Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

McPherson, Morgan R.; Wang, Peng; Marsh, Ellen L.; Mitchell, Robert B.; Schachtman, Daniel P.

doi:10.3791/57932-v

Cited by 19 publications

(9 citation statements)

References 6 publications

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“…Rhizosphere soil was collected according to established protocols (McPherson et al, 2018) after plants had grown in soil for 5 weeks. In brief, soil loosely attached to roots was removed by gentle shaking.…”

Section: Methodsmentioning

confidence: 99%

The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly

Chen

et al. 2023

Molecular Ecology

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Symbiosis with arbuscular mycorrhizal (AM) fungi improves plant nutrient capture from the soil, yet there is limited knowledge about the diversity, structure, functioning, and assembly processes of AM fungi‐related microbial communities. Here, 16S rRNA gene sequencing and metagenomic sequencing were used to detect bacteria in the rhizosphere of Lotus japonicus inoculated with and without AM fungi, and the L. japonicus mutant ljcbx (defective in symbiosis) inoculated with AM fungi in southern grassland soil. Our results show that AM symbiosis significantly increased bacterial diversity and promoted deterministic processes of bacterial community construction, suggesting that mycorrhizal symbiosis resulted in the directional enrichment of bacterial communities. AM fungi promoted the enrichment of nine bacteria, including Ohtaekwangia, Niastella, Gemmatimonas, Devosia, Sphingomonas, Novosphingobium, Opitutus, Lysobacter, Brevundimonas, which are positively correlated with NPK‐related parameters. Through a functional identification experiment, we found that six of these genera, including Brevundimonas, Lysobacter, Ohtaekwangia, Sphingomonas, Devosia, and Gemmatimonas, demonstrated the ability to mineralize organophosphate and dissolve inorganic phosphorus, nitrogen, and potassium. Our study revealed that AM fungi can regulate rhizosphere bacterial community assembly and attract specific rhizosphere bacteria to promote soil nutrient turnover in southern grasslands.

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Section: Methodsmentioning

confidence: 99%

The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly

Chen

et al. 2023

Molecular Ecology

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“…The disease incidence was calculated by dividing the number of plants with visible gall formation by the total number of inoculated plants. The sections with crown gall were cut out and sterilized in 35 mL of sterilization solution (3% NaOCl, 0.01% Tween 20) for 30 s, and then transferred to 35 mL of 70% ethanol and washed in 35 mL of sterile H 2 O three times ( 48 ). The sterilization was evaluated by spreading 100 μL of liquid from the third wash onto 523 agar plates and observing for 2 days to make sure there was no growth of bacteria.…”

Section: Methodsmentioning

confidence: 99%

Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome

Wang

Chen

Chou

et al. 2023

mBio

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“…Soil between rows samples were excavated from the top 30 cm of soil in between plots from different locations of the field. Soil within rows, rhizosphere, and root samples were collected as described previously (McPherson et al, 2018). Leaf samples were collected from the newest, unexpanded leaves inside the whorl that had never been exposed because they were considered to be absent of leaf epiphytic microbes.…”

Section: Methodsmentioning

confidence: 99%

“…All the samples for microbiome and metabolome analyses were brought back to the laboratory on ice and processed as described previously (McPherson et al, 2018; Sheflin et al, 2019). The soil between rows were processed with the same procedure as the soil within rows.…”

Section: Methodsmentioning

confidence: 99%

Root associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

Chai

Goren

et al. 2023

Preprint

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Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly influenced the root-associated bacterial communities and root metabolite composition of sorghum. Sorghum NUE was positively correlated with the bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to N stress and indicate that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our study provides new insight into the links between host genetic regulation of root metabolites and root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.

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Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Cited by 19 publications

References 6 publications

The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly

The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly

Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome

Root associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

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