Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water

Effects of running time on biological activated carbon filters: water purification performance and microbial community evolution

Ozone-biologically activated carbon (BAC) filtration is an advanced treatment process that can be applied to remove recalcitrant organic micro-pollutants in drinking water treatment plants (DWTPs). In this study, we continuously monitored a new and an old BAC filter in a DWTP for 1 year to compare their water purification performance and microbial community evolution. The results revealed that, compared with the new filter, the use of the old BAC filter facilitated a slightly lower rate of dissolved organic carbon (DOC) removal. In the case of the new BAC filter, we recorded general increases in the biomass and microbial diversity of the biofilm with a prolongation of operating time, with the biomass stabilizing after 7 months. For both new and old BAC filters, Proteobacteria and Acidobacteria were the dominant bacterial phyla. At the genus level, the microbial community gradually shifted over the course of operation from a predominance of Herminiimonas and Hydrogenophaga to one predominated by Bradyrhizbium, Bryobacter, Hyphomicrobium, and Pedomicrobium, with Bradyrhizobium being established as the most abundant genus in the old BAC filter. Regarding spatial distribution, we detected reductions in the biomass and number of operational taxonomic units with increasing biofilm depth, whereas there was a corresponding increase in microbial diversity. However, compared with the effects of time, the influence of depth on the composition of the biofilm microbial community was considerably smaller. Furthermore, co-occurrence network analysis revealed that the microbial community network of the new filter after 11 months of operation was the most tightly connected, although its modular coefficient was the lowest of those assessed. We speculate that the positive and negative interactions within the network may be attributable to symbiotic or competitive relationships among species. Moreover, there may have been a significant negative interaction between SWB02 and Acidovorax, plausibly associated with a competition for substrates.

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.

Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991T, a Biopharmaceutical Contaminant

Herminiimonas contaminans was described as a new bacterial species, a contaminant isolated from a biopharmaceutical production process in Sweden. Since the genome sequence was not available, we performed draft genome sequencing. The genome of strain CCM 7991^T (=CCUG 53591^T = DSM 28178^T = Marseille-Q4544^T) was 4,038,814 bp long, with a G+C content of 53.9%; a total of 3,860 genes were identified, along with 3 rRNAs, 44 tRNAs, and 4 noncoding RNAs (ncRNAs).

Herminiimonas contaminans was described as a new bacterial species, a contaminant isolated from a biopharmaceutical production process in Sweden. Since the genome sequence was not available, we performed draft genome sequencing. The genome of strain CCM 7991^T (=CCUG 53591^T = DSM 28178^T = Marseille-Q4544^T) was 4,038,814 bp long, with a G+C content of 53.9%; a total of 3,860 genes were identified, along with 3 rRNAs, 44 tRNAs, and 4 noncoding RNAs (ncRNAs).

Sapientia aquatica gen. nov., sp. nov., isolated from a crater lake

A new aerobic betaproteobacterium, strain SA-152^T, was isolated from the water of a crater lake. 16S rRNA gene sequence analysis revealed that strain SA-152^T belonged to the family Oxalobacteraceae (order Burkholderiales) and was phylogenetically related to Solimicrobium silvestre S20-91^T with 97.09 % and to Herminiimonas arsenicoxydans ULPAs1^T with 96.00 % 16S rRNA gene pairwise sequence similarity. Cells of strain SA-152^T were rod-shaped, non-motile, oxidase-negative and catalase-positive. Its fatty acid profile was dominated by two fatty acids, C_16 : 1 ω7c and C_16 : 0, the major respiratory quinones were Q-8 and Q-7, and the main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA of strain SA-152^T was 48.3 mol%. The new bacterium can be distinguished from closely related genera Solimicrobium, Herminiimonas, Rugamonas and Undibacterium based on its non-motile and oxidase-negative cells. On the basis of the phenotypic, chemotaxonomic and genomic data, strain SA-152^T is considered to represent a novel species of a new genus, for which the name Sapientia aquatica gen. nov., sp. nov. is proposed. The type strain of Sapientia aquatica is SA-152^T (=DSM 29805^T=NCAIM B.02613^T).

