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Han C, Cheng Q, Du X, Liang L, Fan G, Xie J, Wang X, Tang Y, Zhang H, Hu C, Zhao X. Selenium in soil enhances resistance of oilseed rape to Sclerotinia sclerotiorum by optimizing the plant microbiome. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5768-5789. [PMID: 38809805 DOI: 10.1093/jxb/erae238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024]
Abstract
Plants can recruit beneficial microbes to enhance their ability to resist disease. It is well established that selenium is beneficial in plant growth, but its role in mediating microbial disease resistance remains poorly understood. Here, we investigated the correlation between selenium, oilseed rape rhizosphere microbes, and Sclerotinia sclerotiorum. Soil application of 0.5 and 1.0 mg kg-1 selenium [selenate Na2SeO4, Se(VI) or selenite Na2SeO3, Se(IV)] significantly increased the resistance of oilseed rape to Sclerotinia sclerotiorum compared with no selenium application, with a disease inhibition rate higher than 20% in Se(VI)0.5, Se(IV)0.5 and Se(IV)1.0 mg kg-1 treatments. The disease resistance of oilseed rape was related to the presence of rhizosphere microorganisms and beneficial bacteria isolated from the rhizosphere inhibited Sclerotinia stem rot. Burkholderia cepacia and the synthetic community consisting of Bacillus altitudinis, Bacillus megaterium, Bacillus cereus, Bacillus subtilis, Bacillus velezensis, Burkholderia cepacia, and Flavobacterium anhui enhanced plant disease resistance through transcriptional regulation and activation of plant-induced systemic resistance. In addition, inoculation of isolated bacteria optimized the bacterial community structure of leaves and enriched beneficial microorganisms such as Bacillus, Pseudomonas, and Sphingomonas. Bacillus isolated from the leaves were sprayed on detached leaves, and it also performed a significant inhibition effect on Sclerotinia sclerotiorum. Overall, our results indicate that selenium improves plant rhizosphere microorganisms and increase resistance to Sclerotinia sclerotiorum in oilseed rape.
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Affiliation(s)
- Chuang Han
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/ National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang 725000, China
| | - Qin Cheng
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoping Du
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/ National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang 725000, China
| | - Lianming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Guocheng Fan
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou 350013, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yanni Tang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengxiao Hu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohu Zhao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/ National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang 725000, China
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Zhang B, Ma Y, Duan W, Fan Q, Sun J. Pinewood nematode induced changes in the assembly process of gallery microbiomes benefit its vector beetle's development. Microbiol Spectr 2024:e0141224. [PMID: 39258937 DOI: 10.1128/spectrum.01412-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/03/2024] [Indexed: 09/12/2024] Open
Abstract
Microbiomes play crucial roles in insect adaptation, especially under stress such as pathogen invasion. Yet, how beneficial microbiomes assemble remains unclear. The wood-boring beetle Monochamus alternatus, a major pest and vector of the pine wilt disease (PWD) nematode, offers a unique model. We conducted controlled experiments using amplicon sequencing (16S rRNA and ITS) within galleries where beetles and microbes interact. PWD significantly altered bacterial and fungal communities, suggesting distinct assembly processes. Deterministic factors like priority effects, host selection, and microbial interactions shaped microbiome composition, distinguishing healthy from PWN-infected galleries. Actinobacteria, Firmicutes, and Ophiostomataceae emerged as potentially beneficial, aiding beetle's development and pathogen resistance. This study unveils how nematode-induced changes in gallery microbiomes influence beetle's development, shedding light on microbiome assembly amid insect-pathogen interactions. Insights gleaned enhance understanding of PWD spread and suggest novel management strategies via microbiome manipulation.IMPORTANCEThis study explores the assembly process of gallery microbiomes associated with a wood-boring beetles, Monochamus alternatus, a vector of the pine wilt disease (PWD). By conducting controlled comparison experiments and employing amplicon approaches, the study reveals significant changes in taxonomic composition and functional adaptation of bacterial and fungal communities induced by PWD. It identifies deterministic processes, including priority effects, host selection, and microbial interactions, as major drivers in microbiome assembly. Additionally, the study highlights the presence of potentially beneficial microbes such as Actinobacteria, Firmicutes, and Ophiostomataceae, which could enhance beetle development and resistance to pathogens. These findings shed light on the intricate interplay among insects, microbiomes, and pathogens, contributing to a deeper understanding of PWD prevalence and suggesting innovative management strategies through microbiome manipulation.
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Affiliation(s)
- Bin Zhang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yafei Ma
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Wenzhao Duan
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Qi Fan
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jianghua Sun
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Gao W, Chen X, He J, Sha A, Ren Y, Wu P, Li Q. The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants. Front Microbiol 2024; 15:1424687. [PMID: 39314884 PMCID: PMC11417686 DOI: 10.3389/fmicb.2024.1424687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/22/2024] [Indexed: 09/25/2024] Open
Abstract
Introduction Thus far, the impact of kaolin mining activities on the surrounding native plants and rhizosphere microecology has not been fully understood. Methods In this study, we used 16S rRNA high-throughput sequencing to examine the impact of kaolin mining on the rhizosphere bacterial communities and functions of three local plant species: Conyza bonariensis, Artemisia annua, and Dodonaea viscosa. Results The results showed that kaolin mining significantly reduced the diversity of rhizosphere bacteria in these plants, as indicated by the Shannon, Simpson, Chao1, and observed species indices (p < 0.05). Kaolin mining had an impact on the recruitment of three rhizosphere bacteria native to the area: Actinoplanes, RB41, and Mycobacterium. These bacteria were found to be more abundant in the rhizosphere soil of three local plants than in bulk soil, yet the mining of kaolin caused a decrease in their abundance (p < 0.05). Interestingly, Ralstonia was enriched in the rhizosphere of these plants found in kaolin mining areas, suggesting its resilience to environmental stress. Furthermore, the three plants had different dominant rhizosphere bacterial populations in kaolin mining areas, such as Nocardioides, Pseudarthrobacter, and Sphingomonas, likely due to the unique microecology of the plant rhizosphere. Kaolin mining activities also caused a shift in the functional diversity of rhizosphere bacteria in the three local plants, with each plant displaying different functions to cope with kaolin mining-induced stress, such as increased abundance of the GlpM family and glucan-binding domain. Discussion This study is the first to investigate the effects of kaolin mining on the rhizosphere microecology of local plants, thus contributing to the establishment of soil microecological health monitoring indicators to better control soil pollution in kaolin mining areas.
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Affiliation(s)
- Wei Gao
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Xiaodie Chen
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Jing He
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Yuanhang Ren
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Qiang Li
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
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Liu W, Zhang Z, Zhang B, Zhu Y, Zhu C, Chen C, Zhang F, Liu F, Ai J, Wang W, Kong W, Xiang H, Wang W, Gong D, Meng D, Zhu L. Role of bacterial pathogens in microbial ecological networks in hydroponic plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1403226. [PMID: 39290732 PMCID: PMC11405252 DOI: 10.3389/fpls.2024.1403226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/15/2024] [Indexed: 09/19/2024]
Abstract
Plant-associated microbial communities are crucial for plant growth and health. However, assembly mechanisms of microbial communities and microbial interaction patterns remain elusive across vary degrees of pathogen-induced diseases. By using 16S rRNA high-throughput sequencing technology, we investigated the impact of wildfire disease on the microbial composition and interaction network in plant three different compartments. The results showed that pathogen infection significantly affect the phyllosphere and rhizosphere microbial community. We found that the primary sources of microbial communities in healthy and mildly infected plants were from the phyllosphere and hydroponic solution community. Mutual exchanges between phyllosphere and rhizosphere communities were observed, but microbial species migration from the leaf to the root was rarely observed in severely infected plants. Moreover, wildfire disease reduced the diversity and network complexity of plant microbial communities. Interactions among pathogenic bacterial members suggested that Caulobacter and Bosea might be crucial "pathogen antagonists" inhibiting the spread of wildfire disease. Our study provides deep insights into plant pathoecology, which is helpful for the development of novel strategies for phyllosphere disease prediction or prevention.
