1
|
Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
Collapse
Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| |
Collapse
|
2
|
He L, Kim SH, Yu JM. Development of the Droplet Digital PCR Method for the Detection and Quantification of Erwinia pyrifoliae. THE PLANT PATHOLOGY JOURNAL 2023; 39:141-148. [PMID: 36760056 PMCID: PMC9929165 DOI: 10.5423/ppj.nt.08.2022.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Black shoot blight disease caused by Erwinia pyrifoliae has serious impacts on quality and yield in pear production in Korea; therefore, rapid and accurate methods for its detection are needed. However, traditional detection methods require a great deal of time and fail to achieve absolute quantification. In the present study, we developed a droplet digital polymerase chain reaction (ddPCR) method for the detection and absolute quantification of E. pyrifoliae using a pair of species-specific primers. The detection range was 103 - 107 copies/ml (DNA templates) and cfu/ml (cell culture templates). This new method exhibited good linearity and repeatability and was validated by absolute quantification of E. pyrifoliae DNA copies from samples of artificially inoculated immature pear fruits. Here, we present the first study of ddPCR assay for the detection and quantification of E. pyrifoliae. This method has potential applications in epidemiology and for the early prediction of black shoot blight outbreaks.
Collapse
Affiliation(s)
- Lin He
- Department of Applied Biology, Chungnam National University, Daejeon 34134,
Korea
| | - Seong Hwan Kim
- Department of Microbiology, Dankook University, Cheonan 31116,
Korea
| | - Jun Myoung Yu
- Department of Applied Biology, Chungnam National University, Daejeon 34134,
Korea
| |
Collapse
|
3
|
Bao M, Chen Q, Xu Z, Jensen EC, Liu C, Waitkus JT, Yuan X, He Q, Qin P, Du K. Challenges and Opportunities for Clustered Regularly Interspaced Short Palindromic Repeats Based Molecular Biosensing. ACS Sens 2021; 6:2497-2522. [PMID: 34143608 DOI: 10.1021/acssensors.1c00530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, CRISPR, has recently emerged as a powerful molecular biosensing tool for nucleic acids and other biomarkers due to its unique properties such as collateral cleavage nature, room temperature reaction conditions, and high target-recognition specificity. Numerous platforms have been developed to leverage the CRISPR assay for ultrasensitive biosensing applications. However, to be considered as a new gold standard, several key challenges for CRISPR molecular biosensing must be addressed. In this paper, we briefly review the history of biosensors, followed by the current status of nucleic acid-based detection methods. We then discuss the current challenges pertaining to CRISPR-based nucleic acid detection, followed by the recent breakthroughs addressing these challenges. We focus upon future advancements required to enable rapid, simple, sensitive, specific, multiplexed, amplification-free, and shelf-stable CRISPR-based molecular biosensors.
