Orchard Soil Health—Current Challenges and Future Perspectives

Abstract

Globally, orchard soils are facing multiple severe health issues. However, different countries and regions have adopted their own soil classification standards, making many studies only useful for improving soil health in local orchards but not widely applicable to other regions. This fragmentation highlights the urgent need for internationally comparable approaches to orchard soil health assessment. Furthermore, there are currently no unified standards for screening orchard soil health indicators or establishing comprehensive evaluation indices. Many proposed orchard soil health assessment frameworks lack practical applicability. This review introduces and compares several soil health assessment methods, critically analyzes their limitations, and explores directions for improvement in their application to orchards. Additionally, it addresses the primary challenges, currently and in the future, facing orchard soil health—climate change and emerging contaminants. This review also evaluates current orchard soil health management practices, focusing on their advantages and limitations. Finally, this paper offers recommendations for data acquisition and analysis in future orchard soil health assessment frameworks and encourages the establishment of a Decision-Making Platform for Soil Health with Cross-Border Cooperation and Feedback, thereby promoting a more globally consistent perspective on orchard soil health.

1. Introduction

Soil health is widely defined as “the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans” [1]. However, in reality, global soil health is facing serious challenges; according to the report Status of the World’s Soil Resources (2015) by the Food and Agriculture Organization of the United Nations (FAO), global soils face serious degradation, which poses a major challenge to the maintenance of sustainable agriculture [2]. Among the different agricultural systems, orchards, because of their unique ecological and management characteristics, exhibit soil processes and health risks that are significantly different from those of traditional farmland [3].

In this paper, “orchard soils” refer to soil systems formed and evolved under long-term cultivation of perennial crops such as fruit or nut trees, which are typically characterized by a long cultivation cycle and low frequency of land disturbance [4]. Perennial fruit trees have deep, robust, and stably distributed root systems that can continuously absorb nutrients and water from the deeper soil layers, thus attenuating the impact of surface nutrient fluctuations on growth [5]. The organic matter of orchard soil mainly originates from fallen leaves, root apoptosis, and pruning residues, with inputs occurring primarily through surface cover and inter-root deposition [6]. The overall cycle is similar to that of woodland, which is conducive to the long-term accumulation of organic matter [7]. The root system of fruit trees is immobilized for a long period of time and continuously absorbs nutrients from the inter-roots, while the nutrient input is mainly concentrated in the surface layer, thus forming a nutrient gradient in orchard soils that is enriched in the surface layer and gradually depleted in the deeper layers [8]. In contrast, agricultural soils serve annual crops and carry away a large amount of biomass in each harvest season, with rapid nutrient loss and high dependence on exogenous fertility, and frequent soil disturbance but relatively uniform nutrient distribution [9]. The microbial communities of orchard and farmland soils differed in composition and function. The microbial richness and diversity in the 0–10 cm surface layer of orchard soil were higher, and the community distribution was more uniform, while the middle layer of 10–20 cm of farmland soil had higher microbial richness, but the dominant taxa accounted for a large proportion of the total, and the community structure showed obvious dominance. This difference may be related to the differences in vegetation cover, cultivation patterns, and management measures and may further affect the utilization of carbon sources and functional diversity of microorganisms [10]. Although orchard soils have strong nutrient buffering capacity and depletion resilience in the short term, in the long term, nutrient fixation in the tree and inter-root depletion accumulation, as well as the long cultivation cycle and low disturbance frequency limit key management measures such as crop rotation and deep plowing, which are important for optimizing root structure, regulating microbial communities, regulating microbial communities, improving soil fertility, and improving soil physical properties [11,12]. Orchard soils are also prone to “hidden degradation”, i.e., a gradual decline in soil fertility and microbial ecological functioning while surface yields are maintained and soil health problems accumulate. This unique developmental trajectory gives orchard soils the advantages of soil carbon storage [6] and soil and water conservation [13], but they are also more susceptible to specific degradation processes such as soil compaction [14], accumulation of heavy metals [15] and pesticide residues [16], and enrichment of diseased microorganisms in soil [17], among other forms of soil degradation.

The problem of orchard soil degradation has widespread negative impacts. A direct consequence is a decline in orchard productivity [18]. According to the Food and Agriculture Organization Corporate Statistical Database (FAOSTAT) statistics, the fruit trade generates substantial global economic benefits and is an important pillar of global agricultural trade [19]. The decline in productivity directly threatens the stability of this economic benefit and may lead to global economic losses. On the other hand, in addition to economic benefits, orchards also provide important ecosystem services like soil moisture regulation, nutrient cycle regulation, and soil carbon storage [20]. Orchard soil degradation can also harm ecological environment.

Soil classification systems in different countries and regions vary widely, leading to different naming of the same soil in different regions, which increases the complexity of soil health research in cross-regional orchards [21]. If fruit tree cultivation is established on unsuitable soil types, it is difficult to truly reflect the ecological suitability of the soil itself, even if it relies on high-input management to maintain yield. Therefore, mapping fruit tree production to internationally recognized soil classification systems and identifying the suitability of typical soil types are important prerequisites for improving the comparability of soil health assessment in orchards around the world.