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Affiliation(s)
- Wenyi Liu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhihua Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Bin Zhang
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Yi Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Chongwen Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Chaoyong Chen
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Fangxu Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Feng Liu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jixiang Ai
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Wei Wang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Wuyuan Kong
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Haoming Xiang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Weifeng Wang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Daoxin Gong
- College of Environment and Ecology, Hunan Agricultural University, Changsha, China
| | - Delong Meng
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Li Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
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Angelotti F, Hamada E, Bettiol W. A Comprehensive Review of Climate Change and Plant Diseases in Brazil. PLANTS (BASEL, SWITZERLAND) 2024; 13:2447. [PMID: 39273931 PMCID: PMC11396851 DOI: 10.3390/plants13172447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/07/2024] [Accepted: 07/30/2024] [Indexed: 09/15/2024]
Abstract
Analyzing the impacts of climate change on phytosanitary problems in Brazil is crucial due to the country's special role in global food security as one of the largest producers of essential commodities. This review focuses on the effects of climate change on plant diseases and discusses its main challenges in light of Brazil's diverse agricultural landscape. To assess the risk of diseases caused by fungi, bacteria, viruses, oomycetes, nematodes, and spiroplasms, we surveyed 304 pathosystems across 32 crops of economic importance from 2005 to 2022. Results show that diseases caused by fungi account for 79% of the pathosystems evaluated. Predicting the occurrence of diseases in a changing climate is a complex challenge, and the continuity of this work is strategic for Brazil's agricultural defense. The future risk scenarios analyzed here aim to help guide disease mitigation for cropping systems. Despite substantial progress and ongoing efforts, further research will be needed to effectively prevent economic and environmental damage.
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Affiliation(s)
- Francislene Angelotti
- Embrapa Semi-Arid, Brazilian Agricultural Research Corporation, Petrolina 56302-970, Brazil
| | - Emília Hamada
- Embrapa Environment, Brazilian Agricultural Research Corporation, Jaguariúna 13918-110, Brazil
| | - Wagner Bettiol
- Embrapa Environment, Brazilian Agricultural Research Corporation, Jaguariúna 13918-110, Brazil
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Chaudhary P, Bhattacharjee A, Khatri S, Dalal RC, Kopittke PM, Sharma S. Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms. Microbiol Res 2024; 289:127880. [PMID: 39236602 DOI: 10.1016/j.micres.2024.127880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 05/23/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024]
Abstract
Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.
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Affiliation(s)
- Priya Chaudhary
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shivani Khatri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ram C Dalal
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Peter M Kopittke
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Shilpi Sharma
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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Zhao Z, Gao B, Yang C, Wu Y, Sun C, Jiménez N, Zheng L, Huang F, Ren Z, Yu Z, Yu C, Zhang J, Cai M. Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application. ENVIRONMENT INTERNATIONAL 2024; 190:108831. [PMID: 38936065 DOI: 10.1016/j.envint.2024.108831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".
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Affiliation(s)
- Zhengzheng Zhao
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Bingqi Gao
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Chongrui Yang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Yushi Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Chen Sun
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Núria Jiménez
- Department of Chemical Engineering, Vilanova i la Geltrú School of Engineering (EPSEVG), Universitat Politècnica de Catalunya BarcelonaTech, Vilanova i la Geltrú 08800, Spain
| | - Longyu Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Feng Huang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Zhuqing Ren
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China; Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ziniu Yu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jibin Zhang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China.
| | - Minmin Cai
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China.
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Uwaremwe C, Bao W, Daoura BG, Mishra S, Zhang X, Shen L, Xia S, Yang X. Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species. Int Microbiol 2024; 27:1231-1247. [PMID: 38158469 DOI: 10.1007/s10123-023-00470-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss. METHODS In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection. RESULTS Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification. CONCLUSIONS Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.
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Affiliation(s)
- Constantine Uwaremwe
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
| | - Wenjie Bao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bachir Goudia Daoura
- Department of Biology, Faculty of Sciences and Technology, Dan Dicko Dankoulodo University, POBox, 465, Maradi, Niger
| | - Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingjie Shen
- College of Biology and Chemistry, Pu'er University, Pu'er, 665000, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China.
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Liu Q, Zhu J, Sun M, Song L, Ke M, Ni Y, Fu Z, Qian H, Lu T. Multigenerational Adaptation Can Enhance the Pathogen Resistance of Plants via Changes in Rhizosphere Microbial Community Assembly. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14581-14591. [PMID: 38957087 DOI: 10.1021/acs.jafc.4c02200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Plants withstand pathogen attacks by recruiting beneficial bacteria to the rhizosphere and passing their legacy on to the next generation. However, the underlying mechanisms involved in this process remain unclear. In our study, we combined microbiomic and transcriptomic analyses to reveal how the rhizosphere microbiome assembled through multiple generations and defense-related genes expressed in Arabidopsis thaliana under pathogen attack stress. Our results showed that continuous exposure to the pathogen Pseudomonas syringae pv tomato DC3000 led to improved growth and increased disease resistance in a third generation of rps2 mutant Arabidopsis thaliana. It could be attributed to the enrichment of specific rhizosphere bacteria, such as Bacillus and Bacteroides. Pathways associated with plant immunity and growth in A. thaliana, such as MAPK signaling pathways, phytohormone signal transduction, ABC transporter proteins, and flavonoid biosynthesis, were activated under the influence of rhizosphere bacterial communities. Our findings provide a scientific basis for explaining the relationship between beneficial microbes and defense-related gene expression. Understanding microbial communities and the mechanisms involved in plant responses to disease can contribute to better plant management and reduction of pesticide use.
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Affiliation(s)
- Qiuyun Liu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jichao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mengyan Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lin Song
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yinhua Ni
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
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Wang X, Lu T, Yang B, Cao J, Li M. Exposure to resorcinol bis (diphenyl phosphate) induces colonization of alien microorganisms with potential impacts on the gut microbiota and metabolic disruption in male zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172892. [PMID: 38719053 DOI: 10.1016/j.scitotenv.2024.172892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
Organophosphate esters (OPEs) have been demonstrated to induce various forms of toxicity in aquatic organisms. However, a scarcity of evidence impedes the conclusive determination of whether OPEs manifest sex-dependent toxic effects. Here, we investigated the effects of tris (1-chloro-2-propyl) phosphate (TCPP) and resorcinol bis (diphenyl phosphate) (RDP) on the intestines of both female and male zebrafish. The results indicated that, in comparison to TCPP, RDP induced more pronounced intestinal microstructural damage and oxidative stress, particularly in male zebrafish. 16S rRNA sequencing and metabolomics revealed significant alterations in the species richness and oxidative stress-related metabolites in the intestinal microbiota of zebrafish under exposure to both TCPP and RDP, manifesting gender-specific effects. Based on differential species analysis, we defined invasive species and applied invasion theory to analyze the reasons for changes in the male fish intestinal community. Correlation analysis demonstrated that alien species may have potential effects on metabolism. Overall, this study reveals a pronounced gender-dependent impact on both the intestinal microbiota and metabolic disruptions of zebrafish due to OPEs exposure and offers a novel perspective on the influence of pollutants on intestinal microbial communities and metabolism.
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Affiliation(s)
- Xinwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ting Lu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Jiangsu Environmental Engineering Technology Co. Ltd, Nanjing, Jiangsu 210019, China
| | - Bin Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jing Cao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mei Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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11
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Daraz U, Erhunmwunse AS, Dubeux JCB, Mackowiak C, Liao HL, Wang XB. Soil fungal community structure and function response to rhizoma perennial peanut cultivars. BMC PLANT BIOLOGY 2024; 24:582. [PMID: 38898415 PMCID: PMC11186081 DOI: 10.1186/s12870-024-05209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.
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Affiliation(s)
- Umar Daraz
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | | | - José C B Dubeux
- North Florida Research and Education Center, University of Florida, Marianna, FL, USA
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China.
