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1. Alves  MS, Dias  RC, de Castro  AC, Riley  LW, Moreira  BM,     ( 2006 )

Identification of clinical isolates of indole-positive and indole-negative Klebsiella spp.

Journal of clinical microbiology 44 (10)
PMID : 16928968  :   DOI  :   10.1128/JCM.00940-06     PMC  :   PMC1594763    
Abstract >>
Biochemical methods employed to classify bacterial species have limitations and may have contributed to the taxonomic complexity recently reported for the genus Klebsiella. The objective of the present study was to apply a simple biochemical test panel to classify a collection of human Klebsiella isolates. We found that with only three additional tests, it is possible to place most isolates in a defined species. Analysis of a 512-bp sequence of the rpoB gene was used as the reference. A total of 16 conventional and 4 supplementary tests were used to evaluate 122 recent isolates identified as Klebsiella from 120 patients, isolated at the clinical laboratory of a university hospital in Minas Gerais, Brazil. Of these, 102 (84%) isolates were identified as Klebsiella pneumoniae or Klebsiella variicola, 19 (15%) as Klebsiella oxytoca, and 1 (1%) as Raoultella planticola. Enterobacterial repetitive intergenic consensus-PCR typing revealed a diversity of genotypes. rpoB gene sequencing confirmed the phenotypic identification and detected five K. variicola isolates among the K. pneumoniae/K. variicola group. Three additional tests that include growth at 10 degrees C and histamine and d-melezitose assimilation should be considered essential tests for the typing of Klebsiella isolates.
KeywordMeSH Terms
2. Rosenblueth  M, Martínez  L, Silva  J, Martínez-Romero  E,     ( 2004 )

Klebsiella variicola, a novel species with clinical and plant-associated isolates.

Systematic and applied microbiology 27 (1)
PMID : 15053318  :   DOI  :   10.1078/0723-2020-00261     DOI  :   10.1078/0723-2020-00261    
Abstract >>
A new Klebsiella species, K. variicola, is proposed on the basis of total DNA-DNA hybridization, on the monophyly observed in the phylogenetic analysis derived from the sequences of rpoB, gyrA, mdh, infB, phoE and nifH genes and on distinct phenotypic traits. The bacteria from this new species seem to be genetically isolated from K. pneumoniae strains, do not ferment adonitol and were obtained from plants (such as banana, rice, sugar cane and maize) and hospitals. The type strain is F2R9T (= ATCC BAA-830T = CFNE 2004T).
KeywordMeSH Terms
3. Gueneau de Novoa  P, Williams  KP,     ( 2004 )

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts.

Nucleic acids research 32 (Database issue)
PMID : 14681369  :   DOI  :   10.1093/nar/gkh102     PMC  :   PMC308836    
Abstract >>
tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~ tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.
KeywordMeSH Terms
Databases, Nucleic Acid
Evolution, Molecular
Internet
4. Farkas  A, Cr?ciuna?  C, Chiriac  C, Szekeres  E, Coman  C, Butiuc-Keul  A,     ( 2016 )

Exploring the Role of Coliform Bacteria in Class 1 Integron Carriage and Biofilm Formation During Drinking Water Treatment.

Microbial ecology 72 (4)
PMID : 27079455  :   DOI  :   10.1007/s00248-016-0758-0    
Abstract >>
This study investigates the role of coliforms in the carriage of class 1 integron and biocide resistance genes in a drinking water treatment plant and explores the relationship between the carriage of such genes and the biofouling abilities of the strain. The high incidence of class 1 integron and biocide resistance genes (33.3 % of the isolates) highlights the inherent risk of genetic contamination posed by coliform populations during drinking water treatment. The association between the presence of intI1 gene and qac gene cassettes, especially qacH, was greater in biofilm cells. In coliforms recovered from biofilms, a higher frequency of class 1 integron elements and higher diversity of genetic patterns occurred, compared to planktonic cells. The coliform isolates under the study proved to mostly carry non-classical class 1 integrons lacking the typical qacE�G1/sul1 genes or a complete tni module, but bearing the qacH gene. No link was found between the carriage of integron genes and the biofouling degree of the strain, neither in aerobic or in anaerobic conditions. Coliform bacteria isolated from established biofilms rather adhere in oxygen depleted environments, while the colonization ability of planktonic cells is not significantly affected by oxygen availability.
KeywordMeSH Terms
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
Biofilm assay
Class 1 integron
Planktonic versus biofilm phenotype
qac genes
5. Fang  CT, Shih  YJ, Cheong  CM, Yi  WC,     ( 2016 )

Rapid and Accurate Determination of Lipopolysaccharide O-Antigen Types in Klebsiella pneumoniae with a Novel PCR-Based O-Genotyping Method.

