From Microbial Functions to Measurable Indicators: A Framework for Predicting Grassland Productivity and Stability

Abstract

Grassland ecosystems play a key role in global carbon and nutrient cycling, yet their productivity is increasingly affected by changing climate, land use, and nutrient inputs. Recent studies have identified plant–microbe interactions as a crucial biological mechanism regulating these changes. However, comprehensive research across different biomes remains insufficient. This review focuses on the functional characteristics and physiological processes of microorganisms to explore how they influence grassland productivity and stability in the context of global change, and proposes quantifiable indicators to improve model predictions. By integrating evidence from alpine, temperate, and arid grasslands, we summarize how microbial carbon use efficiency(CUE), nutrient cycling enzyme activity, and symbiotic capabilities affect plant nutrient acquisition, carbon allocation, and stress resistance. Meta-analytical data indicate that microbial processes can explain a substantial proportion of productivity variation beyond climatic and edaphic factors. We further outline methodological progress in linking molecular mechanisms with ecosystem dynamics through multi-omics, stable isotope tracing, and structural equation modeling. This synthesis highlights that incorporating microbial mechanisms into grassland productivity frameworks enhances predictive accuracy and provides an empirical basis for sustainable management. Across global grasslands, microbial processes account for roughly 40–50% of the explained variance in productivity beyond abiotic drivers, underscoring their predictive value in ecosystem models. Thes study underscores the broader significance of recognizing soil microbes as active drivers of ecosystem function, offering a biological foundation for carbon sequestration and grassland restoration strategies under global environmental change.

1. Introduction

According to the Food and Agriculture Organization of the United Nations, permanent grasslands and pastures occupy approximately 3200 million hectares, accounting for about 26% of the global land area [1,2]. In this review, “grassland” is used in a broad ecological sense, encompassing both natural and semi-natural systems dominated by herbaceous vegetation. These include alpine meadows, temperate steppes, and savanna-like ecosystems that are either maintained by climatic constraints or by long-term extensive management such as grazing and mowing. As one of the most extensive and ecologically significant terrestrial biomes, grasslands play a vital role in regulating the global carbon cycle, supporting biodiversity, and providing essential ecosystem services such as soil conservation, water regulation, and forage production for livestock [3,4]. As a critical interface between the atmosphere and the pedosphere, grasslands contribute significantly to carbon sequestration, hence influencing climate feedback mechanisms [5,6]. Recent assessments have also highlighted that spatiotemporal variations in grassland productivity are closely linked to global sustainability goals, including carbon neutrality, biodiversity conservation, and land degradation neutrality [1,7]. Moreover, they are basic elements of food security and socioeconomic stability for many areas, especially in arid and semi-arid zones where pastoralism and grassland-based agriculture are widespread [8,9]. Due to their wide coverage and functional importance, grasslands have increasingly been seen as a crucial aspect of worldwide sustainability strategies formulated against the background of current changes within the natural environmental systems [10].

Grasslands for this review encompass alpine meadows, temperate steppes, and tropical savannas across continental regions, such as the Eurasian steppe belt, Indian savannahs, South American Cerrado, and tundra grasslands at high latitudes. The core of grassland ecosystem functioning revolves around productivity, or the rate of biomass accumulation through primary production [11]. Grasslands contribute roughly 20–25% of global terrestrial net primary production, equivalent to 10–12 Pg of carbon annually [1,7]. This productivity is the base for carbon sequestration, herbivore support, soil fertility, and ecosystem resilience [12,13]. Recent evidence indicates productivity declines in several semi-arid and intensively managed regions over the past two decades [14]. Changes in productivity, whether climatic or anthropogenic, can cascade into systems of stability at the ecosystem level, carbon budgets at regional levels, and socio-economic systems at the micro-level [15,16]. Under these conditions of global change—here taken to refer to the combined effects of climate change, land use change, grazing regime shifts, and changes in management—drivers and constraints of grassland productivity have gained increasing attention as central themes of ecological research.

While traditional grassland productivity studies were mainly related to abiotic drivers, such as temperature, precipitation, and nutrient availability in the soil, many drivers have recently been recognized as very important in biotic interactions between plants and soil microbiota. Plants influence ecosystem processes through a variety of mechanisms, including carbon allocation, root exudation, and functional trait expression, which in turn affect nutrient cycling, microbial activity, and overall ecosystem productivity [17,18]. Simultaneously, soil microorganisms—including bacteria, fungi, and archaea—mediate key processes such as organic matter decomposition, nutrient mineralization, and symbiotic nutrient exchange [19,20]. These microbial communities respond sensitively to environmental changes and can either buffer or amplify the effects of such changes on plant growth and ecosystem functioning.

Despite this recognition, a fragmented understanding persists regarding how plant and microbial components interact to jointly regulate grassland productivity. While it is clear that plants and microbes individually influence productivity, the emergent properties of their interactions—such as feedback loops, co-adaptation, and functional complementarity—remain underexplored. This raises a fundamental question: Are plant–microbe interactions the central regulatory mechanism governing grassland productivity under global change?

Addressing this question requires a systematic synthesis of mechanistic pathways, empirical evidence, and methodological advances. To this end, we undertake a narrative synthesis, bolstered by the development of an integrative conceptual framework linking plant and microbial processes across scales. Recent advances in research have begun to uncover how plant-microbe interactions may not be passive responses to environmental shifts but active drivers of ecosystem dynamics [21]. For instance, rhizosphere microbes can enhance plant nutrient acquisition under nutrient-limited conditions, while mycorrhizal fungi may improve water-use efficiency during drought [22,23]. Conversely, pathogenic microbes can reduce plant fitness and alter competitive outcomes, thereby influencing community composition and productivity [24]. These interactions are further modulated by plant functional traits—such as root architecture and leaf economics—which affect microbial community assembly and function [25]. Together, these bidirectional feedbacks create complex, adaptive networks that may stabilize or destabilize grassland productivity under changing conditions.

The growing interest in plant–microbe interactions is reflected in several emerging research fronts. These include the use of molecular tools to characterize microbial functional genes, the application of stable isotope tracing to quantify carbon and nitrogen fluxes, and the integration of machine learning and structural equation modeling to identify key drivers across scales [26,27]. Moreover, cross-biome comparisons and long-term manipulative experiments are beginning to reveal generalizable patterns and context-specific mechanisms [28]. These advances highlight the potential of microbial indicators—such as CUE, pathogen-to-mutualist ratios, and nitrogen-cycle gene abundance—to predict grassland responses to global change.

In this review, we aim to synthesize current knowledge on the role of plant–microbe interactions in regulating grassland productivity under global change. Specifically, we will: (i) Outline the major global change drivers affecting grasslands and their interactions with plant and microbial communities; (ii) Elucidate the core mechanisms through which plants and microbes interact to influence productivity; (iii) Summarize evidence from diverse grassland ecosystems worldwide; (iv) Review emerging methodologies enabling mechanistic insights; (v) Identify key challenges and future research directions.

By integrating mechanistic understanding with empirical evidence and methodological innovations, this review advances the working hypothesis that plant–microbe interactions may constitute a central regulatory axis in grassland productivity—an idea crucial for predicting and managing these ecosystems under future global change scenarios.

2. Regulatory Factors of Grassland Productivity

Grassland productivity, fundamentally defined as the rate of biomass production per unit area per unit time, serves as a paramount indicator of ecosystem function and service provision, including carbon sequestration, forage production, and biodiversity maintenance [29]. Productivity is typically expressed using several complementary indicators: gross primary productivity (GPP) refers to the total amount of carbon fixed by photosynthesis over a given period of time; net primary productivity (NPP) is GPP minus plant autotrophic respiration (carbon consumption by plant metabolism) [30], which represents the amount of carbon actually accumulated in plant biomass that is available for consumption by herbivores and decomposers [31]; aboveground net primary productivity (ANPP) and belowground net primary productivity (BNPP) break down this accumulation into aboveground and belowground portions, respectively. While ANPP is often used as a simpler alternative indicator to gross productivity because it is easier to measure and can be performed by harvesting or remote sensing, the importance of BNPP is increasingly being recognized, especially in grasslands where a large portion (usually more than 50%) of carbon and nutrients is invested in the root system to acquire and store resources and survive disturbances. It is increasingly recognized that different productivity indicators are multifaceted responses to driving factors, and as global change unfolds, the response of grassland ecosystems is expected to exhibit this multifaceted nature as well.