Collapse
Affiliation(s)
- Mengdi Bao
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Qun Chen
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Zhiheng Xu
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Erik C. Jensen
- HJ Science & Technology Inc., San Leandro, California 94710, United States
| | - Changyue Liu
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Jacob T. Waitkus
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Xi Yuan
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Qian He
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Ke Du
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| |
Collapse
|
4
|
Peil A, Hübert C, Wensing A, Horner M, Emeriewen OF, Richter K, Wöhner T, Chagné D, Orellana-Torrejon C, Saeed M, Troggio M, Stefani E, Gardiner SE, Hanke MV, Flachowsky H, Bus VG. Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation. BMC PLANT BIOLOGY 2019; 19:532. [PMID: 31791233 PMCID: PMC6889339 DOI: 10.1186/s12870-019-2154-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/21/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although the most common path of infection for fire blight, a severe bacterial disease on apple, is via host plant flowers, quantitative trait loci (QTLs) for fire blight resistance to date have exclusively been mapped following shoot inoculation. It is not known whether the same mechanism underlies flower and shoot resistance. RESULTS We report the detection of a fire blight resistance QTL following independent artificial inoculation of flowers and shoots on two F1 segregating populations derived from crossing resistant Malus ×robusta 5 (Mr5) with susceptible 'Idared' and 'Royal Gala' in experimental orchards in Germany and New Zealand, respectively. QTL mapping of phenotypic datasets from artificial flower inoculation of the 'Idared' × Mr5 population with Erwinia amylovora over several years, and of the 'Royal Gala' × Mr5 population in a single year, revealed a single major QTL controlling floral fire blight resistance on linkage group 3 (LG3) of Mr5. This QTL corresponds to the QTL on LG3 reported previously for the 'Idared' × Mr5 and an 'M9' × Mr5 population following shoot inoculation in the glasshouse. Interval mapping of phenotypic data from shoot inoculations of subsets from both flower resistance populations re-confirmed that the resistance QTL is in the same position on LG3 of Mr5 as that for flower inoculation. These results provide strong evidence that fire blight resistance in Mr5 is controlled by a major QTL on LG3, independently of the mode of infection, rootstock and environment. CONCLUSIONS This study demonstrates for the first time that resistance to fire blight caused by Erwinia amylovora is independent of the mode of inoculation at least in Malus ×robusta 5.
Collapse
Affiliation(s)
- Andreas Peil
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Christine Hübert
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer str. 101, 69221 Dossenheim, Germany
| | - Annette Wensing
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer str. 101, 69221 Dossenheim, Germany
| | - Mary Horner
- The New Zealand Institute for Plant and Food Research Limited (PFR), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, 4157 New Zealand
| | - Ofere Francis Emeriewen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Klaus Richter
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Thomas Wöhner
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - David Chagné
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | | | - Munazza Saeed
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | - Michela Troggio
- Research and Innovation Centre, Edmund Mach Foundation, 38010 San Michele all’Adige, Italy
| | - Erika Stefani
- Research and Innovation Centre, Edmund Mach Foundation, 38010 San Michele all’Adige, Italy
| | - Susan E. Gardiner
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | - Magda-Viola Hanke
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Vincent G.M. Bus
- The New Zealand Institute for Plant and Food Research Limited (PFR), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, 4157 New Zealand
| |
Collapse
|
5
|
Holeva MC, Morán F, Scuderi G, González A, López MM, Llop P. Development of a real-time PCR method for the specific detection of the novel pear pathogen Erwinia uzenensis. PLoS One 2019; 14:e0219487. [PMID: 31291321 PMCID: PMC6619794 DOI: 10.1371/journal.pone.0219487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/25/2019] [Indexed: 11/24/2022] Open
Abstract
Erwinia uzenensis is a plant-pathogenic bacterium, recently described in Japan, which infects pear trees, causing the ‘bacterial black shoot disease of European pear’ (BBSDP). Like other Erwinia pear pathogens, E. uzenensis causes damp, black lesions on young shoots resembling those of E. amylovora, but not blossom blight, fruitlet blight or wilting of the shoot tip. The distribution of E. uzenensis seems restricted to the country where it was reported up to now, but it may spread to other countries and affect new hosts, as is the current situation with E. piriflorinigrans and E. pyrifoliae. Fast and accurate detection systems for this new pathogen are needed to study its biology and to identify it on pear or other hosts. We report here the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for E. uzenensis, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 101 cfu ml-1 on pure bacterial cultures and 102–103 cfu ml-1 on spiked plant material. The specificity of the protocol was evaluated against E. uzenensis and 46 strains of pear-associated Erwinia species different to E. uzenensis. No cross-reaction with the non-target bacterial species or the loss of sensitivity were observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range of E. uzenensis initially considered restricted to a region and will expand our knowledge of the life cycle and environmental preferences of this pathogen.
