Soil Microbial Diversity Research Articles

Effects of Bacillus subtilis on cotton physiology and growth under water and salt stress

The scarcity of fresh water resources has severely limited agricultural production in arid areas. Although brackish water irrigation or fresh water deficit irrigation can alleviate the water resources crisis, both may cause water and salt stress to crop. Therefore, this study is based on the functional advantages of Bacillus subtilis in soil improvement and crop growth promotion to alleviate water and salt stress and build safe and efficient water-saving irrigation patterns. In this study, cotton (No. 50 Chuangmian) was selected as the research crop, and five application rates of Bacillus subtilis (0, 22.5, 45, 67.5 and 90 kg·ha−1) were combined with three irrigation patterns (brackish water, fresh water and fresh water deficit irrigations) to study the effects of Bacillus subtilis on soil moisture and salinity, soil microbial community, cotton physiology and growth under water and salt stress. The results showed that Bacillus subtilis could enhance soil water retention capacity, promote soil desalination, improve cotton growth indices (plant height, stem diameter, leaf area index, dry matter accumulation), and then increase yield and water use efficiency (WUE). Compared with the control treatment, the yield and WUE of Bacillus subtilis application treatments increased by 3.32–54.67 % and 1.68–41.07 %, respectively. In the cotton physiology characteristics, Bacillus subtilis increased proline content and the activity of superoxide dismutase, peroxidase and catalase while decreased malondialdehyde content in cotton leaves. Bacillus subtilis could enhance the relative abundance of bacteria with the functions of nitrogen fixation, stress resistance and biocontrol. A structural equation model proved that Bacillus subtilis could improve yield and WUE indirectly by directly improving soil microbial diversity, alleviating water and salt stress, and then improving cotton physiology and growth. According to a comprehensive evaluation of cotton physiology and growth, it was determined that the optimal improvement effect was achieved when the application rate of Bacillus subtilis was 45 kg ha−1; the synergistic effect of brackish water irrigation and Bacillus subtilis (45 kg·ha−1) was superior to that of fresh water deficit irrigation combining with Bacillus subtilis (45 kg·ha−1), which could be considered a priority strategy for alleviating the fresh water crisis in arid areas and promoting the efficient increase in cotton yield.

Soil and stone terraces offset the negative impacts of sloping cultivation on soil microbial diversity and functioning by protecting soil carbon

Cultivation of sloping land is a main cause for soil erosion. Conservation practices, such as soil and stone terraces, may reduce the impacts of erosion but their impacts on soil microbial diversity and functioning related to carbon (C) and nutrient metabolisms remain unclear. This study was conducted to evaluate the effects of slope gradients (5°, 8°, 15°, 25°) and conservation practices (cultivated, uncultivated, soil terrace, and stone terrace) on bacterial and fungal diversities, metagenomic and metabolomic functioning associated with basic soil properties. Our results showed that steep slopes at 25° significantly decreased soil pH, silt percentage, and bacterial and fungal abundances, but that soil and stone terraces increased soil organic C (SOC), silt and clay contents, and fungal abundance compared to sloping cultivated lands. In addition, soil and stone terraces increased both bacterial and fungal alpha diversities, and relative abundances of Crenarchaeota, Nitrospirota, and Latescibacterota, but reduced the proportions of Actinobacteriota and Patescibacteria, thus shifting microbial beta diversities, which were significantly associated with increased SOC and silt content. For metagenomics, soil and stone terraces greatly increased the relative abundance of functional genes related to Respiration, Virulence, disease and defense, Stress response, and nitrogen and potassium metabolisms, such as Denitrification and Potassium homeostasis. For soil metabolomics, a total of 22 soil metabolites was enriched by soil and stone terraces, such as Lipids and lipid-like molecules (Arachidonic acid, Gamma-Linolenic acid, and Pentadecanoic acid), and Organoheterocyclic compounds (Adenine, Laudanosine, Methylpyrazine, and Nicotinic acid). To sum up, soil and stone terraces could reduce some of the negative impacts of steep slope cultivation on soil microbial diversity as well as their metagenomic and metabolomic functioning related to C and nutrient metabolism useful for soil health improvement, potentially bolstering the impact of sustainable practices in erosion hotspots around the world.

