Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov.

A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-b(T), was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-b(T) (=DSM 19378(T) =CCUG 55131(T)) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10(T) (=DSM 16106(T) =CCUG 49250(T)).

Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples.

Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic alpha-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation.

Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid.

Three bacterial strains, designated MT1(T), RW10(T) and IpA-2(T), had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genus Pseudomonas. Analysis of the results of DNA-DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA-DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the names Pseudomonas reinekei sp. nov. (type strain MT1(T) =DSM 18361(T)=CCUG 53116(T)), Pseudomonas moorei sp. nov. (type strain RW10(T) =DSM 12647(T)=CCUG 53114(T)) and Pseudomonas mohnii sp. nov. (type strain IpA-2(T) =DSM 18327(T)=CCUG 53115(T)) are proposed.

Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs.

The active bacteria of a biofilm community grown directly on polychlorinated biphenyl (PCB) droplets were analyzed by 16S rRNA fingerprinting, identified by their 16S rRNA gene sequences and fatty acid profiling, and compared with isolates from the biofilm. Although, the multi-species biofilm degraded di- and trichlorinated PCB-congeners these substrates were not attacked by its individual isolated members, which suggests that a metabolic network is responsible for PCB degradation in the biofilm. The community metabolized [U-13C]-2,2'-dichlorobiphenyl incorporating the label into certain phospholipid fatty acids matching those found in Burkholderia species. In contrast, abundant biofilm community members, like Methylobacterium species, did not incorporate the label. These results provide prima faciae evidence for Burkholderia species as the main degraders of PCBs in this type of aerobic soils.

Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora.

A metagenome expression library of bulk DNA extracted from the rumen content of a dairy cow was established in a phage lambda vector and activity-based screening employed to explore the functional diversity of the microbial flora. Twenty-two clones specifying distinct hydrolytic activities (12 esterases, nine endo-beta-1,4-glucanases and one cyclodextrinase) were identified in the library and characterized. Sequence analysis of the retrieved enzymes revealed that eight (36%) were entirely new and formed deep-branched phylogenetic lineages with no close relatives among known ester- and glycosyl-hydrolases. Bioinformatic analyses of the hydrolase gene sequences, and the sequences and contexts of neighbouring genes, suggested tentative phylogenetic assignments of the rumen organisms producing the retrieved enzymes. The phylogenetic novelty of the hydrolases suggests that some of them may have potential for new applications in biocatalysis.

Brevundimonas mediterranea sp. nov., a non-stalked species from the Mediterranean Sea.

Six strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from the Mediterranean Sea. 16S rRNA gene sequence analysis indicated that the strains were affiliated within the alphaproteobacterial genus Brevundimonas, with Brevundimonas intermedia (99.4 %) and Brevundimonas vesicularis (99.2 %) as their closest relatives. This affiliation was supported by chemotaxonomic data (major polar lipids: phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol; major fatty acids: C(18 : 1), C(16 : 0), C(16 : 1), C(15 : 0), C(17 : 1)omega8c, 11-Me-C(18 : 1)omega5t). The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the strains from all recognized Brevundimonas species. The strains therefore represent a novel species, for which the name Brevundimonas mediterranea sp. nov. is proposed, with the type strain V4.BO.10T)(=LMG 21911T=CIP 107934T).

Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids.

Two cauliform bacteria (CM243T and CM251) isolated by J. Poindexter from the Atlantic Ocean were characterized by 16S rRNA gene sequencing, TaqI restriction fragment length polymorphism and single-strand conformation polymorphism analyses of the internally transcribed 16S-23S rDNA spacer (ITS1) region, analysis of fatty acids from cellular lipids, mass spectrometry of polar lipids and physiological properties. The two strains showed very low diversity of polar lipids with diacyl-sulfoquinovosyl glycerols as the predominant lipids. The two bacterial strains were observed to have nearly identical 16S rRNA gene sequences and could not be differentiated by their ITS1 regions. The isolates differed from species of the genus Maricaulis by their 16S rRNA gene sequences, polar lipids and fatty acid patterns. On the basis of the genotypic analyses and estimations of phylogenetic similarities, physiological and chemotaxonomic characteristics, it is proposed that the isolates represent a new genus and species, for which the name Woodsholea maritima gen. nov., sp. nov. (type strain CM243T=VKM B-1512T=LMG 21817T) is proposed.

Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov.