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Jin X, Jia H, Ran L, Wu F, Liu J, Schlaeppi K, Dini-Andreote F, Wei Z, Zhou X. Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates. Nat Commun 2024; 15:5125. [PMID: 38879580 PMCID: PMC11180119 DOI: 10.1038/s41467-024-49218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/27/2024] [Indexed: 06/19/2024] Open
Abstract
The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.
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Affiliation(s)
- Xue Jin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Huiting Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Lingyi Ran
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China.
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13
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Wei F, Feng Z, Yang C, Zhao L, Zhang Y, Zhou J, Feng H, Zhu H, Xu X. Genetic control of rhizosphere microbiome of the cotton plants under field conditions. Appl Microbiol Biotechnol 2024; 108:371. [PMID: 38861165 PMCID: PMC11166756 DOI: 10.1007/s00253-024-13143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 06/12/2024]
Abstract
Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.
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Affiliation(s)
- Feng Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zili Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Chuanzhen Yang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yalin Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Jinglong Zhou
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongjie Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Heqin Zhu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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14
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Cunha IDCMD, Silva AVRD, Boleta EHM, Pellegrinetti TA, Zagatto LFG, Zagatto SDSS, Chaves MGD, Mendes R, Patreze CM, Tsai SM, Mendes LW. The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype. Microbiol Res 2024; 283:127706. [PMID: 38574431 DOI: 10.1016/j.micres.2024.127706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.
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Affiliation(s)
- Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Luiz de Queiroz College of Agriculture ESALQ, University of São Paulo USP, Piracicaba, SP 13418-900, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Eduardo Henrique Marcandalli Boleta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Luis Felipe Guandalin Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Department of Terrestrial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen NL-6700 AB, the Netherlands
| | - Solange Dos Santos Silva Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna 18020-000, Brazil
| | - Camila Maistro Patreze
- Institute of Biosciences, Federal University of the State of Rio de Janeiro, Rio de Janeiro, RJ 22290-240, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil.
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15
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Kwon KM, Kim EH, Sim KH, Lee YJ, Kang EJ, Han KH, Jin JS, Kim DK, Ahn JH, Hwang IH. Phenylacetic acid, an anti-vaginitis metabolite produced by the vaginal symbiotic bacterium Chryseobacterium gleum. Sci Rep 2024; 14:12226. [PMID: 38806600 PMCID: PMC11133378 DOI: 10.1038/s41598-024-62947-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
The human microbiome contains genetic information that regulates metabolic processes in response to host health and disease. While acidic vaginal pH is maintained in normal conditions, the pH level increases in infectious vaginitis. We propose that this change in the vaginal environment triggers the biosynthesis of anti-vaginitis metabolites. Gene expression levels of Chryseobacterium gleum, a vaginal symbiotic bacterium, were found to be affected by pH changes. The distinctive difference in the metabolic profiles between two C. gleum cultures incubated under acidic and neutral pH conditions was suggested to be an anti-vaginitis molecule, which was identified as phenylacetic acid (PAA) by spectroscopic data analysis. The antimicrobial activity of PAA was evaluated in vitro, showing greater toxicity toward Gardnerella vaginalis and Candida albicans, two major vaginal pathogens, relative to commensal Lactobacillus spp. The activation of myeloperoxidase, prostaglandin E2, and nuclear factor-κB, and the expression of cyclooxygenase-2 were reduced by an intravaginal administration of PAA in the vaginitis mouse model. In addition, PAA displayed the downregulation of mast cell activation. Therefore, PAA was suggested to be a messenger molecule that mediates interactions between the human microbiome and vaginal health.
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Affiliation(s)
- Kang Mu Kwon
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Eun-Hye Kim
- Department of Korean Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Kyeong Hwa Sim
- Department of Pharmacology, School of Medicine, Daegu Catholic University, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu, 42472, Republic of Korea
| | - Youn Ju Lee
- Department of Pharmacology, School of Medicine, Daegu Catholic University, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu, 42472, Republic of Korea
| | - Eun-Ji Kang
- Department of Food and Biotechnology, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Dae Keun Kim
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
- Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea
| | - Ji-Hye Ahn
- Department of Korean Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea.
| | - In Hyun Hwang
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea.
- Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea.
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16
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Hirpara KR, Hinsu AT, Kothari RK. Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India. Sci Rep 2024; 14:10525. [PMID: 38720057 PMCID: PMC11079051 DOI: 10.1038/s41598-024-61343-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/05/2024] [Indexed: 05/12/2024] Open
Abstract
The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.
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Affiliation(s)
- Krunal R Hirpara
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
| | - Ankit T Hinsu
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
- Royal Veterinary College, London, AL9 7TA, UK
| | - Ramesh K Kothari
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.
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Zhang P, Huguet-Tapia J, Peng Z, Liu S, Obasa K, Block AK, White FF. Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani. Appl Environ Microbiol 2024; 90:e0224523. [PMID: 38319098 PMCID: PMC10952491 DOI: 10.1128/aem.02245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. Crenshaw (En-Cren), which was isolated from the generalist fungal pathogen Rhizoctonia solani, and examined the genetic potential of the bacterium with regard to the phenotypic traits associated with the fungus. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while some common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved.IMPORTANCEThe genome characterization and comparative genomics analysis of Enterobacter sp. Crenshaw provided the foundation and resources for a better understanding of the ecology and evolution of this endohyphal bacteria in the rhizosphere. The ability to produce indole-3-acetic acid and phenylacetic acid may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction, which have yet to be explored.
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Affiliation(s)
- Peiqi Zhang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jose Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Ken Obasa
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- High Plains Plant Disease Diagnostic Lab, Texas A&M AgriLife Extension Service, Amarillo, Texas, USA
| | - Anna K. Block
- Chemistry Research Unit, US Department of Agriculture-Agricultural Research Service, Gainesville, Florida, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Russ L, Andreo Jimenez B, Nijhuis E, Postma J. Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities. FEMS Microbiol Ecol 2024; 100:fiae024. [PMID: 38499445 PMCID: PMC10959553 DOI: 10.1093/femsec/fiae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/06/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024] Open
Abstract
Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase the suppression potential in agricultural soils is via the addition of organic amendments. This microbe-mediated phenomenon, although not fully understood, prompted our study to explore the microbial taxa and functional properties associated with Rhizoctonia solani disease suppression in sugar beet seedlings after amending soil with a keratin-rich waste stream. Soil samples were analyzed using shotgun metagenomics sequencing. Results showed that both amended soils were enriched in bacterial families found in disease suppressive soils before, indicating that the amendment of keratin-rich material can support the transformation into a suppressive soil. On a functional level, genes encoding keratinolytic enzymes were found to be abundant in the keratin-amended samples. Proteins enriched in amended soils were those potentially involved in the production of secondary metabolites/antibiotics, motility, keratin-degradation, and contractile secretion system proteins. We hypothesize these taxa contribute to the amendment-induced suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate-a potential virulence factor of R. solani-while simultaneously possessing the ability to metabolize keratin.
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Affiliation(s)
- Lina Russ
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Beatriz Andreo Jimenez
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Els Nijhuis
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joeke Postma
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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19
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Van Gerrewey T, Chung HS. MAPK Cascades in Plant Microbiota Structure and Functioning. J Microbiol 2024; 62:231-248. [PMID: 38587594 DOI: 10.1007/s12275-024-00114-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 04/09/2024]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.
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Affiliation(s)
- Thijs Van Gerrewey
- Plant Biotechnology Research Center, Department of Environmental Technology, Food Technology and Molecular Biotechnology, Ghent University Global Campus, Incheon, 21985, Republic of Korea
| | - Hoo Sun Chung
- Plant Biotechnology Research Center, Department of Environmental Technology, Food Technology and Molecular Biotechnology, Ghent University Global Campus, Incheon, 21985, Republic of Korea.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
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20
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Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. SCIENCE ADVANCES 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria
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21
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Xiao Y, Zhang S, Li H, Teng K, Wu S, Liu Y, Yu F, He Z, Li L, Li L, Meng D, Yin H, Wang Y. Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2024; 15:1325141. [PMID: 38434434 PMCID: PMC10904623 DOI: 10.3389/fpls.2024.1325141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.
