Residues of herbicides with the extensive applications may impact the soil ecosystem and ultimately threaten agricultural sustainability. However, the effects of long-term herbicide residues on soil multifunctionality and the soil microbial community remain poorly understood. Here, we evaluated relationships between soil multifunctionality and soil microbial communities with residual herbicide concentrations by surveying and analyzing 62 black soil samples collected from an agricultural area in northeastern China. Total residual herbicide concentrations varied from 35 to 568 μg/kg in the soil samples. The response of soil multifunctionality to increasing residual herbicide concentrations exhibited an inverted U-shaped relationship with a peak at approximately 310 μg/kg, with net mineralized organic nitrogen (Nm) and total nitrogen (TN) exhibiting the same trend. Microbial community richness was significantly lower in soil samples with high residual herbicide concentrations (> 310 μg/kg, HG) compared to low residual herbicide concentrations (< 310 μg/kg, LG). In addition, the relative abundances of specific keystone microbial genera differed significantly between LG and HG: norank_f_Acetobacteraceae, norank_f_Caldilineaceae, Candidatus_Alysiosphaera, and Gonytrichum. The relative abundances of these genera were also significantly correlated with soil multifunctionality. Structural equation models (SEMs) further showed that herbicide residues influenced soil multifunctionality by affecting these specific keystone genera. Our study demonstrates that long-term herbicide residues significantly impact the multifunctionality of agricultural black soil, where low concentrations stimulate while high concentrations inhibit, underscoring the need for reasonable application of herbicides to maintain soil ecosystem health.

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.

Soil desertification is an important challenge in global soil management, and effectively and stably restoring soil function is an urgent problem. Using synthetic microbial communities (SynComs) is a burgeoning microbial strategy aimed at enhancing soil nutrients through functional synergies among diverse microorganisms; nevertheless, their effectiveness in restoring desertified soils remains unknown. In this study, we conducted a two-year field experiment using a SynCom constructed by in situ probiotic bacteria and set up control, chemical fertilizer, and combined SynCom-chemical fertilizer (combined fertilizer) treatments to investigate the linkage between microbial communities and soil multifunctionality in the soil surface layer (0-10 cm). Both the bacterial and fungal communities differed the most under the combined fertilizer treatment compared to the control. The bacterial communities differed more under treatments of the SynCom than the chemical fertilizer, while the fungal communities differed more under the chemical fertilizer treatment than the SynCom treatment. Regarding soil function, the SynCom strengthened the correlation between enzyme activities and both bacterial communities and functional properties. pH and available potassium were the main influencing factors under the chemical fertilizer and combined fertilizer treatments. The beta-diversity of the bacterial communities was significantly correlated with soil multifunctionality. Random forest analyses showed that the SynCom significantly enhanced the bacterial communities, driving soil multifunctionality, and that some potential microbial taxa drove multiple nutrient cycles simultaneously. In summary, the SynCom effectively increased the abundance of most carbon, nitrogen, and phosphorus functional genes as well as soil enzyme activities. The bacterial community composition contributed significantly to soil multifunctionality. Hence, the development of novel microbial agents holds significant potential for improving soil functionality and managing desertification.

The use of green manure can substantially increase the microbial diversity and multifunctionality of soil. Green manuring practices are becoming popular for tobacco production in China. However, the influence of different green manures in tobacco fields has not yet been clarified. Here, smooth vetch (SV), hairy vetch (HV), broad bean (BB), common vetch (CV), rapeseed (RS), and radish (RD) were selected as green manures to investigate their impact on soil multifunctionality and evaluate their effects on enhancing soil quality for tobacco cultivation in southwest China. The biomass of tobacco was highest in the SV treatment. Soil pH declined, and soil organic matter (SOM), total nitrogen (TN), and dissolved organic carbon (DOC) content in CV and BB and activity of extracellular enzymes in SV and CV treatments were higher than those in other treatments. Fungal diversity declined in SV and CV but did not affect soil multifunctionality, indicating that bacterial communities contributed more to soil multifunctionality than fungal communities. The abundance of Firmicutes, Rhizobiales, and Micrococcales in SV and CV treatments increased and was negatively correlated with soil pH but positively correlated with soil multifunctionality, suggesting that the decrease in soil pH contributed to increases in the abundance of functional bacteria. In the bacteria-fungi co-occurrence network, the relative abundance of key ecological modules negatively correlated with soil multifunctionality and was low in SV, CV, BB, and RS treatments, and this was associated with reductions in soil pH and increases in the content of SOM and nitrate nitrogen (NO3--N). Overall, we found that SV and CV are more beneficial for soil multifunctionality, and this was driven by the decrease in soil pH and the increase in SOM, TN, NO3--N, and C- and N-cycling functional bacteria.

