Dokdonella koreensis gen. nov., sp. nov., isolated from soil

Large-scale comparative analysis reveals different bacterial community structures in full- and lab-scale wastewater treatment bioreactors

The activated sludge process is widely used for biological wastewater treatment due to its low cost and high efficiency. Although numerous lab-scale bioreactor experiments have been conducted to investigate the microorganism performance and mechanisms in activated sludge, understanding the bacterial community differences between full- and lab-scale bioreactors has remained elusive. In this study, we investigated the bacterial communities in 966 activated sludge samples obtained from various bioreactors, including both full- and lab-scale ones, from 95 previous studies. Our findings reveal significant differences in the bacterial communities between full- and lab-scale bioreactors, with thousands of bacterial genera exclusive to each scale. We also identified 12 genera that are frequently abundant in full-scale bioreactors but rarely observed in lab-scale reactors. By using a machine-learning method, organic matter and temperature were determined as the primary factors affecting microbial communities in full- and lab-scale bioreactors. Additionally, transient bacterial species from other environments may also contribute to the observed bacterial community differences. Furthermore, the bacterial community differences between full- and lab-scale bioreactors were verified by comparing the results of lab-scale bioreactor experiments to full-scale bioreactor sampling. Overall, this study sheds light on the bacteria overlooked in lab-scale studies and deepens our understanding of the differences in bacterial communities between full- and lab-scale bioreactors.

Regulation of rhizospheric microbial network to enhance plant growth and resist pollutants: Unignorable weak electric field

The union of Plant Growth-Promoting Bacteria (PGPB) and rhizosphere confers a series of functions beneficial to plant. However, the lack of an opearable in situ method limits the further understanding on the mechanism. In this study, a weak electric field was designed to regulate rhizospheric microflora in a constructed root-splitting reactor. Compared with the control, the aboveground and underground biomass of rice seedling increased by 17 % and 18 % (p < 0.05) respectively under the exist of weak electric field of 0.14 V/cm. The joint action of rhizosphere and PGPB displayed the detoxification ability in the condition of soluble petroleum hydrocarbons, where the height, stem diameter, biomass and root vigor of the plant was increased by 58 %, 32 %, 43 % and 48 % respectively than the control. The selective reproduction of endophytes and ectophytes (denitrifying, auxin-producing, hydrocarbon-degrading and electroactive bacteria) was observed under applied weak electric field, which enhanced the nitrogen utilization, cellular metabolic activity and resistance to toxic organics of plant. This was further confirmed by the up-regulated OTUs related to the hydrocarbon degradation function, tryptophan metabolism and metabolism of nicotinate and nicotinamide. Moreover, the weak electric field also enhanced the transfer ability of partial endophytes grown in the root to improve plant stress resistance. The results in this work inspired an exercisable method for in situ enrichment of PGPB in the rhizosphere to cope with food crisis and provided a new way to deal with sudden environmental events.

Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment

This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln³⁺)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by Alpha-, Beta-, and Gammaproteobacteria represented by the four orders Methylococcales, Nitrosomonadales, Rhizobiales, and Xanthomonadales. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with Nitrosomonadales and Rhizobiales, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.

Dynamics of PHA-Accumulating Bacterial Communities Fed with Lipid-Rich Liquid Effluents from Fish-Canning Industries

