Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices

Abstract

Rhizobacteria and endophytic bacteria play important roles in protecting host plants from infection by phytopathogens, which cause soil-borne diseases and severely impair plant health. Panax notoginseng is negatively affected by continuous cropping and becomes vulnerable to attack by microbial pathogens. In the present study, culture-independent Illumina MiSeq was used to investigate root-endophytic and rhizospheric bacteria in response to continuous cropping of P. notoginseng. Numbers of rhizospheric bacteria decreased with continuous P. notoginseng cropping, while the effects of continuous cropping on endophytic bacteria were not statistically significant. Bacterial diversity was higher in healthy P. notoginseng rhizospheric soils and roots than in those of diseased P. notoginseng. The most dominant phyla detected during continuous cropping were Proteobacteria, Cyanobacteria, Actinobacteria, and Acidobacteria. The genera Pseudomonas, Rhodoplanes, Candidatus Solibacter, and Streptomyces were dominant in P. notoginseng rhizospheric soils and roots. Erwinia, Stenotrophomonas, Pseudomonas, and Sphingobium were specifically detected in relatively high proportions among root-rot rhizospheric bacteria and endogenous root bacteria in plants under continuous cropping, suggesting that they may be the pathogens responsible for the negative effects of continuous cropping on P. notoginseng. Based on canonical correspondence analysis of the bacterial communities that were identified from healthy plants and fallow soils, total phosphorus (P), pH, and organic soil matter exerted the greatest impacts upon bacterial community composition during continuous cropping. In general, continuous cropping practices for P. notoginseng and severe root-rot disease notably affected the community structure and the diversity of rhizospheric and root endophytic bacteria. Our study elucidated the ecological significance of microbial communities in healthy plant maintenance, and our results may inform biological control strategies during the continuous cropping of P. notoginseng.

Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping

“…In addition, fallow soils showed relatively higher overall fungal activity, whereas fungal diversity was similar between continuously cropped soil and the S_CK, suggesting that fungal diversity gradually recovers to unplanted control soil with time of fallowing. Severe root-rot disease has long been known as a major problem in continuous cropping (Tan et al, 2017a). Consistently, we detected a relatively higher fungal community diversity in healthy tissues and rhizospheric soils compared to diseased samples.…”

“…Due to limited land access, only one plot was used for each zone. However, we randomly collected 15 soil cores from the plow layer (0-30 cm in depth), thoroughly pooled them as a composite sample and divided the pooled samples into three replicates to make the samples more representative Tan et al, 2017a). Fallow soil zones were left unplanted for the specified number of years after an initial planting and harvesting of A. macrocephala.…”

“…Next, we rarified the OTU table and calculated Observed Species, Shannon's index, and Chao1to calculate Alpha Diversity (Tan et al, 2017a). QIIME and the compute_core_microbiome.py script were used to identify OTUs that occurred within 95% of the A. macrocephala or soil samples (Mahoney, Yin & Hulbert, 2017).…”

“…Plants and rhizospheric soil are colonized by fungal communities that can impact their fitness by influencing nutrient acquisition, causing soil-borne diseases and affecting the activity of plant pathogens (Tan et al, 2017a). Many previous studies have shown that studying plant-microorganism interactions can lead to improvements in several agronomic processes, including crop rotation and tillage (Somenahally et al, 2018), pesticide application (Regar et al, 2019), irrigation (Dang et al, 2019, fertilizer application (Nguyen et al, 2018) and continuous cropping (Ali et al, 2019;Xiong et al, 2015).…”

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

“…Wu et al [23] and Wu et al [24] studied the changes in bacterial community structure in the rhizospheric soil of konjac and vanilla after continuous cropping, and found that continuous cropping changed the composition and structure of bacterial communities, resulting in a reduction in bene cial bacteria and an increase in harmful bacteria. Tan et al [25] used high-throughput sequencing to study changes in the diversity and composition of rhizospheric soil microbes and endophytes of Panax notoginseng after three years of continuous cropping, and found that bacteria decreased over time. Further, the bacterial diversity of the rhizospheric soil of healthy Panax notoginseng was greater than that of diseased plants.…”