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Affiliation(s)
- Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Sai Zhang
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Hongguang Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Kai Teng
- Xiangxi Tobacco Co Hunan Prov, Changsha, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, China
| | - Yongbin Liu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Fahui Yu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Zhihong He
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Lijuan Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yujie Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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22
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Vlasselaer L, Crauwels S, Lievens B, De Coninck B. Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms. FEMS Microbiol Ecol 2024; 100:fiae010. [PMID: 38317643 PMCID: PMC10872686 DOI: 10.1093/femsec/fiae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024] Open
Abstract
Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.
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Affiliation(s)
- Liese Vlasselaer
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Sam Crauwels
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Bart Lievens
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Barbara De Coninck
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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23
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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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24
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Costa LSAS, de Faria MR, Chiaramonte JB, Mendes LW, Sepo E, de Hollander M, Fernandes JMC, Carrión VJ, Bettiol W, Mauchline TH, Raaijmakers JM, Mendes R. Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness. ENVIRONMENTAL MICROBIOME 2023; 18:85. [PMID: 38053159 PMCID: PMC10696838 DOI: 10.1186/s40793-023-00529-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/19/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. RESULTS The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. CONCLUSION Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.
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Affiliation(s)
- Lilian S Abreu Soares Costa
- Embrapa Environment, Jaguariúna, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | | | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Edis Sepo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Departamento de Microbiología y Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | | | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
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25
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Ma CY, Zhang W, Luo DL, Jiang HJ, Wu XH, Sun K, Dai CC. Fungal endophyte promotes plant growth and disease resistance of Arachis hypogaea L. by reshaping the core root microbiome under monocropping conditions. Microbiol Res 2023; 277:127491. [PMID: 37769598 DOI: 10.1016/j.micres.2023.127491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Fungal endophytes play critical roles in helping plants adapt to adverse environmental conditions. The root endophyte Phomopsis liquidambaris can promote the growth and disease control of peanut plants grown under monocropping systems; however, how such beneficial traits are produced is largely unknown. Since the plant endophytic microbiome is directly linked to plant growth and health, and the composition of which has been found to be potentially influenced by microbial inoculants, this study aims to clarify the roles of root endophytic bacterial communities in P. liquidambaris-mediated plant fitness enhancement under monocropping conditions. Here, we found that P. liquidambaris inoculation induced significant changes in the root bacterial community: enriching some beneficial bacteria such as Bradyrhizobium sp. and Streptomyces sp. in the roots, and improving the core microbial-based interaction network. Next, we assembled and simplified a synthetic community (SynII) based on P. liquidambaris-derived key taxa, including Bacillus sp. HB1, Bacillus sp. HB9, Burkholderia sp. MB7, Pseudomonas sp. MB2, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Furthermore, the application of the simplified synthetic community suppressed root rot caused by Fusarium oxysporum, promoted plant growth, and increased peanut yields under continuous monocropping conditions. The resistance of synII to F. oxysporum is related to the increased activity of defense enzymes. In addition, synII application significantly increased shoot and root biomass, and yield by 35.56%, 81.19%, and 34.31%, respectively. Collectively, our results suggest that the reshaping of root core microbiota plays an important role in the probiotic-mediated adaptability of plants under adverse environments.
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Affiliation(s)
- Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xiao-Han Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.
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26
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Bautista D, García D, Dávila L, Caro‐Quintero A, Cotes AM, González A, Zuluaga AP. Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana). ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:757-768. [PMID: 37675926 PMCID: PMC10667652 DOI: 10.1111/1758-2229.13195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023]
Abstract
Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.
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Affiliation(s)
- Daniel Bautista
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
- Department of Biological SciencesUniversidad de Los AndesBogotáColombia
| | - Diana García
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| | - Lorena Dávila
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| | | | - Alba Marina Cotes
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| | - Adriana González
- Department of BiologyUniversidad Nacional de ColombiaBogotáColombia
| | - A. Paola Zuluaga
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
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27
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Sipriyadi S, Khairina Y, Masrukhin M, Yulandi A, Wibowo RH, Nisa DT. Bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Can J Microbiol 2023; 69:439-448. [PMID: 37364294 DOI: 10.1139/cjm-2022-0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The rhizosphere is a narrow soil area directly affected by plant root exudates. Microbes inhabiting the rhizosphere have been widely studied for their beneficial effects on plant nutrition, growth, and disease prevention. Many factors affect the rhizosphere microbial composition, including plant pathogen infection. Here, we analyzed the bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Soil samples were collected from rhizosphere and non-rhizosphere areas of fungi-infected A. titanum. The 16S metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The results showed that the phylum Firmicutes was prevalent in the rhizosphere, whereas the phyla Proteobacteria, Acidobacteria, and Actinobacteria were limited. Some major fungal genera were isolated from infected tubers and rhizosphere soil of A. titanum, including Trichoderma sp., Aspergillus sp., Perenniporia sp., and Cerrena sp. The fungal-isolate Aspergillus spp. is a well-known agricultural pest in several reports. While Cerrena sp. was reported to be pathogenic in plants, including the family of Arecaceae. Overall, the data revealed a potential relationship between fungal infections and the dominant bacterial community in the rhizosphere of A. titanum. Additionally, this research may contribute to the development of microbe-based technology to mitigate diseases in A. titanum.
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Affiliation(s)
- Sipriyadi Sipriyadi
- Department of Biology. Faculty of Mathematics and Natural Sciences, Bengkulu University, Bengkulu, Indonesia
| | - Yeni Khairina
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Cibinong 16911, Indonesia
| | - Masrukhin Masrukhin
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Cibinong 16911, Indonesia
| | - Adi Yulandi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Risky Hadi Wibowo
- Department of Biology. Faculty of Mathematics and Natural Sciences, Bengkulu University, Bengkulu, Indonesia
| | - Dhiatama Tauhida Nisa
- Department of Biology. Faculty of Mathematics and Natural Sciences, Bengkulu University, Bengkulu, Indonesia
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Dubey S, Bhattacharjee A, Pradhan S, Kumar A, Sharma S. Composition of fungal communities upon multiple passaging of rhizosphere microbiome for salinity stress mitigation in Vigna radiata. FEMS Microbiol Ecol 2023; 99:fiad132. [PMID: 37838474 DOI: 10.1093/femsec/fiad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/27/2023] [Accepted: 10/13/2023] [Indexed: 10/16/2023] Open
Abstract
The top-down approach of microbiome-mediated rhizosphere engineering has emerged as an eco-friendly approach for mitigating stress and enhancing crop productivity. It has been established to mitigate salinity stress in Vigna radiata using multi-passaging approach. During the process of acclimatization under increasing levels of salinity stress, the structure of rhizospheric microbial community undergoes dynamic changes, while facilitating stress mitigation in plants. In this study, using ITS-based amplicon sequencing, the dynamics of rhizosphere fungal community was unravelled over successive passages under salinity stress in V. radiata. Clear shifts were evident among the fungal community members under stress and non-stress conditions, upon application of acclimatized rhizosphere microbiome in V. radiata across successive passages. These shifts correlated with enhanced plant biometrics and reduced stress marker levels in plant. Significant changes in the fungal community structure were witnessed in the rhizosphere across specific passaging cycles under salinity stress, which possibly facilitated stress mitigation in V. radiata.
