Soil Microbial Networks Research Articles

Meadow degradation reduces microbial β diversity and network complexity while enhancing network stability

Continuing meadow degradation under the dual impacts of climate change and human activities has altered microbially-mediated biogeochemical cycles. However, microbial diversity and network stability in response to meadow degradation and their relationships to environmental variables remain insufficiently understood. This study focused on alpine meadows with varying degrees of degradation in the hinterland of the Qinghai-Tibetan Plateau. It analyzed the soil microbial diversity (α and β diversity) and ecological network topology characteristics under the degradation of alpine meadows. Furthermore, the extent to which these factors elucidate the environmental changes observed during degradation was explored. The results demonstrated that: (1) the α diversity of soil microbial under degradation of alpine meadows exhibited an increasing trend, although not significantly. The β diversity (community dissimilarity) exhibited a significant decreasing trend. These indicated that meadow degradation resulted in microbial homogenization intra- and inter-community. In the light degradation stage, the β diversity of bacteria and fungi significantly increased with geographic and environmental distance rise. Only bacterial β diversity significantly increased with geographical distance in the moderate degradation stage and environmental distance in the heavy degradation stage, respectively. This indicated that meadow degradation possibly altered microbial assembly, especially for fungi. (2) The degree of soil bacterial nodes exhibited a significant decreasing trend with degradation and fungal eigencentrality demonstrated a significant decreasing trend. After removing the identical nodes, the natural connectivity of the fungal network exhibited a significant decreasing trend with degradation. This suggested that the stability of the soil microbial network increased while the network complexity decreased under meadow degradation. These changes possibly marked the irreversible course of alpine meadow degradation. (3) The Mantel test indicated that bacterial diversity and network topological features were more strongly associated with environmental factors than those of fungi. Akaike information criterion (AIC) values and the upset matrix plots of variance partitioning based on Redundancy analysis (RDA) indicated that higher rates of soil factors, such as soil pH, organic carbon (SOC) content, and total potassium (TK), elucidated changes in microbial community diversity and network topological features. This study highlights the importance of soil microorganisms for ecological stability and the role of microorganisms should be emphasized in future efforts to restore alpine grasslands.

Soil microbial community composition by crop type under rotation diversification

BackgroundCrop rotation is an important agricultural practice that often affects the metabolic processes of soil microorganisms through the composition and combination of crops, thereby altering nutrient cycling and supply to the soil. Although the benefits of crop rotation have been extensively discussed, the effects and mechanisms of different crop combinations on the soil microbial community structure in specific environments still need to be analyzed in detail.Materials and methodsIn this study, six crop rotation systems were selected, for which the spring crops were mainly tobacco or gramineous crops: AT (asparagus lettuce and tobacco rotation), BT (broad bean and tobacco rotation), OT (oilseed rape and tobacco rotation), AM (asparagus lettuce and maize rotation), BM (broad bean and maize rotation), and OR (oilseed rape and rice rotation). All crops had been cultivated for > 10 years. Soil samples were collected when the rotation was completed in spring, after which the soil properties, composition, and functions of bacterial and fungal communities were analyzed.ResultsThe results indicate that spring cultivated crops play a more dominant role in the crop rotation systems than do autumn cultivated crops. Crop rotation systems with the same spring crops have similar soil properties and microbial community compositions. pH and AK are the most important factors driving microbial community changes, and bacteria are more sensitive to environmental responses than fungi. Rotation using tobacco systems led to soil acidification and a decrease in microbial diversity, while the number of biomarkers and taxonomic indicator species differed between rotation patterns. Symbiotic network analysis revealed that the network complexity of OT and BM was the highest, and that the network density of tobacco systems was lower than that of gramineous systems.ConclusionsDifferent crop rotation combinations influence both soil microbial communities and soil nutrient conditions. The spring crops in the crop rotation systems had stronger dominating effects, and the soil bacteria were more sensitive than the fungi were to environmental changes. The tobacco rotation system can cause soil acidification and thereby affect soil sustainability, while the complexity of soil microbial networks is lower than that of gramineous systems. These results provide a reference for future sustainable applications of rotation crop systems.

The structure and function of rhizosphere bacterial communities: impact of chemical vs. bio-organic fertilizers on root disease, quality, and yield of Codonopsis pilosula.

Long-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence. This study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation. Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus, Rubrobacter, Luteitalea, Nakamurella, and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community.

