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Pflanze S, Mukherji R, Ibrahim A, Günther M, Götze S, Chowdhury S, Reimer L, Regestein L, Stallforth P. Nonribosomal peptides protect Pseudomonas nunensis 4A2e from amoebal and nematodal predation. Chem Sci 2023; 14:11573-11581. [PMID: 37886094 PMCID: PMC10599466 DOI: 10.1039/d3sc03335j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/01/2023] [Indexed: 10/28/2023] Open
Abstract
The rhizosphere is a highly competitive environment forcing bacteria to evolve strategies to oppose their enemies. The production of toxic secondary metabolites allows bacteria to counteract predators. In this study, we describe the anti-predator armamentarium of the soil-derived bacterium Pseudomonas nunensis 4A2e. Based on a genome mining approach, we identified several biosynthetic gene clusters coding for nonribosomal peptide synthetases. Generation of gene deletion mutants of the respective clusters shows a loss of defense capabilities. We isolated the novel lipopeptides keanumycin D and nunapeptins B and C, and fully elucidated their structures by a combination of in-depth mass spectrometry experiments, stable isotope labelling, and chemical synthesis. Additionally, investigation of the quorum sensing-dependent biosynthesis allowed us to elucidate parts of the underlying regulation of the biosynthetic machinery. Ecology-inspired bioassays highlight the role of these peptides as a defence strategy against protozoans and led us to find a previously unknown function against the bacterivorous nematode Oscheius myriophilus.
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Affiliation(s)
- Sebastian Pflanze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Ruchira Mukherji
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Markus Günther
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Sebastian Götze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Lisa Reimer
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Lars Regestein
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University (FSU) Jena Germany
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2
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Webster G, Mullins AJ, Petrova YD, Mahenthiralingam E. Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea). Front Microbiol 2023; 14:1240206. [PMID: 37692405 PMCID: PMC10485841 DOI: 10.3389/fmicb.2023.1240206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.
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Shi G, Luan L, Zhu G, Zeng Z, Zheng J, Shi Y, Sun B, Jiang Y. Interaction between nematodes and bacteria enhances soil carbon sequestration under organic material amendments. Front Microbiol 2023; 14:1155088. [PMID: 37250034 PMCID: PMC10213412 DOI: 10.3389/fmicb.2023.1155088] [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: 01/31/2023] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
The process of carbon (C) sequestration plays an important role in soil fertility and productivity, yet most studies have focused on the individual role of the bacterial community. However, an in-depth mechanistic understanding of how soil nematodes interact with the bacterial community to regulate soil C accumulation is still lacking. We conducted a 10-year field experiment to explore the nematode and bacterial communities and determine the influence of nematode-bacteria interactions on C mineralization, microbial metabolic quotient (qCO2), and carbon use efficiency (CUE) under the organic material amendments, including chemical fertilizers with straw (NS), chemical fertilizers with straw and pig manure (NSM), and chemical fertilizer with straw biochar (NB). Here, our results showed the abundance of bacterial and nematode communities was significantly higher under NS, NSM, and NB treatments than under chemical fertilizers (N) treatment, with the highest abundance under the NSM treatment. The enrichment index and functional dispersion index were significantly higher under NSM treatment than under N, NS, and NB treatments, while the channel index followed the opposite pattern. Structural equation modeling indicated that the potential predation pressure induced by nematodes may improve bacterial abundance, with positive cascading effects on C sequestration. Collectively, our study highlights the functional importance of nematode-microorganism interactions in mediating C dynamics under organic material amendments.
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Affiliation(s)
- Guangping Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China
| | - Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoyang Zeng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China
| | - Yue Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China
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4
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Zhang X, Linghu S, Chen Z, Gu H, Chen X, Wei X, Hu X, Yang Y, Gao Y. Bacterial diversity evolution process based on physicochemical characteristics of sludge treating hydroquinone during acclimation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:31686-31699. [PMID: 35001263 DOI: 10.1007/s11356-021-17325-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/29/2021] [Indexed: 06/14/2023]
Abstract
Hydroquinone is one of the main pollutants in coal-gasification wastewater, which is biologically toxic and difficult to remove. The aerobic biodegradation rate, organic toxicity, and microbial community structure at different acclimation stages of degradation of hydroquinone by activated sludge were investigated. In each acclimation cycle, the removal of hydroquinone reached 100% after 5 days, indicating that high-concentration hydroquinone in the activated sludge could be completely biodegraded. When the microbial flora was inhibited by the influent hydroquinone, the enzyme system experienced stress conditions and led to the secretion of secondary metabolites, extracellular protein of 5-10 kDa mainly contributing to the sludge organic toxicity. Microbial diversity analysis showed that with the increase of the concentration of hydroquinone, β-Proteus bacteria such as Azoarcus and Dechloromonas gradually accumulated, which improved the removal of hydroquinone with aerobic activated sludge in the sequencing batch reactor (SBR) system. As the inhibition degree exceeded the appropriate tolerance range of microorganisms, bacteria would secrete much more secondary metabolites, and the organic toxicity of sludge would reach a relatively high level.
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Affiliation(s)
- Xinyu Zhang
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Shanshan Linghu
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhichong Chen
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao Gu
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiurong Chen
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China.
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xiao Wei
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Xueyang Hu
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Yingying Yang
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuqing Gao
- National Engineering Laboratory for High-Concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, 200237, China
- Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
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5
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Clough SE, Jousset A, Elphinstone JG, Friman V. Combining in vitro and in vivo screening to identify efficient
Pseudomonas
biocontrol strains against the phytopathogenic bacterium
Ralstonia solanacearum. Microbiologyopen 2022; 11:e1283. [PMID: 35478286 PMCID: PMC9059233 DOI: 10.1002/mbo3.1283] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth‐promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain‐specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2,4‐diacetylphloroglucinol, pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. Although all these compounds suppressed R. solanacearum growth, only orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the “Micro‐Tom” tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas–Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.