For decades, ecological research has primarily focused on abiotic and direct biotic factors as the principal controllers of grassland productivity, forming a foundational paradigm. These traditional drivers can be broadly categorized into climatic factors, soil properties, and anthropogenic disturbances, as summarized in Figure 1. While this framework provides a crucial first-order understanding, it often fails to capture the full complexity of the system, necessitating a deeper exploration of the biological mediators that translate these drivers into productivity outcomes.

2.1. Climatic Factors: The Ultimate Environmental Filters

Climate sets the ultimate boundary for grassland distribution and function on a global scale, acting as a master switch that enables or constrains biological activity. The interplay between temperature and precipitation largely defines the biome [32,33,34].

Temperature profoundly influences the biochemical enzymatic reactions underlying photosynthesis and respiration. Its effects are biphasic and context-dependent. Moderate warming in cooler regions can extend the growing season, enhance metabolic rates, and accelerate development, thereby boosting GPP. Meta-analyses confirm this trend: experimental warming across global grasslands increased NPP by ~15%, ANPP by 7.6%, and BNPP by 11.6% [35], while a more recent synthesis reported a mean rise of about 9.8% in GPP under warming treatments, though ecosystem respiration increased even more strongly (≈16%), partially offsetting the net gain [36]. However, persistent warming intensifies evapotranspiration, raising the risk of physiological drought even without reduced precipitation [37], and increases respiratory carbon loss, which can suppress NPP when respiration outpaces photosynthesis [38]. In soils, soil microbial activity is also highly temperature-sensitive: warming initially accelerates organic matter decomposition and nutrient mineralization, boosting nutrient supply and plant growth, but long-term exposure shifts microbial communities toward fast-metabolizing taxa with lower CUE and reduced carbon retention [39,40]. These changes intensify soil carbon losses and destabilize the balance between decomposition and stabilization, producing nonlinear NPP responses [41,42]. For instance, warming may initially enhance ANPP in mesic, nutrient-rich grasslands but suppress it in water-limited systems where evaporative demand outweighs metabolic gains [43].

Precipitation regimes, including total annual amount, seasonal timing, intra-annual distribution, and event intensity, are arguably the most dominant drivers in many grassland ecosystems, which are predominantly found in semi-arid regions [44,45,46]. Water availability is a direct prerequisite for photosynthetic activity, plant cell expansion, and nutrient transport in the soil [47]. Reduced precipitation or prolonged drought stress consistently suppresses ANPP by stunting plant growth, inducing stomatal closure, and accelerating senescence. The impact on belowground dynamics is more nuanced. As an adaptive response to water scarcity, plants may initially increase the relative carbon allocation to roots (potentially increasing BNPP or the root-to-shoot ratio) to forage for deeper soil moisture [45]. However, under severe and prolonged soil moisture deficit, both root growth and the activity of rhizosphere microbes responsible for nutrient mineralization are fundamentally restricted, ultimately curtailing overall NPP [48]. The increasing frequency and intensity of extreme climate events, such as heatwaves and compound drought-heat events, act as potent catalysts, often pushing ecosystems beyond their physiological thresholds and triggering rapid, sometimes irreversible, declines in productivity through widespread plant mortality and soil carbon loss [49].

2.2. Soil Nutrient Availability: The Elemental Building Blocks

Beyond the macro-climatic constraints of water and temperature, the local availability of essential soil nutrients, particularly nitrogen (N) and phosphorus (P), strongly constrains grassland productivity at finer spatial scales. These elements are the fundamental building blocks of proteins, nucleic acids, and energy molecules.

Most natural grasslands are nitrogen-limited; meta-analysis shows that nitrogen addition increases above-ground net primary productivity by about 33%, while phosphorus addition results in a smaller 14% increase; hence, nitrogen supply is more closely related to ANPP than the availability of phosphorus [50,51,52]. Nitrogen availability is dynamic and controlled by microbial-mediated processes, such as the mineralization of organic matter. In grassland soils, microbes can convert 20–50 kg N ha⁻¹ yr⁻¹ of organic nitrogen into plant-available forms like ammonium and nitrate, with rates rising sharply under warmer and moister conditions [53]. For instance, in temperate steppe soils, warming experiments have thus far shown a 21.8% increase in net N mineralization, further emphasizing that microbial activity plays the key role in regulating temporal variability in N availability [54].

Phosphorus limitation in most old, highly weathered soils is a common thing, and this is indeed chronic as nitrogen inputs redistribute nutrient imbalance. Prolonged nitrogen enrichment can lower soil pH by 0.25–0.34 units over 1–10 years, enhancing phosphorus immobilization and reducing its availability [55], which in turn can constrain microbial-mediated P mineralization. This reduction in microbially available phosphorus limits plant nutrient acquisition, altering plant–microbe interactions and potentially shifting community composition [56]. Soil N:P ratios provide a useful indicator of such imbalances: plant communities tend to exhibit higher diversity and productivity when N:P exceeds 4.0, whereas lower ratios can intensify phosphorus limitation, reducing microbial activity and biodiversity [57,58]. Maintaining an appropriate soil N:P balance is therefore critical not only for plant growth and ecosystem productivity but also for sustaining functional plant–microbe interactions in grassland soils.

Anthropogenic nutrient enrichment mainly results from the atmospheric nitrogen deposition caused by the combustion of fossil fuels and agricultural activities [59]. This enrichment can initially alleviate nutrient limitation and enhance ANPP, a phenomenon observed in many regions. However, the long-term consequences are often detrimental [60]. Chronic N input can lead to soil acidification, which mobilizes toxic aluminum ions and reduces the availability of other essential cations like calcium and magnesium [61]. It can also cause a decline in plant species richness, as fast-growing, nitrophilic species dominate, and alter the composition and function of soil microbial communities (e.g., suppressing decomposer fungi like mycorrhizae) [62]. These shifts can destabilize productivity in the long term, reduce the ecosystem’s resilience to environmental stress, and lead to increased losses of nitrogen through leaching and gaseous emissions, causing further environmental damage [63].

2.3. Anthropogenic Disturbances: The Overlying Human Imprint

Human activities are powerful driving forces that can regulate and sometimes even have a greater impact than natural climate and soil nutrient gradients. The most common of these are grazing and changes in land use.

Grazing by domestic herbivores influences productivity through a triad of interconnected mechanisms: (1) direct biomass removal (herbivory), which reduces standing crop and can alter plant competitive hierarchies; (2) physical alteration of the soil environment through compaction and root disturbance (trampling), which affects water infiltration, aeration, and root growth; and (3) nutrient recycling via the deposition of dung and urine, which creates spatial heterogeneity in nutrient availability. Herbivore optimization hypothesis (or intermediate disturbance hypothesis) posits that moderate levels of herbivory can enhance plant productivity and biodiversity by preventing competitive exclusion and promoting resource turnover, whereas very low or very high grazing intensities tend to reduce productivity and diversity [64]. Moderate grazing can sometimes stimulate productivity by promoting nutrient cycling, reducing self-shading and senescent material, and favoring more productive plant species [65]. However, when grazing intensity crosses a system-specific threshold, it uniformly leads to ANPP reduction, soil degradation (erosion, compaction), and simplified plant communities dominated by unpalatable or grazing-tolerant species.

Land use changes often lead to irreversible alterations. The conversion of native grasslands to cropland, afforestation, or urbanization completely resets the habitat template. Such changes disrupt the evolved vegetation structure, deplete soil organic matter (SOM) pools through accelerated decomposition or erosion, and alter hydrological cycles through drainage or the expansion of impervious surfaces (e.g., roads, buildings, and compacted soil layers that prevent water infiltration), exerting profound impacts on productivity [66,67]. Even on well-managed grasslands, changes in management intensity, such as the frequency and timing of mowing, can significantly alter the distribution patterns of ANPP and BNPP, soil carbon storage, and community composition.

2.4. The Unexplained Variance and the Path Forward

Despite the well-established and robust importance of these traditional abiotic and disturbance factors, a synthesis of empirical studies from diverse grasslands consistently reveals a significant portion of variation in productivity—often 30–50%—that remains unexplained by climate, soil, and disturbance factors alone [68]. This persistent explanatory shortfall points unequivocally to the existence of critical, yet historically underexplored, biological mechanisms operating within the “black box” of the soil–plant system. As shown in Figure 1, the effects of these main driving factors do not occur directly but are widely mediated and regulated through the biological reactions of resident plants and soil microorganisms [69].

