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a numerical taxonomic study of proteolytic and lipolytic psychrotrophs isolated from caprine milk.lipolytic and proteolytic psychrotrophs were isolated from raw and pasteurized goats' milk, which had been stored at 5 degrees c for 7 d. the 241 strains isolated and 20 reference strains were examined by 149 biochemical, physiological, and morphological tests. the results yielded 195 characters suitable for taxonomic analysis. computer-assisted complete linkage analysis, using the jaccard coefficient, produced 22 phenons at 75% s. the results showed that pseudomonas fluorescens was the predomin ...19892496069
riemerella anatipestifer gen. nov., comb. nov., the causative agent of septicemia anserum exsudativa, and its phylogenetic affiliation within the flavobacterium-cytophaga rrna homology group.the phylogenetic position of the causative agent of septicemia anserum exsudativa, now most often referred to as [moraxella] anatipestifer (brackets indicate a generically misnamed taxon) or "[pasteurella] anatipestifer," was established by performing rrna cistron similarity studies. [moraxella] anatipestifer belongs to rrna superfamily v, together with the genera flavobacterium, cytophaga, flexibacter, weeksella, capnocytophaga, and sphingobacterium. the detailed structure of rrna superfamily v ...19938240957
phylogenetic position of riemerella anatipestifer based on 16s rrna gene sequences.riemerella anatipestifer, the causative agent of septicemia anserum exsudativa (also called new duckling disease), belongs to the family flavobacteriaceae of gram-negative bacteria. we determined the dna sequences of the rrs genes encoding the 16s rrnas of four r. anatipestifer strains by directly sequencing pcr-amplified rrs genes. a sequence similarity analysis confirmed the phylogenetic position of r. anatipestifer in the family flavobacteriaceae in rrna superfamily v and allowed fine mapping ...19979103649
properties of a cold-active protease from psychrotrophic flavobacterium balustinum p104.protease activity was detected in the culture medium of flavobacterium balustinum p104 grown at 10 degrees c, which was isolated from salmon (oncorhynchus keta) intestine. the enzyme, designated as cp-70 protease, was purified to homogeneity from the culture broth by ion exchange and gel filtration chromatographyies. the molecular mass of the protease was 70 kda, and its isoelectric point was close to 3.5. maximal activity toward azocasein was observed at 40 degrees c and from ph 7.0 to 9.0. the ...19989891929
precise detection and tracing of trichoderma hamatum 382 in compost-amended potting mixes by using molecular markers.randomly amplified polymorphic dna (rapd) analysis and the pcr assay were used in combination with dilution plating on a semiselective medium to detect and enumerate propagules of trichoderma hamatum 382, a biocontrol agent utilized in compost-amended mixes. distinct and reproducible fingerprints were obtained upon amplification of purified genomic dna of t. hamatum 382 with the random primers ope-16, oph-19, and oph-20. three amplified dna fragments of 0.35 (ope-16(0.35)), 0.6 (oph-19(0.6)), an ...199910583998
a novel protein-deamidating enzyme from chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil.a novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of chryseobacterium proteolyticum strain 9670(t) isolated from rice field soil in tsukuba, japan. the deamidating activities on carboxybenzoxy (cbz)-gln-gly and caseins and protease activity were produced synchronously by the isolate. both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-sepharose chromatography of the cult ...200010919788
phylogenetic characterization and in situ detection of a cytophaga-flexibacter-bacteroides phylogroup bacterium in tuber borchii vittad. ectomycorrhizal mycelium.mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. in this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus tuber borchii vittad. universal eubacterial primers specific for the 5' and 3' ends of the 16s rrna gene (16s rdna) were used for pcr ampli ...200011055961
phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the cariaco basin.microbial community samples were collected from the anoxic zone of the cariaco basin at depths of 320, 500, and 1,310 m on a november 1996 cruise and were used to construct 16s ribosomal dna libraries. of 60 nonchimeric sequences in the 320-m library, 56 belonged to the epsilon subdivision of the proteobacteria (epsilon-proteobacteria) and 53 were closely related to ectosymbionts of rimicaris exoculata and alvinella pompejana, which are referred to here as epsilon symbiont relatives (esr). the 5 ...200111282619