Journal of clinical microbiology 54 (3)
PMID : 26719438  :   DOI  :   10.1128/JCM.02494-15     PMC  :   PMC4767969    
Abstract >>
Klebsiella pneumoniae, a Gram-negative bacillus that causes life-threatening infections in both hospitalized patients and ambulatory persons, can be classified into nine lipopolysaccharide (LPS) O-antigen serotypes. The O-antigen type has important clinical and epidemiological significance. However, K. pneumoniae O serotyping is cumbersome, and the reagents are not commercially available. To overcome the limitations of conventional serotyping methods, we aimed to create a rapid and accurate PCR method for K. pneumoniae O genotyping. We sequenced the genetic determinants of LPS O antigen from serotypes O1, O2a, O2ac, O3, O4, O5, O8, O9, and O12. We established a two-step genotyping scheme, based on the two genomic regions associated with O-antigen biosynthesis. The first set of PCR primers, which detects alleles at the wzm-wzt loci of the wb gene cluster, distinguishes between O1/O2, O3, O4, O5, O8, O9, and O12. The second set of PCR primers, which detects alleles at the wbbY region, further differentiates between O1, O2a, and O2ac. We verified the specificity of O genotyping against the O-serotype reference strains. We then tested the sensitivity and specificity of O genotyping in K. pneumoniae, using the 56 K-serotype reference strains with known O serotypes determined by an inhibition enzyme-linked immunosorbent assay (iELISA). There is a very good correlation between the O genotypes and classical O serotypes. Three discrepancies were observed and resolved by nucleotide sequencing--all in favor of O genotyping. The PCR-based O genotyping, which can be easily performed in clinical and research microbiology laboratories, is a rapid and accurate method for determining the LPS O-antigen types of K. pneumoniae isolates.
KeywordMeSH Terms
Genotype
6. Madhaiyan  M, Alex  TH, Ngoh  ST, Prithiviraj  B, Ji  L,     ( 2015 )

Leaf-residing Methylobacterium species fix nitrogen and promote biomass and seed production in Jatropha curcas.

Biotechnology for biofuels 8 (N/A)
PMID : 26697111  :   DOI  :   10.1186/s13068-015-0404-y     PMC  :   PMC4687150    
Abstract >>
Jatropha curcas L. (Jatropha) is a potential biodiesel crop that can be cultivated on marginal land because of its strong tolerance to drought and low soil nutrient content. However, seed yield remains low. To enhance the commercial viability and green index of Jatropha biofuel, a systemic and coordinated approach must be adopted to improve seed oil and biomass productivity. Here, we present our investigations on the Jatropha-associated nitrogen-fixing bacteria with an aim to understand and exploit the unique biology of this plant from the perspective of plant-microbe interactions. An analysis of 1017 endophytic bacterial isolates derived from different parts of Jatropha revealed that diazotrophs were abundant and diversely distributed into five classes belonging to �\, �], �^-Proteobacteria, Actinobacteria and Firmicutes. Methylobacterium species accounted for 69.1 % of endophytic bacterial isolates in leaves and surprisingly, 30.2 % which were able to fix nitrogen that inhabit in leaves. Among the Methylobacterium isolates, strain L2-4 was characterized in detail. Phylogenetically, strain L2-4 is closely related to M. radiotolerans and showed strong molybdenum-iron dependent acetylene reduction (AR) activity in vitro and in planta. Foliar spray of L2-4 led to successful colonization on both leaf surface and in internal tissues of systemic leaves and significantly improved plant height, leaf number, chlorophyll content and stem volume. Importantly, seed production was improved by 222.2 and 96.3 % in plants potted in sterilized and non-sterilized soil, respectively. Seed yield increase was associated with an increase in female-male flower ratio. The ability of Methylobacterium to fix nitrogen and colonize leaf tissues serves as an important trait for Jatropha. This bacteria-plant interaction may significantly contribute to Jatropha's tolerance to low soil nutrient content. Strain L2-4 opens a new possibility to improve plant's nitrogen supply from the leaves and may be exploited to significantly improve the productivity and Green Index of Jatropha biofuel.
KeywordMeSH Terms
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
Biofuel
Culturable endophyte
Jatropha curcas L.
Methylobacterium
Nitrogen fixation
7. Brisse  S, Passet  V, Grimont  PA,     ( 2014 )

Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola.

