Effects of wheat root exudates on bacterial communities in the rhizosphere of watermelon

Shi, Jie; Gong, Xiaoya; Rahman, Muhammad Khashi u; Tian, Qing; Zhou, Xingang; Wu, Fengzhi

doi:10.17221/419/2021-pse

Cited by 10 publications

(9 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 59 Therefore, the composition of root-associated microbial community (i.e., in the rhizosphere) is strictly linked with the composition of root exudates of a plant, and any change in root exudation could potentially alter the soil biodiversity in the close vicinity. 60–62 Despite the obvious differences in metabolic profile in the soils of two maize cultivars at each growth stage, similar to the results of most of the previous studies conducted on cry1Ah insecticidal maize, 34 , 63 , 64 , 65 no difference in rhizosphere bacterial community was found in our study. Interestingly, the relative abundances of some bacterial OTUs were yet correlated with the altered metabolites in transgenic maize.…”

Section: Discussionsupporting

confidence: 89%

Comparison of genetically modified insect-resistant maize and non-transgenic maize revealed changes in soil metabolomes but not in rhizosphere bacterial community

et al. 2022

View full text Add to dashboard Cite

The deliberate introduction of the beneficial gene in crop plants through transgenic technology can provide enormous agricultural and economic benefits. However, the impact of commercialization of these crops on the ecosystem particularly on belowground soil biodiversity is still uncertain. Here, we examined and compared the effects of a non-transgenic maize cultivar and an insect-resistant transgenic maize cultivar genetically engineered with cry1Ah gene from Bacillus thuringiensis , on the rhizosphere bacterial community using 16S rDNA amplicon sequencing and soil metabolome profile using UPLC/MS analysis at six different growth stages. We found no significant differences in bacterial community composition and diversity at all growth stages between the two cultivars. The analysis of bacterial beta-diversity showed an evident difference in community structure attributed to plant different growth stages but not to the plant type. In contrast, the soil metabolic profile of transgenic maize differed from that of the non-transgenic plant at some growth stages, and most of the altered metabolites were usually related to the metabolism but not to the plant-microbe interaction related pathways. These results suggest that genetic modification with the cry1Ah gene-altered maize soil metabolism but had no obvious effect on the rhizosphere bacterial community.

show abstract

Section: Discussionsupporting

confidence: 89%

Comparison of genetically modified insect-resistant maize and non-transgenic maize revealed changes in soil metabolomes but not in rhizosphere bacterial community

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Fungi directly and positively affected root diameter. Studies have confirmed that the mycelial network of AM fungi expand the space of mineral and water absorption in root system, which promotes the growth and component accumulation of medicinal plants (Sun et al, 2021). G+ bacteria directly and negatively affected root branching number, rosmarinic acid and salvianolic acid B contents, but G-bacteria only directly and negatively affected rosmarinic acid content.…”

Section: Effect Of Rhizosphere Soil Physicochemical Properties and Mi...mentioning

confidence: 89%

“…Plant root distribution can influence soil physicochemical properties such as substrates and pH along soil profiles (Pietri and Brookes, 2008). Plant root systems are the main medium for exudates into rhizosphere soil, and root exudates can change the physicochemical properties and microbial composition of the rhizosphere soil to a plant's benefit (Bakker et al, 2018;Shi et al, 2021). Zhang et al (2022) reported that ginseng rhizosphere bacterial community structure is affected by genotype, and there is a correlation between ginseng genotypes and the bacterial population structure.…”

Section: Effect Of Genotype and Climatic Factors On Growth And Active...mentioning

confidence: 99%

Deciphering the effects of genotype and climatic factors on the performance, active ingredients and rhizosphere soil properties of Salvia miltiorrhiza

