1
|
Ambreetha S, Zincke D, Balachandar D, Mathee K. Genomic and metabolic versatility of Pseudomonas aeruginosa contributes to its inter-kingdom transmission and survival. J Med Microbiol 2024; 73. [PMID: 38362900 DOI: 10.1099/jmm.0.001791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Pseudomonas aeruginosa is one of the most versatile bacteria with renowned pathogenicity and extensive drug resistance. The diverse habitats of this bacterium include fresh, saline and drainage waters, soil, moist surfaces, taps, showerheads, pipelines, medical implants, nematodes, insects, plants, animals, birds and humans. The arsenal of virulence factors produced by P. aeruginosa includes pyocyanin, rhamnolipids, siderophores, lytic enzymes, toxins and polysaccharides. All these virulent elements coupled with intrinsic, adaptive and acquired antibiotic resistance facilitate persistent colonization and lethal infections in different hosts. To date, treating pulmonary diseases remains complicated due to the chronic secondary infections triggered by hospital-acquired P. aeruginosa. On the contrary, this bacterium can improve plant growth by suppressing phytopathogens and insects. Notably, P. aeruginosa is one of the very few bacteria capable of trans-kingdom transmission and infection. Transfer of P. aeruginosa strains from plant materials to hospital wards, animals to humans, and humans to their pets occurs relatively often. Recently, we have identified that plant-associated P. aeruginosa strains could be pathologically similar to clinical isolates. In this review, we have highlighted the genomic and metabolic factors that facilitate the dominance of P. aeruginosa across different biological kingdoms and the varying roles of this bacterium in plant and human health.
Collapse
Affiliation(s)
- Sakthivel Ambreetha
- Developmental Biology and Genetics, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Diansy Zincke
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
2
|
Xie J, Singh P, Qi Y, Singh RK, Qin Q, Jin C, Wang B, Fang W. Pseudomonas aeruginosa Strain 91: A Multifaceted Biocontrol Agent against Banana Fusarium Wilt. J Fungi (Basel) 2023; 9:1047. [PMID: 37998853 PMCID: PMC10672659 DOI: 10.3390/jof9111047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Banana Fusarium wilt (BFW), caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), poses significant threats to banana cultivation. Currently, effective control methods are lacking, and biological control has emerged as a possible strategy to manage BFW outbreaks. In this investigation, 109 bacterial strains were isolated from the rhizospheric soil surrounding banana plants in search of potent biological agents against Foc. Strain 91 exhibited the highest antifungal activity against the causal agent of Foc and was identified as Pseudomonas aeruginosa through 16S rRNA gene sequencing and scanning electron microscopy (SEM). Elucidation of strain 91's inhibitory mechanism against Foc revealed a multifaceted antagonistic approach, encompassing the production of bioactive compounds and the secretion of cell wall hydrolytic enzymes. Furthermore, strain 91 displayed various traits associated with promoting plant growth and showed adaptability to different carbon sources. By genetically tagging with constitutively expressing GFP signals, effective colonization of strain 91 was mainly demonstrated in root followed by leaf and stem tissues. Altogether, our study reveals the potential of P. aeruginosa 91 for biocontrol based on inhibition mechanism, adaptation, and colonization features, thus providing a promising candidate for the control of BFW.
Collapse
Affiliation(s)
- Jin Xie
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
| | - Pratiksha Singh
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
| | - Yanhua Qi
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
| | - Rajesh Kumar Singh
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Qijian Qin
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
| | - Cheng Jin
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Wang
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
| | - Wenxia Fang
- Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning 530007, China; (J.X.); (P.S.); (Y.Q.); (Q.Q.); (C.J.)
| |
Collapse
|
3
|
Liu Q, Li L, Chen Y, Wang S, Xue L, Meng W, Jiang J, Cao X. Diversity of Endophytic Microbes in Taxus yunnanensis and Their Potential for Plant Growth Promotion and Taxane Accumulation. Microorganisms 2023; 11:1645. [PMID: 37512818 PMCID: PMC10383522 DOI: 10.3390/microorganisms11071645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Taxus spp. are ancient tree species that have survived from the Quaternary glacier period, and their metabolites, such as taxol, have been used as anticancer drugs globally. Plant-endophytic microbial interaction plays a crucial role in exerting a profound impact on host growth and secondary metabolite synthesis. In this study, high-throughput sequencing was employed to explore endophytic microbial diversity in the roots, stems, and leaves of the Taxus yunnanensis (T. yunnanensis). The analysis revealed some dominant genera of endophytic bacteria, such as Pseudomonas, Neorhizobium, Acidovorax, and Flavobacterium, with Cladosporium, Phyllosticta, Fusarium, and Codinaeopsis as prominent endophytic fungi genera. We isolated 108 endophytic bacteria and 27 endophytic fungi from roots, stems, and leaves. In vitro assays were utilized to screen for endophytic bacteria with growth-promoting capabilities, including IAA production, cellulase, siderophore production, protease and ACC deaminase activity, inorganic phosphate solubilization, and nitrogen fixation. Three promising strains, Kocuria sp. TRI2-1, Micromonospora sp. TSI4-1, and Sphingomonas sp. MG-2, were selected based on their superior growth-promotion characteristics. These strains exhibited preferable plant growth promotion when applied to Arabidopsis thaliana growth. Fermentation broths of these three strains were also found to significantly promote the accumulation of taxanes in T. yunnanensis stem cells, among which strain TSI4-1 demonstrated outstanding increase potentials, with an effective induction of taxol, baccatin III, and 10-DAB contents. After six days of treatment, the contents of these metabolites were 3.28 times, 2.23 times, and 2.17 times the initial amounts, reaching 8720, 331, and 371 ng/g of dry weight of stem cells, respectively. These findings present new insight into the industrialization of taxol production through Taxus stem cell fermentation, thereby promoting the conservation of wild Taxus resources by maximizing their potential economic benefits.
