scholarly journals First Report of Enterobacter Bulb Decay of Onions Caused by Enterobacter cloacae in New York

Plant Disease ◽  
2011 ◽  
Vol 95 (12) ◽  
pp. 1581-1581 ◽  
Author(s):  
A. M. Zaid ◽  
J. M. Bonasera ◽  
S. V. Beer
Keyword(s):  
New York ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Carbon Sources ◽  
Enterobacter Cloacae ◽  
Biochemical Properties ◽  
Published Data ◽  
Rrna Gene ◽  
Reference Strains ◽  
The 16S Rrna Gene

During the summer of 2010, onions (Allium cepa L.) of several cultivars growing in muck-land soils in Orange, Genesee, Orleans, and Oswego counties of New York exhibited leaf dieback and bulb decay consistent with disease symptoms caused by Enterobacter cloacae as described previously (1,3,4). Isolations of bacteria from symptomatic tissues and muck soil were made using onion extract medium (OEM), which contains extracts of autoclaved onions, salts, and inhibitors of fungi and gram-positive bacteria. Some presumptive strains of E. cloacae were isolated; 5 from symptomatic onions growing in Genesee County, 2 from muck-land soil, and 27 from bulbs stored for ~2.5 months in a farm storage facility in Oswego County. Tentative identification was based on colony morphology (convex, cream-color colonies, 2 to 3 mm in diameter following incubation at 28°C for 1 day on OEM), which was similar to the morphology of reference strains of E. cloacae ATCC 23355, ATCC 13047, and strain 310 (gift of H. F. Schwartz, which was derived from reference 4; personal communication). Strains were gram-negative rods, negative for oxidase and indole, positive for nitrate reductase and catalase; produced acid from glucose aerobically and anaerobically. Also, all strains produced PCR products from the 16S-23S internal transcribed spacer (ITS) DNA region of the predicted sizes using primers T5A and T3B designed for identification of E. cloacae (2). The growth of eight of the isolated strains and strains ATTC 23355 and 310 were evaluated on several carbon sources with RapiD 20E test strips (bio Mérieux, Inc, Durham, NC). All strains were positive for β-d-galactosidase, ornithine decarboxylase, utilization of citrate and malonate, and production of acetoin. Hydrolysis of esculin by β-glucosidase differed among the eight. All strains were negative for lysine decarboxylase, urease, para-phenylalanine deaminase, indole, and oxidase. All produced acid from arabinose, xylose, rhamnose, cellobiose, melibiose, saccharose, trehalose, raffinose, and glucose; no strains produced acid from adonitol. These characteristics are consistent with published data for E. cloacae. Surface-disinfested onion bulbs and sets were inoculated with 50 to 100 μl of bacterial suspensions containing ~108 CFU/ml, injected with hypodermic needles and syringes, and incubated at 37°C for 2 weeks. Bisected onions revealed dry brown discoloration in each of the four bulbs and sets that had been inoculated with each presumptive strain. Symptoms were indistinguishable from those apparent in onions inoculated with the authentic strains mentioned. Strains recovered on OEM were identified as E. cloacae based on the stated biochemical properties and analysis of the 16S rRNA gene amplified by PCR as above. The sequence of the amplicon from the isolated strains was identical to that of reference strains ATCC 23355 and 310. Amplicon sequences of the 16S rRNA gene of New York strains Ecl3, Ecl6, and Ecl7 were deposited in GenBank as JF832951, JF832952, and JF832953, respectively. The strains were accessioned as ATCC BAA-2271, ATCC BAA-2272, and ATCC BAA-2273, respectively. To our knowledge, this is the first published report of E. cloacae causing Enterobacter bulb decay of onion in New York. References: (1) A. L. Bishop and R. M. Davis. Plant Dis. 74:692, 1990. (2) M. M. Clementino et al. J. Clin. Microbiol. 39:3865, 2004. (3) B. K. Schroeder and L. J. du Toit. Plant Dis. 93:323, 2009. (4) H. F. Schwartz and K. Otto. Plant Dis. 84:808, 2000.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria

2006 ◽  
Vol 56 (5) ◽  
pp. 983-989 ◽  
Author(s):  
Cindy H. Nakatsu ◽  
Krassimira Hristova ◽  
Satoshi Hanada ◽  
Xian-Ying Meng ◽  
Jessica R. Hanson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Methyl Tert Butyl Ether ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Butyl Ether ◽  
The 16S Rrna Gene

