Effects of Rotary Tillage and Fertilization on Chemical Properties and Microbial Communities of Soil Under Continuous Morchella Mushroom Cultivation

Variations in crop yield caused by different ratios of organic substitution are closely related to microbial ecological clusters in a fluvo-aquic soil

Tillage practices can directly affect soil quality, influencing soil properties, crop growth, and soil microbial community characteristics. However, the influence of long-term tillage practices on the rhizosphere bacterial community in lime concretion black soil remains largely unknown. In this study, the effects of nine-year rotary tillage (RT), no-tillage (NT), subsoiling tillage (ST), and plow tillage (PT) on soil chemical properties, microbial community structure, and correlations between bacterial communities and soil properties in the maize rhizosphere were investigated. The results revealed that the maize yield in ST and PT was higher by 10.61% and 10.26% than that in RT and by 10.25% and 9.90% than that in NT, respectively. The soil organic matter (SOM) and total nitrogen (TN) contents in NT and ST were significantly higher than those in RT and PT, whereas the available phosphorus (AP) content in ST and PT was significantly higher than that in NT and RT. The diversity and richness of the soil bacterial communities exhibited a trend of NT > RT > PT > ST. The principal component analysis revealed that the soil bacterial community differed among treatments. Linear discriminant analysis effect size (LEfSe) analysis demonstrated that Proteobacteria, Armatimonadetes, Verrucomicrobia, and Chloroflexi could serve as crucial biomarkers. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) results revealed that genes involved in carbon, lipid, and xenobiotic metabolism were enriched under ST and PT, whereas those involved in nitrogen and carbon fixation were enriched under NT. Besides, Proteobacteria, Verrucomicrobia, and Armatimonadetes were positively associated with AP levels and negatively associated with pH; however, Acidobacteria, Bacteroidetes, and Planctomycetes exhibited an opposite trend. Overall, ST and PT improved the soil properties and environmental suitability by increasing the bacterial keystone taxa; thus, these practices improved crop yield. These findings could enhance our understanding of the rhizosphere functional microbial community in lime concretion black soil for winter wheat–summer maize double-cropping system.

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land. HIGHLIGHTS The effects of different phytoremediation on microbial diversity and community structure were different. Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil. All plants increased the activity of nitrite reductase and decreased the activity of urease.

The responses of soil microbes to climatic and anthropological factors in the Tibetan grasslands

The harsh soil conditions in alpine mining areas severely restrict plant growth, necessitating the urgent development of an optimal fertilization strategy to facilitate soil restoration and ecosystem recovery. Six treatments were incorporated: control with no fertilization (CK), 100% sheep manure (S), 100% commercial organic fertilizer (F), 60% sheep manure + 40% commercial organic fertilizer (M1), 50% sheep manure + 50% commercial organic fertilizer (M2), and 40% sheep manure + 60% commercial organic fertilizer (M3). The treatments' impacts on soil properties, microbial composition, functionality, and their interactions were systematically analyzed. The combined application of sheep manure and commercial organic fertilizer significantly enhanced soil organic matter (SOM) and available nutrients. The findings revealed that the M1 treatment showed the greatest improvement, with total nitrogen (TN), total phosphorus (TP), SOM, available nitrogen (AN), and available phosphorus (AP) increasing by 211.07%, 136.27%, 388.18%, 564.97%, and 282.53%, respectively, in comparison to the CK treatment. Nutrient addition significantly altered the structure of soil microbial communities and the abundance of functional microorganisms. But it had no significant effect on the Shannon and Simpson indices of the soil fungal community. Key factors such as TP, SOM, TN, AP, and AN significantly influenced bacterial distribution, while TP, AN, and AP played a crucial role in fungal distribution. Bacterial diversity and fungal functionality were mainly regulated by TP, while bacterial functionality was primarily controlled by pH and SOM. In conclusion, the M1 treatment appears to be a viable strategy for promoting soil restoration in alpine mining areas.IMPORTANCEEcological restoration in mining areas is a global challenge. We systematically investigated the effects of sheep manure, commercial organic fertilizer, and their combined application on soil physicochemical properties, microbial community structure, and functions in the Muli mining area of the Qinghai-Tibetan Plateau. Results showed that the combined application significantly improved soil quality, with the optimal ratio being 60% sheep manure and 40% commercial organic fertilizer. Furthermore, the study revealed the mechanisms by which nutrient addition enhances soil quality by analyzing the relationships between soil properties and microbial communities under different treatments. These findings provide valuable insights for restoring ecosystem functions in alpine mining areas of the Qinghai-Tibetan Plateau and promoting sustainable grassland agriculture.

