The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

Shi, Wencong; Li, Mingcong; Wei, Guangshan; Tian, Renmao; Li, Cuiping; Wang, Bing; Lin, Runmao; Shi, Chunyu; Chi, Xiuli; Zhou, Bo; Gao, Zheng

doi:10.1186/s40168-019-0629-2

Cited by 156 publications

(112 citation statements)

References 101 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Plant growth-promoting rhizobacteria (PGPR) play an important role in enhancing plant health, promoting plant growth and increasing crop yields [44,45]. Some PGPR, such as Nitrosomonadaceae, Xanthomonadaceae, Arthrobacter and Mycobacterium, presented positive correlations with P. notoginseng yields in our study.…”

Section: Discussionsupporting

confidence: 47%

See 1 more Smart Citation

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

Chen

Qian

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction.Methods: This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields. Results: At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields. Conclusions: This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.

show abstract

Section: Discussionsupporting

confidence: 47%

“…Mycobacterium, as PGPR genera, had positive effect on plant growth, nutrient uptake and increased root dry weight of maize [44,45,48,49]. Arthrobacter acts as antagonistic bacteria against Sclerotinia sclerotiorum [50], which can cause Helianthus annuus L. sclerotinia rot [51].…”

Section: Discussionmentioning

confidence: 99%

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

Chen

Qian

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…To explore the response of functions to the quality of P. notoginseng, soil samples from nine sites (i.e., [33]. The metagenomic libraries were sequenced on a HiSeq 2500 sequencer (Illumina, USA), and 150 bp pairedend reads were generated.…”

Section: Metagenomics Sequencingmentioning

confidence: 99%

WITHDRAWN: Rhizosphere Microbiome is Associated with Yield and Medical Value of the Perennial Panax Notoginseng

Wei

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Rhizosphere microbiome play important roles in promoting plant growth. However, it is not well understood how rhizosphere microbiome were driven by medical plants during growth stages and whether they contribute the accumulation of medical values. Panax notoginseng is a perennial medicinal plant, which belowground biomass and saponin contents are the important indicators of its value. Here, we use high-throughput sequencing method to study the temporal dynamics of perennial P. notoginseng rhizosphere microbiomes and the relationship between the indicators and core rhizosphere microbiomes.Results: The results show that the diversity, composition and network structures of the bacterial and fungal communities are mainly driven by the developmental stages. And succession characteristics of bacterial and fungal diversity show similar parabolic patterns during the developmental stages. Enrichment and depletion of the bacterial and fungal communities are active at the 3-year root growth (3YR) stage. From samples collected at a large-spatial P. notoginseng production area at the 3YR stage, we obtained 639 bacterial and 310 fungal core operational taxonomic units (OTUs). Analysis of the data indicate that the microbiome diversity is related to the belowground biomass and total saponin contents. Some genera, such as Pseudomonas, Massilia, Sphingobium, and Phoma are positively correlated to the belowground biomass, and genera likely Staphylotrichum, Chaetosphaeria, and Podospora are positively correlated with total saponin contents. Additionally, we identified 36 microbial functions involving in plant-microbe and microbe-microbe interactions, nutrition acquisition, and disease resistance. They are related to belowground biomass and saponin contents. Conclusions: In short, this study provides a detailed and systematic survey of rhizosphere microbiome in P. notoginseng and reveals that P. notoginseng rhizosphere microbiomes are largely driven by the developmental stages, while the core microbiomes are related to the belowground biomass and saponins contents of the plant. The finding may enhance our understanding of the interaction between microbes and perennial plants and improve our ability to manage root microbiota for sustainable production of the herb medicine.

show abstract

“…Soil microorganisms play the essential roles in soil formation and development, farmland material circulation, fertility evolution, degradation and purification of toxic substances [11,12]. Soil is an excellent culture medium for the growth and development of various microorganisms due to the availability of nutrients, water, organic and inorganic matter [13].…”

Section: Introductionmentioning

confidence: 99%

Responses of Microbial Communities and Interaction Networks to Different Management Practices in Tea Plantation Soils

Tan

Shi

et al. 2019

Sustainability

View full text Add to dashboard Cite

Soil microorganisms play important roles in the plant health and agricultural production. However, little is known about the complex responses of microbial communities and interaction networks to different agricultural management practices in tea plantation soils. In the present study, Illumina Miseq high-throughput sequencing technology and molecular ecological network (MEN) analysis were used to investigate the soil microbial diversity, community structure and composition, interaction networks of organic tea plantation (OTP), non-polluted tea plantation (NPTP) and conventional tea plantation (CTP). Alpha-diversity indices, Chao1 and richness, of OTP soil were significantly higher than those of NPTP and CTP soils. The beta-diversity analysis showed there were significant differences among bacterial community structures of OTP, NPTP and CTP soils. Composition analysis showed that Proteobacteria, Acidobacteria and Chloroflexi were the most dominant bacteria in all tea plantation soil samples under different management practices, and the beneficial community compositions of OTP soil were significantly different from NPTP and CTP soils at the phylum and genus levels. Canonical correspondence analysis (CCA) and mantel test revealed that TOC and NO3-N contents as well as pH values were the key soil factors to affect the bacterial community structures of tea plantation soils. Furthermore, network analysis showed that the network of OTP soil possessed more functionally interrelated microbial modules than NPTP and CTP soils, indicating that OTP soil possessed the higher ecosystem multi-functionality. These results provided the theoretical basis and reference for improving soil microbial diversity and enhancing community multi-functionality in tea plantation soil ecosystems through effective agricultural management practices.

show abstract

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

Cited by 156 publications

References 101 publications

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

WITHDRAWN: Rhizosphere Microbiome is Associated with Yield and Medical Value of the Perennial Panax Notoginseng

Responses of Microbial Communities and Interaction Networks to Different Management Practices in Tea Plantation Soils

Contact Info

Product

Resources

About