Several soil functions of alpine wetland depend on microbial communities, including carbon storage and nutrient cycling, and soil microbes are highly sensitive to hydrological conditions. Wetland degradation is often accompanied by a decline in water table. With the water table drawdown, the effects of microbial network complexity on various soil functions remain insufficiently understood. In this research, we quantified soil multifunctionality of flooded and non-flooded sites in the Lalu Wetland on the Tibetan Plateau. We employed high-throughput sequencing to investigate the microbial community responses to water table depth changes, as well as the relationships between microbial network properties and soil multifunctionality. Our findings revealed a substantial reduction in soil multifunctionality at both surface and subsurface soil layers (0-20 cm and 20-40 cm) in non-flooded sites compared to flooded sites. The α-diversity of bacteria in the surface soil of non-flooded sites was significantly lower than that in flooded sites. Microbial network properties (including the number of nodes, number of edges, average degree, density, and modularity of co-occurrence networks) exhibited significant correlations with soil multifunctionality. This study underscores the adverse impact of non-flooded conditions resulting from water table drawdown on soil multifunctionality in alpine wetland soils, driven by alterations in microbial community structure. Additionally, we identified soil pH and moisture content as pivotal abiotic factors influencing soil multifunctionality, with microbial network complexity emerging as a valuable predictor of multifunctionality.

Intricate microbial associations contribute greatly to the multiple functions (multifunctionality) of natural ecosystems. However, the relationship between microbial associations and soil multifunctionality (SMF) in artificial ecosystems, particularly in agricultural ecosystem with frequent fertilization, remains unclear. In this study, based on a 28-year paddy field experiment, high-throughput sequencing and networks analysis was performed to investigate changes in soil microbial (archaea, bacteria, fungi, and protists) associations and how these changes correlate with SMF under long-term fertilization. Compared to no fertilization (CK), both chemical fertilization with N, P, and K (CF) and chemical fertilization plus rice straw retention (CFR) treatments showed significantly higher soil nutrient content, grain yield, microbial abundance, and SMF. With the exception of archaeal diversity, the CF treatment exhibited the lowest bacterial, fungal, and protist diversity, and the simplest microbial co-occurrence network. In contrast, the CFR treatment had the lowest archaeal diversity, but the highest bacterial, fungal, and protist diversity. Moreover, the CFR treatment exhibited the most complex microbial co-occurrence network with the highest number of nodes, edges, and interkingdom edges. These results highlight that both chemical fertilization with and without straw retention caused high ecosystem multifunctionality while changing microbial association oppositely. Furthermore, these results indicate that rice straw retention contributes to the development of the soil microbiome and ensures the sustainability of high-level ecosystem multifunctionality.

Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.