Diversification of crops and intensification of canola impact the diversity, community structure, and productivity in successive crop systems: A study on arbuscular mycorrhizal fungal communities in roots and rhizosphere

The widespread cultivation of canola, conventionally still considered a non-host plant for AM fungi, coupled with its increasing frequency in crop rotations, raises concerns about its impacts on soil microbial diversity and overall crop productivity. The main objective of this study is to assess the influence of different crop succession systems, incorporating canola, on AM fungal diversity and community structure in both the roots and in the rhizosphere, as well as on productivity of each crop present within the succession. Doubling the frequency of canola occurrence in a 4-year crop succession did not reduce the productivity of the other crops in the succession, nor did it result in a decrease in AM fungal biodiversity in the roots or rhizosphere of these crops. Interestingly, the diversity of AM fungi was higher in canola roots compared to wheat roots, indicating that canola might serve as a rudimentary host of AM fungi. The succession systems did, however, alter the AM fungal community structure in both roots and rhizosphere environments, exhibiting positive or negative correlations with crop productivity. This suggests that a simple modification of the cropping system could potentially be employed to manipulate root or rhizosphere microbiomes. Results of this study add to the growing body of evidences that plants that were thought to be non-AM fungi host, such as plants from the Brassicaceae family, could in fact interact with AM fungi.

Low impact of Carpobrotus edulis on soil microbiome after manual removal from a climate change field experiment

Synergic effects between climate change and invasive species may alter soil microbial diversity and functioning, as well as cause major shifts in physicochemical properties. Moreover, some of these ecological impacts may manifest even after the removal of the invasive species. We have conducted a field experiment to assess such effects on soil microbial communities (fungi and bacteria) and physicochemical properties seven months after the removal of Carpobrotus edulis (L.), an invasive plant of coastal dune ecosystems. C. edulis grew on the experimental plots for 14 months under current (“invasive species treatment”) and increased warming and drought conditions (“combined treatment”). Then, all plant parts (above and belowground biomass) were removed with a non-aggressive eradication method and soil samples were collected seven months later in the experimental and control plots (no invasive species and current climatic conditions). We predicted a general compositional shift in microbial communities in response to the presence of the invasive species. Moreover, given that water is the most limiting factor in this type of ecosystem, we also predicted a more pronounced compositional shift in the treatment combining invader presence and climate change. While species richness was similar amongst treatments, we observed some taxonomic and functional variation in soil microbial communities. Notably, fungal and bacterial communities exhibited contrasting responses. The species composition of bacteria differed significantly between the “invasive species” and “control” treatments, while, in the case of fungi, the most substantial difference occurred between the “invasive species” treatment and the combined treatment of “invasive species and climate change”. Some chemical properties, such as carbon and nitrogen content or pH, strongly differed amongst treatments, with the “invasive species” showing a different response compared to the other two treatments. Overall, our study suggests smaller short-term effects on the microbial community compared to soil chemical properties. Furthermore and contrary to our initial expectations, the potential impact on the soil microbiome seemed to be weaker in the face of rising temperatures and drought conditions predicted by climate change. This outcome highlights the remarkable complexity of the impact of invasive species and climate change on belowground microbial communities.

