1
|
Yakkou L, Houida S, El Baaboua A, Bilen S, Chelkha M, Okyay Kaya L, Aasfar A, Ameen F, Ahmad Bhat S, Raouane M, Amghar S, El Harti A. Unveiling resilience: coelomic fluid bacteria's impact on plant metabolism and abiotic stress tolerance. PLANT SIGNALING & BEHAVIOR 2024; 19:2363126. [PMID: 38832593 DOI: 10.1080/15592324.2024.2363126] [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: 04/07/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Earthworms' coelomic fluid (CF) has been discovered to possess properties that promote plant development. In particular, the earthworm's coelomic fluid-associated bacteria (CFB) are the primary factor influencing the plants' response. To investigate this, we used bacteria isolated from the CF and selected based on different plant growth-promoting traits, in a mesocosm ecosystem that includes plants. This experiment aimed to assess their impact on the metabolism of plants growing under abiotic stress environments (alkaline soil and nitrogen (N), phosphate (P), and potassium (K) deficit) and compare the lipid profiles of plants under the various treatments. We used seven different bacterial species isolated from the CF of Aporrectodea molleri and as a plant model Zea mays L. For the metabolomic analysis method, we used gas chromatography-mass spectrometry lipidomic. After observing the metabolomic profiles, we found that a few molecular pathways are involved in how plants react to bacterial biostimulants. The bacterial isolates belonging to Pantoea vagans, Pseudomonas aeruginosa, Bacillus paramycoides, and Bacillus thuringiensis have led to a significant increase in synthesizing several metabolites belonging to various chemical categories. Contrary to predictions, abiotic stress did not cause a drop in the composition and concentration of lipids in plants treated with the CFB, demonstrating the rigidity of the protective mechanisms. The statistical analysis based on the Pearson method revealed a positive significant correlation between plant growth parameters (length of the aerial part, surface of the leaves, and biomass) and some metabolites belonging to fatty acids, carboxylic acids, benzene derivatives, and alkanes. Moreover, the standard metabolic components of all treatments in much higher concentrations during bacterial treatments than the control treatment suggests that the bacteria have stimulated the overexpression of these metabolic components. According to these results, we could assume that plants treated with CFB exhibit an adaptability of abiotic stress defense mechanisms, which may be attributed to the upregulation of genes involved in lipid biosynthesis pathways.
Collapse
Affiliation(s)
- Lamia Yakkou
- Laboratory of Microbial Biotechnologies and Plant Protection (LBVRN), Faculty of Sciences Agadir, University Ibn Zohr, Agadir, Morocco
- Faculty of Applied Sciences- Ait Melloul, University Ibn Zohr, Agadir, Morocco
| | - Sofia Houida
- Laboratory of Mycobacteria and Tuberculosis, Institut Pasteur of Morocco, Casablanca, Morocco
| | - Aicha El Baaboua
- Biotechnology and Applied Microbiology Team, Department of Biology, Faculty of Science, Abdelmalek-Essaadi University, Tetouan, Morocco
| | - Serdar Bilen
- Soil Science and Plant Nutrition Department, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Maryam Chelkha
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Leyla Okyay Kaya
- Soil Science and Plant Nutrition Department, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Abderrahim Aasfar
- Plant and Microbial Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Mohammed Raouane
- Research Team «Lumbricidae, Improving Soil Productivity and Environment (LAPSE)», Center "Water, Natural Resources, Environment and Sustainable Development, Ecole Normale Supérieure (ENS), Mohammed V University, Rabat, Morocco
| | - Souad Amghar
- Research Team «Lumbricidae, Improving Soil Productivity and Environment (LAPSE)», Center "Water, Natural Resources, Environment and Sustainable Development, Ecole Normale Supérieure (ENS), Mohammed V University, Rabat, Morocco
| | - Abdellatif El Harti
- Research Team «Lumbricidae, Improving Soil Productivity and Environment (LAPSE)», Center "Water, Natural Resources, Environment and Sustainable Development, Ecole Normale Supérieure (ENS), Mohammed V University, Rabat, Morocco
| |
Collapse
|
2
|
Tian Y, Liu Y, Yue L, Zhao X, Zhou Q, Uwaremwe C, Wang Y, Chen G, Sha Y, Zhang Y, Wang R. Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions. Microbiol Res 2024; 287:127855. [PMID: 39079269 DOI: 10.1016/j.micres.2024.127855] [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: 05/31/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024]
Abstract
Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.
Collapse
Affiliation(s)
- Yuan Tian
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Yue
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Zhao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Zhou
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Constantine Uwaremwe
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin 730900, China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yubao Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ruoyu Wang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
3
|
Anzuay MS, Chiatti MH, Intelangelo AB, Ludueña LM, Viso NP, Angelini JG, Taurian T. Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants. Curr Genet 2024; 70:12. [PMID: 39093429 DOI: 10.1007/s00294-024-01296-4] [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: 05/16/2024] [Revised: 07/02/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.
Collapse
Affiliation(s)
- María Soledad Anzuay
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto, Argentina
| | - Mario Hernán Chiatti
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto, Argentina
| | | | | | - Natalia Pin Viso
- Instituto de Microbiología y Zoología Agrícola, IMyZA, IABiMo, INTA, Hurlingham, Buenos Aires, Argentina
| | | | - Tania Taurian
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto, Argentina.
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal 3, Río Cuarto, Córdoba, 5800, Argentina.
| |
Collapse
|
4
|
Bruger EL, Hying ZT, Singla D, Márquez Reyes NL, Pandey SK, Patel JS, Bazurto JV. Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in Methylorubrum extorquens PA1. Appl Environ Microbiol 2024; 90:e0031024. [PMID: 38934615 PMCID: PMC11323934 DOI: 10.1128/aem.00310-24] [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: 02/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Integration of metabolites into the overall metabolic network of a cell requires careful coordination dependent upon the ultimate usage of the metabolite. Different stoichiometric needs, and thus pathway fluxes, must exist for compounds destined for diverse uses, such as carbon sources, nitrogen sources, or stress-protective agents. Herein, we expand upon our previous work that highlighted the nature of glycine betaine (GB) metabolism in Methylobacteria to examine the utilization of GB-derivative compounds dimethylglycine (DMG) and sarcosine into Methylorubrum extorquens in different metabolic capacities, including as sole nitrogen and/or carbon sources. We isolated gain-of-function mutations that allowed M. extorquens PA1 to utilize dimethylglycine as a carbon source and dimethylglycine and sarcosine as nitrogen source. Characterization of mutants demonstrated selection for variants of the AraC-like regulator Mext_3735 that confer constitutive expression of the GB metabolic gene cluster, allowing direct utilization of the downstream GB derivatives. Finally, among the distinct isolates examined, we found that catabolism of the osmoprotectant used for selection (GB or dimethylglycine) enhanced osmotic stress resistance provided in the presence of that particular osmolyte. Thus, access to the carbon and nitrogen and osmoprotective effects of GB and DMG are made readily accessible through adaptive mutations. In M. extorquens PA1, the limitations to exploiting this group of compounds appear to exist predominantly at the levels of gene regulation and functional activity, rather than being constrained by transport or toxicity.IMPORTANCEOsmotic stress is a common challenge for bacteria colonizing the phyllosphere, where glycine betaine (GB) can be found as a prevalent osmoprotectant. Though Methylorubrum extorquens PA1 cannot use GB or its demethylation products, dimethylglycine (DMG) and sarcosine, as a sole carbon source, utilization is highly selectable via single nucleotide changes for both GB and DMG growth. The innate inability to use these compounds is due to limited flux through steps in the pathway and regulatory constraints. Herein, the characterization of the transcriptional regulator, Mext_3735 (GbdR), expands our understanding of the various roles in which GB derivatives can be used in M. extorquens PA1. Interestingly, increased catabolism of GB and derivatives does not interfere with, but rather improves, the ability of cells to thrive under increased salt stress conditions, suggesting that metabolic flux improves stress tolerance rather than providing a distinct tension between uses.
