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Tian J, Xu L, Sun JQ. Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus. ENVIRONMENTAL RESEARCH 2024; 261:119724. [PMID: 39096995 DOI: 10.1016/j.envres.2024.119724] [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: 06/15/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18T) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.
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Affiliation(s)
- Jing Tian
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ji-Quan Sun
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
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Ferrando L, Rariz G, Martínez-Pereyra A, Fernández-Scavino A. Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties. J Appl Microbiol 2024; 135:lxae157. [PMID: 38925647 DOI: 10.1093/jambio/lxae157] [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: 03/29/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
AIM Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
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Affiliation(s)
- Lucía Ferrando
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Gastón Rariz
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Andrea Martínez-Pereyra
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
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Shi W, Li J, Xie S, Wang X, Zhang Y, Yao H, Chen M, Li J, Deng Z. Selection of the Dominant Endophytes Based on Illumina Sequencing Analysis for Controlling Bacterial Wilt of Patchouli Caused by Ralstonia solanacearum. PLANT DISEASE 2024; 108:996-1004. [PMID: 38613135 DOI: 10.1094/pdis-09-23-1722-re] [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: 04/14/2024]
Abstract
Bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating diseases in patchouli (Pogostemon cablin [Blanco] Benth.), which results in low yield and quality of patchouli. However, no stable and effective control methods have been developed yet. To evaluate the potential of dominant bacterial endophytes in biocontrol, the endophytic bacterial diversity of patchouli was investigated based on Illumina sequencing analysis, and the ability of isolates belonging to the dominant bacterial genera to control RS wilt of patchouli was explored in pot experiments. A total of 245 bacterial genera were detected in patchouli plants, with the highest relative abundance of operational taxonomic units belonging to the genus Pseudomonas detected in roots, leaves, and stems. The Pseudomonas isolates S02, S09, and S26 showed antagonistic activity against RS in vitro and displayed many plant growth-promoting characteristics, including production of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase and phosphate- and potassium-solubilizing capability. Inoculation of patchouli plants with the isolates S02, S09, and S26 significantly improved shoot growth and decreased the incidence of bacterial wilt caused by RS. The results suggest that screening of dominant bacterial endophytes for effective biocontrol agents based on Illumina sequencing analysis is more efficient than random isolation and screening procedures.
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Affiliation(s)
- Wenguang Shi
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Junyan Li
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Siyun Xie
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Xing Wang
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Yuxin Zhang
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Huaxiong Yao
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Meiqi Chen
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Jianbin Li
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Zujun Deng
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
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Wang X, He SW, He Q, Ju ZC, Ma YN, Wang Z, Han JC, Zhang XX. Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages. Microbiol Spectr 2023; 11:e0497822. [PMID: 37655928 PMCID: PMC10580921 DOI: 10.1128/spectrum.04978-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/07/2023] [Indexed: 09/02/2023] Open
Abstract
The core endophytes of plants are regarded as promising resources in future agroecosystems. How they affect the assembly of rice-related bacterial communities after early inoculation remains unclear. Here, we examined bacterial communities across 148 samples, including bulk and rhizosphere soils, sterilized roots, stems, and seeds at the seedling, tillering, booting, and maturity stages. Tissue cultured rice seedlings were inoculated with Xathomonas sacchari JR3-14, a core endophytic bacterium of rice seeds, before transplanting. The results revealed that α-diversity indices were significantly enhanced in the root and stem endosphere at the seedling stage. β-diversity was altered at most plant developmental stages, except for the root and stem at the booting stage. Network complexity consequently increased in the root and stem across rice growth stages, other than the stem endosphere at the booting stage. Four abundant beneficial bacterial taxa, Bacillus, Azospira, Azospirillum, and Arthrobacter, were co-enriched during the early growth stage. Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis revealed a higher relative contribution of drift and other eco-evolutionary processes mainly in root compartments across all growth stages, but the opposite pattern was observed in stem compartments. IMPORTANCE Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant's ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium Xanthomonas sacchari could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding.