Collapse
Affiliation(s)
- Maria C. Holeva
- Laboratory of Bacteriology, Department of Plant Pathology, Benaki Phytopathological Institute, Kifissia, Attica, Greece
| | - Félix Morán
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Giuseppe Scuderi
- Laboratory of Biotechnology, Department of Sustainable agriculture, biodiversity and food security, Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Asier González
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - María M. López
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Pablo Llop
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
- * E-mail: ,
| |
Collapse
|
6
|
Khan N, Zandi P, Ali S, Mehmood A, Adnan Shahid M, Yang J. Impact of Salicylic Acid and PGPR on the Drought Tolerance and Phytoremediation Potential of Helianthus annus. Front Microbiol 2018; 9:2507. [PMID: 30405567 PMCID: PMC6206235 DOI: 10.3389/fmicb.2018.02507] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
The present study was aimed to isolate and characterize plant growth promoting rhizobacteria (PGPR) from the rhizosphere of rainfed area (Karak) in Pakistan. The influence of isolated rhizobacteria, in association with salicylic acid (SA), physiological attributes, drought tolerance potential, and phytoremediation in drought-stressed sunflower exposed was investigated. The isolated bacteria were named P1 and P2 and characterized on the basis of colony morphology and biochemical traits. Both PGPR P1 and P2 were identified on the basis of 16S-rRNA gene sequencing as Planomicrobium chinense strain P1 (Accession No. MF616408) and Bacillus cereus strain P2 (Accession No. MF616406). The fresh cultures (24 h old) of isolates were used to soak the seeds pre-sowing. SA was foliar applied at three-leaf-stage. Likewise, the 30-days-old seedlings (three leaf stage) were exposed to drought stress. Drought stress was imposed to 30-days-old plants (three-leaf stage) by withholding water supply for the next 15 days until the soil water content reached 10%. The PGPR and/or SA treatment resulted in significant accumulation of Cd (84%), Pb (66%), and Ni (65%) in the rhizosphere. PGPR also induced accumulation of Cd and Ni in plant shoot. Combined treatment of PGPR and SA increased the Cu (21%), Co (11%), and Zn (8%) accumulation but decreased (12%) the Fe accumulation as compared to coinoculation of PGPR P1 and P2. Inoculation of plants with PGPR significantly increased shoot length (60%), root length (68%), root fresh (61%), and dry (63%) biomass under water stress. The inoculated plants had increased chlorophyll (67%), carotenoid (70%), leaf protein (64%), sugar (64%), and phenolic (62%) contents while lower leaf proline (62%) content, malondialdehyde (MDA) (64%), and antioxidant enzymes (67%) which suggest their role in drought tolerance. It is concluded that integrative use of PGPR in combination with SA found to be an efficacious strategy to improve the phytoremediation of heavy metals and plant growth under stressed conditions particularly under water-deficient conditions.
Collapse
Affiliation(s)
- Naeem Khan
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Peiman Zandi
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shahid Ali
- Plant Epigenetics and Development Lab, Northeast Forestry University, Harbin, China
| | - Asif Mehmood
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jianjun Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
7
|
Kajiwara H. Direct detection of the plant pathogens Burkholderia glumae, Burkholderia gladioli pv. gladioli, and Erwinia chrysanthemi pv. zeae in infected rice seedlings using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2016; 120:1-5. [DOI: 10.1016/j.mimet.2015.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 11/27/2022]
|
8
|
Aremu BR, Babalola OO. Classification and Taxonomy of Vegetable Macergens. Front Microbiol 2015; 6:1361. [PMID: 26640465 PMCID: PMC4661320 DOI: 10.3389/fmicb.2015.01361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/16/2015] [Indexed: 11/24/2022] Open
Abstract
Macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). These enzymatic actions result in the separation of plant tissues leading to total plant destruction. This can be attributed to soft rot diseases in vegetables. These macergens primarily belong to the genus Erwinia and to a range of opportunistic pathogens namely: the Xanthomonas spp., Pseudomonas spp., Clostridium spp., Cytophaga spp., and Bacillus spp. They consist of taxa that displayed considerable heterogeneity and intermingled with members of other genera belonging to the Enterobacteriaceae. They have been classified based on phenotypic, chemotaxonomic and genotypic which obviously not necessary in the taxonomy of all bacterial genera for defining bacterial species and describing new ones These taxonomic markers have been used traditionally as a simple technique for identification of bacterial isolates. The most important fields of taxonomy are supposed to be based on clear, reliable and worldwide applicable criteria. Hence, this review clarifies the taxonomy of the macergens to the species level and revealed that their taxonomy is beyond complete. For discovery of additional species, further research with the use modern molecular methods like phylogenomics need to be done. This can precisely define classification of macergens resulting in occasional, but significant changes in previous taxonomic schemes of these macergens.