The biosynthesis of polyhydroxyalkanoates (PHAs) from industrial wastes by mixed microbial cultures (MMCs) enriched in PHA-accumulating bacteria is a promising technology to replace petroleum-based plastics. However, the populations’ dynamics in the PHA-accumulating MMCs are not well known. Therefore, the main objective of this study was to address the shifts in the size and structure of the bacterial communities in two lab-scale sequencing batch reactors (SBRs) fed with fish-canning effluents and operated under non-saline (SBR-N, 0.5 g NaCl/L) or saline (SBR-S, 10 g NaCl/L) conditions, by using a combination of quantitative PCR and Illumina sequencing of bacterial 16S rRNA genes. A double growth limitation (DGL) strategy, in which nitrogen availability was limited and uncoupled to carbon addition, strongly modulated the relative abundances of the PHA-accumulating bacteria, leading to an increase in the accumulation of PHAs, independently of the saline conditions (average 9.04 wt% and 11.69 wt%, maximum yields 22.03 wt% and 26.33% SBR-N and SBR-S, respectively). On the other hand, no correlations were found among the PHAs accumulation yields and the absolute abundances of total Bacteria, which decreased through time in the SBR-N and did not present statistical differences in the SBR-S. Acinetobacter, Calothrix, Dyella, Flavobacterium, Novosphingobium, Qipengyuania, and Tsukamurella were key PHA-accumulating genera in both SBRs under the DGL strategy, which was revealed as a successful tool to obtain a PHA-enriched MMC using fish-canning effluents.

Total and Metabolically Active Microbial Community of Aerobic Granular Sludge Systems Operated in Sequential Batch Reactors: Effect of Pharmaceutical Compounds

Two aerobic granular sludge (AGS) sequential batch reactors were operated at a mild (15 °C) temperature for 180 days. One of those bioreactors was exposed to a mixture of diclofenac, naproxen, trimethoprim, and carbamazepine. The AGS system, operating under pressure from emerging contaminants, showed a decrease in COD, BOD5, and TN removal capacity, mainly observed during the first 100 days, in comparison with the removal ratios detected in the control bioreactor. After an acclimatisation period, the removal reached high-quality effluent for COD and TN, close to 95% and 90%, respectively. In the steady-state period, trimethoprim and diclofenac were successfully removed with values around 50%, while carbamazepine and naproxen were more recalcitrant. The dominant bacterial OTUs were affected by the presence of a mixture of pharmaceutical compounds, under which the dominant phylotypes changed to OTUs classified among the Pseudomonas, Gemmobacter, and Comamonadaceae. The RT-qPCR and qPCR results showed the deep effects of pharmaceutical compounds on the number of copies of target genes. Statistical analyses allowed for linking the total and active microbial communities with the physico-chemical performance, describing the effects of pharmaceutical compounds in pollution degradation, as well as the successful adaptation of the system to treat wastewater in the presence of toxic compounds.

Assessing the performance and microbial community of hybrid moving bed and conventional membrane bioreactors treating municipal wastewater

A conventional (SB-CMBR) and a hybrid moving-bed (SB-HMBR) sequencing batch membrane bioreactor treating municipal wastewater were compared during their start-up in terms of organic matter and nutrient removal, membrane fouling characteristics and microbial community. Both systems exhibited similar COD, ammonium, total nitrogen (TN) and phosphorus removal efficiency, amounting up to 96%, 99%, 70% and 85%, respectively. Results from cycle tests revealed that the contribution of attached biomass to the overall ammonium removal in the hybrid reactor was marginal. Moreover, higher despite the similar phosphorus removal efficiency attained in both reactors, nitrate-dosing activity batch assays specifically revealed that the anoxic phosphate uptake rate (PUR) in the SB-HMBR was 1.71 times higher than in the SB-CMBR. Moreover, a higher frequency of Candidatus Accumulibacter-related polyphosphate-accumulating organisms was observed in the biofilm carriers of the hybrid reactor. These findings may explain why the overall PUR was almost 50% higher in the SB-HMBR. By operating the reactors in sequencing batch mode, adhesion of particles on the membrane surface was reduced while fouling was mitigated as compared to continuous MBR systems. Better filterability conditions with lower fouling rate were found in the SB-HMBR, important features of the hybrid reactor for reducing membrane cleaning-related energy demand.

