Comparative Analysis of Soil Microbiome Profiles in the Companion Planting of White Clover and Orchard Grass Using 16S rRNA Gene Sequencing Data

Exploring microbial diversity and function in companion planting systems of white clover and orchard grass

Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.

Soil Microbial Community Characteristics and Their Effect on Tea Quality under Different Fertilization Treatments in Two Tea Plantations

Fertilization is an essential aspect of tea plantation management that supports a sustainable tea production and drastically influences soil microbial communities. However, few research studies have focused on the differences of microbial communities and the variation in tea quality in response to different fertilization treatments. In this work, the soil fertility, tea quality, and soil microbial communities were investigated in two domestic tea plantations following the application of chemical and organic fertilizers. We determined the content of mineral elements in the soil, including nitrogen, phosphorus, and potassium, and found that the supplementation of chemical fertilizer directly increased the content of mineral elements. However, the application of organic fertilizer significantly improved the accumulation of tea polyphenols and reduced the content of caffeine. Furthermore, amplicon sequencing results showed that the different ways of applying fertilizer have limited effect on the alpha diversity of the microbial community in the soil while the beta diversity was remarkably influenced. This work also suggests that the bacterial community structure and abundance were also relatively constant while the fungal community structure and abundance were dramatically influenced; for example, Chaetomiaceae at the family level, Hypocreaceae at the order level, Trichoderma at the genus level, and Fusarium oxysporum at the species level were predominantly enriched in the tea plantation applying organic fertilizer. Moreover, the bacterial and fungal biomarkers were also analyzed and it was found that Proteobacteria and Gammaproteobacteria (bacteria) and Tremellomycetes (fungi) were potentially characterized as biomarkers in the plantation under organic fertilization. These results provide a valuable basis for the application of organic fertilizer to improve the soil of tea plantations in the future.

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria

Plant-microbiome research plays a pivotal role in understanding the relationships between plants and their associated microbial communities, with implications for agriculture and ecosystem dynamics. Metabarcoding analysis on variable regions of the 16S ribosomal RNA (rRNA) gene remains the dominant technology to study microbiome diversity in this field. However, the choice of the targeted variable region might affect the outcome of the microbiome studies. In our in silico analysis, we have evaluated whether the targeted variable region has an impact on taxonomic resolution in 16 plant-related microbial genera. Through a comparison of 16S rRNA gene variable regions with whole-genome data, our findings suggest that the V1-V3 region is generally a more suitable option than the widely used V3-V4 region for targeting microbiome analysis in plant-related genera. However, sole reliance on one region could introduce detection biases for specific genera. Thus, we are suggesting that while transitioning to full-length 16S rRNA gene and whole-genome sequencing for plant-microbiome analysis, the usage of genus-specific variable regions can achieve more precise taxonomic assignments. More broadly, our approach provides a blueprint to identify the most discriminating variable regions of the 16S rRNA gene for genera of interest.

Microbial communities and functions changed in rhizosphere soil of Pinus massoniana provenances with different carbon storage

Introduction

The average carbon storage of Pinus massoniana is much higher than the average carbon storage of Chinese forests, an important carbon sink tree species in subtropical regions of China. However, there are few studies on the differences in rhizosphere microorganisms of P. massoniana with different carbon storages.

Methods

To clarify the relationships between plant carbon storage level, environmental parameters and microbial community structure, we identified three carbon storage levels from different P. massoniana provenances and collected rhizosphere soil samples. We determined chemical properties of soil, extracellular enzyme activity, and microbial community structures at different carbon storage levels and examined how soil factors affect rhizosphere microorganisms under different carbon storage levels.

Results

The results revealed that soil organic carbon (SOC), nitrate nitrogen (NO3--N), ammonium nitrogen (NH4+-N) contents all increased with increasing carbon storage levels, while pH decreased accordingly. In contrast, the available phosphorus (AP) content did not change significantly. The soil AP content was within the range of 0.91 ~ 1.04 mg/kg. The microbial community structure of P. massoniana changed with different carbon storage, with Acidobacteria (44.27%), Proteobacteria (32.57%), and Actinobacteria (13.43%) being the dominant bacterial phyla and Basidiomycota (73.36%) and Ascomycota (24.64%) being the dominant fungal phyla across the three carbon storage levels. Soil fungi were more responsive to carbon storage than bacteria in P. massoniana. C/N, NH4+-N, NO3--N, and SOC were the main drivers (p < 0.05) of changes in rhizosphere microbial communities.

