Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species.

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil.

A new lanthanide (Ln3+)-dependent methanol-utilizing bacterial strain, La3113T, was isolated from rice field soil and its taxonomic position was investigated using polyphasic approaches. The strain was aerobic, Gram-stain-negative, strongly motile, catalase-positive and cytochrome oxidase-positive. It could neither catalyse the hydrolysis of urea nor reduce nitrate to nitrite. Growth was observed within a temperature range of 10-40 °C and a pH range of 6-8, with optimum growth at 28 °C and pH 7. Methylamine was utilized as the single source of energy, carbon and nitrogen, and it was oxidized by methylamine dehydrogenase. C16 : 1 ω7c, C16 : 1 ω6c and C16 : 0 were the dominant cellular fatty acids. Its draft genome (2.67 Mbp and 44.9 mol% G+C content) encodes genes including three Ln3+-dependent methanol dehydrogenase (XoxF-type MDH) genes, those for formaldehyde assimilation (ribulose monophosphate pathway), formate dehydrogenases and methylamine dehydrogenases, but not Ca2+-dependent MDH (MxaFI-MDH), which characterizes the species as a Ln3+-dependent methylotroph. The 16S rRNA gene sequence showed that strain La3113T belongs to the genus Methylotenera and is closely related to Methylotenera mobilis JLW8T (98.29 % identity). The digital DNA-DNA hybridization (dDDH) values (less than 30 %) and average nucleotide identity (ANI) values (less than 85 %) between genomes of strain La3113T and related type strains were lower than the thresholds for species delineation (70 % for dDDH and 95-96 % for ANI). On the basis of these polyphasic approaches, we propose a novel Methylotenera species, Methylotenera oryzisoli sp. nov. (type strain La3113T=NBRC 111954T=DSM 103219T).

Isolation and genomic characterization of Novimethylophilus kurashikiensis gen. nov. sp. nov., a new lanthanide-dependent methylotrophic species of Methylophilaceae.

Recently, it has been found that two types of methanol dehydrogenases (MDHs) exist in Gram-negative bacterial methylotrophs, calcium-dependent MxaFI-MDH and lanthanide-dependent XoxF-MDH and the latter is more widespread in bacterial genomes. We aimed to isolate and characterize lanthanide-dependent methylotrophs. The growth of strain La2-4T on methanol, which was isolated from rice rhizosphere soil, was strictly lanthanide dependent. Its 16S rRNA gene sequence showed only 93.4% identity to that of Methylophilus luteus MimT , and the name Novimethylophilus kurashikiensis gen. nov. sp. nov. is proposed. Its draft genome (ca. 3.69 Mbp, G + C content 56.1 mol%) encodes 3579 putative CDSs and 84 tRNAs. The genome harbors five xoxFs but no mxaFI. XoxF4 was the major MDH in the cells grown on methanol and methylamine, evidenced by protein identification and quantitative PCR analysis. Methylamine dehydrogenase gene was absent in the La2-4T genome, while genes for the glutamate-mediated methylamine utilization pathway were detected. The genome also harbors those for the tetrahydromethanopterin and ribulose monophosphate pathways. Additionally, as known species, isolates of Burkholderia ambifaria, Cupriavidus necator and Dyadobacter endophyticus exhibited lanthanide dependent growth on methanol. Thus, lanthanide can be used as an essential growth factor for methylotrophic bacteria that do not harbor MxaFI-MDH.

Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium, isolated from rice rhizosphere.

A novel facultatively methanol-utilizing bacterial strain, SM30T, was isolated from rice rhizosphere. Strain SM30T was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 °C. It could tolerate 0 to 2 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30T was most closely related to Pleomorphomonas oryzae DSM 16300T, with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30T showed its distinct phylogenetic position with respect to species with validly published names. Polymerase chain reaction (PCR) amplification of the nifH and growth on nitrogen-free medium indicated that strain SM30T is a diazotroph. The major cellular fatty acids were summed feature 8 (containing 18 : 1ω7c and 18 : 1ω6c) and cyclo 19 : 0ω8c. The major quinone was ubiquinone 10. The DNA G+C content was 74.6 mol%. Based on the genotypic and phenotypic characteristics, strain SM30T represents a novel genus and species, for which the name Oharaeibacter diazotrophicus gen. nov., sp. nov. is proposed with the type strain SM30T (=NBRC 111955T=DSM 102969T).

