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Aytenov IS, Bozorov TA, Zhang D, Samadiy SA, Muhammadova DA, Isokulov MZ, Murodova SM, Zakirova OR, Chinikulov BK, Sherimbetov AG. Uncovering the Antifungal Potential of Plant-Associated Cultivable Bacteria from the Aral Sea Region against Phytopathogenic Fungi. Pathogens 2024; 13:585. [PMID: 39057812 PMCID: PMC11279601 DOI: 10.3390/pathogens13070585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Two freshwater rivers, the Amu Darya and Syr Darya, flow into the Aral Sea, but they began to diminish in the early 1960s, and by the 1980s, the lake had nearly ceased to exist due to excessive water consumption for agriculture and the unsustainable management of water resources from rivers, which transformed the Aral Sea into a hypersaline lake. Despite this, the flora and fauna of the region began to evolve in the high-salinity seabed soil, which has received little attention in studies. In this study, we isolated approximately 1400 bacterial strains from the rhizosphere and phyllosphere of plant species of distinct families. Bacterial isolates were examined for antifungal activities against a range of pathogenic fungi such as Rhizoctonia gossypii, Trichothecium ovalisporum, Fusarium annulatum, F. oxysporum, F. culmorum, F. brachygibbosum, F. tricinctum, F. verticillioides, Alternaria alternata, A. terreus, Aspergillus niger, and As. flavus. Eighty-eight bacterial isolates exhibited varying antagonistic ability against pathogenic fungi. Furthermore, DNA barcoding of isolates using the 16S rRNA gene indicated that most antagonistic bacteria belonged to the Bacillus and Pseudomonas genera. The study also explored the activity of hydrolytic and cell-wall-degrading enzymes produced by antagonistic bacteria. The findings revealed that antagonistic bacteria can be utilized to widely protect seabed plants and plants growing in saline areas against pathogenic fungi, as well as agricultural crops.
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Affiliation(s)
- Ilkham S. Aytenov
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (I.S.A.); (D.Z.)
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Tohir A. Bozorov
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (I.S.A.); (D.Z.)
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Daoyuan Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (I.S.A.); (D.Z.)
| | - Sitora A. Samadiy
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
- Department of Microbiology and Biotechnology, National University of Uzbekistan, University Street, 4, Tashkent 100174, Uzbekistan
| | - Dono A. Muhammadova
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Marufbek Z. Isokulov
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Sojida M. Murodova
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Ozoda R. Zakirova
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Bakhodir Kh. Chinikulov
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan; (S.A.S.); (D.A.M.); (S.M.M.)
| | - Anvar G. Sherimbetov
- Laboratory of Plant Immunity, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Kibray 111226, Uzbekistan
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Riera N, Davyt D, Durán R, Iraola G, Lemanceau P, Bajsa N. An antibiotic produced by Pseudomonas fluorescens CFBP2392 with antifungal activity against Rhizoctonia solani. Front Microbiol 2023; 14:1286926. [PMID: 38033591 PMCID: PMC10682437 DOI: 10.3389/fmicb.2023.1286926] [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: 08/31/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Pseudomonas fluorescens CFBP2392 has been recognized as a potential biocontrol agent due to its ability to suppress damping-off and root rot disease. This isolate has antibacterial activity in vitro as many other strains from the Pseudomonas fluorescens complex. In this work, the antibacterial and antifungal activity of the strain were explored. Dual culture assays evidenced the antifungal activity of the strain against different phytopathogens: Alternaria sp., Pythium ultimun, Fusarium oxysporum, and Rhizoctonia solani. Purification of an antifungal fraction was performed by preparative HPLC from the chemical extraction of growth media. The fraction showed altered R. solani growth and ultrastructure. Transmission electron microscopy revealed the purified compound induced hypertrophied mitochondria, membranous vesicles, and a higher number of vacuoles in R. salani cytoplasm. In addition, co-cultivation of P. fluorescens CFBP2392 with R. solani resulted in an enlarged and deformed cell wall. To gain genomic insights on this inhibition, the complete genome of P. fluorescens CFBP2392 was obtained with Oxford Nanopore technology. Different biosynthetic gene clusters (BGCs) involved in specialized metabolites production including a lokisin-like and a koreenceine-like cluster were identified. In accordance with the putative BGCs identified, sequence phylogeny analysis of the MacB transporter in the lokisin-like cluster further supports the similarity with other transporters from the amphisin family. Our results give insights into the cellular effects of the purified microbial metabolite in R. solani ultrastructure and provide a genomic background to further explore the specialized metabolite potential.
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Affiliation(s)
- Nadia Riera
- Laboratorio de Ecología Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Danilo Davyt
- Laboratorio de Química Farmacéutica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Rosario Durán
- Unidad Mixta de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Gregorio Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Philippe Lemanceau
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne—Université de Bourgogne Franche-Comté, Dijon, France
| | - Natalia Bajsa
- Laboratorio de Ecología Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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Xu R, Huang QY, Shen WH, Li XP, Zheng LP, Wang JW. Volatiles of Shiraia fruiting body-associated Pseudomonas putida No.24 stimulate fungal hypocrellin production. Synth Syst Biotechnol 2023; 8:427-436. [PMID: 37409170 PMCID: PMC10319174 DOI: 10.1016/j.synbio.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 07/07/2023] Open
Abstract
Hypocrellins are major bioactive perylenequinones from Shiraia fruiting bodies and have been developed as efficient photosensitizers for photodynamic therapy. Pseudomonas is the second dominant genus inside Shiraia fruiting bodies, but with less known actions on the host fungus. In this work, the effects of bacterial volatiles from the Shiraia-associated Pseudomonas on fungal hypocrellin production were investigated. Pseudomonas putida No.24 was the most active to promote significantly accumulation of Shiraia perylenequinones including hypocrellin A (HA), HC, elsinochrome A (EA) and EC. Headspace analysis of the emitted volatiles revealed dimethyl disulfide as one of active compounds to promote fungal hypocrellin production. The bacterial volatiles induced an apoptosis in Shiraia hyphal cell, which was associated with the generation of reactive oxygen species (ROS). ROS generation was proved to mediate the volatile-induced membrane permeability and up-regulation of gene expressions for hypocrellin biosynthesis. In the submerged volatile co-culture, the bacterial volatiles stimulated not only HA content in mycelia, but also HA secretion into the medium, leading to the enhanced HA production to 249.85 mg/L, about 2.07-fold over the control. This is the first report on the regulation of Pseudomonas volatiles on fungal perylenequinone production. These findings could be helpful to understand the roles of bacterial volatiles in fruiting bodies and also provide new elicitation method using bacterial volatiles to stimulate fungal secondary metabolite production.
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Affiliation(s)
- Rui Xu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Qun Yan Huang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Wen Hao Shen
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Xin Ping Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Li Ping Zheng
- Department of Horticultural Sciences, Soochow University, Suzhou, 215123, China
| | - Jian Wen Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
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Lin T, Tang J, Li S, Li S, Han S, Liu Y, Yang C, Chen G, Chen L, Zhu T. Drought stress-mediated differences in phyllosphere microbiome and associated pathogen resistance between male and female poplars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1100-1113. [PMID: 37177875 DOI: 10.1111/tpj.16283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/15/2023]
Abstract
Phyllosphere-associated microbes play a crucial role in plant-pathogen interactions while their composition and diversity are strongly influenced by drought stress. As dioecious plant species exhibited secondary dimorphism between the two sexes in response to drought stress, whether such difference will lead to sex-specific differences in phyllosphere microbiome and associated pathogen resistance between male and female conspecifics is still unknown. In this study, we subjected female and male full siblings of a dioecious poplar species to a short period of drought treatment followed by artificial infection of a leaf pathogenic fungus. Our results showed that male plants grew better than females with or without drought stress. Female control plants had more leaf lesion area than males after pathogen infection, whereas drought stress reversed such a difference. Further correlation and in vitro toxicity tests suggested that drought-mediated sexual differences in pathogen resistance between the two plant sexes could be attributed to the shifts in structure and function of phyllosphere-associated microbiome rather than the amount of leaf main defensive chemicals contained in plant leaves. Supportively, the microbiome analysis through high-throughput sequencing indicated that female phyllosphere enriched a higher abundance of ecologically beneficial microbes that serve as biological plant protectants, while males harbored abundant phytopathogens under drought-stressed conditions. The results could provide potential implications for the selection of suitable poplar sex to plants in drought or semi-drought habitats.