Depth-dependent effects of forest diversification on soil functionality and microbial community characteristics in subtropical forests

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0–80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

Increasing tree phylogenetic diversity stimulates microbial functional potential in a subtropical forest

Abstract Soil microbial functions are closely related to ecosystem productivity, carbon sequestration and their responses to global change. Tree phylogenetic diversity has been found to impact microbial community composition, diversity, and functions, but how it modulates the linkage between microbial community facets and functions remains unclear. Here, 45 plots covering a natural gradient of tree phylogenetic diversity (TPD) were selected in a subtropical forest of southwest China to explore how increasing TPD impacts soil microbial community facets and microbial functional potential. The microbial functional potential was evaluated based on the abundances of carbon, nitrogen, and phosphorus cycling-related functional genes. Soil fungal alpha diversity increased significantly, but bacterial alpha diversity did not change as TPD increased. Both soil microbial network complexity and stability improved significantly with increasing TPD. Ultimately, increasing TPD promoted soil microbial functional potential by stimulating soil carbon and nitrogen availability, microbial keystone diversity, and network stability collectively. These findings emphasize the critical roles of keystone taxa and network stability as microbial factors in stimulating soil microbial function in response to increasing TPD. Therefore, it is strongly recommended to increase TPD in order to stimulate soil microbial functions and other ecosystem functions when implementing afforestation or ecological restoration projects.

Key bacterial taxa with specific metabolisms and life history strategies sustain soil microbial network stability exposed to carbendazim and deoxynivalenol

Co-contamination of carbendazim (CBD) and deoxynivalenol (DON) is common in agricultural soils, yet their ecological impact on soil microbiome remains poorly assessed. Here, we investigated the influence of CBD and DON on the structure, function, and co-occurrence networks of soil microbiome. The combined treatment of CBD and DON significantly exacerbated the negative impacts on soil microbial diversity, functional diversity, and microbial network stability compared to individual treatments. Specifically, Lysobacter, Gemmatimonas, Nitrospira, Massilia, and Bacillus were identified as indicator species for CBD and DON. Simultaneously, the abundance of genes involved in key ecological functions, such as nitrification (amoA) and organic phosphorus mineralization (phoAD), was significantly reduced. Notably, key bacterial taxa Nitrospira and Gemmatimonas, with K-life history strategy and capabilities for nitrification and organic nitrogen mineralization, played crucial roles in promoting positive interactions in networks. Furthermore, variance partitioning analysis (VPA) and structural equation modeling (SEM) demonstrated that the abundance and niche breadth of key bacterial taxa were the primary drivers of microbial network stability. In conclusion, our study provides new insights into how soil microbiomes and networks respond to pesticides and mycotoxins, aiding in a more comprehensive assessment of exposure risks.

Soil carbon pools and microbial network stability depletion associated with wetland conversion into aquaculture ponds in Southeast China

Wetlands, which are ecosystems with the highest soil surface carbon density, have been severely degraded and replaced by artificial reclamation for fish and shrimp ponds in recent years. This transformation is causing intricate shifts in soil carbon pools and microbial stability. In this study, we examined natural wetlands and reclaimed aquaculture ponds in Southeast China to analyze the structure and network stability of soil microbial communities following the reclamation of estuarine wetlands and to elucidate the microbial-mediated mechanisms for regulating soil organic carbon (SOC). The aquaculture ponds presented significantly less average SOC content than the natural wetlands (p < 0.05). ACE, Chao1, and Shannon's indices of bacteria and fungi were decreased in aquaculture ponds. Less numbers of nodes and edge links in the co-occurrence network of soil fungi and bacteria in aquaculture ponds. This suggests reduced correlation and stability within the microbial network of aquaculture ponds. Decomposers in soil fungi (e.g. Dung Saprotroph) reduced. Reduced proportions of key phyla Ascomycota, Basidiomycota and Rozellomycota in the soil fungal network. Reduced proportions of key phyla Proteobacteria, Chloroflexi and Desulfobacterota in the soil bacterial network. In conclusion, our results suggest that converting wetland paddocks to intensive aquaculture ponds results in carbon pool loss and reduces soil microbial network stability. The results highlight the importance of protecting or moderately restoring mangrove wetlands along the coast of southeastern China. It is also predicted that such measures may enhance the storage capacity of soil carbon pools and improve the stability of carbon sequestration by soil microorganisms, thus offering a potential solution for mitigating global climate change.