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Affiliation(s)
- Xing Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Wen He
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zhi-Cheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yi-Nan Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhe Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia-Cheng Han
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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Guzmán-Altamirano MÁ, Rebollo-Plata B, Joaquín-Ramos ADJ, Gómez-Espinoza MG. Green synthesis and antimicrobial mechanism of nanoparticles: applications in agricultural and agrifood safety. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2727-2744. [PMID: 35941521 DOI: 10.1002/jsfa.12162] [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: 09/26/2021] [Revised: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The growing demand for food and its safety are a challenge for agriculture and agrifood. This has led to the incorporation of alternatives such as organic agriculture, the use of biocontrollers, the development of transgenic plants resistant to pathogens and the incorporation of nanotechnology. In this sense, agrochemicals based on nanoparticles (NPs) have been developed. Recently, the green synthesis of NPs has grown rapidly and, for this reason, molecules, microorganisms, fungi and plants are used. Synthesis from plant extracts offers a broad spectrum and, despite the fact that NPs are usually dispersed in size and shape, extensive antimicrobial effectiveness has been demonstrated at nanomolar concentrations. It has been shown that the mechanism of action can be through the dissipation of the driving force of the protons, the alteration of cellular permeability, the formation of bonds with the thiol group of the proteins, the generation of reactive species of oxygen, and the hyperoxidation of DNA, RNA and even the cell membrane. To improve the efficiency of NPs, modifications have been made such as coating with other metals, the addition of antibiotics, detergents and surfactants, as well as the acidification of the solution. Consequently, NPs are considered as a promising method for achieving safety in the agricultural and agrifood area. However, it is necessary to investigate the side effects of NPs, when applied in agroecological systems, on the textural, nutriment and sensory properties of food, as well as the impact on human health. © 2022 Society of Chemical Industry.
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Affiliation(s)
| | - Bernabe Rebollo-Plata
- Departamento de Ing. Electrónica, Instituto Tecnológico superior de Irapuato, Guanajuato, México
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Zhu Y, Lv X, Li T, Zhong M, Song J, Wang H, Cui J. Cotton straw biochar and compound Bacillus biofertilizer reduce Cd stress on cotton root growth by regulating root exudates and antioxidant enzymes system. FRONTIERS IN PLANT SCIENCE 2022; 13:1051935. [PMID: 36457531 PMCID: PMC9705756 DOI: 10.3389/fpls.2022.1051935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Cotton straw biochar (biochar) and compound Bacillus biofertilizer (biofertilizer) have attracted wide attentions in the remediation of heavy metal-contaminated soils in recent years. However, few studies have explored the metabolomics of lateral roots of Cd-stressed cotton to determine the mechanism of biochar and biofertilizer alleviating Cd stress. METHODS In this pot experiment, biochar and biofertilizer were applied to the soils with different Cd contamination levels (1, 2, and 4 mg kg-1). Then, the responses of cotton root morphology, vitality, Cd content, and antioxidant enzyme activities were analyzed, and the mechanism of biochar and biofertilizer alleviating Cd stress was determined by metabolomic analysis. RESULTS The results showed that exogenous Cd addition decreased the SOD and POD activities in cotton taproot and lateral root. Besides, with the increase of soil Cd content, the maximum Cd content in taproot (0.0250 mg kg-1) and lateral root (0.0288 mg kg-1) increased by 89.11% and 33.95%, respectively compared with those in the control (p< 0.05). After the application of biochar and biofertilizer, the SOD and POD activities in cotton taproot and lateral root increased. The Cd content of cotton taproot in biochar and biofertilizer treatments decreased by 16.36% and 19.73%, respectively, and that of lateral root decreased by 13.99% and 16.68%, respectively. The metabolomic analysis results showed that the application of biochar and biofertilizer could improve the resistance of cotton root to Cd stress through regulating the pathways of ABC transporters and phenylalanine metabolism. DISCUSSION Therefore, the application of biochar and biofertilizer could improve cotton resistance to Cd stress by increasing antioxidant enzyme activities, regulating root metabolites (phenols and amino acids), and reducing Cd content, thus promoting cotton root growth.