Collapse
Affiliation(s)
- Qiao Liu
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Ludan Li
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Yujie Chen
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Sai Wang
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Lina Xue
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Weiying Meng
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Jihong Jiang
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Xiaoying Cao
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| |
Collapse
|
4
|
Parus A, Ciesielski T, Woźniak-Karczewska M, Ślachciński M, Owsianiak M, Ławniczak Ł, Loibner AP, Heipieper HJ, Chrzanowski Ł. Basic principles for biosurfactant-assisted (bio)remediation of soils contaminated by heavy metals and petroleum hydrocarbons - A critical evaluation of the performance of rhamnolipids. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130171. [PMID: 36367467 DOI: 10.1016/j.jhazmat.2022.130171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Despite the fact that rhamnolipids are among the most studied biosurfactants, there are still several gaps which must be filled. The aim of this review is to emphasize and to indicate which issues should be taken into account in order to achieve efficient rhamnolipids-assisted biodegradation or phytoextraction of soils contaminated by heavy metals and petroleum hydrocarbons without harmful side effects. Four main topics have been elucidated in the review: effective concentration of rhamnolipids in soil, their potential phytotoxicity, susceptibility to biodegradation and interaction with soil microorganisms. The discussed elements are often closely associated and often overlap, thus making the interpretation of research results all the more challenging. Each dedicated section of this review includes a description of potential issues and questions, an explanation of the background and rationale for each problem, analysis of relevant literature reports and a short summary with possible application guidelines. The main conclusion is that there is a necessity to establish regulations regarding effective concentrations for rhamnolipids-assisted remediation of soil. The use of an improper concentration is the direct cause of all the other discussed phenomena.
Collapse
Affiliation(s)
- Anna Parus
- Poznan University of Technology, Institute of Chemical Technology and Engineering, Berdychowo 4, 60-965 Poznan, Poland
| | - Tomasz Ciesielski
- Poznan University of Technology, Institute of Chemical Technology and Engineering, Berdychowo 4, 60-965 Poznan, Poland
| | - Marta Woźniak-Karczewska
- Poznan University of Technology, Institute of Chemical Technology and Engineering, Berdychowo 4, 60-965 Poznan, Poland
| | - Mariusz Ślachciński
- Poznan University of Technology, Institute of Chemistry and Technical Electrochemistry, Berdychowo 4, 60-965 Poznan, Poland
| | - Mikołaj Owsianiak
- Quantitative Sustainability Assessment Division, Department of Environmental and Resources Engineering, Technical University of Denmark, Produktionstorvet 424, 2800 Kgs. Lyngby, Denmark
| | - Łukasz Ławniczak
- Poznan University of Technology, Institute of Chemical Technology and Engineering, Berdychowo 4, 60-965 Poznan, Poland
| | - Andreas P Loibner
- Department IFA-Tulln, Institute of Environmental Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Łukasz Chrzanowski
- Poznan University of Technology, Institute of Chemical Technology and Engineering, Berdychowo 4, 60-965 Poznan, Poland; Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.
| |
Collapse
|
5
|
Ambreetha S, Balachandar D. Pathogenesis of plant-associated Pseudomonas aeruginosa in Caenorhabditis elegans model. BMC Microbiol 2022; 22:269. [DOI: 10.1186/s12866-022-02682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Pseudomonas aeruginosa is a globally dreaded pathogen that triggers fatality in immuno-compromised individuals. The agricultural ecosystem is a massive reservoir of this bacterium, and several studies have recommended P. aeruginosa to promote plant growth. However, there were limited attempts to evaluate the health risks associated with plant-associated P. aeruginosa. The current study hypothesized that agricultural P. aeruginosa strains exhibit eukaryotic pathogenicity despite their plant-beneficial traits.
Results
We have demonstrated that feeding with the plant-associated P. aeruginosa strains significantly affects Caenorhabditis elegans health. Out of the 18 P. aeruginosa strain tested, PPA03, PPA08, PPA10, PPA13, PPA14, PPA17, and PPA18 isolated from cucumber, tomato, eggplant, and chili exhibited higher virulence and pathogenicity. Correlation studies indicated that nearly 40% of mortality in C. elegans was triggered by the P. aeruginosa strains with high levels of pyocyanin (> 9 µg/ml) and biofilm to planktonic ratio (> 8).
Conclusion
This study demonstrated that plant-associated P. aeruginosa could be a potential threat to human health similar to the clinical strains. Pyocyanin could be a potential biomarker to screen the pathogenic P. aeruginosa strains in the agricultural ecosystem.
