M Suzuki, Y Nakagawa, S Harayama and S Yamamoto
Marine Biotechnology Institute, Kamaishi Laboratories, Kamaishi, Iwate 026-0001, Japan
Bacterial strains were isolated from sponge and green algae ...which were
collected on the coast of Japan and Palau. The phylogenetic relationships
of these isolates among marine species of the
Cytophaga--Flavobacterium--Bacteroides complex were analysed by using their
gyrB nucleotide sequences and translated peptide sequences (GyrB) in
addition to 16S rDNA sequences. These isolates were closely related to the
previously characterized marine Flexibacter species, Flexibacter
maritimus and Flexibacter ovolyticus. These Flexibacter species are
distantly related to Flexibacter flexilis, the type species of the genus
Flexibacter, and phylogenetically belong to the family Flavobacteriaceae
(according to analysis using both 16S rDNA and GyrB sequences). Their
phylogenetic, chemotaxonomic and phenotypic characteristics prompted the
proposal that these two species should be transferred to the new genus
Tenacibaculum, as Tenacibaculum maritimum and Tenacibaculum ovolyticum,
respectively. Two additional new species of the genus Tenacibaculum,
Tenacibaculum mesophilum gen. nov., sp. nov. (=MBIC 1140(T)=IFO 16307(T))
and Tenacibaculum amylolyticum gen. nov., sp. nov. (=MBIC 4355(T)= IFO
16310(T)), which were isolated from sponges and macro-algae, are also
reported. For taxonomic considerations at the species level, the resolution
of gyrB sequences was superior to that of 16S rDNA sequences, and the
grouping based on the gyrB phylogram was consistent with DNA--DNA
hybridization results.
Many polycyclic aromatic hydrocarbons (PAHs) are known to be mutagenic or carcinogenic, and their contamination in soil and aquifer is of great environmental concern. Limited numbers of ...microorganisms including mycobacteria,
Sphingomonas and white rot fungi were found to be capable of degrading PAHs with four or more fused aromatic rings. In white rot fungi, lignin peroxidases are believed to be involved in the degradation of PAHs. In addition to these enzymes, P450 monooxygenases in some fungi were implicated in the degradation of PAHs. The stimulation of PAH biodegradation by the addition of surfactants was observed with some of these microorganisms although the agents were inhibitory on biodegradation with some other microorganisms. Mathematical models were constructed to explain the effect of surfactants on biodegradation. Further studies should be carried out to select the best microorganisms and surfactants for applications to PAH bioremediation.
Microorganisms form biofilms on various surfaces in different environments and cause diverse problems such as biofouling and biocorrosion. Biofilm formation includes at least three steps: initial ...adhesion, colonisation, and development. In this study, we enriched bacterial populations capable of adhering to a metallic iron surface. The community structure of the enriched populations differed from the structures of those without enrichment. From the enriched populations, we isolated six strains capable of adhering to the surface of metallic iron. A Marinobacter hydrocarbonoclasticus strain M1 showed the highest adhesion rate of approximately 4×10
6
cells cm
−2
min
−1
. Atomic force microscopy showed that a high density monolayer of cells was formed within a few minutes of adherence of single cells of this strain to the surface of metallic iron.
Aims: Investigation of the alkane‐degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill. Methods and Results: Using ...molecular and chemical analyses, the alkane‐degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n‐alkanes ranging from C12 to C38 and branched alkanes (pristane and phytane). 8‐Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane‐degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR‐amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation. Conclusions: The results from this study suggest novel alkane‐degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil‐degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis. Significance and Impact of the Study: This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.
Phylogenetic analysis of the genus Pseudomonas: was conducted by using the combined gyrB and rpoD nucleotide sequences of 31 validly described species of Pseudomonas: (a total of 125 strains). ...Pseudomonas: strains diverged into two major clusters designated intrageneric cluster I (IGC I) and intrageneric cluster II (IGC II). IGC I was further split into two subclusters, the 'P: aeruginosa complex', which included P: aeruginosa, P: alcaligenes, P: citronellolis, P: mendocina, P: oleovorans and P: pseudoalcaligenes, and the 'P: stutzeri complex', which included P: balearica and P: stutzeri. IGC II was further split into three subclusters that were designated the 'P: putida complex', the 'P: syringae complex' and the 'P: fluorescens complex'. The 'P: putida complex' included P: putida and P: fulva. The 'P: syringae complex' was the cluster of phytopathogens including P: amygdali, P: caricapapayae, P: cichorii, P: ficuserectae, P: viridiflava and the pathovars of P. savastanoi and P. syringae. The 'P. fluorescens complex' was further divided into two subpopulations, the 'P. fluorescens lineage' and the 'P. chlororaphis lineage'. The 'P. fluorescens lineage' contained P. fluorescens biotypes A, B and C, P. azotoformans, P. marginalis pathovars, P. mucidolens, P. synxantha and P. tolaasii, while the 'P. chlororaphis lineage' included P. chlororaphis, P. agarici, P. asplenii, P. corrugata, P. fluorescens biotypes B and G and P. putida biovar B. The strains of P. fluorescens biotypes formed a polyphyletic group within the 'P. fluorescens complex'.
1 NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusa-Kamatari, Kisarazu-shi, Chiba 292-0818, Japan
2 Institute of Molecular and Cellular ...Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
3 Coastal Branch, Natural History Museum and Institute, 123 Yoshio, Katsuura, Chiba 299-5242, Japan
Correspondence Yukiyo Fukunaga fukunaga-yukiyo{at}nite.go.jp
Strain FYK2218 T was isolated from a specimen of the chiton Acanthopleura japonica , which had been collected from a beach on the Boso peninsula in Japan. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain belonged to the phylum Acidobacteria . The most closely related type strains to strain FYK2218 T were Holophaga foetida TMBS4 T (83.6 % 16S rRNA gene sequence similarity) and Geothrix fermentans H-5 T (83.6 %) in subdivision 8 of the Acidobacteria . Cells of FYK2218 T were motile, rod-shaped, Gram-negative, mesophilic and strictly aerobic. The G+C content of the strain was 56.7 mol%. The strain had isoprenoid quinones MK-6 and MK-7 as major components. Major fatty acids of the strain were iso-C 15 : 0 , iso-C 17 : 0 , C 16 : 0 and C 20 : 5 3 c ( cis -5,8,11,14,17-eicosapentaenoic acid). From the taxonomic data obtained in this study, it is proposed that the new marine isolate be placed into a novel genus and species named Acanthopleuribacter pedis gen. nov., sp. nov. within the new family, order and class Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov. and Holophagae classis nov. The family Holophagaceae fam. nov. is also described. The type strain of Acanthopleuribacter pedis is FYK2218 T (=NBRC 101209 T =KCTC 12899 T ).
The DDBJ/GenBank/EMBL accession number for the 16S rRNA gene sequence of Acanthopleuribacter pedis FYK2218 T is AB303221 .
Transmission electron micrographs of strain FYK2218 T , a 16S rRNA gene sequence-based tree and a detailed fatty acid profile of strain FYK2218 T are available as supplementary material with the online version of this paper.
In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even ...by June 1999. To investigate the long‐term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil‐contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR‐amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga–Flavobacterium–Bacteroides phylum, α‐Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 × 105 to 1.6 × 106 bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.
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