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Li Y, Yang R, Häggblom MM, Li M, Guo L, Li B, Kolton M, Cao Z, Soleimani M, Chen Z, Xu Z, Gao W, Yan B, Sun W. Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis). MICROBIOME 2022; 10:186. [PMID: 36329505 PMCID: PMC9632085 DOI: 10.1186/s40168-022-01379-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/22/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments. RESULTS Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using 15N2 identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth. CONCLUSIONS This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.
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Affiliation(s)
- Yongbin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Rui Yang
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Lifang Guo
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zhiguo Cao
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Zhimin Xu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Wenlong Gao
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Bei Yan
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China.
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
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Thiebaut F, Urquiaga MCDO, Rosman AC, da Silva ML, Hemerly AS. The Impact of Non-Nodulating Diazotrophic Bacteria in Agriculture: Understanding the Molecular Mechanisms That Benefit Crops. Int J Mol Sci 2022; 23:ijms231911301. [PMID: 36232602 PMCID: PMC9569789 DOI: 10.3390/ijms231911301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Agriculture is facing increasing challenges with regard to achieving sustainable growth in productivity without negatively impacting the environment. The use of bioinoculants is emerging as a sustainable solution for agriculture, especially bioinoculants based on diazotrophic bacteria. Brazil is at the forefront of studies intended to identify beneficial diazotrophic bacteria, as well as in the molecular characterization of this association on both the bacterial and plant sides. Here we highlight the main advances in molecular studies to understand the benefits brought to plants by diazotrophic bacteria. Different molecular pathways in plants are regulated both genetically and epigenetically, providing better plant performance. Among them, we discuss the involvement of genes related to nitrogen metabolism, cell wall formation, antioxidant metabolism, and regulation of phytohormones that can coordinate plant responses to environmental factors. Another important aspect in this regard is how the plant recognizes the microorganism as beneficial. A better understanding of plant–bacteria–environment interactions can assist in the future formulation of more efficient bioinoculants, which could in turn contribute to more sustainable agriculture practices.
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Hernández-Guzmán M, Pérez-Hernández V, Navarro-Noya YE, Luna-Guido ML, Verhulst N, Govaerts B, Dendooven L. Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere. Sci Rep 2022; 12:4110. [PMID: 35260645 PMCID: PMC8904580 DOI: 10.1038/s41598-022-07623-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/01/2022] [Indexed: 12/30/2022] Open
Abstract
Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha−1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha−1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2− was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.
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Affiliation(s)
- Mario Hernández-Guzmán
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico
| | - Valentín Pérez-Hernández
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico.,Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tuxtla Gutiérrez, Mexico
| | - Yendi E Navarro-Noya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, México
| | - Marco L Luna-Guido
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico.,Cornell University, Ithaca, USA
| | - Luc Dendooven
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico.
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Cao P, Wei X, Wang G, Chen X, Han J, Li Y. Microbial inoculants and garbage fermentation liquid reduced root-knot nematode disease and As uptake in Panax quinquefolium cultivation by modulating rhizosphere microbiota community. CHINESE HERBAL MEDICINES 2021; 14:58-69. [PMID: 36120127 PMCID: PMC9476822 DOI: 10.1016/j.chmed.2021.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/18/2021] [Accepted: 06/02/2021] [Indexed: 11/19/2022] Open
Abstract
Objective To find a suitable ecological cultivation measure to solve the problem of root-knot nematode disease of Panax quinquefolium (Panacis Quinquefolii Radix) and the heavy metals accumulating in its roots. Methods Three-year-old P. quinquefolium was treated with four different combinations of microbial inoculant (MI) and garbage fermentation liquid (GFL) [the joint application of ‘TuXiu’ MI and Fifty potassium MI (TF), the combination use of ‘No. 1′ MI and Fifty potassium MI (NF), ‘Gulefeng’ poly-γ-glutamic acid MI (PGA), GFL], and the untreated control (CK). Here, high-throughput sequencing, ICP-MS and UPLC were employed to systematically characterize changes of microbial diversity and structure composition, heavy metals (As, Cd and Pb) content and ginsenoside content among different treatments. Results The results revealed that different MIs and GFL could increase the root dry weight of P. quinquefolium, PGA enhanced it by 83.24%, followed by GFL (49.93%), meanwhile, PGA and GFL were able to lessen root-knot nematode disease incidence by 57.25% and 64.35%. The treatment of PGA and GFL can also effectively reduce heavy metals in roots. The As content in GFL and PGA was decreased by 52.17% and 43.48% respectively, while the Cd and Pb contents of GFL and PGA was decreased somewhat. Additionally, the content of total ginsenosides was increased by 42.14% and 42.07%, in response to TF and NF, respectively. Our metagenomic analysis showed that the relative abundance of particular soil microbial community members related to the biocontrol of root-knot nematode disease and plant pathogen (i.e., Chaetomium in NF, Xylari in GFL, and Microascus in PGA), heavy metal bioremediation (Hyphomacrobium in PGA and Xylaria in GFL), and nitrogen fixation (Nordella and Nitrospira in TF) was significantly increased; notably, potential harmful microflora, such as Plectosaphaerella and Rhizobacter, were more abundant in the control group. Conclusion MI and GFL could improve the quality of P. quinquefolium by modifying its rhizosphere microbial community structure and composition, both of them are beneficial to the development of ecological cultivation of P. quinquefolium.