A strategy for securing unique microbial resources – focusing on Dokdo islands-derived microbial resources

This review focuses on the state of research on the microbial resources of Dokdo, Korea, as a strategy for securing national microbial resources. In the Korean peninsula, studies aimed at securing microbial resources are carried out across diverse natural environments, especially in the Dokdo islands. Until 2017, a total of 61 novel microbial genera, species, or newly recorded strains have been reported. Among these, 10 new taxa have had their whole genome sequenced and published, in order to find novel useful genes. Additionally, there have been multiple reports of bacteria with novel characteristics, including promoting plant growth or inducing systemic resistance in plants, calcite-forming ability, electrical activation, and production of novel enzymes. Furthermore, fundamental studies on microbial communities help to secure and define microbial resources in the Dokdo islands. This study will propose several tactics, based on ecological principles, for securing more microbial resources to cope with the current increase in international competition for biological resources.

A Case of Relapsing Peritoneal Dialysis-Associated Peritonitis by Dokdonella koreensis

Peritonitis is a common and serious complication of peritoneal dialysis (PD) with significant morbidity. We report the first case of relapsing Dokdonella koreensis peritonitis in a patient on peritoneal dialysis. A 63-year-old Chinese man, with history of renal failure on continuous ambulatory peritoneal dialysis, presented with cloudy peritoneal effluent and abdominal pain. There was no sign or symptom suggestive of exit-site/tunnel tract infection. Peritoneal effluent cultures yielded Dokdonella koreensis which was initially misidentified as Weeksella virosa and Brevundimonas species by the API® 20 NE and VITEK® 2 GN ID card, respectively. He was treated with intraperitoneal amikacin, but the infection relapsed within a few days upon completing each antibiotic course. He eventually required removal of catheter and was transferred to hemodialysis. Infections due to unusual organisms may pose a diagnostic issue as currently available commercial tests will not be able to identify them. There is a role for using 16S rRNA sequencing to help identify these organisms and guide patient management.

Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing

Membrane bioreactors (MBRs) are a well-established filtration technology that has become a popular solution for treating wastewater. One of the drawbacks of MBRs, however, is the formation of biofilm on the surface of membrane modules. The occurrence of biofilms leads to biofouling, which eventually compromises water quality and damages the membranes. To prevent this, it is vital to understand the mechanism of biofilm formation on membrane surfaces. In this pilot-scale study, a novel reciprocation membrane bioreactor was operated for a period of 8 months and fed with domestic wastewater from an aerobic tank of a local WWTP. Water quality parameters were monitored and the microbial composition of the attached biofilm and suspended aggregates was evaluated in this reciprocating MBR configuration. The abundance of nitrifiers and composition of microbial communities from biofilm and suspended solids samples were investigated using qPCR and high throughput 16S amplicon sequencing. Removal efficiencies of 29%, 16%, and 15% of chemical oxygen demand, total phosphorus and total nitrogen from the influent were observed after the MBR process with average effluent concentrations of 16 mg/L, 4.6 mg/L, and 5.8 mg/L respectively. This suggests that the energy-efficient MBR, apart from reducing the total energy consumption, was able to maintain effluent concentrations that are within regulatory standards for discharge. Molecular analysis showed the presence of amoA Bacteria and 16S Nitrospira genes with the occurrence of nitrification. Candidatus Accumulibacter, a genus with organisms that can accumulate phosphorus, was found to be present in both groups which explains why phosphorus removal was observed in the system. High-throughput 16S rRNA amplicon sequencing revealed the genus Saprospira to be the most abundant species from the total OTUs of both the membrane tank and biofilm samples.

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration

The decomposition of large stocks of soil organic carbon in thawing permafrost might depend on more than climate change-induced temperature increases: indirect effects of thawing via altered bacterial community structure (BCS) or rooting patterns are largely unexplored. We used a 10-year in situ permafrost thaw experiment and aerobic incubations to investigate alterations in BCS and potential respiration at different depths, and the extent to which they are related with each other and with root density. Active layer and permafrost BCS strongly differed, and the BCS in formerly frozen soils (below the natural thawfront) converged under induced deep thaw to strongly resemble the active layer BCS, possibly as a result of colonization by overlying microorganisms. Overall, respiration rates decreased with depth and soils showed lower potential respiration when subjected to deeper thaw, which we attributed to gradual labile carbon pool depletion. Despite deeper rooting under induced deep thaw, root density measurements did not improve soil chemistry-based models of potential respiration. However, BCS explained an additional unique portion of variation in respiration, particularly when accounting for differences in organic matter content. Our results suggest that by measuring bacterial community composition, we can improve both our understanding and the modeling of the permafrost carbon feedback.