To explore the effects of different long-term fertilization treatments on soil microbial diversity and community structure in the drylands of an agro-pastoral ecotone, a long-term fertilization experiment at the Inner Mongolia cultivated land conservation science observation and experiment station, Ministry of Agriculture, and rural areas was taken as the research object. Four treatments, including no fertilizer (CK), single nitrogen fertilizer (NF), single chemical fertilizer (CF), and the combined application of organic manure and chemical fertilizer (CFM), were selected for the collection of 0-10 cm and 10-20 cm soil at potato maturity 16 years after the experiment (2019). High-throughput sequencing technology was used to assess the soil bacterial and fungal communities to explore the effects of different fertilization measures on soil quality from the perspective of microorganisms, and the partial least squares path model (PLS-PM) was used to reveal the key environmental driving factors of soil microbial community alternation and crop yield improvement in dryland during fertilization mode transformation. The results showed that:① the CF and CFM treatments significantly improved soil fertility, but the effect of the latter was significantly better than that of the former. Soil available nitrogen, available phosphorus, and available potassium in the CFM treatment increased by 131.9%-174.7%, 216.9%-283.3%, and 103.3%-109.3%, respectively, and organic matter and total nitrogen content also increased significantly. The CF treatment still maintained a high soil pH, whereas the NF treatment significantly decreased soil pH and had little effect in improving soil fertility. ② Compared with that under CK, the NF treatment significantly reduced the soil bacterial Chao1 and Shannon index, and the CFM treatment significantly increased the soil bacterial species richness, Chao1 index, and soil fungal Shannon index, whereas soil bacterial and fungal diversity in the CF treatment did not reach a significant difference level with CK. ③ The soil microbial community composition at 0-10 cm and 10-20 cm was similar. The CFM treatment increased the relative abundance of soil beneficial bacteria and decreased the relative abundance of pathogenic bacteria. The relative abundance of dominant bacteria such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes increased. The relative abundances of Actinobacteria, Ascomycota, and Basidiomycota were decreased, whereas the NF and CF treatments showed the opposite trend. ④ PLS-PM analysis showed that with the gradual change in fertilization mode from CK→NF→CF→CFM, the driving factors affecting microbial community succession and yield increase were also changed from soil pH→soil NPK content→soil pH, SOM, and NPK content. In general, long-term fertilization had significant effects on soil chemical properties and microbial communities in drylands in the agro-pastoral ecotone. As the optimal fertilization choice, CFM was significantly better than NF and CF in improving soil fertility and inhibiting the growth of pathogenic microorganisms. The number of pathogens in long-term non-fertilization and unbalanced fertilization soil was significantly increased, and the risk of crop infection to indigenous diseases was increased. The research results can provide scientific reference for farmland nutrient balance management and soil microenvironment improvement of the agricultural ecosystem in the agro-pastoral ecotone in North China.

IntroductionAs the years of mango cultivation progress, pathogens invade the soil, leading to the development of soil borne diseases. These diseases not only change the physical and chemical properties of the soil but also influence the diversity and composition of soil microbes, ultimately impeding the development of the mango industry. In view of this, this study aimed to explore the correlations among the physical and chemical properties of mango root soil, root exudates, soil microbial community and soil borne diseases.MethodsHealthy, diseased and severely diseased mango root soil samples were taken as the investigation objects. The main research methods were: (1)Testing seven soil physicochemical properties, such as total phosphorus and total potassium, in rhizosphere soil. (2) We determined the phenolic acid content in mango rhizosphere soil using high-performance liquid chromatography (HPLC). (3) Soil microbial communities were analyzed using second-generation high-throughput sequencing technology. (4) The characteristics and response mechanisms of changes in soil microbial community structure were analyzed using multivariate statistical methods, such as redundancy analysis (RDA) and correlation analysis, in combination with physical and chemical environmental factors. (5) PICRUSt2 analysis of microbial community function under soil borne diseases.ResultsSoil borne disease had profound impacts on soil physicochemical properties, root exudates (phenolic acid) and microbial community structure. On one hand, with the development of soil—borne disease, the mango’s ability to absorb foreign nutrients is weakened, leading to the accumulation of nutrients in the root soil, which significantly increases total phosphorus, total potassium, alkaline hydrolysis nitrogen, acid—soluble phosphorus, available potassium, organic matter and pH value. On the other hand, soil borne disease also increased the secretion of phenolic acid in mango root, with significantly increased concentrations of vanillic acid, ferulic acid, salicylic acid and coumaric acid. High-throughput sequencing results showed that soil-borne diseases were followed by a decrease in bacterial diversity, an increase in fungal diversity, and the accumulation of pathogenic microorganisms such as Fusarium in the soil. In addition, the physical and chemical properties of the soil as well as phenolic acid exudates also influenced microbial community functioning, particularly with respect to genetic information processing, metabolism and biological systems.DiscussionIn this study, we investigated the mechanism of soil-borne diseases in mango by studying the response mechanism of soil-borne diseases with root secretion and microbial community. It provides theoretical support for the sustainable development of mango industry.