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Affiliation(s)
- Pei Cao
- Key Lab of Chinese Medicine Resources Conservation, National Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xuemin Wei
- Key Lab of Chinese Medicine Resources Conservation, National Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Gang Wang
- Key Lab of Chinese Medicine Resources Conservation, National Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiaochen Chen
- Key Lab of Chinese Medicine Resources Conservation, National Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianping Han
- Key Lab of Chinese Medicine Resources Conservation, National Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Corresponding authors.
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Corresponding authors.
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11
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Li Y, Li Q, Chen S. Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize. Int J Mol Sci 2021; 22:1460. [PMID: 33540521 PMCID: PMC7867140 DOI: 10.3390/ijms22031460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/28/2022] Open
Abstract
Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant.
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Affiliation(s)
| | | | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100094, China; (Y.L.); (Q.L.)
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12
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Kumar M, Kumar A, Sahu KP, Patel A, Reddy B, Sheoran N, Krishnappa C, Rajashekara H, Bhagat S, Rathour R. Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones. Microbiol Res 2021; 246:126704. [PMID: 33486428 DOI: 10.1016/j.micres.2021.126704] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/20/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated influence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Acinetobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.
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Affiliation(s)
- Mukesh Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | | | - Asharani Patel
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Bhaskar Reddy
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelam Sheoran
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Someshwar Bhagat
- ICAR-Central Rainfed Upland Rice Research Station (NRRI), Hazaribagh, Jharkhand, India
| | - Rajeev Rathour
- CSK-Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
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Mushtaq T, Shah AA, Akram W, Yasin NA. Synergistic ameliorative effect of iron oxide nanoparticles and Bacillus subtilis S4 against arsenic toxicity in Cucurbita moschata: polyamines, antioxidants, and physiochemical studies. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 22:1408-1419. [PMID: 32574074 DOI: 10.1080/15226514.2020.1781052] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The present study was intended to assess the potential of iron oxide nanoparticles (IONPs) and Bacillus subtilis S4 in mitigation of arsenic (As) stress in Cucurbita moschata. Cucurbita moschata seedlings were subjected to As stress for 60 days. Reduced level of growth parameters including photosynthetic pigments, rate of photosynthesis and gas exchange characteristics was observed in seedlings subjected to As stress. However, IONPs and B. subtilis S4 improved growth attributes and proline contents in supplemented C. moschata seedlings. Bacillus subtilis S4 inoculated seedlings showed higher activity of peroxidase (POD) and superoxide dismutase (SOD) under As toxicity. Similarly, the co-application of IONPs and B. subtilis S4 further increased the activity of these antioxidative enzymes. The As stress alleviation in inoculated C. moschata seedlings is credited to reduced levels of hydrogen peroxide (H2O2), malondialdehyde (MDA) and electrolyte leakage (EL) in IONPs and B. subtilis S4-treated plants. Furthermore, synergism between plant growth promoting bacteria (PGPB) and IONPs enhanced the biosynthesis of stress mitigating polyamines including spermidine and putrescine in As-stressed seedlings. Current research reveals that synergistic application of IONPs and B. subtilis S4 is an effective sustainable and ecofriendly approach for alleviation of As stress in C. moschata seedlings.