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Affiliation(s)
- Sophie E. Clough
- Department of Biology University of York York UK
- Department of Biosciences Chemistry Durham University Durham UK
| | - Alexandre Jousset
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group Utrecht University Utrecht The Netherlands
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Chen X, Hu X, Lu Q, Yang Y, Linghu S, Zhang X. Study on the differences in sludge toxicity and microbial community structure caused by catechol, resorcinol and hydroquinone with metagenomic analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114027. [PMID: 34872176 DOI: 10.1016/j.jenvman.2021.114027] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
The aerobic biodegradation rate, organic toxicity and microbial community structure of activated sludge acclimated by catechol, resorcinol and hydroquinone were investigated, to study the relationship between microbial structure and sludge organic toxicity caused by phenolic compounds. At the stable operation stage, the degradation rates of the dihydroxy benzenes in a single sequencing batch reactor (SBR) cycle were followed the order: resorcinol (89.71%) > hydroquinone (85.64%) > catechol (59.62%). Sludge toxicity bioassay indicated that the toxicity of sludge was catechol (45.63%) > hydroquinone (40.28%) > resorcinol (38.15%). The accumulation of secondary metabolites such as 5-10 kDa tryptophan and tyrosine protein substances caused the differential sludge toxicity. Microbial metagenomic analysis showed that the toxicity of sludge was significantly related to the microbial community structure. Thauera, Azoarcus, Pseudomonas and other Proteobacteria formed in the sludge during acclimation. Catechol group had the least dominant bacteria and loop ring opening enzyme genes (catA, dmpB, dxnF, hapD) numbers. Therefore, the degradation of catechol was the most difficult than resorcinol and hydroquinone, resulting the highest sludge toxicity.
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Affiliation(s)
- Xiurong Chen
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xueyang Hu
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Quanling Lu
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yingying Yang
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Shanshan Linghu
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xinyu Zhang
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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7
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Khanna K, Kohli SK, Ohri P, Bhardwaj R. Plants-nematodes-microbes crosstalk within soil: A trade-off among friends or foes. Microbiol Res 2021; 248:126755. [PMID: 33845302 DOI: 10.1016/j.micres.2021.126755] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/18/2021] [Accepted: 03/27/2021] [Indexed: 11/28/2022]
Abstract
Plants interact with enormous biotic and abiotic components within ecosystem. For instance, microbes, insects, herbivores, animals, nematodes etc. In general, these interactions are studied independently with plants, that condenses only specific information about the interaction. However, the limitation to study the cross-interactions masks the collaborative role of organisms within ecosystem. Beneficial microbes are most prominent organisms that are needed to be studied due to their bidirectional nature towards plants. Fascinatingly, Plant-Parasitic Nematodes (PPNs) have been profoundly observed to cause mass destruction of agricultural crops worldwide. The huge demand for agriculture for present-day population requires optimization of production potential by curbing the damage caused by PPNs. Chemical nematicides combats their proliferation, but their extended usage has abruptly affected flora, fauna and human populations. Because of consistent pressing issues in regard to environment, the use of biocontrol agents are most favourable alternatives for managing agriculture. However, this association is somehow, tug of war, and understanding of plant-nematode-microbial relation would enable the agriculturists to monitor the overall development of plants along with limiting the use of agrochemicals. Soil microbes are contemporary bio-nematicides emerging in the market, that stimulates the plant growth and impedes PPNs populations. They form natural enemies and trap nematodes, henceforth, it is crucial to understand these interactions for ecological and biotechnological perspectives for commercial use. Moreover, acquiring the diversity of their relationship and molecular-based mechanisms, outlines their cascade of signaling events to serve as biotechnological ecosystem engineers. The omics based mechanisms encompassing hormone gene regulatory pathways and elicitors released by microbes are able to modulate pathogenesis-related (PR) genes within plants. This is achieved via Induced Systemic Resistance (ISR) or acquired systemic channels. Taking into account all these validations, the present review mainly advocates the relationship among microbes and nematodes in plants. It is believed that this review will boost zest and zeal within researchers to effectively understand the plant-nematodes-microbes relations and their ecological perspectives.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Sukhmeen Kaur Kohli
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
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8
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Martin-Rivilla H, Gutierrez-Mañero FJ, Gradillas A, P. Navarro MO, Andrade G, Lucas JA. Identifying the Compounds of the Metabolic Elicitors of Pseudomonas fluorescens N 21.4 Responsible for Their Ability to Induce Plant Resistance. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1020. [PMID: 32806693 PMCID: PMC7463883 DOI: 10.3390/plants9081020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/17/2022]
Abstract
In this work, the metabolic elicitors extracted from the beneficial rhizobacterium Pseudomonas fluorescens N 21.4 were sequentially fragmented by vacuum liquid chromatography to isolate, purify and identify the compounds responsible for the extraordinary capacities of this strain to induce systemic resistance and to elicit secondary defensive metabolism in diverse plant species. To check if the fractions sequentially obtained were able to increase the synthesis of isoflavones and if, therefore, they still maintained the eliciting capacity of the live strain, rapid and controlled experiments were done with soybean seeds. The optimal action concentration of the fractions was established and all of them elicited isoflavone secondary metabolism-the fractions that had been extracted with n-hexane being more effective. The purest fraction was the one with the highest eliciting capacity and was also tested in Arabidopsis thaliana seedlings to induce systemic resistance against the pathogen Pseudomonas syringae pv. tomato DC 3000. This fraction was then analyzed by UHPLC/ESI-QTOF-MS, and an alkaloid, two amino lipids, three arylalkylamines and a terpenoid were tentatively identified. These identified compounds could be part of commercial plant inoculants of biological and sustainable origin to be applied in crops, due to their potential to enhance the plant immune response and since many of them have putative antibiotic and/or antifungal potential.
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Affiliation(s)
- Helena Martin-Rivilla
- Plant Physiology Pharmaceutical and Health Sciences Department, Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (F.J.G.-M.); (J.A.L.)
| | - F. Javier Gutierrez-Mañero
- Plant Physiology Pharmaceutical and Health Sciences Department, Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (F.J.G.-M.); (J.A.L.)