Anoxic biodegradation of BTEX in a biotrickling filter

Emissions of BTEX (benzene, toluene, ethylbenzene and xylene) from the petrochemical industry are characterized by a low pollutants concentration and the absence of oxygen. Biodegradation of these pollutants using nitrate as the electron acceptor is of key interest to reuse the residual gas for inertization purposes. However, the biological mineralization of BTEX is often limited by their recalcitrant nature and the toxicity of the secondary metabolites produced. The potential of an anoxic biotrickling filter for the treatment of a model O₂-free BTEX-laden emission at inlet individual concentrations of ~700mgm^-3 was here evaluated. A UV oxidation step was also tested both in the recycling liquid and in the inlet gas emission prior to biofiltration. Removal efficiencies >90% were achieved for both toluene and ethylbenzene, corresponding to elimination capacities (ECs) of 1.4±0.2gm^-3h^-1 and 1.5±0.3gm^-3h^-1, respectively, while ~45% of xylene (EC=0.6±0.1g m^-3h^-1) was removed at a liquid recycling rate of 2mh^-1. Benzene biodegradation was however limited by the accumulation of toxic metabolites in the liquid phase. The oxidation of these intermediates in the recycling liquid by UV photolysis boosted benzene abatement, achieving an average EC of 0.5±0.2gm^-3h^-1 and removals of ~40%. However, the implementation of UV oxidation as a pretreatment step in the inlet gas emission resulted in the deterioration of the BTEX biodegradation capacity of the biotrickling filter. Finally, a high bacterial diversity was observed throughout the entire experiment, the predominant phyla being Proteobacteria and Deinococcus-thermus.

Distribution and microbial community structure analysis of a single-stage partial nitritation/anammox granular sludge bioreactor operating at low temperature

In the last decade, autotrophic nitrogen removal technologies based on anammox metabolism have become state of the art in urban and industrial wastewater treatment systems, due to their advantages over traditional nitrogen removal processes. However, their application is currently limited to the treatment of warm wastewater (25-40°C) mainly due to the low growth rate of the anammox bacteria. The extension of the application field to wastewater characterized by lower temperatures (8-20°C), such as those typical for municipal sewage, allows the design of treatment systems with a net energy production. In this study, the distribution and bacterial community structure of a lab-scale single-stage partial nitritation/anammox (PN/A) granular sludge bioreactor operating at low temperatures was analysed using next-generation sequencing techniques. The presence of ammonium-oxidizing bacteria and anammox bacteria was found, but the appearance of other bacterial species shows a complex microbial ecosystem. Evaluation of ecological roles of representative species inside the single-stage PN/A bioreactor was accomplished. Results obtained will be helpful for the future design and operation of PN/A systems performing at low temperatures.

Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment

A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).

Dokdonella koreensis bacteremia: A case report and review of the literature

Dokdonella koreensis is a recently discovered organism that was isolated from an island in Korea in 2006. The authors describe a case involving a 75-year-old man undergoing chemotherapy for acute myeloid leukemia who developed a bloodstream infection that was eventually discovered to be due to D koreensis. The authors discuss the similarities between this case and the only other reported case of infection due to D koreensis reported in the literature.

Dokdonella koreensis is a non-spore-forming, aerobic, Gram-negative bacillus that was initially isolated from soil. The pathogenicity of this organism in humans remains unclear. The authors report a case of successfully treated D koreensis bacteremia in a patient with a hematological malignancy who presented with a fever and palmar-plantar erythrodysesthesia.

Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan

The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils.

Chiayiivirga flava gen. nov., sp. nov., a novel bacterium of the family Xanthomonadaceae isolated from an agricultural soil, and emended description of the genus Dokdonella

A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031T was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031T formed a discrete monophyletic lineage in the family Xanthomonadaceae , sharing high pairwise sequence similarity of 93.5–95.2 and 94.8 % with species of the genus Dokdonella (94.9 % similarity to the type strain of the type species) and Aquimonas voraii GPTSA 20T, respectively. The genomic DNA G+C content of strain CC-YHH031T was 68.6±0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5 % of total fatty acids) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 1ω9c, iso-C14 : 0, iso-C11 : 0 and iso-C11 : 0 3-OH. The polar lipid profile of strain CC-YHH031T included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1–2) and four unidentified phospholipids (PL1–4). Strain CC-YHH031T was distinguished particularly from the type species of the genus Dokdonella ( Dokdonella koreensis ) by the presence of major amounts of iso-C14 : 0 and summed feature 3 and minor amounts of iso-C17 : 0 and by the complete absence of anteiso-C17 : 0, the presence of PL1–3 and APL1–2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031T is proposed to represent a novel genus and species within the family Xanthomonadaceae , for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031T ( = BCRC 80273T = DSM 24163T).

Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5T, was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5T was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5T was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16–37 °C (optimum 25 °C) and at pH 5.0–8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5T were rods that measured 0.3–0.5 µm in width and 3.0–5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5T clustered with members of the genus Dokdonella and appeared most closely related to Dokdonella koreensis DS-123T (96.4 % sequence similarity), Dokdonella fugitiva A3T (96.1 %), Dokdonella soli KIS28-6T (95.7 %) and Dokdonella ginsengisoli Gsoil 191T (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5T was considered to represent a novel species of the genus Dokdonella , for which the name Dokdonella immobilis is proposed. The type strain is LM2-5T ( = CGMCC 1.7659T  = JCM 15763T).

Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm

A Gram-stain-negative, non-motile, facultatively anaerobic, acid-tolerant rod, designated strain DKE6T, was isolated from an acidic biofilm (pH 2.5) harvested in the pyrite mine Drei Kronen und Ehrt in Germany. The isolate grew optimally at pH 5.5, between 25 and 30 °C and only with casein as the carbon and energy source; although a variety of sugars were tested as growth substrates, none supported growth of the isolate. During casein consumption, strain DKE6T produced ammonium, which led to an alkalinization of the medium. This is a possible strategy to raise the pH in the direct vicinity of the cell and hence modulate the pH towards the growth optimum. The predominant fatty acids (>5 %) were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 66.6 %. Strain DKE6T was not able to oxidize iron or thiosulfate. Iron reduction was detected. The isolate showed 93.3 % 16S rRNA gene sequence similarity to the most closely related cultivable strain, Dokdonella koreensis DS-123T, but <93.2 % sequence similarity with other type strains of closely related type species of the Gammaproteobacteria . On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Gammaproteobacteria , for which we propose the name Metallibacterium scheffleri gen. nov., sp. nov. The type strain of the type species is DKE6T ( = DSM 24874T = JCM 17596T).

Dokdonella kunshanensis sp. nov., isolated from activated sludge, and emended description of the genus Dokdonella

A Gram-negative, aerobic, non-motile, non-spore-forming rod, designated DC-3T, was isolated from activated sludge of a wastewater treatment plant in China. Comparative 16S rRNA gene sequence analysis showed that strain DC-3T belonged to the family Xanthomonadaceae and formed a lineage within the genus Dokdonella . Strain DC-3T shared the highest 16S rRNA gene sequence similarity with Dokdonella soli KIS28-6T (97.1 %) and Dokdonella fugitiva A3T (97.1 %). The G+C content of the genomic DNA was 71.5 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17 : 1ω9c (31.6 %), iso-C15 : 0 (12.6 %), iso-C16 : 0 (21.3 %), iso-C17 : 0 (13.1 %) and iso-C11 : 0 3-OH (6.5 %), which supported the affiliation of strain DC-3T with the genus Dokdonella . DNA–DNA relatedness between strain DC-3T and its closest phylogenetic neighbours was <30 %. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain DC-3T from the recognized species of the genus Dokdonella . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DC-3T represents a novel species of the genus Dokdonella , for which the name Dokdonella kunshanensis sp. nov. is proposed. The type strain is DC-3T ( = CCTCC AB 2011179T  = KACC 16511T). The description of the genus Dokdonella is also emended.

