Azospira inquinata sp. nov., a nitrate-reducing bacterium of the family Rhodocyclaceae isolated from contaminated groundwater.

Two novel Gram-stain-negative bacterial strains, Azo-3T and Azo-2, were isolated from a toluene-producing enrichment culture that originated from contaminated groundwater at a site in southeast Louisiana (USA). Cells are non-spore forming straight to curved rods with single polar flagella. Strains Azo-3T and Azo-2 are oxidase-positive, catalase-negative, use nitrate and nitrite as electron acceptors, and are able to fix nitrogen. Poly-ß-hydroxybutyrate storage granules are produced. Dominant fatty acids when grown in R2A medium at 37 °C are C16:0, summed feature 3 (C16:1 ω7c and/or C15:0 iso 2OH), C17:0 cyclo and C18:1 ω7c. 16S rRNA gene sequence based phylogenetic analysis indicated that the strains cluster within the family Rhodocyclaceae, class Betaproteobacteria, most closely related to but distinct from type strains of the species Azospira oryzae (96.94% similarity) and Azospira restricta (95.10% similarity). Complete genome sequences determined for strains Azo-3T and Azo-2 revealed DNA G+C content of 62.70 mol%. Genome-wide comparisons based on average nucleotide identity by orthology and estimated DNA-DNA hybridization values combined with phenotypic and chemotaxonomic traits and phylogenetic analysis indicate that strains Azo-3T and Azo-2 represent a novel species within the genus Azospira for which the name Azospira inquinata sp. nov. is proposed. The type strain of Azospira inquinata is Azo-3T (=NRRL B-65590T=DSM 112046T).

Niveibacterium microcysteis sp. nov., isolated from a cyanobacterial bloom sample.

A novel bacterial strain, named HC41T, was isolated from a cyanobacterial bloom sample and was characterized as Gram-stain-negative, rod-shaped and non-motile. According to 16S rRNA phylogenetic analyses, this strain HC41T belongs to the family Rhodocyclaceae and is most closely related to Niveibacterium umoris KACC 17062T (=MIC 2059T; 98.63 %) and Uliginosibacterium gangwonense 5YN10-9 T (=KACC 11603T; 93.64 %). The genome size and DNA G+C content of strain HC41T were 4.8 Mbp and 64.17 mol%, respectively. Moreover, the average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values between strain HC41T and N. umoris KACC 17062T were 81.8, 43.1 and 90.89 %, respectively. Additionally, strain HC41T exhibited weak catalase and oxidase activities and had no motility (swimming and swarming motilities). The cells grew at 11-40 °C (optimum, 30 °C), pH 5.5-8.0 (optimum, pH 7) and with 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl) in Reasoner's 2A medium. Its major respiratory quinone was ubiquinone-8 and its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Furthermore, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; C16 : 1 ω6c and/or C16 : 1 ω7c) were the predominant cellular fatty acids in strain HC41T according to fatty acid methyl ester analysis. Based on its genotypic and phenotypic characteristics, strain HC41T was identified as representing a novel Niveibacterium species, for which the name Niveibacterium microcysteis sp. nov. is proposed (=KACC 22091T=DSM 111425T).

Characterization of nitrous oxide reduction by Azospira sp. HJ23 isolated from advanced wastewater treatment sludge.

A new nitrous oxide (N2O)-reducing bacterium was isolated from a consortium that was enriched using advanced wastewater treatment sludge as an inoculum and N2O as the sole nitrogen source. The isolated facultative anaerobe was identified as Azospira sp. HJ23. Azospira sp. HJ23 exhibited optimum N2O-reducing activity with a C/N ratio of 62 at pH 6 in the temperature range of 37 °C to 40 °C. The optimum carbon source for N2O reduction was a mixture of glucose and acetate. The maximum rate of N2O reduction by Azospira sp. HJ23 was 4.8 mmol·g-dry cell-1·h-1, and its N2O-reducing activity was higher than other known N2O reducers. Azospira sp. HJ23 possessed several functional genes for denitrification. These included narG (NO3- reductase), nirK (NO2- reductase), norB (NO reductase), and nosZ (N2O reductase) genes. These results suggest that Azospira sp. HJ23 can be applied in the denitrification process to minimalize N2O emission.

Genomic resolution of bacterial populations in saccharin and cyclamate degradation.

The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.

