Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil

Wu, Xingjie; Cui, Zhenling; Peng, Jingjing; Zhang, Fusuo; Liesack, Werner

doi:10.1038/s43705-022-00100-z

Cited by 25 publications

(12 citation statements)

References 21 publications

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“…These bacteria can also enhance N fixation especially in legume crops reducing reliance on fertilizer inputs in soils. gcd encoding quinoprotein glucose dehydrogenase (GCD) has been identified as the key biomarker for inorganic phosphate solubilization in bacteria in agriculture soils (Wu et al, 2022). In addition, the phoD encoding alkaline phosphatase, bpp encoding β‐propeller phytase are good biomarkers for evaluating soil organic P transformation abilities in bacteria (Wan et al, 2020).…”

Section: Rhizo‐microbiome: a Complete Solution For Nutrient Interdepe...mentioning

confidence: 99%

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Pathania

Kumar

Sharma

et al. 2022

Journal of Applied Microbiology

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Plant rhizo-microbiome comprises complex microbial communities that colonize at the interphase of plant roots and soil. Plant growth-promoting rhizobacteria (PGPR) in the rhizosphere provide important ecosystem services ranging from the release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though it is evident that nutrient availability in soil is managed through inter-linked mechanisms, how PGPR expedite these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the interplay between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

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Section: Rhizo‐microbiome: a Complete Solution For Nutrient Interdepe...mentioning

confidence: 99%

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Pathania

Kumar

Sharma

et al. 2022

Journal of Applied Microbiology

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“…The accelerated microbial P solubilization could be related to the carbon input from RM. Previous work has found that cellulose, hemicelluloses, and lignin significantly increased the abundance of PSMs and their activity of phosphatase 28,29 . For example, polysaccharide breakdown and sugar metabolism are important for stimulating phosphate solubilization 30 .…”

Section: Discussionmentioning

confidence: 99%

Single‐cell Raman and functional gene analyses reveal microbial P solubilization in agriculture waste‐modified soils

Ding

Zhu

et al. 2023

mLife

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Application of agricultural waste such as rapeseed meal (RM) is regarded as a sustainable way to improve soil phosphorus (P) availability by direct nutrient supply and stimulation of native phosphate-solubilizing microorganisms (PSMs) in soils. However, exploration of the in situ microbial P solubilizing function in soils remains a challenge. Here, by applying both phenotype-based single-cell Raman with D 2 O labeling (Raman-D 2 O) and genotype-based high-throughput chips targeting carbon, nitrogen and P (CNP) functional genes, the effect of RM application on microbial P solubilization in three typical farmland soils was investigated. The abundances of PSMs increased in two alkaline soils after RM application identified by single-cell Raman D 2 O. RM application reduced the diversity of bacterial communities and increased the abundance of a few bacteria with reported P solubilization function. Genotypic analysis indicated that RM addition generally increased the relative abundance of CNP functional genes. A correlation analysis of the abundance of active PSMs with the abundance of soil microbes or functional genes was carried out to decipher the linkage between the phenotype and genotype of PSMs. Myxococcota and C degradation genes were found to potentially contribute to the enhanced microbial P release following RM application. This work provides important new insights into the in situ function of soil PSMs. It will lead to better harnessing of agricultural waste to mobilize soil legacy P and mitigate the P crisis.

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“…have been identified to be capable of both N fixation and P solubilization [ 183 ]. The gcd gene encoding quinoprotein glucose dehydrogenase is considered the core determinant that governs microbial phosphate solubilization [ 194 , 195 ]. The organic acids and exopolysaccharides released by microbes also help increase the contents of P and K in soil [ 196 , 197 ].…”

Section: Roles Of Microorganisms In Soil Bioremediation and The Poten...mentioning

confidence: 99%

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

Gang

Ren

Bai

et al. 2022

Plants

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Medicinal plants (MPs) are important resources widely used in the treatment and prevention of diseases and have attracted much attention owing to their significant antiviral, anti-inflammatory, antioxidant and other activities. However, soil degradation, caused by continuous cropping, excessive chemical fertilizers and pesticide residues and heavy metal contamination, seriously restricts the growth and quality formation of MPs. Microorganisms, as the major biota in soil, play a critical role in the restoration of the land ecosystem. Rhizosphere microecology directly or indirectly affects the growth and development, metabolic regulation and active ingredient accumulation of MPs. Microbial resources, with the advantages of economic efficiency, harmless to environment and non-toxic to organisms, have been recommended as a promising alternative to conventional fertilizers and pesticides. The introduction of beneficial microbes promotes the adaptability of MPs to adversity stress by enhancing soil fertility, inhibiting pathogens and inducing systemic resistance. On the other hand, it can improve the medicinal quality by removing soil pollutants, reducing the absorption and accumulation of harmful substances and regulating the synthesis of secondary metabolites. The ecological and economic benefits of the soil microbiome in agricultural practices are increasingly recognized, but the current understanding of the interaction between soil conditions, root exudates and microbial communities and the mechanism of rhizosphere microecology affecting the secondary metabolism of MPs is still quite limited. More research is needed to investigate the effects of the microbiome on the growth and quality of different medicinal species. Therefore, the present review summarizes the main soil issues in medicinal plant cultivation, the functions of microbes in soil remediation and plant growth promotion and the potential mechanism to further guide the use of microbial resources to promote the ecological cultivation and sustainable development of MPs.

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Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil

Cited by 25 publications

References 21 publications

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Single‐cell Raman and functional gene analyses reveal microbial P solubilization in agriculture waste‐modified soils

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

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