Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm

Cheng, Hongyan; Yuan, Minshu; Tang, Liang; Shen, You-Gen; Yu, Qiang; Li, Shiqing

doi:10.1016/j.scitotenv.2021.152878

Cited by 69 publications

(27 citation statements)

References 95 publications

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“…They can decompose organic matter, promote soil carbon cycle and nitrogen fixation, and play a positive role in improving the soil environment ( Fan et al, 2021 ). In addition, Cheng et al (2022) also found that Solicoccozyma had the strongest correlation with some metabolites, indicating that this microorganism may be involved in the synthesis of most metabolites in soil. These microorganisms were positively correlated with the accumulation of the main active components of RAM.…”

Section: Discussionmentioning

confidence: 87%

Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components

Song

Liu

Huang

et al. 2023

PeerJ

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Rhizosphere microorganisms are the main factors affecting the formation of high quality medicinal materials and promoting the accumulation of secondary metabolites. However, the composition, diversity, and function of rhizosphere microbial communities in endangered wild and cultivated Rhizoma Atractylodis Macrocephalae (RAM) and their relationships with active component accumulation have remained unclear. In this study, high-throughput sequencing and correlation analysis were used to study the rhizosphere microbial community diversity (bacteria and fungi) of three RAM species and its correlation with the accumulation of polysaccharides, atractylone, and lactones (I, II, and III). A total of 24 phyla, 46 classes, and 110 genera were detected. The dominant taxa were Proteobacteria, Ascomycota, and Basidiomycota. The microbial communities in both wild and artificially cultivated soil samples were extremely species-rich, but there were some differences in their structure and the relative abundances of microorganism taxa. Meanwhile, the contents of effective components in wild RAM were significantly higher than those in cultivated RAM. Correlation analysis showed that 16 bacterial and 10 fungal genera were positively or negatively correlated with active ingredient accumulation. These results showed that rhizosphere microorganisms could play an important role in component accumulation and might lay a foundation for future research on endangered materials.

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Section: Discussionmentioning

confidence: 87%

Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components

Song

Liu

Huang

et al. 2023

PeerJ

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“…The importance of soil microorganisms in soil metabolic activity cannot be ignored ( Kalu et al, 2022 ). In addition, the variations in microbial types and their abundance shape the levels and types of soil metabolites, and, in turn, the circulation and metabolism of exogenous nutrients in the soil ( Cheng et al, 2022 ). Uncovering the relationships between soil metabolism and bacterial communities is therefore highly critical to understanding how fertilization can positively affect crop yield without inducing harmful side-effects.…”

Section: Discussionmentioning

confidence: 99%

“…For example, 16S rRNA gene sequencing and gas chromatography–mass spectrometry (GC–MS) metabolomics have been used to study soil microbial communities and the related metabolites ( Zhang H. et al, 2020 ). More recent studies, combining microbiology and non-targeted metabolomics, found that P fertilizer reduced the diversity of the bacterial 16S rRNA and the fungal nuclear ribosomal internal transcribed spacer (ITS) genes, and significantly changed the overall composition of soil bacteria and fungi ( Cheng et al, 2022 ). However, the effects of organic and microbial fertilizers (especially their combined use) on soil metabolites, metabolic pathways, and the structure of soil microbial communities are still largely unknown, especially in bamboo cultivation studies ( Rodríguez et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Wang²,

Xu³

et al. 2023

Front. Microbiol.

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Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC–MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

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“…The 10 year field trial results clearly show that long-term nitrogen fertilization affects soil pH, thereby significantly altering most dominant soil bacterial species ( Ren et al, 2020 ). As well as excessive phosphorus fertilizers reduced microbial diversity and significantly altered microbial community structures and compositions, phosphorus levels also interfered with the complexity of soil bacterial and fungal symbiosis networks ( Cheng et al, 2022 ). Moreover, soil metabolomics provides a window into microbial behavior, as the metabolites secreted by microbes and the residual decomposition products of microbes are the main components of the soil metabolome ( Jones et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Co-analysis of cucumber rhizosphere metabolites and microbial PLFAs under excessive fertilization in solar greenhouse

Wang

Bian²,

Wu³

et al. 2022

Front. Microbiol.

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Fertilizer application is the most common measure in agricultural production, which can promote the productivity of crops such as cucumbers, but the problem of excessive fertilization occurs frequently in solar greenhouses. However, the effects of fertilization levels on cucumber rhizosphere soil microbes and metabolites and their relationships are still unclear. In order to determine how fertilization levels affect the rhizosphere microenvironment, we set up four treatments in the solar greenhouse: no-fertilization (N0P0K0), normal fertilization (N1P1K1), slight excessive fertilization (N2P2K2), and extreme excessive fertilization (N3P3K3). The results showed that fertilization treatments significantly increased cucumber yield compared to no-fertilization, but, the yield of N3P3K3 was significantly lower than that of N1P1K1 and N2P2K2. Fertilization levels had significant effects on rhizosphere microorganisms, and pH, NH4+-N and AP were the main environmental factors that affected the changes in microbial communities. The total PLFAs, the percentages of fungi and arbuscular mycorrhizal fungi (AMF) were significantly reduced and bacteria percentage was significantly increased in N3P3K3 compared to other fertilization treatments. Differential metabolites under different fertilization levels were mainly organic acids, esters and sugars. Soil phenols with autotoxic effect under fertilization treatments were higher than that of N0P0K0. In addition, compared with soil organic acids and alkanes of N0P0K0, N2P2K2 was significantly increased, and N3P3K3 was not significantly different. This suggested that cucumber could maintain microbial communities by secreting beneficial metabolites under slight excessive fertilization (N2P2K2). But under extremely excessive fertilization (N3P3K3), the self-regulating ability of cucumber plants and rhizosphere soil was insufficient to cope with high salt stress. Furthermore, co-occurrence network showed that 16:1ω5c (AMF) was positively correlated with 2-palmitoylglycerol, hentriacontane, 11-octadecenoic acid, decane,4-methyl- and d-trehalose, and negatively correlated with 9-octadecenoic acid at different fertilization levels. This indicated that the beneficial microorganisms in the cucumber rhizosphere soil promoted with beneficial metabolites and antagonized with harmful metabolites. But with the deepening of overfertilization, the content of beneficial microorganisms and metabolites decreased. The study provided new insights into the interaction of plant rhizosphere soil metabolites and soil microbiomes under the different fertilization levels.

show abstract

Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm

Cited by 69 publications

References 95 publications

Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components

Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Co-analysis of cucumber rhizosphere metabolites and microbial PLFAs under excessive fertilization in solar greenhouse

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