Collapse
Affiliation(s)
- Eric L. Bruger
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Zachary T. Hying
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Deepanshu Singla
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Nicole L. Márquez Reyes
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Shubham Kumar Pandey
- Department of Chemical
and Biological Engineering, University of
Idaho, Moscow,
Idaho, USA
| | - Jagdish Suresh Patel
- Department of Chemical
and Biological Engineering, University of
Idaho, Moscow,
Idaho, USA
| | - Jannell V. Bazurto
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| |
Collapse
|
5
|
Khwathisi A, Madala NE, Traore AN, Samie A. Bioprospecting of soil-borne microorganisms and chemical dereplication of their anti-microbial constituents with the aid of UPLC-QTOF-MS and molecular networking approach. PeerJ 2024; 12:e17364. [PMID: 39035159 PMCID: PMC11260408 DOI: 10.7717/peerj.17364] [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: 01/24/2024] [Accepted: 04/18/2024] [Indexed: 07/23/2024] Open
Abstract
Due to the emergence of drug-resistant microorganisms, the search for broad-spectrum antimicrobial compounds has become extremely crucial. Natural sources like plants and soils have been explored for diverse metabolites with antimicrobial properties. This study aimed to identify microorganisms from agricultural soils exhibiting antimicrobial effects against known human pathogens, and to highlight the chemical space of the responsible compounds through the computational metabolomics-based bioprospecting approach. Herein, bacteria were extracted from soil samples and their antimicrobial potential was measured via the agar well diffusion method. Methanolic extracts from the active bacteria were analyzed using the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) technique, and the subsequent data was further analyzed through molecular networking approach which aided in identification of potential anti-microbial compounds. Furthermore, 16S rRNA gene sequencing enabled identification of the active bacterial isolates, where isolate 1 and 2 were identified as strains of Bacillus pumilus, whilst isolate 3 was found to be Bacillus subtilis. Interestingly, isolate 3 (Bacillus subtilis) displayed wide-ranging antimicrobial activity against the tested human pathogens. Molecular networking revealed the presence of Diketopiperazine compounds such as cyclo (D-Pro-D-Leu), cyclo (L-Tyr-L-Pro), cyclo (L-Pro-D-Phe), and cyclo (L-Pro-L-Val), alongside Surfactin C, Surfactin B, Pumilacidin E, and Isarrin D in the Bacillus strains as the main anti-microbial compounds. The application of the molecular networking approach represents an innovation in the field of bio-guided bioprospection of microorganisms and has proved to be an effective and feasible towards unearthing potent antimicrobial compounds. Additionally, the (computational metabolomics-based) approach accelerates the discovery of bioactive compounds and isolation of strains which offer a promising avenue for discovering new clinical antimicrobials. Finally, soil microbial flora could serve an alternative source of anti-microbial compounds which can assist in the fight against emergence of multi-drug resistance bacterial pathogens.
Collapse
Affiliation(s)
- Adivhaho Khwathisi
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| | - Ntakadzeni Edwin Madala
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| | - Afsatou Ndama Traore
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| | - Amidou Samie
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| |
Collapse
|
6
|
Humaira Z, Cho D, Peng Y, Avila F, Park YL, Kim CY, Lee J. Demequina capsici sp. nov., a novel plant growth-promoting actinomycete isolated from the rhizosphere of bell pepper (Capsicum annuum). Sci Rep 2024; 14:15830. [PMID: 38982145 PMCID: PMC11233565 DOI: 10.1038/s41598-024-66202-x] [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: 05/10/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Demequina, commonly found in coastal and marine environments, represents a genus of Actinomycetes. In this study, strains Demequina PMTSA13T and OYTSA14 were isolated from the rhizosphere of Capsicum annuum, leading to the discovery of a novel species, Demequina capsici. Bacteria play a significant role in plant growth, yet there have been no reports of the genus Demequina acting as plant growth-promoting bacteria (PGPB). Comparative genomics analysis revealed ANI similarity values of 74.05-80.63% for PMTSA13T and 74.02-80.54% for OYTSA14, in comparison to various Demequina species. The digital DNA-DNA hybridization (dDDH) values for PMTSA13T ranged from 19 to 39%, and 19.1-38.6% for OYTSA14. Genome annotation revealed the presence of genes associated with carbohydrate metabolism and transport, suggesting a potential role in nutrient cycling and availability for plants. These strains were notably rich in genes related to 'carbohydrate metabolism and transport (G)', according to their Cluster of Orthologous Groups (COG) classification. Additionally, both strains were capable of producing auxin (IAA) and exhibited enzymatic activities for cellulose degradation and catalase. Furthermore, PMTSA13T and OYTSA14 significantly induced the growth of Arabidopsis thaliana seedlings primarily attributed to their capacity to produce IAA, which plays a crucial role in stimulating plant growth and development. These findings shed light on the potential roles of Demequina strains in plant-microbe interactions and agricultural applications. The type strain is Demequina capsici PMTSA13T (= KCTC 59028T = GDMCC 1.4451T), meanwhile OYTSA14 is identified as different strains of Demequina capsici.
Collapse
Affiliation(s)
- Zalfa Humaira
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea
| | - Donghyun Cho
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Forbes Avila
- Animal Model Research Group, Jeonbuk Branch Institute, Korea Institute of Toxicology, Jeongeup, Jeollabuk-do, 56212, Republic of Korea
- Human and Environmental Toxicology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea
| | - Yu Lim Park
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
7
|
Zheng T, Hou J, Wu T, Jin H, Dai Y, Xu J, Yang K, Lin D. Ferric Oxide Nanomaterials and Plant-Rhizobacteria Symbionts Cogenerate Iron Plaque for Removing Highly Chlorinated Contaminants in Dryland Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11063-11073. [PMID: 38869036 DOI: 10.1021/acs.est.4c03133] [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: 06/14/2024]
Abstract
Rhizosphere iron plaques derived from Fe-based nanomaterials (NMs) are a promising tool for sustainable agriculture. However, the requirement for flooded conditions to generate iron plaque limits the scope of the NM application. In this study, we achieved in situ Fenton oxidation of a highly chlorinated persistent organic pollutant (2,2',4,5,5'-pentachlorobiphenyl, PCB101) through iron plaque mediated by the interaction between α-Fe2O3 NMs and plant-rhizobacteria symbionts under dryland conditions. Mechanistically, the coexistence of α-Fe2O3 NMs and Pseudomonas chlororaphis JD37 stimulated alfalfa roots to secrete acidic and reductive agents as well as H2O2, which together mediated the rhizosphere Fenton reaction and converted α-Fe2O3 NMs into iron plaque rich in Fe(II)-silicate. Further verifications reproduced the Fenton reaction in vitro using α-Fe2O3 NMs and rhizosphere compounds, confirming the critical role of •OH in the oxidative degradation of PCB101. Significant reductions in PCB101 content by 18.6%, 42.9%, and 23.2% were respectively found in stem, leaf, and soil after a 120-d treatment, proving the effectiveness of this NMs-plant-rhizobacteria technique for simultaneously safe crop production and soil remediation. These findings can help expand the potential applications of nanobio interaction and its mediated iron plaque generation for both agricultural practice and soil remediation.
Collapse
Affiliation(s)
- Tianying Zheng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Ting Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Hui Jin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Yunbu Dai
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jiang Xu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Kun Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Ecological Civilization Academy, Anji 313300, China
| |
Collapse
|
8
|
Song Y, Yao S, Li X, Wang T, Jiang X, Bolan N, Warren CR, Northen TR, Chang SX. Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems. ECO-ENVIRONMENT & HEALTH 2024; 3:227-237. [PMID: 38680731 PMCID: PMC11047296 DOI: 10.1016/j.eehl.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 05/01/2024]
Abstract
Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.
Collapse
Affiliation(s)
- Yang Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi Yao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaona Li
- School of Environment and Ecology, Jiangnan University, Wuxi 225127, China
| | - Tao Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nanthi Bolan
- School of Agriculture and Environment, The University of Western Australia, Nedland, WA-6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Nedland, WA-6009, Australia
- Healthy Environments and Lives (HEAL) National Research Network, Australia
| | - Charles R. Warren
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building A08, NSW 2006, Australia
| | - Trent R. Northen
- Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Scott X. Chang
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| |
Collapse
|
9
|
Liu Z, Zhang J, Fan C, Sun S, An X, Sun Y, Gao T, Zhang D. Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105875. [PMID: 38685217 DOI: 10.1016/j.pestbp.2024.105875] [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: 02/02/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.
Collapse
Affiliation(s)
- Zhaosha Liu
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Jizong Zhang
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Chenxi Fan
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Shangyi Sun
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Xutong An
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Yanheng Sun
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Tongguo Gao
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Dongdong Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China.
| |
Collapse
|
10
|
Tan W, Nian H, Tran LSP, Jin J, Lian T. Small peptides: novel targets for modulating plant-rhizosphere microbe interactions. Trends Microbiol 2024:S0966-842X(24)00085-4. [PMID: 38670883 DOI: 10.1016/j.tim.2024.03.011] [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: 12/17/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering.
Collapse
Affiliation(s)
- Weiyi Tan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Jing Jin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
| |
Collapse
|
11
|
Olanrewaju OS, Glick BR, Babalola OO. Metabolomics-guided utilization of beneficial microbes for climate-resilient crops. Curr Opin Chem Biol 2024; 79:102427. [PMID: 38290195 DOI: 10.1016/j.cbpa.2024.102427] [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: 04/26/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.