Currently, there is a lack of specialized and widely applied assessment frameworks for orchard soil health; existing mainstream soil health assessment frameworks are primarily based on the concept of agricultural systems [22]. Although these frameworks provide some reference for orchard soil health research, they cannot be perfectly applied to orchards. Because, although orchards belong to the agricultural classification, they also have some characteristics of forestry [4,20]. Their forestry characteristics (such as perennial woody plants, longer planting cycles, and low-frequency interventions) make it difficult for existing agricultural soil assessment frameworks to accurately evaluate orchard soil health and develop effective soil health restoration strategies.

With the ongoing changes in the external environment, orchard soils are facing a series of new health threats, such as extreme weather events driven by climate change [23] and the accumulation of emerging contaminants (ECs) (such as microplastic residues) [24]. To effectively address these challenges, orchard management measures urgently need to be strengthened and updated.

Orchard soil health is an important part of sustainable orchard management, and many practices aimed at improving orchard sustainability prioritize improving soil health [25,26,27]. Currently, various improvement measures have been applied to orchard soil health management, such as planting cover crops [28], implementing organic orchard management [29], and applying biochar [30]. None of these measures is a perfect solution, each with its own advantages and disadvantages. Therefore, analyzing their specific effects and applicability is crucial for addressing orchard soil health issues in a targeted manner.

This review will systematically sort out the key issues facing orchard soil health, summarize and review the strengths and limitations of existing soil health assessment systems, analyze the soil health challenges that orchards may face in the future, and introduce three major orchard soil health enhancement practices. Finally, the development of a more rational and sustainable soil health management model for orchards is discussed.

2. Soil Requirements of Fruit Trees in Orchards Worldwide

An important issue facing current orchard soil research is that different countries and regions use their own soil classification standards, resulting in the fact that the same soil may be given different names in different regions. For example, the International Union of Soil Sciences (IUSS), in its publication World Reference Base for Soil Resources (WRB) 2014, categorizes certain types of soils as Cambisols, while in Germany, they are called Braunerden and Terrae fuscae; in France, Sols bruns; and in Russia, Burozems [21]. This lack of harmonization in the classification system severely limits the accurate assessment of the adaptability of fruit trees to the soils of different countries or regions and makes the comparative study of the effect of soil factors on fruit tree growth complex and uncertain.

The research premise of the concept of soil health in orchards should be based on the cultivation of fruit trees and their ecological suitability to match the soil type. The so-called “health” has practical significance only if the soil’s physical and chemical properties, water retention capacity, nutrient supply potential, and other basic functions can meet the needs of normal growth of fruit trees [31]. On the contrary, if fruit trees are planted in soil environments that are obviously incompatible with their physiological and ecological needs, even if they are maintained in a short period of time through high-intensity fertilization, irrigation, and other human-made means, this will not truly reflect the ecological adaptability and sustainability of the soil itself, and the related soil health research will lack general applicability and guiding value. For example, Ferralsols, Podzols, Solonetz, Solonchaks, Cryosols, Arenosols, Leptosols, Plinthosols, Durisols, Regosols, Retisols, Gleysols, and Technosols, which are classified by WRB, are soils that are not suitable for orchards at all due to salinization, structural hardening, lack of oxygen, freezing or severe waterlogging, all of which directly affect the health of the root system of the fruit trees and water and fertilizer uptake, leading to a decrease in yield and quality of the fruit trees. On the contrary, Chernozems, Phaeozems, Luvisols, Cambisols, Fluvisols, Andosols, Anthrosols, Nitisols, etc., are mostly of good structure, and moderate fertility, water, and nutrients, suitable for most of the fruit trees to grow healthily, and other types of soil need to be improved in accordance with their characteristics [21]. Scientific assessment of orchard soil health should be based on the core premise of “suitability”, and the construction of a unified and standardized soil classification system is the key foundation for achieving this goal.

In view of the global demand for orchard soil health assessment, future research should promote the in-depth connection between major fruit tree production areas and international common classification systems. Based on the existing orchard soil survey, the construction of a database covering the main fruit tree species, typical soil types, and their suitability relationships will help to improve the comparability of research results between different regions and provide a more universal scientific basis for the layout of fruit tree varieties and soil management strategies.

At present, there is still a relative lack of research on the type of soil in which different fruit trees have the best suitability. This is mainly since most research on soil health in orchards focuses on guiding local production, whereas fruit tree suitability studies usually need to cover a wider geographic area, which is more time-consuming and financially demanding, making it difficult for many research teams to afford. To fill this research gap, this study comprehensively utilized the global fruit tree production distribution data provided by the Food and Agriculture Organization of the United Nations (FAO) Agricultural Statistics Database (FAOSTAT) [19], and the global WRB reference soil group distribution map [32] published by the International Union of Soil Science (IUSS), and combined with the results of the previous literature research, a table was organized and produced to show the world’s distribution areas of major fruit trees and their suitable soil types for cultivation (

Table 1. Global distribution and WRB-based suitable soil types for major orchard fruit species.

