Soil microbial communities response to different fertilization regimes in young Catalpa bungei plantation

Responses of soil fertility indicators and fungi community diversity to fertilization strategies in legume-grass mixtures

Introduction

Alfalfa-grass binary mixtures outperformed monocultures in nutrient use, soil nutrient content, and biomass yield. Nonetheless, the impact of fertilization strategies on fungal community composition and ecological functions in legume-Grass mixtures remains under-researched. This study aimed to explore the effects of different fertilization strategies on soil fungal community distribution and soil environmental characteristics.

Methods

A field experiment in Gansu, China, has been conducted to explore the effects of five different fertilization strategies-no fertilization (CK), three partial fertilization methods (+PK, +NK, +NP), and balanced fertilization (+NPK)-on fungal population richness, community composition, and soil environmental drivers. Rhizosphere soils from the five treatments were sampled and investigated using high-throughput ITS sequencing.

Results

Compared to CK, +NPK led to higher soil capabilities (P< 0.05), soil organic matter (SOM), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) increased by an average of 29.7 %, 42.3 %, 101.2 %, and 24.3 %, respectively; alkaline phosphatase (APA), catalase (CAT), and sucrase (SA) increased by an average of 56.6 %, 31.8 %, and 46.7 %, respectively; soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), and soil microbial biomass phosphorus (SMBP) increased by an average of 64.8 %, 65.1 %, and 60.4 %, respectively. The dominant fungi in the rhizosphere soil were Mortierellomycota and Ascomycota, accounting for 82.2%-92.3%. The fungal species richness was the highest in the +PK treatment. From the NMDS and RDA analysis, it can be discerned that SA, AK, and CAT were the key environmental factors influencing the structure of the inter-root soil fungal community in alfalfa; CAT and SOM were the key environmental factors influencing the structure of the inter-root soil fungal community in awnless brome.

Discussion

Our findings investigated the optimal fertilizer strategy for legume-Grass mixtures. Results provided a technical basis for scientific fertilizer application and development of local mixed grassland ecosystems.

Insights into the gut microbiota characteristics between the organic and traditional feeding chickens based on amplicon and metagenomic sequencing

Intestinal microorganisms play a crucial role in chicken health and production performance, especially in the research of traditional and organic feeding methods. The intestinal contents of organic and feed chickens were analyzed by 16S rRNA gene and metagenome technology. The results showed that the microbial diversity of organic chickens was significantly higher than that of the feed chickens, especially the key microorganisms, such as Enterococcus, were more abundant in organic chickens. The functional analysis of metagenome revealed the significant difference in the metabolic function of intestinal microorganisms between them. The present study provides new insights into the gut microbiota characteristics of the organic and feed chicken based on amplicon and metagenomic sequencing. Our results are helpful to fully illustrate the effects of different feeding methods on intestinal microorganisms in chickens and can offer a more scientific basis for chicken production management.

Co-application of cadmium-immobilizing bacteria and organic fertilizers alter the wheat root soil chemistry and microbial communities

Cadmium contamination poses a significant risk to soil ecosystems in certain parts of the world. Using eco-friendly fertilizers alongside beneficial microorganisms offers a viable solution to mitigate Cd pollution in agricultural soil. This study used an outdoor experiment to evaluate the impact of administering a Cd-immobilizing bacterial (Bacillus) inoculant with two biologically-enriched organic fertilizers (either fermentative edible fungi residue or fermented cow dung) on wheat plants and associated microbial populations in a field contaminated with Cd. The mixed application of fermentative cow dung with the Cd-immobilizing bacterium reduced the effective Cd content of wheat root-soil by 13,0 %. Application of Cd-immobilizing Bacillus inoculant reduced the Cd enrichment of wheat roots by 0.07 mg/kg. Co-application of fermentative cow dung with the bacterial inoculant reduced the Cd enrichment of wheat seeds by 20,0 %. Co-application of the two organic fertilizers could improve some of the nutrients related to wheat and soil fertility; however, the diversity of the soil microbial community changed less and its species richness decreased. Applying the Bacillus inoculant inhibited the growth of native pathogenic bacteria, such as Proteobacteria. Whether administering it with either fermented cow manure or fermented edible fungus residue, the relative abundance of nitrate-reducing bacteria such as Rhodobacter increased, which should promote the soil nitrogen cycle. The main factors influencing soil microbial community structure of wheat plants were pH, available potassium, and available Cd content. Symbiotic network analysis revealed bacterial inoculant and organic fertilizer inoculum further altering the ecological relationships of microbial communities. According to the FAPROTAX functional prediction, Rhodanobacter may play a key role in nitrate respiration in the soil nitrogen cycle. In conclusion, this study provides a comprehensive, timely reference for understanding microbial changes caused by the combined application of this type of bacterial inoculant and organic soil amendments in Cd-contaminated fields.