Alterations in carbon and nitrogen cycling mediated by soil microbes due to the conversion of karst mountainous forests into urban parks

The conversion of mountainous karst forests into urban parks necessitates a critical analysis of its impact on existing ecosystems, particularly regarding soil microbial diversity and its role in carbon and nitrogen cycling. Our study targeted three established mountain parks in Guiyang, China, to discern the effects of habitat alteration and park age on the soil microbiota’s functional genes. The findings indicated pronounced differences in functional gene profiles between original remnant forests and created greenspaces. The artificial green spaces exhibited a heightened presence of genes related to aerobic methane oxidation, anaerobic carbon fixation, denitrification and nitrification, indicating that artificial green spaces may cultivate soil microbial communities with enhanced metabolic versatility. We revealed a positive correlation between soil nitrogen levels and the abundance of genes involved in various processes of the carbon and nitrogen cycles in these artificial green areas, highlighting the critical role of nitrogen in influencing the structure of microbial communities. Soil chemical properties (namely C, N, P, K content) and habitat type emerged as the most consequential for the gene composition related to the carbon and nitrogen cycles. The co-occurrence networks of functional genes constructed for these cycles suggest a tendency towards synergistic microbial interactions. To safeguard the interplay between human recreation and the conservation of native ecosystems, we recommend the integration of native flora preservation and meticulous soil condition management into the strategies for developing urban mountain parks.

Effects of Trichoderma harzianum and Bacillus subtilis on the root and soil microbiomes of the soybean plant INTACTA RR2 PRO™.

Soybean is a significant export product for several countries, including the United States and Brazil. There are numerous varieties of soybean. Among them, a genetically modified type known as INTACTA RR2 PRO™ has been designed to demonstrate resistance to glyphosate and to produce toxins that are lethal to several species of caterpillars. Limited information is available on the use of Trichoderma harzianum and Bacillus subtilis to promote plant growth and their impact on the plant microbiome. This study aimed to evaluate the effects of these microorganisms on this soybean cultivar by analyzing parameters, such as root and shoot dry matter, nutritional status, and root and soil microbial diversity. The results indicated that treatments with B. subtilis alone or in combination with T. harzianum as seed or seed and soil applications significantly enhanced plant height and biomass compared to the other treatments and the control. No significant differences in phosphorus and nitrogen concentrations were detected across treatments, although some treatments showed close correlations with these nutrients. Microbial inoculations slightly influenced the soil and root microbiomes, with significant beta diversity differences between soil and root environments, but had a limited overall impact on community composition. The combined application of B. subtilis and T. harzianum particularly enhanced plant growth and promoted plant-associated microbial groups, such as Rhizobiaceae, optimizing plant-microbe interactions. Furthermore, the treatments resulted in a slight reduction in fungal richness and diversity.

Nitrates and Microbiome Components Engaged in Denitrification within Soil Regulate Morchella spp. Growth

Morels (Morchella spp.) are a kind of rare and precious edible fungus and have been successfully cultivated in many places. Currently, the widespread cultivation of morels poses a significant challenge owing to their demanding environmental requirements. Soil properties and the soil microbiome are thought to play pivotal roles in morel growth. However, it remains unknown what factors exert a decisive influence on morel growth. In this study, soils with different morel yields were studied in nine sites from four locations. The basic soil physical and chemical properties were measured. In addition, the soil microbiome was analyzed using high-throughput metagenomic sequencing. We found that soil pH, nitrogen, carbon and conductivity were key indicators for the impact on microbial communities in soil for cultivating morels. Among these, nitrate was more positively associated with morel yield. The soil microbial diversity was more abundant in the soil with a high morel yield. Moreover, certain unknown archaea might be unfavorable to morel growth. The microbes that perform incomplete denitrification (no step of N2O reduction to N2) and nitrogen fixation were positively and negatively correlated with morel growth, respectively. In summary, morels prefer to live in nutrient-rich soils with a variety of microbes and are supported by nitrate and microbiome components involved in denitrification. The findings elucidate a pivotal mechanism in eliciting morel fructification and provide valuable insights for guiding production practices.

Impact of Transgenic Maize Ruifeng125 on Diversity and Dynamics of Bacterial Community in Rhizosphere Soil.

With the development of commercialized planting of genetically modified crops, their ecological security risks remain a key topic of public concern. Insect-resistant genetically modified maize, Ruifeng125, which expresses a fusion Bt protein (Cry1Ab-Cry2Aj), has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw was returned to the field, over 97% of Bt proteins were degraded quickly at the early stages (≤10 d) and then they were degraded at a relatively slow rate. In addition, the variations in bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families, and 842 genera were obtained by 16S rRNA sequencing, among which Proteobacteria, Actinobacia, Acidobacter Acidobacterium, and Chloroflexi were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution to the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establishes a theoretical foundation for their environmental safety assessment.