Collapse
Affiliation(s)
- Bukola R. Aremu
- Department of Biological Sciences, Faculty of Agriculture, Science and Technology, North-West University, Mmabatho, South Africa
| | - Olubukola O. Babalola
- Department of Biological Sciences, Faculty of Agriculture, Science and Technology, North-West University, Mmabatho, South Africa
- Food Security and Safety Niche Area, Faculty of Agriculture, Science and Technology, North-West University, Mmabatho, South Africa
| |
Collapse
|
9
|
Geider K, Gernold M, Jock S, Wensing A, Völksch B, Gross J, Spiteller D. Unifying bacteria from decaying wood with various ubiquitous Gibbsiella species as G. acetica sp. nov. based on nucleotide sequence similarities and their acetic acid secretion. Microbiol Res 2015; 181:93-104. [PMID: 26071988 DOI: 10.1016/j.micres.2015.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/07/2015] [Accepted: 05/09/2015] [Indexed: 11/28/2022]
Abstract
Bacteria were isolated from necrotic apple and pear tree tissue and from dead wood in Germany and Austria as well as from pear tree exudate in China. They were selected for growth at 37 °C, screened for levan production and then characterized as Gram-negative, facultatively anaerobic rods. Nucleotide sequences from 16S rRNA genes, the housekeeping genes dnaJ, gyrB, recA and rpoB alignments, BLAST searches and phenotypic data confirmed by MALDI-TOF analysis showed that these bacteria belong to the genus Gibbsiella and resembled strains isolated from diseased oaks in Britain and Spain. Gibbsiella-specific PCR primers were designed from the proline isomerase and the levansucrase genes. Acid secretion was investigated by screening for halo formation on calcium carbonate agar and the compound identified by NMR as acetic acid. Its production by Gibbsiella spp. strains was also determined in culture supernatants by GC/MS analysis after derivatization with pentafluorobenzyl bromide. Some strains were differentiated by the PFGE patterns of SpeI digests and by sequence analyses of the lsc and the ppiD genes, and the Chinese Gibbsiella strain was most divergent. The newly investigated bacteria as well as Gibbsiella querinecans, Gibbsiella dentisursi and Gibbsiella papilionis, isolated in Britain, Spain, Korea and Japan, are taxonomically related Enterobacteriaceae, tolerate and secrete acetic acid. We therefore propose to unify them in the species Gibbsiella acetica sp. nov.
Collapse
Affiliation(s)
- Klaus Geider
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Marina Gernold
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Susanne Jock
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Annette Wensing
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Beate Völksch
- FSU Jena, Institute of Microbiology, Microbial Phytopathology, Neugasse 25, Jena, Germany.