Responses of soil microbial metabolism, function and soil quality to long-term addition of organic materials with different carbon sources

Biochar and green manure have been widely applied in agricultural production and are important means to achieve sustainable agriculture. However, there is limited research systematically and comprehensively exploring the response of soil microbiota and the changes in soil metabolomics after the addition of two different carbon source amendments to the soil, and the differential mechanisms of soil metabolomics between them remain unclear. In this study, a long-term field experiment (initiated in 2019) was conducted to investigate the effects of biochar and green manure application on soil nutrients and soil functions driven by soil microbes. Compared to the pure fertilizer treatment, biochar increased soil total carbon by 14.54% to 27.04% and soil available potassium by 4.67% to 27.46%. Ryegrass significantly increased soil available phosphorus and organic matter. Under different fertilization regimes, the ecological niches of soil microbes changed significantly. Network analysis revealed that long-term ryegrass returning reduced the complexity of soil microbial networks. Ryegrass and biochar increased dispersal limitation in fungal assemblages (reaching 93.33% and 86.67%, respectively), with biochar particularly enhancing variable selection in bacterial assemblages (accounting for 53.33%). Variation partitioning analysis based on redundancy analysis indicated that humic substances had the highest explanatory power for microbial community variation, with humic substances explaining 38.49% of bacteria and 52.19% of fungi variation. The ryegrass treatment mainly changed the abundance of carbohydrates (CH), amines (AM), c (AH), and lipids (LP), while the BC treatment mainly altered the abundance of organic acids (AC), amines (AM), and carbohydrates (CH). Meanwhile, both treatments significantly reduced the bisphenol A, one of the soil pollutants. Ryegrass incorporation significantly increased the abundance of genes related to soil C, N, P, and S cycling, especially genes involved in carbon decomposition, while biochar significantly enhanced the abundance of nitrogen fixation genes nifH and Hao in soil. Random forest model results indicated that carbohydrates, alcohols, aromatics (AR), and ester (ES) were the main categories of metabolites in soil influenced by differential microbes, and Finegoldia served as a common important metabolic driving species. In summary, this study reveals the processes of soil function, microbial community succession, and metabolism driven by ryegrass and biochar, providing important insights for optimizing soil management and improving soil quality.Graphical

Multiple anthropogenic environmental stressors structure soil bacterial diversity and community network

Microbial communities in many ecosystems are suffering a wide range of environmental stressors induced by anthropogenic perturbations. While the impacts of a single stressor have been extensively estimated in numerous studies, the responses of microbial communities to multiple environmental stressors simultaneously are still poorly understood. In the current study, we investigated the taxonomic diversity, community resistance, and co-occurrence interaction of soil bacterial communities treated with different numbers of environmental stressors by conducting 136 microcosms. We found that the richness and Shannon diversity of the soil community decreased significantly from 1430 to 6.54 in the mono-factor treatments to 920 and 5.77 in the hepta-factor treatments. The counts of nodes and edges of the soil microbial networks decreased with the increasing stressor number, potentially indicating that multiple stressors can reduce the network size. Multiple stressors increased the community resistance potential to environmental disturbance. Additionally, the network cohesion suggested that the cooperative and competitive behaviors between microorganisms were induced by multiple stressors. The observation could be potentially due to the enrichment of the generalists by multiple environmental stressors. Although only a handful of stressors were included, our study still indicated that multiple environmental stressors would lead to diversity loss via deterministic processes.

Difference in microbial community structure along a gradient of crater altitude: insights from the Nushan volcano.

The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.

Linking main ecological clusters of soil bacterial–fungal networks and nitrogen cycling genes to crop yields under diverse cropping systems in the North China Plain