Collapse
|
6
|
Ambreetha S, Marimuthu P, Mathee K, Balachandar D. Plant-associated Pseudomonas aeruginosa strains harbour multiple virulence traits critical for human infection. J Med Microbiol 2022; 71. [PMID: 35947528 DOI: 10.1099/jmm.0.001493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. Pseudomonas aeruginosa causes fatal infections in immunocompromised individuals and patients with pulmonary disorders.Gap Statement. Agricultural ecosystems are the vast reservoirs of this dreaded pathogen. However, there are limited attempts to analyse the pathogenicity of P. aeruginosa strains associated with edible plants.Aim. This study aims to (i) elucidate the virulence attributes of P. aeruginosa strains isolated from the rhizosphere and endophytic niches of cucumber, tomato, eggplant and chili;and (ii) compare these phenotypes with that of previously characterized clinical isolates.Methodology. Crystal-violet microtitre assay, swarm plate experiment, gravimetric quantification and sheep blood lysis were performed to estimate the biofilm formation, swarming motility, rhamnolipid production and haemolytic activity, respectively, of P. aeruginosa strains. In addition, their pathogenicity was also assessed based on their ability to antagonize plant pathogens (Xanthomonas oryzae, Pythium aphanidermatum, Rhizoctonia solani and Fusarium oxysporum) and kill a select nematode (Caenorhabditis elegans).Results. Nearly 80 % of the plant-associated strains produced rhamnolipid and exhibited at least one type of lytic activity (haemolysis, proteolysis and lipolysis). Almost 50 % of these strains formed significant levels of biofilm and exhibited swarming motility. The agricultural strains showed significantly higher and lower virulence against the bacterial and fungal pathogens, respectively, compared to the clinical strains. In C. elegans, a maximum of 40 and 100% mortality were induced by the agricultural and clinical strains, respectively.Conclusion. This investigation shows that P. aeruginosa in edible plants isolated directly from the farm express virulence and pathogenicity. Furthermore, clinical and agricultural P. aeruginosa strains antagonized the tested fungal phytopathogens, Pythium aphanidermatum, Rhizoctonia solani and Fusarium oxysporum. Thus, we recommend using these fungi as simple eukaryotic model systems to test P. aeruginosa pathogenicity.
Collapse
Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.,Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Ponnusamy Marimuthu
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
7
|
Adeleke BS, Babalola OO. Meta-omics of endophytic microbes in agricultural biotechnology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102332] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
8
|
Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens. BIOLOGY 2022; 11:biology11010140. [PMID: 35053136 PMCID: PMC8773043 DOI: 10.3390/biology11010140] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/24/2022]
Abstract
P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent.
Collapse
|
9
|
Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:3-28. [DOI: 10.1007/978-3-031-08491-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
10
|
Tümmler B. What Makes Pseudomonas aeruginosa a Pathogen? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:283-301. [DOI: 10.1007/978-3-031-08491-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
Kaszab E, Radó J, Kriszt B, Pászti J, Lesinszki V, Szabó A, Tóth G, Khaledi A, Szoboszlay S. Groundwater, soil and compost, as possible sources of virulent and antibiotic-resistant Pseudomonas aeruginosa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2021; 31:848-860. [PMID: 31736330 DOI: 10.1080/09603123.2019.1691719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Pseudomonas aeruginosa is a major public health concern all around the world. In the frame of this work, a set of diverse environmental P. aeruginosa isolates with various antibiotic resistance profiles were examined in a Galleria mellonella virulence model. Motility, serotypes, virulence factors and biofilm-forming ability were also examined. Molecular types were determined by pulsed-field gel electrophoresis (PFGE). Based on our results, the majority of environmental isolates were virulent in the G. mellonella test and twitching showed a positive correlation with mortality. Resistance against several antibiotic agents such as Imipenem correlated with a lower virulence in the applied G. mellonella model. PFGE revealed that five examined environmental isolates were closely related to clinically detected pulsed-field types. Our study demonstrated that industrial wastewater effluents, composts, and hydrocarbon-contaminated sites should be considered as hot spots of high-risk clones of P. aeruginosa.
Collapse
Affiliation(s)
- Edit Kaszab
- Department of Environmental Safety and Ecotoxicology, Szent István University, Gödöllő, Hungary
| | - Júlia Radó
- Department of Environmental Safety and Ecotoxicology, Szent István University, Gödöllő, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety and Ecotoxicology, Szent István University, Gödöllő, Hungary
| | - Judit Pászti
- Department of Phage Typing and Molecular Epidemiology, National Center for Epidemiology, Budapest, Hungary
| | - Virág Lesinszki
- Department of Phage Typing and Molecular Epidemiology, National Center for Epidemiology, Budapest, Hungary
| | - Adám Szabó
- Centre for Experimental and Clinical Infection Research, Institute for Molecular Bacteriology TWINCORE, Hannover, Germany
| | - Gergő Tóth
- Department of Environmental Safety and Ecotoxicology, Szent István University, Gödöllő, Hungary
| | - Ariane Khaledi
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sándor Szoboszlay
- Department of Environmental Safety and Ecotoxicology, Szent István University, Gödöllő, Hungary
| |
Collapse
|
12
|
Ambreetha S, Marimuthu P, Mathee K, Balachandar D. Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates. J Appl Microbiol 2021; 132:3226-3248. [PMID: 34608722 DOI: 10.1111/jam.15317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 01/02/2023]
Abstract
AIM Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections, is also commonly found in agricultural settings. However, there are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study investigates the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyses the evolutionary and metabolic relatedness of the agricultural and clinical strains. METHODS AND RESULTS Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical and molecular assays. The genetic and metabolic traits of these plant-associated P. aeruginosa isolates were compared with clinical strains. DNA fingerprinting and 16S rDNA-based phylogenetic analyses revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization to release essential nutrients (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular pyocyanin, siderophore, and indole-3 acetic acid. CONCLUSION These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. In addition, the genotypic and phenotypic traits do not correlate with plant sources or ecosystems. SIGNIFICANCE AND IMPACT OF THE STUDY This study reconfirms that edible plants are the potential source for human and animal transmission of P. aeruginosa.
