Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.

Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa. Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes. Levels of DNA-DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and ß-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga, named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

High frequency of horizontal gene transfer in the oceans.

Oceanic bacteria perform many environmental functions, including biogeochemical cycling of many elements, metabolizing of greenhouse gases, functioning in oceanic food webs (microbial loop), and producing valuable natural products and viruses. We demonstrate that the widespread capability of marine bacteria to participate in horizontal gene transfer (HGT) in coastal and oceanic environments may be the result of gene transfer agents (GTAs), viral-like particles produced by α-Proteobacteria. We documented GTA-mediated gene transfer frequencies a thousand to a hundred million times higher than prior estimates of HGT in the oceans, with as high as 47% of the culturable natural microbial community confirmed as gene recipients. These findings suggest a plausible mechanism by which marine bacteria acquire novel traits, thus ensuring resilience in the face of environmental change.

Reproductive fitness and dietary choice behavior of the genetic model organism Caenorhabditis elegans under semi-natural conditions.

Laboratory breeding conditions of the model organism C. elegans do not correspond with the conditions in its natural soil habitat. To assess the consequences of the differences in environmental conditions, the effects of air composition, medium and bacterial food on reproductive fitness and/or dietary-choice behavior of C. elegans were investigated. The reproductive fitness of C. elegans was maximal under oxygen deficiency and not influenced by a high fractional share of carbon dioxide. In media approximating natural soil structure, reproductive fitness was much lower than in standard laboratory media. In seminatural media, the reproductive fitness of C. elegans was low with the standard laboratory food bacterium E. coli (γ-Proteobacteria), but significantly higher with C. arvensicola (Bacteroidetes) and B. tropica (ß-Proteobacteria) as food. Dietary-choice experiments in semi-natural media revealed a low preference of C. elegans for E. coli but significantly higher preferences for C. arvensicola and B. tropica (among other bacteria). Dietary-choice experiments under quasi-natural conditions, which were feasible by fluorescence in situ hybridization (FISH) of bacteria, showed a high preference of C. elegans for Cytophaga-Flexibacter-Bacteroides, Firmicutes, and ß-Proteobacteria, but a low preference for γ-Proteobacteria. The results show that data on C. elegans under standard laboratory conditions have to be carefully interpreted with respect to their biological significance.

Reclassification of Flexibacter tractuosus (Lewin 1969) Leadbetter 1974 and 'Microscilla sericea' Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov.

The taxonomic position of the misclassified strains [Flexibacter] tractuosus KCTC 2958T and '[Microscilla] sericea' LMG 13021 was studied using a polyphasic approach. The two strains shared 99.1% 16S rRNA gene sequence similarity and 28% DNA-DNA relatedness. On the basis of the phylogenetic evidence supported by genotypic and phenotypic data [Flexibacter] tractuosus KCTC 2958T and '[Microscilla] sericea' LMG 13021 are classified as two distinct species in a novel genus, Marivirga, in the family 'Flammeovirgaceae', as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov., with strains KCTC 2958T (=ATCC 23168T =CIP 106410T =DSM 4126T =NBRC 15989T =NCIMB 1408T =VKM B-1430T) and LMG 13021T (=ATCC 23182T =NBRC 15983T =NCIMB 1403T), respectively, as the type strains. The type species is Marivirga tractuosa.

Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov.

A Gram-negative, rod-shaped, non-spore-forming bacterium, designated strain R2A36-4T, was isolated from greenhouse soil and subjected to a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Sphingobacteriaceae. Its nearest phylogenetic neighbour was the type strain of [Flexibacter] canadensis CIP 104802T (93.2% 16S rRNA gene sequence similarity). Strain R2A36-4T and [F.] canadensis CIP 104802T fell in a distinct cluster within the family Sphingobacteriaceae. Strain R2A36-4T contained MK-7 as the predominant quinone. Strain R2A36-4T and [F.] canadensis CIP 104802T had iso-C15:0, iso-C17:0 3-OH, summed feature 3 and C15:1omega6c as the major fatty acids. Strain R2A36-4T could be distinguished from [F.] canadensis on the basis of several physiological properties and fatty acid compositions. Based on phenotypic characterization and 16S rRNA gene sequence analysis, strain R2A36-4T represents a novel species within a new genus, for which the name Solitalea koreensis gen. nov., sp. nov. is proposed. The type strain of Solitalea koreensis is strain R2A36-4T (=KACC 12953T=DSM 21342T). It is also proposed that [F.] canadensis be transferred to this genus as Solitalea canadensis comb. nov. (type strain UASM 9DT=ATCC 29591T=CIP 104802T=DSM 3403T=NBRC 15130T=JCM 21819T=KACC 13276T=LMG 8368T).