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Affiliation(s)
- Tarifa Mushtaq
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Anis Ali Shah
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Waheed Akram
- Guangdong Key Laboratory for New Technology Research of Vegetables/Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Nasim Ahmad Yasin
- Senior Superintendent Garden, University of the Punjab, Lahore, Pakistan
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14
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Menéndez E, Paço A. Is the Application of Plant Probiotic Bacterial Consortia Always Beneficial for Plants? Exploring Synergies between Rhizobial and Non-Rhizobial Bacteria and Their Effects on Agro-Economically Valuable Crops. Life (Basel) 2020; 10:E24. [PMID: 32178383 PMCID: PMC7151578 DOI: 10.3390/life10030024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 12/13/2022] Open
Abstract
The overgrowth of human population and the demand for high-quality foods necessitate the search for sustainable alternatives to increase crop production. The use of biofertilizers, mostly based on plant probiotic bacteria (PPB), represents a reliable and eco-friendly solution. This heterogeneous group of bacteria possesses many features with positive effects on plants; however, how these bacteria with each other and with the environment when released into a field has still barely been studied. In this review, we focused on the diversity of root endophytic rhizobial and non-rhizobial bacteria existing within plant root tissues, and also on their potential applications as consortia exerting benefits for plants and the environment. We demonstrated the benefits of using bacterial inoculant consortia instead of single-strain inoculants. We then critically discussed several considerations that farmers, companies, governments, and the scientific community should take into account when a biofertilizer based on those PPBs is proposed, including (i) a proper taxonomic identification, (ii) the characterization of the beneficial features of PPB strains, and (iii) the ecological impacts on plants, environment, and plant/soil microbiomes. Overall, the success of a PPB consortium depends on many factors that must be considered and analyzed before its application as a biofertilizer in an agricultural system.
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Affiliation(s)
- Esther Menéndez
- MED—Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research (IIFA), University of Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
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Changes of Root Endophytic Bacterial Community Along a Chronosequence of Intensively Managed Lei Bamboo ( Phyllostachys praecox) Forests in Subtropical China. Microorganisms 2019; 7:microorganisms7120616. [PMID: 31779125 PMCID: PMC6956015 DOI: 10.3390/microorganisms7120616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/17/2022] Open
Abstract
Endophytic bacteria widely exist inside plant tissues and have an important role in plant growth and development and the alleviation of environmental stress. However, little is known about the response of root-associated bacterial endophytes of Lei bamboo (Phyllostachys praecox) to intensive management, which is a common management practice for high bamboo shoot production in subtropical China. In this study, we comparatively investigated the root endophytic bacterial community structures in a chronosequence of intensively managed (5a, 10a, 15a, and 20a) and extensively managed plantations (as control, Con). The results showed that endophytic Proteobacteria was the dominant bacterial phylum in the bamboo roots. Intensive management significantly increased (p < 0.05) the bacterial observed species and Chao1 (except 5a) indices associated with bamboo roots. The relative abundances of Firmicutes, Bacteroidetes, and Actinobacteria (except 15a) in the intensively managed bamboo roots significantly increased (p < 0.05) compared with those in Con, while the relative abundance of Proteobacteria significantly decreased in intensively managed bamboo roots (p < 0.05). The phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the biomarkers in Con, 5a, 15a, and 20a, respectively. Redundancy analysis (RDA) showed that soil alkali-hydrolysable N (AN), available phosphorus (AP), available K (AK), and total organic carbon (TOC) were significantly correlated (p < 0.05) with the bacterial community compositions. Our results suggest that the root endophytic microbiome of Lei bamboo was markedly influenced by intensive management practices, and the available nutrient status could be the main driving factor for such shifts. Although heavy fertilization in the intensive management system increased the diversity indices, the rapid changes in root endophyte communities and their relevant functions might indicate a high risk for sustainable management.
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