For example, warming does not merely increase metabolic rates in a deterministic fashion; it reshapes soil microbial community composition and function, potentially shifting them towards bacterial-dominated communities that are less efficient at stabilizing soil carbon, which in turn alters the long-term nutrient supply to plants [70]. Similarly, the impact of drought on a plant is not solely a function of physical water scarcity [71]; it is critically modulated by the ability of its associated rhizosphere microbes (e.g., mycorrhizal fungi) to enhance water retention, explore a larger soil volume, and maintain nutrient acquisition under stress through the production of compounds like glomalin.

This realization requires us to shift from the simplistic perspective of environmental determinism to a comprehensive perspective that integrates biology and geochemistry. The intricate web of feedbacks and interactions between plants and soil microbes emerges as the central mechanistic pathway through which the traditional drivers ultimately exert their influence on productivity. Plants, through their root architecture, exudation of a diverse cocktail of organic compounds, and functional traits, act as ecosystem engineers, actively architecting the rhizosphere environment and selectively recruiting, supporting, and controlling specific microbial consortia. In return, these microbes become key agents in regulating the very processes that define productivity: they are the primary engines of nutrient cycling (decomposers, nitrifiers), the extended root system for nutrient and water uptake (mycorrhizal fungi), the providers of growth hormones, and the defenders against pathogens [72]. While this review focuses primarily on microbial mechanisms, it is important to acknowledge that soil invertebrates—such as nematodes, collembolans, and earthworms—also contribute substantially to nutrient cycling and soil aggregation, often interacting synergistically with microbial communities.

Therefore, to move beyond correlation and towards mechanistic prediction, the following sections will delve into the specifics of how these plant-microbe interactions—encompassing mutualistic symbioses, pathogenic relationships, and the complex networks of nutrient cycling—form the core regulatory machinery. This biological circuitry translates external environmental forces into the observable patterns of grassland productivity, representing the next frontier in our understanding of these vital ecosystems.

3. Core Mechanisms of Plant–Microbe Interactions in Regulating Grassland Productivity

The dynamic interplay between plants and soil microorganisms (Figure 2) forms the biological foundation of grassland productivity. Moving beyond simplistic cause–effect relationships, these interactions regulate nutrient cycling, symbiotic partnerships, pathogenic feedbacks, and trait-mediated resource allocation. Together, they determine how efficiently ecosystems convert resources into biomass and how resilient they remain under global change.

3.1. Nutrient Cycling and Resource-Use Efficiency: The Microbial Metabolic Engine

Soil microorganisms drive the transformation and availability of nutrients. Their activity determines the rate and efficiency with which plants acquire essential elements such as nitrogen (N), phosphorus (P), and carbon (C) (Figure 2a). The coupled nutrient cycles of nitrogen, phosphorus, and carbon illustrate how microbial processes govern the turnover and availability of essential elements in grassland soils (Figure 3). Recent global syntheses show that microbial processes are the dominant drivers of soil N mineralization in grasslands, accounting for the majority of total N turnover [73,74]. Field observations reveal that realized net N mineralization rates vary widely among sites—from near zero up to 1.4 mg N·kg⁻¹·d⁻¹ [75]—which, depending on soil bulk density and depth, corresponds to roughly several tens to a few hundred kilograms of N per hectare per year.

3.1.1. Nitrogen (N) Cycle

Nitrogen cycling (Figure 3a) in grassland soils is regulated by microbial transformations: diazotrophs (e.g., Rhizobium, Azospirillum) fix atmospheric N₂ into ammonium, nitrifiers (e.g., Nitrosomonas, Nitrososphaera) oxidize ammonium to nitrate, and denitrifiers reduce nitrate to gaseous N forms, closing the cycle. Meta-analysis indicates that experimental warming increases soil net N mineralization by approximately 21.8–25.3%, reflecting enhanced microbial turnover and nutrient release under higher temperatures [76]. However, such warming and nitrogen enrichment can also intensify gaseous N losses. For instance, in a semiarid temperate grassland, high nitrogen input elevated N₂O emissions by ~265%, while methane uptake decreased by ~34%, indicating that faster microbial cycling may come at the cost of lower N-use efficiency [54]. Field and meta-analytical evidence further show that nitrogen enrichment amplifies phosphorus limitation across terrestrial ecosystems [77,78]. At the global scale, grassland aboveground net primary productivity increases by about 33.2% under N addition but only 14.2% under P addition, underscoring nitrogen’s predominant role in driving productivity [50].

3.1.2. Phosphorus (P) Cycle

In P-deficient grasslands, P-solubilizing microorganisms such as Bacillus, Pseudomonas, and certain fungi release organic acids (e.g., citric, gluconic) and phosphatases that mobilize insoluble P compounds [79,80,81]. These processes (Figure 3b) can raise available soil P concentrations by 20–60% compared with non-inoculated soils [82]. Arbuscular mycorrhizal fungi (AMF) further improve P uptake by extending hyphal networks beyond the root depletion zone, accessing P pools up to 10 cm beyond root surfaces [83,84]. Empirical evidence from semi-arid grasslands shows that microbial phosphatase activity explains nearly half of the variance in soil-available P (R² ≈ 0.47, P < 0.001), and each 10 µmol pNP g⁻¹ h⁻¹ increase in enzyme activity corresponds to a ~7–12% rise in above-ground productivity [85]. Such microbial facilitation becomes increasingly important as chronic N deposition shifts many grasslands from N to P limitation [80,86].

According to He [87], the different bacterial families exhibit opposite correlations with inorganic P, implying complementary roles in phosphorus cycling and driving the turnover between organic and inorganic P forms. Similarly, the functions of fungal symbionts are not fixed but context-dependent. For instance, Colletotrichum tofieldiae can act as a pathogen inhibiting the growth of Capsella rubella, yet promote Arabidopsis thaliana growth under low-P conditions [88].

3.1.3. Carbon (C) Cycle

Plants allocate a significant portion (up to 20–40%) of their photosynthetically fixed carbon belowground, where it enters the soil in the form of root exudates, shed cells, and litter (Figure 3c). This form of carbon input has almost become the primary energy source for the entire soil microbial food web [89,90]. The fate of this carbon—whether it is rapidly released as CO₂ through respiration or efficiently converted into microbial biomass and retained in stable SOM—is determined by the microbial community’s CUE, which represents the ratio of carbon allocated to biomass synthesis to carbon lost via respiration [91,92,93].

In grassland ecosystems, CUE is typically approximately 0.3–0.4, meaning that approximately 30–40% of assimilated carbon is converted into microbial biomass, while the remaining approximately 60–70% is lost through respiration or other pathways [94,95]. When vegetation structure is complex, nutrient supply is abundant, and microbial activity is high, CUE can rise to 0.4–0.5 or even higher [96,97]. In systems with limited nutrients, suppressed microbes, or weak plant-microbe interactions, CUE may drop to 0.1–0.3 [92,98]. This suggests that even if plants input 20–40% of their carbon into the belowground system, if microbial CUE is low (e.g., 10–20%), much of this carbon will quickly return to the atmosphere as CO₂, making it less likely to effectively enter microbial biomass or contribute to stable SOM. Conversely, a higher CUE promotes the conversion of more belowground carbon into microbial residues, thereby enhancing soil organic carbon (SOC) storage and playing a key role in nutrient cycling and maintaining ecosystem productivity [99].

Collectively, these interlinked nutrient cycles form the mechanistic basis illustrated in Figure 3, where microbial transformations integrate elemental flows and sustain grassland productivity under global change.

3.2. Mutualism and Symbiosis: Forging Strategic Alliances

Mutualistic relationships represent sophisticated evolutionary strategies for plants to expand their resource acquisition capacity and buffer against environmental stress, forming a foundational pillar for stable productivity. These alliances are based on reciprocal exchange, but they are dynamic and context-dependent, constantly renegotiated based on environmental conditions and the needs of the partners (Figure 2b).

3.2.1. Mycorrhizal Fungi: The Extended Root System

AMF, symbiotic with over 80% of grassland plants, constitute one of Earth’s most widespread mutualisms [24,100]. Meta-analyses show that AMF colonization enhances plant phosphorus uptake by 20–50%, particularly in grassland soils [101,102]. Within cortical arbuscules, plants transfer up to 20% of photosynthates as lipids and carbohydrates to the fungus, which reciprocates with water and nutrients [103,104].