Nitrogen addition changed soil fungal community structure and increased the biomass of functional fungi in Korean pine plantations in temperate northeast China

Nitrogen (N) deposition is a global environmental issue that can have significant impacts on the community structure and function in ecosystems. Fungi play a key role in soil biogeochemical cycles and their community structures are tightly linked to the health and productivity of forest ecosystems. Based on high-throughput sequencing and ergosterol extraction, we examined the changes in community structure, composition, and biomass of soil ectomycorrhizal (ECM) and saprophytic (SAP) fungi in 0-10 cm soil layer after 8 years of continuous N addition and their driving factors in a temperate Korean pine plantation in northeast China. Our results showed that N addition increased fungal community richness, with the highest richness and Chao1 index under the low N treatment (LN: 20 kg N ha-1 yr-1). Based on the FUN Guild database, we found that the relative abundance of ECM and SAP fungi increased first and then decreased with increasing N deposition concentration. The molecular ecological network analysis showed that the interaction between ECM and SAP fungi was enhanced by N addition, and the interaction was mainly positive in the ECM fungal network. N addition increased fungal biomass, and the total fungal biomass (TFB) was the highest under the MN treatment (6.05 ± 0.3 mg g-1). Overall, we concluded that N addition changed soil biochemical parameters, increased fungal activity, and enhanced functional fungal interactions in the Korean pine plantation over an 8-year simulated N addition. We need to consider the effects of complex soil conditions on soil fungi and emphasize the importance of regulating soil fungal community structure and biomass for managing forest ecosystems. These findings could deepen our understanding of the effects of increased N deposition on soil fungi in temperate forests in northern China, which can provide the theoretical basis for reducing the effects of increased N deposition on forest soil.

Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community

Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.

Decrease in beneficial bacteria and increase in harmful bacteria in Gastrodia seedlings and their surrounding soil are mainly responsible for degradation of Gastrodia asexual propagation

Introduction

Asexual reproduction of Gastrodia elata Bl. f. glauca S. chow (GeB) produces degeneration with increasing number of GeB. Therefore, we analyzed the microorganisms of GeB seedlings and surrounding soil by Illumina Miseq high-throughput sequencing technology.

Methods

In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the types and quantities of GeB seedlings and surrounding soil microorganisms in the first to third generations of asexual reproduction, isolated and identified the dominant strains of GeB in the first to third generations and screened the antagonistic bacteria of its pathogenic fungi, and evaluated the effects of beneficial bacteria on the production performance of seedlings planted with GeB.

Results

With an increase in the number of asexual reproductive generations, the number of pathogenic fungi and bacteria in GeB seedlings and the surrounding soil increased, and the number of beneficial fungi and bacteria decreased. Pseudomonas sp., Agrobacterium rhizomes, and Herbaspirillum hiltneri were isolated and identified in the first generation, and Trichoderma harzianum, Penicillium viridiatum, Fusarium oxysporum, and Novosphingobium sp. Were isolated and identified in the third generation. Antagonistic strains of the three pathogenic bacterial strains were screened. In conclusion, beneficial bacteria significantly improved the production performance of asexual reproductive seedlings planted with GeB.

Discussion

In conclusion, our findings suggested that the microorganisms of GeB seedlings and the surrounding soil change as the number of generations of GeB reproduction increases, disrupts the microecological balance of surrounding soil and endophytic microbiomes.This study provides a theoretical basis for the degradation of asexual reproduction in GeB.

Long-term application of nitrogen and phosphorus fertilizers changes the process of community construction by affecting keystone species of crop rhizosphere microorganisms

Keystone species of microbial communities play a very important role in community structure and ecosystem function; however, the effect of long-term nitrogen (N) and phosphorus (P) fertilizers on key taxa and the mechanisms of community construction of rhizosphere microbial communities remain unclear. In this study, the effect of nine fertilization treatments (N0P0, N0P1, N0P2, N1P0, N1P1, N1P2, N2P0, N2P1, and N2P2) on soil microbial community diversity, keystone species, and construction methods in the crop rhizosphere were studied in a loess hilly area after 26 years of fertilization. The results showed that fertilization significantly increased the nutrient contents of the rhizospheric soil and root system and significantly affected microbial community composition (based on the Bray-Curtis distance) and community construction process (β-nearest taxon index: βNTI). The decrease in the abundance of oligotrophic bacteria (from phyla Acidobacteriota and Chloroflexi) in the keystone species of bacterial communities shifted the community construction process from homogenizing dispersal to variable selection process and was significantly regulated by soil factors (total P and carbon-N ratio). However, the decrease in the abundance of keystone species (from phylum Basidiomycota) in the fungal communities did not have a significant effect on community construction, which was mainly affected by root characteristics (root N content and soluble sugar). This study found that long-term N and P fertilization changed the keystone species composition of bacterial communities by affecting the nutrient content of the rhizospheric soil, such as total P, so that the construction mode of communities changed from a stochastic to a deterministic process, and the N2 fertilization, especially the N1P2 treatment was better for increasing network stability (modularity and clustering coefficient).