| | - Jürgen Gross
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Dieter Spiteller
- Max-Planck-Institute for Chemical Ecology, Bioorganic Chemistry, Jena and Chemical Ecology/Biological Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
| |
Collapse
|
10
|
Tokonami S, Nakadoi Y, Nakata H, Takami S, Kadoma T, Shiigi H, Nagaoka T. Recognition of gram-negative and gram-positive bacteria with a functionalized conducting polymer film. RESEARCH ON CHEMICAL INTERMEDIATES 2014. [DOI: 10.1007/s11164-014-1609-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
11
|
Konecki K, Gernold M, Wensing A, Geider K. Growth inhibition of Erwinia amylovora and related Erwinia species by neutralized short-chain fatty acids. Arch Microbiol 2013; 195:759-64. [DOI: 10.1007/s00203-013-0928-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/08/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
|
12
|
Horká M, Šalplachta J, Karásek P, Kubesová A, Horký J, Matoušková H, Šlais K, Roth M. Combination of Capillary Isoelectric Focusing in a Tapered Capillary with MALDI-TOF MS for Rapid and Reliable Identification of Dickeya Species from Plant Samples. Anal Chem 2013; 85:6806-12. [DOI: 10.1021/ac4009176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie Horká
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Jiří Šalplachta
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Pavel Karásek
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Anna Kubesová
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Jaroslav Horký
- Division of Diagnostics, State Phytosanitary Administration, Šlechtitelů
23, 779 00 Olomouc, Czech Republic
| | - Hana Matoušková
- Division of Diagnostics, State Phytosanitary Administration, Šlechtitelů
23, 779 00 Olomouc, Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Michal Roth
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| |
Collapse
|
13
|
Tokonami S, Nakadoi Y, Takahashi M, Ikemizu M, Kadoma T, Saimatsu K, Dung LQ, Shiigi H, Nagaoka T. Label-Free and Selective Bacteria Detection Using a Film with Transferred Bacterial Configuration. Anal Chem 2013; 85:4925-9. [DOI: 10.1021/ac3034618] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shiho Tokonami
- Nanoscience and Nanotechnology Research Center, Research Organization
for the 21st Century, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Yu Nakadoi
- Nanoscience and Nanotechnology Research Center, Research Organization
for the 21st Century, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Mari Takahashi
- Sharp Corporation, 3-1-72, Kitakamei-cho, Yao 581-8585, Japan
| | - Mugihei Ikemizu
- Sharp Corporation, 3-1-72, Kitakamei-cho, Yao 581-8585, Japan
| | - Tetsuya Kadoma
- Sharp Corporation, 3-1-72, Kitakamei-cho, Yao 581-8585, Japan
| | - Kenta Saimatsu
- Department of Applied Chemistry, Graduate School
of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Le Quynh Dung
- Department of Applied Chemistry, Graduate School
of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Hiroshi Shiigi
- Department of Applied Chemistry, Graduate School
of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Tsutomu Nagaoka
- Department of Applied Chemistry, Graduate School
of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| |
Collapse
|
14
|
Jock S, Wensing A, Pulawska J, Drenova N, Dreo T, Geider K. Molecular analyses of Erwinia amylovora strains isolated in Russia, Poland, Slovenia and Austria describing further spread of fire blight in Europe. Microbiol Res 2013; 168:447-54. [PMID: 23570971 DOI: 10.1016/j.micres.2013.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/23/2013] [Accepted: 01/25/2013] [Indexed: 11/27/2022]
Abstract
Fire blight, a bacteriosis of apple and pear, was assayed with molecular tools to associate its origin in Russia, Slovenia and south-eastern Austria with neighboring countries. The identification of all investigated strains was confirmed by MALDI-TOF mass spectroscopy except one. Independent isolation was verified by the level of amylovoran synthesis and by the number of short sequence DNA repeats in plasmid pEA29. DNA of gently lysed E. amylovora strains from Russia, Slovenia, Austria, Hungary, Italy, Spain, Croatia, Poland, Central Europe and Iran was treated with restriction enzymes XbaI and SpeI to create typical banding patterns for PFGE analysis. The pattern Pt2 indicated that most Russian E. amylovora strains were related to strains from Turkey and Iran. Strains from Slovenia exhibited patterns Pt3 and Pt2, both present in the neighboring countries. Strains were also probed for the recently described plasmid pEI70 detected in Pt1 strains from Poland and in Pt3 strains from other countries. The distribution of pattern Pt3 suggests distribution of fire blight from Belgium and the Netherlands to Central Spain and Northern Italy and then north to Carinthia. The PFGE patterns indicate that trade of plants may have introduced fire blight into southern parts of Europe proceeded by sequential spread.