Cultivable Methylobacterium species diversity in rice seeds identified with whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis.

Methylobacterium species are methylotrophic bacteria that widely inhabit plant surfaces. In addition to studies on methylotrophs as model organisms, research has also been conducted on their mechanism of plant growth promotion as well as the species-species specificity of plant-microbe interaction. We employed whole-cell matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (WC-MS) analysis, which enables the rapid and accurate identification of bacteria at the species level, to identify Methylobacterium isolates collected from the rice seeds of different cultivars harvested in Japan, Thailand, and Kenya. Rice seeds obtained from diverse geographical locations showed different communities of Methylobacterium species. We found that M. fujisawaense, M. aquaticum, M. platani, and M. radiotolerans are the most frequently isolated species, but none were isolated as common species from 18 seed samples due to the highly biased communities in some samples. These findings will contribute to the development of formulations containing selected species that promote rice growth, though it may be necessary to customize the formulations depending on the cultivars and farm conditions.

Methylobacterium Species Promoting Rice and Barley Growth and Interaction Specificity Revealed with Whole-Cell Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF/MS) Analysis.

Methylobacterium species frequently inhabit plant surfaces and are able to utilize the methanol emitted from plants as carbon and energy sources. As some of the Methylobacterium species are known to promote plant growth, significant attention has been paid to the mechanism of growth promotion and the specificity of plant-microbe interactions. By screening our Methylobacterium isolate collection for the high growth promotion effect in vitro, we selected some candidates for field and pot growth tests for rice and barley, respectively. We found that inoculation resulted in better ripening of rice seeds, and increased the size of barley grains but not the total yield. In addition, using whole-cell matrix-assister laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, we identified and classified Methylobacterium isolates from Methylobacterium-inoculated rice plants. The inoculated species could not be recovered from the rice plants, and in some cases, the Methylobacterium community structure was affected by the inoculation, but not with predomination of the inoculated species. The isolates from non-inoculated barley of various cultivars grown in the same field fell into just two species. These results suggest that there is a strong selection pressure at the species level of Methylobacterium residing on a given plant species, and that selection of appropriate species that can persist on the plant is important to achieve growth promotion.

Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes.

Pink-pigmented, facultatively methylotrophic bacteria, strains 87e(T) and 99b(T), were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87e(T) and 99b(T) were found to be related to Methylobacterium organophilum ATCC 27886(T) (97.1% and 97.7%, respectively). Strains 87e(T) and 99b(T) showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23e(T) (98.3 and 99.0%, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97%. Major cellular fatty acids of both strains were C(18:1)ω7c and C(18:0). The results of DNA-DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87e(T) and 99b(T) from their phylogenetically closest relatives. We propose that strains 87e(T) and 99b(T) represent novel species within the genus Methylobacterium, for which the names Methylobacterium haplocladii sp. nov. (type strain 87e(T) =DSM 24195(T) =NBRC 107714(T)) and Methylobacterium brachythecii sp. nov. (type strain 99b(T) =DSM 24105(T) =NBRC 107710(T)) are proposed.

Primary obstructive megaureter with giant ureteral stone: a case report.

A 19-year-old male patient was admitted with flank pain, which had lasted intermittently for four years. In X-ray, there was a radiopacity with a dimension of 6 × 4 cm on the left pelvic bone. Intravenous pyelography revealed a huge left megaureter with a stone in the lower end and grade V hydronephrosis. A left ureterolithotomy, left nipple ureteroneocystostomy, and psoas hitch operation was performed. A voiding cystourethrogram taken three months after the operation showed no reflux, and in IVP there was reduced dilatation of the collecting system when compared to the ureter before the operation.