The unusually shaped bacteria of the genera Stella, Labrys and Angulomicrobium have been described based on their cell morphology and biochemistry. However, their phylogenetic relationships remain unresolved. An earlier study that was based on 5S rRNA gene sequences placed the genus Stella within the 'Alphaproteobacteria'. In the present report, polar lipids and 16S rRNA genes of the type strains of the two species in the genus Stella, Stella humosa DSM 5900(T) and Stella vacuolata DSM 5901(T), are studied, as well as the type strains of the monospecific genera Labrys (Labrys monachus VKM B-1479(T)) and Angulomicrobium (Angulomicrobium tetraedrale DSM 5895(T)). It was found that the genus Stella belongs to the order Rhodospirillales in the family Rhodospirillaceae, and not to the Acetobacteraceae. Whilst the position of the genus Angulomicrobium in the family Hyphomicrobiaceae was confirmed, the genus Labrys could not be placed into any known family, but was adjacent to the family 'Beijerinckiaceae'. In addition, data were obtained for strain VKM B-1336, which was shown not to belong to the genus Angulomicrobium, and strain NCIMB 1785(T) (=DSM 15561(T)), for which the name Angulomicrobium amanitiforme sp. nov. is proposed.

Phylogeny of the ring-forming bacterium Arcicella aquatica gen. nov., sp. nov. (ex Nikitin et al. 1994), from a freshwater neuston biofilm.

Arcicella aquatica NO-502(T), obtained from a neuston film on a freshwater lake and belonging to the phylum Bacteroidetes, is characterized by ring-forming cells. The bacterium is a strict aerobe, with optimal growth between 28 and 30 degrees C. Carbohydrates, but no organic acids or amino acids, are used as substrates. The G+C content of strain NO-502(T) is 34.5 mol%; its genome size is 2.9 x 10(9) Da. The genus Arcicella and its type species Arcicella aquatica (type strain NO-502(T)=LMG 21963(T)=CIP 107990(T)) are proposed, and descriptions of this genus and species are given.

Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech.

Five bacterial strains were isolated from a non-toxigenic strain of the marine dinoflagellate Alexandrium tamarense (Lebour) Balech CCMP 116 (NEPCC C116), during a survey of the diversity of bacteria associated with paralytic shellfish toxin-producing cultures of Alexandrium spp. (Dinophyta). All strains were strictly aerobic, Gram-negative, straight or curved rods. Cells were dimorphic, with stalks (or prosthecae) and non-motile or non-stalked and motile, by means of a single polar flagellum. The bacteria grew best at salt concentrations ranging from 2 to 10 % and growth occurred at 10 degrees C, but not at 50 degrees C. The G+C content of the chromosomal DNA of the strains was determined to be 61-62 mol%. Major cellular fatty acids of the bacteria presented a unique profile. 16S rRNA gene sequence analysis showed the five strains to be related to genera of budding bacteria of marine origin in the 'Alphaproteobacteria', namely, Hirschia, Maricaulis and Hyphomonas, although they exhibited substantial differences in morphology, substrate utilization and fatty acid profile to members of these genera. The five strains are proposed to comprise a new species of a new genus, Oceanicaulis alexandrii gen. nov., sp. nov., the type strain of which is C116-18(T) (=DSM 11625(T)=NCIMB 13905(T)).

Phylogeny of Maricaulis Abraham et al. 1999 and proposal of Maricaulis virginensis sp. nov., M. parjimensis sp. nov., M. washingtonensis sp. nov. and M. salignorans sp. nov.

Thirteen marine bacteria isolated from different locations, belonging to the genus Maricaulis, were characterized by 16S rRNA gene sequencing, DNA-DNA hybridizations and analysis of the internally transcribed 16S-23S rDNA spacer (ITS1) region, analysis of fatty acids from total lipids, mass spectrometry of polar lipids and determination of temperature and NaCl tolerances. The data obtained led to the identification of five new sulfoquinovosyl diacylglycerols, using tandem mass spectrometry, and the fragmentation patterns of the individual compounds. Four novel species were identified and described as Maricaulis virginensis sp. nov. (type strain VKM B-1 5139T)), Maricaulis parjimensis sp. nov. (type strain MCS 25(T)), Maricaulis washingtonensis sp. nov. (type strain MCS 6(T)) and Maricaulis salignorans sp. nov. (type strain MCS 18(T)). They differ in their temperature and salt tolerances and can be differentiated by their polar lipids and fatty acid patterns, as well as their ITS1 and 16S rRNA gene sequences.