Collapse
Affiliation(s)
- Susanne Jock
- Julius Kuehn Institute, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, D-69221 Dossenheim, Germany
| | | | | | | | | | | |
Collapse
|
15
|
Braun-Kiewnick A, Lehmann A, Rezzonico F, Wend C, Smits THM, Duffy B. Development of species-, strain- and antibiotic biosynthesis-specific quantitative PCR assays for Pantoea agglomerans as tools for biocontrol monitoring. J Microbiol Methods 2012; 90:315-20. [PMID: 22705381 DOI: 10.1016/j.mimet.2012.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/04/2012] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
Abstract
Pantoea agglomerans is a cosmopolitan plant epiphytic bacterium that includes some of the most effective biological antagonists against the fire blight pathogen Erwinia amylovora, a major threat to pome fruit production worldwide. Strain E325 is commercially available as Bloomtime Biological™ in the USA and Canada. New quantitative PCR (qPCR) assays were developed for species- and strain -specific detection in the environment, and for detection of indigenous strains carrying the biocontrol antibacterial peptide biosynthesis gene paaA. The qPCR assays were highly specific, efficient and sensitive, detecting fewer than three cells per reaction or 700 colony forming units per flower, respectively. The qPCR assays were tested on field samples, giving first indications to the incidence of P. agglomerans E325 related strains, total P. agglomerans and pantocin A producing bacteria in commercial orchards. These assays will facilitate monitoring the environmental behavior of biocontrol P. agglomerans after orchard application for disease protection, proprietary strain-tracking, and streamlined screening for discovery of new biocontrol strains.
Collapse
Affiliation(s)
- Andrea Braun-Kiewnick
- Agroscope Changins-Wädenswil ACW, Plant Protection Division, CH-8820 Wädenswil, Switzerland
| | | | | | | | | | | |
Collapse
|
16
|
Roda A, Mirasoli M, Roda B, Bonvicini F, Colliva C, Reschiglian P. Recent developments in rapid multiplexed bioanalytical methods for foodborne pathogenic bacteria detection. Mikrochim Acta 2012. [DOI: 10.1007/s00604-012-0824-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
17
|
Gehring I, Geider K. Identification of Erwinia species isolated from apples and pears by differential PCR. J Microbiol Methods 2012; 89:57-62. [PMID: 22330936 DOI: 10.1016/j.mimet.2012.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 01/25/2012] [Accepted: 01/25/2012] [Indexed: 11/27/2022]
Abstract
Many pathogenic and epiphytic bacteria isolated from apples and pears belong to the genus Erwinia; these include the species E. amylovora, E. pyrifoliae, E. billingiae, E. persicina, E. rhapontici and E. tasmaniensis. Identification and classification of freshly isolated bacterial species often requires tedious taxonomic procedures. To facilitate routine identification of Erwinia species, we have developed a PCR method based on species-specific oligonucleotides (SSOs) from the sequences of the housekeeping genes recA and gpd. Using species-specific primers that we report here, differentiation was done with conventional PCR (cPCR) and quantitative PCR (qPCR) applying two consecutive primer annealing temperatures. The specificity of the primers depends on terminal Single Nucleotide Polymorphisms (SNPs) that are characteristic for the target species. These PCR assays enabled us to distinguish eight Erwinia species, as well as to identify new Erwinia isolates from plant surfaces. When performed with mixed bacterial cultures, they only detected a single target species. This method is a novel approach to classify strains within the genus Erwinia by PCR and it can be used to confirm other diagnostic data, especially when specific PCR detection methods are not already available. The method may be applied to classify species within other bacterial genera.
Collapse
Affiliation(s)
- I Gehring
- Julius Kühn Institut, Institut für Pflanzenschutz in Obst- und Weinbau, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | | |
Collapse
|