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PubMed2004

Comparison of the API 20E and BBL Crystal E/NF identification systems for differentiating bacterial isolates from apparently healthy reared sea bass (Dicentrarchus labrax).

The ability of two commercial rapid identification systems, API 20E and BBL Crystal E/NF, to reliably identify bacterial isolates from the internal organs of reared sea bass were compared. The tests gave different results: API 20E identified bacteria as Pseudomonas spp. with 37% accuracy, while BBL Crystal E/NF identified them as Flavobacterium odoratum with 99% accuracy. Although F. odoratum is not a marine fish pathogen, conventional tests conducted with the same isolates were more indicative of them being Flavobacterium spp. than Pseudomonas spp., suggesting that BBL Crystal E/NF was more reliable in this identification. Both systems were found to be applicable for diagnostics of marine fish pathogens, but should be used with caution because of possible misinterpretation.

Animals↗

PubMedDate not supplied

Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers.

Flavobacterium sp. KI72 metabolizes 6-aminohexanoic acid cyclic dimer, a by-product of nylon manufacture, through two newly evolved enzymes, 6-aminohexanoic acid cyclic dimer hydrolase (EI) and 6-aminohexanoic acid linear oligomer hydrolase (EII). These enzymes are active towards man-made compounds, the cyclic dimer and linear oligomers of 6-aminohexanoic acid respectively, but not towards any of the natural amide bonds tested. The structural genes of EI (nylA) and EII (nylB) are encoded on pOAD2, one of three plasmids harboured in Flavobacterium sp. KI72. This plasmid contains two kinds of repeated sequence (RS-I and RS-II); one of the two RS-II sequences, RS-IIA, contains the nylB gene, while the other, RS-IIB, contains a homologous nylB' gene. From comparisons of the nucleotide sequences and gene products of the nylB and nylB' genes, we now conclude that EII enzyme is newly evolved by gene duplication followed by base substitutions on the same plasmid.

Amidohydrolases↗

PubMed1999

Influence of carbon and nitrogen sources on Flavobacteriumgrowth and zeaxanthin biosynthesis.

Growth and production of zeaxanthin by Flavobacterium sp were studied using different carbon and nitrogen sources in a chemically defined medium. The best growth was supported by sucrose, but glucose yielded similar carotenoid concentrations. Both asparagine and glutamine stimulated growth and pigment formation. Carotenoid production and glucose consumption increased as a function of asparagine concentration. In the presence of asparagine, high glucose concentrations decreased pigment production without affecting biomass formation. In the absence of glucose, asparagine could not support growth and zeaxanthin production. When compared to the effect of 55 mM glucose, 10 mM oxaloacetate increased growth and carotenoid production. Pyruvate and other intermediates of the citric acid cycle showed a similar stimulatory effect. The intermediates of glycolysis: glucose 6-phosphate and fructose 1,6-diphosphate did not support growth. These results suggest that Flavobacterium sp utilizes asparagine primarily as a nitrogen source for growth and production of zeaxanthin.

Ammonia↗

PubMed1969

A bacterium capable of using phytol as its sole carbon source, isolated from algal sediment of Mud Lake, Florida.

A species of Flavobacterium that consistently attacks pure phytol and can use it as a sole source of carbon has been isolated from the blue-green algal sediment of Mud Lake, Florida. Biochemical tests demonstrate that this bacterium also readily uses various other organic compounds. This bacterium may account for the degradation products of chlorophyll and its side chain phytol, which have been found in the Mud Lake algal sediment. Phytol and its degradation products play a role in Refsum's disease, but phytol is also the most promising precursor of the isoprenoid hydrocarbons found in oil shale of the Green River Formation (Eocene) of Colorado, Utah, and Wyoming. The discovery of this species of Flavobacterium is a significant product of a protracted study of the bacteriology, phycology, zoology, and geochemistry of the algal sediment forming in Mud Lake, which is believed to be a modern analogue of the kind of algal sediment that, through geologic time, became oil shale.

Chlorophyll↗

PubMed1993

Prolyl endopeptidase from Aeromonas hydrophila: cloning, sequencing, and expression of the enzyme gene, and characterization of the expressed enzyme.