Collapse
Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.,Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Ponnusamy Marimuthu
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
13
|
Kumar R, Borker SS, Thakur A, Thapa P, Kumar S, Mukhia S, Anu K, Bhattacharya A, Kumar S. Physiological and genomic evidence supports the role of Serratia quinivorans PKL:12 as a biopriming agent for the biohardening of micropropagated Picrorhiza kurroa plantlets in cold regions. Genomics 2021; 113:1448-1457. [PMID: 33744342 DOI: 10.1016/j.ygeno.2021.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/26/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
The medicinal herb, Picrorhiza kurroa Royle ex Benth has become endangered because of indiscriminate over-harvesting. Although micropropagation has been attempted for mass propagation of the plant, survival of in vitro plantlets under green house/open field poses a major challenge. Biopriming of micropropagated plantlets with plant growth-promoting rhizobacteria (PGPR) are among the successful methods to combat this problem. Serratia quinivorans PKL:12 was the best-characterized PGPR from rhizospheric soil of P. kurroa as it increased the vegetative growth and survival of the micropropagated plantlets most effectively. Complete genome (5.29 Mb) predicted genes encoding proteins for cold adaptation and plant growth-promoting traits in PKL:12. Antibiotic and biosynthetic gene cluster prediction supported PKL:12 as a potential biocontrol agent. Comparative genomics revealed 226 unique genes with few genes associated with plant growth-promoting potential. Physiological and genomic evidence supports S. quinivorans PKL:12 as a potential agent for bio-hardening of micropropagated P. kurroa plantlets in cold regions.
Collapse
Affiliation(s)
- Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India..
| | - Shruti Sinai Borker
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India
| | - Aman Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India
| | - Pooja Thapa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Sanjeet Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Amita Bhattacharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| |
Collapse
|
14
|
Singh P, Singh RK, Guo DJ, Sharma A, Singh RN, Li DP, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Whole Genome Analysis of Sugarcane Root-Associated Endophyte Pseudomonas aeruginosa B18-A Plant Growth-Promoting Bacterium With Antagonistic Potential Against Sporisorium scitamineum. Front Microbiol 2021; 12:628376. [PMID: 33613496 PMCID: PMC7894208 DOI: 10.3389/fmicb.2021.628376] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Sugarcane smut is a significant fungal disease that causes a major loss in sugar yield and quality. In this study, we isolated an endophytic strain B18 from a sugarcane root, which showed plant growth-promotion, hydrolytic enzyme production, antifungal activity against sugarcane pathogens (Sporisorium scitamineum, Ceratocystis paradoxa, Fusarium verticillioides), and the presence of nifH, acdS, and antibiotic genes (hcn, prn, and phCA) under in vitro conditions. BIOLOG(R) phenotypic profiling of B18 established its ability to use various carbon and nitrogen sources and tolerate a range of pH and osmotic and temperature stresses. Whole-genome analysis of B18, identified as Pseudomonas aeruginosa, showed that it consists of a single circular chromosome of 6,490,014 bp with 66.33% GC content. Genome annotation has identified 5,919 protein-coding genes, and 65 tRNA, and 12 rRNA genes. The P. aeruginosa B18 genome encodes genes related to ethylene, nitrogen (nifU, norBCDERQ, gltBDPS, and aatJMPQ), and phosphate (pstABCS and phoBDHRU) metabolism and produce indole-3-acetic acid and siderophores. This also includes genes encoding hydrolases and oxidoreductases, those associated with biocontrol mechanisms (hcnABC, phzA_B, phzDEFGMS, and pchA), colonization (minCDE and lysC), and biofilm formation (efp, hfq, flgBCDEFGHI, and motAB), and those associated with metabolism of secondary metabolites. Collectively, these results suggest a role for P. aeruginosa B18 in plant growth enhancement and biocontrol mechanisms. The P. aeruginosa B18 strain was found to be an efficient colonizer in sugarcane; it can improve growth through modulation of plant hormone production and enhanced host-plant resistance to smut pathogen S. scitamineum in a smut-susceptible sugarcane variety (Yacheng71-374). These biocontrol and plant growth promotion properties of P. aeruginosa B18 area are discussed in this report.
Collapse
Affiliation(s)
- Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China.,College of Agriculture, Guangxi University, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | | | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Mukesh K Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin (CAGD), College of Resources and Environment, Southwest University, Chongqing, China.,Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China.,College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China.,College of Agriculture, Guangxi University, Nanning, China
| |
Collapse
|
15
|
Vishwakarma K, Kumar N, Shandilya C, Mohapatra S, Bhayana S, Varma A. Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review. Front Microbiol 2020; 11:560406. [PMID: 33408698 PMCID: PMC7779480 DOI: 10.3389/fmicb.2020.560406] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.
Collapse
Affiliation(s)
| | - Nitin Kumar
- Department of Biotechnology, Periyar Maniammai Institute of Science and Technology, Thanjavur, India
| | | | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Sahil Bhayana
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
| |
Collapse
|
16
|
Cunningham CJ, Kuyukina MS, Ivshina IB, Konev AI, Peshkur TA, Knapp CW. Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:1110-1124. [PMID: 32236187 DOI: 10.1039/c9em00606k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.