The Changes of Microbial Diversity and Isolation of Microorganism in Soil for Alleviating the Production Decreasing After Continuous Cultivation of Ganoderma lucidum.

Ganoderma lucidum is a medicinal mushroom usually cultivated in logs and covered with soil. Its production decreases after continuous cultivation. Changes of microbial diversity in soil are suggested to be one of the reasons. This study aims to investigate the changes of microbial diversity and abundance in soil during cultivation, and isolate potential microbial strains that affect the yield of G. lucidum. Soil samples were collected at two different ranges from logs during one complete growth cycle of G. lucidum. The changes in fungi and bacteria were investigated by using high-throughput sequencing and real-time PCR. Results indicated that the relative abundance of Firmicutes in the bacterial community decreased at the short-range site. In the fungal community, the relative abundance of Ganoderma increased to 70% at the long-range site at the end of the cultivation. The abundance of bacteria and fungi decreased significantly at the end of the growth cycle. Recovery of microbial changes in soil should be proceeded separately based on different ranges to logs. The microbial strains in these soil samples were also isolated and identified. Potential strains were assessed in the form of bio-fertilizer. The yield of G. lucidum in the field using bio-fertilizer with isolated bacterial strains from the Firmicutes phylum was about 13% higher than that without using bio-fertilizer, suggesting the possibility of alleviating the production decrease of G. lucidum by this method.

Nanoarchitectonics with self-healing hydrogel for hierarchical porous carbons and its application in cadmium-arsenic complex pollution

A cheap and green method for porous carbons (CAC-1) with high surface area (409.41 mg/g) is constructed benefiting from self-healing properties of calcium alginate hydrogel under atmospheric drying. Layered double hydroxides modified CAC-1 (CAC-LDH-1) is applied in cadmium-arsenic complex pollution. The adsorption capacities of the CAC-LDH-1 on Cd(II) and As(V) are 331.03 mg/g and 33.48 mg/g in single system, and 79.87 mg/g and 150.59 mg/g in binary system. In binary system, the synergistic action of Cd(II) ions greatly improve the adsorption capacity and adsorption rate of As(V) ions. The adsorption process of cadmium-arsenic by CAC-LDH-1 mainly follows the second-order kinetic model and Freundlich model, and the adsorption process is endothermic and spontaneous. XPS, FTIR, XRD, SEM-EDS mapping and pore size distribution are carried out to explore the structure and adsorption mechanism of CAC-LDH-1. After treatment with 1 % CAC-LDH-1 for 30 days, the proportions of E1-Cd, F1-As, and F2-As that can be utilized by plants decrease from 46.32 % to 33.15 %, 10.08–2.15 %, and 43.06–35.23 %. Compared with CK group, Cd/As contents in the above/under-ground part of red cherry radish seedlings decrease by 31.41∼59.09 %. CAC-LDH-1 inhibits little effect on the microbial diversity of soil, but change the dominant bacterial colonies.

Field-based assessment of the effect of conventional and biodegradable plastic mulch film on nitrogen partitioning, soil microbial diversity, and maize biomass