Exploring plant diversity and ecosystem functioning in different dimensions is crucial to preserve ecological balance and advance ecosystem conservation efforts. Ecosystem transition zones serve as vital connectors linking two distinct ecosystems, yet the impact of various aspects of plant diversity (including taxonomic, functional, and phylogenetic diversity) on soil multifunctionality in these zones remains to be clarified. This study focuses on the forest-grassland transition zone in the mountains on the northern slopes of the Tianshan Mountains, and investigates vegetation and soil characteristics from forest ecosystems to grassland ecosystems to characterize plant diversity and soil functioning, as well as the driving role of plant diversity in different dimensions. In the montane forest-grassland transition zone, urease (URE) and total nitrogen (TN) play a major role in regulating plant diversity by affecting the soil nutrient cycle. Phylogenetic diversity was found to be the strongest driver of soil multifunctionality, followed by functional diversity, while taxonomic diversity was the least important driver. Diverse species were shown to play an important role in maintaining soil multifunctionality in the transition zone, especially distantly related species with high phylogeny. The study of multidimensional plant diversity and soil multifunctionality in the montane forest-grassland transition zone can help to balance the relationship between these two elements, which is crucial in areas where the ecosystem overlaps, and the application of the findings can support sustainable development in these regions.

Core microbiome has been proven to play crucial roles in soil function. However, we still lack knowledge on how core microbiome responds to crop residue retention, and whether they contribute to this process. Consequently, we examined the effect of residue retention on soil core and non-core microbial communities in maize seedling, mature stage and freezing period based on a multi-site field experiment in Sanjiang Plain, Northeast China. Totally, 247 bacterial amplicon sequence variants (ASVs) and 109 fungal ASVs were identified as core microbiota. Both core and non-core bacterial/fungal community composition were significantly influenced by residue retention across all study sites. Especially, the core fungal community shifted towards a saprotroph-dominated community. Normalized stochastic ratio pattern revealed that that deterministic process dominated both core and non-core microbial community assembly processes. Residue retention enhanced the deterministic process of core microbial community assembly, while exhibited opposite effect on non-core microbial community. This study also revealed that soil fungi were more sensitive to residue retention than bacteria, with a larger proportion of core fungi were enriched or depleted by residue retention. In addition, residue retention complicated core bacterial co-occurrence network, while simplified fungal network. Our results pointed out both no reduction in microbial diversity or collapse in microbial network structure after repeated freezing-thawing cycles. The potential function of core microbiome was evaluated through random forest analysis and structural equation model, the results indicated core microbiome contributed more to multifunctionality than non-core microbiome. Overall, this study strengthened our understanding of soil core microbiome in response to residue retention, and highlighted their importance in maintaining soil multifunctionality.

Although pervasive microplastics (MPs) pollution in terrestrial ecosystems invites increasing global concern, impact of MPs on soil microbial community assembly and ecosystem multifunctionality received relatively little attention. Here, we manipulated a mesocosm experiment to investigate how polyethylene MPs (PE MPs; 0, 1%, and 5%, w/w) influence ecosystem functions including plant production, soil quality, microbial community diversity and assembly, enzyme activities in carbon (C), nitrogen (N) and phosphorus (P) cycling, and multifunctionality in the maize-soil continuum. Results showed that PE MPs exerted negligible effect on plant biomass (dry weight). The treatment of 5% PE MPs caused declines in the availability of soil water, C and P, whereas enhanced soil pH and C storage. The activity of C-cycling enzymes (α/β-1, 4-glucosidase and β-D-cellobiohydrolase) was promoted by 1% PE MPs, while that of β-1, 4-glucosidase was inhibited by 5% PE MPs. The 5% PE MPs reduced the activity of N-cycling enzymes (protease and urease), whereas increased that of the P-cycling enzyme (alkaline phosphatase). The 5% PE MPs shifted soil microbial community composition, and increased the number of specialist species, microbial community stability and networks resistance. Moreover, PE MPs altered microbial community assembly, with 5% treatment decreasing dispersal limitation proportion (from 13.66% to 9.96%). Overall, ecosystem multifunctionality was improved by 1% concentration, while reduced by 5% concentration of PE MPs. The activity of α/β-1, 4-glucosidase, urease and protease, and ammonium-N content were the most important predictors of ecosystem multifunctionality. These results underscore that PE MPs can alter soil microbial community assembly and ecosystem multifunctionality, and thus development and implementation of practicable solutions to control soil MPs pollution become increasingly imperative in sustainable agricultural production.