Composition and Diversity of Soil Microbial Community Associated With Land Use Types in the Agro–Pastoral Area in the Upper Yellow River Basin

Abstract

The microorganisms of soil are sensitive to their living microenvironment, and their community structure and function will change with the environmental conditions. In the agro–pastoral area on the Qinghai–Tibet Plateau, revealing the diversity of the soil microbial communities and its response to different soil physicochemical properties and environmental factors are important for ecosystem management. The microbial (bacteria and archaea) community composition and diversity under different land use types (cultivated land, grazing grassland and planted forest) were analyzed by 16S rRNA (V4 region) method in a typical agro–pastoral region in the upper Yellow River basin. Also, the soil nutrients were studied and correlated with the microbial community. The results showed that the soil nutrient contents in grassland were low, but the available nutrients were relatively high. There was a great spatial variability under different distances to the river. The microbial community diversity was lower in the grassland than the cultivated land and forest land closer to the river. For all land uses, the dominant phyla of soil microorganisms included Proteobacteria, Actinobacteria, and Bacteroidetes, while the abundance of Clostridia was significantly higher than that of the other groups, indicating that Clostridia dominated the Firmicutes and affected soil microbial community composition. The linear discriminant analysis (LDA) effect size (LefSe) analysis showed different biomarkers were more abundant in grassland than other land use types, suggesting that the structure and diversity of soil microorganisms in grassland were significantly different compared with cultivated land and forest land. The distance-based redundancy analysis (db-RDA) results showed that the total phosphorus (TP) and calcium (Ca) were the key environmental factors affecting the diversity and abundance of the soil microbial community in cultivated land and forestland, respectively. However, the microbial diversity in grassland was more related to spatial distance of the river. These results provided a theoretical basis for the changes in the composition, structure, and function of soil microbial communities in agro–pastoral areas.

Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices

“…The lower assay efficiency in paddy field soil (89.3%) was observed as compared to the river water (103.6%) which could be due to the presence of PCR inhibitors in soil samples such as humic substances [ 36 , 38 ]. Moreover, no amplification was observed with total DNA isolated from unspiked water and soil which are the primary habitats of many micro and macroorganisms showing the high degree of specificity of developed multiplex assay S664 [ 39 , 40 ]. These results indicate the potential usefulness of the developed multiplex assay using the cry 1 gene as an internal control for the detection of B. pseudomallei in environmental samples.…”

Characterization of Rhizosphere Microbial Diversity and Selection of Plant-Growth-Promoting Bacteria at the Flowering and Fruiting Stages of Rapeseed

“…The results suggest that the difference between groups was significant. A LefSe was used to determine the magnitude of species and variation in each group by identifying biomarkers that differ significantly in abundance between the two groups [ 34 ]. An LDA score of >4 was considered significantly different.…”

“…Significant differences between different species were determined via a linear discriminant analysis (LDA) effect size (LEfSe) (https: //github.com/biobakery/lefse/, accessed on 22 June 2023) with two as the default filter value for the LDA score. COG functional prediction was carried out following the method of Galperin et al [34].…”

Effect of intercropping of paulownia and buckwheat on soil microbial biodiversity and enzymatic activity

“…Land use patterns have a signi cant impact on the composition and diversity of soil microorganisms, which are extremely sensitive to changes in the soil environment. 25,37 Our metagenomic sequence analysis of 16S rRNA gene fragments and ITS regions has provided unique data on bacterial and fungal population diversity and structure. Intercropping increased the diversity of rhizosphere bacterial populations, while the opposite trend was observed for fungal populations, evidenced by the values of the Shannon and Simpson indices.…”