A strain of Aeromonas hydrophila was found to show prolyl endopeptidase activity. The enzyme gene was cloned and expressed in Escherichia coli JM83. A 12 kbp EcoRI fragment containing the enzyme gene was subcloned at the HincII site of pUC19 to construct plasmid pAPEP-3 with a 3.5 kbp insert. E. coli JM83 transformed with this plasmid showed about 100-fold higher activity than the parent Aeromonas. Analysis of the nucleotide sequence of the insert revealed that the mature enzyme-encoding sequence starts just after the ATG initiation codon of the open reading frame. The enzyme was a single polypeptide composed of 689 amino acid residues with a molecular weight of 76,383. It showed properties very similar to those of Flavobacterium prolyl endopeptidase, except that the isoelectric point was 5.5. The amino acid sequence was 56 and 41% homologous to those of Flavobacterium and porcine brain prolyl endopeptidases, respectively. From a survey of sequence homology with other members of the prolyl endopeptidase family, the amino acid residues involved in the catalytic triad were deduced to be Ser-537, His-656, and Asp-512 (or Asp-621).

Aeromonas hydrophila↗

PubMed1976

Action of chondroitinases. I. The mode of action of two chondroitinase-AC preparations of different origin.

The modes of action of two chondroitinases-AC [EC 4.2.2.5] from Arthrobacter aurescens and Flavobacterium heparinum were examined. By comparison of the increase of viscosity and by analyses of digests using paper chromatography and gel filtration, it was shown that the Arthrobacter enzyme (A-Chase) degrades the substrate by a stepwise attack, while the Flavobacterium enzyme (F-Chase) exhibits a more random attack, though the first attack of both enzymes is of endo-type. Further study was carried out of the initial rate and final extent of the enzymic degradation of various mucopolysaccharides. The order of the initial rates at which the native mucopolysaccharides are degraded was similar for both enzymes. For A-Chase, the initial rate and final extent of degradation of modified chondroitin sulfate C or chondroitin methyl ester, however, were low compared with those of F-Chase. These results also suggested that A-Chase degrades the substrate by stepwise attack and F-Chase by random attack.

Arthrobacter↗

PubMed1989

The taxonomic relationship of certain environmental flavobacteria to the genus Weeksella.

Forty environmental strains and reference cultures of Flavobacterium, Cytophaga and Weeksella spp. were examined by numerical taxonomy. Twenty-seven strains were recovered in four phena. Phena 1A and 1B comprised 48% of the strains and were sufficiently similar to the genus Weeksella as to suggest possible inclusion in this genus. They could not be accommodated in the existing species W. virosa and W. zoohelcum. Strains from phenon 2 appear to belong neither in the Flavobacterium or the Weeksella genus. Although no reference strains were included in phena 3 and 4 they appear phenotypically to be most similar to F. breve and F. odoratum respectively.

Animals↗

PubMed2005

The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization.

This study describes the microbial community structure of three sandy sediment stations that differed with respect to median grain size and permeability in the German Bight of the Southern North Sea. The microbial community was investigated using lipid biomarker analyses and fluorescence in situ hybridization. For further characterization we determined the stable carbon isotope composition of the biomarkers. Biomarkers identified belong to different bacterial groups such as members of the Cytophaga-Flavobacterium cluster and sulfate-reducing bacteria (SRB). To support these findings, investigations using different fluorescent in situ hybridization probes were performed, specifically targeting Cytophaga-Flavobacterium, gamma-Proteobacteria and different members of the SRB. Depth profiles of bacterial fatty acid relative abundances revealed elevated subsurface peaks for the fine sediment, whereas at the other sandy sediment stations the concentrations were less variable with depth. Although oxygen penetrates deeper into the coarser and more permeable sediments, the SRB biomarkers are similarly abundant, indicating suboxic to anoxic niches in these environments. We detected SRB in all sediment types as well as in the surface and at greater depth, which suggests that SRB play a more important role in oxygenated marine sediments than previously thought.

