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E. coli from drinking water
Published in Cara Gleeson, Nick Gray, The Coliform Index and Waterborne Disease, 1996
Numerous commercial identification systems (kits) are also available for the rapid identification of Enterobacteriaceae and other bacteria. One of the more popular systems currently in use is the API 20E (Bio Merieux UK Ltd, Basingstoke). This consists of a plastic strip with 20 microtubes containing dehydrated substrates that can detect certain biochemical characteristics: ONPG, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase, citrate utilization, H2S production, urease production, tryptophan deamination, indole production, acetoin production, gelatin hydrolysis, fermentation of glucose, mannitol, inositol, sorbitol, rhamnose, sucrose, melibiose, amygdalin, arabinose and production of oxidase. The test substances are inoculated with bacteria in sterile physiological saline. Some tests may have to be overlaid with mineral oil to obtain the correct gaseous conditions. Results are usually available after 24 hours incubation and the 20 test results are converted to a seven- or nine-digit profile number (Figure 4.1). This profile number is then used with either a computer or a book called the API Profile Index to find the name of the bacterium (Holmes and Costas, 1992; Prescott, Harley and Klein, 1993). A study by Holmes and Costas (1992) found that 88% of all test strains were correctly identified using the API system. They also reviewed a number of other test kits which had varying results (Table 4.3). While these kits are very convenient and relatively sensitive, cost is a considerable factor which must be taken into consideration.
Salmonids (Salmonidae)
Published in John A Plumb, Health Maintenance Of Cultured Fishes, 1994
Once Y. ruckeri is isolated it can be identified by conventional biochemical characteristics.119,136-137 It is a motile (peritrichous flagellation), Gram-negative, cytochrome oxidase negative rod that measures 1.0 x 1.0 to 3 (xm. The following biochemical reactions, which are fairly homogeneous for the species, are the most informative: positive for fermentative metabolism, production of catalase and p-galactosidase, lysine and ornithine decarboxylation, methyl red test, nitrite reduction, and degradation of gelatin (Table 2). It will grow on media containing up to 3% NaCl and utilizes citrate. Y. ruckeri’s inability to produce H2S, indole, oxidase, and phenylalanine deaminase, and its negative reaction for Voges-Proskauer are significant features. Some strains can vary in the methyl red, Voges-Proskauer, lysine decarboxylase, arginine dihydrolase, and lactose fermentation tests.119,125,132 Fermentation of sorbitol has received some attention in discriminating between pathogenic strains (Serotype I) and nonpathogenic strains (Serotype II). Serotype I does not ferment sorbitol but Serotype II does, consequently Cipriano and Pyle138 developed a sorbitol-based medium that can be used to distinguish between them. However, Valtonen et al.139 questioned the sorbitol reaction as being indicative of pathogenicity for Norwegian isolates. Austin and Austin1 stated that Y. ruckeri could be confused with Hafnia alvei if the API 20 system is used for identification; however, de Grandis et al.140 showed that H. alvei is L-arabinose and L-rhamnose positive while Y. ruckeri is uniformly negative for these characteristics.
Enterobacteriaceae
Published in Maria Csuros, Csaba Csuros, Klara Ver, Microbiological Examination of Water and Wastewater, 2018
Maria Csuros, Csaba Csuros, Klara Ver
The following list explains the operation of the API 20E System. Preparation of bacterial suspension: add 5 ml of buffer solution or 0.85 percent saline solution, pH 5.5 to 7.0, to a sterile test tube.Gently touch the center of a well-isolated colony with the tip of a wooden applicator stick. Insert the applicator stick into the tube of buffer or saline solution and, with the tip of the stick at the base of the tube, rotate the stick in a vortex-like action. Recap the tube.Set up an incubation tray and lid. Record the sample identification on the elongated flap of the tray.Dispense 5 ml of tapwater into the incubation tray to provide a humid atmosphere during incubation.Remove the API strips from the sealed envelope and place one strip in each incubation tray. The API 20E contains 20 microtubes each of which consists of a tube and a cupule section as shown in Figure 20.4. The API 20E microtube system is shown in Figure 20.5.Using a sterile Pasteur pipet, tilt the API 20E tray and fill the tube section of the microtubes with bacterial suspension. Also, fill the cupule section of the CIT (citrate), VP (Voges-Prokauer), and GEL (gelatin) tubes.After inoculation, completely fill the cupule section of the ADH (arginine dihydrolase), LDC (lysine decarboxylase), ODC (ornithine decarboxylase), and URE (urea) tubes with mineral oil.Place the plastic lid on the tray and incubate the strip for 18 to 24 h at 35 to 37°C. If the strip cannot be read after 24 h, the strips should be removed from the incubator and refrigerated until the reaction can be read.Read and record all reactions and follow the tests for TDA (tryptophane deaminase), VP, and indole reactions.Read the number according to the accompanied interpretation guide.The entire incubation unit must be autoclaved, incinerated, or immersed in a germicide prior to disposal.