new degenerate cytophaga-flexibacter-bacteroides-specific 16s ribosomal dna-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon.river microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. in this study the bacterial diversity of river taff epilithon in south wales was investigated. a 16s ribosomal dna (rdna) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. the epilithon was found to be very diverse, with an estimated 59.6% of the bacteri ...200211772628
plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different verticillium host plants.to study the effect of plant species on the abundance and diversity of bacterial antagonists, the abundance, the phenotypic diversity, and the genotypic diversity of rhizobacteria isolated from potato, oilseed rape, and strawberry and from bulk soil which showed antagonistic activity towards the soilborne pathogen verticillium dahliae kleb. were analyzed. rhizosphere and soil samples were taken five times over two growing seasons in 1998 and 1999 from a randomized field trial. bacterial isolates ...200212089011
localisation of identical organophosphorus pesticide degrading (opd) genes on genetically dissimilar indigenous plasmids of soil bacteria: pcr amplification, cloning and sequencing of opd gene from flavobacterium balustinum.plasmid borne organophosphorus pesticide degrading (opd) gene of flavobacterium balustinum has been amplified using polymerase chain reaction (pcr) and the resulting pcr product (1.25 kb) was cloned in puc18. further, a detailed restriction map was determined to pcr product and subcloned as overlapping restriction fragments. the nucleotide sequence was determined for all subclones to obtain complete sequence of pcr amplified fragment. the sequence showed 98% similarity to opd genes cloned from o ...200212602326
transposon-like organization of the plasmid-borne organophosphate degradation (opd) gene cluster found in flavobacterium sp.several bacterial strains that can use organophosphate pesticides as a source of carbon have been isolated from soil samples collected from diverse geographical regions. all these organisms synthesize an enzyme called parathion hydrolase, and in each case the enzyme is encoded by a gene (opd) located on a large indigenous plasmid. these plasmids show considerable genetic diversity, but the region containing the opd gene is highly conserved. two opd plasmids, ppdl2 from flavobacterium sp. and pcm ...200312732518
kaistella koreensis gen. nov., sp. nov., a novel member of the chryseobacterium-bergeyella-riemerella branch.gram-negative, non-spore-forming, rod-shaped, yellow-pigmented bacteria isolated from a freshwater stream in korea were investigated to determine their taxonomic position. complete 16s rrna gene sequence analysis indicated that the organisms should be placed in the chryseobacterium-bergeyella-riemerella branch in the family flavobacteriaceae. phylogenetically, the strains were most closely related to chryseobacterium balustinum atcc 33487(t) and chryseobacterium scophthalmum lmg 13028(t) (94.3 a ...200415545478
characterization of bacteria that suppress rhizoctonia damping-off in bark compost media by analysis of fatty acid biomarkers.examination of cucumber roots (cucumis sativus l.) grown in bark compost media and of the surrounding edaphic substrate showed profiles of polar lipid fatty acids commonly found in bacteria. the composition of fatty acids in these profiles differed significantly between roots grown in a medium naturally suppressive to rhizoctonia damping-off and roots from a conducive medium. cucumber roots from the suppressive medium had higher proportions of cis-vaccenic acid (18:1 omega 7c) and the iso-branch ...198916347930
factors affecting the attachment of rhizospheric bacteria to bean and soybean roots.the plant rhizosphere is an important soil ecological environment for plant-microorganism interactions, which include colonization by a variety of microorganisms in and around the roots that may result in symbiotic, endophytic, associative, or parasitic relationships within the plant, depending on the type of microorganisms, soil nutrient status, and soil environment. rhizosphere competence may be attributable to the differences in the extent of bacterial attachment to the root surface. we prese ...200616684104
soonwooa buanensis gen. nov., sp. nov., a member of the family flavobacteriaceae isolated from seawater.a gram-negative, non-motile, non-gliding, strictly aerobic, pale yellow colony-forming, rod-shaped bacterial strain, designated hm0024(t), was isolated from coastal seawater of the yellow sea and subjected to a polyphasic taxonomy study. based on 16s rrna gene sequence similarities, strain hm0024(t) was most closely related to chryseobacterium balustinum lmg 8329(t) (94.4 %), chryseobacterium scophthalmum lmg 13028(t) (94.4 %), chryseobacterium piscium lmg 23089(t) (94.3 %) and elizabethkingia m ...201019819990