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalyses, Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain;
| | - Miguel O. P. Navarro
- Laboratory of Microbial Ecology, Department of Microbiology, Londrina State University, Londrina 86051-990, Brazil; (M.O.P.N.); (G.A.)
| | - Galdino Andrade
- Laboratory of Microbial Ecology, Department of Microbiology, Londrina State University, Londrina 86051-990, Brazil; (M.O.P.N.); (G.A.)
| | - José A. Lucas
- Plant Physiology Pharmaceutical and Health Sciences Department, Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (F.J.G.-M.); (J.A.L.)
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9
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Yu XQ, Yan X, Zhang MY, Zhang LQ, He YX. Flavonoids repress the production of antifungal 2,4-DAPG but potentially facilitate root colonization of the rhizobacterium Pseudomonas fluorescens. Environ Microbiol 2020; 22:5073-5089. [PMID: 32363709 DOI: 10.1111/1462-2920.15052] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
Abstract
In the well-known legume-rhizobia symbiosis, flavonoids released by legume roots induce expression of the Nod factors and trigger early plant responses involved in root nodulation. However, it remains largely unknown how the plant-derived flavonoids influence the physiology of non-symbiotic beneficial rhizobacteria. In this work, we demonstrated that the flavonoids apigenin and/or phloretin enhanced the swarming motility and production of cellulose and curli in Pseudomonas fluorescens 2P24, both traits of which are essential for root colonization. Using a label-free quantitative proteomics approach, we showed that apigenin and phloretin significantly reduced the biosynthesis of the antifungal metabolite 2,4-DAPG and further identified a novel flavonoid-sensing TetR regulator PhlH, which was shown to modulate 2,4-DAPG production by regulating the expression of 2,4-DAPG hydrolase PhlG. Although having similar structures, apigenin and phloretin could also influence different physiological characteristics of P. fluorescens 2P24, with apigenin decreasing the biofilm formation and phloretin inducing expression of proteins involved in the denitrification and arginine fermentation processes. Taken together, our results suggest that plant-derived flavonoids could be sensed by the TetR regulator PhlH in P. fluorescens 2P24 and acts as important signalling molecules that strengthen mutually beneficial interactions between plants and non-symbiotic beneficial rhizobacteria.
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Affiliation(s)
- Xiao-Quan Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xu Yan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Meng-Yuan Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Li-Qun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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10
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Daura-Pich O, Hernández I, Pinyol-Escala L, Lara JM, Martínez-Servat S, Fernández C, López-García B. No antibiotic and toxic metabolites produced by the biocontrol agent Pseudomonas putida strain B2017. FEMS Microbiol Lett 2020; 367:5826813. [DOI: 10.1093/femsle/fnaa075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
ABSTRACTPseudomonas putida and closely-related species such as Pseudomonas fluorescens and Pseudomonas brassicacearum have been reported as potential biocontrol agents and plant growth-promoters. Recently, we have described the biocontrol activity of P. putida B2017 against several phytopathogens of agricultural relevance. In this study, its ability to produce potential antibiotic / toxic metabolites was assessed by functional, chromatography-mass spectrometry and genomic analysis. Our results show that B2017 is not able to synthesize surfactants and common antibiotics produced by Pseudomonas spp., i.e. pyrrolnitrin, 2,4-diacetylphloroglucinol, pyoluteorin and pyocyanin, but it produces pyoverdine, a siderophore which is involved in its biocontrol activity. The non-production of other metabolites, such as cyanide, safracin, promysalin and lipopeptides between others, is also discussed. Our data suggest that the mode of action of B2017 is not mainly due to the production of antimicrobial / toxic metabolites. Moreover, these features make P. putida B2017 a promising biocontrol microorganism for plant protection without side effects on environment, non-target organisms and human health.
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Affiliation(s)
- Oriol Daura-Pich
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Iker Hernández
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Lola Pinyol-Escala
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Jose M Lara
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Sonia Martínez-Servat
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Carolina Fernández
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Belén López-García
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
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11
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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12
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GC-MS analysis of volatile organic compounds from Bambara groundnut rhizobacteria and their antibacterial properties. World J Microbiol Biotechnol 2019; 35:83. [PMID: 31134356 PMCID: PMC6536467 DOI: 10.1007/s11274-019-2660-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/15/2019] [Indexed: 11/18/2022]
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Khan F, Jain S, Oloketuyi SF. Bacteria and bacterial products: Foe and friends to Caenorhabditis elegans. Microbiol Res 2018; 215:102-113. [DOI: 10.1016/j.micres.2018.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/11/2018] [Accepted: 06/24/2018] [Indexed: 02/07/2023]
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Cyanide Production by Chromobacterium piscinae Shields It from Bdellovibrio bacteriovorus HD100 Predation. mBio 2017; 8:mBio.01370-17. [PMID: 29259082 PMCID: PMC5736907 DOI: 10.1128/mbio.01370-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Predation of Chromobacterium piscinae by Bdellovibrio bacteriovorus HD100 was inhibited in dilute nutrient broth (DNB) but not in HEPES. Experiments showed that the effector responsible was present in the medium, as cell-free supernatants retained the ability to inhibit predation, and that the effector was not toxic to B. bacteriovorus. Violacein, a bisindole secondary metabolite produced by C. piscinae, was not responsible. Further characterization of C. piscinae found that this species produces sufficient concentrations of cyanide (202 µM) when grown in DNB to inhibit the predatory activity of B. bacteriovorus, but that in HEPES, the cyanide concentrations were negligible (19 µM). The antagonistic role of cyanide was further confirmed, as the addition of hydroxocobalamin, which chelates cyanide, allowed predation to proceed. The activity of cyanide against B. bacteriovorus was found to be twofold, depending on the life cycle stage of this predator. For the attack-phase predatory cells, cyanide caused the cells to lose motility and tumble, while for intraperiplasmic predators, development and lysis of the prey cell were halted. These findings suggest that cyanogenesis in nature may be employed by the bacterial strains that produce this compound to prevent and reduce their predation by B. bacteriovorus. Bacterial predators actively attack, kill, and enter the periplasm of susceptible Gram-negative bacteria, where they consume the prey cell components. To date, the activity of B. bacteriovorus HD100 has been demonstrated against more than 100 human pathogens. As such, this strain and others are being considered as potential alternatives or supplements to conventional antibiotics. However, the production of secondary metabolites by prey bacteria is known to mitigate, and even abolish, predation by bacterivorous nematodes and protists. With the exception of indole, which was shown to inhibit predation, the effects of bacterial secondary metabolites on B. bacteriovorus and its activities have not been considered. Consequently, we undertook this study to better understand the mechanisms that bacterial strains employ to inhibit predation by B. bacteriovorus HD100. We report here that cyanogenic bacterial strains can inhibit predation and show that cyanide affects both attack-phase predators and those within prey, i.e., in the bdelloplast.
