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Organic Amendments and Sustainable Agriculture: History
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Contributor: Ayansina Segun Ayangbenro , Chinenyenwa Fortune Chukwuneme , Modupe Stella Ayilara , Funso Raphael Kutu ,
Motlagomang Khantsi
, Bartholomew Saanu Adeleke , Bernard R. Glick , Olubukola Oluranti Babalola

The use of organic amendments (OAs) dates back to the origin of agriculture by humans and has been reported to have a positive influence on soil health and plant yield. OAs may originate from suitable naturally occurring plant species, food and agricultural processing industries, disposed waste materials, or crop residues, and biodegradable wastes, such as sludge to improve soil fertility.

  • soil degradation
  • organic amendments
  • soil microbiota

1. Sources of Organic Amendments (OAs) and Their Impact on Soil Properties

The production and use of organic-based fertilizers from different sources through innovative technologies represent an important fertilization strategy for promoting increased and sustainable crop production. In addition to the various OAs sources listed in the previous section, different wastes from manufacturing industries, including distillery wastes, sugar extraction residues, and paper residues have been investigated and used over the years as soil amendments [1][2][3][4]. Biochar has also been successfully used and reported as a good complementary organic fertilizer material that originates from organic biomass (plant and animal biomass, such as residential plant trimmings, food processing residues, animal manures, or forestry cuttings) and contains large amounts of organic carbon. The high organic carbon content of biochar arising from pyrolysis, which involves the heating of organic biomass at a high temperature with little or no oxygen, has been reported to be highly beneficial for soil and crop growth [1][5].
The application of OAs on agricultural soils directly enhances soil quality by modifying the physical, chemical, and biological properties of the soil. Some studies have demonstrated that applying OAs to the soil directly changes its physical properties. These improvements are due to the following: (1) reducing water and nutrient losses by increasing water holding capacity of soil; (2) enhancing nutrient cycling by stimulating existing microbial activities and populations; (3) increasing biodiversity by creating positive soil carbon budget; (4) improving soil health by suppressing soil-borne diseases; (5) increasing soil porosity and water filtration by decreasing soil bulk density; and (6) enhancing soil pH buffering capacity due to cation exchange capacity of OAs [6][7][8][9][10]. According to Zhang et al. [11], the application of OAs improves the stability of soil particles, increases the pore size, and decreases the density of bulk soil while positively impacting soil aeration and structure. The regulation of soil temperature can also be directly influenced by this practice as soil evapotranspiration decreases soil surface temperatures [12].
Organic amendments are used to offset the organic matter’s decline to improve chemical and physical properties of arable soils. Organic amendments applied topically can increase the soil’s C and N content in the top 5 cm, but they may have little to no impact below this [7]. The dry matter content of the amendment determines how much of an impact there will be. Increased carbon can improve infiltration and reduce runoff due to increased cation exchange capacity and higher resistance of soil aggregates to raindrop impact [7]. Additionally, adding OAs to soil improves its ability to store water, enhances its porosity, and reduces its bulk density [13], as well as creates greater macroporosity at the depth where OAs have been applied. Since the nature, form, and shape of OAs are crucial in the development of soil aggregates, adding OAs alone is not wholly adequate to counteract all the detrimental changes in soil chemical and physical properties [7]. Applying OAs can cause changes to the chemical properties of soil. The amount of organic C in soil can affect the surface charges needed for cation exchange capacity (CEC) and the retention of basic ions, especially magnesium and calcium, which can make the soil more acidic. Applying OAs can also lead to improved CEC. The CEC and organic C content had a direct correlation with soils with less clay [7].
Plant residues are also important soil amendments that positively influence soil structure and soil health [1][4]. The use of plant residues as soil amendment involves the addition of foliar or plant parts into the soil or growing certain crop varieties to improve soil properties. This practice is common and represents a sustainable means of replenishing the soil with important nutrients [14][15]. For example, legume crops used as covers facilitate nitrogen fixation through the help of rhizobacteria. The practice of crop rotation also preserves the soil, which makes it ready for the next crop and prevents autotoxicity [16]. Furthermore, using plant residue helps prevent wind and water erosion and increases soil water retention capacity [14]. Although, the application of plant residues as OA have been reported to produce positive effects on soils, such as the alteration of soil microbial community composition, increasing enzyme activity, and reducing soil-borne diseases. Documented evidence also focuses on species richness of pathogenic Pythium spp. and Rhizoctonia solani, following incorporation of fresh plant residues [17][18].
The addition of OAs to the soil can alter the soil pH, which can either increase or decrease depending on the type of OA and its pH [19]. Cooper et al. [20] reported a significant increase in soil pH and organic carbon compared to the control in a six-year study that included the application of compost and biochar, added separately to an agricultural field under a temperate climate. The addition of compost to the soil resulted in increased cation exchange capacity of the soil whereas biochar had no significant effect. The study also observed an increase in microbial biomass carbon, which is closely linked with an increase in pH due to the addition of compost and biochar [20]. Eventually, there was a shift toward a favorable environment for the rhizospheric microbial population to thrive and an increase in microbial biomass carbon. However, Jones et al. [21] reported that the addition of biosolids to bauxite-processing residue sand led to a decrease in pH and acidification was more evident at the higher addition rate compared to the addition of other OAs (green waste compost, spent mushroom compost, and green waste-derived biochar).
One of the most important indicators of soil fertility and soil health is the diversity of microbial populations in soils. Amending the soil with organic materials stimulates the growth of soil microbial communities and enhances the activities of the biological components of the soil because of high organic carbon present in OAs [22][23]. The application of organic manure increases the availability of micro- and macronutrients in soil, thereby increasing the population of soil microbial communities [24]. Although microbial populations in soils may be increased by the addition of OA, the number of microbes from one OA source may vary from the other [1].
Organically amending the soil for agriculture can indirectly or directly favor the growth of certain microbial communities that contribute to changes in the biological properties of the soil [25]. Previous studies have indicated that soil biological properties, such as microbial enzymes, are good indicators of soil fertility, in addition to microbial properties, which include organic compound decomposition by hydrolytic enzymes [26]. These enzymes are involved in various ongoing decomposition processes in soil. Soil amendments enriched with available carbon may cause plants to select specific microbes, leading to changes in soil biological properties [4]. This change is caused by the induction of changes in soil structure and the amount of accessible nutrients caused by microbial activities, which can influence plant exudation, growth, and health. These changes may influence agricultural productivity by increasing crop yield and suppressing the incidence of diseases by soil-borne pathogens [4]. The increase in soil organic carbon as a result of the addition of OAs provides plants with essential nutrients and improves the microbial activity in soil [27]. It also enhances soil quality by improving soil porosity and soil density, increasing water and nutrient (N, P, K, and Mg) availability for plant use, and enhancing biological activity and cation exchange capacity [1]. These all depend on the amount of nutrients present in the OAs applied.