Collapse
Affiliation(s)
- Colin J Cunningham
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK
| | | | | | | | | | | |
Collapse
|
17
|
Singh S, Singh UB, Malviya D, Paul S, Sahu PK, Trivedi M, Paul D, Saxena AK. Seed Biopriming with Microbial Inoculant Triggers Local and Systemic Defense Responses against Rhizoctonia solani Causing Banded Leaf and Sheath Blight in Maize ( Zea mays L.). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E1396. [PMID: 32098185 PMCID: PMC7068308 DOI: 10.3390/ijerph17041396] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 11/17/2022]
Abstract
Plant growth promoting rhizobacteria Pseudomonas aeruginosa strain MF-30 isolated from maize rhizosphere was characterized for several plant growth stimulating attributes. The strain MF-30 was also evaluated for antifungal properties against Rhizoctonia solani causing banded leaf and sheath blight in maize (Zea mays L.) under in vitro conditions and was found to have higher mycelial growth suppression in the culture suspension (67.41%) followed by volatile organic compounds (62.66%) and crude extract (51.20%) in a dual plate assay. The endophytic and epiphytic colonization ability was tested using Green Fluorescent Protein (GFP)-tagging. Visualization through confocal scanning laser microscope clearly indicated that strain MF-30 colonizes the root and foliar parts of the plants. Further, the effects of seed bio-priming with P. aeruginosa MF-30 was evaluated in the induction and bioaccumulation of defense-related biomolecules, enzymes, natural antioxidants, and other changes in maize under pot trial. This not only provided protection from R. solani but also ensured growth promotion under pathogenic stress conditions in maize. The maximum concentration of hydrogen peroxide (H2O2) was reported in the root and shoot of the plants treated with R. solani alone (8.47 and 17.50 mmol mg-1 protein, respectively) compared to bioagent, P. aeruginosa MF-30 bio-primed plants (3.49 and 7.50 mmol mg-1 protein, respectively). Effects on total soluble sugar content, total protein, and total proline were also found to enhanced significantly due to inoculation of P. aeruginosa MF-30. The activities of anti-oxidative defense enzymes phenylalanine ammonia lyase (PAL), ascorbate peroxidase, peroxidase, superoxide dismutase, and catalase increased significantly in the plants bio-primed with P. aeruginosa MF-30 and subsequent foliar spray of culture suspension of MF-30 compared to pathogen alone inoculated plants. qRT-PCR analysis revealed that seed bio-priming and foliar application of P. aeruginosa MF-30 significantly increased the expression of PR-1 and PR-10 genes with the simultaneous decrease in the disease severity and lesion length in the maize plants under pathogenic stress conditions. A significant enhancement of shoot and root biomass was recorded in MF-30 bio-primed plants as compared to untreated control (p < 0.05). Significant increase in plant growth and antioxidant content, as well as decreased disease severity in the P. aeruginosa MF-30 bio-primed plants, suggested the possibility of an eco-friendly and economical means of achieving antioxidants-rich, healthier maize plants.
Collapse
Affiliation(s)
- Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 227105, India
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Pramod Kumar Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 227105, India
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA;
| | - Anil Kumar Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| |
Collapse
|
18
|
Keswani C, Prakash O, Bharti N, Vílchez JI, Sansinenea E, Lally RD, Borriss R, Singh SP, Gupta VK, Fraceto LF, de Lima R, Singh HB. Re-addressing the biosafety issues of plant growth promoting rhizobacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:841-852. [PMID: 31302549 DOI: 10.1016/j.scitotenv.2019.07.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 05/21/2023]
Abstract
To promote agronomic sustainability, extensive research is being carried out globally, investigating biofertilizer development. Recently, it has been realized that some microorganisms used as biofertilizers behave as opportunistic pathogens and belong to the biosafety level 2 (BSL-2) classification. This poses serious risk to the environmental and human health. Evidence presented in various scientific forums is increasingly favoring the merits of using BSL-2 microorganisms as biofertilizers. In this review, we emphasize that partial characterization based on traditional microbiological approaches and small subunit rRNA gene sequences/conserved regions are insufficient for the characterization of biofertilizer strains. It is advised herein, that research and industrial laboratories developing biofertilizers for commercialization or environmental release must characterize microorganisms of interest using a multilateral polyphasic approach of microbial systematics. This will determine their risk group and biosafety characteristics before proceeding with formulation development and environmental application. It has also been suggested that microorganisms belonging to risk-group-1 and BSL-1 category should be used for formulation development and for field scale applications. While, BSL-2 microorganisms should be restricted for research using containment practices compliant with strict regulations.
Collapse
Affiliation(s)
- Chetan Keswani
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India.
| | - Nidhi Bharti
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India.
| | - Juan I Vílchez
- Department of Plant Growth Promotion Rhizobacteria, Plant Stress Centre for Biology (PSC), Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Estibaliz Sansinenea
- Facultad de Ciencias Químicas, Benemerita Universidad Autonoma de Puebla, Puebla, Pue, Mexico.
| | - Richard D Lally
- Research Department, Alltech, 3031 Catnip Hill Road, Nicholasville, KY 40356, USA.
| | - Rainer Borriss
- Nord Reet UG Greifswald, Germany and Humboldt University, Berlin, Germany.
| | - Surya P Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Leonardo F Fraceto
- São Paulo State University (UNESP), Institute of Science and Technology, Avenida Três de Março, 511, Alto da Boa Vista, Sorocaba, São Paulo, Brazil.
| | - Renata de Lima
- LABiToN - LaboratóriodeAvaliaçãodeBioatividadeeToxicologiade Nanomateriais, University of Sorocaba, Rodovia Raposo Tavares, Sorocaba, São Paulo, Brazil.