biodegradation of organophosphate pesticide chloropyrifos by egyptian bacterial isolates.sixteen microbial isolates capable of growing on dursban as a secondary substrate were isolated from three soil and sewage water samples collected from different localities polluted with pesticides. six developed isolates only were capable of biodegrading dursban and utilizing it as only sole source of carbon, energy and phosphorus. the six bacterial isolates were managed to grow on enrichment medium containing dursban up to 40 ml/liter, for seven days at 25 degrees c. each isolate exhibited gro ...200920218527
molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers.highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ...201426019546
systemic disease protection elicited by plant growth promoting rhizobacteria strains: relationship between metabolic responses, systemic disease protection, and biotic elicitors.a study of plant defensive systemic responses induced by three plant growth promoting rhizobacteria (pgpr) on arabidopsis thaliana col 0 against pseudomonas syringae pv. tomato dc3000 at the biochemical and transcriptional levels is reported in this paper. all three strains decreased disease severity when applied to a. thaliana prior to pathogen inoculation. at the biochemical level, each of the three strains induced ethylene (et) when incubated with 1-amino-cyclopropane-1-carboxylic acid, and s ...200818944194
biotechnology of cold-active proteases.the bulk of earth's biosphere is cold (<5 °c) and inhabited by psychrophiles. biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. proteinases as a class represent the largest category of industrial enzymes. there has been an emphasis on employing cold-active proteases in detergents because this allows laundry operations at ambient temperatures. proteases have been used in environment ...201324832807
dna-dna hybridization study of strains of chryseobacterium, elizabethkingia and empedobacter and of other usually indole-producing non-fermenters of cdc groups iic, iie, iih and iii, mostly from human clinical sources, and proposals of chryseobacterium bernardetii sp. nov., chryseobacterium carnis sp. nov., chryseobacterium lactis sp. nov., chryseobacterium nakagawai sp. nov. and chryseobacterium taklimakanense comb. nov.the taxonomic classification of 182 phenotypically similar isolates was evaluated using dna-dna hybridization and 16s rrna gene sequence analysis. these bacterial isolates were mainly derived from clinical sources; all were gram-negative non-fermenters and most were indole-producing. phenotypically, they resembled species from the genera chryseobacterium, elizabethkingia or empedobacter or belonged to cdc groups iic, iie, iih and iii. based on these analyses, four novel species are described: ch ...201323934253
emerging flavobacterial infections in fish: a review.flavobacterial diseases in fish are caused by multiple bacterial species within the family flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. in addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. the emergence of recent reports linking previously uncharacterized flavobacteria to syst ...201426257926
emerging flavobacterial infections in fish: a review.flavobacterial diseases in fish are caused by multiple bacterial species within the family flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. in addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. the emergence of recent reports linking previously uncharacterized flavobacteria to syst ...201426257926
the soil microbiota harbors a diversity of carbapenem-hydrolyzing β-lactamases of potential clinical relevance.the origin of carbapenem-hydrolyzing metallo-β-lactamases (mbls) acquired by clinical bacteria is largely unknown. we investigated the frequency, host range, diversity, and functionality of mbls in the soil microbiota. twenty-five soil samples of different types and geographical origins were analyzed by antimicrobial selective culture, followed by phenotypic testing and expression of mbl-encoding genes in escherichia coli, and whole-genome sequencing of mbl-producing strains was performed. carba ...201526482314
the soil microbiota harbors a diversity of carbapenem-hydrolyzing β-lactamases of potential clinical relevance.the origin of carbapenem-hydrolyzing metallo-β-lactamases (mbls) acquired by clinical bacteria is largely unknown. we investigated the frequency, host range, diversity, and functionality of mbls in the soil microbiota. twenty-five soil samples of different types and geographical origins were analyzed by antimicrobial selective culture, followed by phenotypic testing and expression of mbl-encoding genes in escherichia coli, and whole-genome sequencing of mbl-producing strains was performed. carba ...201526482314