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Affiliation(s)
- Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Abhay Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
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Li P, Gu S, Zhu Y, Xu T, Yang Y, Wang Z, Deng X, Wang B, Li W, Mei W, Hu Q. Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot. Front Microbiol 2023; 14:1214167. [PMID: 37779693 PMCID: PMC10540700 DOI: 10.3389/fmicb.2023.1214167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Root rot caused by the fungal pathogen Fusarium sp. poses significant challenges to tobacco cultivation in China, leading to major economic setbacks. The interplay between this pathogen and the wider soil microbial community remains poorly understood. Methods High-throughput sequencing technology was utilized to evaluate soil prokaryotic, fungal, and protistan communities. We compared microbial communities in infected soils to those in healthy soils from the same field. Additionally, the influence of pH on the microbial communities was assessed. Results Infected soils displayed elevated levels of soil nutrients but diminished observed richness across prokaryotic, fungal, and protistan groups. The pathogenic fungi Fusarium solani f sp. eumartii's abundance was notably increased in infected soils. Infection with F. solani significantly altered the soil's microbial community structure and interactions, manifested as a decrease in network scale and the number of keystone species. An evaluation of prokaryotes' role in F. solani's invasion revealed an increased number of connecting nodes in infected soils. Additionally, relationships between predatory protists and fungi were augmented, whereas predation on F. solani declined. Discussion The study underscores the significance of comprehending the interactions among soil microorganisms and brings to light the susceptibility of soil microbial communities to pathogen invasion. It offers insights into the multifaceted relationships and potential vulnerabilities within the soil ecosystem in the context of Fusarium sp. invasion.
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Affiliation(s)
- Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanmei Zhu
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Tianyang Xu
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Yishuai Yang
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhengqiang Wang
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiangdong Deng
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Bin Wang
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Wei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Wenqiang Mei
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Qiulong Hu
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
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He H, Huang J, Zhao Z, Du P, Li J, Xin J, Xu H, Feng W, Zheng X. Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide. Heliyon 2023; 9:e19543. [PMID: 37681179 PMCID: PMC10480658 DOI: 10.1016/j.heliyon.2023.e19543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/06/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Rehmannia glutinosa, a valuable medicinal plant, is threatened by ring rot, a condition that greatly affects its yield and quality. Interactions between plant and the rhizosphere soil microbiome in the context of pathogen invasion are generally more specific, with recruitment of specialized microbes potentially antagonistic to a certain pathogen. Isolation of microorganisms from rhizosphere soil of healthy and ring rot-infected R. glutinosa was carried out to screen antifungal microbes. A strain designated RerS4 isolated from ring rot-infected R. glutinosa rhizosphere soil with strong antifungal activities was selected for further study. RerS4 was taxonomically characterized as the genus Streptomyces according to its morphology and 16S rRNA sequences that were most closely related to Streptomyces racemochromogenes NRRL B-5430T (99.72%) and Streptomyces polychromogenes NBRC 13072T (99.72%). A new lipopeptide isolated from RerS4 showed restrained proliferation, but was devoid of significant antibacterial and antioxidant activity with minimum inhibitory concentration (MIC) values of 20.3 ± 2.5 and 70.8 ± 3.7 μg/mL and half-maximal inhibitory concentration (IC50) values of 23.3 ± 0.8 and 58.8 ± 2.9 μg/mL, respectively. In addition, we report the complete genome sequence of Streptomyces sp. RerS4, which consists of a 7,301,482 bp linear chromosome and a 242,139 bp plasmid. Genome analysis revealed that Streptomyces sp. RerS4 contained 25 biosynthetic gene clusters (BGCs) for secondary metabolites, among which 68% had low similarities with known BGCs, leading us to believe that Streptomyces sp. RerS4 could produce valuable bioactive compounds.
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Affiliation(s)
- Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Jiarui Huang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Zhenzhu Zhao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Pengqiang Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jiansong Li
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou, 318000, China
| | - Jile Xin
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Huifang Xu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
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Tang J, Xiao Y, Xu X, Tang M, Zhang X, Yi Y. Root microbiota alters response to root rot in Rhododendron delavayi Franch. Front Microbiol 2023; 14:1236110. [PMID: 37692401 PMCID: PMC10486992 DOI: 10.3389/fmicb.2023.1236110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Root microbiota have a significant effect on plant health. However, the role of root microbiota in the resistance of Rhododendron against root rot is not known. In this study, we employed amplicon 16S and ITS sequencing to investigate the bacterial and fungal communities associated with four distinct niches (bulk soil, rhizosphere, rhizoplane, and endosphere) of both healthy and diseased Rhododendron plants in the Baili Rhododendron nature reserve in China. The amplicon data analysis identified 182 bacterial genera and 141 fungal genera that were impacted by root rot across all niches. Specifically, the rhizoplane appeared to exert a selective gating effect, resulting in a reduction in the complexity of bacterial communities, but not fungal communities, in wild Rhododendron delavayi Franch roots. Nevertheless, the stress induced by root rot led to alterations in the root microbiota and compromised the gating function of the rhizoplane, thereby significantly increasing the complexity of the bacterial community within the plant root. In the root tissue following root rot outbreak, the relative abundance of the pathogenic species Pezicula brunnea and Diaporthe helianthi was enriched by as much as 6.13% and 1.71%, respectively. These findings provide novel insights into the contribution of enrichment of root-associated microbiota to wild plant hosts under the disease stress of root rot. The root rot-causing pathogenic fungi may interact with beneficial bacteria and induce plants to send out "cry for help" signals, which may encourage the specific assembly of microbiota. In the Rhododendron delavayi Franch root microbiota, we found 23 potentially beneficial microbes. Notably, certain beneficial bacteria, such as Sporolactobacillus and Stenotrophomonas, were found to accumulate in the rhizoplane and endosphere under root rot disease stress. Overall, our results lend support to our hypothesis that Rhododendron recruits protective microbes as a strategy to suppress root rot outbreaks. Future endeavors in isolating beneficial microbes capable of mitigating root rot have the potential to enhance plant resilience against root diseases.
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Affiliation(s)
- Jing Tang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yufeng Xiao
- State Key Laboratory of Plant Physiology and Development in Guizhou Province, Guizhou Normal University, Guiyang, China
| | - Xiaorong Xu
- State Key Laboratory of Plant Physiology and Development in Guizhou Province, Guizhou Normal University, Guiyang, China
| | - Ming Tang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Ximin Zhang
- State Key Laboratory of Plant Physiology and Development in Guizhou Province, Guizhou Normal University, Guiyang, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
- State Key Laboratory of Plant Physiology and Development in Guizhou Province, Guizhou Normal University, Guiyang, China
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32
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Li X, Chen D, Carrión VJ, Revillini D, Yin S, Dong Y, Zhang T, Wang X, Delgado-Baquerizo M. Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections. Nat Commun 2023; 14:5090. [PMID: 37607924 PMCID: PMC10444831 DOI: 10.1038/s41467-023-40810-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.
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Affiliation(s)
- Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dele Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
| | - Daniel Revillini
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.
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Li R, Ren C, Wu L, Zhang X, Mao X, Fan Z, Cui W, Zhang W, Wei G, Shu D. Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield. ENVIRONMENTAL RESEARCH 2023; 231:116194. [PMID: 37217131 DOI: 10.1016/j.envres.2023.116194] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.
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Affiliation(s)
- Ruochen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Chengyao Ren
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Likun Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Xinxin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Xinyi Mao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Zhen Fan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Weili Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang, 150086, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
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Mendes LW, Raaijmakers JM, de Hollander M, Sepo E, Gómez Expósito R, Chiorato AF, Mendes R, Tsai SM, Carrión VJ. Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:68. [PMID: 37537681 PMCID: PMC10401788 DOI: 10.1186/s40793-023-00524-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. RESULTS Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. CONCLUSION Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.
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Affiliation(s)
- Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP, 13416-000, Brazil.
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.
| | - Jos M Raaijmakers
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mattias de Hollander
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Edis Sepo
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Ruth Gómez Expósito
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Alisson Fernando Chiorato
- Centro de Análises e Pesquisa Tecnológica do Agronegócio dos Grãos e Fibras, Instituto Agronômico IAC, Campinas, 130001-970, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna, 18020-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP, 13416-000, Brazil
| | - Victor J Carrión
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.
- Institute of Biology, Leiden University, Leiden, the Netherlands.
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain.
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Peng M, Jiang Z, Zhou F, Wang Z. From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants. Front Microbiol 2023; 14:1169809. [PMID: 37426022 PMCID: PMC10327291 DOI: 10.3389/fmicb.2023.1169809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.