Anaerobiosis↗

PubMed1987

Degradation of chlorinated phenols by a pentachlorophenol-degrading bacterium.

A pentachlorophenol (PCP)-degrading Flavobacterium sp. was tested for its ability to dechlorinate other chlorinated phenols by using resting cells that had been grown in the presence or absence of PCP. Phenols with chlorine atoms at positions 2 and 6 of the phenol ring were dechlorinated completely by PCP-induced cells. Other chlorinated phenols were not significantly mineralized. When PCP was added to a culture growing on L-glutamate, there was a lag period before the start of PCP degradation. When similar cells were treated with chloramphenicol prior to the addition of PCP, they did not degrade added PCP, even after prolonged incubations. Thus, the enzymes necessary for PCP degradation appeared to be inducible. Suspensions of cells grown in the presence of 2,4,6-trichlorophenol or 2,3,5,6-tetrachlorophenol did not show a lag period for mineralization of PCP, 2,4,6-trichlorophenol, or 2,3,5,6-tetrachlorophenol, indicating that one enzyme system probably was induced for the biodegradation of all three compounds. Nondegradable chlorophenols were toxic toward the Flavobacterium sp., probably acting as uncouplers of oxidative phosphorylation.

Biodegradation, Environmental↗

PubMed1989

Purification and characterization of three parathion hydrolases from gram-negative bacterial strains.

Three unique parathion hydrolases were purified from gram-negative bacterial isolates and characterized. All three purified enzymes had roughly comparable affinities for ethyl parathion and had broad temperature optima at ca. 40 degrees C. The membrane-bound hydrolase of Flavobacterium sp. strain ATCC 27551 was composed of a single subunit of approximately 35,000 daltons (Da) and was inhibited by sulfhydryl reagents such as dithiothreitol (DTT) and by metal salts such as CuCl2. The cytosolic hydrolase of strain B-1 was composed of a single subunit of approximately 43,000 Da and was stimulated by DTT and inhibited by CuCl2. The membrane-bound hydrolase of strain SC was composed of four identical subunits of 67,000 Da and was inhibited by DTT and stimulated by CuCl2. The substrate ranges of the three enzymes also differed, as evidenced by their relative affinities for parathion and the related organophosphate insecticide O-ethyl-O-4-nitrophenyl phenylphosphonothioate (EPN). The B-1 hydrolase displayed equal affinity for both compounds, the Flavobacterium enzyme showed twofold-lower affinity for EPN than for parathion, and the SC hydrolase displayed no activity toward EPN. The range in characteristics of these three enzymes can be exploited in different waste disposal strategies.

Aryldialkylphosphatase↗

PubMed1999

Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ.

We propose a novel method for studying the function of specific microbial groups in situ. Since natural microbial communities are dynamic both in composition and in activities, we argue that the microbial "black box" should not be regarded as homogeneous. Our technique breaks down this black box with group-specific fluorescent 16S rRNA probes and simultaneously determines 3H-substrate uptake by each of the subgroups present via microautoradiography (MAR). Total direct counting, fluorescent in situ hybridization, and MAR are combined on a single slide to determine (i) the percentages of different subgroups in a community, (ii) the percentage of total cells in a community that take up a radioactively labeled substance, and (iii) the distribution of uptake within each subgroup. The method was verified with pure cultures. In addition, in situ uptake by members of the alpha subdivision of the class Proteobacteria (alpha-Proteobacteria) and of the Cytophaga-Flavobacterium group obtained off the California coast and labeled with fluorescent oligonucleotide probes for these subgroups showed that not only do these organisms account for a large portion of the picoplankton community in the sample examined ( approximately 60% of the universal probe-labeled cells and approximately 50% of the total direct counts), but they also are significant in the uptake of dissolved amino acids in situ. Nearly 90% of the total cells and 80% of the cells belonging to the alpha-Proteobacteria and Cytophaga-Flavobacterium groups were detectable as active organisms in amino acid uptake tests. We suggest a name for our triple-labeling technique, substrate-tracking autoradiographic fluorescent in situ hybridization (STARFISH), which should aid in the "dissection" of microbial communities by type and function.