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Affiliation(s)
- Tiantian Lin
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China and Centre of Invasion Biology, Institute of Biodiversity, Yunnan University, 650504, Kunming, China
| | - Jiayao Tang
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Shuying Li
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Shujiang Li
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Shan Han
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yinggao Liu
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Chunlin Yang
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Gang Chen
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Lianghua Chen
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Tianhui Zhu
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
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Chen W, Modi D, Picot A. Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2736. [PMID: 37514350 PMCID: PMC10384710 DOI: 10.3390/plants12142736] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Dixi Modi
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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Khanal M, Bhatta BP, Malla S. Isolation and Characterization of Bacteria Associated with Onion and First Report of Onion Diseases Caused by Five Bacterial Pathogens in Texas, U.S.A. PLANT DISEASE 2023:PDIS09222206SR. [PMID: 36451309 DOI: 10.1094/pdis-09-22-2206-sr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial diseases pose a severe challenge to growers and cause significant loss to the billion-dollar onion industry in the United States. Texas is the sixth largest onion producing state, yet the bacterial communities associated with short-day onion crops grown in Texas have not been studied. This study was conducted to identify, characterize, and understand the diversity of bacteria associated with onion production in Texas. In 2020, 190 foliar and 210 bulb samples were collected from onion crops in the Rio Grande Valley and Winter Garden regions of Texas. Sequencing of the 16s rRNA gene was used to identify each bacterial strains to a genus. The pathogenicity to onion of each bacterial strain was tested using three assays: a red onion scale assay, a yellow onion bulb assay, and a foliar assay. Whole genome sequencing was done to identify the onion-pathogenic strains to species. Collectively, isolates of 24 genera belonging to three phyla were detected, including 19 genera from foliar samples and nine genera from bulb samples. Isolates in the Phylum Proteobacteria, including 15 genera of Gram-negative bacteria, were the most abundant of the taxa, comprising 90.0% of the strains isolated. The diversity of foliar isolates was evenly distributed between Gram-positive and Gram-negative bacteria, while Gram-negative bacteria dominated the isolates from bulb samples. In total, 83.9% of the bacterial isolates were not pathogenic on onion, with only isolates of Pantoea, Pseudomonas, Burkholderia, Erwinia, Enterobacter, and Curtobacterium proving pathogenic. Strains of Burkholderia gladioli, Pseudomonas alliivorans, Pantoea agglomerans, P. ananatis, and P. allii are the first documented cases of these pathogens of onion in Texas. Identifying and characterizing the nature of onion microflora, including pathogens of onion, is vital to developing rapid disease detection techniques via pathogenomics and minimizing losses through the application of effective disease management measures.
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
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Vicente TFL, Félix C, Félix R, Valentão P, Lemos MFL. Seaweed as a Natural Source against Phytopathogenic Bacteria. Mar Drugs 2022; 21:23. [PMID: 36662196 PMCID: PMC9867177 DOI: 10.3390/md21010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Plant bacterial pathogens can be devastating and compromise entire crops of fruit and vegetables worldwide. The consequences of bacterial plant infections represent not only relevant economical losses, but also the reduction of food availability. Synthetic bactericides have been the most used tool to control bacterial diseases, representing an expensive investment for the producers, since cyclic applications are usually necessary, and are a potential threat to the environment. The development of greener methodologies is of paramount importance, and some options are already available in the market, usually related to genetic manipulation or plant community modulation, as in the case of biocontrol. Seaweeds are one of the richest sources of bioactive compounds, already being used in different industries such as cosmetics, food, medicine, pharmaceutical investigation, and agriculture, among others. They also arise as an eco-friendly alternative to synthetic bactericides. Several studies have already demonstrated their inhibitory activity over relevant bacterial phytopathogens, some of these compounds are known for their eliciting ability to trigger priming defense mechanisms. The present work aims to gather the available information regarding seaweed extracts/compounds with antibacterial activity and eliciting potential to control bacterial phytopathogens, highlighting the extracts from brown algae with protective properties against microbial attack.
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Affiliation(s)
- Tânia F. L. Vicente
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Carina Félix
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
| | - Rafael Félix
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marco F. L. Lemos
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
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Ye S, Yan R, Li X, Lin Y, Yang Z, Ma Y, Ding Z. Biocontrol potential of Pseudomonas rhodesiae GC-7 against the root-knot nematode Meloidogyne graminicola through both antagonistic effects and induced plant resistance. Front Microbiol 2022; 13:1025727. [PMID: 36386722 PMCID: PMC9651087 DOI: 10.3389/fmicb.2022.1025727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
Plant-parasitic nematodes (PPNs) cause serious damage to agricultural production worldwide. Currently, because of a lack of effective and environmental-friendly chemical nematicides, the use of microbial nematicides has been proposed as an eco-friendly management strategy to control PPNs. A nematicidal bacterium GC-7 was originally isolated from the rice rhizosphere, and was identified as Pseudomonas rhodesiae. Treatment with the fermentation supernatant of GC-7 in vitro showed a highly lethal effect on second-stage juveniles of Meloidogyne graminicola, with the mortality rate increasing to 95.82% at 24 h and egg hatching significantly inhibited, with a hatch inhibition rate of 60.65% at 96 h. The bacterium significantly reduced the level of damage caused by M. graminicola infestations to rice (Oryza sativa) in greenhouse and field experiments. Under greenhouse conditions, the GC-7 culture efficiently reduced the gall index and nematode population in rice roots and soils, as well as inhibited nematode development compared to the control. Under field conditions, application of the GC-7 consistently showed a high biocontrol efficacy against M. graminicola (with a control efficiency of 58.85%) and promoted plant growth. In addition, the inoculation of GC-7 in M. graminicola-infested rice plant fields significantly suppressed final nematode populations in soil under natural conditions. Furthermore, activities of plant defense-related enzymes, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase were remarkably increased in plant roots treated with GC-7 compared with roots that were challenge to M. graminicola. Moreover, quantitative real-time PCR analysis showed that GC-7 significantly enhanced the expression of defense genes (PR1a, WRKY45, JaMYB, AOS2, ERF1, and ACS1) related to salicylic acid, jasmonic acid, and ethylene signaling pathways in rice roots after inoculation with GC-7 at different levels. The results indicated that GC-7 could be an effective biological component in the integrated management of M. graminicola infecting rice.
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Affiliation(s)
- Shan Ye
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
- Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha, Hunan, China
| | - Rui Yan
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Xinwen Li
- Agriculture and Rural Department of Hunan Province, Plant Protection and Inspection Station, Changsha, Hunan, China
| | - Yufeng Lin
- Agriculture and Rural Department of Hunan Province, Plant Protection and Inspection Station, Changsha, Hunan, China
| | - Zhuhong Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
- Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha, Hunan, China
| | - Yihang Ma
- Department of Chemical Metrology and Reference Materials, Hunan Institute of Metrology and Test, Changsha, Hunan, China
| | - Zhong Ding
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
- Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha, Hunan, China
- *Correspondence: Zhong Ding,
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Mahdi I, Allaoui A, Fahsi N, Biskri L. Bacillus velezensis QA2 Potentially Induced Salt Stress Tolerance and Enhanced Phosphate Uptake in Quinoa Plants. Microorganisms 2022; 10:microorganisms10091836. [PMID: 36144437 PMCID: PMC9505587 DOI: 10.3390/microorganisms10091836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Plant Growth-Promoting Rhizobacteria (PGPR) have attracted much attention in agriculture biotechnology as biological inputs to sustain crop production. The present study describes a halotolerant phosphate solubilizing bacterium associated with quinoa plant roots. Based on a metabolic screening, one bacterial isolate, named QA2, was selected and screened for PGPR traits. This isolate solubilized both inorganic phosphate and zinc, produced indole-3-acetic acid, ammonia, hydrogen cyanide, cellulase, and (to be deleted) protease, and induced biofilm formation. We demonstrated that QA2 exhibited both antimicrobial and ion metabolism activities and tolerated high salt concentration at up to 11% NaCl. Genotyping analyses, using 16S rRNA and chaperonin cpn60 genes, revealed that QA2 belongs to the species of Bacillus velezensis. Using the quinoa model cultivated under a saline condition, we demonstrated that QA2 promoted plant growth and mitigated the saline irrigation effects. Analysis of harvested plants revealed that QA2 induced a significant increase of both leaf chlorophyll index by 120.86% (p < 0.05) and P uptake by 41.17% (p < 0.05), while the content of Na+ was drastically decreased. Lastly, a bibliometric data analysis highlighted the panoramic view of studies carried out so far on B. velezensis strains. Our investigation presents a holistic view of the potential application of B. velezensis as a biological inoculant to promote plant growth, control pathogen attacks, and mitigate the salinity effect of quinoa plants. Further investigations are still needed to demonstrate these effects in field conditions.
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Affiliation(s)
- Ismail Mahdi
- Microbiology Laboratory, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Abdelmounaaim Allaoui
- Microbiology Laboratory, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Nidal Fahsi
- Microbiology Laboratory, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Latefa Biskri
- Microbiology Laboratory, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
- African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
- Correspondence: ; Tel.: +212-52502926
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10
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Agarwal R, Gupta M, Antony A, Sen R, Raychoudhury R. In Vitro Studies Reveal that Pseudomonas, from Odontotermes obesus Colonies, can Function as a Defensive Mutualist as it Prevents the Weedy Fungus While Keeping the Crop Fungus Unaffected. MICROBIAL ECOLOGY 2022; 84:391-403. [PMID: 34495359 DOI: 10.1007/s00248-021-01798-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, take over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the weedy fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification, and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of O. obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the widespread prevalence of Pseudomonas within this termite. These lines of evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.
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Affiliation(s)
- Renuka Agarwal
- Department of Biological Sciences, Indian Institute of Science and Education Research Mohali (IISER Mohali), Knowledge City, Sector 81, Manauli, SAS Nagar, Punjab, PO 140306, India
| | - Manisha Gupta
- Department of Biological Sciences, Indian Institute of Science and Education Research Mohali (IISER Mohali), Knowledge City, Sector 81, Manauli, SAS Nagar, Punjab, PO 140306, India
| | - Abin Antony
- Department of Biological Sciences, Indian Institute of Science and Education Research Mohali (IISER Mohali), Knowledge City, Sector 81, Manauli, SAS Nagar, Punjab, PO 140306, India
| | - Ruchira Sen
- Sri Guru Gobind Singh College, Sector 26, Chandigarh, 160019, India
| | - Rhitoban Raychoudhury
- Department of Biological Sciences, Indian Institute of Science and Education Research Mohali (IISER Mohali), Knowledge City, Sector 81, Manauli, SAS Nagar, Punjab, PO 140306, India.