Under drought conditions, AMF hyphae enhance plant water uptake and sustain growth by accessing soil micropores beyond the reach of roots. In a field rainfall-exclusion experiment, AMF colonization increased above-ground biomass by ~47% in the C3 grass Leymus chinensis and by ~37% in the C4 grass Hemarthria altissima compared with non-mycorrhizal controls [105]. AMF-derived glomalin enhances soil aggregation, with glomalin-related soil protein (GRSP) closely linked to water-stable aggregates and mean weight diameter. Increases in GRSP typically raise aggregate stability by 10–40%, improving soil water retention [106,107]. In colder or woody-dominated grasslands, ectomycorrhizal (ECM) fungi fulfill similar roles through sheathing root tips, influencing carbon cycling and below-ground carbon storage dynamics [108].

These mutualisms are increasingly critical under global change: meta-analyses and field experiments show that nitrogen enrichment and experimental warming typically reduce AMF colonization or abundance by 8–15%, weakening plant nutrient balance and stress resilience. In contrast, sustainable grazing regimes and organic amendments consistently enhance AMF activity and glomalin production, leading to improved soil aggregation and structure [109,110].

3.2.2. Plant Growth-Promoting Rhizobacteria (PGPR) and Endophytes: The Bio-Stimulants and Bodyguards

This diverse group of bacteria (e.g., Pseudomonas, Bacillus, Azospirillum) and endophytic fungi (e.g., Epichloë in grasses) residing in the rhizosphere or within plant tissues enhances productivity through a multi-pronged approach:

(i)

Bio-fertilization: PGPR fix atmospheric N₂ (up to 60 kg N ha⁻¹ yr⁻¹), solubilize inorganic P by 20–60%, and produce siderophores that improve Fe availability [111,112].

(ii)

Phytohormone modulation: PGPR that produce auxins (IAA), cytokinins, and gibberellins can enhance root length and branching by about 20–40%, thereby improving water and nutrient uptake [113].

(iii)

Biocontrol: PGPR suppress pathogens through antibiotic production and competition for infection sites, achieving~40–80% reductions in disease incidence and frequently inducing systemic resistance [114,115].

(iv)

Stress tolerance amelioration: By synthesizing osmoprotectants (proline, glycine betaine) and antioxidants, PGPR and endophytes enhance drought and heat tolerance. Epichloë in cool-season grasses produces alkaloids that deter herbivores and reduce evapotranspiration losses [116].

These microbial consortia reduce the plant’s metabolic costs for defense and stress responses—allowing more carbon to be allocated to growth. Bio-inoculants combining PGPR and AMF have been shown in meta-analyses and field trials to raise plant biomass by up to ~30–40% and improve nutrient/fertilizer use efficiency by around 10–20% under certain conditions [117,118].

3.2.3. The Carbon Cost of Mutualism: A Dynamic Trade-Off

Maintaining microbial partners imposes a considerable carbon cost—up to 30–40% of plant-fixed C can be allocated belowground to support mutualists [119,120]. This defines a dynamic trade-off at the core of plant allocation strategy: balancing the benefit of enhanced resource acquisition against the direct carbon expense.

Under nutrient limitation or drought, plants invest more carbon in roots and exudates, often increasing rhizosphere C allocation by 20–50% to reinforce symbioses [121]. Conversely, under nutrient-rich or chronically nitrogen-enriched conditions, arbuscular mycorrhizal colonization often decreases by 30–60%, and plants may activate immune pathways that restrict microbial colonization. Long-term nitrogen addition suppresses both AMF and PGPR abundance, leading to lower microbial carbon use efficiency CUE (typically declining from ~0.4 to ~0.2) and weakened soil carbon stabilization capacity [63,122].

Understanding and managing this trade-off is crucial for sustaining productivity under global change. Practices such as moderate grazing, maintaining balanced N:P ratios, and minimizing chemical disturbance can help preserve functional mutualisms and stabilize grassland C and N cycles.

3.3. Pathogenic and Saprotrophic Effects: The Antagonistic and Competitive Forces

Not all plant-microbe interactions are beneficial. Pathogenic and saprotrophic microbes exert critical negative and competitive feedbacks that can suppress productivity, influence plant community assembly, and drive ecosystem state transitions (Figure 2c).

3.3.1. Pathogenic Effects: The Regulators of Plant Fitness and Diversity

Soil-borne pathogens such as Fusarium (wilt fungi), Phytophthora (oomycetes) and plant-parasitic nematodes act as potent agents of selection by reducing host growth, reproduction and survival; field pathogen-exclusion experiments indicate ~15–45% losses in above-ground biomass, and nematode infections alone can reduce shoot biomass by ~30% in susceptible hosts [123,124]. At the community level, they can shift competitive hierarchies: dominant species are often more targeted, which suppresses their abundance and releases subordinate species from competitive exclusion [125]. This host-specific suppression underpins the Janzen–Connell effect, a mechanism that maintains grassland diversity and prevents dominance by any single species [126].

Diversity, in turn, feeds back to productivity through complementarity effects. For instance, pathogen exclusion experiments in temperate grasslands showed that removing soil pathogens increased dominance of one or two species and reduced community-level ANPP by ~25% [127,128]. Hence, moderate pathogen pressure supports diversity and long-term stability, while excessive pathogen outbreaks can lead to large-scale mortality, vegetation thinning, and eventual ecosystem collapse.

Environmental stress—drought, eutrophication, or nitrogen imbalance—often amplifies pathogenic effects. Drought can reduce plant defense enzyme activity by 30–60%, increasing fungal infection rates. Under chronic nitrogen enrichment, pathogen biomass can rise by twofold while AMF colonization declines by half, tipping the beneficial–pathogenic balance. In management terms, practices that maintain moderate grazing pressure, enhance SOM, and avoid nutrient overloading help sustain this equilibrium and prevent pathogen-dominated degradation [129,130].

3.3.2. Saprotrophic Effects: The Decomposers and Competitors

Across grasslands, heterotrophic (microbial) respiration contributes the majority of annual soil CO₂ efflux, averaging ~73% at the China-grassland scale and reaching 76–95% in site-level partitioning studies; globally, Rh/Rs (the proportion of heterotrophic respiration to total soil respiration) centers around ~61% with moisture exerting primary control in grasslands [131,132]. During early litter decomposition, microbes frequently immobilize nitrogen and phosphorus into microbial biomass, creating short-term competition with plants. Field and mesocosm studies show that this immobilization typically spans weeks and can extend to months, with plant-available inorganic N often dropping by several tens of percent following litterfall pulses, before later recovery as mineralization resumes [133,134].

The competitive balance between plants and saprotrophs depends strongly on litter quality and climate. When decomposing high C:N ratio litter, microbes invest more energy in respiration, lowering microbial CUE from ~0.45 to ~0.25 [135,136]. Experimental evidence indicates that a soil warming of approximately +3 °C can increase decomposition rates by about 25–35%, while leading to an 8–12% decline in SOC stocks over decadal timescales [137].

Saprotrophic and pathogenic processes often reinforce each other during degradation. Overgrazing or drought weakens plants, increasing susceptibility to pathogens [138]. Mortality adds litter input, fueling saprotroph growth, which in turn heightens nutrient immobilization and limits the regrowth of surviving plants. This self-reinforcing feedback—plant stress → pathogen attack → mortality → saprotroph bloom → nutrient immobilization → further stress—can trigger rapid transitions from a carbon-sinking to a carbon-emitting grassland.

Moderating grazing intensity, retaining surface litter, and restoring arbuscular mycorrhizal functioning can slow decomposition and enhance soil carbon stabilization in grasslands, whereas balanced fertilization that avoids nitrogen oversupply helps maintain microbial diversity and reduces the risk of runaway carbon loss [139,140,141].

These measures align with global frameworks that prioritize soil-carbon–centric mitigation in agriculture, including the UNFCCC Koronivia Joint Work on Agriculture and IPCC’s 2019 Refinement for AFOLU reporting, as well as the “4 per 1000” initiative that highlights the technical potential of soil carbon sequestration [142,143].

3.4. Plant Functional Trait–Microbe Feedbacks: Shaping the Ecosystem from the Bottom Up

This mechanism represents a higher-order of interaction, where plants and microbes engage in bidirectional feedbacks mediated by plant functional traits, which ultimately shape ecosystem-level properties like productivity, stability, and resilience. It links plant evolutionary strategies directly to microbial community assembly and function (Figure 2d).