Small cell prostate carcinoma: a case report and review of the literature.

Small cell prostate cancer constitutes less than 1% of all prostate cancers and has a poor prognosis. A 60-year-old male patient presented with dysuria, pollakiuria, and nocturia of about 1-year duration.The total PSA level at admission was 47.50 ng/mL. The prostate needle biopsy result was reported as adenocarcinoma Gleason 5 + 3. The patient underwent transurethral prostate resection (TUR-P) and bilateral orchiectomy. The TUR-P pathology result was consistent with small cell neuroendocrine carcinoma. He was offered systemic chemotherapy but refused it. Examinations and tests at the third postoperative month showed diffuse liver metastasis and vertebral bone metastasis. He died at the 6 months after surgery.

Azorhizobium oxalatiphilum sp. nov., and emended description of the genus Azorhizobium.

A gram-negative, motile, non-spore-forming rod, designated NS12(T), was isolated from macerated petioles of Rumex sp. after enrichment with oxalate. On the basis of 16S rRNA gene sequence similarity, strain NS12(T) was phylogenetically related to the genera Azorhizobium and Xanthobacter in the class Alphaproteobacteria. Strain NS12(T) was most closely related to Azorhizobium doebereinerae BR 5401(T) and Azorhizobium caulinodans ORS 571(T) (98.3 and 97.3 % 16S rRNA gene sequence similarity, respectively). Membership of the genus Xanthobacter was excluded by phenotypic characterization. The whole-cell fatty acid compositions of the isolate was typical of members of the genus Azorhizobium with C18 : 1ω7c, cyclo-C19 : 0ω8c, 11-methyl-C18 : 1ω7c and C16 : 0 as the main components. The results of DNA-DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strain NS12(T) from the two members of the genus Azorhizobium. Therefore it is concluded that the isolate represents a novel species of the genus Azorhizobium, for which the name Azorhizobium oxalatiphilum sp. nov. is proposed. The type strain is NS12(T) ( = DSM 18749(T) = CCM 7897(T)). The description of the genus Azorhizobium is also emended.

High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis.

Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.

Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata.

A pink-pigmented, facultatively methylotrophic bacterium, strain 35a(T), was isolated from the leaves of Oxalis corniculata. Cells of strain 35a(T) were Gram-reaction-negative, motile, non-spore-forming rods. The highest 16S rRNA gene pairwise sequence similarities for strain 35a(T) were found with the strains of Methylobacterium iners 5317S-33(T) (96.7%), 'Methylobacterium soli' YIM 48816 (96.6%) and Methylobacterium jeotgali S2R03-9(T) (96.3%). 16S rRNA gene sequence similarities with the type strains of all other recognized species of the genus Methylobacterium were below 96%. Major cellular fatty acids were C(18:1)ω7c, C(18:0) and C(16:0). The results of DNA-DNA hybridization experiments, analysis of cpn60 gene sequences, fatty acid profiles, whole-cell MALDI-TOF/MS spectral pattern analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 35a(T) from its nearest phylogenetic neighbours. Strain 35a(T) is therefore considered to represent a novel species within the genus Methylobacterium, for which the name Methylobacterium oxalidis sp. nov. is proposed. The type strain is 35a(T) (=DSM 24028(T)=NBRC 107715(T)).

Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum.

A pink-pigmented, facultatively methylotrophic bacterium, strain 23e(T), was isolated from the leaves of Gnaphalium spicatum (cudweed). The cells of strain 23e(T) were Gram-reaction negative, motile and non-spore-forming rods. On the basis of 16S rRNA gene sequence similarities, strain 23e(T) was related to Methylobacterium organophilum ATCC 27886(T) (97.1%) and Methylobacterium marchantiae JT1(T) (97%), and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 97%. Major cellular fatty acids were C(18:1)ω7c, C(16:00) and C(18:0). The results of DNA-DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted laser desorption/ionization time of flight/MS analysis, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 23e(T) from the phylogenetically closest relatives. We propose that strain 23e(T) represents a novel species within the genus Methylobacterium, for which the name Methylobacterium gnaphalii sp. nov. is proposed. The type strain is 23e(T) (=DSM 24027(T)=NBRC 107716(T)).