Flavobacterium psychrophilum y su patología en alevines de Onchorhynchus mykiss del centro piscícola El Ingenio, Huancayo / Flavobacterium psychrophilum and its pathology in alevins of Onchorhynchus

En el presente trabajo se reporta la presencia de Flavobacterium psychrophilum, como agente causante de la patología “enfermedad bacteriana del agua fría” en alevines de Onchorhynchus mykiss “trucha arco iris”del Centro Piscícola El Ingenio, Junín (3250 m de altitud). La lesión macroscópica externa más frecuente fue la ulceración profunda de la región dorsal del pez acompañado de un ennegrecimiento localizado de la piel. Internamente se observó una marcada esplenomegalia, palidez del hígado, riñón y branquias, inflamación del intestino y acumulación de líquido ascítico en el peritoneo. No se detectó hemorragia interna. En Agar Cytophaga Modificado (ACM) según Anaker & Ordal (1959) fueron aisladas inicialmente 29 Gram negativas, de las cuales según la caracterización fenotípica y pruebas bioquímicas 9 fueron consideradas como F. psychrophilum. Pruebas de susceptibilidad antibiótica mostraron alta sensibilidad de las cepas a Gentamicina, Ceftazidina, oxitetraciclina, Norfloxacina, furazolidona, Ciprofloxacina y Cefoxitina.

The present paper reports the presence of Flavobacterium psychrophilum such as pathological agent of "bacterial disease of cold water" on juvenile Onchorhynchus mykiss "rainbow trout" from El Ingenio fish farm,Junín (3250 m). The ulceration of the dorsal area was the most frequent macroscopic external injury as well the localized blackening of the skin. Internally there was a marked splenomegaly, pallor of the liver, kidney and gills, inflammation of the intestine and ascitic fluid in the peritoneum. Internal hemorrhage was not detected. 29 strain Gram negative were isolated in Modified Cytophaga Agar (MCA) (Anaker & Ordal, 1959), which according to the phenotypic characterization and the biochemical tests 9 were considered as F. psychrophilum. Tests of antibiotic susceptibility showed high sensitivity of this strains to Gentamicin, Ceftazidine, oxytetracycline, Norfloxacine, furazolidone, Ciprofloxacine and Cefoxitine.

The effect of starvation stress on the protein profiles in Flexibacter chinensis.

BACKGROUND: Analysis of many proteins produced during the transition into the stationary phase and under stress conditions (including starvation stress) demonstrated that a number of novel proteins were induced in common to each stress and could be the reason for cross-protection in bacterial cells. It is necessary to investigate the synthesis of these proteins during different stress conditions. METHODS: The changes in protein profile of Flexibacter chinensis at various stages of the starvation process and the other stresses were investigated using two-dimensional gel electrophoresis which has proven to be a powerful tool for investigation of the changes in protein profiles under such conditions. RESULTS: Most starvation proteins were synthesized during the early stationary phase and many of these proteins remained during long-term starvation. Some of these proteins were transiently synthesized. The sequencing result of one of the proteins showed that there was a 62.5% identity in 8 amino acids overlapped with the 5' residue of a 10 kDa chaperon protein which is known to be involved in the starvation stress response in other organisms. CONCLUSION: There are many proteins synthesized in common with many stresses in Flexibacter chinensis. Some of these proteins must play a major role in the stability of the cell under different stresses.

Effect of an acute necrotic bacterial gill infection and feed deprivation on the metabolic rate of Atlantic salmon Salmo salar.

In this study, experiments were conducted to examine the effect of an acute necrotic bacterial gill infection on the metabolic rate (M(O2)) of Atlantic salmon Salmo salar. Fed and unfed Atlantic salmon smolts were exposed to a high concentration (5 x 10(12) CFU ml(-1)) of the bacteria Tenacibaculum maritimum, their routine and maximum metabolic rates (M(O2rout) and M(O2max), respectively) were measured, and relative metabolic scope determined. A significant decrease in metabolic scope was found for both fed and unfed infected groups. Fed infected fish had a mean +/- standard error of the mean (SEM) decrease of 2.21 +/- 0.97 microM O2 g(-1) h(-1), whilst unfed fish a mean +/- SEM decrease of 3.16 +/- 1.29 microM O2 g(-1) h(-1). The decrease in metabolic scope was a result of significantly increased M(O2rout) of both fed and unfed infected salmon. Fed infected fish had a mean +/- SEM increase in M(O2rout) of 1.86 +/- 0.66 microM O2 g(-1) h(-1), whilst unfed infected fish had a mean +/- SEM increase of 2.16 +/- 0.72 microM O2 g(-1) h(-1). Interestingly, all groups maintained M(O2max) regardless of infection status. Increases in M(O2rout) corresponded to a significant increase in blood plasma osmolality. A decrease in metabolic scope has implications for how individuals allocate energy; fish with smaller metabolic scope will have less energy to allocate to functions such as growth, reproduction and immune response, which may adversely affect the efficiency of fish growth.

Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm.