3.4.1. Root Traits as the Primary Filter for the Rhizosphere Microbiome

Root morphology and chemistry govern which microbial taxa thrive in the rhizosphere. Traits such as specific root length (SRL; root length per unit mass, m g⁻¹), root diameter, and exudate composition act as selective filters shaping microbial communities [144]. Species with an acquisitive root strategy (e.g., SRL, fine diameter) have been shown to access substantially larger soil volumes per gram of root biomass and to allocate more labile carbon compounds (such as sugars and organic acids) to the rhizosphere compared with more conservative species [145]. These exudates stimulate copiotrophic, r-strategist bacteria (e.g., Pseudomonas, Arthrobacter), accelerating mineralization and nutrient turnover.

In contrast, conservative plants with thicker roots (low SRL and fewer exudates) promote fungal-dominated communities, especially mycorrhizal and decomposer fungi [146]. Microbial communities with a higher fungal/bacterial biomass ratio tend to exhibit higher CUE and slower nutrient cycling rates, which may contribute to ecosystem patterns such as higher short-term productivity but lower long-term nutrient retention in grasslands dominated by acquisitive species [147,148].

From a management perspective, grazing intensity, nutrient enrichment, and species composition shifts can all reshape these root–microbe linkages. Moderate grazing tends to favor fine-rooted species and higher microbial activity, while chronic N deposition reduces SRL and favors conservative root types, thereby slowing nutrient cycling.

3.4.2. Leaf Traits and the Afterlife Effects on Decomposition

Aboveground traits influence productivity both during life and after senescence. High- Specific Leaf Area (SLA), nutrient-rich leaves consistently decompose faster than lignin-rich, low-SLA leaves [149,150]. Across species, deciduous woody litters decompose about 60% faster than evergreen woody litters, and first-year mass turnover averages 43% in broadleaf forests vs. 29% in coniferous forests (≈48% higher), while trait-based models attribute ~8% of decomposition variation to SLA relative to cellulose (40%) and lignin (36%) [151,152]. This accelerated decay supports a specialized bacterial decomposer community that efficiently mineralizes N and P, returning nutrients to the soil and sustaining ANPP in subsequent seasons [153].

Conservative species with low SLA and high lignin concentrations favor fungal decomposers and slower nutrient turnover. This “afterlife effect” stabilizes nutrient cycling but reduces short-term productivity. In grasslands undergoing global change, increasing aridity or N deposition often selects for tougher, low-SLA leaves, leading to more fungal-dominated decomposition and reduced carbon turnover efficiency [154,155]. Maintaining a balance of fast- and slow-decomposing species through species-rich plant mixtures can help stabilize nutrient flow and productivity across climatic extremes.

3.4.3. Biodiversity-Stability Feedback Loops

Functional trait diversity among plants determines the heterogeneity of root exudates, litter quality, and physical soil niches—key drivers of microbial diversity [156]. Functionally diverse plant communities harbor significantly richer and more redundant microbial assemblages than monocultures—microbial biomass and respiration increase by roughly 10–15%, supporting an ecological insurance effect whereby diverse taxa compensate for nutrient and carbon cycling under drought or disturbance [157,158].

High plant diversity increases soil microbial biomass by 10–15% and α-diversity, while long-term experiments show it reduces ANPP variability through species asynchrony [159]. This positive feedback between plant and microbial diversity is a key mechanism underpinning grassland stability under environmental fluctuations. In contrast, the loss of plant diversity simplifies the soil microbiome, reduces resilience, and amplifies productivity variability—effects already documented in intensively managed and nutrient-enriched grasslands.

Thus, conserving functional diversity is not only a matter of biodiversity preservation but a strategy for maintaining microbial-mediated stability and ecosystem productivity in a rapidly changing world.

3.5. Interactions at the Community and Network Level: The Emergence of System-Level Properties

The cumulative outcome of countless plant–microbe exchanges emerges at the community and network level, where interactions among plants, bacteria, and fungi form highly interconnected ecological systems. These networks integrate the functional roles described in previous sections—mutualism, competition, decomposition, and trait feedbacks—into collective properties such as stability, resistance, and productivity that cannot be inferred from isolated interactions.

3.5.1. Network Complexity as a Predictor of Ecosystem Stability

Theoretical and empirical evidence both indicate that network complexity and modular architecture are tightly linked to ecosystem stability [160,161]. In grassland soils, higher microbial network complexity and robustness are linked to greater resilience under drought: experiments show that drought destabilizes bacterial but not fungal co-occurrence networks, while enhancing arbuscular mycorrhizal (AMF) diversity and network modularity/robustness by ~20% increases stability. Keystone taxa such as AMF, Bradyrhizobium and Mortierella frequently underpin these network properties [162].

Common mycorrhizal networks (CMNs) physically link multiple plant species, allowing redistribution of water and nutrients from deep-rooted to shallow-rooted plants during stress events [163]. This cross-species buffering creates a form of “biological insurance”, sustaining community productivity even when individual species decline. Conversely, the loss of keystone taxa or the breakdown of network modularity can cause cascading failures—pathogen outbreaks, nutrient leakage, and long-term soil carbon depletion.

3.5.2. Microbial Indicators as Proxies for Network Function and Productivity Trends

Several measurable indicators link microbial networks to ecosystem performance. Microbial CUE typically ranges from 0.2 to 0.6, with higher CUE communities showing greater soil carbon and nutrient retention [164]. The balance between mutualistic AMF and pathogenic fungi reflects ecosystem resilience: global nutrient-enrichment experiments show that increased N and P inputs favor pathogens over AMF, weakening soil stability [129]. Meanwhile, the nifH gene, a marker of biological N fixation, declines markedly under chronic N deposition, indicating reduced nutrient self-sufficiency [165].

Together, these indicators summarize the emergent behavior of the plant–microbe–soil continuum. Monitoring network structure and these functional markers offers a powerful diagnostic framework for grassland management—linking belowground biodiversity to aboveground productivity and providing early warning of ecosystem instability under intensifying global change.

4. Regional and Global Case Studies: Context-Dependent Manifestations of Plant-Microbe Interactions

The fundamental mechanisms that govern plant–microbe interactions are broadly conserved across ecosystems, yet their expression and ecological consequences are heavily filtered by local climate regimes, soil evolutionary history, and anthropogenic pressures. Grasslands, encompassing both natural and semi-natural systems managed for grazing or hay production, provide an ideal setting to examine how these processes operate under contrasting resource constraints and management intensities. Comparing case studies across Chinese grasslands and representative global biomes elucidates how a common mechanistic framework—nutrient cycling, mutualisms, pathogenic dynamics, and trait-mediated feedbacks—plays out in regionally distinct “dialects.” These contrasts both challenge universal generalizations and identify actionable microbial indicators for targeted management under global change.

4.1. Chinese Grasslands: A Natural Laboratory Along Environmental Gradients

China’s grasslands span a steep environmental gradient from the high, cold Qinghai–Tibet Plateau to the temperate semi-arid steppes of Inner Mongolia and the hyper-arid desert margins of Xinjiang [166]. This transect showcases how similar processes are re-weighted according to dominant abiotic limitations.

4.1.1. Qinghai–Tibet Plateau (Alpine Meadow): Cold and Nitrogen-Limited Dynamics

Alpine meadows are characterized by low mean annual temperatures, short growing seasons, and pervasive nitrogen limitation [167]. These alpine grasslands lie mostly above 4000 m elevation with mean annual temperatures around –2 to +3 °C and low N-input rates (0.32–1.23 g N m⁻² yr⁻¹) on the Qinghai–Tibet Plateau [168]. Microbial processes that underpin N availability operate slowly and seasonally; ammonia-oxidizing archaea (AOA) frequently dominate nitrification, and freeze–thaw cycles generate pulsed nutrient release that plants and microbes must rapidly exploit. Experimental warming tends to increase microbial mineralization and nitrification rates, but these shifts can uncouple plant uptake from microbial supply, producing transient increases in nitrate leaching and nitrous oxide emissions rather than durable productivity gains [169,170]. Grazing pressure further modulates the system: moderate grazing can create nutrient hotspots and maintain plant–microbe heterogeneity, whereas chronic overgrazing reduces legume abundance, diminishes mycorrhizal networks, and simplifies microbial co-occurrence structure [171,172]. Management interventions such as rotational grazing exclusion or targeted reseeding with legumes can partially restore microbial functional diversity and improve nitrogen retention, suggesting that microbial indicators (AOA/AOB ratios, mycorrhizal richness, network modularity) are useful for early assessment of system trajectory [173].