Discussion

The results revealed that in the rhizosphere there were significant differences in soil carbon cycle and microorganism nutrient preferences at different carbon storages of P. massoniana provenance, which were significantly related to the changes in rhizosphere microbial community structure. Jiangxi Anyuan (AY) provenance is more suitable for the construction of high carbon storage plantation.

Microbiome composition of disturbed soils from sandy-gravel mining complexes with different reclamation approaches

Activities connected to mineral mining disrupt the soil layer and bring parent rock material to the surface. It leads to altering the environmental conditions and leaves behind vast areas of disturbed lands. Returning these lands to natural ecosystems is an important contemporary challenge, which can be acquired by reclamation practices. Soil microbiome composition reflects changes happening to disturbed lands; thus, its analysis is a powerful tool for evaluating the disturbance degree and estimating the effect of the implementation of reclamation techniques. Additionally, factors connected to the characteristics of a particular geographical region have a certain impact on the microbiome and should be taken into account. Thereby, studies of soil microbiomes of disturbed soils of different origins are essential in understanding the dynamics of soil restoration. Here, we focus on soil microbiomes from two sandy-gravel mining complexes in mountainous areas with a moderate continental climate of the Central Caucasus. These quarries share the same parent rock material, but differ in benchmark soil type and reclamation approach - one was left for passive recovery and the other was technically reclaimed with overburden material. Comparative analysis of microbiome composition, based on sequencing of 16S rRNA gene libraries, showed that region and disturbance are the key factors explaining microbiome variation, which surpass the influence of local factors. However, the application of reclamation techniques greatly reduces the dissimilarity of soil microbiomes caused by disturbance. Linking of soil chemical parameters to microbiome composition showed that the disturbance factor correlates with a lack of organic carbon. Other chemical parameters, like pH, ammonium, nitrates and total carbon explain microbiome variability on a smaller scale between sampling sites. Thus, while regional and disturbance factors reflected differentiation of soil microbiomes, soil chemical parameters explained local variation of certain groups of microorganisms.

Plant-Growth-Promoting Potential of PGPE Isolated from Dactylis glomerata L

Plant-growth-promoting endophytes (PGPE) are a kind of beneficial microorganisms which could inhabit plant tissues to antagonize certain plant pathogens and promote the host plant’s growth and development. At present, many studies have confirmed the mutualistic effect of endophytes with plants, but there are few systematic studies on beneficial roles between endophytes and Dactylis glomerata, especially on the PGPE characteristics of the forage and environmental restoration plant. This study aimed to isolate PGPE from D. glomerata, evaluate their effects on plant growth, and ultimately acquire desirable microbial inoculants for agricultural use. First, endophytes were isolated from D. glomerata by plant re-inoculation experiment, and identified by morphological and molecular analyses. Fixation medium and methods were carried out to assess the nitrogen fixation ability of the strains. Then, the ability to dissolve phosphorus was determined by the Olsen and silicate medium methods; secretory IAA was measured by Salkowski colorimetric method; and the inhibitive effects on phytopathogen were observed by confrontation culture. Twenty-one strains were isolated from four varieties of D. glomerata, among which 14 strains with plant-growth-promoting characteristics were obtained by re-inoculation experiments, including seven endophytic bacteria and seven endophytic fungi. Further evaluation of three selected strains with the most significant PGP attributes were performed by using the pot re-inoculation experiment which revealed that TG2-B derived from Myroides odoratimimus was the most effective plant-growth-promoting agent due to its ability to produce high levels of IAA; the strain Bacillus cereus exhibited the most robust ability in dissolving inorganic phosphorus; and Trichoderma harzianum manifested a conspicuously antagonistic effect against a variety of plant pathogens. For the first time, this study reports the identification of D. glomerata endophytes that were able to promote plant growth and have a considerable antagonistic effects on plant pathogens, which could be considered as microbial inoculants for using in improving crop production and plant disease control.