Small molecule metabolites drive plant rhizosphere microbial community assembly patterns

The assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant sampl...

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Main Authors: Yanwei Ma, Heqi Wang, Yalong Kang, Tao Wen
Format: Article
Language:English
Published: Frontiers Media S.A. 2025-02-01
Series:Frontiers in Microbiology
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Online Access:https://www.frontiersin.org/articles/10.3389/fmicb.2025.1503537/full
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author Yanwei Ma
Heqi Wang
Yalong Kang
Tao Wen
author_facet Yanwei Ma
Heqi Wang
Yalong Kang
Tao Wen
author_sort Yanwei Ma
collection DOAJ
description The assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant samples and evaluated root traits, plant growth characteristics, soil enzyme activities, rhizosphere metabolites, and soil chemical properties to identify the primary determinants of rhizosphere community assembly. Across 36 soil samples, we obtained 969,634 high-quality sequences, clustering into 6,284 ASVs predominantly classified into Proteobacteria (57.99%), Actinobacteria (30%), and Bacteroidetes (5.13%). Our findings revealed that rhizosphere metabolites accounted for more variance in microbial community composition compared to chemical properties (ANOVA, F = 1.53, p = 0.04), enzyme activities, or root traits (ANOVA, F = 1.04, p = 0.001). Seven small molecule metabolites, including glycerol, sorbitol, phytol, and alpha-ketoglutaric acid, were significantly correlated with βNTI, underscoring their role as critical drivers of microbial community assembly. The genus Rhizobium, significantly associated with βNTI (R = 0.25, p = 0.009), emerged as a keystone taxon shaping community structure. Soil culture experiments further validated that small molecule metabolites can modulate microbial community assembly. The ST treatment, enriched with these metabolites, produced 1,032,205 high-quality sequences and exhibited significant shifts in community composition (Adonis, p = 0.001, R = 0.463), with Rhizobium showing higher abundance compared to the control (CK). Variable selection (βNTI >2) drove phylogenetic turnover in ST, while stochastic processes (|βNTI| < 2) dominated in CK. This study provides quantitative insights into the role of rhizosphere metabolites in shaping microbial community assembly and highlights their potential for targeted modulation of rhizosphere microbiomes.
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spelling doaj-art-93816687e2a84776991c03aabd7caae12025-02-11T17:20:25ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-02-011610.3389/fmicb.2025.15035371503537Small molecule metabolites drive plant rhizosphere microbial community assembly patternsYanwei Ma0Heqi Wang1Yalong Kang2Tao Wen3Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, ChinaJiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, ChinaCollege of Resources and Environmental Science, Yunnan Agricultural University, Kunming, ChinaJiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, ChinaThe assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant samples and evaluated root traits, plant growth characteristics, soil enzyme activities, rhizosphere metabolites, and soil chemical properties to identify the primary determinants of rhizosphere community assembly. Across 36 soil samples, we obtained 969,634 high-quality sequences, clustering into 6,284 ASVs predominantly classified into Proteobacteria (57.99%), Actinobacteria (30%), and Bacteroidetes (5.13%). Our findings revealed that rhizosphere metabolites accounted for more variance in microbial community composition compared to chemical properties (ANOVA, F = 1.53, p = 0.04), enzyme activities, or root traits (ANOVA, F = 1.04, p = 0.001). Seven small molecule metabolites, including glycerol, sorbitol, phytol, and alpha-ketoglutaric acid, were significantly correlated with βNTI, underscoring their role as critical drivers of microbial community assembly. The genus Rhizobium, significantly associated with βNTI (R = 0.25, p = 0.009), emerged as a keystone taxon shaping community structure. Soil culture experiments further validated that small molecule metabolites can modulate microbial community assembly. The ST treatment, enriched with these metabolites, produced 1,032,205 high-quality sequences and exhibited significant shifts in community composition (Adonis, p = 0.001, R = 0.463), with Rhizobium showing higher abundance compared to the control (CK). Variable selection (βNTI >2) drove phylogenetic turnover in ST, while stochastic processes (|βNTI| < 2) dominated in CK. This study provides quantitative insights into the role of rhizosphere metabolites in shaping microbial community assembly and highlights their potential for targeted modulation of rhizosphere microbiomes.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1503537/fullmicrobiome assemblymicrobial communityrhizosphere metabolitesneutral modelecological process
spellingShingle Yanwei Ma
Heqi Wang
Yalong Kang
Tao Wen
Small molecule metabolites drive plant rhizosphere microbial community assembly patterns
Frontiers in Microbiology
microbiome assembly
microbial community
rhizosphere metabolites
neutral model
ecological process
title Small molecule metabolites drive plant rhizosphere microbial community assembly patterns
title_full Small molecule metabolites drive plant rhizosphere microbial community assembly patterns
title_fullStr Small molecule metabolites drive plant rhizosphere microbial community assembly patterns
title_full_unstemmed Small molecule metabolites drive plant rhizosphere microbial community assembly patterns
title_short Small molecule metabolites drive plant rhizosphere microbial community assembly patterns
title_sort small molecule metabolites drive plant rhizosphere microbial community assembly patterns
topic microbiome assembly
microbial community
rhizosphere metabolites
neutral model
ecological process
url https://www.frontiersin.org/articles/10.3389/fmicb.2025.1503537/full
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AT taowen smallmoleculemetabolitesdriveplantrhizospheremicrobialcommunityassemblypatterns