2. Impact of Organic Amendments on the Structure and Diversity of Microbial Communities in the Rhizosphere

The structure and functions of microbial communities in the plant rhizosphere are affected by a plethora of biotic and abiotic factors, some of which are soil properties [28], genotype [29], plant species [30], plant developmental stage [29], and fertilization [31]. Moreover, long-term fertilization is a critical factor that determines the properties of both the rhizosphere and bulk soils and their microbial inhabitants.
Organic materials and mineral fertilizer provide bulk soil with large amounts of nutrients. Without these additional nutrients, this soil would have otherwise been regarded as an oligotrophic environment. These nutrients both increase the activity of several dormant microbes and decrease the rhizosphere microbiome’s reliance on being plant-derived [32]. Therefore, prolonged fertilization modifies both the structure and function of the soil microbial population as well as the interactions between plants and microbial communities [32]. Another significant factor influencing soil microbial communities is pH, which is significantly decreased when nitrogen fertilizers comprising urea and ammonia are applied [33]. The metabolic capabilities of microbial communities in decomposing C pools can potentially change as a result of N addition [34]. Organic fertilizers on the other hand, add a significant amount of C, other nutrients, and associated microbes to the soil, in addition to N. Previous research has demonstrated that the condition of cultivated soil determines which native microbes will be exposed to its roots and this could be activated by root exudates [28][35]. As a result, the addition of OAs to agricultural soils would modify the bulk soil microbiome. This opens the door to the possibility of modifying the native microbial communities in the rhizosphere of plants by introducing different kinds of substrates into the soil to improve microbial functions in the rhizosphere soil and increase crop yield.
Studies have suggested that fertilization shapes the composition of rhizosphere microbiomes compared to other factors, such as plant, soil properties, and rhizosphere effect [36][37]. OAs change the composition of rhizosphere soil microbiota, with an increase in prokaryotic richness and the formation of prokaryotic groups known to be associated with the breakdown of complex organic compounds, such as compost and manure [38][39][40]. Semenov et al. [36] also reported a higher abundance of nitrifiers and denitrifiers within prokaryotic communities in NPK-amended soils compared to manured soils. However, increased soil properties and nutrients were observed in manure-amended soils compared to NPK-amended soils. The authors suggested that fertilization affects soil properties, which has significant effects on microbial composition and diversity; hence, the higher total porosity and aggregation observed in manure-amended soils resulted in a more conducive environment, with optimal nutrient and water balance for bacterial communities to thrive.
On the other hand, soil protists are so responsive to environmental factors. Their mode of response to biotic and abiotic factors from fungi and bacteria also differs [41]. Among the environmental factors, the effects of nitrogen fertilizer on protists communities, particularly the phagotrophs, were more pronounced than those on bacterial and fungal communities [42][43]. This could be partially explained by higher ammonia levels caused by nitrogen fertilizers, which can inhibit protist growth by disrupting their cells [44]. In paddy soils, it was shown that phagotrophic protist communities consume bacteria, thereby altering their communities [45][46]. The studies reported that in the paddy soils, the predatory activities of phagotrophic protists influence methane cycling [47][48], fungal, as well as bacterial communities, particularly, those associated with nitrogen cycling [46][49][50], which in turn promotes the growth of rice plants [45][46][50].