BackgroundCrop rotation changes crop species and the associated management strategies, significantly influencing soil fertility and soil microbial communities. Interactions among the species in microbial communities are important for soil nutrient cycling. Yet, the contribution of soil microbial interactions to crop yield and soil nitrogen-cycle function under wheat–maize and wheat–soybean rotation conversion remains unclear. An 8-year field experiment was conducted to investigate the impact of simple [8-year wheat–maize rotation (8WM) and 8-year wheat–soybean rotation (8WS)] and diverse cropping systems [4-year wheat–soybean followed by 4-year wheat–maize rotation (4WS4WM) and 4-year wheat–maize followed by 4-year wheat–soybean rotation (4WM4WS)] on crop yield, soil properties, bacterial–fungal co-occurrence networks and nitrogen functional potentials. The abundances of genes with nitrogen fixation (nifH), nitrification (AOB and nxrA) and denitrification (narG, nirK, norB and nosZ) potentials were quantified and bacterial and fungal communities were characterized.Results4WS4WM led to higher succeeding maize yields and lower bacterial–fungal network complexity, nitrogen fixation potentials and denitrifying potentials than 8WM. Meanwhile, 4WM4WS exhibited higher succeeding wheat and soybean yields, network complexity and lower nitrifying potentials than 8WS. The ecological cluster with the most nitrifying and denitrifying bacterial species (Module#5) and that with the least species (Module#3) dominated the potentials of nitrogen fixation, nitrification and denitrification and succeeding maize yields in 4WS4WM and 8WM. Module#4 with the highest abundances of nitrifying bacteria (Nitrosomonadaceae) and Module#2 with the most species dominated the nitrifying potentials and succeeding wheat and soybean yields in 4WM4WS and 8WS. Soil water content, organic carbon, dissolved organic carbon, NO3− and pH were key drivers influencing Module#3 and Module#5, while only NH4+ significantly affected Module#2 and Module#4.ConclusionsThese findings demonstrate the importance of ecological clusters within soil microbial network in regulating crop yield and soil nitrogen cycling, and identify specific ecological clusters dominating nitrogen functional potentials in wheat–maize and wheat–soybean rotations, offering science-based recommendations for sustainable crop rotation practices.Graphical

No tillage and organic fertilization improved kiwifruit productivity through shifting soil properties and microbiome

AbstractThe preservation of edaphic quality and productivity is critical for the ecological sustainability of vine orchards. The heavy utilization of intensified tillage and singular chemical fertilizers can shift changes in edaphic physicochemical and biological features, thus exerting significant pressure on agroecosystems. In current research, we assessed the shifts in soil physicochemical features and soil microbiome composition over 11 years carrying out no tillage and organic fertilizer substitution in a typical Chinese Guanzhong kiwifruit production area, and explore the fundamental factors that contribute to alterations in the microbial community and the influence on kiwifruit performance. Results showed that long‐term no tillage and organic fertilizer improved the soil condition by significantly increasing the proportion of soil macroaggregates, bulk density, and nutrient content (e.g., organic matter, nitrogen, and ammonia), as compared to conventional tillage with chemical fertilization. Moreover, no tillage significantly increased soil bacterial α‐diversity but had no significant effects on fungal. No tillage also enhanced the abundance of potential beneficial soil bacteria (e.g., Acidobacteria, Actinobacteria, and Nitrospira), while decreasing the abundance of Proteobacteria, Pseudomonas, and Fusarium. In addition, no tillage and mixed fertilized soil microbial network exhibited higher complexity (i.e., node and edge numbers, and positive edge proportion) and connectivity (i.e., average number of neighbors) than conventional tillage and chemical fertilization group. Changes in nitrate, ammonia, available phosphorus, and pH values accounted for the variation in the structure of soil microbial community. Hence, the utilization of both no tillage and organic fertilization practices could serve as a suitable and sustainable approach for managing kiwifruit production in the fragile environmental conditions of the Chinese Guanzhong region, and lead to an improvement in soil nutrient levels and help regulate the soil microbial community.

Linking phosphorus fertility to soil microbial diversity and network complexity in citrus orchards: Implications for sustainable agriculture

Continuous input of chemical fertilizers causes soil acidification, land degradation, and water eutrophication, but its impact on soil microbial communities and co-occurrence patterns of microboes is unclear. In this study, we evaluated the impact of chemical fertilizer on bacterial community diversity and ecological network at 75 citrus sites in a watershed where chemical fertilizer is continuously applied. In addition, 25 natural forest sites adjacent to citrus sites were used as references to compare the potential effects of land conversion from natural forests to citrus orchards on soil bacterial diversity and microbial network. The results showed that the cultivation of citrus results in soil phosphorus (P) accumulation, with significantly higher available and mineral-bound phosphate contents than those found in soils of natural forests. Citrus soil average soil available P was 73.2 mg/kg, which was 20 times higher than that in forest soils. As the P content accumulates, soil bacterial Shannon index linearly decreases from 7.06 to 5.93 and is significantly lower than that of adjacent natural forest soils (7.13). Low P fertility soils have higher microbial network complexity and stability, containing more microbial communities and tighter relationships between microbes compared to higher P fertility soils. Soil P content and soil pH regulates soil microbial network complexity and stability. In addition, soil bacterial community structure in soils of natural forests is significantly different from that in citrus soils, and the bacterial community structure in high P soils is different from that in medium and low P soils. Soil P fertility reduces the relative abundance of dominant communities including Proteobacteria, Bacteroidetes, and Gemmatimonadetes, and also changes the relative abundance of some functional microbial communities, such as some phosphorus cycling microorganisms, including Acetobacteraceae and Beijerinckiaceae. In conclusion, soil phosphate accumulation severely alters soil bacterial community diversity, complexity, stability, and functionality. This could have negative impacts on soil functional stability and the sustainability of citrus orchards.

