Labrys okinawensis sp. nov. and Labrys miyagiensis sp. nov., budding bacteria isolated from rhizosphere habitats in Japan, and emended descriptions of the genus Labrys and Labrys monachus

Three strains, MAFF 210191T, G24103T and G24116, assumed to be members of two novel species, were isolated from several rhizosphere habitats in different parts of Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates formed a distinct monophyletic group together with the two known species of the genus Labrys, suggesting that the isolates have a close affiliation with this genus. In this study, a polyphasic approach was used to characterize and compare the three isolates with the two species of the genus Labrys, Labrys monachus and Labrys methylaminiphilus. All three isolates were aerobic, Gram-negative, motile and non-sporulating and they ranged in shape from spherical to short rods. The cells multiplied by budding and utilized a wide variety of monosaccharides, disaccharides and sugar alcohols as sole carbon and energy sources, but they did not utilize C1 compounds, salicin or d-melezitose. The strains were inhibited by dl-α-alanine and glycine (both at 10 mM). The major cellular fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C18 : 0 and C18 : 1 ω7c. The three isolates shared <12 % and <11 % DNA–DNA relatedness with L. monachus DSM 5896T and L. methylaminiphilus DSM 16812T, respectively. The G+C content of the isolates (61–62 mol%) was also significantly lower than those of the two previously characterized species. In spite of many morphological, physiological and chemotaxonomic similarities among the three isolates, strain MAFF 210191T could be differentiated from strains G24103T and G24116 on the basis of 16S rRNA gene sequence divergence, DNA–DNA relatedness (<46 %) and gelatin hydrolysis. Two novel species are therefore proposed, namely Labrys okinawensis sp. nov., with the type strain MAFF 210191T (=DSM 18385T), and Labrys miyagiensis sp. nov., with the type strain G24103T (=NBRC 101365T=NCIMB 14143T) and also including strain G24116 (=NBRC 101366=NCIMB 14144). Emended descriptions of the genus Labrys and Labrys monachus are also presented.

Taxonomic heterogeneity within the Planctomycetales as derived by DNA–DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula

Ninety-seven strains of budding bacteria originating from various aquatic habitats and morphologically resembling planctomycetes were investigated taxonomically. Taxonomic differentiation was based on DNA–DNA hybridization, physiological properties and chemotaxonomic tests. Nineteen hybridization groups, containing 79 of the tested strains, were established. Eighteen strains, however, did not fit into any of these groups. Rhodopirellula baltica gen. nov., sp. nov. is described, with strain SH 1T (=IFAM 1310T=DSM 10527T=NCIMB 13988T) as the type strain. Pirellula marina is transferred to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov., with strain SH 106T (=IFAM 1313T=DSM 3645T=ATCC 49069T) as the type strain. An emended description of the genus Pirellula is also provided. Differentiation between R. baltica, B. marina and Pirellula staleyi was achieved by the integration of morphological, physiological, chemotaxonomic and genetic characteristics.

Distribution of denitrification and nitrogen fixation genes inHyphomicrobiumspp. and other budding bacteria

Genomic DNA of Hyphomicrobium spp., Hirschia baltica ATCC 49814T, Hyphomonas oceanitis ATCC 33897T, and Pedomicrobium ferrugineum S-1290Twas investigated with gene probes specific for nitrate reductase (narG), cytochrome cd1containing nitrite reductase (nirS), Cu-containing nitrite reductase (nirK), nitrous oxide reductase (nosZ), ammonia monooxygenase (amoA), and nitrogenase reductase (nifH) by Southern or dot blot hybridization. The presence of denitrification genes could be demonstrated for Hyphomicrobium denitrificans 1869T, Hyphomicrobium aestuarii IFAM NQ-521GrT, Hyphomicrobium zavarzinii IFAM ZV-580, Hyphomicrobium zavarzinii subsp. chengduense, in the Hyphomicrobium DNA-DNA hybridization groups 3, 12, 13, 18, 26a1, 26a2, 26c, 26d, 26e, 26f, 26g2, and 29, and in three isolates from a denitrifying sand filter in a municipal wastewater treatment plant. The Cu-containing nitrite reductase appeared to be more frequent than the cytochrome cd1containing nitrite reductase in hyphomicrobia. Resulting positive DNA-DNA hybridization signals correlated with physiological activity measurements of intact cells in all cases determined. The nifH-like gene fragment was found in Hyphomicrobium aestuarii, Hyphomicrobium zavarzinii, Hyphomicrobium zavarzinii subsp. chengduense, Hyphomicrobium facilis and eight additional DNA-DNA hybridization groups. Ammonia monooxygenase was not genetically detected in any of the strains investigated. The results significantly extended the previous findings that genetically different hyphomicrobia of a sewage treatment plant and its adjacent receiving lake could occupy different ecological niches. Denitrification genes or the nifH-like gene fragment were not found in the other budding bacteria investigated.Key words: Hyphomicrobium, denitrification, nitrification, nitrogen fixation, activated sludge, biofilm.