Insights into the shift of microbial community related to nitrogen cycle, especially N2O in vanadium-polluted soil

Liu, Xuna; Pang, Lina; Yue, Yao; Li, Hongna; Chatzisymeon, Efthalia; Lu, Yuanyuan; Yang, Ping

doi:10.1016/j.envpol.2023.121253

Cited by 11 publications

(5 citation statements)

References 60 publications

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“…Furthermore, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the four dominant bacterial phyla in legume rhizosphere soil . The increase in Acidobacteriota in legume rhizosphere soil suggests an increase in the degradation and utilization of soil organic matter and total nitrogen, and increases in Proteobacteria and Actinobacteriota may reflect an increase in nitrogen cycle activity . An increase in the nitrogen-fixing bacterial genera Bradyrhizobium , Rhodoplanes , Pseudolabrys , Allorhizobium - Neorhizobium - Pararhizobium - Rhizobium , and Mesorhizobium could result in an increase in nitrogen availability in the soil, increasing crop yields. − …”

Section: Discussionmentioning

confidence: 97%

“…51 The increase in Acidobacteriota in legume rhizosphere soil suggests an increase in the degradation and utilization of soil organic matter and total nitrogen, 52 and increases in Proteobacteria and Actinobacteriota may reflect an increase in nitrogen cycle activity. 53 An increase in the nitrogen-fixing bacterial genera Bradyrhizobium, Rhodoplanes, Pseudolabrys, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Mesorhizobium could result in an increase in nitrogen availability in the soil, increasing crop yields. 54−58 Microbial network analyses can improve the understanding of microbial interactions and ecological processes beyond simple richness and composition analyses.…”

Section: Microbial Assembly Patterns and Network Structures Differ Be...mentioning

confidence: 99%

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Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Yang,

Xu,

Zhang

et al. 2024

J. Agric. Food Chem.

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Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

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Section: Discussionmentioning

confidence: 97%

Section: Microbial Assembly Patterns and Network Structures Differ Be...mentioning

confidence: 99%

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Yang,

Xu,

Zhang

et al. 2024

J. Agric. Food Chem.

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“…For the nonrhizosphere soil and rhizosphere soil samples, the relative abundances of ammonia oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus in Akihime was significantly higher than those in F. nilgerrensis . These archaea may play important roles in the soil nitrogen cycle of cultivated strawberry ( Wu et al, 2021 ; Kraft et al, 2022 ; Sun et al, 2022 ; Liu et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

Wang,

Dai,

et al. 2024

Front. Microbiol.

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Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.

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“…Nocardioides participate in bioremediation, especially organochlorine degradation such as lindane pesticide and chloroaromatics, making them a crucial candidate for soil remediation strategy ( Ito et al, 2019 ; Singh and Singh, 2019 ). Lysobacter is a well-known biocontrol agent ( Lin et al, 2021 ) while Ilumatobacter and Marmoricola participate in C and N cycling, respectively ( Edgmont et al, 2012 ; Liu et al, 2023 ). Although soil microbes have been extensively classified, the high proportion of unclassified sequences in this study gave credence to the fact that the majority of soil microbiomes are yet to be fully identified and characterized ( Delgado-Baquerizo, 2019 ; Furtak et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production

Raimi,

Ezeokoli,

Adeleke

2023

Front. Microbiol.

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IntroductionRhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types.MethodsRhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline.ResultsOverall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms.DiscussionModule hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.

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Insights into the shift of microbial community related to nitrogen cycle, especially N2O in vanadium-polluted soil

Cited by 11 publications

References 60 publications

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production

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