Collapse
Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Unit for Environmental Sciences and Management, Potchefstroom Campus, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa.
| |
Collapse
|
12
|
Silva E, Dantas R, Barbosa JC, Berlinck RGS, Fill T. Metabolomics approach to understand molecular mechanisms involved in fungal pathogen-citrus pathosystems. Mol Omics 2024; 20:154-168. [PMID: 38273771 DOI: 10.1039/d3mo00182b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Citrus is a crucial crop with a significant economic impact globally. However, postharvest decay caused by fungal pathogens poses a considerable threat, leading to substantial financial losses. Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii and Phyllosticta citricarpa are the main fungal pathogens, causing green mold, blue mold, sour rot and citrus black spot diseases, respectively. The use of chemical fungicides as a control strategy in citrus raises concerns about food and environmental safety. Therefore, understanding the molecular basis of host-pathogen interactions is essential to find safer alternatives. This review highlights the potential of the metabolomics approach in the search for bioactive compounds involved in the pathogen-citrus interaction, and how the integration of metabolomics and genomics contributes to the understanding of secondary metabolites associated with fungal virulence and the fungal infection mechanisms. Our goal is to provide a pipeline combining metabolomics and genomics that can effectively guide researchers to perform studies aiming to contribute to the understanding of the fundamental chemical and biochemical aspects of pathogen-host interactions, in order to effectively develop new alternatives for fungal diseases in citrus cultivation. We intend to inspire the scientific community to question unexplored biological systems, and to employ diverse analytical approaches and metabolomics techniques to address outstanding questions about the non-studied pathosystems from a chemical biology perspective.
Collapse
Affiliation(s)
- Evandro Silva
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
- University of São Paulo, Institute of Chemistry, CEP 13566-590, São Carlos, SP, Brazil
| | - Rodolfo Dantas
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| | - Júlio César Barbosa
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| | - Roberto G S Berlinck
- University of São Paulo, Institute of Chemistry, CEP 13566-590, São Carlos, SP, Brazil
| | - Taicia Fill
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| |
Collapse
|
13
|
Yang Y, Hu J, Wei X, Huang K, Li C, Yang G. Deciphering core microbiota in rhizosphere soil and roots of healthy and Rhizoctonia solani-infected potato plants from various locations. Front Microbiol 2024; 15:1386417. [PMID: 38585705 PMCID: PMC10995396 DOI: 10.3389/fmicb.2024.1386417] [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: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Black scurf caused by Rhizoctonia solani severely affects potato production. Through amplification of V3-V4 and ITS1-5f variable regions of 16S and internal transcribed spacer (ITS) rRNA, the study was based on the location (Kunming, Qujing, and Zhaotong), plant components (rhizosphere soil and roots), and sample types (healthy and diseased) to assess the diversity of bacterial and fungal communities. We found plant components significantly influence microbial diversity, with rhizosphere soil being more diverse than roots, and the microbial community in the root is mainly derived from the rhizosphere soil. Moreover, the rhizosphere soil and roots of healthy potato plants exhibit greater microbial diversity compared to those of potato plants infected by Rhizoctonia solani. Bacterial phyla Actinobacteriota and Acidobacteriota were enriched in rhizosphere soil compared to that of roots, whereas Proteobacteria and Cyanobacteria showed the opposite trend. Fungal phylum Ascomycota was found in low relative abundance in rhizosphere soil than in roots, whereas Basidiomycota showed the opposite trend. Bacterial genera including Streptomyces, Lysobacter, Bacillus, Pseudomonas, Ensifer, Enterobacter, and the Rhizobium group (Allorhizobium, Neorhizobium, Pararhizobium, Rhizobium), along with fungal genera such as Aspergillus, Penicillium, Purpureocillium, and Gibberella moniliformis, have the potential ability of plant growth promotion and disease resistance. However, most fungal species and some bacterial species are pathogenic to potato and could provide a conducive environment for black scurf infection. Interaction within the bacterial network increased in healthy plants, contrasting with the trend in the fungal network. Our findings indicate that R. solani significantly alters potato plant microbial diversity, underscoring the complexity and potential interactions between bacterial and fungal communities for promoting potato plant health and resistance against black scurf.
Collapse
Affiliation(s)
| | | | | | | | | | - Genhua Yang
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| |
Collapse
|
14
|
Musa OI, Akande SA, Ijah UJJ, Abioye OP, Maude AM, Samuel JO, Mustapha A, Abdulrahim AM, Gusdanis ACG. Biofilms communities in the soil: characteristic and interactions using mathematical model. Res Microbiol 2024; 175:104149. [PMID: 37923049 DOI: 10.1016/j.resmic.2023.104149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
There are many different kinds of microorganisms in the soil, and many of them are biofilms because they can make supracellular compounds. Surface-associated microorganisms in a biofilm are encased in a hydrated extracellular polymeric substance that aids in adherence and survival. Numerous different kinds of microorganisms call the soil home. Strong interactions with and among species are made possible by biofilms; this, in turn, might increase the effectiveness with which organic compounds and poisons in soil are degraded. This encouraged us to take a close look at soil biofilm ecosystems, which we do in this paper. In this research, we will look at how soil biofilms arise and how that affects the composition of microbial communities and their function in the soil. Recent years have seen an uptick in interest in questions about biofilm structure and the social interactions of various bacteria. Many concepts elucidating the underlying mathematics of biofilm growth are also presented. Since biofilms are so widespread, this breakthrough in soil biofilm inquiry might help scientists understand soil microbiomes better. Mathematical models further extrapolate the relationships between microbial communities and gives a more precise information as to what is happening in a biofilm. Biofilms can help plants cope with a variety of environmental challenges. Soil quality, plant nourishment, plant protection, bioremediation, and climate change are all influenced by the interplay of biofilm communities. Thus, biofilms play an important role in the development of environmentally friendly and sustainable agriculture.
Collapse
Affiliation(s)
- Ojeba Innocent Musa
- Department of Microbiology, Skyline University Nigeria, Kano State, Nigeria.
| | | | | | - Olabisi Peter Abioye
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Asmau Mohammed Maude
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Job Oloruntoba Samuel
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Adamu Mustapha
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Al-Musbahu Abdulrahim
- Department of Mathematics, Federal University of Technology, Minna Niger State, Nigeria
| | | |
Collapse
|
15
|
Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
Collapse
Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
16
|
Wu W, Wang J, Wang Z, Yan X, Wang Y, He X. Comparative Transcriptome Analysis Reveals the Molecular Mechanism of Bacillus velezensis GJ-7 Assisting Panax notoginseng against Meloidogyne hapla. Int J Mol Sci 2023; 24:17581. [PMID: 38139410 PMCID: PMC10743745 DOI: 10.3390/ijms242417581] [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: 10/13/2023] [Revised: 12/03/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The rhizosphere bacteria Bacillus velezensis GJ-7, as a biological control agent (BCA), has significant biological control effects on Meloidogyne hapla, and has strong colonization ability in the root of Panax notoginseng. In this study, we conducted a comparative transcriptome analysis using P. notoginseng plant roots treated with B. velezensis GJ-7 or sterile water alone and in combination with M. hapla inoculation to explore the interactions involving the P. notoginseng plant, B. velezensis GJ-7, and M. hapla. Four treatments from P. notoginseng roots were sequenced, and twelve high-quality total clean bases were obtained, ranging from 3.57 to 4.74 Gb. The Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that numerous DEGs are involved in the phenylpropane biosynthesis pathway and the MAPK signaling pathway in the roots of P. notoginseng with B. velezensis GJ-7 treatments. The analysis results of the two signaling pathways indicated that B. velezensis GJ-7 could enhance the expression of lignin- and camalexin-synthesis-related genes in plant roots to resist M. hapla. In addition, B. velezensis GJ-7 could enhance plant resistance to M. hapla by regulating the expression of resistance-related genes and transcription factors (TFs), including ETR, ERF, ChiB, WRKY22, and PR1. The expression of plant disease resistance genes in the roots of P. notoginseng with different treatments was validated by using real-time quantitative PCR (qRT-PCR), and the results were consistent with transcriptome sequencing. Taken together, this study indicated that B. velezensis GJ-7 can trigger a stronger defense response of P. notoginseng against M. hapla.
Collapse
Affiliation(s)
- Wentao Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.W.)
| | - Jingjing Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.W.)
| | - Zhuhua Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.W.)
| | - Xirui Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.W.)
| | - Yang Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.W.)
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.W.)