Fruit	Top Producing Countries	Soil Types
Apple	China, Russia, Turkey, Poland, Uzbekistan	Cambisols [33], Luvisols [34]
Apricot	Turkey, Iran, Uzbekistan, Algeria, Afghanistan	Cambisol [35], Chernozem [36], Fluvisol [37], Luvisol [38]
Pear	China, India, Italy, Turkey, Argentina	Cambisols [39], Fluvisol [40]
Olive	Spain, Tunisia, Morocco, Italy, Turkey	Calcisols [41], Cambisols [42], Leptosols [43], Regosols [44],
Avocado	Mexico, Colombia, Indonesia, Peru, Dominican Republic	Andosols [45], Ferralsols [46], Vertisols [47]
Mangoes & Related	India, China, Côte d’Ivoire, Indonesia, Mexico	Acrisols [48], Ferralsols [49], Fluvisols [50]
Citrus Fruits	Nigeria, China, India, Mexico, Guinea	Acrisols [51], Calcisols [52], Fluvisols [40], Luvisols [53]

). It should be noted that the WRB classification system emphasizes the natural properties of soils, so the table is only used as a reference material, not an absolute planting guidance basis.

3. Rethinking Soil Health Assessment for Orchard Systems

Soil indicators can be divided into three major categories: chemical indicators, physical indicators, and biological indicators [54]. Physical and chemical indicators are more traditional indicators, accounting for at least 40% of the indicators in 90% of soil health assessment systems in the past [1]. Soil biological communities are considered the most sensitive indicators of soil health and play a crucial role in soil function [55]. A major challenge for future orchard soil health assessments is to enhance the availability and interpretability of biological indicators. The selected indicators for orchard soil health should possess the following characteristics: relevance, representativeness, sensitivity, reproducibility, and the ability to reflect the connection between soil function and plant productivity [56]. Orchard soil health assessment cannot rely on a single indicator but requires a comprehensive assessment using multiple soil indicators to obtain accurate results [22]. Currently, our research indicates that there is no universally recognized standardized framework for assessing orchard soil health. The health status of orchard soils is primarily assessed based on locally developed soil health index (SHI) standards, and the construction of these indices is highly dependent on expert experience [57]. Although existing comprehensive soil health assessment frameworks have limitations when applied to orchard soils, they can serve as a reference for developing an orchard soil health framework that can be adjusted according to specific assessment needs. The following is a brief introduction to several mainstream soil health assessment methods and a discussion of their shortcomings in orchard applications. The main characteristics of these mainstream soil health assessment methods have been summarized in

Table 2. Characteristics of the global mainstream soil health assessment system.

System Name	Developer	Indicators	Scoring System	Advantages	Application Scope
SMAF	Karlen’s team	Tailored to management goals and site-specific factors	Nonlinear scoring curves (0 to 1)	Adaptable to local conditions and management goals Provides comprehensive assessment through integration	Used in multiple countries (e.g., Brazil, Spain, Italy, India)
CASH	Cornell University	Simplified from SMAF; now has 39 indicators	Cumulative normal distribution functions (0 to 100)	Standardized approach with fewer indicators Easy to use with practical field assessment	Used in multiple countries (e.g., USA, China, Kenya)
Soil Health Card (SHC)	India	18 indicators (physical, chemical, biological)	Nonlinear scoring functions (0 to 100) Based on expert opinion and principal component analysis	Practical tool for farmers Includes detailed recommendations and easy-to-understand results	Mainly used in India
Muencheberg Soil Quality Rating (M-SQR)	Muencheberg	20 indicators (8 basic, 12 hazard)	Quasi 5-ball scale ranking (0 to 2)	Considers hazard indicators for comprehensive soil quality assessment	Mainly used in Europe

.

The Soil Management Assessment Framework (SMAF) is one of the earliest tools used to quantify soil health, with its composite index reflecting the impact of management measures on soil function. The framework consists of three steps: indicator selection, indicator interpretation, and composite index construction. By combining management objectives with local environmental conditions, SMAF selects a minimum data set (MDS) of indicators, standardizes their scores, and integrates them into a single index that reflects the overall health of the soil [58]. Many subsequent soil health assessment tools have been optimized and improved based on the SMAF.

The Cornell University Soil Health Comprehensive Assessment (CASH) was developed by Cornell University. The CASH algorithm was initially based on a simplified SMAF. Unlike SMAF, CASH uses a cumulative normal distribution function to convert indicator values into scores ranging from 0 to 100 and has developed different scoring functions for coarse, medium, and fine-textured soils. Cornell University continues to release new versions of the CASH system, with the latest version being the third edition published in 2017. Compared to SMAF, CASH incorporates more newly proposed soil health indicators that have emerged with the times and covers soil characteristics from a broader range of regions. The construction of the soil health index emphasizes the integrated assessment of soil biological, physical, and chemical indicators, using a smaller yet more representative set of indicators in the index construction process [59].

In recent years, the yield of major food crops in the Ganges Plain region of India has stagnated or declined. To achieve efficient soil management and improve soil health, India has developed a Soil Health Card. This card is also based on SMAF and was created using expert opinions and principal component analysis to establish a minimum data set (MDS). The indicator scores use a nonlinear scoring function. The soil health index is calculated by summing the scores of each soil function multiplied by their respective weights. Compared to most soil assessment methods, the Soil Health Card has lower accuracy. But, in many developing countries with limited economic and knowledge resources, the Soil Health Card is highly valuable due to its simplicity in implementation and use [60].

The Muencheberg Soil Quality Rating (M-SQR) is a simple method for assessing farmland soil quality in the field. It includes eight basic indicators and twelve risk indicators. The M-SQR is a visual assessment method, and expert experience is key to its accuracy. It incorporates risk indicators into the scoring system, making soil health status easier to understand intuitively than other methods [61].