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Flury P, Vesga P, Péchy-Tarr M, Aellen N, Dennert F, Hofer N, Kupferschmied KP, Kupferschmied P, Metla Z, Ma Z, Siegfried S, de Weert S, Bloemberg G, Höfte M, Keel CJ, Maurhofer M. Antimicrobial and Insecticidal: Cyclic Lipopeptides and Hydrogen Cyanide Produced by Plant-Beneficial Pseudomonas Strains CHA0, CMR12a, and PCL1391 Contribute to Insect Killing. Front Microbiol 2017; 8:100. [PMID: 28217113 PMCID: PMC5289993 DOI: 10.3389/fmicb.2017.00100] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/13/2017] [Indexed: 01/30/2023] Open
Abstract
Particular groups of plant-beneficial fluorescent pseudomonads are not only root colonizers that provide plant disease suppression, but in addition are able to infect and kill insect larvae. The mechanisms by which the bacteria manage to infest this alternative host, to overcome its immune system, and to ultimately kill the insect are still largely unknown. However, the investigation of the few virulence factors discovered so far, points to a highly multifactorial nature of insecticidal activity. Antimicrobial compounds produced by fluorescent pseudomonads are effective weapons against a vast diversity of organisms such as fungi, oomycetes, nematodes, and protozoa. Here, we investigated whether these compounds also contribute to insecticidal activity. We tested mutants of the highly insecticidal strains Pseudomonas protegens CHA0, Pseudomonas chlororaphis PCL1391, and Pseudomonas sp. CMR12a, defective for individual or multiple antimicrobial compounds, for injectable and oral activity against lepidopteran insect larvae. Moreover, we studied expression of biosynthesis genes for these antimicrobial compounds for the first time in insects. Our survey revealed that hydrogen cyanide and different types of cyclic lipopeptides contribute to insecticidal activity. Hydrogen cyanide was essential to full virulence of CHA0 and PCL1391 directly injected into the hemolymph. The cyclic lipopeptide orfamide produced by CHA0 and CMR12a was mainly important in oral infections. Mutants of CMR12a and PCL1391 impaired in the production of the cyclic lipopeptides sessilin and clp1391, respectively, showed reduced virulence in injection and feeding experiments. Although virulence of mutants lacking one or several of the other antimicrobial compounds, i.e., 2,4-diacetylphloroglucinol, phenazines, pyrrolnitrin, or pyoluteorin, was not reduced, these metabolites might still play a role in an insect background since all investigated biosynthetic genes for antimicrobial compounds of strain CHA0 were expressed at some point during insect infection. In summary, our study identified new factors contributing to insecticidal activity and extends the diverse functions of antimicrobial compounds produced by fluorescent pseudomonads from the plant environment to the insect host.
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Affiliation(s)
- Pascale Flury
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Pilar Vesga
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Maria Péchy-Tarr
- Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland
| | - Nora Aellen
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Francesca Dennert
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Nicolas Hofer
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | | | - Peter Kupferschmied
- Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland
| | - Zane Metla
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
- Laboratory of Experimental Entomology, Institute of Biology, University of LatviaRiga, Latvia
| | - Zongwang Ma
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Sandra Siegfried
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Sandra de Weert
- Microbial Biotechnology and Health, Institute of Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Guido Bloemberg
- Microbial Biotechnology and Health, Institute of Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Christoph J. Keel
- Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
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Canchignia H, Altimira F, Montes C, Sánchez E, Tapia E, Miccono M, Espinoza D, Aguirre C, Seeger M, Prieto H. Candidate nematicidal proteins in a new Pseudomonas veronii isolate identified by its antagonistic properties against Xiphinema index. J GEN APPL MICROBIOL 2016; 63:11-21. [PMID: 27989999 DOI: 10.2323/jgam.2016.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The nematode Xiphinema index affects grape vines and transmits important viruses associated with fanleaf degeneration. Pseudomonas spp. are an extensive bacterial group in which important biodegradation and/or biocontrol properties can occur for several strains in the group. The aim of this study was to identify new Pseudomonas isolates with antagonist activity against X. index. Forty bacterial isolates were obtained from soil and root samples from Chilean vineyards. Thirteen new fluorescent pseudomonads were found and assessed for their antagonistic capability. The nematicide Pseudomonas protegens CHA0 was used as a control. Challenges of nematode individuals in King's B semi-solid agar Petri dishes facilitated the identification of the Pseudomonas veronii isolate R4, as determined by a 16S rRNA sequence comparison. This isolate was as effective as CHA0 as an antagonist of X. index, although it had a different lethality kinetic. Milk-induced R4 cultures exhibited protease and lipase activities in cell supernatants using both gelatin/tributyrin Petri dish assays and zymograms. Three proteins with these activities were isolated and subjected to mass spectrometry. Amino acid partial sequences enabled the identification of a 49-kDa protease similar to metalloprotease AprA and two lipases of 50 kDa and 69 kDa similar to LipA and ExoU, respectively. Electron microscopy analyses of challenged nematodes revealed degraded cuticle after R4 supernatant treatment. These results represent a new and unexplored property in this species associated with the presence of secretable lipases and protease, similar to characterized enzymes present in biocontrol pseudomonads.