In an agricultural context, the use of conventional low-density polyethylene (LDPE) and biodegradable plastic mulch film has been actively promoted, however, the effects on physical and biochemical soil properties, crop growth dynamics, yield, and nutrient cycling of conventional and biodegradable mulch film use in a temperate climate remain largely undetermined. Here, we conducted a field experiment, exploring the effects of no mulch (control), conventional (LDPE), and biodegradable (PLA/PBAT) plastic mulch film on soil and crop (Zea mays L.) nitrogen (N) partitioning after application of 15N-labelled ammonium-nitrate fertiliser. Further, we also investigated the treatment effects on soil physical and biochemical properties (e.g., microbial diversity, compound-specific microbial 15N incorporation, N dynamics), plant development, as well as monitoring the biotic and abiotic degradation of the plastic mulch films. We found that conventional mulch film increased crop yield by 25 % and 15N uptake by 34 % compared to the control, simultaneously reducing 15N retention by 40 % in the topsoil (0–10 cm), but not affecting microbial N use efficiency and N transformation and incorporation into the protein pool. Biodegradable film application resulted in similar biomass (306 ± 14 g plant−1) to both control (275 ± 14 g plant−1) and conventional mulch (344 ± 20 g plant−1) treatments, but significantly reduced 15N crop uptake by 63 % compared to the conventional mulch film. We ascribe this to the accelerated mechanical breakdown and faster degradation of the biodegradable mulch film during the growing season. These findings suggest that current biodegradable plastic mulch film polymer blends may not be a suitable alternative to conventional mulch film in terms of short-term productivity and N use efficiency in a temperate climate for maize production.

Molecular Diversity of Ectomycorrhizal Fungi in Relation to the Diversity of Neighboring Plant Species.

(1) Background: Plant diversity has long been assumed to predict soil microbial diversity. The mutualistic symbiosis between forest trees and ectomycorrhizal (EM) fungi favors strong correlations of EM fungal diversity with host density in terrestrial ecosystems. Nevertheless, in contrast with host tree effects, neighboring plant effects are less well studied. (2) Methods: In the study presented herein, we examined the α-diversity, community composition, and co-occurrence patterns of EM fungi in Quercus acutissima across different forest types (pure forests, mixed forests with Pinus tabuliformis, and mixed forests with other broadleaved species) to ascertain how the EM fungi of focal trees are related to their neighboring plants and to identify the underlying mechanisms that contribute to this relationship. (3) Results: The EM fungal community exhibited an overall modest but positive correlation with neighboring plant richness, with the associations being more pronounced in mixed forests. This neighboring effect was mediated by altered abiotic (i.e., SOC, TN, LC, and LP) and biotic (i.e., bacterial community) factors in rhizosphere soil. Further analysis revealed that Tomentella_badia, Tomentella_galzinii, and Sebacina_incrustans exhibited the most significant correlations with plant and EM fungal diversity. These keystone taxa featured low relative abundance and clear habitat preferences and shared similar physiological traits that promote nutrient uptake through contact, short-distance and medium-distance smooth contact-based exploration types, thereby enhancing the potential correlations between EM fungi and the neighboring plant community. (4) Conclusions: Our findings contribute to the comprehension of the effect of neighboring plants on the EM fungal community of focal trees of different forest communities and the biodiversity sensitivity to environmental change.

Effects of Streptomyces melanosporofaciens X216 on microbial diversity in oilseed rape soil.

Clubroot disease is a devastating soil borne disease caused by infection with Plasmodiophora brassicae, which primarily affects cruciferous plants. The microbial diversity of the soil is an essential indicator of its quality. This study measured the physicochemical properties of the soil to study the effect of its microbial diversity on the infection of oilseed rape with P. brassicae. High-throughput sequences of the soil bacteria and fungi in the inter-root soils of P. brassicae were analyzed under different treatment conditions. In the study, it was found that the efficiency of strain X216 in preventing and controlling the root disease of rapeseed was positively correlated with the amount of solution used to irrigate the root system. The results of the greenhouse and field trials showed that the efficiency of strain X216 against the root disease of rapeseed was 43.16% in the field and 62.14% in the greenhouse. Proteobacteria, Chloroflexi, Rozellomycota, and Basidiomycota are critical phylum in the development of clubroot disease. The application of biocontrol increased the relative abundance of Actinobacteria, Bacillus, Mesorhizobium, Mycobacterium, Streptomyces and Filobasidium, which affected the structure and abundance of microbial communities. A principal coordinate analysis showed that the microbial structure in the soil varied substantially in the bacterial community, and there was no significant difference in soil structure in the fungal community. The occurrence of clubroot disease affected the structure of inter-root microbial community composition in the soil, which resulted in a decrease in its community diversity. The application of the biocontrol bacterium X216 increased the soil microbial diversity. It effectively reduced the occurrence of P. brassicae, and this study provides a basis to study the microbial diversity in cruciferous crops.