| | - Harikesh B Singh
- Department of Mycology and Plant Pathology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
19
|
Martínez-Hidalgo P, Maymon M, Pule-Meulenberg F, Hirsch AM. Engineering root microbiomes for healthier crops and soils using beneficial, environmentally safe bacteria. Can J Microbiol 2019; 65:91-104. [DOI: 10.1139/cjm-2018-0315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Green Revolution developed new crop varieties, which greatly improved food security worldwide. However, the growth of these plants relied heavily on chemical fertilizers and pesticides, which have led to an overuse of synthetic fertilizers, insecticides, and herbicides with serious environmental consequences and negative effects on human health. Environmentally friendly plant-growth-promoting methods to replace our current reliance on synthetic chemicals and to develop more sustainable agricultural practices to offset the damage caused by many agrochemicals are proposed herein. The increased use of bioinoculants, which consist of microorganisms that establish synergies with target crops and influence production and yield by enhancing plant growth, controlling disease, and providing critical mineral nutrients, is a potential solution. The microorganisms found in bioinoculants are often bacteria or fungi that reside within either external or internal plant microbiomes. However, before they can be used routinely in agriculture, these microbes must be confirmed as nonpathogenic strains that promote plant growth and survival. In this article, besides describing approaches for discovering plant-growth-promoting bacteria in various environments, including phytomicrobiomes and soils, we also discuss methods to evaluate their safety for the environment and for human health.
Collapse
Affiliation(s)
- Pilar Martínez-Hidalgo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
| | - Maskit Maymon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
| | - Flora Pule-Meulenberg
- Department of Crop Science and Production, Botswana University of Agriculture and Natural Resources, Private Bag 0027, A1 Sebele Content Farm, Gaborone, Botswana
| | - Ann M. Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
| |
Collapse
|
20
|
Oni FE, Geudens N, Omoboye OO, Bertier L, Hua HGK, Adiobo A, Sinnaeve D, Martins JC, Höfte M. Fluorescent Pseudomonas and cyclic lipopeptide diversity in the rhizosphere of cocoyam (Xanthosoma sagittifolium). Environ Microbiol 2019; 21:1019-1034. [PMID: 30623562 DOI: 10.1111/1462-2920.14520] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/21/2022]
Abstract
Cocoyam (Xanthosoma sagittifolium (L.)), an important tuber crop in the tropics, is severely affected by the cocoyam root rot disease (CRRD) caused by Pythium myriotylum. The white cocoyam genotype is very susceptible while the red cocoyam has some field tolerance to CRRD. Fluorescent Pseudomonas isolates obtained from the rhizosphere of healthy red and white cocoyams from three different fields in Cameroon were taxonomically characterized. The cocoyam rhizosphere was enriched with P. fluorescens complex and P. putida isolates independent of the plant genotype. LC-MS and NMR analyses revealed that 50% of the Pseudomonas isolates produced cyclic lipopeptides (CLPs) including entolysin, lokisin, WLIP, putisolvin and xantholysin together with eight novel CLPs. In general, CLP types were linked to specific taxonomic groups within the fluorescent pseudomonads. Representative CLP-producing bacteria showed effective control against CRRD while purified CLPs caused hyphal branching or hyphal leakage in P. myriotylum. The structure of cocoyamide A, a CLP which is predominantly produced by P. koreensis group isolates within the P. fluorescens complex is described. Compared with the white cocoyam, the red cocoyam rhizosphere appeared to support a more diverse CLP spectrum. It remains to be investigated whether this contributes to the field tolerance displayed by the red cocoyam.
Collapse
Affiliation(s)
- Feyisara Eyiwumi Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Niels Geudens
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Olumide Owolabi Omoboye
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Lien Bertier
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Hoang Gia Khuong Hua
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Amayana Adiobo
- Jay PJ Biotechnology Laboratory, Institute for Agricultural Research for Development (IRAD), Ekona, P.M.B 25, Buea, Cameroon
| | - Davy Sinnaeve
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - José C Martins
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| |
Collapse
|
21
|
Li Y, Jiang L, Lv W, Cui S, Zhang L, Wang Q, Meng F, Li B, Liu P, Suonan J, Renzeng W, Li X, Luo C, Zhang Z, Dorji T, Wang Y, Wang S. Fungal pathogens pose a potential threat to animal and plant health in desertified and pika-burrowed alpine meadows on the Tibetan Plateau. Can J Microbiol 2018; 65:365-376. [PMID: 30566369 DOI: 10.1139/cjm-2018-0338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intact Tibetan meadows provide significant defense against soil-borne pathogen dispersal. However, dramatic meadow degradation has been observed due to climate change and pika damage, but their impacts on soil-borne pathogens are still unclear. With approximately 40% of the world's population living in Tibetan Plateau and its downstream watersheds, this lack of knowledge should be of great concern. Here, we used Illumina amplicon sequencing to characterize the changes in potential human, domestic animal, plant, and zoonotic bacterial and fungal pathogens in nondegraded, desertified, and pika-burrowed meadows. The relative abundance of bacterial domestic animal pathogens and zoonotic pathogens were significantly increased by desertification. Pika burrowing significantly increased the relative abundance of bacterial human pathogens and zoonotic pathogens. The species richness and relative abundance of fungal pathogens was significantly increased by desertification and pika burrowing. Accordingly, fungal plant and animal pathogens categorized by FUNGuid significantly increased in desertified and pika-burrowed meadows. Soil chemical and plant properties explained 38% and 64% of the bacterial and fungal pathogen community variance, respectively. Therefore, our study indicates for the first time that both alpine meadow desertification and pika burrowing could potentially increase infectious disease risks in the alpine ecosystem, especially for fungal diseases.