Soil depth exerts a stronger impact on microbial communities and the sulfur biological cycle than salinity in salinized soils

The distribution of microbial communities along salinity gradients in the surface layer of salinized soils has been widely studied. However, it is unknown whether microbial communities exhibit similar distribution patterns in surface and deep soils. Additionally, the relationship between soil depth, salinity, and sulfur metabolism remains unclear. Herein, bulk soils in the surface (S, 5-10 cm) and deep (D, 20-25 cm) layers from high- and low-salinity soils were analyzed using metagenomic and physicochemical analyses. Soil depth was significantly correlated to the concentration of sulfur compounds in the soil and exerted a stronger effect than salinity. Non-metric multidimensional scaling analysis revealed significant differences in microbial community structure with varying soil depths and salinities. However, soil depth clearly influenced microbial community abundance, homogeneity, and diversity, while salinity had a limited effect on microbial abundance. Archaea and bacteria were enriched in the surface and deep soils, respectively. Gene abundance analysis revealed significant differences in the abundance of sulfur-related genes at different soil depths. The abundance of sulfur oxidation genes was lower in deep soil than in surface soil, whereas the abundance of other sulfur-related genes showed the opposite trend. Redundancy analysis (RDA) showed that environmental factors and sulfur compounds have a significant impact on sulfur metabolism genes, with sulfide significantly affecting low-salinity soils in the surface and deep layers, whereas salinity and sulfane sulfur had a greater correlation with high-salinity soils. Correlation analysis further showed that Euryarchaeota clustered with Bacteroidetes and Balneolaeota, while Proteobacteria clustered with many phyla, such as Acidobacteria. Various sulfur metabolism genes were widely distributed in both clusters. Our results indicate that microorganisms actively participate in the sulfur cycle in saline soils and that soil depth can affect these processes and the structure of microbial communities to a greater extent than soil salinity.

Elucidating the impact of biochar with different carbon/nitrogen ratios on soil biochemical properties and rhizosphere bacterial communities of flue-cured tobacco plants

Background and aims

In agriculture, biochar (BC) and nitrogen (N) fertilizers are commonly used for improving soil fertility and crop productivity. However, it remains unclear how different levels of BC and N fertilizer affect soil fertility and crop productivity.

Methods

This study elucidates the impact of different application rates of BC (0, 600, and 1200 kg/ha) and N fertilizer (105 and 126 kg/ha) on biomass accumulation, soil microbial biomass of carbon (SMC) and nitrogen (SMN), and soil biochemical properties, including soil organic carbon (SOC), total nitrogen (TN), soil nitrate nitrogen (NO3--N), ammonium nitrogen (NH4+-N), urease (UE), acid phosphatase (ACP), catalase (CAT), and sucrase (SC) of tobacco plants. In addition, a high throughput amplicon sequencing technique was adopted to investigate the effect of different application rates of BC/N on rhizosphere bacterial communities of tobacco plants.

Results

The results confirm that high dosages of BC and N fertilizer (B1200N126) significantly enhance dry matter accumulation by 31.56% and 23.97% compared with control B0N105 and B0N126 under field conditions and 23.94% and 24.52% under pot experiment, respectively. The soil biochemical properties, SMC, and SMN significantly improved under the high application rate of BC and N fertilizer (B1200N126), while it negatively influenced the soil carbon/nitrogen ratio. Analysis of rhizosphere bacteriome through amplicon sequencing of 16S rRNA revealed that the structure, diversity, and composition of rhizosphere bacterial communities dramatically changed under different BC/N ratios. Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Acidobacteria were highly abundant bacterial phyla in the rhizosphere of tobacco plants under different treatments. Co-occurrence network analysis displayed fewer negative correlations among rhizosphere bacterial communities under high dosages of biochar and nitrogen (B1200N126) than other treatments, which showed less competition for resources among microbes. In addition, a redundancy analysis further proved a significant positive correlation among SMC, SMN, soil biochemical properties, and high dosage of biochar and nitrogen (B1200N126).

Conclusions

Thus, we conclude that a high dosage of BC (1200 kg/ha) under a high application rate of N fertilizer (126 kg/ha) enhances the biomass accumulation of tobacco plants by improving the soil biochemical properties and activities of rhizosphere bacterial communities.