4.1.2. Inner Mongolia Steppe (Temperate Arid and Semi-Arid): Water-Limited Resilience

Water availability is the principal constraint in temperate steppe ecosystems, with nitrogen frequently a secondary limitation [174]. Under drought, plants reallocate carbon belowground, enhancing root exudation that sustainsAMF and drought-tolerant rhizobacteria [170,175]. AMF hyphal networks and exopolysaccharide-producing bacteria contribute to aggregate stability and improve soil water retention and plant water uptake from micropores inaccessible to roots. However, persistent atmospheric nitrogen deposition and fertilization can transiently raise aboveground productivity while reducing plant and microbial diversity: fast-growing grasses outcompete forbs and legumes, root exudate diversity narrows, and AMF colonization declines. Restoration experiments indicate that reintroducing legumes, reducing external N inputs, and implementing grazing rotations can rebuild belowground mutualist networks [176]. Metrics such as AMF: saprotroph ratio, hyphal length density, and drought recovery of ANPP provide integrative measures of resilience.

4.1.3. Xinjiang Desert Grassland (Hyper-Arid): Survival Under Multiple Stresses

Hyper-arid desert margins combine extreme water limitation, salinity, and often P scarcity in alkaline soils. Plants frequently rely on highly specialized microbial consortia—halotolerant PGPR that synthesize osmoprotectants, and P-solubilizing bacteria and fungi that mobilize calcium-bound phosphorus [177]. Biological soil crusts (biocrusts) formed by cyanobacteria, lichens, and mosses are central ecosystem engineers: they stabilize soils, fix atmospheric N, reduce evaporation, and create microsites for plant establishment. Crust successional stage strongly influences nitrogen inputs and seedling recruitment; disturbance of mature crusts commonly triggers long-term degradation and reduced recovery potential [178]. Consequently, monitoring crust coverage and functional stage, together with assessments of P-solubilization capacity and halotolerant microbiome composition, offers practical diagnostics for desert grassland integrity and restoration readiness [179].

4.2. Global Comparative Analysis: Contrasting Responses to Global Change Drivers

Comparative examples from major global grasslands reveal how local evolutionary histories and primary resource constraints redirect otherwise similar plant–microbe mechanisms.

4.2.1. North American Great Plains (Temperate Prairie): CUE and Management Interactions

Long-term manipulative studies in the Great Plains indicate that warming and elevated CO₂ can reduce the microbial CUE’s temperature sensitivity by approximately 28.7% [39], leading to higher microbial respiration relative to biomass accrual [180,181]. This shift reduces the potential for long-term soil carbon stabilization despite short-term increases in ANPP [182]. Land use intensity modulates these dynamics: conversion to cropping systems or intensive tillage accelerates declines in CUE and organic matter, whereas managed rangelands with reduced soil disturbance retain more efficient microbial processing. Thus, CUE and soil aggregation metrics function as integrative early-warning indicators for carbon balance vulnerability.

4.2.2. Pampas of Argentina (Subtropical Grassland): Functional Simplification Under Intensive Conversion

Conversion of species-rich grasslands to soybean monocultures and intensive pastures has driven a marked loss of microbial functional diversity. Chronic fertilization suppresses diazotrophs, while monoculture promotes pathogen build-up and narrow decomposer communities [183]. The combined loss of nifH gene abundance and elevated pathogen load signals a shift from self-sustaining nutrient regimes to systems dependent on continual external inputs, with reduced resilience to perturbation [184].

4.2.3. African Sahel (Tropical Dry Savanna): Degradation Feedback Loops and Fire Interactions

The Sahel exemplifies synergistic stressors—recurring droughts, overgrazing, and fire—that reduce plant carbon allocation to the rhizosphere and erode mutualist populations (AMF, beneficial PGPR). As plant mortality increases, saprotrophic fungi and soil pathogens proliferate, immobilizing nutrients and reinforcing vegetation decline. Fire interacts with these processes by volatilizing nutrients and restructuring microbial communities, often compounding recovery difficulties [185]. The saprotroph: mutualist ratio and post-fire microbial reassembly trajectories provide critical measures of degradation state and restoration potential [33].

4.2.4. Australian Drylands (Arid and Semi-Arid): Phosphorus Constraints and Partner Specificity

Ancient, highly weathered soils in Australia impose severe P limitation, shaping plant–microbe dynamics around P acquisition [186]. Productivity hinges on specialized P-solubilizing microbes and compatible AMF associations; introduced pasture species frequently fail when unable to establish appropriate mycorrhizal partnerships. Soil disturbance or mistimed fertilizer application can rapidly disrupt these finely tuned P-cycling relationships, precipitating pasture decline. Indicators such as soil phosphatase activity and the presence of P-mobilizing gene assemblages are therefore particularly informative for management in these systems.

4.3. Synthesis: Universal Principles and Contextual Divergences

Across biomes, several universal mechanisms reappear: plants expend carbon exudates as a currency to recruit microbial services that alleviate limiting resources [187]; mutualists (AMF, PGPR) commonly buffer abiotic stress; and functional shifts in microbial communities often precede visible vegetation collapse, rendering microbial metrics powerful early-warning tools [188]. Yet the operative microbial players and pathways are context-dependent. Nitrogen cycling microbes dominate alpine responses; water-mediating mutualists are critical in semi-arid steppes; phosphorus solubilizers and partner specificity govern productivity in ancient, P-poor landscapes. Anthropogenic drivers—N deposition, land conversion, grazing, and fire—interact with these contexts idiosyncratically, sometimes providing short-term yields while degrading long-term resilience.

For management, this duality implies two priorities: (1) leverage universal microbial indicators—such as CUE, nifH abundance, AMF diversity, phosphatase activity, and microbial network complexity—for early diagnosis; and (2) design interventions that respect local “dialects” of plant–microbe interactions, restoring mutualist networks where they have been lost, protecting biocrust succession in deserts, and minimizing soil disturbance to preserve CUE in temperate systems. These diagnostic metrics and their recent quantitative evidence are summarized in

Table 1. Key microbial indicators and their quantitative relationships with ecosystem performance.

Indicator	What It Captures	Recent Quantitative/Directional Evidence
Microbial CUE	Balance of biomass production vs. respiration; predictor of SOC retention	Global analyses: microbial CUE is a dominant control on SOC storage: a 2% increase in CUE can raise global SOC by ~10%, and CUE is at least four times as important as other evaluated factors (carbon inputs, decomposition rates, etc.) in explaining SOC variation [99,189].
AMF status (diversity/abundance)	Strength of mutualist network	A global meta-analysis nutrient enrichment significantly reduced AMF diversity (by 12–20%) and abundance, with root colonization, spore density, and extrarhioidal hyphae decreasing by approximately 18–25%, 15–30%, and 20–40%, respectively. This negative effect was further exacerbated with longer trial durations and higher MAT and MAP [190].
nifH abundance	Proxy for biological N fixation capacity	In multiple grassland fertilization experiments, especially under relatively high N inputs, N addition often reduces diazotrophic nifH gene abundance by ~30–50% [191]. However, a recent grassland meta-analysis found no consistent overall response of N-fixation genes to global change factors, suggesting strong Environmental dependence [192].
Phosphatase activity	P-mineralization potential, P stress signal	Phosphatase activity rises under P limitation and declines with P addition: meta-analyses show monoesterase activity increases by ~+70% under low P but decreases by ~−20% with inorganic P fertilization [193,194]
Microbial network complexity (connectance/modularity)	Community robustness, multifunctionality under stress	Long-term warming experiments in grasslands show consistent losses of soil microbial biodiversity, with bacterial, fungal and protistan richness decreasing by ~8–15% under experimental warming [195], and global meta-analyses reporting average declines of 2–4% across multiple global change drivers [196].

, which highlights their ecological significance and management relevance. Predicting grassland responses to global change therefore requires integrating mechanistic understanding with regionally tailored monitoring strategies that recognize both shared principles and local contingencies.