Collapse
Affiliation(s)
- Yaoming Li
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Lili Jiang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wangwang Lv
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Shujuan Cui
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Lirong Zhang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Qi Wang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Fandong Meng
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Bowen Li
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Peipei Liu
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Ji Suonan
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wangmu Renzeng
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xine Li
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Caiyun Luo
- c Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, P.R. China
| | - Zhenhua Zhang
- c Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, P.R. China
| | - Tsechoe Dorji
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,d CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, P.R. China.,e Naqu Integrated Observation and Research Station of Ecology and Environment, Tibet University and Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, Lasa 850012, P.R. China
| | - Yanfen Wang
- b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Shiping Wang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,d CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, P.R. China.,e Naqu Integrated Observation and Research Station of Ecology and Environment, Tibet University and Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, Lasa 850012, P.R. China
| |
Collapse
|
22
|
Alegbeleye OO, Singleton I, Sant'Ana AS. Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review. Food Microbiol 2018; 73:177-208. [PMID: 29526204 PMCID: PMC7127387 DOI: 10.1016/j.fm.2018.01.003] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/31/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
Foodborne illness resulting from the consumption of contaminated fresh produce is a common phenomenon and has severe effects on human health together with severe economic and social impacts. The implications of foodborne diseases associated with fresh produce have urged research into the numerous ways and mechanisms through which pathogens may gain access to produce, thereby compromising microbiological safety. This review provides a background on the various sources and pathways through which pathogenic bacteria contaminate fresh produce; the survival and proliferation of pathogens on fresh produce while growing and potential methods to reduce microbial contamination before harvest. Some of the established bacterial contamination sources include contaminated manure, irrigation water, soil, livestock/ wildlife, and numerous factors influence the incidence, fate, transport, survival and proliferation of pathogens in the wide variety of sources where they are found. Once pathogenic bacteria have been introduced into the growing environment, they can colonize and persist on fresh produce using a variety of mechanisms. Overall, microbiological hazards are significant; therefore, ways to reduce sources of contamination and a deeper understanding of pathogen survival and growth on fresh produce in the field are required to reduce risk to human health and the associated economic consequences.
Collapse
Affiliation(s)
| | - Ian Singleton
- School of Applied Sciences, Sighthill Campus, Edinburgh Napier University, Edinburgh, UK
| | - Anderson S Sant'Ana
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil.
| |
Collapse
|
23
|
Puri A, Padda KP, Chanway CP. Plant Growth Promotion by Endophytic Bacteria in Nonnative Crop Hosts. ENDOPHYTES: CROP PRODUCTIVITY AND PROTECTION 2017. [DOI: 10.1007/978-3-319-66544-3_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
24
|
Plant Growth-Promoting Microorganisms for Environmental Sustainability. Trends Biotechnol 2016; 34:847-850. [PMID: 27265889 DOI: 10.1016/j.tibtech.2016.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/22/2022]
Abstract
Agrochemicals used to meet the needs of a rapidly growing human population can deteriorate the quality of ecosystems and are not affordable to farmers in low-resource environments. Here, we propose the use of plant growth-promoting microorganisms (PGPMs) as a tool for sustainable food production without compromising ecosystems services.
Collapse
|
25
|
Thomas P, Sekhar AC. Effects Due to Rhizospheric Soil Application of an Antagonistic Bacterial Endophyte on Native Bacterial Community and Its Survival in Soil: A Case Study with Pseudomonas aeruginosa from Banana. Front Microbiol 2016; 7:493. [PMID: 27199897 PMCID: PMC4844927 DOI: 10.3389/fmicb.2016.00493] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/27/2016] [Indexed: 01/31/2023] Open
Abstract
Effective translation of research findings from laboratory to agricultural fields is essential for the success of biocontrol or growth promotion trials employing beneficial microorganisms. The rhizosphere is to be viewed holistically as a dynamic ecological niche comprising of diverse microorganisms including competitors and noxious antagonists to the bio-inoculant. This study was undertaken to assess the effects due to the soil application of an endophytic bacterium with multiple pathogen antagonistic potential on native bacterial community and its sustenance in agricultural soil. Pseudomonas aeruginosa was employed as a model system considering its frequent isolation as an endophyte, wide antagonistic effects reported against different phytopathogens and soil pests, and that the species is a known human pathogen which makes its usage in agriculture precarious. Employing the strain ‘GNS.13.2a’ from banana, its survival in field soil and the effects upon soil inoculation were investigated by monitoring total culturable bacterial fraction as the representative indicator of soil microbial community. Serial dilution plating of uninoculated control versus P. aeruginosa inoculated soil from banana rhizosphere indicated a significant reduction in native bacterial cfu soon after inoculation compared with control soil as assessed on cetrimide- nalidixic acid selective medium against nutrient agar. Sampling on day-4 showed a significant reduction in P. aeruginosa cfu in inoculated soil and a continuous dip thereafter registering >99% reduction within 1 week while the native bacterial population resurged with cfu restoration on par with control. This was validated in contained trials with banana plants. Conversely, P. aeruginosa showed static cfu or proliferation in axenic-soil. Lateral introduction of soil microbiome in P. aeruginosa established soil under axenic conditions or its co-incubation with soil microbiota in suspension indicated significant adverse effects by native microbial community. Direct agar-plate challenge assays with individual environmental bacterial isolates displayed varying interactive or antagonistic effects. In effect, the application of P. aeruginosa in rhizospheric soil did not serve any net benefit in terms of sustained survival. Conversely, it caused a disturbance to the native soil bacterial community. The findings highlight the need for monitoring the bio-inoculant(s) in field-soil and assessing the interactive effects with native microbial community before commercial recommendation. varying interactive or antagonistic effects. In effect, the application of P. aeruginosa in rhizospheric soil did not serve any net benefit in terms of sustained survival. Conversely, it caused a disturbance to the native soil bacterial community. The findings highlight the need for monitoring the bio-inoculant(s) in field-soil and assessing the interactive effects with native microbial community before commercial recommendation.