Solimicrobium silvestre gen. nov., sp. nov., isolated from alpine forest soil

A Gram-stain-negative, rod-shaped, motile, catalase and cytochrome c oxidase-positive bacterial strain, designated S20-91^T, was isolated from alpine forest soil. Growth occurred within a temperature range of 0-25 °C. Yeast extract was required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain S20-91^T was related to the genus Herminiimonas and had the highest 16S rRNA gene sequence similarity to Herminiimonas arsenicoxydans ULPAs1^T (96.5 %). The strain contained ubiquinone 8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. The major cellular fatty acids (>10 %) were C16 : 1ω7c (55.3 %) and C16 : 0 (25.6 %). The genomic DNA G+C content was 47.6 mol%. Combined data of genomic, phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-91^T represents a novel genus and species, for which the name Solimicrobium silvestre gen. nov., sp. nov. is proposed. The type strain is S20-91^T (=DSM 104733^T=LMG 30010).

Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans

Arsenic, a representative toxic metalloid, is responsible for serious global health problems. Most organisms possess arsenic resistance strategies to mitigate this toxicity. Here, we reported a microorganism, strain AS8, from heavy metal/metalloid-contaminated soil that is able to oxidize arsenite, and investigated its physiological and genomic traits. Its cells were rod-shaped and Gram-negative, and formed small beige-pigmented colonies. 16S rRNA-based phylogenetic analysis indicated that the strain belongs to the genus Herminiimonas and is closely related to Herminiimonas glaciei UMB49^T (98.7% of 16S rRNA gene sequence similarity), Herminiimonas arsenicoxydans ULPAs1^T (98.4%), and Herminiimonas saxobsidens NS11^T (98.4%). Under chemolithoheterotrophic conditions, the strain utilized some organic acids and amino acids as carbon and/or nitrogen sources but not electron sources. Further, the strain grew as a sulfur oxidizer in a complex medium (trypticase soy agar). Unexpectedly, most carbohydrates failed to support its growth as sole carbon sources. Genome sequencing supported these observations, and very few ABC transporters capable of oligo/monosaccharide uptake were identified in the AS8 genome. The genome harbored genes required for the colonization, flagella biosynthesis, urea degradation, and heavy metal and antibiotic resistance. Based on these polyphasic and genomic analyses, we propose that the strain AS8 be named Herminiimonas arsenitoxidans.

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages

The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages.

Developing an ecologically relevant heterogeneous biofilm model for dental-unit waterlines

This study monitored the biodiversity of microbes cultured from a heterogeneous biofilm which had formed on the lumen of a section of dental waterline tubing over a period of 910 days. By day 2 bacterial counts on the outlet-water showed that contamination of the system had occurred. After 14 days, a biofilm comparable to that of clinical waterlines, consisting of bacteria, fungi and amoebae had formed. This showed that the proprietary silver coating applied to the luminal surface of the commercial waterline tubing failed to prevent biofilm formation. Molecular barcoding of isolated culturable microorganisms showed some degree of the diversity of taxa in the biofilm, including the opportunistic pathogen Legionella pneumophila. Whilst the system used for isolation and identification of contaminating microorganisms may underestimate the diversity of organisms in the biofilm, their similarity to those found in the clinical environment makes this a promising test-bed for future biocide testing.

Ozone treatment of conditioned wastewater selects antibiotic resistance genes, opportunistic bacteria, and induce strong population shifts

An ozone treatment system was investigated to analyze its impact on clinically relevant antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). A concentration of 0.9±0.1g ozone per 1g DOC was used to treat conventional clarified wastewater. PCR, qPCR analyses, Illumina 16S Amplicon Sequencing, and PCR-DGGE revealed diverse patterns of resistances and susceptibilities of opportunistic bacteria and accumulations of some ARGs after ozone treatment. Molecular marker genes for enterococci indicated a high susceptibility to ozone. Although they were reduced by almost 99%, they were still present in the bacterial population after ozone treatment. In contrast to this, Pseudomonas aeruginosa displayed only minor changes in abundance after ozone treatment. This indicated different mechanisms of microorganisms to cope with the bactericidal effects of ozone. The investigated ARGs demonstrated an even more diverse pattern. After ozone treatment, the erythromycin resistance gene (ermB) was reduced by 2 orders of magnitude, but simultaneously, the abundance of two other clinically relevant ARGs increased within the surviving wastewater population (vanA, blaVIM). PCR-DGGE analysis and 16S-Amplicon-Sequencing confirmed a selection-like process in combination with a substantial diversity loss within the vital wastewater population after ozone treatment. Especially the PCR-DGGE results demonstrated the survival of GC-rich bacteria after ozone treatment.

Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil

A bacterial strain, designated JS5-2(T), was isolated from soil collected from Jeju Island, Republic of Korea. The cells of the strain were Gram-negative, nonspore forming, catalase- and oxidase-positive, aerobic, nonmotile and rod-shaped. Strain JS5-2(T) exhibited 96.2-97.2, 95.1-96.3, and 95.4-95.8% 16S rRNA gene sequence similarities to the genera Herbaspirillum, Oxalicibacterium, and Herminiimonas, respectively. The highest sequence similarities were with Herbaspirillum autotrophicum IAM 14942(T) (97.2%) and Herbaspirillum frisingense GSF30(T) (97.1%). The major fatty acids of strain JS5-2(T) were C16:0 (35.0%), C17:0 cyclo (19.9%), C18:1 ω7c (11.4%), and summed feature 3 (C16:1 ω7c/C15:0 iso 2-OH) (15.2%), and the major polar lipids of strain JS5-2(T) were diphosphatidylglycerol and an unknown aminophospholipid. The strain contained Q-8 as the predominant ubiquinone. DNA-DNA relatedness values between strain JS5-2(T) and H. autotrophicum IAM 14942(T), and H. frisingense GSF30(T) were 32 and 35%, respectively. The DNA G+C content of strain JS5-2(T) was 59.0 mol%. On the basis of phenotypic, genotypic, and physiological evidence, strain JS5-2(T) represents a novel species of a new genus, for which the name Paraherbaspirillum soli gen. nov., sp. nov. is proposed. The type strain JS5-2(T) (=KACC 12633(T) =NBRC 106496(T)) is proposed.

Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals

A Gram-staining-negative, rod-shaped, non-spore-forming bacterium isolated as a contaminant from a biopharmaceutical process (strain CCUG 53591(T)) was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity data, this strain was clearly allocated to the genus Herminiimonas. Herminiimonas saxobsidens was shown to be the most closely related species on the basis of 16S rRNA gene sequence similarity (99.9 %), followed by Herminiimonas glaciei (99.6 %) and Herminiimonas arsenicoxydans (98.8 %). Strain ND5, previously reported as H. glaciei, but showing 100 % 16S rRNA gene sequence similarity to strain CCUG 53591(T), was included in the comparative study. Similarities to all other species of the genus Herminiimonas were below 98.0 %. Chemotaxonomic data (major ubiquinone, Q-8; major polar lipids, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; and major fatty acids, C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(16 : 0,) with C(10 : 0) 3-OH as hydroxylated fatty acid) supported the affiliation of the isolate to the genus Herminiimonas. DNA-DNA hybridization results (mean values) for strain CCUG 53591(T) with H. saxobsidens CCUG 59860(T) (34 %), H. glaciei DSM 21140(T) (57 %), H. arsenicoxydans DSM 17148(T) (17 %) and Herminiimonas fonticola S-94(T) (11 %) clearly supported the separate taxonomic position of this strain. Strain ND5 showed DNA-DNA similarities of 78, 56 and 52 % to strain CCUG 53591(T), H. glaciei DSM 21140(T) and H. saxobsidens CCUG 59860(T), respectively. Phenotypic differentiation of the isolate from the most closely related species was possible by various features. Hence, strain CCUG 53591(T) represents a novel species, for which the name Herminiimonas contaminans sp. nov. is proposed, with the type strain CCUG 53591(T) ( = CCM 7991(T)). Strain ND5 is a second strain of this species.

