Potentially Mobile Denitrification Genes Identified in Azospirillum sp. Strain TSH58.

Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested potential occurrences of horizontal gene transfer (HGT) for the denitrification genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 denitrifying Azospirillum sp. strains and searched for mobile genetic elements that contain denitrification genes. All Azospirillum sp. strains examined in this study possessed multiple replicons (4 to 11 replicons), with their sizes ranging from 7 to 1,031 kbp. Among those, the nitrite reductase gene nirK was located on large replicons (549 to 941 kbp). Genome sequencing showed that Azospirillum strains that had similar nirK sequences also shared similar nir-nor gene arrangements, especially between the TSH58, Sp7T, and Sp245 strains. In addition to the high similarity between nir-nor gene clusters among the three Azospirillum strains, a composite transposon structure was identified in the genome of strain TSH58, which contains the nir-nor gene cluster and the novel IS6 family insertion sequences (ISAz581 and ISAz582). The nirK gene within the composite transposon system was actively transcribed under denitrification-inducing conditions. Although not experimentally verified in this study, the composite transposon system containing the nir-nor gene cluster could be transferred to other cells if it is moved to a prophage region and the phage becomes activated and released outside the cells. Taken together, strain TSH58 most likely acquired its denitrification ability by HGT from closely related Azospirillum sp. denitrifiers.IMPORTANCE The evolutionary history of denitrification is complex. While the occurrence of horizontal gene transfer has been suggested for denitrification genes, most studies report circumstantial evidences, such as disagreement between denitrification gene phylogenies and the 16S rRNA gene phylogeny. Based on the comparative genome analyses of Azospirillum sp. denitrifiers, we identified denitrification genes, including nirK and norCBQD, located on a mobile genetic element in the genome of Azospirillum sp. strain TSH58. The nirK was actively transcribed under denitrification-inducing conditions. Since this gene was the sole nitrite reductase gene in strain TSH58, this strain most likely benefitted by acquiring denitrification genes via horizontal gene transfer. This finding will significantly advance our scientific knowledge regarding the ecology and evolution of denitrification.

Flaw-Containing Alumina Hollow Nanostructures Have Ultrahigh Fracture Strength To Be Incorporated into High-Efficiency GaN Light-Emitting Diodes.

In the present study, we found that α-alumina hollow nanoshell structure can exhibit an ultrahigh fracture strength even though it contains a significant number of nanopores. By systematically performing in situ mechanical testing and finite element simulations, we could measure that the fracture strength of an α-alumina hollow nanoshell structure is about four times higher than that of the conventional bulk size α-alumina. The high fracture strength of the α-alumina hollow nanoshell structure can be explained in terms of conventional fracture mechanics, in that the position and size of the nanopores are the most critical factors determining the fracture strength, even at the nanoscales. More importantly, by deriving a fundamental understanding, we would be able to provide guidelines for the design of reliable ceramic nanostructures for advanced GaN light-emitting diodes (LEDs). To that end, we demonstrated how our ultrastrong α-alumina hollow nanoshell structures could be successfully incorporated into GaN LEDs, thereby greatly improving the luminous efficiency and output power of the LEDs by 2.2 times higher than that of conventional GaN LEDs.

Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-ß-lactamase, in an urban river in South Korea.