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China
| |
Collapse
|
17
|
Manickam S, Rajagopalan VR, Kambale R, Rajasekaran R, Kanagarajan S, Muthurajan R. Plant Metabolomics: Current Initiatives and Future Prospects. Curr Issues Mol Biol 2023; 45:8894-8906. [PMID: 37998735 PMCID: PMC10670879 DOI: 10.3390/cimb45110558] [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: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.
Collapse
Affiliation(s)
- Sudha Manickam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Rohit Kambale
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Raghu Rajasekaran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Selvaraju Kanagarajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| |
Collapse
|
18
|
Garaycochea S, Altier NA, Leoni C, Neal AL, Romero H. Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:352-369. [PMID: 37162018 PMCID: PMC10472533 DOI: 10.1111/1758-2229.13159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.
Collapse
Affiliation(s)
- Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Nora Adriana Altier
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Andrew L. Neal
- Net‐Zero and Resilient FarmingRothamsted Research, North WykeOkehamptonUK
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma/Genómica Evolutiva, Departamento de Ecología y Evolución, Facultad de Ciencias/CUREUniversidad de la RepúblicaMaldonadoUruguay
| |
Collapse
|
19
|
Hamany Djande CY, Tugizimana F, Steenkamp PA, Piater LA, Dubery IA. Metabolomic Reconfiguration in Primed Barley ( Hordeum vulgare) Plants in Response to Pyrenophora teres f. teres Infection. Metabolites 2023; 13:997. [PMID: 37755277 PMCID: PMC10537252 DOI: 10.3390/metabo13090997] [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: 08/08/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023] Open
Abstract
Necrotrophic fungi affect a wide range of plants and cause significant crop losses. For the activation of multi-layered innate immune defences, plants can be primed or pre-conditioned to rapidly and more efficiently counteract this pathogen. Untargeted and targeted metabolomics analyses were applied to elucidate the biochemical processes involved in the response of 3,5-dichloroanthranilic acid (3,5-DCAA) primed barley plants to Pyrenophora teres f. teres (Ptt). A susceptible barley cultivar ('Hessekwa') at the third leaf growth stage was treated with 3,5-DCAA 24 h prior to infection using a Ptt conidia suspension. The infection was monitored over 2, 4, and 6 days post-inoculation. For untargeted studies, ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-MS) was used to analyse methanolic plant extracts. Acquired data were processed to generate the data matrices utilised in chemometric modelling and multi-dimensional data mining. For targeted studies, selected metabolites from the amino acids, phenolic acids, and alkaloids classes were quantified using multiple reaction monitoring (MRM) mass spectrometry. 3,5-DCAA was effective as a priming agent in delaying the onset and intensity of symptoms but could not prevent the progression of the disease. Unsupervised learning methods revealed clear differences between the sample extracts from the control plants and the infected plants. Both orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and 'shared and unique structures' (SUS) plots allowed for the extraction of potential markers of the primed and naïve plant responses to Ptt. These include classes of organic acids, fatty acids, amino acids, phenolic acids, and derivatives and flavonoids. Among these, 5-oxo-proline and citric acid were notable as priming response-related metabolites. Metabolites from the tricarboxylic acid pathway were only discriminant in the primed plant infected with Ptt. Furthermore, the quantification of targeted metabolites revealed that hydroxycinnamic acids were significantly more prominent in the primed infected plants, especially at 2 d.p.i. Our research advances efforts to better understand regulated and reprogrammed metabolic responses that constitute defence priming in barley against Ptt.
Collapse
Affiliation(s)
| | | | | | | | - Ian A. Dubery
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa; (C.Y.H.D.); (F.T.); (P.A.S.); (L.A.P.)
| |
Collapse
|
20
|
Vogel D, Hills P, Moore JP. Strigolactones GR-24 and Nijmegen Applications Result in Reduced Susceptibility of Tobacco and Grapevine Plantlets to Botrytis cinerea Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:3202. [PMID: 37765366 PMCID: PMC10535315 DOI: 10.3390/plants12183202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Priming agents are plant defence-inducing compounds which can prompt a state of protection but may also aid in plant growth and interactions with beneficial microbes. The synthetic strigolactones (±)-GR24 and Nijmegen-1 were evaluated as potential priming agents for induced resistance against Botrytis cinerea in tobacco and grapevine plants. The growth and stress response profiles of B. cinerea to strigolactones were also investigated. Soil drench treatment with strigolactones induced resistance in greenhouse-grown tobacco plants and restricted lesion development. The mode of action appeared to function by priming redox-associated compounds to produce an anti-oxidant protective response for limiting the infection. The results obtained in the in vitro assays mirrored that of the greenhouse-grown plants. Exposure of B. cinerea to the strigolactones resulted in increased hyphal branching, with (±)-GR24 stimulating a stronger effect than Nijmegen-1 by affecting colony diameter and radial growth. An oxidative stress response was observed, with B. cinerea exhibiting increased ROS and SOD levels when grown with strigolactones. This study identified the application of strigolactones as potential priming agents to induce disease resistance in both tobacco and grapevine plants. In addition, strigolactones may alter the ROS homeostasis of B. cinerea, resulting in both morphological and physiological changes, thereby reducing virulence.
Collapse
Affiliation(s)
- Dominic Vogel
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Paul Hills
- Institute for Plant Biotechnology, Department of Genetics, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7602, South Africa
| | - John P Moore
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7600, South Africa
| |
Collapse
|
21
|
Zulfiqar U, Haider FU, Maqsood MF, Mohy-Ud-Din W, Shabaan M, Ahmad M, Kaleem M, Ishfaq M, Aslam Z, Shahzad B. Recent Advances in Microbial-Assisted Remediation of Cadmium-Contaminated Soil. PLANTS (BASEL, SWITZERLAND) 2023; 12:3147. [PMID: 37687393 PMCID: PMC10490184 DOI: 10.3390/plants12173147] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Soil contamination with cadmium (Cd) is a severe concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Industries such as mining, manufacturing, building, etc., rapidly produce a substantial amount of Cd, posing environmental risks. Cd toxicity in crop plants decreases nutrient and water uptake and translocation, increases oxidative damage, interferes with plant metabolism and inhibits plant morphology and physiology. However, various conventional physicochemical approaches are available to remove Cd from the soil, including chemical reduction, immobilization, stabilization and electro-remediation. Nevertheless, these processes are costly and unfriendly to the environment because they require much energy, skilled labor and hazardous chemicals. In contrasting, contaminated soils can be restored by using bioremediation techniques, which use plants alone and in association with different beneficial microbes as cutting-edge approaches. This review covers the bioremediation of soils contaminated with Cd in various new ways. The bioremediation capability of bacteria and fungi alone and in combination with plants are studied and analyzed. Microbes, including bacteria, fungi and algae, are reported to have a high tolerance for metals, having a 98% bioremediation capability. The internal structure of microorganisms, their cell surface characteristics and the surrounding environmental circumstances are all discussed concerning how microbes detoxify metals. Moreover, issues affecting the effectiveness of bioremediation are explored, along with potential difficulties, solutions and prospects.
Collapse
Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- University of Chinese Academy of Sciences, Beijing 100039, China
| | | | - Waqas Mohy-Ud-Din
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan;
- Department of Soil and Environmental Sciences, Ghazi University, D. G. Khan 32200, Pakistan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Muhammad Shabaan
- Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan;
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; (M.A.); (M.I.)
| | - Muhammad Kaleem
- Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Muhammad Ishfaq
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; (M.A.); (M.I.)