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Affiliation(s)
- Hayron Canchignia
- Biotechnology Doctoral Program, Universidad Técnica Federico Santa María-Pontificia Universidad Católica de Valparaíso
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Castaneda-Alvarez C, Aballay E. Rhizobacteria with nematicide aptitude: enzymes and compounds associated. World J Microbiol Biotechnol 2016; 32:203. [PMID: 27804103 DOI: 10.1007/s11274-016-2165-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
Abstract
The use of rhizobacteria to control plant parasitic nematodes has been widely studied. Currently, the research focuses on bacteria-nematode interactions that can mitigate this complex microbiome in agriculture. Various enzymes, toxins and metabolic by-products from rhizobacteria antagonize plant parasitic nematodes, and many different modes of action have been proposed. Hydrolytic enzymes, primarily proteases, collagenases and chitinases, have been related to the nematicide effect in rhizobacteria, proving to be an important factor involved in the degradation of different chemical constituents of nematodes at distinct developmental stages. Exuded metabolites may also alter the nematode-plant recognition process or create a hostile environment for nematodes in the rhizosphere. Specific bacteria strains responsible for the production of toxins, such as Cry proteins, are one of the strategies used by rhizobacteria. Characterization of the rhizobacteria mode of action could strengthen the development of commercial products to control populations of plant parasitic nematodes. This review aims to provide an overview of different enzymes and compounds produced by rhizobacteria related to the process of antagonism to plant-parasitic nematodes.
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Affiliation(s)
- C Castaneda-Alvarez
- Department of Crop Protection, Faculty of Agronomical Sciences, University of Chile, P.O. Box 1004, Santiago, Chile.
| | - E Aballay
- Department of Crop Protection, Faculty of Agronomical Sciences, University of Chile, P.O. Box 1004, Santiago, Chile
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Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, Raaijmakers JM, Duffy B, Höfte M, Blom J, Smits THM, Keel C, Maurhofer M. Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. THE ISME JOURNAL 2016; 10:2527-42. [PMID: 26894448 PMCID: PMC5030700 DOI: 10.1038/ismej.2016.5] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/09/2015] [Accepted: 12/22/2015] [Indexed: 11/09/2022]
Abstract
Bacteria of the genus Pseudomonas occupy diverse environments. The Pseudomonas fluorescens group is particularly well-known for its plant-beneficial properties including pathogen suppression. Recent observations that some strains of this group also cause lethal infections in insect larvae, however, point to a more versatile ecology of these bacteria. We show that 26 P. fluorescens group strains, isolated from three continents and covering three phylogenetically distinct sub-clades, exhibited different activities toward lepidopteran larvae, ranging from lethal to avirulent. All strains of sub-clade 1, which includes Pseudomonas chlororaphis and Pseudomonas protegens, were highly insecticidal regardless of their origin (animals, plants). Comparative genomics revealed that strains in this sub-clade possess specific traits allowing a switch between plant- and insect-associated lifestyles. We identified 90 genes unique to all highly insecticidal strains (sub-clade 1) and 117 genes common to all strains of sub-clade 1 and present in some moderately insecticidal strains of sub-clade 3. Mutational analysis of selected genes revealed the importance of chitinase C and phospholipase C in insect pathogenicity. The study provides insight into the genetic basis and phylogenetic distribution of traits defining insecticidal activity in plant-beneficial pseudomonads. Strains with potent dual activity against plant pathogens and herbivorous insects have great potential for use in integrated pest management for crops.
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Affiliation(s)
- Pascale Flury
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Nora Aellen
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Beat Ruffner
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Maria Péchy-Tarr
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shakira Fataar
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Zane Metla
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Laboratory of Experimental Entomology, Institute of Biology, University of Latvia, Riga, Latvia
| | | | - Guido Bloemberg
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zürich University of Applied Sciences, Wädenswil, Switzerland
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zürich University of Applied Sciences, Wädenswil, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
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Adam E, Groenenboom AE, Kurm V, Rajewska M, Schmidt R, Tyc O, Weidner S, Berg G, de Boer W, Falcão Salles J. Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut. Front Microbiol 2016; 7:1079. [PMID: 27468279 PMCID: PMC4942455 DOI: 10.3389/fmicb.2016.01079] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022] Open
Affiliation(s)
- Eveline Adam
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | | | - Viola Kurm
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
| | - Magdalena Rajewska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of GdańskGdańsk, Poland
| | - Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Simone Weidner
- Department of Biology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Joana Falcão Salles
- Institute of Evolutionary Life sciences, Groningen UniversityGroningen, Netherlands
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21
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Guo J, Jing X, Peng WL, Nie Q, Zhai Y, Shao Z, Zheng L, Cai M, Li G, Zuo H, Zhang Z, Wang RR, Huang D, Cheng W, Yu Z, Chen LL, Zhang J. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316. Sci Rep 2016; 6:29211. [PMID: 27384076 PMCID: PMC4935845 DOI: 10.1038/srep29211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 02/07/2023] Open
Abstract
We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis, and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316.
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Affiliation(s)
- Jing Guo
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xueping Jing
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wen-Lei Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiyu Nie
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yile Zhai
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Guangyu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China
| | - Huaiyu Zuo
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhitao Zhang
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Rui-Ru Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Dian Huang
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wanli Cheng
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ling-Ling Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Meyer SLF, Everts KL, Gardener BM, Masler EP, Abdelnabby HME, Skantar AM. Assessment of DAPG-producing Pseudomonas fluorescens for Management of Meloidogyne incognita and Fusarium oxysporum on Watermelon. J Nematol 2016; 48:43-53. [PMID: 27168652 PMCID: PMC4859617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 06/05/2023] Open
Abstract
Pseudomonas fluorescens isolates Clinto 1R, Wayne 1R, and Wood 1R, which produce the antibiotic 2,4-diacetylphloroglucinol (DAPG), can suppress soilborne diseases and promote plant growth. Consequently, these beneficial bacterial isolates were tested on watermelon plants for suppression of Meloidogyne incognita (root-knot nematode: RKN) and Fusarium oxysporum f. sp. niveum (Fon). In a greenhouse trial, Wayne 1R root dip suppressed numbers of RKN eggs per gram root on 'Charleston Gray' watermelon by 28.9%. However, in studies focused on 'Sugar Baby' watermelon, which is commercially grown in Maryland, a Wayne 1R root dip did not inhibit RKN reproduction or plant death caused by Fon. When all three isolates were applied as seed coats, plant stand in the greenhouse was reduced up to 60% in treatments that included Fon ± P. fluorescens, and eggs per gram root did not differ among treatments. In a microplot trial with Clinto 1R and Wayne 1R root dips, inoculation with P. fluorescens and/or Fon resulted in shorter vine lengths than treatment with either P. fluorescens isolate plus RKN. Root weights, galling indices, eggs per gram root, and second-stage juvenile (J2) numbers in soil were similar among all RKN-inoculated treatments, and fruit production was not affected by treatment. Plant death was high in all treatments. These studies demonstrated that the tested P. fluorescens isolates resulted in some inhibition of vine growth in the field, and were not effective for enhancing plant vigor or suppressing RKN or Fon on watermelon.