Han

Liu

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

IntroductionSalvia miltiorrhiza Bunge is an important medicinal herb, which is widely cultivated in most parts of China. It has attracted considerable attention because of its pharmacological properties and potential health benefits.MethodsWe used a field experiment to determine the effects of different genotypes and climatic factors on the performance (plant biomass, morphological parameters), active ingredients, rhizosphere soil physicochemical properties and microbial composition of S. miltiorrhiza at five cultivation locations.ResultsThe results showed that these parameters were significantly different in the six different genotypes of S. miltiorrhiza from five producing areas. Genotype and soil physicochemical properties were the main factors affecting the growth traits of S. miltiorrhiza, while genotype, climate and soil physicochemical properties were the main factors affecting the content of active components of S. miltiorrhiza. Microbial phospholipid fatty acid analysis showed that the biomass of Gram-positive and Gram-negative bacteria was affected by the genotypes of S. miltiorrhiza plants, while the biomass of arbuscular mycorrhizal fungi, fungi, Gram-positive and Gram-negative bacteria was affected by climate factors.DiscussionBased on the main results, DS993 was the most suitable genotype for S. miltiorrhiza in the five producing areas from the perspective of comprehensive growth traits and medicinal components, while DS993 and DS2000 were suitable for planting in Shandong province from the perspective of origin. DS996 is not suitable for all of the above production areas. These results are helpful to understand the ecological adaptability of different genotypes of S. miltiorrhiza resources, and to select appropriate S. miltiorrhiza genotypes for specific planting areas, so as to maximize yield and quality.

show abstract

“…Six genera, including Sphigomonas, Pedobacter, Parablastomonas, Paracoccus, Pir4_lineage, and Nocardioides, were identified as biomarkers in good-quality samples. These six biomarkers for good-quality samples were reported to be related to agriculture rhizosphere soil [56][57][58][59][60][61]. Three genera, Sphigomonas, Pedobacter, and Nocardioides, were also identified as core microbiota in healthy samples in the Kusstatscher et al ( 2019) study [9].…”

Section: Integrated Taxonomic Analysis Identifies Generalizable Taxa ...mentioning

confidence: 91%

Alignment-free microbiome-based classification of fresh produce safety and quality

Liao

Wang

Quon

2022

Preprint

View full text Add to dashboard Cite

Background: While next generation sequencing has enriched our knowledge about native microbial populations present in fresh produce, the loss of up to 50-70% of data during the alignment and denoising steps of data preprocessing may lead to the missing of important bacterial species information and decrease our ability to identify species associated with poor produce quality and contamination. Microbial studies are also often limited by small sample sizes, making generalization of results beyond individual studies difficult. Results: In this study, we explored separate strategies to mitigate the challenges of data preprocessing and small sample sizes. First, we explored an alignment-free analysis strategy using k-mer hashes to identify DNA signatures predictive of produce safety (contaminated vs. non-contaminated) and produce quality (good-quality vs. decreasing-quality), and compared it against the amplicon sequence variant (ASV) strategy that uses a typical alignment and denoising step. Random forests (RF)-based classifiers were trained on publicly available fresh produce microbiome datasets with data preprocessed using either the k-mer hash or ASV approach. RF-based classifiers for fresh produce safety and quality using 7-mer hash datasets had significantly higher classification accuracy than those using the ASV datasets, supporting the hypothesis that data preprocessing strategies that keep more data (k-mer hash) retain more useful information about bacterial species than approaches that lose data during preprocessing (ASV). We also demonstrated that integrating multiple datasets together also led to higher classification accuracy compared to those trained with individual datasets. Integrated datasets also enabled the identification of more consistent and generalizable biomarkers (ASV, 7-mer hash, or bacterial taxa) associated with fresh produce safety and quality. Conclusions:The proposed combination of integrating multiple datasets and leveraging an alignment-free 7-mer hash strategy substantially mitigates the loss of sequencing data due to the ASV denoising step and leads to better classification performance for fresh produce safety and quality. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing datasets (generated from different studies or different laboratories) for the application of machine learning in the area of microbial safety and quality of food.

show abstract

Effects of wheat root exudates on bacterial communities in the rhizosphere of watermelon

Cited by 10 publications

References 27 publications

Comparison of genetically modified insect-resistant maize and non-transgenic maize revealed changes in soil metabolomes but not in rhizosphere bacterial community

Comparison of genetically modified insect-resistant maize and non-transgenic maize revealed changes in soil metabolomes but not in rhizosphere bacterial community

Deciphering the effects of genotype and climatic factors on the performance, active ingredients and rhizosphere soil properties of Salvia miltiorrhiza

Alignment-free microbiome-based classification of fresh produce safety and quality

Contact Info

Product

Resources

About