- Department of Agriculture, Extension, Azad Jammu & Kashmir, Pakistan
| | - Zoya Aslam
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Babar Shahzad
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| |
Collapse
|
22
|
Wahab A, Muhammad M, Munir A, Abdi G, Zaman W, Ayaz A, Khizar C, Reddy SPP. Role of Arbuscular Mycorrhizal Fungi in Regulating Growth, Enhancing Productivity, and Potentially Influencing Ecosystems under Abiotic and Biotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:3102. [PMID: 37687353 PMCID: PMC10489935 DOI: 10.3390/plants12173102] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with the roots of nearly all land-dwelling plants, increasing growth and productivity, especially during abiotic stress. AMF improves plant development by improving nutrient acquisition, such as phosphorus, water, and mineral uptake. AMF improves plant tolerance and resilience to abiotic stressors such as drought, salt, and heavy metal toxicity. These benefits come from the arbuscular mycorrhizal interface, which lets fungal and plant partners exchange nutrients, signalling molecules, and protective chemical compounds. Plants' antioxidant defence systems, osmotic adjustment, and hormone regulation are also affected by AMF infestation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress conditions. As a result of its positive effects on soil structure, nutrient cycling, and carbon sequestration, AMF contributes to the maintenance of resilient ecosystems. The effects of AMFs on plant growth and ecological stability are species- and environment-specific. AMF's growth-regulating, productivity-enhancing role in abiotic stress alleviation under abiotic stress is reviewed. More research is needed to understand the molecular mechanisms that drive AMF-plant interactions and their responses to abiotic stresses. AMF triggers plants' morphological, physiological, and molecular responses to abiotic stress. Water and nutrient acquisition, plant development, and abiotic stress tolerance are improved by arbuscular mycorrhizal symbiosis. In plants, AMF colonization modulates antioxidant defense mechanisms, osmotic adjustment, and hormonal regulation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress circumstances. AMF-mediated effects are also enhanced by essential oils (EOs), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), hydrogen peroxide (H2O2), malondialdehyde (MDA), and phosphorus (P). Understanding how AMF increases plant adaptation and reduces abiotic stress will help sustain agriculture, ecosystem management, and climate change mitigation. Arbuscular mycorrhizal fungi (AMF) have gained prominence in agriculture due to their multifaceted roles in promoting plant health and productivity. This review delves into how AMF influences plant growth and nutrient absorption, especially under challenging environmental conditions. We further explore the extent to which AMF bolsters plant resilience and growth during stress.
Collapse
Affiliation(s)
- Abdul Wahab
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Murad Muhammad
- University of Chinese Academy of Sciences, Beijing 100049, China;
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Asma Munir
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan;
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran;
| | - Wajid Zaman
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
| | - Asma Ayaz
- Faculty of Sports Science, Ningbo University, Ningbo 315211, China;
| | - Chandni Khizar
- Institute of Molecular Biology and Biochemistry, University of the Lahore, Lahore 51000, Pakistan;
| | | |
Collapse
|
23
|
Parker GD, Hanley L, Yu XY. Mass Spectral Imaging to Map Plant-Microbe Interactions. Microorganisms 2023; 11:2045. [PMID: 37630605 PMCID: PMC10459445 DOI: 10.3390/microorganisms11082045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.
Collapse
Affiliation(s)
- Gabriel D. Parker
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Luke Hanley
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiao-Ying Yu
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| |
Collapse
|
24
|
Mazoyon C, Firmin S, Bensaddek L, Pecourt A, Chabot A, Faucon MP, Sarazin V, Dubois F, Duclercq J. Optimizing Crop Production with Bacterial Inputs: Insights into Chemical Dialogue between Sphingomonas sediminicola and Pisum sativum. Microorganisms 2023; 11:1847. [PMID: 37513019 PMCID: PMC10385058 DOI: 10.3390/microorganisms11071847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The use of biological inputs is an interesting approach to optimize crop production and reduce the use of chemical inputs. Understanding the chemical communication between bacteria and plants is critical to optimizing this approach. Recently, we have shown that Sphingomonas (S.) sediminicola can improve both nitrogen supply and yield in pea. Here, we used biochemical methods and untargeted metabolomics to investigate the chemical dialog between S. sediminicola and pea. We also evaluated the metabolic capacities of S. sediminicola by metabolic profiling. Our results showed that peas release a wide range of hexoses, organic acids, and amino acids during their development, which can generally recruit and select fast-growing organisms. In the presence of S. sediminicola, a more specific pattern of these molecules took place, gradually adapting to the metabolic capabilities of the bacterium, especially for pentoses and flavonoids. In turn, S. sediminicola is able to produce several compounds involved in cell differentiation, biofilm formation, and quorum sensing to shape its environment, as well as several molecules that stimulate pea growth and plant defense mechanisms.
Collapse
Affiliation(s)
- Candice Mazoyon
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80039 Amiens, France
| | - Stéphane Firmin
- Agroécologie, Hydrogéochimie, Milieux et Ressources (AGHYLE, UP2018.C101) UniLaSalle, 60026 Beauvais, France
| | - Lamine Bensaddek
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80039 Amiens, France
| | - Audrey Pecourt
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80039 Amiens, France
- AgroStation, 68700 Aspach-le-Bas, France
| | - Amélie Chabot
- UFR des Sciences, Université de Picardie Jules Verne (UPJV), 80039 Amiens, France
| | - Michel-Pierre Faucon
- Agroécologie, Hydrogéochimie, Milieux et Ressources (AGHYLE, UP2018.C101) UniLaSalle, 60026 Beauvais, France
| | | | - Fréderic Dubois
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80039 Amiens, France
| | - Jérôme Duclercq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80039 Amiens, France
| |
Collapse
|
25
|
Dos Santos C, Franco OL. Pathogenesis-Related Proteins (PRs) with Enzyme Activity Activating Plant Defense Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112226. [PMID: 37299204 DOI: 10.3390/plants12112226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/12/2023]
Abstract
Throughout evolution, plants have developed a highly complex defense system against different threats, including phytopathogens. Plant defense depends on constitutive and induced factors combined as defense mechanisms. These mechanisms involve a complex signaling network linking structural and biochemical defense. Antimicrobial and pathogenesis-related (PR) proteins are examples of this mechanism, which can accumulate extra- and intracellular space after infection. However, despite their name, some PR proteins are present at low levels even in healthy plant tissues. When they face a pathogen, these PRs can increase in abundance, acting as the first line of plant defense. Thus, PRs play a key role in early defense events, which can reduce the damage and mortality caused by pathogens. In this context, the present review will discuss defense response proteins, which have been identified as PRs, with enzymatic action, including constitutive enzymes, β-1,3 glucanase, chitinase, peroxidase and ribonucleases. From the technological perspective, we discuss the advances of the last decade applied to the study of these enzymes, which are important in the early events of higher plant defense against phytopathogens.
Collapse
Affiliation(s)
- Cristiane Dos Santos
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
| |
Collapse
|
26
|
Hamany Djande CY, Steenkamp PA, Piater LA, Tugizimana F, Dubery IA. Metabolic Reprogramming of Barley in Response to Foliar Application of Dichlorinated Functional Analogues of Salicylic Acid as Priming Agents and Inducers of Plant Defence. Metabolites 2023; 13:metabo13050666. [PMID: 37233707 DOI: 10.3390/metabo13050666] [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: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Designing innovative biological crop protection strategies to stimulate natural plant immunity is motivated by the growing need for eco-friendly alternatives to conventional biocidal agrochemicals. Salicylic acid (SA) and analogues are known chemical inducers of priming plant immunity against environmental stresses. The aim of the study was to study the metabolic reprogramming in barley plants following an application of three proposed dichlorinated inducers of acquired resistance. 3,5-Dichloroanthranilic acid, 2,6-dichloropyridine-4-carboxylic acid, and 3,5-dichlorosalicylic acid were applied to barley at the third leaf stage of development and harvested at 12, 24, and 36 h post-treatment. Metabolites were extracted using methanol for untargeted metabolomics analyses. Samples were analysed by ultra-high performance liquid chromatography coupled to high-definition mass spectrometry (UHPLC-HDMS). Chemometric methods and bioinformatics tools were used to mine and interpret the generated data. Alterations in the levels of both primary and secondary metabolites were observed. The accumulation of barley-specific metabolites, hordatines, and precursors was observed from 24 h post-treatment. The phenylpropanoid pathway, a marker of induced resistance, was identified among the key mechanisms activated by the treatment with the three inducers. No salicylic acid or SA derivatives were annotated as signatory biomarkers; instead, jasmonic acid precursors and derivatives were found as discriminatory metabolites across treatments. The study highlights differences and similarities in the metabolomes of barley after treatment with the three inducers and points to the triggering chemical changes associated with defence and resistance. This report is the first of its kind, and the knowledge acquired provides deeper insight into the role of dichlorinated small molecules as inducers of plant immunity and can be used in metabolomics-guided plant improvement programmes.
Collapse
Affiliation(s)
- Claude Y Hamany Djande
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Paul A Steenkamp
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Lizelle A Piater
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Fidele Tugizimana
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Ian A Dubery
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| |
Collapse
|
27
|
Qi S, Wang J, Zhang Y, Naz M, Afzal MR, Du D, Dai Z. Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091860. [PMID: 37176919 PMCID: PMC10181282 DOI: 10.3390/plants12091860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.