Actimicrobium antarcticum gen. nov., sp. nov., of the family Oxalobacteraceae, isolated from Antarctic coastal seawater

A Gram-negative, non-motile, catalase- and oxidase- positive, strictly aerobic, and short rod-shaped bacterium that was designated strain KOPRI 25157(T) was isolated from coastal seawater sample in Antarctica. The temperature and pH ranges for growth on R2A agar were 10-20°C, and 5.0-10.0, respectively. Phylogenetic analyses of the 16S rRNA gene sequence of strain KOPRI 25157(T) showed it to belong to the family Oxalobacteraceae of the class Betaproteobacteria, and it formed a distinct clade from other recognized members of the family. DNA G + C content was 65.9 mol%. Major ubiquinone was Q-8. Predominant cellular fatty acids were C(16:1) ω7c/15 iso 2OH (56.4%) and C(16:1) (30.5%). Major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and unknown lipid. On the basis of these data, it is proposed that strain KOPRI 25157(T) is the representative of a novel genus, for which the name Actimicrobium gen. nov. is proposed in the family Oxalobacteraceae. The type strain for Actimicrobium antarcticum sp. nov. is KOPRI 25157(T) (=JCM 16673(T)=KCTC 23040(T)).

Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum

A Gram-negative, oxidase- and catalase-positive, flagellated, rod-shaped bacterium, designated strain EM 1(T), was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belonged to the family Oxalobacteraceae within the class Betaproteobacteria; the closest phylogenetic relative was Undibacterium pigrum DSM 19792(T) (96.7 % gene sequence similarity). The new isolate could be distinguished from the type strain of U. pigrum DSM 19792(T) (=CCUG 49009(T)=CIP 109318(T)) and from strain CCUG 49012(T), which has been described as a second genomovar of this species, on the basis of genotypic data and several phenotypic properties. An S-layer was present in the cell envelope in U. pigrum DSM 19792(T), but was absent in strains EM 1(T) and CCUG 49012(T). Test conditions were established that enabled strain CCUG 49012(T) to be distinguished from U. pigrum DSM 19792(T). As found for U. pigrum, the main fatty acids of strains EM 1(T) and CCUG 49012(T) were summed feature 3 (including unsaturated C(16 : 1)ω7c), straight-chain C(16 : 0) and unsaturated C(18 : 1)ω7c (low percentage in strain CCUG 49012(T)), and C(10 : 0) 3-OH was the sole hydroxylated fatty acid. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile was mainly composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. In contrast to U. pigrum and strain CCUG 49012(T), where ubiquinone Q8 was reported as the sole quinone component, the quinone system of strain EM 1(T) consisted of ubiquinone Q-8 (64 %) and Q-7 (36 %). The 16S rRNA gene sequence similarity, the polar lipid profile and the absence of C(12)-hydroxylated fatty acids all indicated that strain EM 1(T) was affiliated with the genus Undibacterium. 16S rRNA gene sequence similarity values lower than 97.0 % and several differentiating phenotypic traits demonstrated that strain EM 1(T) represents a novel species for which the name Undibacterium oligocarboniphilum sp. nov. is proposed (type strain EM 1(T)=DSM 21777(T)=CCUG 57265(T)). In addition, based on previously published results and this study, a separate species, Undibacterium parvum sp. nov., is proposed with strain CCUG 49012(T) (=DSM 23061(T)=CIP 109317(T)) as the type strain.

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.

Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice

A Gram-negative ultramicrobacterium (designated strain UMB49(T)) was isolated from a 120,000-year-old, 3,042 m deep Greenland glacier ice core using a 0.2 mum filtration enrichment procedure. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Herminiimonas of the family Oxalobacteraceae of the class Betaproteobacteria. Strain UMB49(T) was most closely related to Herminiimonas saxobsidens (99.6 % sequence similarity), Herminiimonas arsenicoxydans (98.4 %), Herminiimonas aquatilis (97.6 %) and Herminiimonas fonticola (97.9 %). Genomic DNA-DNA hybridization showed low levels of relatedness (below 57 %) to H. saxobsidens and H. arsenicoxydans. Cells of strain UMB49(T) were small thin rods with a mean volume of 0.043 mum(3) and possessed 1 or 2 polar and/or 1-3 lateral very long flagella. The original colony pigmentation was brown-purple but after recultivation the colonies were translucent white to tan coloured. Strain UMB49(T) grew aerobically and under microaerophilic conditions. The strain produced catalase and oxidase, but did not reduce nitrate. Sole carbon sources included citrate, succinate, malate, lactate and alanine. The strain produced acid from l-arabinose, d-arabinose, l-xylose, d-xylose and d-ribose. The DNA G+C content was 59.0 mol%. Based on differential characteristics of strain UMB49(T) and recognized Herminiimonas species, it was concluded that strain UMB49(T) represents a novel species of the genus Herminiimonas, for which the name Herminiimonas glaciei sp. nov. is proposed. The type strain is UMB49(T) (=ATCC BAA-1623(T)=DSM 21140(T)).