Understanding the responses, adaptations and feedback mechanisms of biological communities to climate change is critical to project future state of earth and climate systems. Although significant amount of knowledge is available on the feedback responses of aboveground communities to climate change, little is known about the responses of belowground microbial communities due to the challenges in analyzing soil microbial community structure. Thus the goal overall goal of this study is to provide system-level, predictive mechanistic understanding of the temperature sensitivity of soil carbon (C) decomposition to climate warming by using cutting-edge integrated metagenomic technologies. Towards this goal, the following four objectives will be pursued: (i) To determine phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems; (ii) To delineate the responses of microbial community structure, functions and activities to climate change in the temperate grassland and tundra ecosystems; (iii) To determine the temperature sensitivity of microbial respiration in soils with different mixtures of labile versus recalcitrant C, and the underlying microbiological basis for temperature sensitivity of these pools; and (iv) To synthesize all experimental data for revealing microbial control of ecosystem carbon processes in responses to climate change. We have achieved our goals for all four proposed objectives. First, we determined the phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems. For this objective, we have developed a novel phasing amplicon sequencing (PAS) approach for MiSeq sequencing of amplicons. This approach has been used for sequencing various phylogenetic and functional genes related to ecosystem functioning. A comprehensive functional gene array (e.g., GeoChip 5.0) has also been developed and used for soil microbial community analysis in this study. In addition, shot-gun metagenome sequencing along with the above approaches have been used to understand the phylogenetic and functional diversity, composition, and structure of soil microbial communities in both temperature grassland and tundra ecosystems. Second, we determined the response of soil microbial communities to climate warming in both temperate grassland and tundra ecosystems using various methods. Our major findings are: (i) Microorganisms are very rapid to respond to climate warming in the tundra ecosystem, AK, which is vulnerable, too. (ii) Climate warming also significantly shifted the metabolic diversity, composition and structure of microbial communities, and key metabolic pathways related to carbon turnover, such as cellulose degradation (~13%) and CO2 production (~10%), and to nitrogen cycling, including denitrification (~12%) were enriched by warming. (iii) Warming also altered the expression patterns of microbial functional genes important to ecosystem functioning and stability through GeoChip and metatranscriptomic analysis of soil microbial communities at the OK site. Third, we analyzed temperature sensitivity of C decomposition to climate warming for both AK and OK soils through laboratory incubations. Key results include: (i) Alaska tundra soils showed that after one year of incubation, CT in the top 15 cm could be as high as 25% and 15% of the initial soil C content at 25°C and 15°C incubations, respectively. (ii) analysis of 456 incubated soil samples with 16S rRNA gene, ITS and GeoChip hybridization showed that warming shifted the phylogenretic and functional diversity, composition, structure and metabolic potential of soil microbial communities, and at different stages of incubation, key populations and functional genes significantly changed along with soil substrate changes. Functional gene diversity and functional genes for degrading labile C components decrease along incubation when labile C components are exhausting, but the genes related to degrading recalcitrant C increase. These molecular data will be directly used for modeling. Fourth, we have developed novel approaches to integrate and model experimental data to understand microbial control of ecosystem C processes in response to climate change. We compared different methods to calculate Q10 for estimating temperature sensitivity, and new approaches for Q10 calculation and molecular ecological network analysis were also developed. Using those newly developed approaches, our result indicated that Q10s increased with the recalcitrance of C pools, suggesting that longer incubation studies are needed in order to assess the temperature sensitivity of slower C pools, especially at low temperature regimes. This project has been very productive, resulting in 42 papers published or in press, 4 submitted, and 13 in preparation.

Summary Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient‐poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2 years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate‐induced respiration rate and a 5‐fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P‐fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro‐organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram‐positive : Gram‐negative ratio. The Fungi : Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.