Collapse
Affiliation(s)
- Shanshan Qi
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yi Zhang
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Muhammad Rahil Afzal
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Zhicong Dai
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| |
Collapse
|
28
|
Hernández-Soberano C, López-Bucio J, Valencia-Cantero E. The Bacterial Volatile Organic Compound N,N-Dimethylhexadecylamine Induces Long-Lasting Developmental and Immune Responses throughout the Life Cycle of Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1540. [PMID: 37050166 PMCID: PMC10096718 DOI: 10.3390/plants12071540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
N,N-dimethylhexadecylamine (DMHDA) is a bacterial volatile organic compound that affects plant growth and morphogenesis and is considered a cross-kingdom signal molecule. Its bioactivity involves crosstalk with the cytokinin and jasmonic acid (JA) pathways to control stem cell niches and induce iron deficiency adaptation and plant defense. In this study, through genetic analysis, we show that the DMHDA-JA-Ethylene (ET) relations determine the magnitude of the defensive response mounted during the infestation of Arabidopsis plants by the pathogenic fungus Botrytis cinerea. The Arabidopsis mutants defective in the JA receptor CORONATINE INSENSITIVE 1 (coi1-1) showed a more severe infestation when compared to wild-type plants (Col-0) that were partially restored by DMHDA supplements. Moreover, the oversensitivity manifested by ETHYLENE INSENSITIVE 2 (ein2) by B. cinerea infestation could not be reverted by the volatile, suggesting a role for this gene in DMHDA reinforcement of immunity. Growth of Col-0 plants was inhibited by DMHDA, but ein2 did not. Noteworthy, Arabidopsis seeds treated with DMHDA produced more vigorous plants throughout their life cycle. These data are supportive of a scenario where plant perception of a bacterial volatile influences the resistance to a fungal phytopathogen while modulating plant growth.
Collapse
|
29
|
Sharma I, Kashyap S, Agarwala N. Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community. FRONTIERS IN PLANT SCIENCE 2023; 14:1132824. [PMID: 36968415 PMCID: PMC10036841 DOI: 10.3389/fpls.2023.1132824] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.
Collapse
|
30
|
Zhang F, Xu N, Zhang Z, Zhang Q, Yang Y, Yu Z, Sun L, Lu T, Qian H. Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:35972-35984. [PMID: 36539666 DOI: 10.1007/s11356-022-24835-3] [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: 09/08/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.
Collapse
Affiliation(s)
- Fan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhitao Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| |
Collapse
|
31
|
Miao S, Liang J, Xu Y, Yu G, Shao M. Bacillaene, sharp objects consist in the arsenal of antibiotics produced by Bacillus. J Cell Physiol 2023. [PMID: 36790954 DOI: 10.1002/jcp.30974] [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: 10/24/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Bacillus species act as plant growth-promoting rhizobacteria (PGPR) that can produce a large number of bioactive metabolites. Bacillaene, a linear polyketide/nonribosomal peptide produced by Bacillus strains, is synthesized by the trans-acyltransferase polyketide synthetase. The complexity of the chemical structure, particularity of biosynthesis, potent bioactivity, and the important role of competition make Bacillus an ideal antibiotic weapon to resist other microbes and maintain the optimal rhizosphere environment. This review provides an updated view of the structural features, biological activity, biosynthetic regulators of biosynthetic pathways, and the important competitive role of bacillaene during Bacillus survival.
Collapse
Affiliation(s)
- Shuang Miao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Jianhao Liang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Yuan Xu
- College of Pharmaceutical Engineering, XinYang College Of Agriculture And Forestry, Xinyang, P.R. China
| | - Guohui Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Mingwei Shao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| |
Collapse
|
32
|
Jain R, Bhardwaj P, Guleria S, Pandey A, Kumar S. Polyamine metabolizing rhizobacteria Pseudomonas sp. GBPI_506 modulates hormone signaling to enhance lateral roots and nicotine biosynthesis in Nicotiana benthamiana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 195:193-205. [PMID: 36641943 DOI: 10.1016/j.plaphy.2023.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 12/21/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Beneficial rhizobacteria in the soil are important drivers of plant health and growth. In this study, we provide the draft genome of a root colonizing and auxin-producing Pseudomonas sp. strain GBPI_506. The bacterium was investigated for its contribution in the growth of Nicotiana benthamiana (Nb) and biosynthesis of nicotine. The bacterium showed chemotaxis towards root exudates potentially mediated by putrescine, a polyamine compound, to colonize the roots of Nb. Application of the bacterium with the roots of Nb, increased plant biomass and total soluble sugars in the leaves, and promoted lateral root (LR) development as compared to the un-inoculated plants. Confocal analysis using transgenic (DR5:GFP) Arabidopsis showed increased auxin trafficking in the LR of inoculated plants. Upregulation of nicotine biosynthesis genes and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling in the roots of inoculated plants suggested increased nicotine biosynthesis as a result of bacterial application. An increased JA content in roots and nicotine accumulation in leaves provided evidence on JA-mediated upregulation of nicotine biosynthesis in the bacterized plants. The findings suggested that the bacterial root colonization triggered networking between auxin, SA, and JA to facilitate LR development leading to enhanced plant growth and nicotine biosynthesis in Nb.
Collapse
Affiliation(s)
- Rahul Jain
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
| | - Priyanka Bhardwaj
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
| | - Shweta Guleria
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
| | - Anita Pandey
- Graphic Era Deemed to be University, Dehradun, 248002, Uttarakhand, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
| |
Collapse
|
33
|
Thakur R, Srivastava S, Yadav S. Multitrait Pseudomonas sp. isolated from the rhizosphere of Bergenia ciliata acts as a growth-promoting bioinoculant for plants. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1097587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Multifunctional plant growth-promoting bioinoculants are used to enhance growth, harvest yields, and add economic value to agricultural crops. In this study, such bioinoculant, BC-II-20 (Pseudomonas sp.), was isolated from the rhizospheric soil of a medicinal plant Bergenia ciliata from the Garhwal Himalayas, Uttarakhand, India. After characterization, supplementation with Pseudomonas sp. was used to study growth stimulation in a commercially important medicinal plant, Andrographis paniculata (Kalmegh), and it depicted enhanced physiological growth parameters under controlled conditions. Bacterial seed priming and also supplementation led to early and increased germination and plants displayed better vegetative growth during the entire growth stages. Early initiation of flowers and the appearance of pods occurred in inoculated plants, ultimately leading to the reduction in the life cycle of the plant. At the time of harvesting, there was an increase in the physiological parameters such as shoot length (38%), root length (14%), fresh weight (57%), dry weight (60%), number of panicles, and root branching. Photosynthetic efficiency was also higher, and ultimately, overall plant growth was improved by bacterial inoculation. The eco-friendly and sustainable use of this bioinoculant will provide an alternative to harmful chemical fertilizers and has become increasingly important. In conclusion, we reported a promising bioinoculant having plant growth-promoting traits, which promotes growth and development in A. paniculata and may be applied to other plants also.
Collapse
|
34
|
de Moraes Pontes JG, da Silva Pinheiro MS, Fill TP. Unveiling Chemical Interactions Between Plants and Fungi Using Metabolomics Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:1-20. [PMID: 37843803 DOI: 10.1007/978-3-031-41741-2_1] [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: 10/17/2023]
Abstract
Metabolomics has been extensively used in clinical studies in the search for new biomarkers of human diseases. However, this approach has also been highlighted in agriculture and biological sciences, once metabolomics studies have been assisting researchers to deduce new chemical mechanisms involved in biological interactions that occur between microorganisms and plants. In this sense, the knowledge of the biological role of each metabolite (virulence factors, signaling compounds, antimicrobial metabolites, among others) and the affected biochemical pathways during the interaction contribute to a better understand of different ecological relationships established in nature. The current chapter addresses five different applications of the metabolomics approach in fungal-plant interactions research: (1) Discovery of biomarkers in pathogen-host interactions, (2) plant diseases diagnosis, (3) chemotaxonomy, (4) plant defense, and (5) plant resistance; using mass spectrometry and/or nuclear magnetic resonance spectroscopy, which are the techniques most used in metabolomics.