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Affiliation(s)
- Susan L F Meyer
- USDA, ARS, Nematology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center (BARC)-West, Beltsville, MD 20705
| | - Kathryne L Everts
- University of Maryland College Park/University of Delaware, The Lower Eastern Shore Research and Education Center, Salisbury, MD 21801
| | - Brian McSpadden Gardener
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - Edward P Masler
- USDA, ARS, Nematology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center (BARC)-West, Beltsville, MD 20705
| | - Hazem M E Abdelnabby
- Department of Plant Protection, Faculty of Agriculture, Benha University, Qaliubia, Egypt
| | - Andrea M Skantar
- USDA, ARS, Nematology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center (BARC)-West, Beltsville, MD 20705
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23
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L. F. MEYER SUSAN, L. EVERTS KATHRYNE, MCSPADDEN GARDENER BRIAN, P. MASLER EDWARD, M. E. ABDELNABBY HAZEM, M. SKANTAR ANDREA. Assessment of DAPG-producing Pseudomonas fluorescens for Management of Meloidogyne incognita and Fusarium oxysporum on Watermelon. J Nematol 2016. [DOI: 10.21307/jofnem-2017-008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans. Clin Microbiol Rev 2015; 27:927-48. [PMID: 25278578 DOI: 10.1128/cmr.00044-14] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the "species" P. fluorescens are now being reclassified as novel Pseudomonas species within the P. fluorescens "species complex." Although most widely studied for its role in the soil and the rhizosphere, P. fluorescens possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent than P. aeruginosa, P. fluorescens can cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association between P. fluorescens and human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies to P. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans and P. fluorescens during health and disease.
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Nandi M, Selin C, Brassinga AKC, Belmonte MF, Fernando WGD, Loewen PC, de Kievit TR. Pyrrolnitrin and Hydrogen Cyanide Production by Pseudomonas chlororaphis Strain PA23 Exhibits Nematicidal and Repellent Activity against Caenorhabditis elegans. PLoS One 2015; 10:e0123184. [PMID: 25901993 PMCID: PMC4406715 DOI: 10.1371/journal.pone.0123184] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas chlororaphis strain PA23 is a biocontrol agent able to suppress growth of the fungal pathogen Sclerotinia sclerotiorum. This bacterium produces an arsenal of exometabolites including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN), and degradative enzymes. Production of these compounds is controlled at both the transcriptional and posttranscriptional levels by the Gac-Rsm system, RpoS, PsrA, and the Phz quorum-sensing system. Beyond pathogen-suppression, the success of a biocontrol agent is dependent upon its ability to establish itself in the environment where predation by bacterivorous organisms, including nematodes, may threaten persistence. The focus of this study was to investigate whether PA23 is able to resist grazing by Caenorhabditis elegans and to define the role played by exoproducts in the bacterial-nematode interaction. We discovered that both PRN and HCN contribute to fast- and slow-killing of C. elegans. HCN is well-established as having lethal effects on C. elegans; however, PRN has not been reported to be nematicidal. Exposure of L4 stage nematodes to purified PRN reduced nematode viability in a dose-dependent fashion and led to reduced hatching of eggs laid by gravid adults. Because bacterial metabolites can act as chemoattractants or repellents, we analyzed whether PA23 exhibited attractant or repulsive properties towards C. elegans. Both PRN and HCN were found to be potent repellents. Next we investigated whether the presence of C. elegans would elicit changes in PA23 gene activity. Co-culturing the two organisms increased expression of a number of genes associated with biocontrol, including phzA, hcnA, phzR, phzI, rpoS and gacS. Exoproduct analysis showed that PHZ and autoinducer signals were upregulated, consistent with the gene expression profiles. Collectively, these findings indicate that PA23 is able to sense the presence of C. elegans and it is able to both repel and kill the nematodes, which should facilitate environmental persistence and ultimately biocontrol.
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Affiliation(s)
- Munmun Nandi
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carrie Selin
- Department of Plant Science University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Mark F. Belmonte
- Department of Biological Sciences University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Peter C. Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teresa R. de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Spence C, Alff E, Johnson C, Ramos C, Donofrio N, Sundaresan V, Bais H. Natural rice rhizospheric microbes suppress rice blast infections. BMC PLANT BIOLOGY 2014; 14:130. [PMID: 24884531 PMCID: PMC4036093 DOI: 10.1186/1471-2229-14-130] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease. RESULTS Naturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by 16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70-15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice. CONCLUSIONS Out of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with current disease protection strategies could aid in global food security.