Objectives: To examine the presence of pathogenic bacteria carrying New Delhi metallo-ß-lactamase in the environment and to characterize the genome structures of these strains. Methods: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river. Results: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess bla NDM-9 genes. Antimicrobial susceptibility testing indicated resistance of these strains to aminoglycosides, carbapenems, cephems, folate pathway inhibitors, fosfomycin and penicillins, but susceptibility to fluoroquinolones, phenicols, tetracyclines and miscellaneous agents. WGS revealed that the 108 kb IncFII(Y)-like plasmids carry bla NDM-9 sandwiched between IS 15 for the GJ1 strain, IS 26 for the GJ2 strain, IS 15D1 for the GJ3 strain and IS Vsa3 , and further bracketed by IS 26 and Tn AS3 along with the mercury resistance operon upstream and the class 1 integron composed of gene cassettes of aadA2 , dfrA12 and sul1 downstream. An aph(3')-Ia gene conferring resistance to aminoglycosides is located after the integrons. Chromosomally encoded bla LEN-13 , fosA , aqxA and oqxB genes, as well as plasmid-mediated bla TEM-1B and bla CTX-M-65 encoding ESBL, ant(3')-Ia and mph (A) genes, were also identified. Conclusions: The findings of the present study provide us with the information that NDM-9 has been spreading into the environment. Dissemination of NDM-9 in the environment has raised a health risk alarm as this variant of NDM carries MDR genes with highly transferable mobile genetic elements, increasing the possibility of resistance gene transfer among microorganisms in the environment.

Season-Specific Occurrence of Potentially Pathogenic Vibrio spp. on the Southern Coast of South Korea.

Vibrio species are widely distributed in warm estuarine and coastal environments, and they can infect humans through the consumption of raw and mishandled contaminated seafood. In this study, we aimed to isolate and observe the distribution of enteropathogenic Vibrio spp. from environments of the southern coast of South Korea over a season cycle. A total of 10,983 isolates of Vibrio spp. were obtained from tidal water and mud samples over a 1-year period from five sampling sites along the southwest coast of South Korea. We found that Vibrio alginolyticus (n = 6,262) and Vibrio parahaemolyticus (n = 1,757) were ubiquitous in both tidal water and mud year round, whereas Vibrio cholerae (n = 24) and Vibrio vulnificus (n = 130) were seasonally specific to summer. While all V. cholerae isolates were nontoxigenic (non-O1 and non-O139), more than 88% of V. vulnificus isolates possessed the virulence factor elastolytic protease (encoded by vvp). Interestingly, V. parahaemolyticus, which was omnipresent in all seasons, contained the virulence factors thermostable direct hemolysin (encoded by tdh) and thermostable direct hemolysin-related hemolysin (encoded by trh) in larger amounts in June (29 trh-positive strains) and September (14 tdh-, 36 trh-, and 12 tdh- and trh-positive strains) than in December (4 trh-positive strains) and February (3 tdh-positive strains), and virulence factors were absent from isolates detected in April. To understand why virulence factors were detected only in the warm season and were absent in the cold season although the locations are static, long-term monitoring and particularly seasonal study are necessary. IMPORTANCE: The presence of enteropathogenic Vibrio species (Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus), which cause acute diarrheal infection, septicemia, and wound infections upon ingestion through food and water, is usually associated with temperature. The World Health Organization (WHO) has estimated that there are 1.4 to 4.3 million cases and 28,000 to 142,000 deaths per year worldwide caused by cholera disease. In South Korea alone, consumption is as much as 52.4 kg of fish and shellfish per year per capita. Our findings suggested that seasonally specific acceleration of these possible pathogenic Vibrio spp. may threaten seafood safety and increase the risk of illness in South Korea, where local people consume raw fish during warmer months.

Microstructured Air Cavities as High-Index Contrast Substrates with Strong Diffraction for Light-Emitting Diodes.