Animals↗

PubMed2003

Diversity and abundance of uncultured cytophaga-like bacteria in the Delaware estuary.

The Cytophaga-Flavobacterium group is known to be abundant in aquatic ecosystems and to have a potentially unique role in the utilization of organic material. However, relatively little is known about the diversity and abundance of uncultured members of this bacterial group, in part because they are underrepresented in clone libraries of 16S rRNA genes. To circumvent a suspected bias in PCR, a primer set was designed to amplify 16S rRNA genes from the Cytophaga-Flavobacterium group and was used to construct a library of these genes from the Delaware Estuary. This library had several novel Cytophaga-like 16S rRNA genes, of which about 40% could be grouped together into two clusters (DE clusters 1 and 2) defined by sequences initially observed only in the Delaware library; the other 16S rRNA genes were classified into an additional four clades containing sequences from other environments. An oligonucleotide probe was designed for the cluster with the most clones (DE cluster 2) and was used in fluorescence in situ hybridization assays. Bacteria in DE cluster 2 accounted for about 10% of the total prokaryotic abundance in the Delaware Estuary and in a depth profile of the Chukchi Sea (Arctic Ocean). The presence of DE cluster 2 in the Arctic Ocean was confirmed by results from 16S rRNA clone libraries. The contribution of this cluster to the total bacterial biomass is probably larger than is indicated by the abundance of its members, because the average cell volume of bacteria in DE cluster 2 was larger than those of other bacteria and prokaryotes in the Delaware Estuary and Chukchi Sea. DE cluster 2 may be one of the more abundant bacterial groups in the Delaware Estuary and possibly other marine environments.

Cytophaga↗

PubMed1975

Chondroitinase-producing bacteria in natural habitats.

A search was undertaken for bacteria which degrade chondroitin sulfate in nature and to find bacteria with a usefully high rate of chondroitinase (ChSase) productivity. First, 253 ChSase-producing bacteria were obtained from aquatic and land environments in Japan by aerobic and anaerobic screening methods. Identification according to Bergey's Manual of Determinative Bacteriology or Bain and Shewan (1968) permitted assignment of the majority of the isolates to seven genera, Aeromonas, Vibrio, Flavobacterium, Beneckea, Proteus, Micrococcus, and Arthrobacter. Next, ChSase productivities of all the isolates were compared with those of two established ChSase-producing stock strains, Proteus vulgaris NCTC 4636 and Flavobacterium heparinum ATCC 13125. As a result, special attention was given to production by a strain of Aeromonas sp. of large quantities of extracellular ChSase-AC. None of the isolates from the current study displayed significant ChSase-ABC productivity. Finally, ChSase-AC was prepared from the culture fluid of the Aeromonas strain by fractional precipitation with ammonium sulfate, chromatography on phospho-cellulose and diethylaminoethyl-cellulose, and gel filtration on Sephadex G-200. It was concluded that the Aeromonas strain may represent a profitable source of the enzyme ChSase-AC.

Aerobiosis↗

PubMed1976

Serum bactericidal activity in the horseshoe crab, Limulus polyphemus.

Serum from the horseshoe crab, Limulus polyphemus, was examined for bactericidal activity against five species of bacteria. Greatest activity was found against Pseudomonas putida and Flavobacterium sp.; with the former, serum dilutions as high as 1:20 were capable of reducing viable counts by 50% within 2 h. Bactericidal activity of a significantly lesser magnitude was demonstrated against Serratia marcesencs and Salmonella minnesota. No killing was seen when the lobster pathogen Aerococcus viridans (formerly Gaffkya homari) was used. The cidal activity against Flavobacterium sp. remained relatively consistent for 6 months.

Animals↗

PubMed1984

DNA-DNA hybridization analysis of nylon oligomer-degradative plasmid pOAD2: identification of the DNA region analogous to the nylon oligomer degradation gene.