International journal of systematic and evolutionary microbiology 64 (Pt 9)
PMID : 24958762  :   DOI  :   10.1099/ijs.0.062737-0     DOI  :   10.1099/ijs.0.062737-0    
Abstract >>
Strains previously classified as members of Klebsiella pneumoniae phylogroups KpI, KpII-A, KpII-B and KpIII were characterized by 16S rRNA (rrs) gene sequencing, multilocus sequence analysis based on rpoB, fusA, gapA, gyrA and leuS genes, average nucleotide identity and biochemical characteristics. Phylogenetic analysis demonstrated that KpI and KpIII corresponded to K. pneumoniae and Klebsiella variicola, respectively, whereas KpII-A and KpII-B formed two well-demarcated sequence clusters distinct from other members of the genus Klebsiella. Average nucleotide identity between KpII-A and KpII-B was 96.4 %, whereas values lower than 94 % were obtained for both groups when compared with K. pneumoniae and K. variicola. Biochemical properties differentiated KpII-A, KpII-B, K. pneumoniae and K. variicola, with acid production from adonitol and l-sorbose and ability to use 3-phenylproprionate, 5-keto-d-gluconate and tricarballylic acid as sole carbon sources being particularly useful. Based on their genetic and phenotypic characteristics, we propose the names Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and K. quasipneumoniae subsp. similipneumoniae subsp. nov. for strains of KpII-A and KpII-B, respectively. The type strain of K. quasipneumoniae sp. nov. and of K. quasipneumoniae subsp. quasipneumoniae subsp. nov. is 01A030(T) (= SB11(T) = CIP 110771(T) = DSM 28211(T)). The type strain of K. quasipneumoniae subsp. similipneumoniae subsp. nov. is 07A044(T) (= SB30(T) = CIP 110770(T) = DSM 28212(T)). Both strains were isolated from human blood cultures. This work also showed that Klebsiella singaporensis is a junior heterotypic synonym of K. variicola.
KeywordMeSH Terms
Phylogeny
Phylogeny
8. Lin  L, Li  Z, Hu  C, Zhang  X, Chang  S, Yang  L, Li  Y, An  Q,     ( 2012 )

Plant growth-promoting nitrogen-fixing enterobacteria are in association with sugarcane plants growing in Guangxi, China.

Microbes and environments 27 (4)
PMID : 22510648  :   DOI  :   10.1264/jsme2.me11275     PMC  :   PMC4103546    
Abstract >>
The current nitrogen fertilization for sugarcane production in Guangxi, the major sugarcane-producing area in China, is very high. We aim to reduce nitrogen fertilization and improve sugarcane production in Guangxi with the help of indigenous sugarcane-associated nitrogen-fixing bacteria. We initially obtained 196 fast-growing bacterial isolates associated with the main sugarcane cultivar ROC22 plants in fields using a nitrogen-deficient minimal medium and screened out 43 nitrogen-fixing isolates. Analysis of 16S rRNA gene sequences revealed that 42 of the 43 nitrogen-fixing isolates were affiliated with the genera Enterobacter and Klebsiella. Most of the nitrogen-fixing enterobacteria possessed two other plant growth-promoting activities of IAA production, siderophore production and phosphate solubilization. Two Enterobacter spp. strains of NN145S and NN143E isolated from rhizosphere soil and surface-sterilized roots, respectively, of the same ROC22 plant were used to inoculate micropropagated sugarcane plantlets. Both strains increased the biomass and nitrogen content of the sugarcane seedlings grown with nitrogen fertilization equivalent to 180 kg urea ha(-1), the recommended nitrogen fertilization for ROC22 cane crops at the seedling stage. (15)N isotope dilution assays demonstrated that biological nitrogen fixation contributed to plant growth promotion. These results suggested that indigenous nitrogen-fixing enterobacteria have the potential to fix N(2) associated with sugarcane plants grown in fields in Guangxi and to improve sugarcane production.
KeywordMeSH Terms

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