Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions

Wang, Bo; Chen, Chen; Xiao, Yuan-Ming; Chen, Kai-Yang; Wang, Juan; Zhao, Shuo; Liu, Na; Li, Jia-Nan; Zhou, Guo-Ying

doi:10.1016/j.micres.2024.127603

Cited by 5 publications

(3 citation statements)

References 53 publications

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“…PCR was conducted in triplicate with an ABI GeneAmp 9700 PCR thermocycler (ABI, Vernon, CA, USA) under the following conditions: initial denaturation at 95 • C for 3 min, followed by 27 cycles (95 • C for 30 s, 55 • C for 30 s, 72 • C for 30 s), followed by a single extension at 72 • C for 10 min, and finally ending at 4 • C. After amplification, 3 µL of the PCR product underwent 2.0% agarose gel electrophoresis and subsequent purification using the AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA, USA). The PCR product's quantity was determined using a Quantus Fluorometer (Promega, Madison, WI, USA) [27].…”

Section: Dna Extraction and High-throughput Sequencing Analysismentioning

confidence: 99%

Effect of Mild Organic Substitution on Soil Quality and Microbial Community

Wang,

Xu,

Jiang

et al. 2024

Agronomy

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Mild organic substitution is advantageous for sustainable agricultural development. In order to determine the proper fertilization strategy, it is essential to investigate the impact of substituting chemical fertilizers with varying levels of organic manure on soil nutrients, microbial communities, and crop productivity. Four treatments were implemented: no fertilizer, sole chemical fertilizer, 20% organic manure substitution, and 40% organic manure substitution. Bacterial and fungal communities were characterized through high-throughput sequencing of the 16S rRNA gene V3–V4 region and the V4 region, respectively. The 20% and 40% organic manure substitutions increased soil organic matter (SOM) content, total nitrogen (TN) content, and reduced soil pH compared to the control (CK). The 20% organic manure substitution showed the most significant improvements in soil alkaline phosphatase, urease, and invertase activities. Soil nutrient enhancement increased bacterial alpha diversity, with a milder impact on fungal alpha diversity compared to bacteria. Different fertilization treatments elevated the relative abundance of bacterial Bacteroidetes (8.11%, 21.25%, and 1.88%), Actinomycetes (12.65%, 26.36%, and 15.33%), and fungal Ascomycota (16.19%, 10.44%, and 12.69%), known for degrading recalcitrant organic matter. The sole chemical fertilizer treatment increased the pathogenic Cheatotryiales. Shared species, primarily from bacterial Actinomycetes, Firmicutes, Proteobacteria, and fungal Ascomycota phyla, were found at 20% and 40% organic manure substitution levels. Specifically, the 20% organic manure substitution level promoted the relative abundance of beneficial plant growth-promoting taxa, Oxalobacteraceae and Massilia, and suppressed pathogens, with an increase in the relative abundance of the Purpureocillium genus and Mortierellomycota. These findings suggest that a 20% OF substitution can maintain crop yield, enhance soil nutrients and enzyme activities by fostering beneficial soil bacteria, inhibiting soil-borne pathogens, and refining microbial community structure.

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Section: Dna Extraction and High-throughput Sequencing Analysismentioning

confidence: 99%

Effect of Mild Organic Substitution on Soil Quality and Microbial Community

Wang,

Xu,

Jiang

et al. 2024

Agronomy

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“…The rhizosphere microorganisms of plants are considered as the "second genome of plants" (Wang et al 2024).The growth, development, yield, secondary metabolites, and disease defense of medicinal plants are crucial. The community structure and diversity of rhizosphere microorganisms are in uenced by soil environment, which is related to factors such as forest type.…”

Section: Introductionmentioning

confidence: 99%

Correlation analysis between ginsenoside content and rhizosphere soil microbial species in different forest types

Pang,

Ruan,

Gao

et al. 2024

Preprint

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Inter-root microorganisms are major factors influencing the formation of high-quality herbs and promoting the accumulation of secondary metabolites, and this relationship has been well characterised in many supra-herbal medicinal herbs, but there is limited information on whether ginseng saponin accumulation is mediated by microorganisms in different forest types.Inter-root soil samples of ginseng and ginseng samples were collected from four different forest types (Theropencedrymion, Larch forest, Broad-leaved forest and Camphor pine forest) in the mountainous areas of Jingyu County, Jilin Province, China. The content of ginsenosides in the collected ginseng samples was determined by high performance liquid chromatography (HPLC). The results showed that the content of ginsenosides in Camphor pine forest was significantly higher than that in the other three forest types.The microorganisms in the soil samples were isolated and purified, and subsequently sequenced and analyzed by high-throughput sequencing methods, and a total of seven bacterial species were isolated and identified in the inter-root soil of ginseng from four different forest types. In broad-leaved forests (BF) and larch forests (LF), Bacillus megaterium is the most abundant microorganism. In the camphor pine forests (CPF) and theropencedrymion (TH), Luteibactor rhizovicinais the largest proportion of microorganisms. Relevant analysis shows that several identified strains from the four forest types, including Bacillus pseudomycoides, Bacillus subtilis, Pseudomonas alcaliphila, Luteibacter rhizovicinus and Pseudomonas alcaliphilacan promote the biosynthesis and accumulation of monomeric saponins Rc, Rb1, Rb2, Rb3, Rg2, Rb3, and Rh4. Our research findings emphasize the crucial role of different forest stand types in soil microbial community structure, and explore the accumulation mechanism of ginsenosides from a microbial perspective. In summary, this study provides more theoretical basis for the relationship between different forest types and the bioactive components of medicinal plants.

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“…This may be partially explained by the fact that soil microbial communities are influenced by both biotic and abiotic attributes. On the one hand, soil properties such as pH and moisture may contribute to filter out some microbial community members (Philippot et al., 2023 ; Wang et al., 2024 ). On the other hand, biotic factors such as symbiosis, competition, trade‐offs, and predation influence how the different taxa interact in the soil (Wardle et al., 2004 ).…”

Section: Introductionmentioning

confidence: 99%

Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities

Kayiranga,

Isabwe,

Yao

et al. 2024

Ecology and Evolution

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Environmental change exerts a profound effect on soil microbial domains—including bacteria, fungi, and protists—that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.

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Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions

Cited by 5 publications

References 53 publications

Effect of Mild Organic Substitution on Soil Quality and Microbial Community

Effect of Mild Organic Substitution on Soil Quality and Microbial Community

Correlation analysis between ginsenoside content and rhizosphere soil microbial species in different forest types

Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities

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