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11
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Rangel LI, Bolton MD. The unsung roles of microbial secondary metabolite effectors in the plant disease cacophony. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102233. [PMID: 35679804 DOI: 10.1016/j.pbi.2022.102233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Plants counter disease with an array of responses to styme pathogen ingress. In contrast to this cacophony, plant pathogens orchestrate a finely tuned repertoire of virulence mechanisms in their attempt to cause disease. One such example is the production of secondary metabolite effectors (SMEs). Despite many attempts to functionally categorize SMEs, their many roles in plant disease have proven they march to the beat of their producer's drum. Some lesser studied features of SMEs in plant disease include self-resistance (SR) and manipulation of the microbiome to enhance pathogen virulence. SR can be accomplished in three general compositions, with the first being the transport of the SME to a benign location; the second being modification of the SME so it cannot harm the producer; and the third being metabolic regulation of the SME or the producer homolog of the SME target. SMEs may also play an interlude prior to disease by shaping the plant microbial community, allowing producers to better establish themselves. Taken together, SMEs are integral players in the phytopathology canon.
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Affiliation(s)
- Lorena I Rangel
- Edward T. Schafer Agricultural Research Center, U.S. Dept. Agriculture, Fargo, ND, USA
| | - Melvin D Bolton
- Edward T. Schafer Agricultural Research Center, U.S. Dept. Agriculture, Fargo, ND, USA.
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12
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Gu Q, Qiao J, Wang R, Lu J, Wang Z, Li P, Zhang L, Ali Q, Khan AR, Gao X, Wu H. The Role of Pyoluteorin from Pseudomonas protegens Pf-5 in Suppressing the Growth and Pathogenicity of Pantoea ananatis on Maize. Int J Mol Sci 2022; 23:ijms23126431. [PMID: 35742879 PMCID: PMC9223503 DOI: 10.3390/ijms23126431] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 01/24/2023] Open
Abstract
The rhizospheric bacterium Pseudomonas protegens Pf-5 can colonize the seed and root surfaces of plants, and can protect them from pathogen infection. Secondary metabolites, including lipopeptides and polyketides produced by Pf-5, are involved in its biocontrol activity. We isolated a crude extract from Pf-5. It exhibited significant surface activity and strong antibacterial activity against Pantoea ananatis DZ-12, which causes maize brown rot on leaves. HPLC analysis combined with activity tests showed that the polyketide pyoluteorin in the crude extract participated in the suppression of DZ-12 growth, and that the lipopeptide orfamide A was the major biosurfactant in the crude extract. Further studies indicated that the pyoluteorin in the crude extract significantly suppressed the biofilm formation of DZ-12, and it induced the accumulation of reactive oxygen species in DZ-12 cells. Scanning electron microscopy and transmission electron microscopy observation revealed that the crude extract severely damaged the pathogen cells and caused cytoplasmic extravasations and hollowing of the cells. The pathogenicity of DZ-12 on maize leaves was significantly reduced by the crude extract from Pf-5 in a dose-dependent manner. The polyketide pyoluteorin had strong antibacterial activity against DZ-12, and it has the potential for development as an antimicrobial agent.
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Affiliation(s)
- Qin Gu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Junqing Qiao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Ruoyi Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Juan Lu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Zhengqi Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Pingping Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Lulu Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Abdur Rashid Khan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Xuewen Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
| | - Huijun Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Q.G.); (R.W.); (J.L.); (Z.W.); (P.L.); (L.Z.); (Q.A.); (A.R.K.); (X.G.)
- Correspondence: ; Tel./Fax: +86-25-84395268
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13
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Caccavo V, Forlano P, Mang SM, Fanti P, Nuzzaci M, Battaglia D, Trotta V. Effects of Trichoderma harzianum Strain T22 on the Arthropod Community Associated with Tomato Plants and on the Crop Performance in an Experimental Field. INSECTS 2022; 13:418. [PMID: 35621754 PMCID: PMC9147967 DOI: 10.3390/insects13050418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022]
Abstract
Fungi belonging to the genus Trichoderma have received much attention in recent years due to their beneficial effects on crop health and their use as pest control agents. Trichoderma activates direct plant defenses against phytophagous arthropods and reinforces indirect plant defense through the attraction of predators. Although the plant defenses against insect herbivores were demonstrated in laboratory experiments, little attention has been paid to the use of Trichoderma spp. in open field conditions. In the present study, we investigated the effects of the inoculation of the commercial Trichoderma harzianum strain T22 on the arthropod community associated with tomato plants and on the crop performance in an experimental field located in South Italy. Our results showed that inoculation with T. harzianum could alter the arthropod community and reduce the abundance of specific pests under field conditions with respect to the sampling period. The present study also confirmed the beneficial effect of T. harzianum against plant pathogens and on tomato fruit. The complex tomato-arthropod-microorganism interactions that occurred in the field are discussed to enrich our current information on the possibilities of using Trichoderma as a green alternative agent in agriculture.
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Affiliation(s)
- Vittoria Caccavo
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (V.C.); (P.F.); (S.M.M.); (M.N.); (D.B.)
| | - Pierluigi Forlano
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (V.C.); (P.F.); (S.M.M.); (M.N.); (D.B.)
| | - Stefania Mirela Mang
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (V.C.); (P.F.); (S.M.M.); (M.N.); (D.B.)
| | - Paolo Fanti
- Department of Science, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy;
| | - Maria Nuzzaci
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (V.C.); (P.F.); (S.M.M.); (M.N.); (D.B.)
| | - Donatella Battaglia
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (V.C.); (P.F.); (S.M.M.); (M.N.); (D.B.)
| | - Vincenzo Trotta
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (V.C.); (P.F.); (S.M.M.); (M.N.); (D.B.)
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Di Lelio I, Coppola M, Comite E, Molisso D, Lorito M, Woo SL, Pennacchio F, Rao R, Digilio MC. Temperature Differentially Influences the Capacity of Trichoderma Species to Induce Plant Defense Responses in Tomato Against Insect Pests. FRONTIERS IN PLANT SCIENCE 2021; 12:678830. [PMID: 34177994 PMCID: PMC8221184 DOI: 10.3389/fpls.2021.678830] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/14/2021] [Indexed: 05/31/2023]
Abstract
Species of the ecological opportunistic, avirulent fungus, Trichoderma are widely used in agriculture for their ability to protect crops from the attack of pathogenic fungi and for plant growth promotion activity. Recently, it has been shown that they may also have complementary properties that enhance plant defense barriers against insects. However, the use of these fungi is somewhat undermined by their variable level of biocontrol activity, which is influenced by environmental conditions. Understanding the source of this variability is essential for its profitable and wide use in plant protection. Here, we focus on the impact of temperature on Trichoderma afroharzianum T22, Trichoderma atroviride P1, and the defense response induced in tomato by insects. The in vitro development of these two strains was differentially influenced by temperature, and the observed pattern was consistent with temperature-dependent levels of resistance induced by them in tomato plants against the aphid, Macrosiphum euphorbiae, and the noctuid moth, Spodoptera littoralis. Tomato plants treated with T. afroharzianum T22 exhibited enhanced resistance toward both insect pests at 25°C, while T. atroviride P1 proved to be more effective at 20°C. The comparison of plant transcriptomic profiles generated by the two Trichoderma species allowed the identification of specific defense genes involved in the observed response, and a selected group was used to assess, by real-time quantitative reverse transcription PCR (qRT-PCR), the differential gene expression in Trichoderma-treated tomato plants subjected to the two temperature regimens that significantly affected fungal biological performance. These results will help pave the way toward a rational selection of the most suitable Trichoderma isolates for field applications, in order to best face the challenges imposed by local environmental conditions and by extreme climatic shifts due to global warming.
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Affiliation(s)
- Ilaria Di Lelio
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Mariangela Coppola
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Ernesto Comite
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Donata Molisso
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Matteo Lorito
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
| | - Sheridan Lois Woo
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Francesco Pennacchio
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
| | - Rosa Rao
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
| | - Maria Cristina Digilio
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
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15
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Candicidin Isomer Production Is Essential for Biocontrol of Cucumber Rhizoctonia Rot by Streptomyces albidoflavus W68. Appl Environ Microbiol 2021; 87:AEM.03078-20. [PMID: 33608297 DOI: 10.1128/aem.03078-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/13/2021] [Indexed: 01/10/2023] Open
Abstract
Diseases caused by soilborne fungal pathogens result in significant crop yield losses and quality reduction. Streptomyces albidoflavus strain W68 is effective in controlling several soilborne fungal diseases. To identify antifungal substances critical for biocontrol activity of W68, the genome of W68 was sequenced and a linear chromosome of 6.80 Mb was assembled. A total of 21 secondary metabolite biosynthesis gene clusters (BGCs), accounting for 12.27% of the genome, were identified. Core gene deletion mutants for each of all 8 BGCs for nonribosomal peptide synthetases and polyketide synthases were created. Among them, only the mutant lacking ctg1-5755 (the gene was renamed as fscD W68) in BGC 19, which shares 100% sequence similarity with the BGC for candicidin synthesis, showed obvious reduction in antifungal activity. A pot experiment revealed that biocontrol effects of the ΔfscD W68 mutant in Rhizoctonia rot of cucumber were also significantly compromised relative to W68. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed that W68 but not the ΔfscD W68 mutant can produce candicidin isomers, indicating that the production of candicidin isomers is key for antifungal activity and biocontrol activity of S. albidoflavus W68.IMPORTANCE This study reports that candicidin-like secondary metabolites produced by microbial cells in natural soil environments can effectively control soilborne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 are attributable to the production of candicidin isomers, suggesting that gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.