Uliginosibacterium sediminicola sp. nov., isolated from freshwater sediment.

Strain M1-21T is a Gram-stain-negative, strictly aerobic and short-rod-shaped bacterium, motile by means of a single polar flagellum; it was isolated from freshwater sediment in Korea. It grew at 10-40 °C (optimum 25 °C), pH 6.0-8.0 (optimum pH 7.0) and with 0-0.75 % (w/v) NaCl (optimal growth occurred in the absence of NaCl) on R2A agar, and it accumulated poly-ß-hydroxybutyrate granules inside the cells. According to 16S rRNA gene sequence analysis, strain M1-21T showed highest sequence similarity with Uliginosibacterium gangwonense (94.7 %) and Uliginosibacterium paludis (94.4 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain M1-21T belongs to the genus Uliginosibacterium. The DNA G+C content of strain M1-21T was 61.9 mol%. The predominant respiratory quinone was ubiquinone-8. The major fatty acids (>10 % of the total) were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain M1-21T showed distinct phenotypic characteristics that differentiated it from species of the genus Uliginosibacterium. Based on these results, strain M1-21T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium sediminicola sp. nov. is proposed. The type strain is M1-21T (=KACC 19271T=JCM 32000T).

Viridibacterium curvum gen. nov., sp. nov., isolated from freshwater.

A Gram stain-negative, yellowish green-pigmented, facultatively anaerobic, motile, curved rod-shaped bacterium designated as strain JJ016T was isolated from an artificial lake in South Korea, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ016T indicated that the isolate belonged to the family Rhodocyclaceae and exhibited 95.0% identity to Uliginosibacterium gangwonense 5YN10-9T. The major cellular fatty acids of the novel strain were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:0, C14:0, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The DNA G+C content of strain JJ016T was 61.9 mol%. The major respiratory quinone and major polar lipid of strain JJ016T were ubiquinone-8 and phosphatidylethanolamine, respectively. Based on the morphological and physiological properties and the biochemical evidence presented, we concluded that strain JJ016T represents a novel species of a new genus in the family Rhodocyclaceae, for which the name Viridibacterium curvum gen. nov., sp. nov. is proposed. The type strain is JJ016T (=KACC 16899T =JCM 18715T).

Spatio-Temporal Variations in the Abundance and Structure of Denitrifier Communities in Sediments Differing in Nitrate Content.

Spatial and temporal variations related to hydric seasonality in abundance and diversity of denitrifier communities were examined in sediments taken from two sites differing in nitrate concentration along a stream Doñana National Park during a 3-year study. We found a positive relationship between the relative abundance of denitrifiers, determined as narG, napA, nirK, nirS and nosZ denitrification genes, and sediment nitrate content, with similar spatial and seasonal variations. However, we did not find association between denitrification activity and the community structure of denitrifiers. Because nosZ showed the strongest correlation with the content of nitrate in sediments, we used this gene as a molecular marker to construct eight genomic libraries. Analysis of these genomic libraries revealed that diversity of the nosZ-bearing communities was higher in the site with higher nitrate content. Regardless of nitrate concentration in the sediments, the Bradyrhizobiaceae and Rhodocyclaceae were the most abundant families. On the contrary, Rhizobiaceae was exclusively present in sediments with higher nitrate content. Results showed that differences in sediment nitrate concentration affect the composition and diversityof nosZ-bearing communities.

Carbon-driven enrichment of the crucial nitrate-reducing bacteria in limed peat soil microcosms.

Bacteria of Dechloromonas were recognized as potential functional important denitrifiers in a long-term shell sand-amended peat soil. Different microcosms in a solid matrix and slurry systems with the addition of carbon and nitrogen sources, for example, clover leaves, glutamate and nitrate, were established. The bacterial community structures were analysed by pyrosequencing of the 16S rRNA gene to select the conditions for enriching bacteria of Dechloromonas. The results showed that a relatively even bacterial community in the initial soil shifted to communities dominated by a few types of nitrate-reducing bacteria after the incubation, which strongly responded to the carbon substrates addition and consumption. The bacteria of several genera including Dechloromonas, Pseudomonas, Clostridium, Aeromonas and Ferribacterium were significantly enriched after a certain period of time. The bacteria of Dechloromonas became one of the most predominant bacteria in the incubated community. Especially when added the mixed carbon substrates into the solid soil matrix, as high as 34% of abundance was detected. This study proved that the functional important bacteria from the genus of Dechloromonas could be enriched to an extremely high abundance by using proper culture condition which will benefit to the isolation or direct metagenomics study for Dechloromonas. SIGNIFICANCE AND IMPACT OF THE STUDY: The study of key players in a microbial community is always of important. In this study, the functional important denitrifiers in a shell sand-amended peat soil were investigated. Using different carbon sources in the incubation, we found the bacteria from the genus of Dechloromonas were enriched to an abundance of higher than 34% with several other denitrifiers together. This work provides us helpful insights not only for knowing the diversity of denitrifiers in the studied peat soil, but also for understanding their response to the carbon sources and the culture conditions.

Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.

A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.

Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae).

The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500 years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ hybridization, suggesting maternal inheritance. Bacterial genomes recovered from metagenomic data derived from whole insects or tissues both from D. coccus and from D. opuntiae were around 3.6 Mb in size. Phylogenomics showed that dactylopiibacteria constituted a closely related clade neighbor to nitrogen fixing bacteria from soil or from various plants including rice and other grass endophytes. Metabolic capabilities were inferred from genomic analyses, showing a complete operon for nitrogen fixation, biosynthesis of amino acids and vitamins and putative traits of anaerobic or microoxic metabolism as well as genes for plant interaction. Dactylopiibacterium nif gene expression and acetylene reduction activity detecting nitrogen fixation were evidenced in D. coccus hemolymph and ovaries, in congruence with the endosymbiont fluorescent in situ hybridization location. Dactylopiibacterium symbionts may compensate for the nitrogen deficiency in the cochineal diet. In addition, this symbiont may provide essential amino acids, recycle uric acid, and increase the cochineal life span.

Oryzomicrobium terrae gen. nov., sp. nov., of the family Rhodocyclaceae isolated from paddy soil.

A polyphasic approach was used to characterize a novel bacterium, designated strain TPP412T, isolated from a paddy soil in Taiwan. Strain TPP412T was Gram-stain-negative, facultatively anaerobic, rod-shaped, motile with a single polar flagellum and lacked bacteriochlorophyll. Growth was observed at 24-45 °C (optimal 25 °C), at pH 5.0-10.0 (optimal pH 7.0) and with 0-0.75 % (w/v) NaCl. Strain TPP412T showed highest 16S rRNA gene sequence similarity to members of the genera Rhodocyclus (94.1-94.5 %), Azospira (93.9-94.5 %) and Propionivibrio (93.4-94.4 %) and established a discrete taxonomic lineage in phylogenetic analysis. The major fatty acids found in strain TPP412T were C12 : 0, C12 : 0 3-OH, iso-C15 : 0 3-OH, C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids consisted of phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified lipid. The polyamine pattern showed a predominance of putrescine and a minor amount of spermidine. The DNA G+C content was 58.4 mol% and the predominant quinone system was ubiquinone-8 (Q-8). The low 16S rRNA gene sequence similarity values (≤94.5%) and distinct phylogenetic clustering clearly distinguished strain TPP412T from other representatives of the family Rhodocyclaceae. Based on the discrete phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain TPP412T is considered to represent a novel species of a new genus in the family Rhodocyclaceae, for which the name Oryzomicrobium terrae gen. nov., sp. nov. is proposed. The type strain of Oryzomicrobium terrae is TPP412T (=BCRC 80905T=JCM 30814T).

Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds.

A bacterial strain designated Ca6T was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil from the site of a former manufactured gas plant in Charlotte, NC, USA, and linked phylogenetically to the family Rhodocyclaceae of the class Betaproteobacteria. Its 16S rRNA gene sequence was highly similar to globally distributed environmental sequences, including those previously designated 'Pyrene Group 1' demonstrated to grow on the PAHs phenanthrene and pyrene by stable-isotope probing. The most closely related described relative was Sulfuritalea hydrogenivorans strain sk43HT (93.6 % 16S rRNA gene sequence identity). In addition to a limited number of organic acids, Ca6T was capable of growth on the monoaromatic compounds benzene and toluene, and the azaarene carbazole, as sole sources of carbon and energy. Growth on the PAHs phenanthrene and pyrene was also confirmed. Optimal growth was observed aerobically under mesophilic temperature, neutral pH and low salinity conditions. Major fatty acids present included summed feature 3 (C16 : 1ω7c or C16 : 1ω6c) and C16 : 0. The DNA G+C content of the single chromosome was 55.14  mol% as determined by complete genome sequencing. Due to its distinct genetic and physiological properties, strain Ca6T is proposed as a member of a novel genus and species within the family Rhodocyclaceae, for which the name Rugosibacter aromaticivorans gen. nov., sp. nov. is proposed. The type strain of the species is Ca6T (=ATCC TSD-59T=DSM 103039T).

Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant.

The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp. in the family Rhodocyclaceae dominated in the oxidation ditch reactor. This dominant Dechloromonas sp. was successfully isolated and subjected to fluorescent staining for polyphosphate, followed by microscopic observations and a spectrofluorometric analysis, which clearly demonstrated that the Dechloromonas isolate exhibited a strong ability to accumulate polyphosphate within its cells. These results indicate the potential key role of Dechloromonas spp. in efficient P removal in the oxidation ditch wastewater treatment process.

Uliginosibacterium paludis sp. nov., isolated from a marsh.

A novel bacterial strain, designated KBP-13T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain KBP-13T were Gram-stain-negative, aerobic, poly-ß-hydroxybutyrate-accumulating, motile rods that formed light yellow colonies. Growth occurred at 15-40 °C (optimum, 30-40 °C), at pH 6.0-8.0 (optimum, pH 6.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-13T belonged to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and its most closely related neighbour was Uliginosibacterium gangwonense 5YN10-9T with sequence similarity of 96.0 %. Strain KBP-13T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 as predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid, one uncharacterized aminolipid, two uncharacterized phospholipids and three uncharacterized glycolipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-13T represents a novel species in the genus Uliginosibacterium, for which the name Uliginosibacterium paludis sp. nov. is proposed. The type strain is KBP-13T (=BCRC 80903T=LMG 28837T=KCTC 42655T).

Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites.

A novel perchlorate- and nitrate-reducing bacterium, Azospira sp. PMJ.

A novel perchlorate-reducing bacterium (PCRB), PMJ, was isolated from the mixed liquor suspended solids in the aerobic tank of a wastewater treatment plant. The 16S ribosomal RNA (rRNA), perchlorate reductase, and chlorite dismutase gene sequences revealed that PMJ belonged to the genus Azospira. PMJ was removed high-strength (700 mg/L) perchlorate and also removed low-strength (≤50 mg/L) perchlorate below the detection limit (2 µg/L) when acetate was used as a sole and carbon source. The maximum specific perchlorate utilization rate, q max, was 0.96 mg ClO4 (-)/mg dry cell weight day, and the half-saturation constant, K S , was lower than 0.002 mg ClO4 (-)/L. PMJ also utilized inorganic electron donors [(H2, S(0), and Fe(II)] with perchlorate as an electron acceptor. Perchlorate reduction by PMJ was completely inhibited by oxygen and chlorate but was not inhibited by nitrate. In the presence of similar concentrations (100∼140 mg/L) of nitrate and perchlorate, PMJ simultaneously removed both electron acceptors. Therefore, it was concluded that the strains PMJ might possess separate pathways for perchlorate and nitrate reduction. These results indicated that Azospira sp. PMJ could be efficiently used for treating perchlorate-contaminated groundwater and wastewater because many of these water bodies are known to contain both perchlorate and nitrate. In addition, low K S value and autotrophic perchlorate reduction of PMJ might be useful to design the biological treatment systems.

Altererythrobacter terrae sp. nov., isolated from mountain soil.

A Gram-negative, non-motile, non-spore-forming, ovoid-shaped bacterium designated as SWU3(T) was isolated from mountain soil collected at Seoul Women's University, South Korea. Based on 16S rRNA sequence analysis, strain SWU3(T) was found to belong to the genus Altererythrobacter. It shares high sequence similarities with A. dongtanensis JM27(T) (96.6 %), A. epoxidivorans JCS350(T) (96.6 %), and A. troitsensis KMM 6042(T) (96.5 %). Growth was observed between 15 and 37 °C (optimum, 30 °C) with pH of 6-9 (optimum, pH 7.0). It could tolerate 0-2 % (w/v) NaCl. Its predominant quinone was found to be ubiquinone (Q-10). Its major cellular fatty acids were determined to be C17:1 ω6c, C18:1 ω7c, and summed featured 3 (C16:1 ω7c/C16:1 ω6c), all of which are similar characteristics to those of species within the genus Altererythrobacter. Its G + C molar content was found to be 58.4 mol%. Phylogenetic evidence, together with phenotypic characteristics showed that strain SWU3(T) represents a new species of the genus Altererythrobacter. The name Altererythrobacter terrae sp. nov. is proposed and the type strain is SWU3(T) (=KEMB 9004-128(T) = JCM 19177(T)).