noncontiguous finished genome sequence and description of weeksella massiliensis sp. nov.strain ff8(t) (= csur p860 = dsm 28259) was isolated in dakar, senegal, from the urine of a 65-year-old man with acute cystitis. this strain shows a similarity of sequence of 16s rrna of 98.38% with weeksella virosa, and its genbank accession numbers are hg931340 and ccmh00000000. matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. using a polyphasic study made of ph ...201526649182
chryseobacterium piscium sp. nov., isolated from fish of the south atlantic ocean off south africa.four isolates from freshly caught fish samples obtained from the south atlantic ocean off the south african coastline were shown to represent a novel species in the genus chryseobacterium by means of a polyphasic taxonomic study. the four isolates had virtually identical whole-cell protein profiles, fatty acid profiles and biochemical properties. analysis of the 16s rrna sequence of strain lmg 23089(t) revealed 99.3 and 98.9 % similarity to the 16s rrna sequences of the type strains of chryseoba ...200616738109
identification and characterization of repetitive extragenic palindromes (rep)-associated tyrosine transposases: implications for rep evolution and dynamics in bacterial genomes.bacterial repetitive extragenic palindromes (reps) compose a distinct group of genomic repeats. they usually occur in high abundance (>100 copies/genome) and are often arranged in composite repetitive structures - bacterial interspersed mosaic elements (bimes). in bimes, regularly spaced reps are present in alternating orientations. bimes and reps have been shown to serve as binding sites for several proteins and suggested to play role in chromosome organization and transcription termination. th ...201020085626
first isolation and characterization of chryseobacterium shigense from rainbow trout.there have been an increasing number of infections in fish associated with different species of chryseobacterium, being considered potentially emerging pathogens. nevertheless the knowledge of the diversity of species associated with fish disease is partial due to the problems for a correct identification at the species level based exclusively on phenotypic laboratory methods.201222676434
catalytic mechanisms for phosphotriesterases.phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. a wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (pte), methyl parathion hydrolase (mph), organophosphorus acid anhydrolase (opaa), diisopropylfluorophosphatase (dfp), and paraoxonase 1 (pon1). t ...201222561533
plant growth-promoting rhizobacteria and root system functioning.the rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. among the latter, plant growth-promoting rhizobacteria (pgpr) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. modification of root system architecture by pgpr implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development ...201324062756
pneumonia and meningitis caused by a new nonfermentative unknown gram-negative bacterium.seven isolates of an unclassified bacterium resembling flavobacterium spp. were characterized by growth requirements, microscopic examination, biochemical characteristics, antimicrobial susceptibility tests, protein profile analysis, and serologic data. the unclassified isolates were differentiated from flavobacterium meningosepticum, flavobacterium odoratum, flavobacterium balustinum, flavobacterium strain iib, chromobacterium violaceum, aquaspirillum serpens, and pseudomonas spp. the bacterium ...19892504766
catalytic mechanisms for phosphotriesterases.phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. a wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (pte), methyl parathion hydrolase (mph), organophosphorus acid anhydrolase (opaa), diisopropylfluorophosphatase (dfp), and paraoxonase 1 (pon1). t ...201222561533
natural rice rhizospheric microbes suppress rice blast infections.the natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. in rice (oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen magnaporthe oryzae. capitalizing on the abilities of naturally occurring rice soil bacteria to reduce m. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to ...201424884531