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Kang Y, Kim M, Shim C, Bae S, Jang S. Potential of Algae-Bacteria Synergistic Effects on Vegetable Production. FRONTIERS IN PLANT SCIENCE 2021; 12:656662. [PMID: 33912211 PMCID: PMC8072153 DOI: 10.3389/fpls.2021.656662] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 05/31/2023]
Abstract
Modern agriculture has become heavily dependent on chemical fertilizers, which have caused environmental pollution and the loss of soil fertility and sustainability. Microalgae and plant growth-promoting bacteria (PGPB) have been identified as alternatives to chemical fertilizers for improving soil fertility. This is because of their biofertilizing properties, through the production of bioactive compounds (e.g., phytohormones, amino acids, and carotenoids) and their ability to inhibit plant pathogens. Although treatment based on a single species of microalgae or bacteria is commonly used in agriculture, there is growing experimental evidence suggesting that a symbiotic relationship between microalgae and bacteria synergistically affects each other's physiological and metabolomic processes. Moreover, the co-culture/combination treatment of microalgae and bacteria is considered a promising approach in biotechnology for wastewater treatment and efficient biomass production, based on the advantage of the resulting synergistic effects. However, much remains unexplored regarding the microalgal-bacterial interactions for agricultural applications. In this review, we summarize the effects of microalgae and PGPB as biofertilizing agents on vegetable cultivation. Furthermore, we present the potential of the microalgae-PGPB co-culture/combination system for the environmentally compatible production of vegetables with improved quality.
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Affiliation(s)
- Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, Jeollabuk-do, South Korea
| | - Minjeong Kim
- Organic Agricultural Division, National Institute of Agricultural Sciences, RDA, Wanju-gun, Jeollabuk-do, South Korea
| | - Changki Shim
- Organic Agricultural Division, National Institute of Agricultural Sciences, RDA, Wanju-gun, Jeollabuk-do, South Korea
| | - Suyea Bae
- World Vegetable Center Korea Office, Wanju-gun, Jeollabuk-do, South Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, Jeollabuk-do, South Korea
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Rhizospheric Phosphate Solubilizing Bacillus atrophaeus GQJK17 S8 Increases Quinoa Seedling, Withstands Heavy Metals, and Mitigates Salt Stress. SUSTAINABILITY 2021. [DOI: 10.3390/su13063307] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction of quinoa (Chenopodium quinoa willd.), a gluten-free nutritious pseudo-cereal, outside its traditional growing areas exposed it to seedling damping-off. Here, we isolated eleven phosphate-solubilizing bacteria from the quinoa rhizosphere and assessed their effect on germination and seedlings growth. All isolates solubilized phosphate, produced indole3-acetic acid, hydrocyanic acid, siderophores, and ammonia. Genotypic analysis revealed that our strains are related to the genus of Bacillus, Pseudomonas, and Enterobacter. Strains Enterobacter asburiae (QD14, QE4, QE6, and QE16), Enterobacter sp. QE3, and Enterobacter hormaechei QE7 withstood 1.5 mg·L−1 of cadmium sulfate, 0.5 mg·mL−1 of nickel nitrate, and 1 mg·mL−1 of copper sulfate. Moreover, all strains solubilized zinc from ZnO; P. Stutzeri QD1 and E. asburiae QD14 did not solubilize Zn3(PO4)2 and CO3Zn, whereas CO3Zn was not solubilized by E. asburiae QE16. Bacillus atrophaeus S8 tolerated 11% NaCl. P. frederiksbergensis S6 and Pseudomonas sp. S7 induced biofilm formation. Anti-fusarium activity was demonstrated for E.asburiae QE16, P. stutzeri QD1, P. frederiksbergensis S6, Pseudomonas sp. S7, and B. atrophaeus S8. Lastly, inoculation of quinoa seeds with B. atrophaeus S8 and E. asburiae QB1 induced the best germination rate and seedling growth, suggesting their potential use as inoculants for salty and heavy metal or zinc contaminated soils.
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Amacker N, Gao Z, Agaras BC, Latz E, Kowalchuk GA, Valverde CF, Jousset A, Weidner S. Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads. Front Microbiol 2020; 11:614194. [PMID: 33384680 PMCID: PMC7769776 DOI: 10.3389/fmicb.2020.614194] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.
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Affiliation(s)
- Nathalie Amacker
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Zhilei Gao
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Betina C. Agaras
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Departamento de Ciencia y Tecnología, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Ellen Latz
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - George A. Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Claudio F. Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Departamento de Ciencia y Tecnología, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Simone Weidner
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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Adedeji AA, Häggblom MM, Babalola OO. Sustainable agriculture in Africa: Plant growth-promoting rhizobacteria (PGPR) to the rescue. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Dobler L, Ferraz HC, Araujo de Castilho LV, Sangenito LS, Pasqualino IP, Souza Dos Santos AL, Neves BC, Oliveira RR, Guimarães Freire DM, Almeida RV. Environmentally friendly rhamnolipid production for petroleum remediation. CHEMOSPHERE 2020; 252:126349. [PMID: 32443257 DOI: 10.1016/j.chemosphere.2020.126349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/25/2020] [Accepted: 02/25/2020] [Indexed: 06/11/2023]
Abstract
Biosurfactants have potential applications in the remediation of petroleum-contaminated sites. Several strategies can be used to reduce the production costs of these surfactants and make the process more environmentally friendly. In this study, we combined some of these strategies to produce the rhamnolipid-type biosurfactant, including the use of the genetically modified strain Pseudomonas aeruginosa-estA, an industrial coproduct as a carbon source, a simple and low-cost medium, and a simple downstream process. The process resulted in a high yield (17.6 g L-1), even using crude glycerin as the carbon source, with substrate in product conversion factor (YRML/s) of 0.444. The cell-free supernatant (CFS) was not toxic to Artemia salina and selected mammalian cell lineages, suggesting that it can be used directly in the environment without further purification steps. Qualitative analysis showed that CFS has excellent dispersion in the oil-displacement test, emulsifying (IE24 = 65.5%), and tensoactive properties. When salinity, temperature and pressure were set to seawater conditions, the values for interfacial tension between crude oil and water were below 1.0 mN m-1. Taken together, these results demonstrate that it is possible to obtain a nontoxic crude rhamnolipid product, with high productivity, to replace petroleum-based surfactants in oil spill cleanups and other environmental applications.
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Affiliation(s)
- Leticia Dobler
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Helen Conceição Ferraz
- Instituto Alberto Luiz Coimbra de Pós Graduação e Pesquisa, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Livia Vieira Araujo de Castilho
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto Alberto Luiz Coimbra de Pós Graduação e Pesquisa, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leandro Stefano Sangenito
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ilson Paranhos Pasqualino
- Instituto Alberto Luiz Coimbra de Pós Graduação e Pesquisa, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Luis Souza Dos Santos
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca Cruz Neves
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Contribution of Hydrogen Cyanide to the Antagonistic Activity of Pseudomonas Strains Against Phytophthora infestans. Microorganisms 2020; 8:microorganisms8081144. [PMID: 32731625 PMCID: PMC7464445 DOI: 10.3390/microorganisms8081144] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022] Open
Abstract
Plants face many biotic and abiotic challenges in nature; one of them is attack by disease-causing microbes. Phytophthora infestans, the causal agent of late blight is one of the most prominent pathogens of the potato responsible for multi-billion-dollar losses every year. We have previously reported that potato-associated Pseudomonas strains inhibited P. infestans at various developmental stages. A comparative genomics approach identified several factors putatively involved in this anti-oomycete activity, among which was the production of hydrogen cyanide (HCN). Here, we report the relative contribution of HCN emission to the overall anti-Phytophthora activity of two cyanogenic Pseudomonas strains, P. putida R32 and P. chlororaphis R47. To quantify this contribution, we generated HCN-negative mutants (Δhcn) and compared their activities to those of their respective wild types in different experiments assessing P. infestans mycelial growth, zoospore germination, and infection of potato leaf disks. Using in vitro experiments allowing only volatile-mediated interactions, we observed that HCN accounted for most of the mycelial growth inhibition (57% in R47 and 80% in R32). However, when allowing both volatile and diffusible compound-mediated interactions, HCN only accounted for 1% (R47) and 18% (R32) of mycelial growth inhibition. Likewise, both mutants inhibited zoospore germination in a similar way as their respective wild types. More importantly, leaf disk experiments showed that both wild-type and Δhcn strains of R47 and R32 were able to limit P. infestans infection to a similar extent. Our results suggest that while HCN is a major contributor to the in vitro volatile-mediated restriction of P. infestans mycelial growth, it does not play a major role in the inhibition of other disease-related features such as zoospore germination or infection of plant tissues.