Collapse
Affiliation(s)
- João Guilherme de Moraes Pontes
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil
| | - Mayra Suelen da Silva Pinheiro
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil
| | - Taícia Pacheco Fill
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil.
| |
Collapse
|
35
|
Li TY, Ye C, Zhang YJ, Zhang JX, Yang M, He XH, Mei XY, Liu YX, Zhu YY, Huang HC, Zhu SS. 2,3-Butanediol from the leachates of pine needles induces the resistance of Panax notoginseng to the leaf pathogen Alternaria panax. PLANT DIVERSITY 2023; 45:104-116. [PMID: 36876306 PMCID: PMC9975478 DOI: 10.1016/j.pld.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/19/2022] [Accepted: 02/24/2022] [Indexed: 06/03/2023]
Abstract
Compared with the use of monocultures in the field, cultivation of medicinal herbs in forests is an effective strategy to alleviate disease. Chemical interactions between herbs and trees play an important role in disease suppression in forests. We evaluated the ability of leachates from needles of Pinus armandii to induce resistance in Panax notoginseng leaves, identified the components via gas chromatography-mass spectrometry (GC-MS), and then deciphered the mechanism of 2,3-Butanediol as the main component in the leachates responsible for resistance induction via RNA sequencing (RNA-seq). Prespraying leachates and 2,3-Butanediol onto leaves could induce the resistance of P. notoginseng to Alternaria panax. The RNA-seq results showed that prespraying 2,3-Butanediol onto leaves with or without A. panax infection upregulated the expression of large number of genes, many of which are involved in transcription factor activity and the mitogen-activated protein kinase (MAPK) signaling pathway. Specifically, 2,3-Butanediol spraying resulted in jasmonic acid (JA) -mediated induced systemic resistance (ISR) by activating MYC2 and ERF1. Moreover, 2,3-Butanediol induced systemic acquired resistance (SAR) by upregulating pattern-triggered immunity (PTI)- and effector-triggered immunity (ETI)-related genes and activated camalexin biosynthesis through activation of WRKY33. Overall, 2,3-Butanediol from the leachates of pine needles could activate the resistance of P. notoginseng to leaf disease infection through ISR, SAR and camalexin biosynthesis. Thus, 2,3-Butanediol is worth developing as a chemical inducer for agricultural production.
Collapse
Affiliation(s)
- Tian-Yao Li
- School of Agriculture, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yi-Jie Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Xing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Xia-Hong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
- Southwest Forestry University, Kunming, 650224, China
| | - Xin-Yue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yi-Xiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - You-Yong Zhu
- School of Agriculture, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Hui-Chuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Shu-Sheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| |
Collapse
|
36
|
Wang Y, Teng Y, Zhang J, Zhang Z, Wang C, Wu X, Long X. Passion fruit plants alter the soil microbial community with continuous cropping and improve plant disease resistance by recruiting beneficial microorganisms. PLoS One 2023; 18:e0281854. [PMID: 36809377 PMCID: PMC9943001 DOI: 10.1371/journal.pone.0281854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Passion fruit (Passiflora edulis) is widely grown in tropical and subtropical regions, showing high economic and ornamental value. Microorganisms are indicators for the stability and health of the soil ecosystem, which can affect the yield and quality of passion fruit under continuous cropping. High-throughput sequencing and interactive analysis were used to analyse the variation of microbial communities in the noncultivated soil (NCS), cultivated soil (CS), and the rhizosphere soil of purple passion fruit (Passiflora edulis f. edulis ×Passiflora edulis f. flavicarpa, RP) and yellow passion fruit (Passiflora edulis f. flavicarpa, RY). An average of 98,001 high-quality fungal internal transcribed spacer (ITS) sequences, mainly from Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Glomeromycota, as well as an average of 71,299 high-quality bacterial 16S rRNA sequences, mainly from Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi, were obtained per sample. It was found that the continuous cropping of passion fruit increased the richness but reduced the diversity of soil fungi, while it dramatically increased the richness and diversity of soil bacteria. In addition, during the continuous cropping, grafting different scions in the same rootstock contributed to the aggregation of differential rhizosphere microbial communities. Among fungal genera, Trichoderma showed higher abundance in RY than in RP and CS, while the opposite was observed in the pathogen Fusarium. Moreover, the co-occurrence network and potential function analyses also showed that the appearance of Trichoderma was related to Fusarium and its contribution to plant metabolism was significantly greater in RY than in RP and CS. In conclusion, the rhizosphere of yellow passion fruit may be beneficial for the enrichment of disease-resistant microbes, such as Trichoderma, which may be an important factor inducing stronger resistance to stem rot. It will help to form a potential strategy for overcoming the pathogen-mediated obstacles in passion fruit and improve its yield and quality.
Collapse
Affiliation(s)
- Ye Wang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
- Institute of Mountain Resources of Guizhou Province, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Yao Teng
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
- Institute of Mountain Resources of Guizhou Province, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Jianli Zhang
- College of Eco-environmental Engineering, Guizhou Minzu University, Guiyang, Guizhou, China
| | - Zixiong Zhang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Chen Wang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Xiukun Wu
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Xiuqin Long
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
- * E-mail:
| |
Collapse
|
37
|
Sarkar AK, Sadhukhan S. Unearthing the alteration in plant volatiles induced by mycorrhizal fungi: A shield against plant pathogens. PHYSIOLOGIA PLANTARUM 2023; 175:e13845. [PMID: 36546667 DOI: 10.1111/ppl.13845] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Plants produce a large range of structurally varied low molecular weight secondary metabolites, which evaporate, known as volatile organic compounds (VOCs). Several of them are emitted in response to biotic stress as a defensive measure against pathogen attacks. Arbuscular Mycorrhizal Fungi (AMFs) can change the VOC pattern in parts of the plant and may promote plant defense via direct or indirect mechanisms. Mycorrhization of plants positively affects plant immunization along with growth and yield. The presence of AMF may raise the concentration of phenolic compounds and the activity of critical defense-related enzymes. AMF-induced changes in plant chemistry and associated volatile emissions lead to stronger immunity against pathogenic microorganisms. Despite substantial research into the origins of diversity in VOC-mediated plant communication, very little is known about the mechanism of influence of several AMFs on plant VOC emissions and modulation of plant immunization. Moreover, the molecular mechanism for VOC sensing in plants and mycorrhizal association is still unclear. In the present review, we have presented an up-to-date understanding of the cross-talk of AMF and VOC patterns in plants and the subsequent modulation of resistance against microbial pathogens.
Collapse
Affiliation(s)
- Anup Kumar Sarkar
- Department of Botany, Dukhulal Nibaran Chandra College, Murshidabad, West Bengal, India
- Plant Molecular Biology Laboratory, Department of Botany, Raiganj University, Uttar Dinajpur, West Bengal, India
| | - Sanjoy Sadhukhan
- Plant Molecular Biology Laboratory, Department of Botany, Raiganj University, Uttar Dinajpur, West Bengal, India
| |
Collapse
|
38
|
Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
Collapse
Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
| |
Collapse
|
39
|
Afridi MS, Ali S, Salam A, César Terra W, Hafeez A, Ali B, S AlTami M, Ameen F, Ercisli S, Marc RA, Medeiros FHV, Karunakaran R. Plant Microbiome Engineering: Hopes or Hypes. BIOLOGY 2022; 11:biology11121782. [PMID: 36552290 PMCID: PMC9774975 DOI: 10.3390/biology11121782] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.
Collapse
Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Willian César Terra
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Aqsa Hafeez
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Mona S AlTami
- Biology Department, College of Science, Qassim University, Burydah 52571, Saudi Arabia
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănă ̧stur Street, 400372 Cluj-Napoca, Romania
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Rohini Karunakaran
- Unit of Biochemistry, Centre of Excellence for Biomaterials Engineering, Faculty of Medicine, AIMST University, Semeling, Bedong 08100, Malaysia
- Department of Computational Biology, Institute of Bioinformatics, Saveetha School of Engineering (SSE), SIMATS, Thandalam, Chennai 602105, Tamil Nadu, India
- Centre of Excellence for Biomaterials Science, AIMST University, Semeling, Bedong 08100, Malaysia
| |
Collapse
|
40
|
Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
|
41
|
Aoki W, Kogawa M, Matsuda S, Matsubara K, Hirata S, Nishikawa Y, Hosokawa M, Takeyama H, Matoh T, Ueda M. Massively parallel single-cell genomics of microbiomes in rice paddies. Front Microbiol 2022; 13:1024640. [PMID: 36406415 PMCID: PMC9669790 DOI: 10.3389/fmicb.2022.1024640] [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: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.
Collapse
Affiliation(s)
- Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan,*Correspondence: Wataru Aoki,
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | | | | | | | - Yohei Nishikawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Hosokawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan,Haruko Takeyama,
| | - Toru Matoh
- Kyoto Agriculture Research Institute KARI, Kyoto, Japan,Toru Matoh,
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan,Mitsuyoshi Ueda,
| |
Collapse
|
42
|
Illuminating the signalomics of microbial biofilm on plant surfaces. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
43
|
Pantigoso HA, Newberger D, Vivanco JM. The rhizosphere microbiome: Plant-microbial interactions for resource acquisition. J Appl Microbiol 2022; 133:2864-2876. [PMID: 36648151 PMCID: PMC9796772 DOI: 10.1111/jam.15686] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 01/21/2023]
Abstract
While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant's own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant-microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.
