial biomass in paddy soil

To plan a sustainable agricultural management system, the effect of elevated atmospheric CO₂ on agricultural ecosystem should be investigated. At first, effects of elevated CO₂ levels on soil biological functions were investigated in microcosm experiments without rice plants. It was found that the soil microbial biomass was increased but CH₄ emissions were decreased by elevated CO₂ due to the higher O₂ content produced by higher photosynthesis rates in flooded water, as well as due to methane oxidation (Inubushi, Cheng, and Chander 1999; Cheng, Chander, and Inubushi 2000). However, in a paddy field under free-air CO₂ enrichment (FACE) conditions in Shizukuishi, Iwate, an elevated CO₂ also increased CH₄ emission, due more to enhanced rice plant growth rather than CH₄ oxidation (Inubushi et al. 2003a), which indicates positive feedback loop exacerbating global warming. Under normal N fertilizer application levels, available N decreased for the rice plants, soil microbial biomass N content also decreased, while biological N₂ fixation activity increased (Hoque et al. 2001). However, under a higher application rate of N fertilizer, research in China showed that CH₄ emissions increased with an increase in N application rate under elevated CO₂ conditions (Zheng et al. 2006). These are important insights to inform and manage future agroecosystems that will live under elevated atmospheric CO₂ conditions. Further investigations in rice FACE in Tsukubamirai, Ibaraki, are continuing on elevated soil temperature, with results being evaluated using carbon isotope signature changes (as seen in Hayashi et al. 2014; Matsushima et al. 2018)

7. Tropical peat soil, wetland, and permafrost forest soil

Similar to paddy soil, peat soil is found in wetlands under waterlogged conditions. Although wetlands occupy only 4%–6% of the land surface area of the world (Aselmann and Crutzen 1989), it holds about 20%–25% of the terrestrial carbon and nitrogen (Batjes 1996). Approximately 29 million ha of peat is in the tropical region, and a large proportion of that is on Borneo Island (Driesen 1978; Takai 1997). Tropical peatlands can become a source of greenhouse gas emissions because they store large amounts of soil carbon and nitrogen. However, these emissions are strongly influenced by soil moisture conditions. The tropical monsoon climate is characterized typically by its wet and dry seasons. Seasonal changes in the emission of CO₂, CH₄ and nitrous oxide (N₂O) were measured using the closed chamber method for over a year at three sites (secondary forest, paddy field and upland field) in the tropical peatland in South Kalimantan, Indonesia (Inubushi et al. 2003b; Hadi et al. 2000, 2005). The quantity of gases emitted from the fields varied tremendously according to the seasonal pattern of precipitation; methane emission rates, in particular, were strongly correlated with precipitation. Converting secondary forest peatland into paddy fields tended to increase the annual emissions of CO₂ and CH₄ to the atmosphere, while changing land cover from secondary forest to upland field tended to decrease these emissions. However, no clear trend was observed for N₂O, which had both positive and negative values at all three sites. Similarly, monthly measurements of CO₂, CH₄, and N₂O fluxes in peat soils were recorded and compared with the groundwater level for over a year at four sites (drained forest, upland cassava (Manihot esculenta) plantation, upland paddy fields, lowland paddy fields) located in Jambi province, Indonesia (Furukawa et al. 2005). Land-use change from drained forest to lowland paddy field significantly decreased CO₂ and N₂O fluxes but increased the CH₄ flux in the soils. Changing a drained forest into a cassava field significantly increased the N₂O flux, but had no significant influence on CO₂ and CH₄ fluxes in the soil. Groundwater levels of the drained forest and the upland crop fields had gone down due to drainage ditches getting dug out, while swamp forest and lowland paddy fields were flooded. Groundwater levels were also affected by precipitation. Groundwater levels were found to be negatively correlated to CO₂ flux but positively related to CH₄ flux at all investigation sites. The greatest N₂O flux was observed a groundwater level of −20 cm. The effects of land-use changes factors such as intensity of drainage, forest fires, and agricultural land use conversion, on the control of gas emission factors were also investigated by looking at the characteristics of the microbes in tropical peat soils in Central Kalimantan, Indonesia (Arai et al. 2014a). The influences of water depth and soil amelioration on greenhouse gas emissions from peat soil columns has also been investigated, which were similar in tendency as in the field and were easier method to monitor over a short period but not over a long period (Susilawati et al. 2016). Another factors controlling CH₄ fluxes in peat soil is the water-filled pore space (WFPS), which showed a significantly positive relationship with CH₄ fluxes and a negative relationship with the of methanotrophs populations. However, the methanotrophic community was unaffected by drainage and forest fires (Arai et al. 2014b). In oil palm plantations, even with well-managed drainage, tropical peat soil can become significant sources of CO₂ and N₂O (Sakata et al. 2015). On the other hand, natural mangrove ecosystems in Vietnam and India showed limited amounts of CH₄ flux, that was influenced by the chemical properties, natural vegetation, and tidal water movement of this unique ecosystem with its salt-tolerant methanogenic community (Arai et al. 2016). The methanogenic and methanotrophic activity and community structure and how they relate to CO₂ and CH₄ emissions in the frozen soil core samples taken from Alaskan permafrost forest have also been investigated (Nagano et al. 2018), with results indicating that global warming is affecting CH₄ release from the thawing of frozen soil.

