Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping

Lv Su; Huatai Li; Jing Wang; Wenting Gao; Xia Shu; Xiting Sun; Kesu Wang; Yan Duan; Yunpeng Liu; Eiko E. Kuramae; Ruifu Zhang; Biao Shen

doi:10.1007/s00374-023-01731-7

Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping

Lv Su, Huatai Li, Jing Wang, Wenting Gao, Xia Shu, Xiting Sun, Kesu Wang, Yan Duan, Yunpeng Liu, Eiko E. Kuramae, Ruifu Zhang^*, Biao Shen^*

^*Corresponding author for this work

NIOO - Microbial Ecology (ME)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

Abstract

The bacteria that dominate and become enriched in the rhizosphere during continuous cropping are of increasing interest, as they can greatly adapt to the rhizosphere. However, there are still little knowledge about the general composition and function of these bacteria. In this study, we planted tomatoes in three different soils for three planting cycles and used both high-throughput sequencing and culture-dependent workflows. Despite significant differences in bacterial communities from the initial soils, we observed a similar succession in the rhizosphere bacterial community compositions. We identified certain bacteria that were gradually enriched and potentially beneficial, such as Rhizobium and Flavobacterium. However, some other potentially beneficial bacteria, such as Massilia and Lysobacter, were gradually depleted. Additionally, we found that predicted functions related to xenobiotic biodegradation, nutrient metabolism and antibiotic biosynthesis were enriched in different rhizosphere soils. Beijerinckia fluminensis GR2, which was gradually enriched in all tested soils, significantly inhibited the growth of Ralstonia solanacearum and protected the host from infection. Our study provides new insights into the assembly mechanism of gradually enriched bacteria and their role as plant-beneficial microbes that adapt well to the rhizosphere.

Original language	English
Journal	Biology and Fertility of Soils
DOIs	https://doi.org/10.1007/s00374-023-01731-7
Publication status	Published - 2023

Keywords

Beneficial microbes
Continuous cropping system
Ralstonia solanacearum
Rhizosphere bacteria
Soil types

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Su et al 2023b AAM
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title = "Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping",

abstract = "The bacteria that dominate and become enriched in the rhizosphere during continuous cropping are of increasing interest, as they can greatly adapt to the rhizosphere. However, there are still little knowledge about the general composition and function of these bacteria. In this study, we planted tomatoes in three different soils for three planting cycles and used both high-throughput sequencing and culture-dependent workflows. Despite significant differences in bacterial communities from the initial soils, we observed a similar succession in the rhizosphere bacterial community compositions. We identified certain bacteria that were gradually enriched and potentially beneficial, such as Rhizobium and Flavobacterium. However, some other potentially beneficial bacteria, such as Massilia and Lysobacter, were gradually depleted. Additionally, we found that predicted functions related to xenobiotic biodegradation, nutrient metabolism and antibiotic biosynthesis were enriched in different rhizosphere soils. Beijerinckia fluminensis GR2, which was gradually enriched in all tested soils, significantly inhibited the growth of Ralstonia solanacearum and protected the host from infection. Our study provides new insights into the assembly mechanism of gradually enriched bacteria and their role as plant-beneficial microbes that adapt well to the rhizosphere.",

keywords = "Beneficial microbes, Continuous cropping system, Ralstonia solanacearum, Rhizosphere bacteria, Soil types",

author = "Lv Su and Huatai Li and Jing Wang and Wenting Gao and Xia Shu and Xiting Sun and Kesu Wang and Yan Duan and Yunpeng Liu and Kuramae, {Eiko E.} and Ruifu Zhang and Biao Shen",

note = "Data archiving: Data with publication",

year = "2023",

doi = "10.1007/s00374-023-01731-7",

language = "English",

journal = "Biology and Fertility of Soils",

issn = "0178-2762",

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TY - JOUR

T1 - Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping

AU - Su, Lv

AU - Li, Huatai

AU - Wang, Jing

AU - Gao, Wenting

AU - Shu, Xia

AU - Sun, Xiting

AU - Wang, Kesu

AU - Duan, Yan

AU - Liu, Yunpeng

AU - Kuramae, Eiko E.

AU - Zhang, Ruifu

AU - Shen, Biao

N1 - Data archiving: Data with publication

PY - 2023

Y1 - 2023

N2 - The bacteria that dominate and become enriched in the rhizosphere during continuous cropping are of increasing interest, as they can greatly adapt to the rhizosphere. However, there are still little knowledge about the general composition and function of these bacteria. In this study, we planted tomatoes in three different soils for three planting cycles and used both high-throughput sequencing and culture-dependent workflows. Despite significant differences in bacterial communities from the initial soils, we observed a similar succession in the rhizosphere bacterial community compositions. We identified certain bacteria that were gradually enriched and potentially beneficial, such as Rhizobium and Flavobacterium. However, some other potentially beneficial bacteria, such as Massilia and Lysobacter, were gradually depleted. Additionally, we found that predicted functions related to xenobiotic biodegradation, nutrient metabolism and antibiotic biosynthesis were enriched in different rhizosphere soils. Beijerinckia fluminensis GR2, which was gradually enriched in all tested soils, significantly inhibited the growth of Ralstonia solanacearum and protected the host from infection. Our study provides new insights into the assembly mechanism of gradually enriched bacteria and their role as plant-beneficial microbes that adapt well to the rhizosphere.

AB - The bacteria that dominate and become enriched in the rhizosphere during continuous cropping are of increasing interest, as they can greatly adapt to the rhizosphere. However, there are still little knowledge about the general composition and function of these bacteria. In this study, we planted tomatoes in three different soils for three planting cycles and used both high-throughput sequencing and culture-dependent workflows. Despite significant differences in bacterial communities from the initial soils, we observed a similar succession in the rhizosphere bacterial community compositions. We identified certain bacteria that were gradually enriched and potentially beneficial, such as Rhizobium and Flavobacterium. However, some other potentially beneficial bacteria, such as Massilia and Lysobacter, were gradually depleted. Additionally, we found that predicted functions related to xenobiotic biodegradation, nutrient metabolism and antibiotic biosynthesis were enriched in different rhizosphere soils. Beijerinckia fluminensis GR2, which was gradually enriched in all tested soils, significantly inhibited the growth of Ralstonia solanacearum and protected the host from infection. Our study provides new insights into the assembly mechanism of gradually enriched bacteria and their role as plant-beneficial microbes that adapt well to the rhizosphere.

KW - Beneficial microbes

KW - Continuous cropping system

KW - Ralstonia solanacearum

KW - Rhizosphere bacteria

KW - Soil types

U2 - 10.1007/s00374-023-01731-7

DO - 10.1007/s00374-023-01731-7

M3 - Article

AN - SCOPUS:85160089245

SN - 0178-2762

JO - Biology and Fertility of Soils

JF - Biology and Fertility of Soils

ER -

Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping

Abstract

Keywords

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