Not all countries have a soil health assessment framework, but most have established local soil parameter databases, such as the Australian National Soil Information System (ANSIS), the European Soil Data Centre (ESDAC), the Canadian Soil Information Service (CanSIS), the Russian Soil Geographic Database (ISSGDB), and the Latin American Soil Information System (SISLAC). In reality, most soil databases face the issue of low utilization rates, with many countries failing to promote practical application methods for farmers.

In summary, most soil health assessment methods primarily consist of three steps: (1) selecting soil indicators based on soil texture, management objectives, expert opinions, or statistical methods to construct a minimum data set (MDS); (2) converting measured values into dimensionless scores using different scoring systems; and (3) integrating all soil indicator scores into a soil health index for comprehensive assessment of soil health status [56].

SMAF and CASH are similar and widely validated standardized soil health assessment methods, akin to two different versions within the same system [58,59]. When reviewing the crop codes in CASH, we can see that fruit tree crops are not included, with most being field crops. This means that the method was originally designed with a stronger focus on use in field soils rather than orchard soils. As in the pecan case, if one wishes to use SMAF to assess fruit tree soil health, it is necessary to develop specific crop codes for tree species to enhance the framework’s accuracy and applicability [62]. In farmland dominated by annual crops, the crop growth cycle is short, nutrient requirements are relatively concentrated [63], and soil health indicators can typically be assessed based on three response patterns: the more, the better; the less, the better; and moderate is optimal. A single measurement at a specific time point can generally determine the overall soil health status. In contrast, fruit trees in orchards have longer life cycles, with each growth stage lasting for an extended period. Their nutrient requirements exhibit stage-specific characteristics [64]. A low level of certain nutrients measured at a specific stage does not necessarily indicate poor soil health, as the tree may not have a significant demand for that nutrient during that stage. Therefore, if a uniform assessment method is applied across different growth stages and relies solely on soil data from a single time point, it may be difficult to accurately reflect soil nutrient dynamics and their alignment with the physiological needs of fruit trees. Thus, the validity of these data in representing soil health status may be questionable. Additionally, the number of measured indicators is not insignificant, and specific data still relies on laboratory testing. Is the economic cost of measurement affordable for ordinary fruit farmers? SHC is also based on SMAF design and shares the same issues, but it has advantages worth considering for future orchard soil health assessment designs. Its scoring function is simple, easy to promote, low-cost, and widely applicable. However, unfortunately, its precision is somewhat lacking for soil health assessment [60]. M-SQR is a distinctive method in soil health assessment, incorporating soil risk indices as a reference. Since orchards are often located on slopes or in mountainous areas, combining the slope, erosion, and soil structure indicators from M-SQR could be used for orchard site selection or assessing soil degradation risks in slope-cultivated orchards. However, M-SQR itself notes that it is not suitable for East Asia or South Asia but is more appropriate for Europe and regions with similar ecosystems, thus limiting its applicability [61]. As for the soil databases established by various countries, they constitute a vast repository of information. In the current era of big data, by feeding these databases with data, it should be possible to develop AI systems capable of predicting soil health with high accuracy.

The application of current mainstream soil health assessment frameworks in orchard systems still faces multiple challenges. For example, there is a lack of crop specificity, as methods such as SMAF and CASH are mostly designed around field crops and lack fruit tree crop codes. Additionally, there is a lack of long-term phased assessment logic, while fruit trees have relatively clear long-term growth cycles. The lengthy sample testing cycle poses a limitation for the applicability of current methods. This is particularly problematic in small-scale orchards or in remote mountainous regions. Furthermore, existing frameworks inadequately consider topographical and risk factors, which are significant in orchards, particularly in regions with widespread hilly and sloped orchards.

To better align with orchard systems, the future soil health assessment framework urgently needs to be improved in the following areas: first, establish corresponding crop codes based on major fruit tree species (such as apples, peaches, and avocados) to enhance the framework’s adaptability and biological rationality; second, introduce a long-term, phased dynamic assessment mechanism that integrates fruit tree growth cycles and key nutrient stages, using multi-point measurements to capture the alignment between soil function and fruit tree growth, rather than relying solely on a single time point; third, develop low-cost visualization diagnostic tools to enhance ordinary fruit farmers’ real-time perception of soil health status; fourth, integrate risk assessment indicators, incorporating factors such as slope, erosion risk, and hydraulic stability into soil health scoring to adapt to the complex topographical conditions of orchards; and fifth, leverage soil big data and artificial intelligence models to integrate and train regional soil databases, meteorological data, and historical yield data, thereby constructing an intelligent prediction and management decision-support system applicable to different orchard types. This will overcome the current framework’s limitations in terms of applicability, timeliness, and scalability in orchards.