A Gram-negative, rod-shaped, motile, non-pigmented, facultative aerobe that grew optimally at pH 6.5 and 30 °C (strain PM1T) was isolated for its ability to completely degrade the gasoline additive methyl tert-butyl ether. Analysis of the 16S rRNA gene sequence indicated that this bacterium was a member of the class Betaproteobacteria in the Sphaerotilus–Leptothrix group. The 16S rRNA gene sequence identity to other genera in this group, Leptothrix, Aquabacterium, Roseateles, Sphaerotilus, Ideonella and Rubrivivax, ranged from 93 to 96 %. The chemotaxonomic data including Q-8 as the major quinone, C16 : 1ω7c and C16 : 0 as the major fatty acids and a DNA G+C content of 69 mol%, support the inclusion of strain PM1T in the class Betaproteobacteria. It differed from other members of the Sphaerotilus–Leptothrix group by being a facultative methylotroph that used methanol as a sole carbon source, and by also being able to grow heterotrophically in defined media containing ethanol, toluene, benzene, ethylbenzene and dihydroxybenzoates as sole carbon sources. On the basis of the morphological, physiological, biochemical and genetic information, a new genus and species, Methylibium petroleiphilum gen. nov., sp. nov., is proposed, with PM1T (=ATCC BAA-1232T=LMG 22953T) as the type strain.

scholarly journals Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelis Kämpfer et al. 2011

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2187-2193 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Zea Mays ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sweet Corn ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Elizabethkingia Meningoseptica ◽  
The 16S Rrna Gene

A slightly yellow bacterial strain (JM-87T), isolated from the stem of healthy 10 day-old sweet corn (Zea mays), was studied for its taxonomic allocation. The isolate revealed Gram-stain-negative, rod-shaped cells. A comparison of the 16S rRNA gene sequence of the isolate showed 99.1, 97.8, and 97.4 % similarity to the 16S rRNA gene sequences of the type strains of Elizabethkingia anophelis, Elizabethkingia meningoseptica and Elizabethkingia miricola, respectively. The fatty acid profile of strain JM-87T consisted mainly of the major fatty acids C15:0 iso, C17:0 iso 3-OH, and C15:0 iso 2-OH/C16:1ω7c/t. The quinone system of strain JM-87T contained, exclusively, menaquinone MK-6. The major polyamine was sym-homospermidine. The polar lipid profile consisted of the major lipid phosphatidylethanolamine plus several unidentified aminolipids and other unidentified lipids. DNA–DNA hybridization experiments with E. meningoseptica CCUG 214T ( = ATCC 13253T), E. miricola KCTC 12492T ( = GTC 862T) and E. anophelis R26T resulted in relatedness values of 17 % (reciprocal 16 %), 30 % (reciprocal 19 %), and 51 % (reciprocal 54 %), respectively. These DNA–DNA hybridization results, in addition to some differentiating biochemical properties, clearly indicate that strain JM-87T is a representative of a novel species, for which the name Elizabethkingia endophytica sp. nov. is proposed. The type strain is JM-87T ( = CIP 110885T = LMG 28604T = CCM 8570T).

Microbispora sitophila sp. nov., a novel actinobacterium isolated from rhizosphere soil of wheat (Triticum aestivum L.)

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Lifeng Guo ◽  
Zhiqi Li ◽  
Xi Xu ◽  
Qiuying Pang ◽  
Junwei Zhao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rhizosphere Soil ◽  
Triticum Aestivum L ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A novel actinobacterium, designated strain NEAU-D428T, was isolated from rhizosphere soil of wheat and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with members of the genus Microbispora . The 16S rRNA gene sequence analysis showed that the isolate was most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.2 %). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain clustered with Microbispora clausenae CLES2T (99.1 %), but formed a separate subclade in the phylogenomic tree within the genus Microbispora . The menaquinones were identified as MK-9(H4), MK-9(H2) and MK-9(H0). The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, ninhydrin-positive glycophospholipid, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C16 : 0, C16 : 0, 10-methyl C17 : 0 and C18 : 0. Digital DNA–DNA hybridization and average nucleotide identity values between strain NEAU-D428T and M. bryophytorum NEAU-TX2-2T, Microbispora camponoti 2C-HV3T, M. clausenae CLES2T, ‘Microbispora cellulosiformans’ Gxj-6T and Microbispora fusca NEAU-HEGS1-5T were 47.6 and 92.2 %, 47.5 and 92.2 %, 55.9 and 94.0 %, 33.1 and 86.8 %, and 33.6 and 87.1 %, respectively. These results and some physiological and biochemical properties demonstrated that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-D428T should be classified as representative of a novel species of the genus Microbispora , for which the name Microbispora sitophila sp. nov. is proposed. The type strain is NEAU-D428T (=CGMCC 4.7523T=DSM 109822T).

scholarly journals Pseudomonas knackmussii sp. nov.