Human activities have significantly increased nitrogen (N) and phosphorous (P) inputs to terrestrial ecosystems. However, the impact of N and P enrichment on soil microbial community structure and functioning in temperate and alpine grassland ecosystems remains unclear. In this study, we investigated the responses of soil microbial communities to nutrient (N and P) additions in two temperate and one alpine grassland ecosystems in China. We measured soil chemical properties, microbial community composition (indicated by the phospholipid fatty acids, PLFA) and potential enzyme activities related to carbon (C), N, and P cycling in the peak growing season after 4 years of nutrient addition. We found that N addition reduced soil pH and increased soil total N content at two meadow sites, P addition increased soil total P content at all three sites, but both N and P additions had minimal effects on soil organic C content. Bacteria and total microbial abundances did not change after N and P additions, while fungi and arbuscular mycorrhizal fungi (AMF) abundances were suppressed by N addition. Moreover, the activity of soil extracellular enzymes involved in C, N and P cycling and their stoichiometric ratios were not responsive to N and P additions, except for inhibition of acid phosphatase by P addition at the temperate meadow site. Despite significant changes in soil chemistry (e.g., pH and available nutrients), soil microbial biomass (except fungi and AMF abundances), community structure, and enzyme activities (except phosphatase) were generally resistant to 4 years of N and P addition in the three temperate and alpine grassland ecosystems in China.

Effect of repeated drying-rewetting cycles on soil extracellular enzyme activities and microbial community composition in arid and semi-arid ecosystems

Dynamic changes of soil microbial community in Pinus sylvestris var. mongolica plantations in the Mu Us Sandy Land

Effects of land-use conversion from paddy field to orchard farm on soil microbial genetic diversity and community structure

Parallel shifts in plant and soil microbial communities in response to biosolids in a semi-arid grassland

Fungal residue is a unique abundant organic material undervalued in agricultural production. The application of chemical fertilizer combined with fungal residue can not only improve soil quality but also regulate the microbial community. However, it is unclear whether the response of soil bacteria and fungi to the combined application of fungal residue and chemical fertilizer is consistent. Therefore, a long-term positioning experiment in a rice field was conducted with a total of nine treatments. Chemical fertilizer (C) and fungal residue (F) were applied at 0, 50%, and 100% to evaluate 1 the change in soil fertility properties and microbial community structure and 2 the main driving factors of soil microbial diversity and species composition. The results showed that soil total nitrogen (TN) was highest after treatment C0F100 (55.56% higher than in the control), and the carbon to nitrogen ratio (C/N), total phosphorus (TP), dissolved organic carbon (DOC), and available phosphorus (AP) contents were highest after treatment with C100F100(26.18%, 26.46%, 17.13%, and 279.54% higher than in the control, respectively). The amounts of soil organic carbon (SOC), available nitrogen (AN), available potassium (AK), and pH were highest after treatment with C50F100 (85.57%, 41.61%, 29.33%, and 4.62% higher than in the control, respectively). Following the application of fungal residue with chemical fertilizer, there were significant changes in the α-diversity of bacteria and fungi in each treatment. Compared with that of the control (C0F0), different long-term applications of fungal residue with chemical fertilizer did not significantly change soil bacterial β-diversity but resulted in significant differences in fungal β-diversity, and the relative abundance of soil fungal Ascomycota and Sordariomycetes significantly decreased after the application of C50F100. The random forest prediction model indicated that AP and C/N were the main driving factors of bacterial and fungal α-diversity, respectively, and AN, pH, SOC, and DOC were the main driving factors of bacterial β-diversity, whereas AP and DOC were the main driving factors of fungal β-diversity. Correlation analysis suggested that the relative abundance of soil fungal Ascomycota and Sordariomycetes had a significantly negative correlation with SOC, TN, TP, AN, AP, AK, and C/N. PERMANOVA showed that variation in soil fertility properties, dominant species of soil bacteria at the phylum and class level, and dominant species of soil fungi at the phylum and class level were all best explained by fungal residue (46.35%, 18.47%, and 41.57%, respectively), and variation in bacterial diversity was best explained by fungal residue (23.84%) and to a lesser extent by the interaction between fungal residue and chemical fertilizer (9.90%). In contrast, the variation in fungal diversity was best explained by the interaction between fungal residue and chemical fertilizer (35.00%) and to a lesser extent by fungal residue (10.42%). In conclusion, the application of fungal residue has more advantages than chemical fertilizer in influencing soil fertility properties and microbial community structure changes.