Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge.

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98.1-98.3 % similarity), Nocardia brasiliensis (97.9-98.0 %) and Nocardia tenerifensis (97.8-97.9 %). However, the results of DNA-DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

Monitoring behaviour of catabolic genes and change of microbial community structures in seawater microcosms during aromatic compound degradation.

The behaviour of microbial populations responsible for degradation of the aromatic compounds, phenol, benzoate, and salicylate, and changes of microbial community structures in seawater microcosms were analysed quantitatively and qualitatively using MPN-PCR and PCR-DGGE. The purpose of the study was to investigate the ecology of the entire microbial community during bioremediation. Bacterial populations possessing catechol 1,2-dioxygenase (C12O) DNA were evidently the primary degraders of phenol and benzoate, but others possessing catechol 2,3-dioxygenase (C23O) DNA increased to enhance substrate degradation under high-load conditions when the substrates were present for long periods. However, salicylate degradation was evidently facilitated by specific bacterial populations possessing C23O DNA. PCR-DGGE analyses suggested that bacterial populations already relatively dominant in the original microcosm contributed to phenol degradation. Bacteria composing a minor fraction of the original population apparently increased and contributed to benzoate degradation. Bacterial populations possessing C23O DNA were responsible for salicylate degradation, however, and different degrading bacteria were evidently selected for, depending on the initial salicylate concentration. Microbial community structure tended to be simplified by aromatic compound degradation. Thus, microbial monitoring can elucidate the behaviour of bacterial populations responsible for aromatic compound degradation and be used to assess the effects of bioremediation on intact microbial ecosystems.

Monitoring of alkane-degrading bacteria in a sea-water microcosm during crude oil degradation by polymerase chain reaction based on alkane-catabolic genes.

Behaviour of microbial populations responsible for degrading n-alkanes, a major component of crude oil, was monitored during crude oil degradation in a sea-water microcosm by both traditional colony culturing and molecular techniques. A DNA extraction method applicable to crude oil-amended sea-water samples was developed to obtain DNA applicable to most probable number (MPN) polymerase chain reaction (PCR). The population of alkane-degrading bacteria responsible for degradation of n-alkanes in a crude oil-amended microcosm altered, so that shorter alkanes were degraded first by alkane-degrading bacteria possessing alkane hydroxylase genes from group I (Kohno et al., 2002, Microb Environ 17: 114-121) and longer ones afterwards by those possessing alkane hydroxylase genes from group II. Thus, the degradation mechanism of the n-alkanes can be clarified during crude oil degradation. Application of the method of detecting different types of alkane-catabolic genes, as shown in the present study, enabled bacterial groups preferring alkanes of either shorter or longer chain lengths to be enumerated selectively.

Characterization of filamentous Eikelboom type 021N bacteria and description of Thiothrix disciformis sp. nov. and Thiothrix flexilis sp. nov.

The phenotypic and genotypic characteristics of 15 strains of Eikelboom type 021 N bacteria isolated from wastewater treatment plants were investigated. The strains shared many characters with Thiothrix species. However, the Eikelboom type 021N bacteria had only 88.3-92.0% 16S rDNA sequence similarity to members of the Thiothrix nivea group, including T. nivea, 'Thiothrix ramosa', Thiothrix unzii and Thiothrix fructosivorans, and were differentiated from them in sugar utilization and other properties, suggesting that the Eikelboom type 021N bacteria belong to species distinct from the T. nivea group. The 15 Eikelboom type 021N bacteria that were investigated were divided into three distinct groups (I to III) on the basis of their genotypic and phenotypic characteristics. The creation of two novel species is proposed, Thiothrix disciformis sp. nov. for the group I strains (type strain B3-1T = JCM 11364T = DSM 14473T) and Thiothrix flexilis sp. nov. for the group III strains (type strain EJ2M-BT = JCM 11135T = DSM 14609T). Thiothrix eikelboomii AP3T was included in group II and shared many characters with the other group II strains. The inclusion of all group II strains within the species T. eikelboomii is proposed,together with emendation of the description of T. eikelboomii.