8. Andosols

In Japan, about half of all arable lands are paddy fields, while the other half are upland fields (MAFF (Ministry of Agriculture, Fishery and Forestry) 1991). A quarter of the total of arable lands is covered by Andosols or Andisols that are derived from volcanic parent material, and similar conditions are found in other Asian countries with volcanos, such as the Philippines and Indonesia (Parfitt and Clayden 1991). The microbial biomass and greenhouse gas dynamics in Andosol and non-Andosol soils were also compared. The ratio of microbial biomass C to total C in Andosol was found to be much smaller than in non-Andosol soils (Inubushi, Sakamoto, and Sawamoto 2005), which indicates a much slower soil organic matter turnover and stability in Andosols. The effect of organic fertilizer on microbial biomass was also examined in Andosols in vegetable fields, in the context of crop growth and greenhouse gas emissions (Goyal et al. 1999; Goyal, Sakamoto, and Inubushi 2000, 2006a, b; Inubushi et al. 2000; Nagano et al. 2012a). Several organic treatments, even over a short period (<2 years) increased both microbial biomass and crop growth to some extent. The environmental impact of recycling organic residues in grassland was also investigated (Ushiwata, Sasa, and Inubushi 2007). The effects can be seen not only in the surface soil but also in the subsurface soils (Zaman et al. 2002a, b, 2004; Matsushima, Choi, and Inubushi 2009). The ratio of soil microbial biomass C (MBC) and soil organic C (SOC) was compared in an Andosol and non-Andosol (sand-dune Regosol) soils from Japan and at Rothamsted Experimental Station, UK (Inubushi and Kong 2014). A significant linear correlation was found between MBC and SOC in Japanese Andosols, but the slope of the linear regression (MBC/SOC) was significantly less steep for Andosols than for non-Andosols. This indicates that MBC was relatively lower at the same SOC level in the Andosol than non-Andosol. Subsurface Andosol buried in paleosol had a higher MBC than the upper subsoil layer, indicating that the accumulated soil C may become a substrate for microorganisms even thousands of years after eruption and surface horizon formation (Inubushi and Kong 2014). These findings highlight the unique characteristics of microbial biomass and C turnover in Andosols. Even when Andosols naturally contain large amounts of soil organic matter due to acidic soil conditions, microbial biomass and activity are sensitive indicators that can show how soil organic matter changes.

Microbial biomass and greenhouse gas production and consumption potential of Andosols and non-Andosols under different land-use types were compared in central Japan and eastern Hungary, respectively, showing that aside from climatic conditions, also soil type and land-use type were principal factors influencing soil microbial properties and greenhouse gas dynamics (Kong et al. 2013a; 2013b). Another field investigation into land-use history was conducted in semi-dry Eurasian steppe soil. The effects of land-use change history (cultivated land changing back to preserved grassland after 18 years) on microbial biomass and activity were examined by taking soil and gas samples from nearby sites with a similar soil type but with different land-use history. Microbial biomass C was significantly larger in former pastures than in former crop land, both having been converted and currently under preserved grassland. However, there was no significant difference in CO₂ efflux between the two sites, indicating that the microbial biomass was affected not only by the current land-use type but also by prior land-use (Nagano et al. 2012b). Soil microbial biomass can therefore be a useful environmental index, especially under such critical or extreme conditions.

Research has been done on the influence of vegetation types and soil properties on microbial biomass carbon and metabolic quotients in temperate volcanic and tropical forest soils (Xu, Inubushi, and Sakamoto 2006. Xu et al. 2007; Nagano et al. 2012a). An investigation using multiple timescale variations and controls of soil/root respiration and soil microbial biomass in a tropical dry Dipterocarp forest in western Thailand found that soil microbial biomass played a crucial role in the magnitude and temporal variation of soil respiration. In this forest ecosystem, large seasonal variations in soil respiration were observed and were mainly attributed to the response of soil microbial biomass to soil moisture (Hanpattanakit et al. 2015).

9. Future research challenges

In paddy soil ecosystems, modern technology such as heavy machinery and low-cost soil management are used not only in Japan but also in many other rice-growing countries. However, their effects on soil microbes, organic matter, soil fertility, and climate change is still not clearly understood. Consequently, the effectiveness of these technologies in sustainable agriculture and land management is not yet proven. Similarly, human impact is also increasing in wetland ecosystems, via interventions such as drainage, wild-fire, and the thawing of the permafrost. Other global issues such as soil C sequestration (Lal 2020), greenhouse gas emission and consumption, climate change, land use and land cover changes, desertification, and deforestation have become more and more critical issues in many countries and regions. Soil has many characteristics and features, such as productivity, soil fertility, water holding capacity, ability to moderate climate change, biodiversity, soil health for environmental and human health, in relation to bio-elements’ (C, N, P, K, Fe, Si, etc.) cycling and air and water dynamics, which interact with each other (Figure 4). Further research with a multi-disciplinary approach to soil science is urgently needed to assess current sustainable practices and to provide long-term prospects for more sustainable agriculture and nature.

Figure 4. Bio-elements and soil multi-functions

Acknowledgments

This research was initiated under the guidance of Professor Emeritus Yasuo Takai and the late Dr. Hidenori Wada of the University of Tokyo.

Disclosure statement

No potential conflict of interest was reported by the author.

Supplementary material

Supplemental data for this article can be accessed here.