Fine structure of the gene of 6-aminohexanoic acid cyclic dimer hydrolase, one of the enzymes responsible for the degradation of the nylon oligomer (6-aminohexanoic acid cyclic dimer), on the plasmid pOAD2 harbored in Flavobacterium sp. KI72 was determined by constructing miniplasmids from plasmid pNDH5 (a hybrid plasmid consisting of pBR322 and a 9.1-kilobase-pair HindIII fragment of pOAD2 ). The 6-aminohexanoic acid cyclic dimer hydrolase produced by cells of Escherichia coli C600 harboring pNDH5 or its miniplasmid was examined immunologically and electrophoretically and was found to be identical to that of Flavobacterium sp. KI72 . A fragment of pOAD2 (17.2- to 19.1-kilobase-pair region on pOAD2 ) was detected as hybridized fragment by Southern blotting experiments, indicating the presence of the DNA region analogous to the 6-aminohexanoic acid cyclic dimer hydrolase gene on the plasmid.

Amidohydrolases↗

PubMed1975

A cluster analysis of some bacteria in the water column of Green Lake, Washington.

Mass inoculation and computer clustering techniques were used in an abbreviated procedure to group similar bacteria isolated from four depths in the water column of Green Lake, Washington. Four groups of bacteria were differentiable and were catagorized as orange-yellow Flavobacterium-Cytophaga, yellow Flavobacterium-Cytophaga, Vibrio-Aeromonas-, and Pseudomonas-like. Some of the groups were most prevalent in certain sample depths in the water column.

Aeromonas↗

PubMed1977

The history, biology, and taxonomy of the Cytophaga group.

The first section of this review covers the important characteristics of the genera Cytophaga and Sporocytophaga. The topics discussed include vegetative cell structure, the spreading habit, and degradation of macromolecules. A historical account of these two genera follows, together with a discussion on the definition of, and species differentiation with the genus Cytophaga, and on the taxonomy of Sporocytophaga. The third section deals with the relationships of the cytophagas with the flavobacteria and includes a brief history of Flavobacterium, reassignation of some species to Cytophaga, differentiation from Cytophaga, and a discussion on the definition of the genus Flavobacterium. This is followed by a section dealing with the relationship of Cytophaga with the flexibacteria, starting with an introduction to the diversity of flexing organisms and taxonomic developments, and proceeding with the differentiation within the family Cytophagaceae, and species differentiation in Flexibacter. The concluding section includes a proposed redefinition of Cytophaga, a proposal regarding species conservation in this genus, and discussions on the relationship between the cytophagas and the myxobacteria and on the significance of cytophagas in the environment. The characteristics of all described species of Cytophaga, Flexibacter, and relevant flavobacteria are tabulated and a bibliography is presented.

Bacteriology↗

PubMed2005

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals.

Bacterial diversity was assessed in water samples collected from several uranium mining wastes in Ger many and in the United States by using 16S rDNA and ribosomal intergenic spacer amplification retrievals. The results obtained using the 16S rDNA retrieval showed that the samples collected from the uranium mill tailings of Schlema/Alberoda, Germany, were predominated by Nitrospina-like bacteria, whereas those from the mill tailings of Shiprock, New Mexico, USA, were predominated by gamma-Pseudomonas and Frauteria spp. Additional smaller populations of the Cytophaga-Flavobacterium-Bacteroides group and alpha- and delta-Proteobacteria were identified in the Shiprock samples as well. Proteobacteria and Cytophaga-Flavobacterium-Bacteroides were also found in the third uranium mill tailings studied, Gittersee/Coschütz, Germany, but the groups of the predominant clones were rather small. Most of the clones of the Gittersee/Coschütz samples represented individual sequences, which indicates a high level of bacterial diversity. The samples from the fourth uranium waste studied, Steinsee Deponie B1, Germany, were predominantly occupied by Acinetobacter spp. The ribosomal intergenic spacer amplification retrieval provided results complementary to those obtained by the 16S rDNA analyses. For instance, in the Shiprock samples, an additional predominant bacterial group was identified and affiliated with Nitrosomonas sp., whereas in the Gittersee/Coschütz samples, anammox populations were identified that were not retrieved by the applied 16S rDNA approach.

Bacteria↗