5. Methodology and Research Approaches

5.1. Multi-Omics and Isotopic Tracing

Understanding grassland productivity in the context of global change requires integrating plant physiology, microbial ecology, and soil biogeochemistry within a single analytical framework. Temperature acts as a master regulator, shaping enzymatic activity that controls photosynthesis, respiration, and nutrient uptake. Moderate warming in cold regions can lengthen the growing season and raise gross primary productivity (GPP), whereas chronic or extreme warming accelerates respiration and evapotranspiration, intensifying soil water deficits and reducing net primary productivity (NPP) [39]. Precipitation regimes—including total rainfall, seasonal timing, and event intensity—interact with temperature to determine soil moisture, plant turgor, and nutrient transport. In semi-arid grasslands, moderate drought may initially stimulate root proliferation for deeper water access, yet prolonged water limitation suppresses microbial activity and nutrient mineralization, constraining productivity. Nitrogen (N) and phosphorus (P) availability further modulate these dynamics [197,198].

Multi-omics technologies reveal the microbial mechanisms underpinning these ecosystem-scale patterns. Metagenomics reconstructs microbial genomes from environmental DNA, identifying taxa capable of N fixation, P solubilization, and cellulose degradation. Metatranscriptomics extends this to gene expression, exposing the active metabolic pathways responding to drought, warming, or nutrient enrichment [199]. Metabolomics quantifies signaling compounds—root exudates, phytohormones, siderophores, and antibiotics—that mediate plant–microbe communication. Proteomics connects these molecular profiles to enzymatic function [200,201].

Stable-isotope probing (SIP) links these molecular insights to biogeochemical fluxes. ¹³C-CO₂ pulse-labeling traces photosynthetic carbon into root exudates and microbial biomass, quantifying the carbon cost of mutualistic interactions [202]. ¹⁵N tracers elucidate N uptake and microbial assimilation pathways, and dual ¹³C/¹⁵N labeling reveals C–N coupling and priming effects [203]. Recent SIP–omics integrations in temperate steppe soils show that 40–55% of root-exuded carbon is assimilated by Pseudomonas and Bacillus within 48 h, corresponding to a microbial CUE of ≈0.45. Such quantitative coupling demonstrates how microbial metabolism governs the resource fluxes sustaining productivity.

5.2. Experimental and Observational Frameworks

While omics and isotopic methods clarify mechanism, field manipulations and long-term observations provide ecosystem validation. Experiments simulating nutrient enrichment, warming, altered precipitation, or herbivore exclusion reveal threshold responses of plant–microbe–soil systems [204]. Nutrient-addition trials identify relative N versus P limitation and show how enrichment shifts microbial composition toward fast-cycling, nitrophilic taxa. Warming treatments quantify temperature sensitivity of enzymatic rates and soil respiration, while precipitation manipulations isolate water-stress thresholds. Grazing-exclusion and herbivory-control experiments illuminate how top-down pressures restructure microbial and plant communities [205].

Long-term networks such as NutNet and ILTER standardize protocols across sites, capturing slow dynamics and cumulative effects. Chronic N enrichment, for instance, may initially raise productivity but eventually reduce microbial diversity and drought resilience [206]. Integrating manipulative experiments with decadal datasets allows identification of lagged feedbacks between soil microbes, nutrient cycling, and vegetation structure.

Mechanistically, these coordinated observations demonstrate that declines in microbial biomass and CUE (often 15–25% under sustained warming) directly explain measured decreases in above-ground NPP. However, most field manipulations remain short (<5 years) and geographically narrow, limiting inference about long-term adaptation. Expanding temporal and spatial coverage is essential to link microbial processes to regional carbon and nutrient budgets.

5.3. Data Integration, Modeling, and Scaling

The diverse datasets generated by omics, isotopes, and experiments demand integrative analysis. Structural equation modeling (SEM) quantifies direct and indirect pathways among climate, soil, microbes, and productivity, distinguishing correlation from causation [39]. Machine learning (ML) algorithms, including random forests, support vector machines, and neural networks, handle high-dimensional, nonlinear data, enabling identification of key predictors among hundreds of environmental, microbial, and plant variables. ML also facilitates predictive modeling, allowing extrapolation of site-specific observations to regional scales or forecasting under future climate scenarios [207].

Remote sensing provides spatially extensive data that bridge fine-scale mechanisms with landscape-level patterns. Spectral indices, such as normalized difference vegetation index (NDVI), enhanced vegetation index (EVI), and solar-induced chlorophyll fluorescence (SIF), correlate with aboveground productivity and photosynthetic activity, while integration with ground-based measurements, including microbial activity and soil nutrient content, allows inference of belowground processes [208]. Remote sensing can identify areas where productivity is decoupled from climatic expectations, potentially signaling microbial-mediated degradation, nutrient limitation, or stress responses. Coupling these data with mechanistic insights from omics and isotope studies enables multi-scale understanding, from molecular processes to landscape dynamics.

5.4. Methodological Integration Framework

Combining isotope tracing with microbial metagenomics and SEM enables simultaneous identification of functional fluxes and causal pathways in plant–microbe–soil systems [209]. Linking these process-level datasets to ML-based spatial extrapolations and remote-sensing indices establishes a coherent, multi-scale predictive framework that connects molecular mechanisms to ecosystem patterns [210]. This integration transforms disparate experimental and observational results into a unified understanding of how microbial processes regulate grassland productivity from genes to landscapes.

Cross-study synthesis further depends on the standardization of biogeochemical and microbial indicators. Core metrics include microbial CUE [180], enzyme activity ratios reflecting C:N:P stoichiometry, arbuscular mycorrhizal-to-pathogen abundance ratios, and plant root traits such as Specific Root Length (SRL; m g−1) [211]. Establishing unified definitions, consistent analytical methods, and shared reporting units will enhance comparability across studies and improve the meta-analytic strength of global syntheses [110].

Despite these advances, key limitations remain. Multi-omics datasets are often correlative and lack quantitative flux calibration, while isotopic and manipulative experiments are typically short-term and spatially limited, restricting extrapolation to decadal or continental scales. Analytical pipelines for omics and remote-sensing data vary widely, reducing reproducibility and complicating cross-site integration. Moreover, remote-sensing proxies effectively capture vegetation dynamics but still struggle to resolve subsurface microbial processes [212].

Future research should focus on integrating omics-based functional predictions with isotope-constrained biogeochemical modeling and long-term ecosystem observation. Establishing standardized protocols for data normalization, indicator calibration, and temporal replication will improve reproducibility. Ultimately, bridging molecular mechanisms with ecosystem-scale evidence is essential for building predictive, management-relevant models of grassland productivity under accelerating global change.

6. Implications for Application and Management

However, applying microbial models in real-world management requires extensive, seasonally resolved datasets, as microbial composition and function can fluctuate strongly across temperature and moisture gradients within and among years.

6.1. Microbial-Driven Grassland Restoration and Rehabilitation

Conventional grassland restoration often focuses on re-vegetation and soil physical amendments, with limited attention to the re-establishment of critical soil microbial communities. The recognition of plant-microbe interactions as a core regulator opens the door for microbial biotechnology in restoration ecology. A primary application is the inoculation of specific beneficial microbes, such as AMF and plant growth-promoting rhizobacteria (PGPR), into degraded soils. These microbial consortia can be selected for their ability to enhance plant drought tolerance, improve nutrient acquisition (particularly in impoverished soils), and suppress soil-borne pathogens [100]. For instance, inoculating bare patches in degraded grasslands with native AMF strains can significantly accelerate the establishment and growth of key grass species by forming a supportive “mycorrhizal network” that facilitates water and nutrient sharing among plants. Nevertheless, field inoculation success is often constrained by climatic variability and soil heterogeneity; thus, repeated sampling and temporal monitoring are essential to confirm microbial establishment and persistence across growing seasons.

6.2. Carbon Sequestration and the “Dual Carbon” Strategy

Grasslands represent massive carbon stocks, and their management is integral to China’s and the global “Dual Carbon” goals (carbon peak and neutrality) [213]. The role of microbes is dualistic: they can be major agents of carbon loss through respiration but also key drivers of carbon stabilization through the formation of microbial necromass and SOM. Management practices can be tailored to steer microbial communities towards higher CUE. This can be achieved by promoting plant communities with high root exudate quality that support a more efficient microbial metabolism, or by applying moderate grazing and organic amendments that enhance fungal-dominated communities, which are generally associated with greater carbon retention than bacterial-dominated ones. Therefore, managing grasslands for carbon sequestration shifts from a purely plant-centric view to a plant-microbe co-management paradigm. Monitoring microbial indicators like CUE and the fungal-to-bacterial ratio can serve as a sensitive gauge for the carbon sink strength of grassland ecosystems, informing policies and carbon credit schemes [214]. In practice, however, quantifying these indicators at management-relevant scales is data-intensive and seasonally dependent, requiring repeated measurements to capture fluctuations in microbial respiration and substrate turnover.