Two-dimensional high-index-contrast dielectric gratings exhibit unconventional transmission and reflection due to their morphologies. For light-emitting devices, these characteristics help guided modes defeat total internal reflections, thereby enhancing the outcoupling efficiency into an ambient medium. However, the outcoupling ability is typically impeded by the limited index contrast given by pattern media. Here, we report strong-diffraction, high-index-contrast cavity engineered substrates (CESs) in which hexagonally arranged hemispherical air cavities are covered with a 80 nm thick crystallized alumina shell. Wavelength-resolved diffraction measurements and Fourier analysis on GaN-grown CESs reveal that the high-index-contrast air/alumina core/shell patterns lead to dramatic excitation of the low-order diffraction modes. Large-area (1075 × 750 µm(2)) blue-emitting InGaN/GaN light-emitting diodes (LEDs) fabricated on a 3 µm pitch CES exhibit ∼39% enhancement in the optical power compared to state-of-the-art, patterned-sapphire-substrate LEDs, while preserving all of the electrical metrics that are relevant to LED devices. Full-vectorial simulations quantitatively demonstrate the enhanced optical power of CES LEDs and show a progressive increase in the extraction efficiency as the air cavity volume is expanded. This trend in light extraction is observed for both lateral- and flip-chip-geometry LEDs. Measurements of far-field profiles indicate a substantial beaming effect for CES LEDs, despite their few-micron-pitch pattern. Near-to-far-field transformation simulations and polarization analysis demonstrate that the improved extraction efficiency of CES LEDs is ascribed to the increase in emissions via the top escape route and to the extraction of transverse-magnetic polarized light.

Pathogenic Escherichia coli strains producing extended-spectrum ß-lactamases in the Yeongsan River basin of South Korea.

A total of 3564 E. coli isolates obtained from Yeongsan River basin of South Korea were investigated for their production of extended-spectrum ß-lactamases (ESBLs) and potential pathogenicity to better understand the linkage between antibiotic-resistant pathogens in the environment and their public health risks. Interestingly, 60% (53 of 89) of the screen-positive ESBL producers were determined to be potentially one or both of the diarrheagenic and extraintestinal pathogenic (ExPEC) pathotypes, suggesting that trade-off between resistance and virulence of E. coli may not apply to this study. In addition, 67% (60 of 89) of the screen-positive ESBL producers possessed more than one ß-lactamase gene, and most (59 of 63) of the ESBL producers had the CTX-M-14 enzyme, which is the most dominant ESBL and seems to be related to urban anthropogenic activities. About 68% (36 of 53) of the potential pathogenic strains were resistant to more than 2 non-ß-lactam antibiotics. Results from this study indicate that the Yeongsan River basin has been contaminated with antibiotic-resistant and potential pathogenic E. coli strains. While few studies have examined pathogenecity of ESBL-producing bacteria, this study reports the possible public health risk which could be caused by the fecal indicator bacterium itself containing both ESBL genes and virulence factors. This will likely impact the dissemination of potential pathogenic E. coli producing ESBLs in the environment and suggests the need for further investigations of antibiotic-resistant pathogens to prevent public health impacts in the Yeongsan River basin.

Whole-genome sequence of Bacillus pseudomycoides strain I32, a nitrous oxide-producing bacterium isolated from a woodchip bioreactor.

We report here the draft whole-genome sequence of Bacillus pseudomycoides strain I32, a bacterium isolated from the denitrifying woodchip bioreactor and showing rhizoidal colony morphology with filamentous swirling pattern on the agar medium plate. The isolate produced nitrous oxide without known nitric oxide reductase genes on the genome.

Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review.

Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.

Draft Genome sequence of Escherichia coli AI27, a porcine isolate belonging to phylogenetic group B1.

Escherichia coli AI27 is a putatively commensal strain isolated from feces of a pig. Here we report the draft genome sequence of E. coli AI27. This is the first porcine strain in the phylogenetic group B1 whose genome sequence has been determined.

Draft genome sequence of Escherichia coli W26, an enteric strain isolated from cow feces.

An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging to E. coli phylogroup B1.

Integrated online system for a pyrosequencing-based microbial source tracking method that targets Bacteroidetes 16S rDNA.