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Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Zhihui Jiang
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Fangzhen Zhou
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Zhiyong Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
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36
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Yang F, Jiang H, Chang G, Liang S, Ma K, Cai Y, Tian B, Shi X. Effects of Rhizosphere Microbial Communities on Cucumber Fusarium wilt Disease Suppression. Microorganisms 2023; 11:1576. [PMID: 37375078 DOI: 10.3390/microorganisms11061576] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Cucumber Fusarium wilt is a worldwide soil-borne disease that seriously restricts the yield and quality of cucumber. The rhizosphere soil microbiome, as the first line of defense against pathogens invading plant roots, plays a key role in rhizosphere immune formation and function. The purpose of this study was to reveal the key microecological factors and dominant microbial flora affecting cucumber resistance and susceptibility to Fusarium wilt by analyzing the physical and chemical properties and microbial flora of rhizosphere soil with different degrees of susceptibility and resistance to cucumber Fusarium wilt, thereby laying a foundation to establish cucumber resistance to the Fusarium wilt rhizosphere core microbiome. Firstly, Illumina Miseq sequencing technology was used to evaluate the physical and chemical properties and microbial groups of cucumber rhizosphere soil at different health levels, and the key environmental factors and microbial factors related to cucumber Fusarium wilt were screened out. Subsequently, PICRUSt2 and FUNGuild were used to predict the functions of rhizosphere bacteria and fungi. Combined with functional analysis, the possible interactions among soil physical and chemical properties, cucumber rhizosphere microorganisms, and Fusarium wilt were summarized. The results showed that the available potassium content in the rhizosphere soil of healthy cucumber decreased by 10.37% and 0.56%, respectively, compared with the rhizosphere soil of severely susceptible cucumber and mildly susceptible cucumber. Exchangeable calcium content increased by 25.55% and 5.39%; the α diversity Chao1 index of bacteria and fungi in the rhizosphere soil of healthy cucumber was significantly lower than that in the rhizosphere soil of seriously infected cucumber, and the MBC content of its physical and chemical properties was also significantly lower than that in the rhizosphere soil of seriously infected cucumber. There was no significant difference in the Shannon and Simpson diversity indexes between healthy cucumber rhizosphere soil and seriously infected cucumber rhizosphere soil. The results of the β diversity analysis showed that the bacterial and fungal community structure of healthy cucumber rhizosphere soil was significantly different from that of severely and mildly infected cucumber rhizosphere soil. At the genus level, through statistical analysis, LEfSe analysis, and RDA analysis, the key bacterial and fungal genera with potential biomarker values were screened out as SHA_26, Subgroup_22, MND1, Aeromicrobium, TM7a, Pseudorhodoplanes, Kocuria, Chaetomium, Fusarium, Olpidium, and Scopulariopsis, respectively. The bacteria SHA_26, Subgroup_22, and MND1 related to cucumber Fusarium wilt inhibition belong to Chloroflexi, Acidobacteriota, and Proteobacteria, respectively. Chaetomiacea belongs to Sordariomycates. The results of functional prediction showed that changes to the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in the bacterial microbiota were concentrated in tetracycline biosynthesis, selenocompound metabolism, lipopolysaccharide biosynthesis, etc., which were mainly involved in the metabolism of terpenoids and polyketides, energy metabolism, metabolism of other amino acids, glycan biosynthesis and metabolism, lipid metabolism, cell growth and death, transcription, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The difference in fungi was mainly dung saprotroph-ectomycorrhizal-soil saprotroph-wood saprotroph. Through the correlation analysis and functional predictions of the key environmental factors, microbial flora, and cucumber health index in cucumber rhizosphere soil, we determined that the inhibition of cucumber Fusarium wilt was a synergistic effect of environmental factors and microbial flora, and a model diagram was drawn to briefly explain its mechanism. This work will provide a basis for the biological control of cucumber Fusarium wilt in the future.
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Affiliation(s)
- Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Huayan Jiang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gaozheng Chang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Shen Liang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Kai Ma
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yuxin Cai
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Baoming Tian
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xuanjie Shi
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
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Hong S, Yuan X, Yang J, Yang Y, Jv H, Li R, Jia Z, Ruan Y. Selection of rhizosphere communities of diverse rotation crops reveals unique core microbiome associated with reduced banana Fusarium wilt disease. THE NEW PHYTOLOGIST 2023; 238:2194-2209. [PMID: 36797661 DOI: 10.1111/nph.18816] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/10/2023] [Indexed: 05/04/2023]
Abstract
Crop rotation can assemble distinct core microbiota as functionally specific barriers against the invasion of banana Fusarium oxysporum pathogens. However, the taxonomic identity of rotation-unique core taxa and their legacy effects are poorly understood under field conditions. Pepper and eggplant rotations were employed to reveal rotation crop- and banana-unique antagonistic core taxa by in situ tracking of the soil microbiome assembly patterns for 2 yr. The rotation crop-unique antagonistic taxa were isolated and functionally verified by culture-dependent techniques, high-throughput sequencing, and pot experiments. Pepper and eggplant rotations resulted in eight and one rotation-unique antagonistic core taxa out of 12 507 microbial taxa, respectively. These nine antagonistic taxa were retained the following year and significantly decreased banana wilt disease incidence via legacy effects, although the cultivated strains were exclusively of the genera Bacillus and Pseudomonas. The fermentation broth and volatiles of these two taxa showed strong antagonistic activity, and pot experiments demonstrated high suppression of wilt disease and significant promotion of banana growth. Our study provides a mechanistic understanding of the identification of rotation crop-unique antagonistic taxa and highlights the importance of targeted cultivation of beneficial microorganisms for optimizing crop rotation-based scenarios in support of banana agriculture sustainability.
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Affiliation(s)
- Shan Hong
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, Hainan Province, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
- Hainan Key Laboratory of Vegetable Biology, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, 570228, China
| | - Xianfu Yuan
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, Anhui Province, 239000, China
| | - Jinming Yang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yue Yang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hongling Jv
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Zhongjun Jia
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, Hainan Province, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin Province, 130000, China
| | - Yunze Ruan
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, Hainan Province, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
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Jiang X, Lu C, Hu R, Shi W, Zhou L, Wen P, Jiang Y, Lo YM. Nutritional and microbiological effects of vermicompost tea in hydroponic cultivation of maple peas ( Pisum sativum var. arvense L.). Food Sci Nutr 2023; 11:3184-3202. [PMID: 37324884 PMCID: PMC10261758 DOI: 10.1002/fsn3.3299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 09/20/2024] Open
Abstract
Hydroponics receives considerable attentions due to population expansion, soil pollution, and farmland scarcity. However, one significant problem is that its residual effluents are detrimental to the surrounding ecosystem. There is a dire need to find an organic, alternative, biodegradable substrate. Vermicompost tea (VCT) was investigated on its suitability as a hydroponic substrate to provide both nutritional and microbiological benefits. It was found VCT increased the biomass of maple peas (Pisum sativum var. arvense L.), increased stem length, raised the potassium ion content, and promoted the uptake of nitrogen by the roots. Meanwhile, the microorganisms associated with earthworm guts were detected in the maple peas root system, namely the inter-rhizosphere of maple peas, including Enterobacteriaceae, Pseudomonadaceae, and Flavobacteriaceae. The presence of these microorganisms in large number indicated the ability for VCT to retain earthworm intestinal microbes via intestinal tract movement, excreting, and other vital activities. In addition, Rhizobia spp., such as Burkholderiaceae and Rhizobiaceae were also identified in VCT. They are critical for legumes as they can form root or stem nodule symbioses to produce growth hormone, vitamins, nitrogen fixation, and protection against plant stress. These findings are consistent with our chemical analysis that VCT-treated maple peas had increased nitrate and ammonium nitrogen content relative to the control in roots, stems, and leaves, hence increasing maple peas' biomass. The abundance and species of the inter-root bacterial population were found to change during the experimental period, indicating the importance of microbial balance to the growth and nutrient uptake of maple peas.
