Evaluation of a commercial microbial identification system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria

1992 ◽  
Vol 72 (4) ◽  
pp. 315-321 ◽  
Author(s):  
D.E. Stead ◽  
J.E. Sellwood ◽  
J. Wilson ◽  
I. Viney
Plant Disease ◽  
2009 ◽  
Vol 93 (11) ◽  
pp. 1219-1219 ◽  
Author(s):  
B. Li ◽  
G. L. Wang ◽  
Z. Y. Wu ◽  
W. Qiu ◽  
Q. M. Tang ◽  
...  

During warm and humid periods in the winters from 2005 to 2008, head rot symptoms on broccoli (cv. Sijilv) (Brassica oleracea L. var italica Planch) were observed in commercial fields in Ningbo, Zhejiang Province, China. In agreement with the report of Cui and Harling (1), water-soaked lesions developed on the buds and then progressed into a brown-black soft rot. Longitudinal sections of the symptomatic inflorescences showed brown discoloration and rotting of the internal tissues. Broccoli production is hampered by the disease, with disease incidence ranging from 65 to 81%. Bacteria were isolated by streaking on nutrient agar (3) and individual colonies formed after 2 to 3 days of incubation at 28°C. Fifteen of thirty isolates induced hypersensitive reactions (HR) on tobacco leaves (Nicotiana tabacum cv. Samsun) within 48 h. All the HR-positive strains were fluorescent on King's medium B and the colonies were smooth, convex, entire, and round. Classical bacteriological tests indicated that the fluorescent strains were gram negative, obligate aerobes, arginine dihydrolase positive, and oxidase positive. Also, the fluorescent strains were positive for the production of levan from sucrose. Five representative strains were further characterized by the Biolog Microbial Identification System, version 4.2 (Biolog Inc., Hayward, CA) and gas chromatography of fatty acid methyl esters (FAME) using the Microbial Identification System (MIDI Inc., Newark, DE) with the aerobic bacterial library (TSBA50). The five strains were identified as Pseudomonas fluorescens with Biolog and FAME similarity indexes of 0.61 to 0.68 and 0.52 to 0.58, respectively. The 16S rRNA gene sequence of broccoli strain PFB-01 (GenBank Accession No. GQ352649) was determined according to Li et al. (2). A subsequent GenBank search showed that this sequence had 98% nucleotide identity with the type strain of P. fluorescens (ATCC 17386T, GenBank Accession No. AF094726). Koch's postulates were completed by the inoculation of broccoli heads (cv. Sijilv) with cell suspensions (107 CFU/ml) of the above five strains by spraying on the surface of subcorymbs. Each treatment had five replicates. All strains induced head rot symptoms similar to those observed in natural infections. No symptoms were noted on the control plants inoculated with sterile water. Bacteria were successfully reisolated from symptomatic heads and confirmed by the cellular fatty acid composition. To our knowledge, this is the first report in China that P. fluorescens is the causal pathogen of bacterial head rot of broccoli. References: (1) X. Cui and R. Harling. Phytopathology 96:408, 2006. (2) B. Li et al. J. Phytopathol. 154:711, 2006. (3) N. W. Schaad et al. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society. St. Paul, MN, 2001.


2002 ◽  
Vol 65 (6) ◽  
pp. 993-998 ◽  
Author(s):  
ARTHUR HINTON ◽  
J. A. CASON ◽  
KIMBERLY D. INGRAM

Yeasts associated with broiler carcasses taken from various stages of commercial poultry processing operations and broiler carcasses stored at refrigerated temperatures were enumerated and identified. Whole carcass rinses were performed to recover yeasts from carcasses taken from a processing facility and processed carcasses stored at 4°C for up to 14 days. Yeasts in the carcass rinsates were enumerated on acidified potato dextrose agar and identified with the MIDI Sherlock Microbial Identification System. Dendrograms of fatty acid profiles of yeast were prepared to determine the degree of relatedness of the yeast isolates. Findings indicated that as the carcasses are moved through the processing line, significant decreases in the number of yeasts associated with broiler carcasses usually occur, and the composition of the yeast flora of the carcasses is altered. Significant (P < 0.05) increases in the yeast population of the carcasses generally occur during storage at 4°C, however. Furthermore, it was determined that the same strain of yeast may be recovered from different carcasses at different points in the processing line and that the same strain of yeast may be isolated from carcasses processed on different days in the same processing facility.


2003 ◽  
Vol 31 (2) ◽  
pp. 133-140 ◽  
Author(s):  
A Ozbek ◽  
O Aktas

The cellular fatty acid profiles of 67 strains belonging to three different species of the genus Mycobacterium were determined by gas chromatography of the fatty acid methyl esters, using the MIDI Sherlock® Microbial Identification System (MIS). The species M. tuberculosis, M. xenopi and M. avium complex were clearly distinguishable and could be identified based on the presence and concentrations of 12 fatty acids: 14:0, 15:0, 16:1ω7c, 16:1ω6c, 16:0, 17:0, 18:2ω6,9c, 18:1ω9c, 18:0, 10Me-18:0 tuberculostearic acid, alcohol and cyclopropane. Fatty acid analysis showed that there is great homogeneity within and heterogeneity between Mycobacterium species. Thus the MIS is an accurate, efficient and relatively rapid method for the identification of mycobacteria.


