Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields

Abstract

Soil microorganisms are critical factors of plant productivity in terrestrial ecosystems. Coptis chinensis Franch is one of the most important medicinal plants in China. Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. In the current study, we provide detailed information regarding the diversity and composition of the rhizospheric bacterial communities of the C. chinensis plants in continuously cropped fields and fallow fields in two seasons (i.e., winter and summer) using next-generation sequencing. The alpha diversity was higher in the five-year cultivated C. chinensis field (CyS5) and lower in fallow fields (NCS). Significant differences analysis confirmed more biomarkers in the cultivated field soil than in fallow fields. Additionally, the principal coordinate analysis (PcoA) of the beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Besides, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the top bacterial phyla. Among these phyla, Proteobacteria were found predominantly and showed a decreasing trend with the continuous cropping of C. chinensis. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the abundance of C and N functional genes had a significant difference between the soil samples from cultivated (CyS1, CyS3, and CyS5) and fallow (NCS) fields in two seasons (winter and summer). The principal coordinate analysis (PCoA) based on UniFrac distances (i.e., unweighted and weighted) revealed the variations in bacterial community structures in the soil samples. This study could provide a reference for solving the increasingly severe cropping obstacles and promote the sustainable development of the C. chinensis industry.

Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato

“…Soil pH can affect soil microbial physiological metabolism and change the competitive relationship between microbial communities or inhibit the growth of non-adapted microbes [26], thus affecting microbial community structures. In terms of the three bacteria phyla with the most relative content, there was a positive correlation between Acidobacteria and pH, which was consistent with the results of Yang et al [34]; Further, there was a negative correlation between Actinobacteria and pH, which was consistent with that reported by Alami et al [47] and Wu et al [24]. However, the results were different from that reported by Li et al [8], which might have been caused by different plant age or genotype [48].…”

Diversity of the Bacterial Community of Three Soils Revealed by Illumina-Miseq Sequencing of 16S rRNA Gene in the South of Brazzaville, Congo

“…In this study, alpha diversity represented by richness (S observed and Chao1) and diversity index (Shannon and Simpson indexes, equitability) declined from the cultivated soils of MFILOU and SNR to the soil of ORSTOM that was exempt of culture. This result is in accordance with several other studies in which it was demonstrated that continuous cultivation resulted in decrease of bacterial diversity [20]. According to Alami et al [20] and Kennedy et al [24], microbial richness and diversity have a crucial role in soil quality, health and ecosystem sustainability.…”

“…We found that Proteobacteria was the most dominant phylum in all sites (45,59% -29,92%). Alami et al [20] found in their study on the rhizospheric soil of Coptis chinensis that Proteobacteria, Actinibacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the dominant bacterial phyla. Among these phyla, Proteobacteria was the most dominant phylum as in our study.…”

Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato 

“…Soil pH can affect soil microbial physiological metabolism and change the competitive relationship between microbial communities or inhibit the growth of non-adapted microbes [26], thus affecting microbial community structures. In terms of the three bacteria phyla with the most relative content, Acidobacteria was positively correlated with pH, which was consistent with Yang et al [34]; Further, Actinobacteria was negatively correlated with pH, which was in accordance with previous studies [24,47]. However, the results were different from that reported by Li et al [8], which might have been caused by different plant age or genotype [48].…”