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Affiliation(s)
- Xinyi Jiang
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Ci Lu
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Runmeng Hu
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Wenyang Shi
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Libang Zhou
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Puzhao Wen
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Yizhou Jiang
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
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Qiao Y, Hou D, Lin Z, Wei S, Chen J, Li J, Zhao J, Xu K, Lu L, Tian S. Sulfur fertilization and water management ensure phytoremediation coupled with argo-production by mediating rhizosphere microbiota in the Oryza sativa L.-Sedum alfredii Hance rotation system. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131686. [PMID: 37270958 DOI: 10.1016/j.jhazmat.2023.131686] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/22/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Sulfur (S) fertilizers, water management and crop rotation are important agronomic practices, related to soil heavy metal bioavailability. However, the mechanisms of microbial interactions remain unclear. Herein, we investigated how S fertilizers (S0 and Na2SO4) and water management affected plant growth, soil cadmium (Cd) bioavailability, and rhizospheric bacterial communities in the Oryza sativa L. (rice)-Sedum alfredii Hance (S. alfredii) rotation system through 16S rRNA gene sequencing and ICP-MS analysis. During rice cultivation, continuous flooding (CF) was better than alternating wetting and drying (AWD). CF treatment decreased soil Cd bioavailability by the promotion of insoluble metal sulfide production and soil pH, thus lowering Cd accumulation in grains. S application recruited more S-reducing bacteria in the rhizosphere of rice, whilst Pseudomonas promoted metal sulfide production and rice growth. During S. alfredii cultivation, S fertilizer recruited S-oxidizing and metal-activating bacteria in the rhizosphere. Thiobacillus may oxidize metal sulfides and enhance Cd and S absorption into S. alfredii. Notably, S oxidation decreased soil pH and elevated Cd content, thereby promoting S. alfredii growth and Cd absorption. These findings showed rhizosphere bacteria were involved in Cd uptake and accumulation in the rice-S. alfredii rotation system, thus providing useful information for phytoremediation coupled with argo-production.
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Affiliation(s)
- Yabei Qiao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Zhi Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Shuai Wei
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jiuzhou Chen
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jiahao Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Kuan Xu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Lingli Lu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Shengke Tian
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China.
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Leal C, Gramaje D, Fontaine F, Richet N, Trotel-Aziz P, Armengol J. Evaluation of Bacillus subtilis PTA-271 and Trichoderma atroviride SC1 to control Botryosphaeria dieback and black-foot pathogens in grapevine propagation material. PEST MANAGEMENT SCIENCE 2023; 79:1674-1683. [PMID: 36573682 DOI: 10.1002/ps.7339] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/12/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Grapevine trunk diseases (GTDs) are a complex group of diseases that lead to major economic losses in all wine-producing countries. The investigation of biocontrol agents (BCAs) capable of forestalling or at least minimizing the development of GTDs has, recently, become a priority. Nursery experiments were set up to (i) assess the biocontrol effect of Trichoderma atroviride (Ta) SC1 and Bacillus subtilis (Bs) PTA-271, alone and in simultaneous application, against Botryosphaeria dieback (BOT)- and black-foot (BF)- associated pathogens during the grapevine propagation process and (ii) evaluate the success of the BCA inoculation during the grapevine propagation process, using quantitative reverse-transcription polymerase chain reaction techniques. RESULTS The results demonstrated a significant reduction in the percentage of potentially infected plants and the percentage of fungal isolation from wood fragments of BOT and BF pathogens in nursery material treated with Ta SC1 and Bs PTA-271, respectively. In one of the experiments, simultaneous treatments with Bs PTA-271 and Ta SC1 caused a reduction in percentages of potentially infected plants and fungal isolation, from wood fragments containing BOT and BF pathogens. CONCLUSION These biological treatments may be relevant components of an integrated approach, using complementary management strategies to limit infection by GTD pathogens, but further research is still needed to elucidate the effectiveness of Bs PTA-271 and the benefits of simultaneous application with Ta SC1 for the control of GTD pathogens in nurseries. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Catarina Leal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja, Logroño, Spain
| | - Florence Fontaine
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Nicolas Richet
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Patricia Trotel-Aziz
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
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Zhang M, Wang Y, Hu Y, Wang H, Liu Y, Zhao B, Zhang J, Fang R, Yan Y. Heterosis in root microbiota inhibits growth of soil-borne fungal pathogens in hybrid rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1059-1076. [PMID: 36426878 DOI: 10.1111/jipb.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
In nature, plants are colonized by various microbes that play essential roles in their growth and health. Heterosis is a natural genetic phenomenon whereby first-generation hybrids exhibit superior phenotypic performance relative to their parents. It remains unclear whether this concept can be extended to the "hybridization" of microbiota from two parents in their descendants and what benefits the hybrid microbiota might convey. Here, we investigated the structure and function of the root microbiota from three hybrid rice varieties and their parents through amplicon sequencing analysis of bacterial 16S ribosomal DNA (rDNA) and fungal internal transcribed spacer (ITS) regions. We show that the bacterial and fungal root microbiota of the varieties are distinct from those of their parental lines and exhibit potential heterosis features in diversity and composition. Moreover, the root bacterial microbiota of hybrid variety LYP9 protects rice against soil-borne fungal pathogens. Systematic analysis of the protective capabilities of individual strains from a 30-member bacterial synthetic community derived from LYP9 roots indicated that community members have additive protective roles. Global transcription profiling analyses suggested that LYP9 root bacterial microbiota activate rice reactive oxygen species production and cell wall biogenesis, contributing to heterosis for protection. In addition, we demonstrate that the protection conferred by the LYP9 root microbiota is transferable to neighboring plants, potentially explaining the observed hybrid-mediated superior effects of mixed planting. Our findings suggest that some hybrids exhibit heterosis in their microbiota composition that promotes plant health, highlighting the potential for microbiota heterosis in breeding hybrid crops.
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Affiliation(s)
- Mengting Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yinyue Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyi Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Huacai Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yawen Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongsheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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Pereira LB, Thomazella DPT, Teixeira PJPL. Plant-microbiome crosstalk and disease development. CURRENT OPINION IN PLANT BIOLOGY 2023; 72:102351. [PMID: 36848753 DOI: 10.1016/j.pbi.2023.102351] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Plants harbor a complex immune system to fight off invaders and prevent diseases. For decades, the interactions between plants and pathogens have been investigated primarily through the lens of binary interactions, largely neglecting the diversity of microbes that naturally inhabit plant tissues. Recent research, however, demonstrates that resident microbes are more than mere spectators. Instead, the plant microbiome extends host immune function and influences the outcome of a pathogen infection. Both plants and the interacting microbes produce a large diversity of metabolites that form an intricate chemical network of nutrients, signals, and antimicrobial molecules. In this review, we discuss the involvement of the plant microbiome in disease development, focusing on the biochemical conversation that occurs between plants and their associated microbiota before, during and after infection. We also highlight outstanding questions and possible directions for future research.
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Affiliation(s)
- Letícia B Pereira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Daniela P T Thomazella
- Department of Genetics, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil.
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Sagova-Mareckova M, Omelka M, Kopecky J. The Golden Goal of Soil Management: Disease-Suppressive Soils. PHYTOPATHOLOGY 2023; 113:741-752. [PMID: 36510361 DOI: 10.1094/phyto-09-22-0324-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.