Biodegradable film mulching increases soil microbial network complexity and decreases nitrogen-cycling gene abundance

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes.

Organic management pattern improves microbial community diversity and alters microbial network structure in karst tea plantation

Soil microbiomes play a crucial role in enhancing plant growth, health, and overall agricultural productivity. Nevertheless, the influence of distinct agricultural management practices on the microbial diversity and community structure within tea (Camellia sinensis) plantations has remained enigmatic. This study postulates that organic agricultural management models can enhance microbial diversity and optimise the microbial community structure within tea plantations, indirectly augmenting soil fertility and tea quality. We employed metagenome technology and conducted molecular ecological network analysis to explore the impact of organic management, pollution-free management, and conventional management on the microbial network structure of tea plantation soil in Weng'an County in the southwestern karst region. Soils subjected to organic management exhibited a higher relative abundance of soil microbial and carbohydrate-active enzyme functional genes than those subjected to other management regimes. Additionally, the relative abundance and diversity of dominant bacteria and keystone species were notably higher under organic management than under the other management regimes. Correlation analysis showed that soil microorganisms were closely related to soil fertility and tea quality, respectively. One-way analysis of variance and the structural equation modelling results showed significant variability in soil fertility under the three agricultural management modes and that soil fertility and soil microbial diversity had a direct impact on tea quality (P > 0.05). In conclusion, this study underscores the profound impact of management modes on microbial diversity and community structure within tea plantations. These management practices alter the soil microbial network structure and potential function, ultimately regulating the microecological dynamics of the soil community in tea plantations.

Positive associations fuel soil biodiversity and ecological networks worldwide

Microbial interactions are key to maintaining soil biodiversity. However, whether negative or positive associations govern the soil microbial system at a global scale remains virtually unknown, limiting our understanding of how microbes interact to support soil biodiversity and functions. Here, we explored ecological networks among multitrophic soil organisms involving bacteria, protists, fungi, and invertebrates in a global soil survey across 20 regions of the planet and found that positive associations among both pairs and triads of soil taxa governed global soil microbial networks. We further revealed that soil networks with greater levels of positive associations supported larger soil biodiversity and resulted in lower network fragility to withstand potential perturbations of species losses. Our study provides unique evidence of the widespread positive associations between soil organisms and their crucial role in maintaining the multitrophic structure of soil biodiversity worldwide.

Response of soil microbial properties in the life cycle of potatoes to organic substitution regimes in North China

Organic substitution regimes (OSR) can improve soil microbial properties in crop production. However, the dynamic responses of soil microbial flora and its driving factors in crop growth periods under OSR are still unclear. Here, a 2-year fertilizer field trial was conducted to explore the response of soil chemistry and microbial properties to OSR in the life cycle of potatoes (Solanum tuberosum L.) in North China. The fertilization treatment included only mineral fertilizer (ConN), substitution of 30% mineral N with organic N (M30), and substitution of 60% mineral N with organic N (M60); soil samples were collected and analyzed in the early flowering period (EP), flowering period (MP), and maturity period (LP) of potatoes. As the potato growth period progressed, M30 and M60 increased soil organic carbon (SOC) compared with ConN. Soil total nitrogen (pH) increased (decreased) under M60, while soil available potassium was similar across three treatments. Compared with ConN, soil bacterial Chao, Shannon, and PD indexes significantly increased under M30 and M60 in MP and LP, and the fungal Shannon index increased in LP. Soil bacterial and fungal community structures under M30 and M60 were only significantly separated from ConN in MP. The bacterial communities of dominant phyla or genera responded more sensitively to the fertilization regimes than the flora of fungi, and the changes in the flora mainly occur in EP and MP. Redundancy analysis revealed that SOC and available phosphorus were highly correlated with soil microbial community compositions. Compared with ConN, soil microbial network complexity and fungal network robustness were higher under M30 and M60, while bacterial network robustness showed the opposite trend. Partial least squares pathway modeling showed that the conversion in the fertilization system or growth period had a direct positive effect on the C/N-cycling function of soil bacteria, but not on the C-degradation function of fungi. Our research has important theoretical implications for the development of microbial fertilizers and fertilization management in different potato growth periods.