A novel, strictly aerobic, heterotrophic, gliding, Gram-negative, oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6220(T), was isolated from seawater and studied by using a polyphasic taxonomic approach. The DNA G+C content of strain KMM 6220(T) was 59.9 mol%. The predominant fatty acids were iso-C(15 : 1), iso-C(15 : 0), iso-C(15 : 0) 3-OH, iso-C(17 : 0) 3-OH and C(16 : 1)omega7/iso-C(15 : 0) 2-OH. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain KMM 6220(T) formed a cluster with the misclassified strains [Flexibacter] aggregans NBRC 15974 and [Flexibacter] tractuosus NBRC 16035 and with the type strains of Reichenbachiella agariperforans and Roseivirga ehrenbergii with levels of similarity of 95.9, 94.4, 92.0 and 91.8 %, respectively. On the basis of its phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain KMM 6220(T) is considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Fulvivirga kasyanovii gen. nov., sp. nov. is proposed. The type strain of the type species is KMM 6220(T) (=CCTCC AB 206119(T)=KCTC 12832(T)).

Reclassification of Flexibacter aggregans (Lewin 1969) Leadbetter 1974 as a later heterotypic synonym of Flexithrix dorotheae Lewin 1970.

The taxonomic relationship between [Flexibacter] aggregans IAM 14894(T) and Flexithrix dorotheae NBRC 15987(T) was investigated by means of DNA-DNA hybridization and phenotypic characteristics. On the basis of these results, it is proposed that Flexibacter aggregans (Lewin 1969) Leadbetter 1974 be considered a later heterotypic synonym of Flexithrix dorotheae Lewin 1970. Emended descriptions of the species Flexithrix dorotheae and the genus Flexithrix are also given.

Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.

Analysis of the 16S rRNA gene sequences of species currently assigned to the genus Flexibacter has shown extensive intrageneric phylogenetic heterogeneity. It has been shown in previous studies that the species [Flexibacter] sancti, [Flexibacter] filiformis and [Flexibacter] japonensis were most closely related to Chitinophaga pinensis. In addition, [Cytophaga] arvensicola and species of the genus Terrimonas also clustered into this phylogenetic group. Although the similarities of 16S rRNA gene sequences were low (88.5-96.4 %), there is no evidence for clear phenotypic differences between these organisms that justify assignment to different genera. A proposal is made to transfer these species to the genus Chitinophaga as Chitinophaga sancti comb. nov., Chitinophaga filiformis comb. nov., Chitinophaga japonenis comb. nov. and Chitinophaga arvensicola comb. nov. on the basis of phylogenetic and phenotypic data. Furthermore, a novel species is described within this genus, Chitinophaga skermanii sp. nov., with strain CC-SG1B(T) (=CCUG 52510(T)=CIP 109140(T)) as the type strain.

Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator.

A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum 'Bacteroidetes'; its nearest neighbour was Spirosoma linguale (88.8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (= NCIMB 14103T) as the type strain.

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium.

A microbial consortium (AM) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (PAH) mixture of three- and four-ringed PAHs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (DGGE), and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and seven by both DGGE and clone libraries were obtained. The comparison of three variable regions (V3-V5) of the 16S rRNA gene between the sequences obtained yielded 19 different microbial components. Proteobacteria were the dominant group, representing 83% of the total, while the Cytophaga-Flexibacter-Bacteroides group (CFB) was 11% and the Ascomycota fungi 6%. Beta-proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences were achieved by the cultivation method that showed members of the alpha-, beta-, and gamma-Proteobacteria; CFB bacterial group; and Ascomycota fungi. Only six of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1), which were similar to Sphingomonas sp. and Fusarium sp., respectively, achieved the greatest PAH depletion. The results indicate that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium.

Modifications to the fathead minnow (Pimephales promelas) chronic test method to remove mortality due to pathogenic organisms.

Whole effluent toxicity testing is used to evaluate the discharge of materials that may be harmful to indigenous aquatic life. Unlike most environmental analyses, receiving water (the water body into which the effluent is discharged) often is used as dilution water in whole effluent toxicity tests to simulate the aquatic environment into which the effluent is introduced. In approximately 26% of whole effluent toxicity tests conducted by Wisconsin (USA) certified labs between 1988 and 1998, a pathogenic effect caused failure of the receiving water controls during the fathead minnow chronic test (i.e., > 20% mortality). We performed microbiological work to isolate pathogenic organisms from receiving waters, the fish, and their food. We found pathogenic organisms such as Flexibacter columnaris, Aeromonas hydrophila, and Flavobacter spp. to be ubiquitous and were not able to remove them from the test (e.g., through decontamination of the fish food and carefully following sterility procedures). To eliminate the pathogenic effect, we evaluated manipulations of the sample and the test method including filtering receiving water, irradiating receiving water, using older fish (48 h), using clean test beakers each day of the test, and using smaller test beakers (30 ml) with two fish per beaker. In samples demonstrating the pathogenic effect, most of these manipulations significantly reduced mortality. The use of smaller tests cups was significantly better at reducing the effect than all of the other sample and method manipulations. These results indicate that a simple method modification to the fathead minnow chronic test will improve test reliability when diluting effluents with receiving waters.