Genotypic microbial source tracking (MST) methods are now routinely used to determine sources of fecal contamination impacting waterways. We previously reported the development of a pyrosequencing-based MST method that assigns contamination sources based on shared operational taxonomic units (OTUs) between fecal and environmental bacterial communities. Despite decreasing sequencing costs, pyrosequencing-based MST approaches are not used in routine water quality monitoring studies due in large part to difficulties in handling massive data sets and difficulties in determining sources of fecal contamination. In the studies presented here we describe the development of an online MST tool, PyroMiST ( http://env1.gist.ac.kr/∼aeml/MST.html) that uses total bacterial or Bacteroidetes 16S rDNA pyrosequencing reads to determine fecal contamination of waterways. The program cd-hit was used for OTU assignment and a Perl script was used to calculate the number of shared OTUs. The analyses require only a small number of pyrosequencing reads from environmental samples. Our results indicate that PyroMiST provides a user-friendly web interface for pyrosequence data that significantly reduces analysis time required to determine potential sources of fecal contamination in the environment.

Probable role of Cutibacterium acnes in the gut of the polychaete Capitella teleta.

Capitella teleta, a marine polychaete that feeds on a refractory diet consisting of sediment, was shown to contain unique gut microbiota comprised of microbial functional groups involved in fermentation. Results of our previous studies showed that C. teleta's core gut microbiota were dominated by propionibacteria, and that these bacteria were more abundant in worms than in sediment and feces. In order to test the hypothesis that the worm nutritionally benefits from its gut microbiota, we identified, and genetically and biochemically characterized Cutibacterium acnes strains (formerly Propionibacterium acnes) that were isolated from the gut of C. teleta. Here we show that 13 worm-isolated Cutibacterium acnes strains primarily belonged to phylotype group IB, likely as a clonal population. We also provide evidence that all tested strains produced propionate and vitamin B12, which are essential host-requiring microbial metabolites. The presence of C. acnes in C. teleta was not unique to our worm culture and was also found in those obtained from geographically distant laboratories located in the U.S. and Europe. Moreover, populations of worm gut-associated C. acnes increased following antibiotic treatment. Collectively, results of this study demonstrated that C. acnes is a member of the worm's core functional microbiota and is likely selectively favored by the physiology and chemistry of the host gut environment. To our knowledge, this is the first report of the presence of C. acnes in the C. teleta gut. Our data strongly suggest that C. acnes, a bacterium previously studied as an opportunistic pathogen, can likely act as a symbiont in C. teleta providing the host essential nutrients for survival, growth, and reproduction.

Prevalence of season-specific Escherichia coli strains in the Yeongsan River Basin of South Korea.

Seasonal and spatial variation in the genotypic richness of 3480 Escherichia coli isolates obtained from the Yeongsan River basin in South Korea was investigated by using the horizontal fluorophore-enhanced rep-PCR (HFERP) DNA fingerprinting technique. The relationship between 60 E. coli isolates from each of 58 freshwater samples was determined by using multidimensional scaling (MDS) analysis and self-organized maps (SOMs). The MDS analysis, done based on HFERP DNA fingerprints, showed that E. coli isolates obtained in October through December clustered tightly, while those obtained in other sampling periods were more genetically diverse. However, site-specific E. coli genotypes were not observed. SOMs analysis, done using the 10 most frequently isolated E. coli genotypes, showed the occurrence of season-specific E. coli genotypes and the main SOMs clusters were most influenced by temperature, strain diversity and biochemical oxygen demand. Diversity among E. coli genotypes tended to decrease as water temperature decreased, and the numbers of E. coli genotypes observed in urban area were greater, more diverse and less dependent on water temperature than those obtained from agricultural areas. Taken together, our findings indicate that that an ecological approach needs to be considered in order to obtain a better understanding of E. coli community dynamics in the environment and that SOMs analysis is useful to visualize the multidimensional dependent variables that are influencing the types and dynamics of specific E. coli genotypes in the environment.

Bioturbation by the marine polychaete Capitella teleta alters the sediment microbial community by ingestion and defecation of sediment particles.