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Affiliation(s)
- Carla Spence
- Department of Biological Sciences, University of Delaware, Newark, USA
- Delaware Biotechnology Institute, Newark, USA
| | - Emily Alff
- Delaware Biotechnology Institute, Newark, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, USA
| | - Cameron Johnson
- Department of Plant Biology, University of California, Davis, USA
| | - Cassandra Ramos
- Department of Plant Biology, University of California, Davis, USA
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, USA
| | | | - Harsh Bais
- Delaware Biotechnology Institute, Newark, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, USA
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Keller-Costa T, Jousset A, van Overbeek L, van Elsas JD, Costa R. The freshwater sponge Ephydatia fluviatilis harbours diverse Pseudomonas species (Gammaproteobacteria, Pseudomonadales) with broad-spectrum antimicrobial activity. PLoS One 2014; 9:e88429. [PMID: 24533086 PMCID: PMC3922812 DOI: 10.1371/journal.pone.0088429] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/07/2014] [Indexed: 11/18/2022] Open
Abstract
Bacteria are believed to play an important role in the fitness and biochemistry of sponges (Porifera). Pseudomonas species (Gammaproteobacteria, Pseudomonadales) are capable of colonizing a broad range of eukaryotic hosts, but knowledge of their diversity and function in freshwater invertebrates is rudimentary. We assessed the diversity, structure and antimicrobial activities of Pseudomonas spp. in the freshwater sponge Ephydatia fluviatilis. Polymerase Chain Reaction--Denaturing Gradient Gel Electrophoresis (PCR-DGGE) fingerprints of the global regulator gene gacA revealed distinct structures between sponge-associated and free-living Pseudomonas communities, unveiling previously unsuspected diversity of these assemblages in freshwater. Community structures varied across E. fluviatilis specimens, yet specific gacA phylotypes could be detected by PCR-DGGE in almost all sponge individuals sampled over two consecutive years. By means of whole-genome fingerprinting, 39 distinct genotypes were found within 90 fluorescent Pseudomonas isolates retrieved from E. fluviatilis. High frequency of in vitro antibacterial (49%), antiprotozoan (35%) and anti-oomycetal (32%) activities was found among these isolates, contrasting less-pronounced basidiomycetal (17%) and ascomycetal (8%) antagonism. Culture extracts of highly predation-resistant isolates rapidly caused complete immobility or lysis of cells of the protozoan Colpoda steinii. Isolates tentatively identified as P. jessenii, P. protegens and P. oryzihabitans showed conspicuous inhibitory traits and correspondence with dominant sponge-associated phylotypes registered by cultivation-independent analysis. Our findings suggest that E. fluviatilis hosts both transient and persistent Pseudomonas symbionts displaying antimicrobial activities of potential ecological and biotechnological value.
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Affiliation(s)
- Tina Keller-Costa
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, Portugal
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Leo van Overbeek
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Rodrigo Costa
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, Portugal
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Friman VP, Jousset A, Buckling A. Rapid prey evolution can alter the structure of predator-prey communities. J Evol Biol 2013; 27:374-80. [DOI: 10.1111/jeb.12303] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 11/28/2022]
Affiliation(s)
- V.-P. Friman
- Department of Biosciences; University of Exeter; Penryn UK
- Imperial College London; Ascot UK
| | - A. Jousset
- Division of Ecology and Biodiversity; Utrecht University; Utrecht The Netherlands
| | - A. Buckling
- Department of Biosciences; University of Exeter; Penryn UK
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Host-Microbe Interactions in Caenorhabditis elegans. ISRN MICROBIOLOGY 2013; 2013:356451. [PMID: 23984180 PMCID: PMC3747393 DOI: 10.1155/2013/356451] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/16/2013] [Indexed: 01/09/2023]
Abstract
A good understanding of how microbes interact with hosts has a direct bearing on our capability of fighting infectious microbial pathogens and making good use of beneficial ones. Among the model organisms used to study reciprocal actions among microbes and hosts, C. elegans may be the most advantageous in the context of its unique attributes such as the short life cycle, easiness of laboratory maintenance, and the availability of different genetic mutants. This review summarizes the recent advances in understanding host-microbe interactions in C. elegans. Although these investigations have greatly enhanced our understanding of C. elegans-microbe relationships, all but one of them involve only one or few microbial species. We argue here that more research is needed for exploring the evolution and establishment of a complex microbial community in the worm's intestine and its interaction with the host.
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Pleiotropic effects of GacA on Pseudomonas fluorescens Pf0-1 in vitro and in soil. Appl Environ Microbiol 2013; 79:5405-10. [PMID: 23811507 DOI: 10.1128/aem.00819-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas species can exhibit phenotypic variation resulting from gacS or gacA mutation. P. fluorescens Pf0-1 is a gacA mutant and exhibits pleiotropic changes following the introduction of a functional allele. GacA enhances biofilm development while reducing dissemination in soil, suggesting that alternative Gac phenotypes enable Pseudomonas sp. to exploit varied environments.
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Müller MS, Scheu S, Jousset A. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities. PLoS One 2013; 8:e66200. [PMID: 23840423 PMCID: PMC3694078 DOI: 10.1371/journal.pone.0066200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 05/05/2013] [Indexed: 11/18/2022] Open
Abstract
Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.
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Affiliation(s)
- Maren Stella Müller
- Georg August University Göttingen, J. F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
| | - Stefan Scheu
- Georg August University Göttingen, J. F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
| | - Alexandre Jousset
- Georg August University Göttingen, J. F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
- * E-mail:
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Barret M, Egan F, Moynihan J, Morrissey JP, Lesouhaitier O, O'Gara F. Characterization of the SPI-1 and Rsp type three secretion systems in Pseudomonas fluorescens F113. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:377-86. [PMID: 23754718 DOI: 10.1111/1758-2229.12039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/10/2013] [Indexed: 05/21/2023]
Abstract
Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar beet rhizosphere. The recent annotation of the F113 genome sequence has revealed that this strain encodes a wide array of secretion systems, including two complete type three secretion systems (T3SSs) belonging to the Hrp1 and SPI-1 families. While Hrp1 T3SSs are frequently encoded in other P. fluorescens strains, the presence of a SPI-1 T3SS in a plant-beneficial bacterial strain was unexpected. In this work, the genetic organization and expression of these two T3SS loci have been analysed by a combination of transcriptional reporter fusions and transcriptome analyses. Overexpression of two transcriptional activators has shown a number of genes encoding putative T3 effectors. In addition, the influence of these two T3SSs during the interaction of P. fluorescens F113 with some bacterial predators was also assessed. Our data revealed that the transcriptional activator hilA is induced by amoeba and that the SPI-1 T3SS could potentially be involved in resistance to amoeboid grazing.