2007 ◽  
Vol 57 (3) ◽  
pp. 572-576 ◽  
Author(s):  
Andreas Stolz ◽  
Hans-Jürgen Busse ◽  
Peter Kämpfer
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Fatty Acid Profile ◽  
Rrna Gene ◽  
Pseudomonas Nitroreducens ◽  
High Degree ◽  
Reference Strains ◽  
Degree Of Similarity ◽  
The 16S Rrna Gene

The taxonomic position of Pseudomonas sp. B13T, isolated as a 3-chlorobenzoate-degrading organism and used for several groundbreaking studies on the enzymology and genetics of the degradative pathway for haloaromatic compounds, was studied in detail. The previously performed physiological studies, the detection of ubiquinone Q-9, the polyamine pattern with putrescine and spermidine as major polyamines, a fatty acid profile with C18 : 1 ω7c, summed feature 3 and C16 : 0 as quantitatively the most important constituents and the 16S rRNA gene sequence demonstrated that Pseudomonas sp. B13T indeed belongs to the genus Pseudomonas. The sequence of the Pseudomonas sp. B13T 16S rRNA gene demonstrated a high degree of similarity with that of Pseudomonas citronellolis DSM 50332T (98.9 %), Pseudomonas nitroreducens DSM 14399T (98.7 %), Pseudomonas jinjuensis DSM 16612T (98.1 %) and Pseudomonas multiresinivorans DSM 17553T (98.7 %). Thus it was shown that strain Pseudomonas sp. B13T can be distinguished from related species by the ability/inability to assimilate N-acetylgalactosamine, d-galactose, putrescine, trans-aconitate and mesaconate and some differences in the fatty acid profile. The positioning of Pseudomonas sp. B13T as a separate taxon was finally verified by DNA hybridization, which demonstrated less than 45 % DNA–DNA similarity between strain Pseudomonas sp. B13T and the reference strains. On the basis of these results, Pseudomonas sp. B13T represents a novel species for which the name Pseudomonas knackmussii sp. nov. is proposed. The type strain is B13T (=DSM 6978T=LMG 23759T).

Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger)

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 495-500 ◽  
Author(s):  
Wensheng Xiang ◽  
Chao Yu ◽  
Chongxi Liu ◽  
Junwei Zhao ◽  
Lingyu Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Close Phylogenetic Relationship ◽  
Polyrhachis Vicina ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain NEAU-ycm2T, was isolated from edible Chinese black ants (Polyrhachis vicina Roger) and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora . The 16S rRNA gene sequence of strain NEAU-ycm2T showed highest similarity to those of Micromonospora sonneratiae 274745T (99.12 %), Micromonospora pattaloongensis TJ2-2T (98.85 %), Micromonospora pisi GUI 15T (98.76 %), Polymorphospora rubra TT 97-42T (98.42 %) and Micromonospora eburnea LK2-10T (98.21 %). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that strain NEAU-ycm2T is a member of the genus Micromonospora and supported the close phylogenetic relationship to M. sonneratiae 274745T, M. pattaloongensis JCM 12833T and M. pisi GUI 15T. Furthermore, a combination of DNA–DNA hybridization and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from its closest phylogenetic relatives. Therefore, it is proposed that NEAU-ycm2T represents a novel species of the genus of Micromonospora , for which the name Micromonospora polyrhachis sp. nov. is proposed. The type strain is NEAU-ycm2T ( = CGMCC 4.7100T = DSM 45886T).

Identification of Coagulase-Negative Staphylococci Isolated from Continuous Ambulatory Peritoneal Dialysis Fluid using 16s Ribosomal RNA,tuf, andSodAGene Sequencing

2011 ◽  
Vol 31 (3) ◽  
pp. 340-346 ◽  
Author(s):  
Jeong Hwan Shin ◽  
Si Hyun Kim ◽  
Haeng Soon Jeong ◽  
Seung Hwan Oh ◽  
Hye Ran Kim ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Rna ◽  
Species Distribution ◽  
Gene Sequencing ◽  
Rrna Gene ◽  
Tuf Gene ◽  
Reference Strains ◽  
The 16S Rrna Gene