Assessment of the effects of zoledronic Acid therapy on bone metabolic indicators in hormone-resistant prostate cancer patients with bone metastatasis.

Purpose. Assessment of effects of zoledronic acid therapy on bone metabolic indicators in hormone-resistant prostate cancer patients with bone metastasis. Material and Methods. Hormone-resistant prostate cancer patients who were identified to have metastases in their bone scintigraphy were taken to trial group. Before administration of zoledronic acid, routine tests for serum calcium, total alkalen phosphates were studied. Sample sera for bone metabolic indicators BALP, PINP, and ICTP were collected. Bone pain was assessed via visual analogue scale and performance via Karnofsky performance scale. Four mg zoledronic acid was administered intravenously once a month. Results. When serum levels of bone forming indicators PINP; BALP were compared before and after therapy, there were insignificant decreases (P = .33, P = .21, resp.). Serum levels of bone destruction indicator ICTP was compared, and there was a significant decrease after zoledronic acid therapy (P = .04). When performances of the patients were compared during therapy period, performances decreased significantly due to progress of illness (P = .01). All patients had ostalgia caused by bone metastases at various degrees. Significant decrease in pain scores was observed (P < .01). Conclusion. Zoledronic acid therapy decreased bone destruction and was effective in palliation of pain in patient with bone metastasis. Using bone metabolic indicators during followup of zoledronic acid therapy might be useful.

Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture.

Five isolates, designated TA2, TA4, TA25(T), KOx(T) and NS15(T) were isolated in previous studies by enrichment in mineral medium with potassium oxalate as the sole carbon source and were characterized using a polyphasic approach. The isolates were Gram-reaction-negative, aerobic, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA and DNA gyrase B subunit (gyrB) gene sequences confirmed that the isolates belonged to the genus Pandoraea and were most closely related to Pandoraea sputorum and Pandoraea pnomenusa (97.2-99.7 % 16S rRNA gene sequence similarity). The isolates could be differentiated from their closest relatives on the basis of several phenotypic characteristics. The major cellular fatty acid profiles of the isolates comprised C16:0, C18:1ω7c, C17:0 cyclo and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). On the basis of DNA-DNA hybridization studies and phylogenetic analyses, the isolates represent three novel species within the genus Pandoraea, for which the names Pandoraea oxalativorans sp. nov. (TA25(T)  = NBRC 106091(T)  = CCM 7677(T)  = DSM 23570(T)), Pandoraea faecigallinarum sp. nov. (KOx(T)  = NBRC 106092(T)  = CCM 2766(T)  = DSM 23572(T)) and Pandoraea vervacti sp. nov. (NS15(T)  = NBRC 106088(T)  = CCM 7667(T)  = DSM 23571(T)) are proposed.

Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov.

Two strains of aerobic, non-spore-forming, Gram-negative, rod-shaped bacteria (ND5 and MY14(T)), previously isolated from urban soil using the membrane-filter enrichment technique, were characterized. Analysis of their 16S rRNA gene sequence grouped strains ND5 and MY14(T) within the family Oxalobacteraceae (Betaproteobacteria). The highest pairwise sequence similarities for strain ND5 were found with members of the genus Herminiimonas, namely with Herminiimonas saxobsidens NS11(T) (99.8%) and Herminiimonas glaciei UMB49(T) (99.6%). Although some fatty acid profiles, physiological and biochemical differences exist between strain ND5 and the respective Herminiimonas-type strains, DNA-DNA hybridization experiments confirm that strain ND5 is a member of the H. glaciei genospecies. Taxonomical analyses revealed a wider range of variability within this genus than considered previously. The highest pairwise nucleotide similarity for strain MY14(T) was found with Oxalicibacterium flavum (96.8%). Phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, DNA-DNA hybridization, fatty acid profiles, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MY14(T) from other Oxalicibacterium species representing a new species, for which the name Oxalicibacterium solurbis sp. nov. (type strain MY14(T)=NBRC 102665(T),=CCM 7664(T)) is proposed.