Improved Straw Decomposition Products Promote Peanut Growth by Changing Soil Chemical Properties and Microbial Diversity

The ameliorative effects of straw decomposition products on soil acidification have been extensively studied. However, the impact of chemically treated straw decomposition products on crop productivity and the underlying microbial mechanisms remain unclear. This study aimed to investigate the effects of two dosages of Ca(OH)2-treated straw decomposition products of peanuts on red soil acidity, fertility, and bacterial and fungal diversity through a pot experiment. The pot experiment included four treatments: chemical nitrogen, phosphorus, and potassium (NPK) fertilization alone (CK), NPK chemical fertilization combined with peanut straw decomposition products (PS), NPK chemical fertilization combined with 4% Ca(OH)2-treated peanut straw decomposition products (PS4Ca), and NPK chemical fertilization combined with 8% Ca(OH)2-treated straw decomposition products (PS8Ca). High-throughput sequencing was performed to investigate the effects of these treatments on soil microbial diversity. The treatments with PS, PS4Ca, and PS8Ca significantly increased soil pH, exchangeable base cations, and nutrient content, whereas they decreased the exchangeable acid, especially exchangeable aluminum. The peanut growth improved substantially with the application of straw decomposition products. Specifically, PS4Ca significantly increased the Shannon and Richness indices of fungi. The principal coordinate analysis showed that the soil microbial communities in the straw decomposition product treatments were significantly different from CK. Linear discriminant analysis effect size identified unique bacteria and fungi between treatments. The Mantel test indicated that exchangeable base cations and pH were significantly positively correlated with bacterial communities, whereas available potassium was positively correlated with fungal communities. The partial least squares path modeling revealed that the bacterial communities positively and directly affected all peanut agronomic traits. In contrast, the fungal communities had a negative and direct effect only on peanut 100-pod weight. Therefore, adding Ca(OH)2-treated straw decomposition products could effectively improve crop productivity by alleviating soil acidification, increasing soil nutrients, and subsequently changing microorganisms.

Dicranopteris dichotoma rhizosphere-derived Bacillus sp. MQB12 acts as an enhancer of plant growth via increasing phosphorus utilization, hormone synthesis, and rhizosphere microbial abundance

In recent years, microbial inoculants have showed a great potential to replace chemical fertilizers as a new generation of soil amendment agents, however, the understanding of their effects on nutrient cycling within plants and rhizosphere microbial diversity are still limited. In this study, the rhizosphere growth-promoting bacteria MQB12 was used to inoculate Vigna radiata to evaluate the effects of external inoculants on plant transcriptomics and rhizosphere soil microbial diversity. Enrichment analysis using GO and KEGG revealed significant enrichment in DNA-binding transcription factor activity, transcriptional regulatory factor activity, and phenylpropanoid biosynthesis among the differentially expressed genes. MQB12 inoculation positively responded to phosphorus starvation response, increased the expression of phosphorus starvation response genes (PHT/PAP), enhanced the synthesis of ethylene and salicylic acid to cope with external stress, and improved the expression of plant disease resistance genes to strengthen the disease resistance of plants to pathogens. At the same time, microbial diversity analysis further revealed the positive effect of MQB12 inoculum. MQB12 inoculum enriched beneficial flora, improved flora abundance, changed the structure and diversity of V. radiata rhizosphere microbial community, enhanced the interconnections between the flora, and positively promoted growth. MQB12 was found to adjust the microflora of the rhizosphere, which subsequently changed the environment for plant colonization. This change led to the enrichment of beneficial bacteria and removal of pathogenic bacteria, which positively affected the internal pathways of plants. Additionally, changes in gene expression levels of plants resulted in the formation of different phenotypes and various metabolites, further influencing the formation of rhizosphere microbial communities through close contact between roots and soil. This study provides new insights into the effects of microbial agents on plant growth and root environment construction and is conducive to the further development and application of microbial agents.Graphical

Effects of Long-Term Application of Nitrogen Fertilizer on Soil Acidification and Biological Properties in China: A Meta-Analysis.