Chemical fertilizers do not only affect the diversity of soil protists, but agricultural land-use also impacts protist communities by modifying the pH, organic matter, and moisture contents of soils [51]. Phagotrophic and autotrophic protists reacted differently to changes in soil porosity and nutrients induced by biochar amendments [52]. Altogether, earlier studies demonstrated that protists are more vulnerable to environmental changes than their bacterial and fungal counterparts, especially in relation to climate, soil nutrients, soil water nutrients, and plant rhizosphere effects [41]. Furthermore, previous studies using T-RFLP and DGGE highlighted that the major drivers of protist community changes are organic and inorganic fertilizers [53], soil oxygen and water availability, and the rhizosphere effect [54][55]. However, a study using the high throughput sequencing method reported a significantly higher richness and diversity of protist community in bulk soils compared to those observed in the rhizosphere soils of the three fertilizer treatments [56]. Moreover, bio-fertilizer application to bulk soils resulted in significantly higher richness and diversity of protists, as opposed to the chemical fertilizer treatment. In the research, organic fertilizer and bio-fertilizer treatments showed higher richness and diversity in both the rhizosphere and bulk soils compared to the chemical fertilizer-treated soils, although, the differences were not significant.
Microbial communities within the plant rhizosphere play major roles in plant growth and health. For example, an increase in the community diversity of rhizosphere microbes promoted the growth of strawberry (Fragaria × ananassa Duch.) seedlings [57]. The research investigated the effects of using apple fruit fermentation (AFF) alone or in conjunction with Bacillus licheniformis on strawberry tissue culture seedlings in vitro. The rhizosphere of the control matrix (water treated) had the most bacterial species, whereas the rhizosphere soil treated with B. licheniformis alone had the least diversity. Coprinus atramentarius, B. megaterium, B. licheniformis, Weissella, and B. subtilis were found to be the most common bacteria in AFF. When AFF and B. licheniformis were combined in one treatment, the leaf area, plant height, root length, plant weight, and antioxidant enzyme activities were all significantly increased. The research concludes that treating the matrix with AFF and B. licheniformis increases antioxidant enzyme activity in strawberry seedlings, improves rhizosphere microbial status, and promotes plant growth [57].
The composition of microbial communities and soil enzyme activities can be manipulated through the application of OAs [58][59]. According to Zhang et al. [60], OA (a mixture of cassava residue, ground tobacco, mushroom compost, concentrated molasses, and filter mud from a sugar factory) can stimulate the activities of soil microbes and improve synergistic interactions within microbial populations in a given habitat, thus increasing plant biomass. Soils amended with organic fertilizer were reported to be dominated by specific microbial groups, known to be associated with the degradation of complex organic compounds such as manure and compost [38]. Some field studies have also reported that the application of bio-organic fertilizer over a long term can alter the rhizosphere community composition of tomato and banana plants [61][62]. The bacterial diversity and relative abundance of the plant growth-promoting bacteria Pseudomonas, Burkholderia, and Chrysosporium were increased in the rhizosphere of kiwifruit after the application of composted pig and sheep dung [63]. The authors concluded that long-term application of OA may improve the productivity of kiwifruit by increasing the populations of plant growth-promoting microbes and simultaneously suppressing the growth of plant pathogens. Other studies have shown that OAs, such as manure and composted plant residues, can inhibit the growth of Fusarium populations by promoting the growth of potential biocontrol populations in the plant rhizosphere. For example, the application of compost amendments resulted in the suppression of the population of Fusarium wilt-causing strains and increased the populations of beneficial fungi, bacteria, and actinomycetes in spinach [64]. In another study, the application of bio-organic fertilizers increased the abundance of Sphingomonas and Gemmatimonas and reduced the incidence of Fusarium wilt disease in banana plants [65].

