Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

Grazing intensity alters network complexity and predator-prey relationships in the soil microbiome

Grasslands are recognized as important reservoirs of soil biodiversity. Livestock grazing is implemented as a grassland management strategy to improve soil quality and enhance plant diversity. Soil microbial communities play a pivotal role in grassland ecosystems, so it is important to examine whether grazing practices affect the soil microbiome. Previous studies on grazing have primarily focused on bacteria and fungi, overlooking an important group-protists. Protists are vital in soil microbiomes as they drive nutrient availability and trophic interactions. Determining the impact of grazing on protists and their relationships with bacterial and fungal communities is important for understanding soil microbiome dynamics in grazed ecosystems. In this study, we investigated soil bacterial, fungal, and protist communities under four grazing levels: no grazing, moderate-use grazing, full-use grazing, and heavy-use grazing. Our results showed that heavy grazing led to a greater diversity of protists with specific groups, such as Discoba and Conosa, increasing in abundance. We also found strong associations between protist and bacterial/fungal members, indicating their intricate relationships within the soil microbiome. For example, the abundance of predatory protists increased under grazing while arbuscular mycorrhizal fungi decreased. Notably, arbuscular mycorrhizae were negatively associated with predatory groups. Furthermore, we observed that microbial network complexity increased with grazing intensity, with fungal members playing an important role in the network. Overall, our study reports the impact of temporal grazing intensity on soil microbial dynamics and highlights the importance of considering protist ecology when evaluating the effects of grazing on belowground communities in grassland ecosystems.

IMPORTANCE

The significance of this study lies in its exploration of the effects of temporal grazing intensity on the dynamics of the soil microbiome, specifically focusing on the often-neglected role of protists. Our findings provide insights into the complex relationships between protists, bacteria, and fungi, emphasizing their impact on trophic interactions in the soil. Gaining a better understanding of these dynamics is essential for developing effective strategies for grassland management and conservation, underscoring the importance of incorporating protist ecology into microbiome studies in grasslands.

Characteristics of rhizosphere and bulk soil microbial community of Chinese cabbage (Brassica campestris) grown in Karst area

Understanding the rhizosphere soil microbial community and its relationship with the bulk soil microbial community is critical for maintaining soil health and fertility and improving crop yields in Karst regions. The microbial communities in the rhizosphere and bulk soils of a Chinese cabbage (Brassica campestris) plantation in a Karst region, as well as their relationships with soil nutrients, were examined in this study using high-throughput sequencing technologies of 16S and ITS amplicons. The aim was to provide theoretical insights into the healthy cultivation of Chinese cabbage in a Karst area. The findings revealed that the rhizosphere soil showed higher contents of organic matter (OM), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), total potassium (TK), total nitrogen (TN), catalase (CA), urease (UR), sucrase (SU), and phosphatase (PHO), in comparison with bulk soil, while the pH value showed the opposite trend. The diversity of bacterial and fungal communities in the bulk soil was higher than that in the rhizosphere soil, and their compositions differed between the two types of soil. In the rhizosphere soil, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla, while Olpidiomycota, Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungal phyla. In contrast, the bulk soil was characterized by bacterial dominance of Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota and fungal dominance of Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota. The fungal network was simpler than the bacterial network, and both networks exhibited less complexity in the rhizosphere soil compared with the bulk soil. Moreover, the rhizosphere soil harbored a higher proportion of beneficial Rhizobiales. The rhizosphere soil network was less complicated than the network in bulk soil by building a bacterial-fungal co-occurrence network. Furthermore, a network of relationships between soil properties and network keystone taxa revealed that the rhizosphere soil keystone taxa were more strongly correlated with soil properties than those in the bulk soil; despite its lower complexity, the rhizosphere soil contains a higher abundance of bacteria which are beneficial for cabbage growth compared with the bulk soil.

Taxonomic Structure of Rhizosphere Bacterial Communities and Its Association With the Accumulation of Alkaloidal Metabolites in Sophora flavescens

Plant secondary metabolites (SMs) play a crucial role in plant defense against pathogens and adaptation to environmental stresses, some of which are produced from medicinal plants and are the material basis of clinical efficacy and vital indicators for quality evaluation of corresponding medicinal materials. The influence of plant microbiota on plant nutrient uptake, production, and stress tolerance has been revealed, but the associations between plant microbiota and the accumulation of SMs in medicinal plants remain largely unknown. Plant SMs can vary among individuals, which could be partly ascribed to the shift in microbial community associated with the plant host. In the present study, we sampled fine roots and rhizosphere soils of Sophora flavescens grown in four well-separated cities/counties in China and determined the taxonomic composition of rhizosphere bacterial communities using Illumina 16S amplicon sequencing. In addition, the association of the rhizosphere bacterial microbiota with the accumulation of alkaloids in the roots of S. flavescens was analyzed. The results showed that S. flavescens hosted distinct bacterial communities in the rhizosphere across geographic locations and plant ages, also indicating that geographic location was a larger source of variation than plant age. Moreover, redundancy analysis revealed that spatial, climatic (mean annual temperature and precipitation), and edaphic factors (pH and available N and P) were the key drivers that shape the rhizosphere bacterial communities. Furthermore, the results of the Mantel test demonstrated that the rhizosphere bacterial microbiota was remarkably correlated with the contents of oxymatrine, sophoridine, and matrine + oxymatrine in roots. Specific taxa belonging to Actinobacteria and Chloroflexi were identified as potential beneficial bacteria associated with the total accumulation of matrine and oxymatrine by a random forest machine learning algorithm. Finally, the structural equation modeling indicated that the Actinobacteria phylum had a direct effect on the total accumulation of matrine and oxymatrine. The present study addresses the association between the rhizosphere bacterial communities and the accumulation of alkaloids in the medicinal plant S. flavescens. Our findings may provide a basis for the quality improvement and sustainable utilization of this medicinal plant thorough rhizosphere microbiota manipulation.