Collapse
Affiliation(s)
- Pious Thomas
- Endophytic and Molecular Microbiology Laboratory, Division of Biotechnology, ICAR-Indian Institute of Horticultural Research Bengaluru, India
| | - Aparna C Sekhar
- Endophytic and Molecular Microbiology Laboratory, Division of Biotechnology, ICAR-Indian Institute of Horticultural Research Bengaluru, India
| |
Collapse
|
26
|
Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose
N
,
N
-Dimethyl Formamide. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01609-15. [PMID: 26847883 PMCID: PMC4742680 DOI: 10.1128/genomea.01609-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium, which uses a variety of organic chemicals as carbon sources. Here, we report the genome sequence of the Cu1510 isolate from wastewater containing a high concentration of N,N-dimethyl formamide.
Collapse
|
27
|
Zohara F, Akanda MAM, Paul NC, Rahman M, Islam MT. Inhibitory effects of Pseudomonas spp. on plant pathogen Phytophthora capsici in vitro and in planta. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2015.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
Sekhar AC, Thomas P. Isolation and Identification of Shoot-Tip Associated Endophytic Bacteria from Banana cv. Grand Naine and Testing for Antagonistic Activity against <i>Fusarium oxysporum</i> f. sp. <i>cubense</i>. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.67101] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
29
|
Zhou J, Zhao X, Dai C. Antagonistic mechanisms of endophytic Pseudomonas fluorescens
against Athelia rolfsii. J Appl Microbiol 2014; 117:1144-58. [DOI: 10.1111/jam.12586] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/20/2014] [Accepted: 06/20/2014] [Indexed: 10/25/2022]
Affiliation(s)
- J.Y. Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics; Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources; College of Life Sciences; Nanjing Normal University; Jiangsu Province Nanjing China
| | - X.Y. Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics; Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources; College of Life Sciences; Nanjing Normal University; Jiangsu Province Nanjing China
| | - C.C. Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics; Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources; College of Life Sciences; Nanjing Normal University; Jiangsu Province Nanjing China
| |
Collapse
|
30
|
Grosso-Becerra MV, Santos-Medellín C, González-Valdez A, Méndez JL, Delgado G, Morales-Espinosa R, Servín-González L, Alcaraz LD, Soberón-Chávez G. Pseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity. BMC Genomics 2014; 15:318. [PMID: 24773920 PMCID: PMC4234422 DOI: 10.1186/1471-2164-15-318] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 03/24/2014] [Indexed: 12/28/2022] Open
Abstract
Background Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. In addition, genetic variability of all the P. aeruginosa strains whose genomes have been sequenced is extremely low. This low genomic variability might be explained if clinical strains constitute a subpopulation of this bacterial species present in environments that are close to human populations, which preferentially produce virulence associated traits. Results In this work, we sequenced the genomes and performed phenotypic descriptions for four non-human P. aeruginosa isolates collected from a plant, the ocean, a water-spring, and from dolphin stomach. We show that the four strains are phenotypically diverse and that this is not reflected in genomic variability, since their genomes are almost identical. Furthermore, we performed a detailed comparative genomic analysis of the four strains studied in this work with the thirteen previously reported P. aeruginosa genomes by means of describing their core and pan-genomes. Conclusions Contrary to what has been described for other bacteria we have found that the P. aeruginosa core genome is constituted by a high proportion of genes and that its pan-genome is thus relatively small. Considering the high degree of genomic conservation between isolates of P. aeruginosa from diverse environments, including human tissues, some implications for the treatment of infections are discussed. This work also represents a methodological contribution for the genomic study of P. aeruginosa, since we provide a database of the comparison of all the proteins encoded by the seventeen strains analyzed.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 México, DF, México.
| |
Collapse
|
31
|
van Overbeek LS, van Doorn J, Wichers JH, van Amerongen A, van Roermund HJW, Willemsen PTJ. The arable ecosystem as battleground for emergence of new human pathogens. Front Microbiol 2014; 5:104. [PMID: 24688484 PMCID: PMC3960585 DOI: 10.3389/fmicb.2014.00104] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/27/2014] [Indexed: 01/10/2023] Open
Abstract
Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.
Collapse
Affiliation(s)
- Leonard S van Overbeek
- Plant Research International, Wageningen University and Research Centre Wageningen, Netherlands
| | - Joop van Doorn
- Applied Plant Research, Wageningen University and Research Centre Lisse, Netherlands
| | - Jan H Wichers
- Food and Biobased Research, Wageningen University and Research Centre Wageningen, Netherlands
| | - Aart van Amerongen
- Food and Biobased Research, Wageningen University and Research Centre Wageningen, Netherlands
| | - Herman J W van Roermund
- Central Veterinary Institute, Wageningen University and Research Centre Lelystad, Netherlands
| | - Peter T J Willemsen
- Central Veterinary Institute, Wageningen University and Research Centre Lelystad, Netherlands
| |
Collapse
|
32
|
Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 2013; 37:634-63. [DOI: 10.1111/1574-6976.12028] [Citation(s) in RCA: 1382] [Impact Index Per Article: 125.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/22/2013] [Accepted: 05/27/2013] [Indexed: 12/18/2022] Open
|
33
|
A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences. J Biosci 2013; 38:267-78. [DOI: 10.1007/s12038-013-9312-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|