4. Challenges to Orchard Soil Health

4.1. Climate Change

According to the assessment by the United Nations climate panel, the continued rise in greenhouse gas emissions is exacerbating global climate change, with both the speed and intensity exceeding earlier expectations [65]. Rising temperatures will accelerate the release of carbon dioxide from the soil, which in turn reinforces the greenhouse effect [66]. Climate change leads to more frequent extreme weather events, such as excessive heat, torrential rains, floods, and droughts [67,68] (Figure 1). Climate change threatens orchard soil health by affecting soil structure, water balance, and erosion processes [69]. According to a process-based model of apple orchards in Southeast France under climate change, C fixation is expected to increase overall, while Soil Organic Carbon (SOC) levels are expected to decrease [70]. In northern Iran, different models yielded inconsistent predictions for SOC reserves, but all indicated that temperature is a more decisive factor than precipitation [71]. Orchard soils generally face severe erosion issues [72,73], with runoff coefficients and soil loss rates reaching 2.6 times and 11.5 times those under normal conditions, respectively, under extreme rainfall conditions [74]. In addition, climate warming has led to an increase in soil temperatures. Sixty years of data from an experimental orchard monitoring site in the Eifel Mountains near Bonn, Germany, show that soil temperatures at a depth of 20 cm have increased by about 0.9 °C in summer and 1.2 °C in winter [75]. This trend is particularly pronounced in the Mediterranean region: some orchards may face higher drought risks [76], and elevated soil temperatures may disrupt the physiological functioning of fruit trees, thereby reducing fruit set and compromising fruit quality [77]. Rising temperatures may also alter soil microbial community structures, particularly in organic orchards [78]. Meanwhile, climate warming and drought trends have significantly increased the risk of orchard soil salinization. For example, using saline irrigation water during extreme drought years can significantly exacerbate soil salinity accumulation [79,80]. Given the long life cycle of fruit trees, the long-term effects of climate change on soil will ultimately impact fruit tree growth and productivity. Fruit farmers and researchers must take proactive measures to mitigate the potential impacts of climate change on orchard soil health. Enhancing soil carbon sequestration capacity not only helps reduce greenhouse gas emissions but also enhances the sustainability of orchard systems [81]. Recycling of fruit tree residues has potential for long-term carbon sequestration [82]. In addition, soil amendment techniques such as biochar [83] and organic fertilizers [84,85] have been shown to have a positive impact on orchard soil carbon sequestration. Sustainable land management practices (e.g., no-till or minimum tillage) are widely recognized as effective interventions against soil erosion and water stress in orchards [86]. Controlled water deficit irrigation techniques have been demonstrated in several orchard systems to improve soil moisture conditions and reduce the risk of salinization [80,87]. In addition, rainwater harvesting facilities and conservation tillage practices can improve rainfall utilization efficiency in orchards and increase soil water retention capacity [88,89]. These integrated strategies will help orchards better adapt to climate change challenges.

4.2. Emerging Contaminants (ECs) in Orchard Soil

Emerging pollutants have not appeared in soil only in recent years; rather, they have been present at typically low concentrations in the environment. With the development of more sensitive detection technologies, these pollutants have gradually begun to attract attention. Emerging pollutants are difficult to remove using traditional technologies and have a longer residual time; hence, they are classified as “pseudo-persistent pollutants (i.e., pollutants that do not necessarily have a long single residual time but accumulate in the environment over time as a result of sustained release).” Additionally, despite their low environmental concentrations, they may still cause abnormalities in human or animal physiological functions. In the process of ensuring the health of orchard soils, identifying and effectively managing these emerging pollutants will become an important challenge following traditional pollution issues [90].

Microplastics are currently one of the major emerging soil pollutants, and soil microplastic abundance in orchards is usually at a higher level among different land use types, lower than agricultural land, and higher than forest land [91,92]. The abundance of microplastics in orchards was positively correlated with the population density of the study site [91], and the correlation with wind speed and rainfall varied geographically [92,93]; future climate change is likely to affect the accumulation of microplastics in different regions. Microplastics in orchards mainly originate from the use of conventional plastic mulch [94]. The abundance of microplastics in orchard soils increased with the prolongation of the use of conventional plastic mulch [24], but after accumulating for many years in some orchards, their content may have decreased, which may be related to the increased expression of functional genes related to microplastic degradation in microbial communities [95]. The input of microplastics not only changed the physical properties such as soil porosity, water-holding capacity, and organic carbon content [24] but also reduced the effectiveness of certain trace elements in orchard soils, broke the balance of the normal expression of functional genes for soil nutrient cycling, and significantly altered the structure of microbial communities, which manifested itself in the enhancement of oligotrophic bacteria and a decrease in eutrophic flora [96]. Although all countries in the world are promoting environmental protection issues and reducing the use of plastic products in daily life [97], given the practicality of conventional plastic mulch in orchard production activities and the wide range of sources of microplastics in the orchard [94,95], the desire to reduce the abundance of microplastics in the orchard soil is still a more difficult issue. Mulches in orchards are expected to be long-lasting or recyclable, and replacing common plastic mulches in orchards with soil-biodegradable plastic mulches is an alternative to consider, as is cultivating microorganisms that decompose plastics and inoculating them in orchards as a potential possibility [98]. Today’s research on microplastics in orchards focuses on the abundance of differences in the source of microplastics, and future research should focus more on the specific effects of microplastics on different orchard ecosystems, such as the presence or absence of microplastics within the fruit, and explore feasible options for reducing microplastic abundance in orchard soils.