Collapse
Affiliation(s)
- Hugo A. Pantigoso
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Derek Newberger
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Jorge M. Vivanco
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| |
Collapse
|
44
|
Metabology: Analysis of metabolomics data using community ecology tools. Anal Chim Acta 2022; 1232:340469. [DOI: 10.1016/j.aca.2022.340469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/15/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022]
|
45
|
De Palma M, Scotti R, D’Agostino N, Zaccardelli M, Tucci M. Phyto-Friendly Soil Bacteria and Fungi Provide Beneficial Outcomes in the Host Plant by Differently Modulating Its Responses through (In)Direct Mechanisms. PLANTS (BASEL, SWITZERLAND) 2022; 11:2672. [PMID: 36297696 PMCID: PMC9612229 DOI: 10.3390/plants11202672] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Sustainable agricultural systems based on the application of phyto-friendly bacteria and fungi are increasingly needed to preserve soil fertility and microbial biodiversity, as well as to reduce the use of chemical fertilizers and pesticides. Although there is considerable attention on the potential applications of microbial consortia as biofertilizers and biocontrol agents for crop management, knowledge on the molecular responses modulated in host plants because of these beneficial associations is still incomplete. This review provides an up-to-date overview of the different mechanisms of action triggered by plant-growth-promoting microorganisms (PGPMs) to promote host-plant growth and improve its defense system. In addition, we combined available gene-expression profiling data from tomato roots sampled in the early stages of interaction with Pseudomonas or Trichoderma strains to develop an integrated model that describes the common processes activated by both PGPMs and highlights the host's different responses to the two microorganisms. All the information gathered will help define new strategies for the selection of crop varieties with a better ability to benefit from the elicitation of microbial inoculants.
Collapse
Affiliation(s)
- Monica De Palma
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| | - Riccardo Scotti
- CREA Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Massimo Zaccardelli
- CREA Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy
| | - Marina Tucci
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| |
Collapse
|
46
|
Deng H, He R, Xia H, Xu N, Deng Q, Liang D, Lin L, Liao L, Xiong B, Xie X, Gao Z, Kang Q, Wang Z. Ultra-HPLC-MS pseudo-targeted metabolomic profiling reveals metabolites and associated metabolic pathway alterations in Asian plum ( Prunus salicina) fruits in response to gummosis disease. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:936-945. [PMID: 35817541 DOI: 10.1071/fp21168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Plum (Prunus spp.) is an economically and nutritionally important stone fruit that is grown worldwide. Gummosis disease (GD) is one of the most common limiting factors that adversely affects the yield and quality of stone fruits such as plum. Elucidating plum fruit metabolomics responses is essential to develop sustainable agricultural practices to combat GD in the future. Herein, an ultra-high-performance liquid chromatography coupled to mass-spectrometry (UHPLC-MS) pseudo-targeted metabolomic profiling was first performed to elucidate the overall metabolic alterations in Asian plum (Prunus salicina Lindl.) fruit in response to GD. The most pivotal differential metabolites, including certain amino acids and proanthocyanidins, in GD and control groups were identified by combining multivariate data analysis with strict statistical criteria. Metabolic pathway enrichment analysis showed that GD induced a series of coordinated defence responses and reprogramming of various metabolic pathways, including glucosinolate biosynthesis, 2-oxocarboxylic acid metabolism, valine, leucine and isoleucine degradation, and isoquinoline alkaloid biosynthesis pathways. Using UHPLC-MS-based pseudo-targeted metabolomic profiling, we systematically evaluated overall metabolic modifications in Asian plum fruits in response to GD for the first time. The identified metabolic pathway alterations helped to better understand the internal relationships and related metabolic networks.
Collapse
Affiliation(s)
- Honghong Deng
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Runmei He
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hui Xia
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Nuo Xu
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qunxian Deng
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Dong Liang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ling Liao
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Xiong
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinyu Xie
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhijian Gao
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingxuan Kang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhihui Wang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
47
|
Li S, Xiao Q, Yang H, Huang J, Li Y. Characterization of a new Bacillus velezensis as a powerful biocontrol agent against tomato gray mold. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 187:105199. [PMID: 36127070 DOI: 10.1016/j.pestbp.2022.105199] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/30/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Biocontrol microbes are environment-friendly and safe for humans and animals. To seek biocontrol microbes effective in suppressing tomato gray mold is important for tomato production. Therefore, serial experiments were conducted to characterize the antagonism of Bacillus velezensis HY19, a novel self-isolated biocontrol bacterium, against Botrytis cinerea in vitro and the control on tomato gray mold in greenhouse. This bacterium produced extracellular phosphatase, protease, cellulose and siderophores, and considerably inhibited the growth of B. cinerea. A liquid chromatography-mass spectrometry (LC-MS) detected salicylic acid and numerous antifungal substances present in B. velezensis HY19 fermentation liquid (BVFL). When B. cinerea was grown on potato glucose agar, BVFL crude extract remarkably suppressed the fungal growth and reduced protein content and the activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD). Transcriptome studies showed that BVFL crude extract significantly induced different expression of numerous genes in B. cinerea, most of which were down-regulated. Theses differently expressed genes were involved in the biological process, cell compartment, molecular functions, and metabolisms of glycine, serine, threonine, and sulfur in pathogen hyphae. Thus, this biocontrol bacterium antagonized B. cinerea in multiple ways due to the production of numerous antifungal substances that acted on multiple targets in the cells. BVFL significantly increased antioxidant enzyme activities in tomato leaves and decreased the incidence of tomato gray mold, with the control efficacies of 73.12-76.51%. Taken together, B. velezensis HY19 showed a promising use potential as a powerful bioagent against tomato gray mold.
Collapse
Affiliation(s)
- Suping Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Qingliang Xiao
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Hongjun Yang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Jianguo Huang
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
| | - Yong Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
| |
Collapse
|
48
|
Solanki MK, Solanki AC, Rai S, Srivastava S, Kashyap BK, Divvela PK, Kumar S, Yandigeri MS, Kashyap PL, Shrivastava AK, Ali B, Khan S, Jaremko M, Qureshi KA. Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere. Front Microbiol 2022; 13:990850. [PMID: 36225362 PMCID: PMC9548980 DOI: 10.3389/fmicb.2022.990850] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/18/2022] [Indexed: 12/28/2022] Open
Abstract
Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.
Collapse
Affiliation(s)
- Manoj Kumar Solanki
- Faculty of Natural Sciences, Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | | | - Shalini Rai
- Department of Biotechnology, Society of Higher Education and Practical Application (SHEPA), Varanasi, UP, India
| | - Supriya Srivastava
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, UP, India
| | | | - Sudheer Kumar
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | - Mahesh S. Yandigeri
- National Bureau of Agricultural Insect Resources (ICAR), Bengaluru, KA, India
- *Correspondence: Mahesh S. Yandigeri,
| | - Prem Lal Kashyap
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Khan
- Department of Agriculture, University of Swabi, Swabi, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Swat, Peshawar, Pakistan
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
- Kamal Ahmad Qureshi,
| |
Collapse
|
49
|
Tsotetsi T, Nephali L, Malebe M, Tugizimana F. Bacillus for Plant Growth Promotion and Stress Resilience: What Have We Learned? PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192482. [PMID: 36235347 PMCID: PMC9571655 DOI: 10.3390/plants11192482] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 06/12/2023]
Abstract
The rhizosphere is a thin film of soil that surrounds plant roots and the primary location of nutrient uptake, and is where important physiological, chemical, and biological activities are occurring. Many microbes invade the rhizosphere and have the capacity to promote plant growth and health. Bacillus spp. is the most prominent plant growth promoting rhizobacteria due to its ability to form long-lived, stress-tolerant spores. Bacillus-plant interactions are driven by chemical languages constructed by a wide spectrum of metabolites and lead to enhanced plant growth and defenses. Thus, this review is a synthesis and a critical assessment of the current literature on the application of Bacillus spp. in agriculture, highlighting gaps that remain to be explored to improve and expand on the Bacillus-based biostimulants. Furthermore, we suggest that omics sciences, with a focus on metabolomics, offer unique opportunities to illuminate the chemical intercommunications between Bacillus and plants, to elucidate biochemical and molecular details on modes of action of Bacillus-based formulations, to generate more actionable insights on cellular and molecular events that explain the Bacillus-induced growth promotion and stress resilience in plants.
Collapse
Affiliation(s)
- Teboho Tsotetsi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Motumiseng Malebe
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
- International R&D Division, Omnia Nutriology, Omnia Group (Pty) Ltd., Johannesburg 2021, South Africa
| |
Collapse
|
50
|
Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review. PLANTS 2022; 11:plants11182437. [PMID: 36145836 PMCID: PMC9502053 DOI: 10.3390/plants11182437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 01/10/2023]
Abstract
Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil–plant–microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.
Collapse
|