3. Organic Amendment and Disease Suppressive Soils

The term “suppressive soils” refers to those where the development of disease is minimal even in the presence of a virulent pathogen and a susceptible plant host [66]. Contrarily, in non-suppressive soils, where abiotic and biotic factors encourage the pathogen, disease is easily transmitted [67]. Suppressive soils are also described as soils where a pathogen either does not persist or establish, establishes but causes little to no disease, or develops and initially causes disease but subsequently the disease declines with subsequent crops of a susceptible host despite the pathogens perhaps still persisting in the soil [68][69]. Some disease-suppressive soils are naturally occurring and reliant upon the chemical or physical characteristics of the soil, whereas in other systems, a soil’s ability to slow the spread of disease evolves over time in response to particular agronomic practices [68], such as the addition of OAs, such as green manure.
The activity of disease-suppressive soils depends on a combination of “general” and “specific” suppression. General suppression is the ability of soils to restrict the growth and activity of soilborne pathogens to some extent, caused by the overall competitive and antagonistic activity of the entire soil microbiome that is in completion with the pathogen(s) [68][69]. It is a natural and inherent property of soil that is effective against a wide range of soilborne diseases. It is not transferrable from one soil to another or a field to the other with very small amounts of microbial inoculum or soil [69]. General suppression is reduced by steaming and is eliminated by soil sterilization but can be enhanced by agronomic practices that increase the diversity, population size, and activity of soil microbiomes [69].
Specific suppression is highly effective and specific species or select groups of microorganisms cause it. It can be transferred by mixing pure cultures or very small amounts, between 1–10% of suppressive soil with conducive soil [69]. Specific suppression is eliminated by pasteurization at 55–60 °C for 30 min [70] and soil fumigation with methyl bromide [69]. The key element that distinguishes specific suppression from general suppression is the ability to transfer by adding a small amount of soil or an inoculum of the responsible microbial species. Transferring 1% or 10% to a favorable soil ultimately results in a same level of suppression. It does not take much for a population of a particular organism to get established in its niche since specific suppression is caused by a population rather than a community [69].
By selectively enriching for populations of pathogen antagonists, OAs are frequently investigated as an environmentally benign method of controlling soilborne pathogens. The most popular OAs used in this context has been composts, which have shown notable levels of efficacy, especially in controlled environments or container-based production systems. The most frequent explanation for effectiveness has been an increase in biological activity in a soil system; however, in other systems, a distinct component of the microbial community and an operational mechanism have been identified [66]. The inability to accurately duplicate compost composition, both from a substrate and microbial perspective, is a significant drawback of this method [66].
Studies have demonstrated that OAs can effectively control diseases caused by pathogens, such as Ralstonia solanacearum [71], Rosellinia necatrix [25], and Fusarium spp. [64][65]. Different mechanisms have been proposed to be responsible for the suppressive nature of OAs and these include increased antagonistic microbial activity, increased competition against pathogen for natural resources that causes antibiosis, parasitism, release of toxic compounds during organic matter decomposition, or the induction of systemic resistance in the host plant [67][72]. Competition for carbon by non-pathogenic Fusarium oxysporum [73] and competition for iron by rhizosphere bacteria through the production of siderophores [74] were demonstrated to be important processes for Fusarium wilt suppressive soils. The all-encompassing pathogens of wheat and barley, F. oxysporum and Gaeumannomyces graminis, were suppressed by the addition of siderophore-producing Pseudomonas from suppressive soils or their siderophores into conducive soils [75].
The efficacy of rhizosphere organisms can also be increased through the addition of OAs to increase their activities against pathogens. Streptomyces, an efficient soil saprophytes, are particularly likely to react to the incorporation of organic material into soil and are frequently the microbial agents responsible for causing amendment-induced suppression [66][69]. Klein et al. [76] studied root-associated microbial communities in connection to suppression and supplemented soils with wild rocket (Diplotaxis tenuifolia) to boost the general suppressiveness to F. oxysporum f. sp. radicis-cucumerinum. In contrast to the unamended (conducive) soil, the amended soil had a higher relative abundance of root-associated Streptomyces. This shift also occurred in non-inoculated controls, and the induced suppression was thought to happen regardless of the presence of the pathogen. The research discovered that 3 days after amendment, a population of S. humidus thought to be hostile to phytopathogenic fungi predominated root actinobacteria by observing changes in the actinobacterial community. However, suppressive soils also saw a surge in other potential antagonists [76].