Soil acidification is a global environmental problem with significant impacts on agricultural production, environmental protection, and ecosystem health. Soil acidification is widespread in China, affecting crop yields, agricultural product quality, and biodiversity. Since the 1980s, much work has been done on acidic soils in China, but it is controversial whether excessive nitrogen fertilizer application can lead to soil acidification mechanisms. To address the above issues, we conducted a meta-analysis of 115 published papers to integrate and analyze the effects of N fertilizer application on soil acidification and biological properties from 1980 to 2024. We also quantified the effect of nitrogen fertilization on soil acidification and biological changes under different climatic conditions. The results showed that under long-term application of nitrogen fertilizers in China from 1980 to 2024, soil pH decreased by an average of 15.27%, and the activities of soil urease, nitrate reductase, nitrite reductase, catalase, glutamate dehydrogenase, and glutamate synthetase decreased by an average of 9.82-22.37%. The soil microbial community richness (Chao1 index) increased by 6.53%, but the community diversity (Shannon index) decreased by 15.42%. Among the dominant soil microorganisms, the relative abundance of bacteria decreased by an average of 9.67-29.38% and the abundance of gene expression of nifH, amoA-AOA, amoA-AOB, and qnorB decreased by 9.92-19.83%. In addition, we found that the mean annual temperature and rainfall impacted soil acidification via their effect on soil microbial diversity and community composition. This study provides a scientific basis for an in-depth understanding of the spatial and temporal variation of soil acidification and biological properties in China.

Aboveground and belowground biodiversity have complementary effects on ecosystem functions across global grasslands.

Grasslands are integral to maintaining biodiversity and key ecosystem services and are under threat from climate change. Plant and soil microbial diversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, it remains virtually unknown whether plant and soil microbial diversity explain a unique portion of total variation or shared contributions to supporting multifunctionality across global grasslands. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that plant and soil microbial diversity independently predict a unique portion of total variation in above- and belowground functioning, suggesting that both types of biodiversity complement each other. Interactions between plant and soil microbial diversity positively impacted multifunctionality including primary production and nutrient storage. Our findings were also climate context dependent, since soil fungal diversity was positively associated with multifunctionality in less arid regions, while plant diversity was strongly and positively linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands.

Rare rather than abundant taxa of soil bacteria and fungi regulate soil multifunctionality in Eucalyptus plantations

Soil multifunctionality not only contributes to the production of ecosystem services (e.g., nutrient cycling, boosts in plant production, and provision of biological processes), but also supports the survival of species (protecting biodiversity) in an ecosystem. Multi-generational planting (sprouting from logging stumps) of Eucalyptus is widely adopted for timber production in southern China, which distinctly induces the decline of soil properties and destroys soil microbial communities. However, research on various Eucalyptus management practices has predominantly concentrated on soil nutrients and microbial populations. The effects of these practices on soil multifunctionality remain unexplored. Furthermore, the underlying mechanisms influencing the abundant and rare microorganisms have not been fully understood. Here, an 18-year Eucalyptus plantation experiment, including single-generation continuous planting (Y18), multiple-generation felling of the same years (D4), and evergreen broadleaf forest control (CK), was designed. Twenty-three parameters associated with soil nutrient cycling were obtained to quantify soil multifunctionality, and partial least squares path modeling (PLS-PM) was used to reveal the main driving force regulating soil multifunctionality. Our results demonstrated that multi-generational Eucalyptus planting significantly reduced soil multifunctionality, microbial diversity, and network stability. Comparatively, single-generational planting showed slight effects on soil multifunctionality and microbial communities. Stochastic processes dominated the assembly of abundant taxa in Eucalyptus plantations, whereas deterministic processes dominated rare taxa. PLS-PM results revealed that soil organic carbon (SOC), dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorus (TP) directly regulated soil multifunctionality or indirectly through modifying the diversity and networks of rare taxa. The total effect analysis showed that the diversity and network of rare taxa had a greater impact on soil multifunctionality than abundant taxa. SOC and DOC played a crucial role in driving changes in soil multifunctionality. Our findings highlight the need to decrease rotation intensity and conserve rare taxa to mitigate soil quality degradation in artificial Eucalyptus plantations.