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).

Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water

Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (strains CCUG 49009T and CCUG 49012), both isolated from drinking water, were characterized. On the basis of chemotaxonomic data [major ubiquinone, Q-8; predominant polyamines, putrescine and 2-hydroxyputrescine; major polar lipids, phosphatidylethanolamine, moderate amounts of diphosphatidylglycerol and phosphatidylglycerol and minor amounts of three aminolipids and phosphatidylserine; major fatty acids, C16 : 0 and summed feature 3 (C16 : 1 ω7c/C15 : 0 iso 2-OH)] and 16S rRNA gene sequence similarities, both strains clearly belong to the family Oxalobacteraceae of the Betaproteobacteria. 16S rRNA gene sequence similarities with members of the most closely related genera of this group (Herminiimonas, Massilia, Duganella, Telluria, Herbaspirillum, Janthinobacterium, Naxibacter and Paucimonas) were less than 96.5 % for both strains. The two strains also shared a relatively low 16S rRNA gene sequence similarity (96.8 %). Although phylogenetic analysis based on 16S rRNA gene sequence similarities clearly showed that the two organisms formed a separate branch, their phenotypes (including chemotaxonomic features) were hardly distinguishable and showed high similarities to those reported for the most closely related genera. On the basis of DNA–DNA hybridization results, the two strains were shown to represent separate species (sharing only 20 % DNA–DNA relatedness), but they could not be clearly differentiated phenotypically from each other. It is evident that these organisms represent a new genus, Undibacterium gen. nov., with one species, Undibacterium pigrum sp. nov. The type strain of Undibacterium pigrum is strain CCUG 49009T (=CIP 109318T). Strain CCUG 49012 (=CIP 108976) probably represents a second species of this genus, but is described here as a second genomovar of this species because of the lack of differentiating characters.

A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.

Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium

An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genusHerminiimonasof the familyOxalobacteraceae, orderBurkholderialesin theBetaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1TandHerminiimonas fonticolaS-94Tand between strain ULPAs1TandHerminiimonas aquatilisCCUG 36956Trevealed levels of relatedness of <10 %, well below the recommended 70 % species cut-off value. Thus, strain ULPAs1T(=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species ofHerminiimonas, for which the nameHerminiimonas arsenicoxydanssp. nov. is proposed.

Herminiimonas aquatilis sp. nov., a new species from drinking water

A bacterial strain (CCUG 36956T) isolated from drinking water was taxonomically studied in detail. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that it belongs to family Oxalobacteraceae of the beta-subclass of the Proteobacteria, with the highest sequence similarity of 99.3% to the type strain of Herminiimonas fonticola. In the polyamine pattern putrescine and 2-hydroxyputrescine were the predominant compounds. In the polar lipid profile major compounds were phosphatidyl ethanolamine and diphosphatidyl glycerol. Phosphatidyl glycerol and an unknown phospholipid were detected in moderate proportions. The major respiratory quinone was a ubiquinone Q-8 and the major whole cell fatty acids were 16:1 omega7c, 17:1 omega6c, and 16:0. The strain also contained 10:0 3-OH and other fatty acids typical for members of the genus Herminiimonas. The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain CCUG 36956T from H. fonticola. For this reason, we propose that strain CCUG 36956T represents a new species of the genus Herminiimonas for which we propose the name Herminiimonas aquatilis sp. nov.

Validation of publication of new names and new combinations previously effectively published outside the IJSEM

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.