Comparison of the bacterial communities in anaerobic, anoxic, and oxic chambers of a pilot A(2)O process using pyrosequencing analysis

A(2)O process is a sequential wastewater treatment process that uses anaerobic, anoxic, and oxic chambers for nitrogen and phosphorus removal. In this study, the bacterial communities among these chambers were compared, and the diversity of the bacteria involved in nitrogen and phosphorus removal was surveyed. A pilot-scale A(2)O process (50 m(3) day(-1)) was operated for more than 6 months, and bacterial 16S rRNA gene diversity was analyzed using pyrosequencing. A total of 7,447 bacterial sequence reads were obtained from anaerobic (1,546), anoxic (2,158), and oxic (3,743) chambers. Even though there were differences in the atmospheric condition and functionality, no prominent differences could be found in the bacterial community of the three chambers of the pilot A(2)O process. All sequence reads, which were taxonomically analyzed using the Eztaxon-e database, were assigned into 638 approved or tentative genera. Among them, about 72.2 % of the taxa were contained in the phyla Proteobacteria and Bacteroidetes. Phosphate-accumulating bacteria, Candidatus Accumulibacter phosphatis, and two other Accumulibacter were found to constitute 3.1 % of the identified genera. Ammonia-oxidizing bacteria, Nitrosomonas oligotropha, and four other phylotypes in the same family, Nitrosomonadaceae, constituted 0.2 and 0.9 %, respectively. Nitrite-oxidizing bacteria, Nitrospira defluvii, and other three phylotypes in the same family, Nitrospiraceae, constituted 2.5 and 0.1 %, respectively. In addition, Dokdonella and a phylotype of the phylum Chloroflexi, function in nitrogen and/or phosphate removal of which have not been reported in the A(2)O process, constituted the first and third composition among genera at 4.3 and 3.8 %, respectively.

Arenimonas metalli sp. nov., isolated from an iron mine

A Gram-staining-negative, aerobic, rod-shaped bacterium (CF5-1T) was isolated from Hongshan Iron Mine, Daye City, Hubei province, China. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c alcohol and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. The genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CF5-1T was most closely related to Arenimonas malthae (95.3 % gene sequence similarity), Arenimonas oryziterrae (94.7 %), Arenimonas donghaensis (94.6 %) and Arenimonas composti (94.5 %). A taxonomic study using a polyphasic approach showed that strain CF5-1T represents a novel species of the genus Arenimonas , for which the name Arenimonas metalli sp. nov. is proposed. The type strain is CF5-1T ( = CGMCC 1.10787T = KCTC 23460T = CCTCC AB 2010449T).

Aspromonas composti gen. nov., sp. nov., a novel member of the family Xanthomonadaceae

Two novel bacteria, strains TR7-09T and P2-12-1, were isolated from samples of compost and river sediment, respectively. The strains comprised Gram-negative, motile, non-spore-forming rods, produced creamy white colonies on R2A agar, contained Q-8 as the predominant ubiquinone, contained iso-15 : 0, iso-17 : 0ω9c and iso-11 : 0 3-OH as the major fatty acids, and had polar lipid profiles consisting of phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and an unknown phospholipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains were most closely related to Thermomonas haemolytica DSM 13605T, Silanimonas lenta KCTC 12236T and Xanthomonas campestris LMG 568T (with 92.5, 92.0 and 92.0 % sequence similarity, respectively) and formed a separate lineage within the family Xanthomonadaceae. The combined genotypic and phenotypic data supported the conclusion that the strains represent a novel genus and species, for which the name Aspromonas composti gen. nov., sp. nov. is proposed. The type strain is TR7-09T (=KCTC 12666T=DSM 18010T).

Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia

A Gram-negative, motile, aerobic and oval- or rod-shaped bacterial strain, DS-56T, which is phylogenetically closely related to the genus Devosia, was isolated from soil from Dokdo, Korea. Strain DS-56T grew optimally at pH 6.5–7.5 and 25 °C in the presence of 0.5 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DS-56T joins the cluster comprising Devosia species, at a bootstrap resampling value of 100 %. The levels of 16S rRNA gene sequence similarity between strain DS-56T and the type strains of recognized Devosia species ranged from 95.4 to 96.4 %. Strain DS-56T contained Q-11 as the predominant ubiquinone, unlike Devosia species, which contain Q-10 as the predominant ubiquinone. The novel strain also contained some fatty acids, including branched and hydroxy fatty acids, that are not detected in Devosia species. The DNA G+C content of strain DS-56T was 66.2 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-56T represents a novel species of the genus Devosia, for which the name Devosia insulae sp. nov. is proposed. The type strain is DS-56T (=KCTC 12821T=DSM 17955T).

First reported infections caused by three newly described genera in the family Xanthomonadaceae

Members of the family of Xanthomonadaceae are typically characterized as environmental organisms. With the exception of Stenotrophomonas maltophilia, these organisms are infrequently implicated as human pathogens. We describe three cases of central venous catheter-associated bloodstream infections caused by Dokdonella koreensis, Aquimonas voraii, and a Luteibacter sp., all newly named genera within the family Xanthomonadaceae. The three patients all had histories of underlying hematological disorders, presented with fever, and recovered fully following treatment. These isolates required 16S rRNA gene sequencing for identification and, unlike S. maltophilia, demonstrated susceptibility to most antibiotics tested. This report represents the first description of human infections caused by these organisms.

Sphingomonas dokdonensis sp. nov., isolated from soil

A Gram-negative, rod-shaped, Sphingomonas-like bacterial strain, DS-4T, was isolated from soil of Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. Strain DS-4T grew optimally on trypticase soy agar medium without NaCl at pH 6.0–6.5 and 25 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c, C16 : 0, C14 : 0 2-OH and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. Sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipid were the major polar lipids. The DNA G+C content was 66.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-4T fell within the evolutionary radiation comprising Sphingomonas species. Levels of 16S rRNA gene sequence similarity between strain DS-4T and the type strains of Sphingomonas species ranged from 93.0 to 97.6 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DS-4T differs from the recognized Sphingomonas species. On the basis of phenotypic, phylogenetic and genetic data, this strain represents a novel species of the genus Sphingomonas, for which the name Sphingomonas dokdonensis sp. nov. is proposed, with DS-4T (=KCTC 12541T=CIP 108841T) as the type strain.

Dokdonella fugitiva sp. nov., a Gammaproteobacterium isolated from potting soil

A Gram-negative bacterium designated A3(T) was isolated from a potting soil produced in Portugal. This organism formed rod-shaped cells, was non-motile and strictly aerobic. Strain A3(T) was catalase-negative, weakly oxidase positive, with an optimum growth temperature of 40 degrees C and an optimum pH value for growth of 7.0. The predominant cellular fatty acids detected were iso-17:1 omega9c, iso-17:0, iso-15:0, iso-16:0 and iso-11:0 3OH and the major respiratory quinone was ubiquinone 8. The G+C content of DNA was 68.3%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relative of strain A3(T) was the type strain of Dokdonella koreensis indicating that the organism is a member of the family Xanthomonadaceae, class Gammaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain A3(T), represents a novel species of the genus Dokdonella for which we propose the name Dokdonella fugitiva sp.nov.