Soil microbial community structure, function and network along a mangrove forest restoration chronosequence

Mangrove forests have high ecological, social and economic values, but due to environmental changes and human activities, natural mangrove forests have experienced serious degradations and reductions in distribution area worldwide. In the coastal zones of southern China, an introduced mangrove species, Sonneratia apetala, has been extensively used for mangrove restoration because of its rapid growth and strong environmental adaptability. However, little is known about how soil microorganisms vary with the restoration stages of the afforested mangrove forests. Here, we examined the changes in soil physicochemical properties and microbial biomass, community structure and function, and network in three afforested S. apetala forests with restoration time of 7, 12, and 18 years and compared them with a bare flat and a 60-year-old natural Kandelia obovata forest in a mangrove nature reserve. Our results showed that the contents of soil salinity, organic carbon, total nitrogen, ammonium nitrogen, and microbial biomass increased, while soil pH and bacterial alpha diversity decreased with afforestation age. Soil microbial community structure was significantly affected by soil salinity, organic carbon, pH, total nitrogen, ammonium nitrogen, available phosphorus, and available kalium, and susceptibility to environmental factors was more pronounced in bacterial than fungal community structure. The relative abundances of aerobic chemoheterotrophy were significantly higher in 12- and 18-year-old S. apetala than in K. obovata forest, while that of sulfate-reducing bacteria showed a decreasing trend with afforestation age. The abundance of dung saprotroph was significantly higher in 12- and 18-year-old S. apetala forests than in the natural forest. With the increasing afforestation age, the modularity of microbial networks increased, while stability and robustness decreased. Our results suggest that planting S. apetala contributes to improving soil fertility and microbial biomass but may make soil microbial networks more vulnerable.

Characteristics of the microbial communities regulate soil multi-functionality under different cover crop amendments in Ultisol

The use of cover crops is a promising strategy for influencing the soil microbial consortium, which is essential for the delivery of multiple soil functions (i.e., soil multifunctionality). Nonetheless, relatively little is known about the role of the soil microbial consortium in mediating soil multifunctionality under different cover crop amendments in dryland Ultisols. Here, we assessed the multifunctionality of soils subjected to four cover crop amendments (control, non-amended treatment; RD, radish monoculture; HV, hairy vetch monoculture; and RDHV, radish–hairy vetch mixture), and we investigated the contributions of soil microbial richness, network complexity, and ecological clusters to soil multifunctionality. Our results demonstrated that cover crops whose chemical composition differed from that of the main plant crop promoted higher multifunctionality, and the radish–hairy vetch mixture rendered the highest enhancement. We obtained evidence that changes in soil microbial richness and network complexity triggered by the cover crops were associated with higher soil multifunctionality. Specifically, specialized microbes in a key ecological cluster (ecological cluster 2) of the soil microbial network were particularly important for maintaining soil multifunctionality. Our results highlight the importance of cover crop-induced variations in functionally important taxa for promoting the soil multifunctionality of dryland Ultisols.

PH is the major predictor of soil microbial network complexity in Chinese forests along a latitudinal gradient

Patterns in the network structure of microbial communities may give indications of their degree of interaction and interdependence, and their resilience to environmental disturbance. Geographical differences in network patterns of forest communities may reflect broad-scale differences in ecosystem structure and responses to environmental change. We analyzed a large dataset of 144 samples of soil bacterial and fungal communities characterized by 16S and ITS amplicon sequencing from forests in eastern China, along a 4,100 km latitudinal transect. This showed that fungal-bacterial network complexity was most closely related to soil pH. Results showed that pH was the strongest predictor of variation in community network structure across the forest soils of eastern China. Lower network complexity and stability were found around neutral pH, which was the strongest environmental predictor. This may be due to the optimal conditions that neutral soils provide for microorganism survival, reducing the necessity for physiological interdependence, consequently leading to fewer positive connections. Additionally, neutral soils provide more generalized niches, resulting in less specific niche exclusion, showing up as fewer negative connections. Unlike the trend for overall connectivity, the richness and relative abundances of keystone taxa were significantly and negatively correlated with pH. Overall, both connectivity and numbers of keystones were consistent in suggesting that network complexity was greatest overall at acidic pH. It appears that at the broad scale studied here, pH plays a more significant role in shaping microbial community integration than such factors as ecosystem productivity or climate.