Antibiotics are another emerging contaminant represented in orchards and were once widely used in North America for being the most effective control for fire blight management [99]. Antimicrobial resistance is a major threat to humanity, and a major factor in the emergence of resistant microorganisms is the excessive or incorrect use of antibiotics [100]. Unlike in the human body, where antibiotics are injected or swallowed, antibiotics are released into the open environment through spraying in fruit trees [101], and the use of manure in organic orchards has resulted in the introduction of large quantities of antibiotics into orchard soils [102,103]. The threat of antibiotics to the health of orchard soil is mainly focused on soil microorganisms. Antibiotics not only are effective against pathogenic microorganisms but also inhibit or kill all antibiotic-sensitive bacteria in the orchard soil, resulting in a decrease in bacterial abundance and diversity, and breaking the balance of orchard soil microorganisms [104]. The emergence of resistant strains in orchard soils and the spread of antibiotic resistance genes (ARGs) are considered to be one of the triggers of soil-borne disease outbreaks [105]. As far as we know, there are no significant means to manage antibiotics in soil, only to reduce the use of antibiotics at the source, similar to what European governments are doing [99], or to find alternatives to antibiotics [106]. In future research, we should strive to develop means of targeted killing of pathogenic bacteria in orchards to minimize damage to soil microbial communities at the source [107], and investigate means of blocking the spread of antibiotic-resistant genes to reduce the transfer of antibiotic-resistant genes throughout the food chain, thus avoiding further harm to humans and the orchard soil environment.

In addition to the two typical cases mentioned above, other types of emerging contaminants (e.g., Persistent Organic Pollutants, nanomaterials, endocrine disruptors, etc.) may also potentially affect orchard soil ecosystems and the health of fruit trees through a complex process of environmental transport and transformation [108]. However, research on these emerging contaminants in orchard soils is still very limited, and many questions remain to be solved, such as whether there is a compound effect between different emerging contaminants. What are the long-term effects of emerging contaminants on orchard soils? How effective are different soil remediation measures for different emerging contaminants? In addition, how to realize the comprehensive identification and quantitative analysis of emerging contaminants in orchard soils in a low-cost, rapid, and high-throughput way is also a major technical bottleneck in the current soil health assessment. Future research should strengthen the development of monitoring technologies and mechanisms for these emerging contaminants to fill the gaps in the existing orchard soil health assessment system and provide scientific support for the sustainable management of orchard ecosystems. Effective management of emerging contaminants in orchard soils relies on source tracking [109], regulatory controls [90], and the adoption of safer alternatives [110]. Monitoring, treatment, and risk prevention measures can further reduce their long-term impacts on orchard soils and fruit tree health.

5. Improved Orchard Soil Management Practices

5.1. Organic Agriculture

Organic orchards are often more economically productive and produce more nutritious, pesticide-free food [111]. Scientific studies continue to demonstrate the benefits of organic practices [112]. However, conventional farming is not friendly to the environment, as it can easily cause soil degradation [113]. For example, in Spain, organically managed olive orchards were found to support more complex microbial co-occurrence networks in the rhizosphere compared to conventionally managed orchards [114], indicating that orchard soil under organic management had positive effects on soil microbes. The orchards in the Mediterranean region using rainfed systems usually face high rates of soil erosion [86]. By analyzing different soil management strategies, researchers found that organic farming systems were effective in improving soil properties in olive and almond orchards [113,114]. These findings strongly suggest that organic agriculture has an important role to play in promoting the sustainable management of orchards. Although challenges such as soil erosion remain, organic farming methods show clear advantages in improving soil health, promoting microbial diversity, and enhancing the long-term resilience of agriculture. Future policies should encourage the promotion of organic farming methods in ecologically fragile areas, such as the Mediterranean, in order to mitigate environmental degradation while safeguarding the economic viability of farmers.

5.2. Cover Crop

There is no specific crop species for cover crops; any plant that is not a major cash crop can be used as a cover crop [115]. Planting cover crops in orchards has been associated with a variety of soil health benefits [116]. For example, in areas of high soil erosion and water stress, such as the Mediterranean, cover crops can help improve soil quality and reduce erosion [117]. Studies have shown that certain cover crop systems (e.g., intercropping olive trees with artificially cut natural vegetation) result in higher soil quality indices compared to bare ground systems [118].

In order to maximize benefits, it is crucial to rationally select the cover crop species and determine the optimal time of mowing [119]. Native cover crop species often outperform introduced species in maintaining soil moisture and health [120]. Cover crops also contribute to increasing orchard SOC and nitrogen (N) pools [84], mixture cover crops have a higher potential for SOC sequestration [117], and acceleration of N cycling is mainly due to the increase in the abundance of the related gene [121]. However, one study pointed out that these genes mainly occurred in the top 0 ~ 10 cm soil layer, whereas differences in these variables in deeper layers were not statistically significant [122]. Using Trifolium subterraneum as a cover crop significantly decreases the weed seed bank size [123], and it has great potential as an eco-friendly strategy for orchard soil weed management. Cover crops enhance the soil microbiome and resource availability for soil microorganisms [124,125], which in turn precisely corresponds to the situation in orchard soil, the earlier mentioned acceleration of the C and N cycle.

5.3. Biochar

Biochar, a product of biomass pyrolysis, offers a sustainable solution for improving orchard soil health [126]. We all say that the wide applicability of biochar is due to its extensive and excellent properties, such as high specific surface area (SSA), high carbon content, aromaticity, and abundant surface [127]. However, not all biochar has the same properties; the properties of biochar from varied biomass feedstock or even the same biomass could differ significantly [128]. Thus, the applications of varied biochars improve the orchard soil health from multiple perspectives.