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Affiliation(s)
- Matthieu Barret
- BIOMERIT Research Centre, University College Cork, Cork, Ireland
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Li PF, Li SG, Li ZF, Zhao L, Wang T, Pan HW, Liu H, Wu ZH, Li YZ. Co-cultivation ofSorangium cellulosumstrains affects cellular growth and biosynthesis of secondary metabolite epothilones. FEMS Microbiol Ecol 2013; 85:358-68. [DOI: 10.1111/1574-6941.12125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/18/2013] [Accepted: 03/24/2013] [Indexed: 12/18/2022] Open
Affiliation(s)
- Peng-fei Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Shu-guang Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Zhi-feng Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Lin Zhao
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Ting Wang
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Hong-wei Pan
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Hong Liu
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Zhi-hong Wu
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
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Hol WHG, Bezemer TM, Biere A. Getting the ecology into interactions between plants and the plant growth-promoting bacterium Pseudomonas fluorescens. FRONTIERS IN PLANT SCIENCE 2013; 4:81. [PMID: 23596447 PMCID: PMC3622252 DOI: 10.3389/fpls.2013.00081] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/19/2013] [Indexed: 05/03/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are increasingly appreciated for their contributions to primary productivity through promotion of growth and triggering of induced systemic resistance in plants. Here we focus on the beneficial effects of one particular species of PGPR (Pseudomonas fluorescens) on plants through induced plant defense. This model organism has provided much understanding of the underlying molecular mechanisms of PGPR-induced plant defense. However, this knowledge can only be appreciated at full value once we know to what extent these mechanisms also occur under more realistic, species-diverse conditions as are occurring in the plant rhizosphere. To provide the necessary ecological context, we review the literature to compare the effect of P. fluorescens on induced plant defense when it is present as a single species or in combination with other soil dwelling species. Specifically, we discuss combinations with other plant mutualists (bacterial or fungal), plant pathogens (bacterial or fungal), bacterivores (nematode or protozoa), and decomposers. Synergistic interactions between P. fluorescens and other plant mutualists are much more commonly reported than antagonistic interactions. Recent developments have enabled screenings of P. fluorescens genomes for defense traits and this could help with selection of strains with likely positive interactions on biocontrol. However, studies that examine the effects of multiple herbivores, pathogens, or herbivores and pathogens together on the effectiveness of PGPR to induce plant defenses are underrepresented and we are not aware of any study that has examined interactions between P. fluorescens and bacterivores or decomposers. As co-occurring soil organisms can enhance but also reduce the effectiveness of PGPR, a better understanding of the biotic factors modulating P. fluorescens-plant interactions will improve the effectiveness of introducing P. fluorescens to enhance plant production and defense.
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Affiliation(s)
- W. H. Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
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35
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Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator. ISME JOURNAL 2013; 7:1126-38. [PMID: 23426012 DOI: 10.1038/ismej.2013.9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bacteriovorous nematode Caenorhabditis elegans has been used to investigate many aspects of animal biology, including interactions with pathogenic bacteria. However, studies examining C. elegans interactions with bacteria isolated from environments in which it is found naturally are relatively scarce. C. elegans is frequently associated with cultivation of the edible mushroom Agaricus bisporus, and has been reported to increase the severity of bacterial blotch of mushrooms, a disease caused by bacteria from the Pseudomonas fluorescens complex. We observed that pseudomonads isolated from mushroom farms showed differential resistance to nematode predation. Under nutrient poor conditions, in which most pseudomonads were consumed, the mushroom pathogenic isolate P. fluorescens NZI7 was able to repel C. elegans without causing nematode death. A draft genome sequence of NZI7 showed it to be related to the biocontrol strain P. protegens Pf-5. To identify the genetic basis of nematode repellence in NZI7, we developed a grid-based screen for mutants that lacked the ability to repel C. elegans. The mutants isolated in this screen included strains with insertions in the global regulator GacS and in a previously undescribed GacS-regulated gene cluster, 'EDB' ('edible'). Our results suggest that the product of the EDB cluster is a poorly diffusible or cell-associated factor that acts together with other features of NZI7 to provide a novel mechanism to deter nematode grazing. As nematodes interact with NZI7 colonies before being repelled, the EDB factor may enable NZI7 to come into contact with and be disseminated by C. elegans without being subject to intensive predation.
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Wang J, Nakad R, Schulenburg H. Activation of the Caenorhabditis elegans FOXO family transcription factor DAF-16 by pathogenic Bacillus thuringiensis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:193-201. [PMID: 21945834 DOI: 10.1016/j.dci.2011.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 05/31/2023]
Abstract
The FOXO family of transcription factors have recently been implicated in innate immunity, especially in case of DAF-16 from the nematode Caenorhabditis elegans. However, previous studies with this nematode proposed that DAF-16 is not directly activated by pathogens. Rather, DAF-16 mediates resistance if activated by some other cue as part of a general stress response. We specifically tested this notion by analysis of DAF-16 nuclear translocation and thus regulatory activity upon exposure to pathogenic Bacillus thuringiensis. Our results demonstrate that DAF-16 nuclear translocation is indeed particularly induced in response to bacterial pathogenicity, whereas infection load alone has little effect. Translocation is strongest at an early time point, suggesting a role during the immediate immune response. The increased DAF-16 availability is associated with higher resistance and a reduction in feeding behaviour. Taken together, our data highlight that a FOXO transcription factor directly responds to pathogens and thus contributes to immune defence.
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Affiliation(s)
- Jun Wang
- Department of Animal Evolutionary Ecology, Zoological Institute, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
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Raaijmakers JM, Mazzola M. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:403-24. [PMID: 22681451 DOI: 10.1146/annurev-phyto-081211-172908] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Soil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.
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Affiliation(s)
- Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands.
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38
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Abstract
Bacterial communities are often heavily consumed by microfaunal predators, such as protozoa and nematodes. Predation is an important cause of mortality and determines the structure and activity of microbial communities in both terrestrial and aquatic ecosystems, and bacteria evolved various defence mechanisms helping them to resist predation. In this review, I summarize known antipredator defence strategies and their regulation, and explore their importance for bacterial fitness in various environmental conditions, and their implications for bacterial evolution and diversification under predation pressure. I discuss how defence mechanisms affect competition and cooperation within bacterial communities. Finally I present some implications of bacterial defence mechanisms for ecosystem services provided by microbial communities, such as nutrient cycling, virulence and the biological control of plant diseases.
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Affiliation(s)
- Alexandre Jousset
- Georg-August University Göttingen, JF Blumenbach Institute of Zoology and Anthropology, Animal Ecology, Berliner Str. 28, 37073 Göttingen, Germany.
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