Short-Term Effects of Cenchrus fungigraminus/Potato or Broad Bean Interplanting on Rhizosphere Soil Fertility, Microbial Diversity, and Greenhouse Gas Sequestration in Southeast China.

Cenchrus fungigraminus is a new species and is largely used as forage and mushroom substrate. However, it can usually not be planted on farmland on account of local agricultural land policy. Interplanting Cenchrus fungigraminus with other crops annually (short-term) is an innovative strategy to promote the sustainable development of the grass industry in southern China. To further investigate this, C. fungigraminus mono-planting (MC), C. fungigraminus-potato interplanting (CIP) and C. fungigraminus-broad bean interplanting (CIB) were performed. Compared to MC, soil microbial biomass carbon (SMBC), soil organic matter (SOM), ammoniacal nitrogen (AMN), pH and soil amino sugars had a positive effect on the rhizosphere soil of CIP and CIB, as well as enhancing soil nitrogenase, nitrite reductase, and peroxidase activities (p < 0.05). Moreover, CIP improved the root vitality (2.08 times) and crude protein (1.11 times). In addition, CIB enhanced the crude fiber of C. fungigraminus seedlings. These two interplanting models also improved the microbial composition and diversity (Actinobacteria, Firmicutes, and Bacteroidota, etc.) in the rhizosphere soil of C. fungigraminus seedlings. Among all the samples, 189 and 59 genes were involved in methane cycling and nitrogen cycling, respectively, which improved the presence of the serine cycle, ribulose monophosphate, assimilatory nitrate reduction, methane absorption, and glutamate synthesis and inhibited denitrification. Through correlation analysis and the Mantel test, the putative functional genes, encoding functions in both nitrogen and methane cycling, were shown to have a significant positive effect on pH, moisture, AMN, SOM, SMBC, and soil peroxidase activity, while not displaying a significant effect on soil nitrogenase activity and total amino sugar (p < 0.05). The short-term influence of the interplanting model was shown to improve land use efficiency and economic profitability per unit land area, and the models could provide sustainable agricultural production for rural revitalization.

Harmonizing soil restoration and microbial diversity: Insights from a Two-Year field experiment with Sedum-Rice rotation systems

Phytoremediation coupled with agroproduction (PCA) model contributes to sustainable agriculture and environmental management. This study investigated the impact of continuous cropping early/late season rice (RR) and Sedum alfredii-rice rotation (SR) on soil physical and chemical properties, as well as their relationships with soil microbial community. In 2022, SR treatment significantly increased pH value and organic matter content by 7 % and 17 %, respectively, compared to the levels in 2020, while RR treatment showed no change. RR treatment resulted in a significant decrease in soil concentrations of Ca, Mg, and K by 18.42 %, 29.01 %, and 7.77 %, respectively. Furthermore, SR treatment saw reductions of 29.62 % in total Cd and 38.30 % in DTPA extractable Cd in the soil. Over the two years, both treatments notably influenced the diversity, structure, and network of the rhizosphere bacterial and fungal communities, which are crucial for nutrient cycling and plant health. Notably, SR treatment exhibited a more complex network compared to RR, suggesting a greater impact on the interconnected systems. Therefore, these findings highlight the potential of Sedum rotation system to rehabilitate contaminated soils while supporting agricultural practices, which is essential for food security and environmental sustainability. This research direction holds promise for future exploration and application in the fields of phytoremediation and agroecology.