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22
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Hyperosmotic Adaptation of Pseudomonas protegens SN15-2 Helps Cells to Survive at Lethal Temperatures. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0430-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Mahdi I, Fahsi N, Hafidi M, Allaoui A, Biskri L. Plant Growth Enhancement using Rhizospheric Halotolerant Phosphate Solubilizing Bacterium Bacillus licheniformis QA1 and Enterobacter asburiae QF11 Isolated from Chenopodium quinoa Willd. Microorganisms 2020; 8:E948. [PMID: 32599701 PMCID: PMC7356859 DOI: 10.3390/microorganisms8060948] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Plant growth-promoting rhizobacteria represent a promising solution to enhancing agricultural productivity. Here, we screened phosphate solubilizing bacteria from the rhizospheric soil of Chenopodium quinoa Willd and assessed their plant-growth promoting rhizobacteria (PGPR) properties including production of indole-3-acetic acid (IAA), siderophores, hydrogen cyanide (HCN), ammonia and extracellular enzymes. We also investigated their tolerance to salt stress and their capacity to form biofilms. Two isolated strains, named QA1 and QF11, solubilized phosphate up to 346 mg/L, produced IAA up to 795.31 µg/mL, and tolerated up to 2 M NaCl in vitro. 16S rRNA and Cpn60 gene sequencing revealed that QA1 and QF11 belong to the genus Bacillus licheniformis and Enterobacter asburiae, respectively. In vivo, early plant growth potential showed that quinoa seeds inoculated either with QA1 or QF11 displayed higher germination rates and increased seedling growth. Under saline irrigation conditions, QA1 enhanced plant development/growth. Inoculation with QA1 increased leaf chlorophyll content index, enhanced P and K+ uptake and decreased plant Na+ uptake. Likewise, plants inoculated with QF11 strain accumulated more K+ and had reduced Na+ content. Collectively, our findings support the use of QA1 and QF11 as potential biofertilizers.
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Affiliation(s)
- Ismail Mahdi
- Medical Application Interface Center (CIAM), Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco; (I.M.); (N.F.)
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, 40000 Marrakesh, Morocco;
| | - Nidal Fahsi
- Medical Application Interface Center (CIAM), Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco; (I.M.); (N.F.)
- Laboratory of Genetic, Neuroendocrinology and Biotechnology, Faculty of Sciences, Ibn Tofail University, 14000 Kénitra, Morocco
| | - Mohamed Hafidi
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, 40000 Marrakesh, Morocco;
- Microbiome Team and African genome center (AGC), AgrobioSciences department (AgBS), Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco;
| | - Abdelmounaaim Allaoui
- Microbiome Team and African genome center (AGC), AgrobioSciences department (AgBS), Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco;
- Laboratory of Molecular Microbiology, CIPEM (Coalition Center, for Innovation, and Prevention of Epidemies in Morocco) Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco
| | - Latefa Biskri
- Medical Application Interface Center (CIAM), Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco; (I.M.); (N.F.)
- Laboratory of Molecular Microbiology, CIPEM (Coalition Center, for Innovation, and Prevention of Epidemies in Morocco) Mohammed VI Polytechnic University (UM6P), 43150 Benguérir, Morocco
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24
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Levenfors JJ, Nord C, Bjerketorp J, Ståhlberg J, Larsson R, Guss B, Öberg B, Broberg A. Antibacterial pyrrolidinyl and piperidinyl substituted 2,4-diacetylphloroglucinols from Pseudomonas protegens UP46. J Antibiot (Tokyo) 2020; 73:739-747. [PMID: 32439988 DOI: 10.1038/s41429-020-0318-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
In the search for new antibiotic compounds, fractionation of Pseudomonas protegens UP46 culture extracts afforded several known Pseudomonas compounds, including 2,4-diacetylphloroglucinol (DAPG), as well as two new antibacterial alkaloids, 6-(pyrrolidin-2-yl)DAPG (1) and 6-(piperidin-2-yl)DAPG (2). The structures of 1 and 2 were determined by nuclear magnetic resonance spectroscopy and mass spectrometry. Compounds 1 and 2 were found to have antibacterial activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus cereus, with minimal inhibitory concentration (MIC) 2 and 4 μg ml-1, respectively, for 1, and 2 μg ml-1 for both pathogens for 2. The MICs for 1 and 2, against all tested Gram-negative bacteria, were >32 μg ml-1. The half maximal inhibitory concentrations against HepG2 cells for compounds 1 and 2 were 11 and 18 μg ml-1, respectively, which suggested 1 and 2 be too toxic for further evaluation as possible new antibacterial drugs. Stable isotope labelling experiments showed the pyrrolidinyl group of 1 to originate from ornithine and the piperidinyl group of 2 to originate from lysine. The P. protegens acetyl transferase (PpATase) is involved in the biosynthesis of monoacetylphloroglucinol and DAPG. No optical rotation was detected for 1 or 2, and a possible reason for this was investigated by studying if the PpATase may catalyse a stereo-non-specific introduction of the pyrrolidinyl/piperidinyl group in 1 and 2, but unless the PpATase can be subjected to major conformational changes, the enzyme cannot be involved in this reaction. The PpATase is, however, likely to catalyse the formation of 2,4,6-triacetylphloroglucinol from DAPG.
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Affiliation(s)
- Jolanta J Levenfors
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.,Ultupharma AB, Södra Rudbecksgatan 13, SE-752 36, Uppsala, Sweden
| | - Christina Nord
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Joakim Bjerketorp
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.,Ultupharma AB, Södra Rudbecksgatan 13, SE-752 36, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Rolf Larsson
- Department of Medical Sciences, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Bengt Guss
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P.O. Box 7036, SE-750 07, Uppsala, Sweden
| | - Bo Öberg
- Ultupharma AB, Södra Rudbecksgatan 13, SE-752 36, Uppsala, Sweden.,Department of Medicinal Chemistry, Uppsala University, P.O. Box 574, SE-751 23, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
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25
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Messan KS, Jones RM, Doherty SJ, Foley K, Douglas TA, Barbato RA. The role of changing temperature in microbial metabolic processes during permafrost thaw. PLoS One 2020; 15:e0232169. [PMID: 32353013 PMCID: PMC7192436 DOI: 10.1371/journal.pone.0232169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Approximately one fourth of the Earth's Northern Hemisphere is underlain by permafrost, earth materials (soil, organic matter, or bedrock), that has been continuously frozen for at least two consecutive years. Numerous studies point to evidence of accelerated climate warming in the Arctic and sub-Arctic where permafrost is located. Changes to permafrost biochemical processes may critically impact ecosystem processes at the landscape scale. Here, we sought to understand how the permafrost metabolome responds to thaw and how this response differs based on location (i.e. chronosequence of permafrost formation constituting diverse permafrost types). We analyzed metabolites from microbial cells originating from Alaskan permafrost. Overall, permafrost thaw induced a shift in microbial metabolic processes. Of note were the dissimilarities in biochemical structure between frozen and thawed samples. The thawed permafrost metabolomes from different locations were highly similar. In the intact permafrost, several metabolites with antagonist properties were identified, illustrating the competitive survival strategy required to survive a frozen state. Interestingly, the intensity of these antagonistic metabolites decreased with warmer temperature, indicating a shift in ecological strategies in thawed permafrost. These findings illustrate the impact of change in temperature and spatial variability as permafrost undergoes thaw, knowledge that will become crucial for predicting permafrost biogeochemical dynamics as the Arctic and Antarctic landscapes continue to warm.
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Affiliation(s)
- Komi S. Messan
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Robert M. Jones
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Stacey J. Doherty
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Karen Foley
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Thomas A. Douglas
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Fairbanks, Alaska, United States of America
| | - Robyn A. Barbato
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
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26
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Yi W, Ge ZW, Wu B, Zhang Z. New metabolites from the marine-derived bacterium Pseudomonas sp. ZZ820R. Fitoterapia 2020; 143:104555. [PMID: 32194170 DOI: 10.1016/j.fitote.2020.104555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 11/25/2022]
Abstract
Six previously undescribed compounds, named monaxanthones A and B, monaphenol A, monathioamide A, monaprenylindole A, and monavalerolactone A, were isolated from the culture of a marine-sourced bacterium Pseudomonas sp. ZZ820R in rice medium. Their structures were elucidated based on the HRESIMS data, NMR and MS-MS spectroscopic analyses, optical rotation and ECD calculations. Monathioamide A is an unprecedented sulfur-contained compound and monavalerolactone A represents the first example of this type of natural products. Monaprenylindole A showed antibacterial activity against methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- Wenwen Yi
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China
| | - Zhi-Wei Ge
- Analysis Center for Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Bin Wu
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China.
| | - Zhizhen Zhang
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China.