Plant Disease ◽  
1998 ◽  
Vol 82 (7) ◽  
pp. 831-831 ◽  
Author(s):  
D. O. Chellemi ◽  
H. A. Dankers ◽  
K. Hill ◽  
R. E. Cullen ◽  
G. W. Simone ◽  
...  

In September 1997, wilted 4-week-old tomato (Lycopersicon esculentum Mill.) plants were observed in a commercial production field in St. Lucie County, FL. Closer inspection of affected plants revealed hollow stems and petioles with dark, water-soaked lesions. Diseased tissue was macerated and streaked onto nutrient agar (NA) and crystal violet pectate (CVP) agar. After incubation for 2 days at 30°C, isolates produced pits on the CVP agar. Isolates were transferred onto NA and the incubation and transfer procedure was performed two additional times to obtain pure cultures. Suspensions of bacterial cells were injected into tomato and tobacco leaves to test for a hypersensitive or pathogenic reaction. Isolates produced collapsed necrotic tissue on tomato while no reaction was observed on tobacco. Tests for differentiating species and subspecies in the ‘carotovora’ group of Erwinia were conducted following the protocol of Dickey and Kelman (1). With known cultures of E. carotovora subsp. carotovora and E. chrysanthemi as controls, the isolate from tomato was determined to function as a facultative anaerobe, utilize asparagine as a sole source of carbon and nitrogen, and give positive reactions for pectate degradation, phosphatase, and growth at 37°C. Known cultures of E. carotovora subsp. carotovora, E. chrysanthemi, and the tomato isolate were grown on trypticase soy broth agar for 24 h at 28°C and their cellular fatty acids derivatized to fatty acid methyl esters (FAMEs). Statistical analyses of FAME profile data (MIDI Microbial Identification System, Newark, DE, version 3.60) identified the tomato isolate as Erwinia chrysanthemi. Pathogenicity was determined by inoculating 50-day-old tomato plants (cv. SunPride) with a suspension of E. chrysanthemi obtained from nutrient broth plates incubated at 24°C for 60 h. Three plants each were inoculated with the E. chrysanthemi identified from tomato, sterile water, and known cultures of E. chrysanthemi and E. carotovora subsp. carotovora by placing a drop at the junction of the petiole and stem and passing a sterile needle through the drop into the stem. Plants were maintained in a greenhouse. Dark, water-soaked cankers were observed on the stems of plants inoculated with E. chrysanthemi, including the tomato isolate and E. carotovora subsp. carotovora, after 7 days. No symptoms were observed on plants inoculated with sterile water. Reisolation of the pathogen and identification was performed with tissue from one of the symptomatic inoculated plants. Analyses of FAMEs confirmed E. chrysanthemi as the causal agent. This is the first report of E. chrysanthemi causing a vascular disease of field-grown tomato in Florida. Reference: (1) R. S. Dickey and A. Kelman. 1988. Pages 44–59 in: Laboratory Guide for Identification of Plant Pathogenic Bacteria. N. W. Schaad, ed. American Phytopathological Society, St. Paul, MN.


Plant Disease ◽  
2000 ◽  
Vol 84 (7) ◽  
pp. 785-788 ◽  
Author(s):  
R. E. Baird ◽  
R. D. Gitaitis ◽  
D. E. Carling ◽  
S. M. Baird ◽  
P. J. Alt ◽  
...  

Fatty acid methyl esters (FAMEs) of isolates of Rhizoctonia solani AG-4 and AG-7 were characterized by gas chromatography and analyzed with Microbial Identification System software. Palmitic, stearic, and oleic acids were common in all isolates from both anastomosis groups (AGs) and accounted for 95% of the C14 to C18 fatty acids present. Oleic acid, most common in both R. solani AG-4 and AG-7 isolates, accounted for the greatest percentages of total FAMEs. The presence, quantities, or absence of individual fatty acids could not be used for distinguishing AG-4 and AG-7 isolates. Anteisopentadecanoic and 9-heptadecanoic acids, however, were specific to all three AG-7 isolates from Japan but absent in other AG-7 isolates and all AG-4 isolates. Pentadecanoic acid occurred in only two of the R. solani AG-4 isolates, but was not found in any of the AG-7 isolates. The AG-4 isolates could be distinguished from AG-7 isolates when quantities of FAMEs and key FAME ratios were analyzed with cluster analysis and principle components were plotted. Isolates of AG-7 from Arkansas, Indiana, and Georgia appeared to be more closely related to each other than to AG-7 isolates from Japan and Mexico. These differences in FAMEs were sufficiently distinct that isolate geographical variability could be determined. A dendrogram analysis cluster constructed from the FAMEs data showed results similar to that of the principal component analysis. Euclidean distances of total AG-4 isolates were distinct from total AG-7 isolates. The Arkansas and Indiana AG-7 isolates had a similar Euclidean distance to each another but the percentages were different for the AG-7 isolates from Japan and Mexico. In conclusion, variability of the FAMEs identified in this study would not be suitable as the main diagnostic tool for distinguishing individual isolates of R. solaniAG-4 from AG-7.


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