Study on the characterization of endosulfan-degrading bacterial strains isolated from contaminated rhizospheric soil
Published in Journal of Environmental Science and Health, Part C, 2022
Vandana Singh, Shubhi Srivastava, Namrata Singh, Suchi Srivastava, Alok Lehri, Nandita Singh
The results of the biochemical tests show that all the strains have shown positive reaction for the Voges–Proskauer, nitrate, deoxyribonuclease, and catalase tests and negative for the indole, starch hydrolysis, and urease tests. Strains EAG-EC-12, 13, and 14 have shown negative result for arginine dihydrolase and oxidase tests, while the same strains have shown positive response for citrate, lysine decarboxylase, esculin hydrolysis, and lypase tests. Strain EAG-EC-15 has shown negative response to methyl red, citrate, lysin decarboxylate, ornithine decarboxylase, gelatin hydrolysis, esculin hydrolysis, and lipase and positive response to Voges–Proskauer test, arginine dihydrolase, and oxidase test. Biochemical response in terms of acid production showed that all four strains have shown positive response toward xylose and fructose test, while negative toward maltose test. Strains EAG-EC-12, 13, and 14 have shown negative response toward galactose and dextrose test, whereas EAG-EC-15 has shown negative response to trehalose and positive to dextrose and galactose test. Based on the results of morphological, physiological, and biochemical characterization tests, three strains were identified as Serratia sp. and one as Ochrobactrum daejeonensis.
Heavy metal remediation and resistance mechanism of Aeromonas, Bacillus, and Pseudomonas: A review
Published in Critical Reviews in Environmental Science and Technology, 2022
Ali Fakhar, Bushra Gul, Ali Raza Gurmani, Shah Masaud Khan, Shafaqat Ali, Tariq Sultan, Hassan Javed Chaudhary, Mazhar Rafique, Muhammad Rizwan
Genus Pseudomonas was first described in 1894 on the basis of morphological characteristics and was subsequently subdivided into five groups based on rRNA–DNA hybridization and DNA–DNA hybridization in 1984. Later, several authors reviewed the different circumstances of the taxonomic status of genus Pseudomonas at different times, which included 96 species; only 31 species fulfilled the criteria of the taxonomy (Gomila et al., 2015). Pseudomonas aeruginosa is a well-known human pathogen that causes pneumonia, acute nosocomial infections of burn wounds, cancer, and cystic fibrosis. Pseudomonas syringae is a well-known plant pathogen responsible for developing stress conditions in plants, such as frost damage (Ha & Denver, 2018; Tran et al., 2017). In addition, Pseudomonas species such as P. chlororaphis and P. fluorescens have some important traits, such as plant growth-promotion properties. This genus includes some bacteria that are biocontrol agents and are considered to be plant beneficial microorganisms because they protect plants from pathogens through competitive colonization (Dorjey et al., 2017; Fishman et al., 2018). These bacteria can grow efficiently in any environment. They have an optimal temperature of 37 °C and can tolerate temperature of 4–42 °C within a pH range of 4–8 (W. Li, Ten, et al., 2018). Many Pseudomonas sp. process fluorescent pigments, such as pyoverdines, and can produce a variety of endoenzymes, including catalase, arginine dihydrolase, and lysine decarboxylase, that are capable of fermentation of carbohydrate to process glucose fermentation (Burns, 2018).
Removal of phosphate by Staphylococcus aureus under aerobic and alternating anaerobic–aerobic conditions
Published in Environmental Technology, 2018
Malairajan Sumathi, Namasivayam Vasudevan
The isolated bacterium, PAO33, is a gram-positive coccus arranged in clusters, nonmotile, facultative anaerobe and non-spore forming. PAO 33 utilized carbohydrates such as mannose, sucrose, mannitol, maltose, trehalose and galactose and produced enzymes such as arginine dihydrolase 1, l-pyrrolidonyl-arylamidase and phosphatase. PAO 33 was resistant to antibiotics such as optochin, polymixin B and bacitracin (Table 1). The data obtained after the analysis were compared with the respective database to determine the quantitative value of proximity to each of the taxa in the database. Furthermore, the molecular identification by 16s rDNA sequencing confirmed PAO 33 as Staphylococcus aureus with 97% homology to S. aureus subsp. anaerobius and S. aureus subsp. aureus and 95% homology to Staphylococcus simiae (Figure 3). Most of the earlier studies on phosphate-accumulating bacteria report the metabolism of phosphate removal by Acinetobacter sp. [45] with various carbon sources under different growth conditions [11,46–54] since it was considered to be the predominant phosphate-accumulating bacterium in the activated sludge. Very few studies have reported Staphylococcus sp as phosphate-accumulating bacteria from a lab-scale reactor [17] and Staphylococcus auricularis isolated from the activated sludge at Ju-Ho University, Tokyo, Japan [24]. Staphylococcus sp was found to be one of the phosphate-accumulating bacteria among 40% of the gram-positive population isolated from the activated sludge of a full-scale Johannesburg type BNR system [34].