Description of Oxalicibacterium horti sp. nov. and Oxalicibacterium faecigallinarum sp. nov., new aerobic, yellow-pigmented, oxalotrophic bacteria.

Three strains of aerobic, Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacteria (OD1(T), YOx(T) and NS13), which were isolated in previous studies by enrichment in a mineral medium with potassium oxalate as the sole carbon source, were characterized. On the basis of 16S rRNA gene sequence similarity, strains OD1(T), YOx(T) and NS13 belong to the Betaproteobacteria, most closely related to Oxalicibacterium flavum TA17(T) (97.2-99.7% sequence similarity). The major whole-cell fatty acids were C(16:0), C(16:1)omega7c and C(17:0) cyclo. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains OD1(T) and YOx(T) from O. flavum TA17(T) and from each other. Therefore, it is concluded that the strains OD1(T) and YOx(T) represent novel species within the genus Oxalicibacterium, for which the names Oxalicibacterium horti sp. nov. (type strain OD1(T)=DSM 21640(T)=NBRC 13594(T)) and Oxalicibacterium faecigallinarum sp. nov. (type strain YOx(T)=DSM 21641(T)=CCM 2767(T)) are proposed.

Description of Ancylobacter oerskovii sp. nov. and two additional strains of Ancylobacter polymorphus.

A Gram-negative, pleomorphic, rod-shaped, non-spore-forming bacterium, designated strain NS05T, was isolated from soil after enrichment with oxalate. On the basis of 16S rRNA gene sequence similarity, strain NS05T was shown to be phylogenetically related to the genera Ancylobacter, Starkeya and Angulomicrobium (96.3-98.1% sequence similarity), class Alphaproteobacteria. Strain NS05T was most closely related to Ancylobacter rudongensis AS 1.1761T (98.1% sequence similarity). The whole-cell fatty acid pattern of strain NS05T was typical of those found in members of the genus Ancylobacter. Its main components were C(18:1)omega7c (60.4%), C(19:0)omega8c cyclo (28.3%) and C(16:0) (7.4%) and hydroxylated compounds were absent. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS05T with respect to the four Ancylobacter species with validly published names. Therefore, it is concluded that NS05T represents a novel species of the genus Ancylobacter, for which the name Ancylobacter oerskovii sp. nov. is proposed. The type strain is NS05T (=DSM 18746T=CCM 7435T). Two other oxalate-utilizing strains, NS03 and NS04, isolated from paper-mill effluents, were shown by 16S rRNA gene sequence analysis to be affiliated to the species Ancylobacter polymorphus. The study of their physiological properties extends the knowledge of the physiological variability within this species.

Taxonomy of oxalotrophic Methylobacterium strains.

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching (S (SM)) and Jaccard (S (J)) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing > or =85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock.

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain NS11T) was isolated from a lichen-colonized rock surface. On the basis of 16S rRNA gene sequence similarity, strain NS11T was shown to belong to the Betaproteobacteria, and was most closely related to Herminiimonas arsenicoxydans ULPAs1T (98.8%), Herminiimonas aquatilis CCUG 36956T (98.0%) and Herminiimonas fonticola S-94T (98.0%). Major whole-cell fatty acids were C16:0, C17:0 cyclo and C16:1omega7c. Strain NS11T also contained high proportions of C10:0 3-OH and C18:1omega7c. This pattern is typical for members of the genus Herminiimonas. The results of DNA-DNA hybridization experiments and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS11T from the three recognized Herminiimonas species. It is therefore concluded that strain NS11T represents a novel species of the genus Herminiimonas, for which the name Herminiimonas saxobsidens sp. nov. is proposed. The type strain is NS11T (=DSM 18748T=CCM 7436T).