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Affiliation(s)
- Marketa Sagova-Mareckova
- Group Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6-Ruzyne, 161 06, Czechia
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamycka 129, 165 00, Prague-Suchdol, Czechia
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovska 83, Prague 8, 186 75, Czechia
| | - Jan Kopecky
- Group Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6-Ruzyne, 161 06, Czechia
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Lv N, Tao C, Ou Y, Wang J, Deng X, Liu H, Shen Z, Li R, Shen Q. Root-Associated Antagonistic Pseudomonas spp. Contribute to Soil Suppressiveness against Banana Fusarium Wilt Disease of Banana. Microbiol Spectr 2023; 11:e0352522. [PMID: 36786644 PMCID: PMC10100972 DOI: 10.1128/spectrum.03525-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Members of the microbiotas colonizing the plant endophytic compartments and the surrounding bulk and rhizosphere soil play an important role in determining plant health. However, the relative contributions of the soil and endophytic microbiomes and their mechanistic roles in achieving disease suppression remain elusive. To disentangle the relative importance of the different microbiomes in the various plant compartments in inhibiting pathogen infection, we conducted a field experiment to track changes in the composition of microbial communities in bulk and rhizosphere soil and of root endophytes and leaf endosphere collected from bananas planted on Fusarium-infested orchards in disease-suppressive and disease-conducive soils. We found that the rhizosphere and roots were the two dominant plant parts whose bacterial communities contributed to pathogen suppression. We further observed that Pseudomonas was potentially a key organism acting as a pathogen antagonist, as illustrated by microbial community composition and network analysis. Subsequently, culturable pathogen-antagonistic Pseudomonas strains were isolated, and their potential suppressive functions or possible antibiosis in terms of auxin or siderophore synthesis and phosphate solubilization were screened to analyze the mode of action of candidate disease-suppressive Pseudomonas strains. In a follow-up in vivo and greenhouse experiment, we revealed that microbial consortia of culturable Pseudomonas strains P8 and S25 (or S36), isolated from banana plantlet rhizosphere and roots, respectively, significantly suppressed the survival of pathogens in the soil, manipulated the soil microbiome, and stimulated indigenous beneficial microbes. Overall, our study demonstrated that root-associated microbiomes, especially the antagonistic Pseudomonas sp. components, contribute markedly to soil suppression of banana Fusarium wilt. IMPORTANCE Soil suppression of Fusarium wilt disease has been proven to be linked with the local microbial community. However, the contribution of endophytic microbes to disease suppression in wilt-suppressive soils remains unclear. Moreover, the key microbes involving in Fusarium wilt-suppressive soils and in the endophytic populations have not been fully characterized. In this study, we demonstrate that root-associated microbes play vitally important roles in disease suppression. Root-associated Pseudomonas consortia were recognized as a key component in inhibiting pathogen abundance associated with the host banana plants. This finding is crucial to developing alternate strategies for soilborne disease management by harnessing the plant microbiome.
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Affiliation(s)
- Nana Lv
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Jiabao Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
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Ali S, Tyagi A, Bae H. Plant Microbiome: An Ocean of Possibilities for Improving Disease Resistance in Plants. Microorganisms 2023; 11:microorganisms11020392. [PMID: 36838356 PMCID: PMC9961739 DOI: 10.3390/microorganisms11020392] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plant diseases pose a serious threat to crop production and the agricultural economy across the globe. Currently, chemical pesticides are frequently employed to combat these infections, which cause environmental toxicity and the emergence of resistant pathogens. Moreover, the genetic manipulation of plant defense pathways and the breeding of resistant genes has attained limited success due to the rapid evolution of pathogen virulence and resistance, together with host range expansion. Additionally, due to climate change and global warming, the occurrence of multiple stresses during disease outbreak has further impacted overall crop growth and productivity, posing a serious threat to food security. In this regard, harnessing the plant beneficial microbiome and its products can provide novel avenues for disease resistance in addition to boosting agricultural output, soil fertility and environmental sustainability. In plant-beneficial microbiome interactions, induced systemic resistance (ISR) has emerged as a key mechanism by which a beneficial microbiome primes the entire plant system for better defense against a wide range of phytopathogens and pests. In this review, we provide the recent developments on the role of plant beneficial microbiomes in disease resistance. We also highlight knowledge gaps and discuss how the plant immune system distinguishes pathogens and beneficial microbiota. Furthermore, we provide an overview on how immune signature hormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), shape plant beneficial microbiome. We also discuss the importance of various high-throughput tools and their integration with synthetic biology to design tailored microbial communities for disease resistance. Finally, we conclude by highlighting important themes that need future attention in order to fill the knowledge gaps regarding the plant immune system and plant-beneficial-microbiome-mediated disease resistance.
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Li Y, Deng X, Zhang N, Shen Z, Li R, Shen Q, Salles JF. Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion. One Health 2023; 16:100481. [PMID: 36683960 PMCID: PMC9845992 DOI: 10.1016/j.onehlt.2023.100481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere is an extremely important component of the "one health" scenario by linking the soil microbiome and plants, in which the potential enrichment of antibiotic resistance genes (ARGs) might ultimately flow into the human food chain. Despite the increased occurrence of soil-borne diseases, which can lead to increased use of pesticides and antibiotic-producing biocontrol agents, the understanding of the dynamics of ARG spread in the rhizosphere is largely overlooked. Here, tomato seedlings grown in soils conducive and suppressive to the pathogen Ralstonia solanacearum were selected as a model to investigate ARG spread in the rhizosphere with and without pathogen invasion. Metagenomics data revealed that R. solanacearum invasion increased the density of ARGs and mobile genetic elements (MGEs). Although we found ARGs originating from human pathogenic bacteria in both soils, the enrichment was alleviated in the suppressive soil. In summary, the suppressive soil hindered ARG spread through pathogen suppression and had a lower number of taxa carrying antibiotic resistance.
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Affiliation(s)
- Yuchan Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China,Sanya Institute of Nanjing Agricultural University, Sanya 572025, Hainan, China,Corresponding authors at: College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Na Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China,Sanya Institute of Nanjing Agricultural University, Sanya 572025, Hainan, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China,Sanya Institute of Nanjing Agricultural University, Sanya 572025, Hainan, China,Corresponding authors at: College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Joana Falcao Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747AG, the Netherlands
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Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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Moneda APC, de Carvalho LAL, Teheran-Sierra LG, Funnicelli MIG, Pinheiro DG. Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure. Sci Rep 2022; 12:19174. [PMID: 36357461 PMCID: PMC9649670 DOI: 10.1038/s41598-022-23562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.
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Affiliation(s)
- Ana Paula Corrêa Moneda
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Lucas Amoroso Lopes de Carvalho
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Luis Guillermo Teheran-Sierra
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Michelli Inácio Gonçalves Funnicelli
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Daniel Guariz Pinheiro
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
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Deng C, Zhang N, Liang X, Huang T, Li B. Bacillus aryabhattai LAD impacts rhizosphere bacterial community structure and promotes maize plant growth. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6650-6657. [PMID: 35603593 DOI: 10.1002/jsfa.12032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plant growth-promoting rhizobacteria may significantly impact the soil microbial community and the growth of plant roots and have critical roles in soil ecosystem functioning. However, the interactions between rhizobacteria and plants are extremely complicated and remain understudied. RESULTS In this study, a Bacillus strain was isolated from a long-term maize colonization soil and identified as Bacillus aryabhattai strain LAD. Laboratory tests showed that B. aryabhattai LAD had phosphate-solubilizing and nitrogen-fixing functions that benefit plant growth. The effects of LAD cultures on the root system development of corn seedlings and the structure of rhizosphere bacterial communities were studied. The most significant stimulations of LAD culture on plant growth were observed at a cell density of 102 CFU mL-1 . Treatment with LAD culture in hydroponics caused an increase of 107%, 197%, and 25% in the shoot length, total root length, and main root thickness respectively. The LAD treatment also significantly affected the rhizosphere microbial abundance and community structure. The rhizobacterial abundance and species richness in the corn seedlings treated with LAD culture were significantly lower than those in the control group. However, the LAD-treated samples had higher relative abundances of plant growth-promoting rhizobacteria like Bacillus and Burkholderia than the control samples did, suggesting that LAD treatment may facilitate the mutualistic relation between the rhizosphere microbiome and the plant. CONCLUSION These results collectively demonstrated that LAD is capable of shaping the rhizosphere microbial community structure and functions as a plant growth-promoting agent, which makes it a strong candidate for application as bio-fertilizer in agricultural systems. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Chao Deng
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Tao Huang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
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