IntroductionCoagulase-negative staphylococcus (CoNS) is the most common pathogen in continuous ambulatory peritoneal dialysis (CAPD)–associated peritonitis. There is no well-organized, standardized database for CoNS, and few studies have used gene sequencing in reporting species distribution in CAPD peritonitis. In the present study, we used 3 housekeeping genes to evaluate the prevalence of CoNS isolated from CAPD peritonitis episodes and to estimate the accuracy of, and the characteristic differences between, these genes for species identification.MethodsAll 51 non-duplicated CoNS isolates obtained from CAPD peritonitis between April 2006 and May 2008 were used. The strains were identified by polymerase chain reaction and by direct sequencing using the 16S ribosomal RNA (rRNA), tuf, and sodA genes. We determined species distribution, and using selected databases, we analyzed the characteristics and diagnostic utility of the individual genes for species identification.ResultsIn GenBank (National Institutes of Health, Bethesda, MD, USA), we found 49 type or reference strains for CoNS 16S rRNA, 17 for tuf, and 46 for sodA, and we used those data for sequence-similarity comparisons with CAPD isolates. Among our 51 strains, S. epidermidis (66.7%) was the most common, followed by S. haemolyticus (11.8%), S. warneri (7.8%), S. caprae (5.9%), S. capitis (3.9%), and S. pasteuri (2.0%). For 1 strain, different species results were obtained with each gene. The identification rates with 16S rRNA, sodA, and tuf gene sequencing were 84.0%, 96.0%, and 92.2% respectively. The discrimination capability of 16S rRNA gene was lower in a few individual species, and for the sodA gene, the percentage similarity to sequences from reference strains was also lower. The tuf gene had excellent identification capacity, but relatively few type strains are available in public databases. The 16S rRNA gene did not discriminate between S. caprae and S. capitis. The sodA gene showed a similarity rate that was lower than that for sequences of the 16S rRNA gene. The tuf type strain sequences for S. caprae and S. pasteuri are not available in public databases.ConclusionsThe sodA, tuf, and 16S rRNA genes were very useful for CoNS identification. Each has its own characteristics of similarity, discriminative power, and inclusion in databases.

scholarly journals Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences

2005 ◽  
Vol 55 (1) ◽  
pp. 263-270 ◽  
Author(s):  
Soon-Wo Kwon ◽  
Jin-Young Park ◽  
Jong-Shik Kim ◽  
Jun-Won Kang ◽  
Yang-Hee Cho ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Its Region ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Group I ◽  
Internally Transcribed Spacer ◽  
Reference Strains ◽  
The 16S Rrna Gene

A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were revealed between phylogenetic dendrograms based on 16S rRNA gene and ITS region sequences for members of the genus Rhizobium, reflecting their taxonomic heterogeneity. The amalgamation of Rhizobium and former members of Agrobacterium was confirmed using the 16S rRNA tree. Phylogenetic analysis of ITS region sequences showed that the Rhizobium giardinii clade (group II) and the Rhizobium radiobacter/Rhizobium rubi clade (group III) could be tentatively recognized as groups that are separable from the core group (group I), which includes Rhizobium leguminosarum. Dendrograms based on the 16S rRNA gene and ITS region sequences of Mesorhizobium strains were highly conflicting due to the poor taxonomic resolution of the 16S rRNA gene sequences and the low confidence in the ITS dendrogram. Several Korean isolates within the genus Mesorhizobium are thought to represent novel taxa when considering their relatively low ITS region sequence similarities (<80 %) to the reference strains.

scholarly journals Anaerostipes Faecalis Sp. Nov. Isolated from Swine Faeces

2021 ◽  
Author(s):  
Seung-Hyeon Choi ◽  
Ji Young Choi ◽  
Jam-Eon Park ◽  
Ji-Sun Kim ◽  
Se Won Kang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Sequencing Analysis ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Ph Range ◽  
Reference Strains ◽  
The 16S Rrna Gene

Abstract A novel, strictly anaerobic, gram-negative, segmented filamentous bacterium (SFB), strain AGMB03513T, was isolated from the faeces of a 5-month-old pig. Comparative analysis of 16S rRNA gene sequences indicated that strain AGMB03513T forms a lineage within the genus Anaerostipes and is most closely related to Anaerostipes butyraticus DSM 22094T (= KCTC 15125T, 95.8%), Anaerostipes hadrus DSM 3319T (= KCTC 15606T, 95.5%), Anaerostipes caccae DSM 14662T (= KCTC 15019T, 94.0%), and Anaerostipes rhamnosivorans DSM 26241T (= KCTC 15316T, 93.4%). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequencing analysis revealed that its closest relatives are members of the family Lachnospiraceae and that the closest related is Anaerostipes butyraticus. Strain AGMB03513T grows at temperatures of between 30 and 45°C within a pH range of 7.0 to 9.0, and in medium containing up to 1.5% NaCl. Cells were found to utilize d-glucose, d-mannitol, d-lactose, d-saccharose, d-maltose, d-xylose, l-arabinose, d-mannose, and d-sorbitol, and acetate was identified as the major end product of metabolism. The DNA G+C content of the strain is 37.0 mol%. Average nucleotide identity (ANI) values obtained in comparisons of strain AGMB03513T with reference strains of species in the genus Anaerostipes were between 71.0% and 75.7%, which are below the ANI criterion for interspecies identity. The major components of cellular fatty acids were C12:0, C16:0, and C18:0. On the basis of phenotypic, phylogenetic, biochemical, chemotaxonomic, and genomic characteristics, we consider it reasonable to assign novel species status to strain AGMB03513T, for which we propose the name Anaerostipes faecalis sp. nov. The type strain AGMB03513T (=KCTC 25020T=NBRC 114896T).

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