4. Potential Negative Effects of Organic Amendment

The application of OA can be either beneficial or harmful to plant growth and soil ecosystems. The harmful agents, such as organic pollutants, heavy metals, human pathogens, and antibiotic-resistance genes, that may be present in OAs negatively influence soil health [77]. In addition, excess, inappropriate and uncontrollable use of OAs can pose hazardous effects on terrestrial and aquatic habitats [78]. For instance, soil acidification, the release of greenhouse gases, nutrient immobilization, eutrophication, and excess nutrient discharge into bodies of water result from surface run-off and create undesirable ecological disturbances [79].
Another negative impact of OAs is metal toxicity, which alters soil chemistry and health. Metal toxicity depends on the metal concentration in the soil, although this can be different from the actual values when measured [80]. The long-term persistence and non-biodegradable nature of heavy metals coupled with continuous OA application have resulted in metal accumulation in soil, thus posing potential risks of metal biomagnification and bioaccumulation along different trophic levels [81]. The biotransformation of organic pollutants in the soil through the activities of soil microbes can reduce the effect of metal toxicity on soil microbes [82]. Hence, there is a need to investigate the ecotoxicity of organic pollutants present in OAs, relative to their continuous use for soil health sustainability and ecological safety.
One of the major concerns of using OA derived from animal waste is the presence of pathogenic microorganisms and parasites [79]. Some identifiable pathogenic bacteria from certain organic waste include Bacillus anthracis, Bordetella pertussis, Escherichia coli, and Klebsiella pneumoniae [83][84]. To avoid soil contamination and intrusion of pathogens into the food chain, there is a need to measure the safety level of OA before applying it to agricultural soils to avoid human health complications.
Cumulatively, the aforementioned-negative effect of OAs on the ecosystem threatens their usage in agriculture with the potential risk associated with environmental and human health [7]. These challenges vary depending on the type of OAs applied; therefore, the need to choose appropriate organic manure with less toxic effects to amend soils is important for enhancing microbial activities for plant growth and survival in diverse environments. To further avert this potential problem, research innovations, legislation guidelines, and policies on waste disposal in many countries are geared toward regulating a number of contaminants in organic waste beyond a set threshold.
The Waste Directive (EU) 2018/851, the Directive on the Landfill of Waste (1999/31/EC), the Animal Waste Directive (90/667/EEC), and the Sewage Sludge Directive (86/278/EEC) are only a few of the legislative instruments that Europe developed in an effort to mitigate these potential negative effects. Intriguingly, these laws specify threshold values for the pollutants present in organic waste and offer advice for waste disposal [77]. Accordingly, the US environmental protection agency reported that it is critical to monitor the concentrations of NH3+, NO3−, phosphate, and trace elements (Ni, Pb, and Cd) in native soil that has been amended with sewage sludge and animal manure as well as their movement into runoff and seepage water and any potential bioaccumulation in edible plants at harvest. Ten elements (As, Cd, Cr, Cu, Hg, Mo, Ni, Pb, Se, and Zn) in sewage sludge applied to soil are controlled under the USEPA Part 503 biosolids rule. In terms of trace element composition (Cu 1500, Cr 1200, Mo 75, Ni 420, Pb 300 and Zn 1400 mg kg−1), the USEPA has established standards for clean sludge and said that, if these elements fall below the typical disposal requirements, sludge may be added to agricultural land [85].

This entry is adapted from the peer-reviewed paper 10.3390/agronomy12123179

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