Biochar prepared from organic waste in an orchard is an ideal choice [129]. In the citrus orchard, the finished rate of biochar produced from pruned citrus branches and interrow grass reached approximately 37%, and the C content of the finished product was as high as 80% [130]. Orange peel biochar effectively increased the SOC content [131]. In pomelo orchards, bamboo-derived biochar is a suitable candidate for the adsorption of Titanium from orchard soils [132]. Biochar applications in orchards improve microbial diversity, soil enzyme activity, and SOC sequestration [30,133,134]. Biochar can not reduce the promotion effect of N deposition on soil respiration [135], but it can promote SOC sequestration, which similarly contributes to mitigating global warming [83].

Biochar is suitable for the circular economy concept; an economic analysis of biochar shows that the production cost of biochar is between 448 and 1846 (USD Mg⁻¹) [136]. Another study shows that the application of biochar did result in a positive net financial benefit in the avocado orchard, but this was dependent on a low biochar price and was sensitive to biochar price increases [137]. Biochar demonstrates multifaceted potential for orchard soil health—enhanced carbon sequestration, microbial activity, and heavy metal remediation, among others.

6. Future Directions in Orchard Soil Health

6.1. Orchard Soil Health Data Acquisition

Sustainable orchard soil management strategies are essential for the future of agriculture to ensure long-term soil health and productivity of orchards [138]. Currently, widely used soil health assessment frameworks such as the Soil Management Assessment Framework (SMAF) and the Comprehensive Assessment of Soil Health Framework (CASH) soil health monitoring frameworks, although proposed earlier, are still well-practiced. However, if some of the shortcomings can be improved by incorporating the scientific and technological developments in recent years, they can be more relevant to the application of soil health management in orchards. Here, we propose an orchard soil health assessment and management system that combines the current new science and technology (Figure 2).

In the past, sample collection for soil health assessments often relied on human collection; the collection range was limited; most sampling methods used for the same day, for the same location, and with the multi-plot sampling method were vulnerable to environmental impact; the collection of data was limited; and the data error was larger [139]. This study suggests that soil data can be collected by combining remote sensing technology, in situ sensor technology, and macrogenomic technology. Remote sensing (RS) technology, including satellite and unmanned aerial vehicle (UAV) imagery, allows soil data to be collected over a great range through high-resolution, non-invasive measurements, and spectral analysis can be used to understand certain physicochemical parameters of the soil (e.g., soil moisture, organic matter, etc.) [140,141]. In addition to soil data, satellites and UAVs are more important for obtaining data on environmental factors that have been lacking in previous soil monitoring, such as local climate at a given time, overall vegetation cover of the land, landforms, and other data that have been less often or not taken into account in previous soil health monitoring, which makes the monitoring model data more three-dimensional [142, 143, 144]. In situ sensor technology, on the other hand, can monitor the physical and chemical data of the land over a long period time, which is more consistent and trending than the previous data volume, and will not be affected by accidental environmental factors, resulting in sampling data anomalies, which may lead to the misjudgment of the soil health status [145]. The physical and chemical data that soil sensors can monitor at present are not comprehensive, but the range of data that can be monitored is being gradually improved by the development of technology in recent years. In the future, with the improvement of soil sensor accuracy and AI technology, it may be possible to indirectly measure the activities of soil animals through vibration, soil aeration, and hydraulic conductivity data to make up for the lack of soil health monitoring of soil animal data; in short, soil sensors have a great potential in the future.

In the past, the monitoring of soil microbial indicators, often a single aspect of the data, such as soil enzyme activity, microbial volume, soil respiration, etc., has involved the acquisition of data that is too shallow [146]. Soil microorganisms are an extremely complex whole; their changes are highly dynamic, and superficial static indicators cannot predict their activities and good intervention. The use of macro-genomics technology to comprehensively analyze soil microbial communities in complex environments, analyze their complex interactions, and strengthen the network structure of microbial communities by guiding instead of destroying them can more effectively facilitate the role of microorganisms in maintaining the health of the soil and enhancing soil fertility [147].