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27
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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28
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Wang X, Tang D, Wang W. Adaptation strategies of
Pseudomonas protegens
SN15‐2 to hyperosmotic growth environment. J Appl Microbiol 2020; 128:1720-1734. [DOI: 10.1111/jam.14582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- X. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - D. Tang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - W. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
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29
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Breitkreuz C, Buscot F, Tarkka M, Reitz T. Shifts Between and Among Populations of Wheat Rhizosphere Pseudomonas, Streptomyces and Phyllobacterium Suggest Consistent Phosphate Mobilization at Different Wheat Growth Stages Under Abiotic Stress. Front Microbiol 2020; 10:3109. [PMID: 32038552 PMCID: PMC6987145 DOI: 10.3389/fmicb.2019.03109] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change models predict more frequent and prolonged drought events in Central Europe, which will exert extraordinary pressure on agroecosystems. One of the consequences is drought-related nutrient limitations for crops negatively affecting agricultural productivity. These effects can be mitigated by beneficial plant growth promoting rhizobacteria. In this study, we investigated the potential of cultivable bacterial species for phosphate solubilization in the rhizosphere of winter wheat at two relevant growth stages - stem elongation and grain filling stages. Rhizosphere samples were collected in the Global Change Experimental Facility in Central Germany, which comprises plots with conventional and organic farming systems under ambient and future climate. Phosphate-solubilizing bacteria were selectively isolated on Pikovskaya medium, phylogenetically classified by 16S rRNA sequencing, and tested for in vitro mineral phosphate solubilization and drought tolerance using plate assays. The culture isolates were dominated by members of the genera Phyllobacterium, Pseudomonas and Streptomyces. Cultivation-derived species richness and abundance of dominant taxa, especially within the genera Phyllobacterium and Pseudomonas, as well as composition of Pseudomonas species were affected by wheat growth stage. Pseudomonas was found to be more abundant at stem elongation than at grain filling, while for Phyllobacterium the opposite pattern was observed. The abundance of Streptomyces isolates remained stable throughout the studied growth stages. The temporal shifts in the cultivable fraction of the community along with considerable P solubilization potentials of Phyllobacterium and Pseudomonas species suggest functional redundancy between and among genera at different wheat growth stages. Phosphate-solubilizing Phyllobacterium species were assigned to Phyllobacterium ifriqiyense and Phyllobacterium sophorae. It is the first time that phosphate solubilization potential is described for these species. Since Phyllobacterium species showed the highest drought tolerance along all isolates, they may play an increasingly important role in phosphate solubilization in a future dryer climate.
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Affiliation(s)
- Claudia Breitkreuz
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mika Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Thomas Reitz
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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30
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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31
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Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate. Appl Environ Microbiol 2019; 85:AEM.01741-18. [PMID: 30478234 PMCID: PMC6344628 DOI: 10.1128/aem.01741-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/17/2018] [Indexed: 01/08/2023] Open
Abstract
Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens. The rhizobacterium Pseudomonas pseudoalcaligenes AVO110, isolated by the enrichment of competitive avocado root tip colonizers, controls avocado white root rot disease caused by Rosellinia necatrix. Here, we applied signature-tagged mutagenesis (STM) during the growth and survival of AVO110 in fungal exudate-containing medium with the goal of identifying the molecular mechanisms linked to the interaction of this bacterium with R. necatrix. A total of 26 STM mutants outcompeted by the parental strain in fungal exudate, but not in rich medium, were selected and named growth-attenuated mutants (GAMs). Twenty-one genes were identified as being required for this bacterial-fungal interaction, including membrane transporters, transcriptional regulators, and genes related to the metabolism of hydrocarbons, amino acids, fatty acids, and aromatic compounds. The bacterial traits identified here that are involved in the colonization of fungal hyphae include proteins involved in membrane maintenance (a dynamin-like protein and ColS) or cyclic-di-GMP signaling and chemotaxis. In addition, genes encoding a DNA helicase (recB) and a regulator of alginate production (algQ) were identified as being required for efficient colonization of the avocado rhizosphere. IMPORTANCE Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens.
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32
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Whole-Genome Sequence of Pseudomonas putida Strain 1312, a Potential Biostimulant Developed for Agriculture. Microbiol Resour Announc 2018; 7:MRA01073-18. [PMID: 30533614 PMCID: PMC6256590 DOI: 10.1128/mra.01073-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/15/2018] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of strain 1312 of Pseudomonas putida, which could be interesting to develop as a biostimulant for agriculture and soil depollution treatments. We report the draft genome sequence of strain 1312 of Pseudomonas putida, which could be interesting to develop as a biostimulant for agriculture and soil depollution treatments.
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33
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Assessment of plant growth promoting activities of five rhizospheric Pseudomonas strains. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Analysis of the genome sequence of plant beneficial strain Pseudomonas sp. RU47. J Biotechnol 2018; 281:183-192. [DOI: 10.1016/j.jbiotec.2018.07.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 11/22/2022]
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35
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Adeniji AA, Babalola OO. Tackling maize fusariosis: in search of Fusarium graminearum biosuppressors. Arch Microbiol 2018; 200:1239-1255. [PMID: 29934785 DOI: 10.1007/s00203-018-1542-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 05/17/2018] [Accepted: 06/16/2018] [Indexed: 12/16/2022]
Abstract
This review presents biocontrol agents employed to alleviate the deleterious effect of the pathogen Fusarium graminearum on maize. The control of this mycotoxigenic phytopathogen remains elusive despite the elaborate research conducted on its detection, identification, and molecular fingerprinting. This could be attributed to the fact that in vitro and greenhouse biocontrol studies on F. graminearum have exceeded the number of field studies done. Furthermore, along with the variances seen among these F. graminearum suppressing biocontrol strains, it is also clear that the majority of research done to tackle F. graminearum outbreaks was on wheat and barley cultivars. Most fusariosis management related to maize targeted other members of Fusarium such as Fusarium verticillioides, with biocontrol strains from the genera Bacillus and Pseudomonas being used frequently in the experiments. We highlight relevant current techniques needed to identify an effective biofungicide for maize fusariosis and recommend alternative approaches to reduce the scarcity of data for indigenous maize field trials.
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Affiliation(s)
- Adetomiwa Ayodele Adeniji
- Food Security and Safety Niche Area, Faculty of Agriculture, Science and Technology, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Agriculture, Science and Technology, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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Tshikantwa TS, Ullah MW, He F, Yang G. Current Trends and Potential Applications of Microbial Interactions for Human Welfare. Front Microbiol 2018; 9:1156. [PMID: 29910788 PMCID: PMC5992746 DOI: 10.3389/fmicb.2018.01156] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/14/2018] [Indexed: 01/06/2023] Open
Abstract
For a long time, it was considered that interactions between microbes are only inhibitory in nature. However, latest developments in research have demonstrated that within our environment, several classes of microbes exist which produce different products upon interaction and thus embrace a wider scope of useful and potentially valuable aspects beyond simple antibiosis. Therefore, the current review explores different types of microbial interactions and describes the role of various physical, chemical, biological, and genetic factors regulating such interactions. It further explains the mechanism of action of biofilm formation and role of secondary metabolites regulating bacteria-fungi interaction. Special emphasis and focus is placed on microbial interactions which are important in medicine, food industry, agriculture, and environment. In short, this review reveals the recent contributions of microbial interaction for the benefit of mankind.
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Affiliation(s)
| | - Muhammad Wajid Ullah
- Department of Biomedical Engineering Huazhong University of Science and Technology, Wuhan, China
| | - Feng He
- College of Life Sciences Huanggang Normal University, Huanggang, China
| | - Guang Yang
- Department of Biomedical Engineering Huazhong University of Science and Technology, Wuhan, China
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Anderson JA, Staley J, Challender M, Heuton J. Safety of Pseudomonas chlororaphis as a gene source for genetically modified crops. Transgenic Res 2018; 27:103-113. [PMID: 29427161 PMCID: PMC5847145 DOI: 10.1007/s11248-018-0061-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/30/2018] [Indexed: 11/25/2022]
Abstract
Genetically modified crops undergo extensive evaluation to characterize their food, feed and environmental safety prior to commercial introduction, using a well-established, science-based assessment framework. One component of the safety assessment includes an evaluation of each introduced trait, including its source organism, for potential adverse pathogenic, toxic and allergenic effects. Several Pseudomonas species have a history of safe use in agriculture and certain species represent a source of genes with insecticidal properties. The ipd072Aa gene from P. chlororaphis encodes the IPD072Aa protein, which confers protection against certain coleopteran pests when expressed in maize plants. P. chlororaphis is ubiquitous in the environment, lacks known toxic or allergenic properties, and has a history of safe use in agriculture and in food and feed crops. This information supports, in part, the safety assessment of potential traits, such as IPD072Aa, that are derived from this source organism.
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Affiliation(s)
| | - Jamie Staley
- DuPont Pioneer, 8325 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Mary Challender
- DuPont Pioneer, 8325 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Jamie Heuton
- DuPont Pioneer, 8325 NW 62nd Avenue, Johnston, IA, 50131, USA
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Abdullah AS, Moffat CS, Lopez-Ruiz FJ, Gibberd MR, Hamblin J, Zerihun A. Host-Multi-Pathogen Warfare: Pathogen Interactions in Co-infected Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1806. [PMID: 29118773 PMCID: PMC5660990 DOI: 10.3389/fpls.2017.01806] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/04/2017] [Indexed: 05/04/2023]
Abstract
Studies of plant-pathogen interactions have historically focused on simple models of infection involving single host-single disease systems. However, plant infections often involve multiple species and/or genotypes and exhibit complexities not captured in single host-single disease systems. Here, we review recent insights into co-infection systems focusing on the dynamics of host-multi-pathogen interactions and the implications for host susceptibility/resistance. In co-infection systems, pathogen interactions include: (i) Competition, in which competing pathogens develop physical barriers or utilize toxins to exclude competitors from resource-dense niches; (ii) Cooperation, whereby pathogens beneficially interact, by providing mutual biochemical signals essential for pathogenesis, or through functional complementation via the exchange of resources necessary for survival; (iii) Coexistence, whereby pathogens can stably coexist through niche specialization. Furthermore, hosts are also able to, actively or passively, modulate niche competition through defense responses that target at least one pathogen. Typically, however, virulent pathogens subvert host defenses to facilitate infection, and responses elicited by one pathogen may be modified in the presence of another pathogen. Evidence also exists, albeit rare, of pathogens incorporating foreign genes that broaden niche adaptation and improve virulence. Throughout this review, we draw upon examples of co-infection systems from a range of pathogen types and identify outstanding questions for future innovation in disease control strategies.