research progress on the use of plant allelopathy in agriculture and the physiological and ecological mechanisms of allelopathy.allelopathy is a common biological phenomenon by which one organism produces biochemicals that influence the growth, survival, development, and reproduction of other organisms. these biochemicals are known as allelochemicals and have beneficial or detrimental effects on target organisms. plant allelopathy is one of the modes of interaction between receptor and donor plants and may exert either positive effects (e.g., for agricultural management, such as weed control, crop protection, or crop re- ...201526635845
biochemical and molecular mechanisms of plant-microbe-metal interactions: relevance for phytoremediation.plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (pgpms), may alleviate metal phytotoxicity and stimulate p ...201627446148
root exudate-induced alterations in bacillus cereus cell wall contribute to root colonization and plant growth promotion.the outcome of an interaction between plant growth promoting rhizobacteria and plants may depend on the chemical composition of root exudates (res). we report the colonization of tobacco, and not groundnut, roots by a non-rhizospheric bacillus cereus (mtcc 430). there was a differential alteration in the cell wall components of b. cereus in response to the res from tobacco and groundnut. attenuated total reflectance infrared spectroscopy revealed a split in amide i region of b. cereus cells expo ...201324205213
phylum- and class-specific pcr primers for general microbial community analysis.amplification of a particular dna fragment from a mixture of organisms by pcr is a common first step in methods of examining microbial community structure. the use of group-specific primers in community dna profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. other uses for group-specific primers include quantitative pcr and library screening. the purpose of the present study was to develop several primer sets targeting commonly occ ...200516204538
pseudomonas fluorescens n21.4 metabolites enhance secondary metabolism isoflavones in soybean (glycine max) calli cultures.phytopharmaceuticals are plant secondary metabolites that are strongly inducible and especially sensitive to biotic changes. plant cell cultures are a good alternative to obtain secondary metabolites, in case effective stimulation can be achieved. in this study, metabolic elicitors from two rhizobacteria able to enhance isoflavone content in soybean seedlings were tested on three different soybean calli cell lines. results show that metabolic elicitors from chryseobacterium balustinum aur9 were ...201223039196
over-expression of parathion hydrolase of flavobacterium balustinum in e. coli: purification and characterization of his-tagged parathion hydrolase.the organophosphorus pesticide degrading (opd) gene was cloned downstream to the transcriptional and translational signals of expression vectors ptrc99a and pet32a. the resulting recombinant expression plasmids pnh2 and phh2 were introduced into e. coli jm105 and e. coli bl21 respectively. on induction the e. coli cells containing pnh2 produced high levels of parathion hydrolase. a 60 kd fusion protein was produced in e. coli cultures containing recombinant plasmid phh2. the molecular mass of th ...200222896893
chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.a gram-reaction-negative, non-motile and rod-shaped bacterium, designated as thg-dn3.6(t), was isolated from an ancient tree trunk from republic of korea. on the basis of 16s rrna gene sequence analysis, strain thg-dn3.6(t) was shown to belong to the genus chryseobacterium and the highest similarity to chryseobacterium indoltheticum lmg 4025(t) (97.2%) and the closest phylogenetic relatives were chryseobacterium scophthalmum (96.8%), chryseobacterium piscium (96.7%) and chryseobacterium balustin ...201526210236
microbe associated molecular patterns from rhizosphere bacteria trigger germination and papaver somniferum metabolism under greenhouse conditions.ten pgpr from different backgrounds were assayed on papaver somniferum var. madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (mamps) are able to trigger plant metabolism. first, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. then, the best three strains were tested for their ability to increase seedling growth ...201424296249
plasmid mediated organophosphate pesticide degradation by flavobacterium balustinum.a bacterium capable of degrading methyl parathion, an organophosphorus insecticide into paranitrophenol (as evidenced by tlc) and other metabolites, was isolated from the agricultural soils of anantapur district, andhra pradesh, india. this bacterium, identified as flavobacterium balustinum was found to harbour an indigenous plasmid of approximately 86 kb in size. the degradative enzyme, parathion hydrolase, was found to be encoded by this plasmid. no enzyme activity was observed in plasmid cure ...19957549962
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