6.2. Orchard Soil Data Analysis and Processing

In soil health assessment, the selection of diverse and comprehensive monitoring indicators helps to reflect soil health more accurately. However, with the increase in data dimensions, traditional data processing methods often face problems such as high computational costs and long data processing cycles, which limit their application in large-scale soil health assessment. Therefore, building a unified orchard big data cloud platform to integrate and efficiently process multi-source soil data is a strategy worth considering in orchard soil health monitoring. Soil monitoring data acquired by the remote sensing, in situ sensor, and genomics technologies mentioned above can be directly imported into the cloud platform for automated analysis. The big data cloud platform enables more effective screening and integration of environmental factors, soil physicochemical factors, and microbial community data, thereby reducing data processing time and errors and improving the accuracy of the assessment, as well as reducing the technical and economic burden of the soil health framework on agricultural producers in the promotion process. Traditional soil health assessment methods are usually based on a linear combination of a single or a small number of indicators, which directly maps soil physicochemical and biological indicators to soil health status [56]. However, there are limitations to this approach because soil health involves complex nonlinear dynamic interactions of physical, chemical, and biological processes that go far beyond the additive and summative relationships of simple indicators. In fact, the core of soil health lies in the interactions among soil components and the overall functions they form, and the existing single indicators may not fully reflect the real status of local soil health. Therefore, integrating individual indicators into multiple soil function indices and constructing mathematical models based on different land use objectives to assess soil health is a more scientific approach and represents the current research trend. For example, the European 2021 LANDMARK program (Land Management: Assessment, Research, Knowledge) proposes to integrate soil health indicators into the five basic soil functions and use them as the basis for soil health assessment to improve the systematicity and applicability of the assessment [148]. In addition, besides positive indicators, the introduction of negative indicators should also be emphasized in soil health assessment. As done by M-SQR in Germany, negative factors such as soil heavy metal pollution, pesticide residues, microplastic pollution, etc., can be introduced into the system to comprehensively examine soil degradation and environmental risks [61]. Similarly, in the soil health assessment of orchards, the soil risk index (SRI) can be constructed based on the above pollution factors, and combined with the soil function index (SFI) to comprehensively assess the soil health status in both positive and negative dimensions. Agricultural production should not only focus on crop yield and quality but also fully consider the potential impact of soil health on human health and the ecological environment. At the decision-making level, artificial intelligence (AI) can be used to optimize soil health management strategies because it can take into account more variables than traditional methods [149]. Through AI algorithms, the soil function index and soil risk index can be comprehensively analyzed, and environmental factors (e.g., future climate change prediction, soil texture, land use type, etc.) can be combined to form a comprehensive soil health management plan that covers physical, chemical, and biological aspects, thus improving the accuracy and adaptability of soil management (Figure 3).

6.3. Decision-Making Platform for Soil Health with Cross-Border Cooperation and Feedback

No matter what kind of soil health management program is implemented, it still needs to be implemented by human beings, and how effective it is, whether it needs to be improved, and whether it can be widely promoted are closely related, but they involve different decision-making bodies, i.e., farmers, researchers, and the government, respectively. However, there is currently a lack of effective communication mechanisms among these three parties, which limits the efficiency of applying scientific research results and affects the relevance of policies. Therefore, it is of great practical significance to establish an organized communication platform where scientists, farmers, and policy makers can engage in regular dialogues to jointly discuss and develop practical solutions. Direct communication between the three parties on this platform can bring multiple benefits. Farmers are able to express their needs to the government, receive more targeted policy support, receive technical guidance from researchers, and provide timely feedback on the data they collect in the course of practicing, so as to avoid wasting data resources. Researchers can optimize artificial intelligence (AI) models through the practical data provided by farmers to make them more adaptable, and receive government funding through the platform to promote technology development and application transformation. The government, in turn, can adjust its policies based on the results of scientific research to improve the effectiveness of agricultural support measures and more accurately meet farmers’ needs (Figure 4). In addition, soil degradation is a cross-regional problem, but current policies rarely promote regional or transnational cooperation. Therefore, the exchange platform should have an international perspective at the governmental level so that neighboring countries can share research results, collaborate on standards, and then build a regional soil health alliance to jointly address transboundary soil degradation challenges.

Combining the soil health assessment framework with an interdisciplinary and multi-initiative exchange platform can not only break the information barriers between different decision-making entities but also build a complete closed-loop “monitoring-analysis-decision-making-feedback” management system. This system can promote the change in soil health management from relying on empirical judgment to data-driven and realize the synergistic optimization of multiple goals, such as the improvement of agricultural productivity, ecological environmental protection, and climate change adaptation.

7. Conclusions

Existing soil health assessment frameworks, while valuable, face limitations in scalability, predictive capacity, and adaptability to dynamic environmental changes. Reliance on static indicators and labor-intensive sampling protocols restricts their utility in real-time decision-making. Future methodologies must prioritize dynamic, data-driven models that leverage advances in remote sensing, genomic profiling, and machine learning to capture the nonlinear interactions within soil ecosystems. The integration of negative indicators (e.g., microplastic contamination) alongside traditional metrics will provide a more holistic evaluation of soil health risks.

Climate change exacerbates challenges such as soil erosion, salinization, and carbon loss, necessitating adaptive strategies like enhanced carbon sequestration through agroecological practices. Meanwhile, soil pollution—particularly from persistent microplastics—demands urgent interdisciplinary solutions, as current remediation technologies remain inadequate for large-scale implementation. Developing nations, where soil degradation disproportionately impacts agricultural livelihoods, require targeted policy interventions and technological transfers to adopt sustainable practices.

To address these challenges, a paradigm shift toward collaborative governance is essential. Establishing international platforms for knowledge exchange, harmonizing soil health standards, and incentivizing regenerative practices through policy frameworks will bridge the gap between research, policymaking, and on-ground implementation. By fostering innovation in monitoring technologies and prioritizing soil health as a cornerstone of climate resilience, the agricultural sector can ensure the long-term productivity of orchards while safeguarding planetary health and contributing to a more globally consistent perspective on soil health that supports cross-regional collaboration and international sustainability initiatives.

Moreover, in addition to international cooperation and technological innovation, practical action at the local level is equally important. Farmers can regularly monitor their soils; adjust fertilizer, irrigation, and organic amendments accordingly; and provide timely feedback about field observations. Researchers can use these data to optimize models and guide best practices. Additionally, policymakers can develop regional soil management guidelines and organize farmer training. Together, these measures can support data-driven decision-making, increase soil resilience, and promote sustainable orchard production.