6.3. Enhancing Productivity for Livestock and Food Security

Sustainable livestock production in grassland-based systems is directly dependent on the quantity and quality of forage. By leveraging plant-microbe interactions, it is possible to enhance pasture productivity without resorting to unsustainable levels of chemical fertilizer input. Managing grazing intensity to maintain a healthy, diverse plant community ensures a continuous supply of root exudates that support a robust and beneficial rhizosphere microbiome [215]. Furthermore, the future may see the development of microbial biofertilizers specifically designed for pasture grasses. These formulations, containing N-fixing bacteria for legumes and P-solubilizing microbes for grasses, can reduce dependency on external inputs, lower production costs, and minimize environmental pollution [216]. In a world facing climate uncertainty, enhancing the intrinsic biotic mechanisms that stabilize forage production is a crucial strategy for safeguarding the livelihoods of pastoralists and contributing to broader food security. However, scaling such bioinoculant strategies to heterogeneous and seasonally dynamic rangelands requires coordinated field trials across climatic zones to validate efficacy under variable soil moisture and grazing pressure.

6.4. Grassland Health and Socioeconomic Benefits

Ultimately, the health of grassland ecosystems, mediated by plant-microbe interactions, underpins a wide range of socioeconomic benefits. Healthy, productive grasslands prevent soil erosion, maintain watershed functions, and conserve biodiversity. The degradation of these ecosystems, often initiated by the collapse of beneficial plant-microbe partnerships, leads to dust storms, reduced water quality, and loss of cultural values for indigenous and local communities [217]. Investing in the restoration and sustainable management of grasslands through a microbial-informed lens is therefore an investment in ecological security and human well-being. It can create green jobs in restoration ecology and biotechnology, support sustainable tourism and recreation, and protect the cultural heritage tied to grassland landscapes. By recognizing soil microbes as invisible engineers of ecosystem services, policymakers and land managers can make more informed decisions that balance short-term economic gains with the long-term preservation of the natural capital that grasslands provide.

Integrating plant–microbe interactions into grassland management represents a fundamental shift from mitigating symptoms to sustaining the underlying biological foundations of ecosystem function. This framework provides a scientifically grounded pathway to enhance sustainability and resilience under increasing environmental pressures. Nevertheless, effective implementation requires careful consideration of data intensity, seasonal variability, and spatial heterogeneity to ensure that microbial models remain both credible and applicable in real-world management contexts.

7. Frontiers and Challenges

Research on plant-microbe interactions and their influence on grassland productivity has advanced rapidly, yet the field stands at a critical juncture. While observational studies have revealed extensive correlations between microbial diversity, functional traits, and productivity metrics, transitioning from descriptive knowledge to predictive, mechanistic understanding remains challenging [39,218]. Grasslands are inherently complex, with interactions among plants, soil microbes, nutrients, and environmental factors occurring across multiple spatial and temporal scales. Addressing these challenges provides unique opportunities for fundamental discoveries, offering insights into ecosystem functioning and guiding the sustainable management of these vital systems under global change.

7.1. From Correlation to Causal Mechanisms

Much of the current evidence linking microbes to grassland productivity remains correlative. Specific microbial taxa, such as diazotrophs or AMF, often coincide with high aboveground net primary productivity (ANPP), yet it is unclear whether they actively drive productivity or respond to plant-mediated environmental changes [219]. Establishing causal relationships is essential for predictive modeling and for designing microbial-based interventions that enhance ecosystem function. Experimental approaches are crucial in this regard. Inoculation with synthetic microbial communities (SynComs) in sterile or microbially depleted soils allows direct assessment of microbial contributions to plant growth and nutrient cycling. Stable isotope tracing, employing ¹³C and ¹⁵N, can track carbon and nitrogen flows from microbial genes to plant tissues, providing direct evidence of microbial-mediated nutrient transfer [220]. Moreover, selective suppression of functional microbial groups, for instance through targeted inhibitors or gene editing approaches, can reveal how loss of specific microbial functions affects productivity and ecosystem stability. Together, these approaches enable a transition from observation to causation, illuminating the mechanisms through which microbes regulate grassland function, and offering pathways for applying microbial knowledge in restoration and management practices.

7.2. Multi-Factor Interactions Under Global Change

Grasslands are simultaneously exposed to multiple, interacting environmental pressures, including warming, altered precipitation patterns, elevated atmospheric CO₂, nitrogen deposition, and grazing. Many existing studies focus on one or two factors, yet real-world responses are shaped by complex, nonlinear interactions. For example, drought-induced declines in ANPP can be exacerbated by elevated temperatures due to increased evapotranspiration, while elevated CO₂ can partially mitigate these effects by improving plant water-use efficiency [221,222,223]. Microbial communities, in turn, respond to these combined stressors in ways that may alter nutrient availability, carbon allocation, and productivity in unpredictable manners. Multi-factor manipulative experiments that simulate realistic future conditions are therefore essential, despite their logistical complexity and cost [224]. Such studies capture interactions among multiple drivers, enabling the identification of synergistic, antagonistic, or compensatory effects, while also revealing potential legacy effects of repeated or chronic stress [225,226]. Understanding these multi-factor dynamics is critical for developing accurate predictive models and for designing management strategies that maintain productivity and ecosystem resilience under multifaceted global change scenarios.

7.3. Microbial Tipping Points and Grassland Resilience

Grasslands are susceptible to abrupt shifts from productive, carbon-sequestering states to degraded, carbon-emitting conditions. These transitions are often mediated by ecological tipping points, and microbial communities are central actors in determining system stability. Identifying microbial thresholds that signal impending ecosystem collapse is a key frontier [217]. For example, a critical decline in the AMF-to-pathogen ratio, loss of microbial functional diversity, or shifts in key nutrient-cycling taxa could serve as early-warning indicators. Conversely, during restoration, re-establishing keystone microbial taxa may trigger positive feedback loops that accelerate recovery, stabilize nutrient cycling, and enhance carbon sequestration. Monitoring these microbial indicators provides actionable metrics for conservation and restoration, allowing managers to intervene before irreversible transitions occur. Furthermore, integrating microbial thresholds with plant and soil parameters can improve predictive capacity, enabling the anticipation of ecosystem responses to combined environmental pressures and management interventions.

7.4. Cross-Scale and Cross-System Integration

A major challenge lies in linking fine-scale microbial processes to broader ecosystem and landscape patterns. Mechanisms observed in laboratory microcosms or small experimental plots may not scale linearly to heterogeneous landscapes, where variations in soil properties, plant community composition, topography, and microclimate influence ecosystem outcomes. Moreover, principles derived from one grassland type may not directly apply to others due to differences in evolutionary history, functional traits, and abiotic constraints [227]. Addressing this challenge requires hierarchical models that connect molecular and microbial processes with ecosystem-level outcomes such as productivity, carbon fluxes, and nutrient cycling. Cross-biome comparisons, enabled by coordinated networks like NutNet and ILTER, facilitate identification of universal versus context-dependent patterns. Macroecological tools, including meta-analysis, spatial modeling, and network analyses, can synthesize findings from multiple studies to reveal large-scale drivers and general principles [228]. By integrating mechanistic insights across scales, researchers can bridge the gap between localized observations and predictive, landscape-level models, enhancing our ability to forecast ecosystem responses under complex global change scenarios.

7.5. Towards a Microbially Explicit Productivity Framework

The ultimate goal is the development of an integrated “Microbially Explicit Grassland Productivity Framework,” which positions soil microbes as central regulators rather than peripheral actors. This framework emphasizes microbial functional traits, including growth rates, enzyme production, CUE, and nutrient processing capacity, while explicitly incorporating dynamic feedbacks between plant carbon allocation, microbial community assembly, and nutrient cycling [99,229]. It also integrates stoichiometric and energetic constraints to predict outcomes under resource limitation or environmental stress. By combining empirical data, manipulative experiments, and hierarchical modeling, this framework would allow quantitative predictions of productivity and resilience, guide interventions that leverage microbial processes, and improve understanding of tipping points and restoration potential. Achieving this vision requires interdisciplinary collaboration among microbiologists, plant ecologists, soil scientists, and computational biologists, ultimately transforming grassland research from descriptive observations into predictive, mechanistic science capable of informing sustainable management and conservation under global change.