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Affiliation(s)
- Araz S. Abdullah
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Caroline S. Moffat
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Francisco J. Lopez-Ruiz
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Mark R. Gibberd
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - John Hamblin
- Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
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Hennessy RC, Glaring MA, Olsson S, Stougaard P. Transcriptomic profiling of microbe-microbe interactions reveals the specific response of the biocontrol strain P. fluorescens In5 to the phytopathogen Rhizoctonia solani. BMC Res Notes 2017; 10:376. [PMID: 28807055 PMCID: PMC5557065 DOI: 10.1186/s13104-017-2704-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 07/29/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Few studies to date report the transcriptional response of biocontrol bacteria toward phytopathogens. In order to gain insights into the potential mechanism underlying the antagonism of the antimicrobial producing strain P. fluorescens In5 against the phytopathogens Rhizoctonia solani and Pythium aphanidermatum, global RNA sequencing was performed. METHODS Differential gene expression profiling of P. fluorescens In5 in response to either R. solani or P. aphanidermatum was investigated using transcriptome sequencing (RNA-seq). Total RNA was isolated from single bacterial cultures of P. fluorescens In5 or bacterial cultures in dual-culture for 48 h with each pathogen in biological triplicates. RNA-seq libraries were constructed following a default Illumina stranded RNA protocol including rRNA depletion and were sequenced 2 × 100 bases on Illumina HiSeq generating approximately 10 million reads per sample. RESULTS No significant changes in global gene expression were recorded during dual-culture of P. fluorescens In5 with any of the two pathogens but rather each pathogen appeared to induce expression of a specific set of genes. A particularly strong transcriptional response to R. solani was observed and notably several genes possibly associated with secondary metabolite detoxification and metabolism were highly upregulated in response to the fungus. A total of 23 genes were significantly upregulated and seven genes were significantly downregulated with at least respectively a threefold change in expression level in response to R. solani compared to the no fungus control. In contrast, only one gene was significantly upregulated over threefold and three transcripts were significantly downregulated over threefold in response to P. aphanidermatum. Genes known to be involved in synthesis of secondary metabolites, e.g. non-ribosomal synthetases and hydrogen cyanide were not differentially expressed at the time points studied. CONCLUSION This study demonstrates that genes possibly involved in metabolite detoxification are highly upregulated in P. fluorescens In5 when co-cultured with plant pathogens and in particular the fungus R. solani. This highlights the importance of studying microbe-microbe interactions to gain a better understanding of how different systems function in vitro and ultimately in natural systems where biocontrol agents can be used for the sustainable management of plant diseases.
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Affiliation(s)
- Rosanna C Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Mikkel A Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Singh VK, Singh AK, Kumar A. Disease management of tomato through PGPB: current trends and future perspective. 3 Biotech 2017; 7:255. [PMID: 28730550 PMCID: PMC5519495 DOI: 10.1007/s13205-017-0896-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 07/15/2017] [Indexed: 12/29/2022] Open
Abstract
Tomato is the world's second most cultivated vegetable. During cultivation or post-harvest storage, it is susceptible to more than 200 diseases caused by an array of pathogenic fungi, nematodes, bacteria, and viruses. Although wide range of chemical pesticides are currently available to manage plant diseases, continuous application of pesticides not only affect the nutritional contents of tomato but also the texture or productivity of soil. In this context, plant growth promoting bacteria (PGPB) are one of the nature friendly, safe, and effective alternatives for the management of diseases and pathogens of tomato. Currently, numbers of microbes have been used as soil or plant inoculants in different plants including tomato as biocontrol. Besides disease inhibition, these inoculants also act as growth modulators. The present article describes the biocontrol potential of PGPB strains and mechanisms for the diseases management in tomato.
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Affiliation(s)
- Vipin Kumar Singh
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Amit Kishore Singh
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ajay Kumar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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Li HB, Singh RK, Singh P, Song QQ, Xing YX, Yang LT, Li YR. Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere. Front Microbiol 2017; 8:1268. [PMID: 28769881 PMCID: PMC5509769 DOI: 10.3389/fmicb.2017.01268] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/23/2017] [Indexed: 01/09/2023] Open
Abstract
The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP) traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL-1 in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg-1 h-1. For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C2H2 h-1 mL-1). All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR) amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 (Pseudomonas koreensis) and CN11 (Pseudomonas entomophila) showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP)-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The Biolog phenotypic profiling, which comprised utilization of C and N sources, and tolerance to osmolytes and pH, revealed the metabolic versatility of the selected strains. The colonization ability of the selected strains was evaluated by genetically tagging them with a constitutively expressing GFP-pPROBE-pTetr-OT plasmid. qRT-PCR results showed that both strains had the ability to express the nifH gene at 90 and 120 days, as compared to a control, in both sugarcane varieties GT11 and GXB9. Therefore, our isolated strains, P. koreensis and P. entomophila may be used as inoculums or in biofertilizer production for enhancing growth and nutrients, as well as for improving nitrogen levels, in sugarcane and other crops. The present study, to the best of our knowledge, is the first report on the diversity of Pseudomonas spp. associated with sugarcane in Guangxi, China.
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Affiliation(s)
- Hai-Bi Li
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Rajesh K Singh
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Pratiksha Singh
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Qi-Qi Song
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Yong-Xiu Xing
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Li-Tao Yang
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Yang-Rui Li
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement Guangxi, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
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Michavila G, Adler C, De Gregorio PR, Lami MJ, Caram Di Santo MC, Zenoff AM, de Cristobal RE, Vincent PA. Pseudomonas protegens CS1 from the lemon phyllosphere as a candidate for citrus canker biocontrol agent. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:608-617. [PMID: 28194866 DOI: 10.1111/plb.12556] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
Citrus canker is a worldwide-distributed disease caused by Xanthomonas citri subsp. citri. One of the most used strategies to control the disease is centred on copper-based compounds that cause environmental problems. Therefore, it is of interest to develop new strategies to manage the disease. Previously, we reported the ability of the siderophore pyochelin, produced by the opportunistic human pathogen Pseudomonas aeruginosa, to inhibit in vitro several bacterial species, including X. citri subsp. citri. The action mechanism, addressed with the model bacterium Escherichia coli, was connected to the generation of reactive oxygen species (ROS). This work aimed to find a non-pathogenic strain from the lemon phyllosphere that would produce pyochelin and therefore serve in canker biocontrol. An isolate that retained its capacity to colonise the lemon phyllosphere and inhibit X. citri subsp. citri was selected and characterised as Pseudomonas protegens CS1. From a liquid culture of this strain, the active compound was purified and identified as the pyochelin enantiomer, enantio-pyochelin. Using the producing strain and the pure compound, both in vitro and in vivo, we determined that the action mechanism of X. citri subsp. citri inhibition also involved the generation of ROS. Finally, the potential application of P. protegens CS1 was evaluated by spraying the bacterium in a model that mimics the natural X. citri subsp. citri infection. The ability of P. protegens CS1 to reduce canker formation makes this strain an interesting candidate as a biocontrol agent.
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Affiliation(s)
- G Michavila
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - C Adler
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - P R De Gregorio
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - M J Lami
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - M C Caram Di Santo
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - A M Zenoff
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - R E de Cristobal
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - P A Vincent
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
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Kotasthane AS, Agrawal T, Zaidi NW, Singh US. Identification of siderophore producing and cynogenic fluorescent Pseudomonas and a simple confrontation assay to identify potential bio-control agent for collar rot of chickpea. 3 Biotech 2017; 7:137. [PMID: 28593521 DOI: 10.1007/s13205-017-0761-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/01/2017] [Indexed: 11/29/2022] Open
Abstract
In soil, plant roots coexist with bacteria and fungi that produce siderophores capable of sequestering the available iron. Microbial cyanogenesis has been demonstrated in many species of fungi and in a few species of bacteria (e.g., Chromobacterium and Pseudomonas). Fluorescent Pseudomonas isolates P29, P59, P144, P166, P174, P187, P191 and P192 were cyanogenic and produced siderophores in the presence of a strong chelater 8-Hydroxyquinoline (50 mg/l). A simple confrontation assay for identifying potential antagonists was developed. Fluorescent Pseudomonas isolates P66, P141, P144, P166 and P174 were antagonistic against both Rhizoctonia solani and Sclerotium rolfsii. Vigorous plant growth was observed following seed bacterization with P141, P200 and P240. In field experiments, seed bacterization with selected bacterial isolates resulted in reduced collar rot (S. rolfsii) incidence.
