Core microbiota drive multi-functionality of the soil microbiome in the Cinnamomum camphora coppice planting

Sun, Luyuan; Li, Guilong; Zhao, Jiao; Zhang, Ting; Liu, Jia; Zhang, Jie

doi:10.1186/s12866-023-03170-8

Cited by 3 publications

(1 citation statement)

References 78 publications

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“…Similarly, Chen et al reported that the core microorganisms identified in soil were associated with the nitrogen cycle . Several studies have demonstrated that the core microbiota plays a crucial role in maintaining the functional stability of the soil microbiota and driving soil nutrient cycling. − In addition, core microbiota were prevalent in multiple ecological environments and used a wide range of ecological niches and resources to improve the productivity of soil ecological environments and plant quality. Therefore, identifying the core microbiota and screening potential nitrogen cycling microbes are key steps in the artificial construction of microbiota to improve soil nitrogen availability.…”

Section: Discussionmentioning

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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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: 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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Beneath the apple trees - Exploring soil microbial properties under Malus domestica concerning various land management practices

Zawadzka,

Oszust,

Pylak

et al. 2024

Applied Soil Ecology

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Phylogenetic Measures of the Core Microbiome

Bewick,

Camper

2024

Preprint

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BackgroundA fundamental concept in microbial ecology is the ‘core microbiome.’ Typically, core microbiomes are defined as the microbial taxa, genes, or functions shared by a threshold number of microbiome samples from a particular type of habitat (e.g., a particular type of host or a particular type of environment/ecosystem). In defining the core microbiome, the goal is to capture the portion of the microbial community that is conserved across samples from the focal habitat. Recently, there has been growing interest in developing methods to better characterize core microbiomes. As a result, numerous occurrence- and abundance-based measures have been defined. However, none have included phylogenetically aware metrics for analyzing core microbiomes.ResultsIn this paper, we develop the concept of the ‘core community phylogeny’ – a phylogeny where branches are selected based on their presence in multiple samples from a single type of habitat. We then use the core community phylogeny to define phylogenetic metrics for the diversity of core microbiomes from a single type of habitat, for turnover between core microbiomes from two different types of habitat, and for shared diversity across core microbiomes from two or more different types of habitat. As compared to non-phylogenetic metrics, our phylogenetic metrics show greater consistency across taxonomic rank and less sensitivity to strain variation across microbiome samples. Thus, our metrics address key challenges in the interpretation of core microbiomes.ConclusionsWe provide a phylogenetic framework for characterizing and comparing core microbiomes. Importantly, the methods that we propose allows integration of microbiome properties across taxonomic rank. Ultimately, this will provide both a more consistent picture of the core microbiome, as well as novel biological insight into the conserved components of microbial communities.

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Core microbiota drive multi-functionality of the soil microbiome in the Cinnamomum camphora coppice planting

Cited by 3 publications

References 78 publications

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Beneath the apple trees - Exploring soil microbial properties under Malus domestica concerning various land management practices

Phylogenetic Measures of the Core Microbiome

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