[Enrichment and Characterization of A Denitrifying Bacteria Consortium from Lihe River's Sediment].

A denitrifying bacteria consortium was enriched from LiHe River's sediment, the dynamics of total nitrogen (TN), nitrate (NO3- -N), nitrite (NO2- -N), ammonium (NH4+ -N) and COD at different enrichment cultivation stages were studied, and the total volume, the releasing rates and the composition of gas released during the denitrification process were analyzed. The full-length 16S rDNA clone library was constructed, enclosing the diversity of the denitrifying bacteria consortium. The results showed, in the enrichment phase 4, under the load of TN 330 mg x L(-1), the best nitrogen removal effect was obtained, which the TN and NO3- -N removal rates reached 90.9% and 100% within 9 hours, respectively. The accumulation amounts of NO2- -N and NH4+ -N were merely 3.39 mg x L(-1) and 16.64 mg x L(-1). And the COD removal rate was 85%. The process released 260 mL of the compound gas, in which the main ingredient was N2 associated with a small quantity of CH4 and CO2. The denitrifying bacteria consortium consisted of the family Pseudomonadaceae and the family Rhodocyclaceae, belonging to Proteobacteria phylum, in which the OUT abundances were 57.8% and 31.6%, respectively. The family Pseudomonadaceae was the predominant group.

Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov.

Three strains of methylotrophic Rhodocyclaceae (FAM1(T), RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus Methyloversatilis. Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7c (49-59%) and 16:0 (32-29%). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the strains FAM1T, RZ18-153 and RZ94 are closely related to each other and almost equally distant from two previously described species of the genus Methyloversatilis, Methyloversatilis universalis and Methyloversatilis thermotolerans. Like other methylotrophic species of the genus Methyloversatilis, all three strains possess one-subunit PQQ-dependent ethanol/methanol dehydrogenase (Mdh-2), the N-methylglutamate pathway and the serine cycle (isocitrate lyase/malate synthase, Icl/ms(+) variant). Like M. universalis, strains FAM1(T), RZ18-153 and RZ94 have a quinohemoprotein amine dehydrogenase, a tungsten-containing formaldehyde ferredoxin oxidoreductase, phenol hydroxylase, and the complete Calvin cycle. Similarly to M. thermotolerans, the three strains possess two-subunit methanol dehydrogenase (MxaFI), monoamine oxidase (MAO) and nitrogenase. Based on the phenotypic and genomic data, the strains FAM1(T), RZ18-153 and RZ94 represent a novel species of the genus Methyloversatilis, for which the name Methyloversatilis discipulorum sp. nov. is proposed. The type strain is FAM1(T) ( = JCM 30542(T) = VKM = B-2888(T)).

Uranium removal and microbial community in a H2-based membrane biofilm reactor.

We evaluated a hydrogen-based membrane biofilm reactor (MBfR) for its capacity to reduce and remove hexavalent uranium [U(VI)] from water. After a startup period that allowed slow-growing U(VI) reducers to form biofilms, the MBfR successfully achieved and maintained 94-95% U(VI) removal over 8 months when the U surface loading was 6-11 e(-) mEq/m(2)-day. The MBfR biofilm was capable of self-recovery after a disturbance due to oxygen exposure. Nanocrystalline UO2 aggregates and amorphous U precipitates were associated with vegetative cells and apparently mature spores that accumulated in the biofilm matrix. Despite inoculation with a concentrated suspension of Desulfovibrio vulgaris, this bacterium was not present in the U(VI)-reducing biofilm. Instead, the most abundant group in the biofilm community contained U(VI) reducers in the Rhodocyclaceae family when U(VI) was the only electron acceptor. When sulfate was present, the community dramatically shifted to the Clostridiaceae family, which included spores that were potentially involved in U(VI) reduction.