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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Frontiers Media S.A.
2025-02-01
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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 |
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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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institution | Kabale University |
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language | English |
publishDate | 2025-02-01 |
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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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