Soil microbial characteristics are considered to be an index for soil quality evaluation. It is generally believed that organic amendments replacing chemical fertilizers have positive effects on changing microbial activity and community structure. However, their effects on different agro-ecosystems on a global scale and their differences in different environmental conditions and experimental durations are unclear. This study performed a meta-analysis based on 94 studies with 204 observations to evaluate the overall effects and their differences in different experimental conditions and duration. The results indicated that compared to chemical fertilizer, organic amendments significantly increased total microbial biomass, bacterial biomass, fungal biomass, Gram-positive bacterial biomass and Gram-negative bacterial biomass, and had no effect on the ratio of fungi to bacteria and ratio of Gram-positive bacteria to Gram-negative bacteria. Meanwhile, land use type, mean annual precipitation and soil initial pH are essential factors affecting microbial activity response. Organic-amendment-induced shifts in microbial biomass can be predominantly explained by soil C and nutrient availability changes. Additionally, we observed positive relationships between microbial functionality and microbial biomass, suggesting that organic-amendment-induced changes in microbial activities improved soil microbial functionality.

Grazing exclusion (GE) is considered an effective strategy for restoring the degradation of overgrazed grasslands on the global scale. Soil microbial diversity plays a crucial role in supporting multiple ecosystem functions (multifunctionality) in grassland ecosystems. However, the impact of grazing exclusion on soil microbial diversity remains uncertain. Here, we conducted a meta-analysis using a dataset comprising 246 paired observations from 46 peer-reviewed papers to estimate how GE affects microbial diversity and how these effects vary with climatic regions, grassland types, and GE duration ranging from 1 to 64 years. Meanwhile, we explored the relationship between microbial diversity and its functionality under grazing exclusion. Overall, grazing exclusion significantly increased microbial Shannon (1.9%) and microbial richness (4.9%) compared to grazing group. For microbial groups, GE significantly increased fungal richness (8.6%) and bacterial richness (5.3%), but decreased specific microbial richness (-11.9%). The responses of microbial Shannon to GE varied among climatic regions, grassland types, and GE duration. Specifically, GE increased microbial diversity in in arid, semi-arid, and dry sub-humid regions, but decreased it in humid regions. Moreover, GE significantly increased microbial Shannon in semidesert grasslands (5.9%) and alpine grasslands (3.0%), but not in temperate grasslands. Long-term (>20 year) GE had greater effects on microbial diversity (8.0% for Shannon and 6.7% for richness) compared to short-term (<10 year) GE (-0.8% and 2.4%). Furthermore, grazing exclusion significantly increased multifunctionality, and both microbial and plant Shannon positively correlated with multifunctionality. Overall, our findings emphasize the importance of considering climate, GE duration, and grassland type for biodiversity conservation and sustainable grassland ecosystem functions.

Application of organic fertilizers or their combination with chemical fertilizers is a feasible practice for improving soil fertility and reducing soil degradation in agroecosystems, and these regulations are mainly mediated though soil microbial communities. Despite bacteria ranking among the most abundant and diverse groups of soil microorganisms, the effects of long-term organic fertilization (OF) and chemical–organic fertilization (COF) on soil bacterial diversity and community composition remain unclear. In this study, we conducted a meta-analysis and demonstrated that OF had no significant effect on bacterial alpha diversity. Application of chemical fertilizer and crop residue significantly decreased bacterial Richness index. Both OF and COF significantly altered bacterial community structure, with these changes being predominately attributed to shifts in soil pH. For bacterial phyla, both OF and COF significantly increased the relative abundance of Proteobacteria and Bacteroidetes, suggesting that OF and COF may cause the enrichment of copiotrophic taxa. In addition, COF significantly increased the relative abundance of Gammaproteobacteria but decreased the relative abundance of Acidobacteria. Overall, our results suggest that organic and chemical–organic fertilization can effectively maintain bacterial diversity and enhance soil fertility in agroecosystems, and the alteration of soil bacterial community structure is closely intertwined with soil pH.

Bacterial synthetic microbial communities (SynCom) have exhibited significant effects for enhancing plant growth and delivering ecological benefits. However, persistent challenges, including structural instability, limited environmental adaptability, and transient efficacy, remain critical barriers to their practical application. Herein, we propose Arbuscular Mycorrhizal fungi (AMF) as the keystone component to optimize SynCom’s ecological fitness in sustainable agricultural systems. AMF modulate microbiome assembly through hyphal networks, enhancing community stability via facilitative interactions and augmenting nutrient cycling functionalities. This review systematically evaluates methodologies for AMF-based SynCom design and construction, investigates the dynamics of AMF-microbe interactions, delineates plant growth-promoting mechanisms, identifies candidate microbial taxa, and addresses implementation bottlenecks with corresponding strategies. We posit that AMF-Based SynComs represent a transformative management tool for ensuring global food security amid impending climatic perturbations and declining agricultural productivity.

Soil bacterial communities are crucial drivers of nutrient cycling and ecosystem functioning; however, their temporal dynamics under arbuscular mycorrhizal (AM) fungi colonization remain insufficiently characterized. In this study, we used a non-destructive continuous sampling method and undertook a 90-day pot experiment to examine the process of shaping the bacterial community of hyphosphere soil. Following inoculation with AM fungi, we found an increase in the α-diversity index of the hyphosphere bacterial community. The community diversity and richness and the key bacterial taxa in the hyphosphere both gradually increased from 30 to 60 days and stabilized thereafter. Principal coordinated (PCoA) analysis and network analysis further confirmed these findings. Stabilized by 60 days post-inoculation, with deterministic processes dominating assembly in inoculated AM fungi soils, while stochastic processes prevailed in non-inoculated controls. Inoculation strengthened bacterial associations with available phosphorus, while making the key bacterial communities more responsive to multiple soil physicochemical properties (available P, CEC, N, and TOC). These findings provide critical insights into AM fungi mediation of soil microbiome dynamics, with the identified 60-day stabilization period offering a key temporal framework for understanding tripartite soil–AM fungi-bacteria interactions.