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Affiliation(s)
- Anil S Kotasthane
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar, Raipur, CG, 492006, India.
| | - Toshy Agrawal
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar, Raipur, CG, 492006, India
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Shah N, Klaponski N, Selin C, Rudney R, Fernando WGD, Belmonte MF, de Kievit TR. PtrA Is Functionally Intertwined with GacS in Regulating the Biocontrol Activity of Pseudomonas chlororaphis PA23. Front Microbiol 2016; 7:1512. [PMID: 27713742 PMCID: PMC5031690 DOI: 10.3389/fmicb.2016.01512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/09/2016] [Indexed: 11/13/2022] Open
Abstract
In vitro inhibition of the fungal pathogen Sclerotinia sclerotiorum by Pseudomonas chlororaphis PA23 is reliant upon a LysR-type transcriptional regulator (LTTR) called PtrA. In the current study, we show that Sclerotinia stem rot and leaf infection are significantly increased in canola plants inoculated with the ptrA-mutant compared to the wild type, establishing PtrA as an essential regulator of PA23 biocontrol. LTTRs typically regulate targets that are upstream of and divergently transcribed from the LTTR locus. We identified a short chain dehydrogenase (scd) gene immediately upstream of ptrA. Characterization of a scd mutant revealed that it is phenotypically identical to the wild type. Moreover, scd transcript abundance was unchanged in the ptrA mutant. These findings indicate that PtrA regulation does not involve scd, rather this LTTR controls genes located elsewhere on the chromosome. Employing a combination of complementation and transcriptional analysis we investigated whether connections exist between PtrA and other regulators of biocontrol. Besides ptrA, gacS was the only gene able to partially rescue the wild-type phenotype, establishing a connection between PtrA and the sensor kinase GacS. Transcriptomic analysis revealed decreased expression of biosynthetic (phzA, prnA) and regulatory genes (phzI, phzR, rpoS, gacA, rsmX, rsmZ, retS) in the ptrA mutant; conversely, rsmE, and rsmY were markedly upregulated. The transcript abundance of ptrA was nine-fold higher in the mutant background indicating that this LTTR negatively autoregulates itself. In summary, PtrA is an essential regulator of genes required for PA23 biocontrol that is functionally intertwined with GacS.
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Affiliation(s)
- Nidhi Shah
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | - Natasha Klaponski
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | - Carrie Selin
- Department of Plant Science, University of Manitoba Winnipeg, MB, Canada
| | - Rachel Rudney
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | | | - Mark F Belmonte
- Department of Biological Science, University of Manitoba Winnipeg, MB, Canada
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Ordoñez YM, Fernandez BR, Lara LS, Rodriguez A, Uribe-Vélez D, Sanders IR. Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities. PLoS One 2016; 11:e0154438. [PMID: 27253975 PMCID: PMC4890779 DOI: 10.1371/journal.pone.0154438] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/13/2016] [Indexed: 11/18/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing Pseudomonas bacteria (PSB) could potentially interact synergistically because PSB solubilize phosphate into a form that AMF can absorb and transport to the plant. However, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. We tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along AMF hyphae and differentially influence the growth of AMF both outside the roots of carrot in in vitro conditions and inside the roots of potato in the presence of a microbial community. We found strong effects of AMF on the growth of the different bacterial strains. Different bacterial strains also had very strong effects on the growth of AMF extraradical hyphae outside the roots of carrot and on colonization of potato roots by AMF. The differential effects on colonization occurred in the presence of a microbial community. Our results show that these two important groups of rhizosphere microorganisms indeed interact with each other. Such interactions could potentially lead to synergistic effects between the two groups but this could depend on whether the bacteria truly solubilize phosphate in the rhizosphere in the presence of microbial communities.
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Affiliation(s)
- Yuli Marcela Ordoñez
- Biology Department, Faculty of Science, Universidad Nacional de Colombia, Ciudad Universitaria—Avenida Carrera 30 N° 45–03, Bogotá, Colombia
| | - Belen Rocio Fernandez
- Faculty of Agronomy, Universidad Nacional de Colombia, Ciudad Universitaria—Avenida Carrera 30 N° 45–03, Bogotá, Colombia
| | - Lidia Susana Lara
- Biotechnology Institute, Universidad Nacional de Colombia, Ciudad Universitaria—Avenida Carrera 30 N° 45–03, Bogotá, Colombia
| | - Alia Rodriguez
- Biology Department, Faculty of Science, Universidad Nacional de Colombia, Ciudad Universitaria—Avenida Carrera 30 N° 45–03, Bogotá, Colombia
| | - Daniel Uribe-Vélez
- Biotechnology Institute, Universidad Nacional de Colombia, Ciudad Universitaria—Avenida Carrera 30 N° 45–03, Bogotá, Colombia
| | - Ian R. Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
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Chen X, Pizzatti C, Bonaldi M, Saracchi M, Erlacher A, Kunova A, Berg G, Cortesi P. Biological Control of Lettuce Drop and Host Plant Colonization by Rhizospheric and Endophytic Streptomycetes. Front Microbiol 2016; 7:714. [PMID: 27242735 PMCID: PMC4874062 DOI: 10.3389/fmicb.2016.00714] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/29/2016] [Indexed: 12/17/2022] Open
Abstract
Lettuce drop, caused by the soil borne pathogen Sclerotinia sclerotiorum, is one of the most common and serious diseases of lettuce worldwide. Increased concerns about the side effects of chemical pesticides have resulted in greater interest in developing biocontrol strategies against S. sclerotiorum. However, relatively little is known about the mechanisms of Streptomyces spp. as biological control agents against S. sclerotiorum on lettuce. Two Streptomyces isolates, S. exfoliatus FT05W and S. cyaneus ZEA17I, inhibit mycelial growth of Sclerotinia sclerotiorum by more than 75% in vitro. We evaluated their biocontrol activity against S. sclerotiorum in vivo, and compared them to Streptomyces lydicus WYEC 108, isolated from Actinovate®. When Streptomyces spp. (10(6) CFU/mL) were applied to S. sclerotiorum inoculated substrate in a growth chamber 1 week prior lettuce sowing, they significantly reduced the risk of lettuce drop disease, compared to the inoculated control. Interestingly, under field conditions, S. exfoliatus FT05W and S. cyaneus ZEA17I protected lettuce from drop by 40 and 10% respectively, whereas S. lydicus WYEC 108 did not show any protection. We further labeled S. exfoliatus FT05W and S. cyaneus ZEA17I with the enhanced GFP (EGFP) marker to investigate their rhizosphere competence and ability to colonize lettuce roots using confocal laser scanning microscopy (CLSM). The abundant colonization of young lettuce seedlings by both strains demonstrated Streptomyces' capability to interact with the host from early stages of seed germination and root development. Moreover, the two strains were detected also on 2-week-old roots, indicating their potential of long-term interactions with lettuce. Additionally, scanning electron microscopy (SEM) observations showed EGFP-S. exfoliatus FT05W endophytic colonization of lettuce root cortex tissues. Finally, we determined its viability and persistence in the rhizosphere and endorhiza up to 3 weeks by quantifying its concentration in these compartments. Based on these results we conclude that S. exfoliatus FT05W has high potential to be exploited in agriculture for managing soil borne diseases barely controlled by available plant protection products.
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Affiliation(s)
- Xiaoyulong Chen
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Cristina Pizzatti
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Maria Bonaldi
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
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Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex. PLoS One 2016; 11:e0150183. [PMID: 26915094 PMCID: PMC4767706 DOI: 10.1371/journal.pone.0150183] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/10/2016] [Indexed: 01/22/2023] Open
Abstract
The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain
| | - Jan P. Meier-Kolthoff
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain
- * E-mail:
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Yasumiba K, Bell S, Alford R. Cell Density Effects of Frog Skin Bacteria on Their Capacity to Inhibit Growth of the Chytrid Fungus, Batrachochytrium dendrobatidis. MICROBIAL ECOLOGY 2016; 71:124-130. [PMID: 26563320 DOI: 10.1007/s00248-015-0701-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/29/2015] [Indexed: 06/05/2023]
Abstract
Bacterial symbionts on frog skin can reduce the growth of the chytrid fungus Batrachochytrium dendrobatidis (Bd) through production of inhibitory metabolites. Bacteria can be effective at increasing the resistance of amphibians to chytridiomycosis when added to amphibian skin, and isolates can be screened for production of metabolites that inhibit Bd growth in vitro. However, some bacteria use density-dependent mechanism such as quorum sensing to regulate metabolite production. It is therefore important to consider cell density effects when evaluating bacteria as possible candidates for bioaugmentation. The aim of our study was to evaluate how the density of cutaneous bacteria affects their inhibition of Bd growth in vitro. We sampled cutaneous bacteria isolated from three frog species in the tropical rainforests of northern Queensland, Australia, and selected ten isolates that were inhibitory to Bd in standardised pilot trials. We grew each isolate in liquid culture at a range of initial dilutions, sub-sampled each dilution at a series of times during the first 48 h of growth and measured spectrophotometric absorbance values, cell counts and Bd-inhibitory activity of cell-free supernatants at each time point. The challenge assay results clearly demonstrated that the inhibitory effects of most isolates were density dependent, with relatively low variation among isolates in the minimum cell density needed to inhibit Bd growth. We suggest the use of minimum cell densities and fast-growing candidate isolates to maximise bioaugmentation efforts.
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Affiliation(s)
- Kiyomi Yasumiba
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.
| | - Sara Bell
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia
| | - Ross Alford
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia
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Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01153-15. [PMID: 26450728 PMCID: PMC4599087 DOI: 10.1128/genomea.01153-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture.
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Pan HQ, Hu JC. Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment. Mar Genomics 2015; 23:55-7. [DOI: 10.1016/j.margen.2015.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 12/01/2022]
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