Deposit-feeding benthic invertebrates are known to modify sediment structure and impact microbial processes associated with biogeochemical cycles in marine sedimentary environments. Despite this, however, there is limited information on how sediment ingestion and defecation by marine benthos alters microbial community structure and function in sediments. In the current study, we used high-throughput sequencing data of 16S rRNA genes obtained from a previous microcosm study to examine how sediment processing by the marine polychaete Capitella teleta specifically affects sediment microbiota. Here we show that both sediment ingestion and defecation by C. teleta significantly alters overall microbial community structure and function. Sediment processing by C. teleta resulted in significant enrichment of sediment microbial communities involved in sulfur and carbon cycling in worm fecal pellets. Moreover, C. teleta's microbiota was predominantly comprised of bacterial functional groups involved in fermentation, relative to microbiota found outside of the host. Collectively, results of this study indicate that C. teleta has the ability to alter microbial biogeochemical cycles in the benthic sedimentary environment by altering microbial assemblages in the worm gut, and in the sediment ingested and defecated by worms as they feed on sediment particles. In this sense, C. teleta plays an important role as an ecosystem engineer and in shaping nutrient cycling in the benthic environment.

A hybrid DNA sequencing approach is needed to properly link genotype to phenotype in multi-drug resistant bacteria.

Antibiotic resistance genes (ARGs) are now viewed as emerging contaminants posing a potential worldwide human health risk. The degree to which ARGs are transferred to other bacteria via mobile genetic elements (MGEs), including insertion sequences (ISs), plasmids, and phages, has a strong association with their likelihood to function as resistance transfer determinants. Consequently, understanding the structure and function of MGEs is paramount to assessing future health risks associated with ARGs in an environment subjected to strong antibiotic pressure. In this study we used whole genome sequencing, done using MinION and HiSeq platforms, to examine antibiotic resistance determinants among four multidrug resistant bacteria isolated from fish farm effluent in Jeju, South Korea. The combined data was used to ascertain the association between ARGs and MGEs. Hybrid assembly using HiSeq and MinION reads revealed the presence of IncFIB(K) and pVPH2 plasmids, whose sizes were verified using pulsed field gel electrophoresis. Twenty four ARGs and 95 MGEs were identified among the 955 coding sequences annotated on these plasmids. More importantly, 22 of 24 ARGs conferring resistance to various antibiotics were found to be located near MGEs, whereas about a half of the ARGs (11 out of 21) were so in chromosomes. Our results also suggest that the total phenotypic resistance exhibited by the isolates was mainly contributed by these putatively mobilizable ARGs. The study gives genomic insights into the origins of putatively mobilizable ARGs in bacteria subjected to selection pressure.

Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds.

While many current microbial source tracking (MST) methods rely on the use of specific molecular marker genes to identify sources of fecal contamination, these methods often fail to determine all point and nonpoint contributors of fecal inputs into waterways. In this study, we developed a new library-dependent MST method that uses pyrosequencing-derived shared operational taxonomy units (OTUs) to define sources of fecal contamination in waterways. A total 56,841 pyrosequencing reads of 16S rDNA obtained from the feces of humans and animals were evaluated and used to compare fecal microbial diversity in three freshwater samples obtained from the Yeongsan river basin in Jeonnam Province, South Korea. Sites included an urbanized agricultural area (Y1) (Escherichia coli counts ≥ 1600 CFU/100 mL), an open area (Y2) with no major industrial activities (940 CFU/100 mL), and a typical agricultural area (Y3) (≥ 1600 CFU/100 mL). Data analyses indicated that the majority of bacteria in the feces of humans and domesticated animals were comprised of members of the phyla Bacteroidetes or Firmicutes, whereas the majority of bacteria in wild goose feces and freshwater samples were classified to the phylum Proteobacteria. Analysis of OTUs shared between the fecal and environmental samples suggested that the potential sources of the fecal contamination at the sites were of human and swine origin. Quantification of fecal contamination was also examined by comparing the density of pyrosequencing reads in each fecal sample within shared OTUs. Taken together, our results indicated that analysis of shared OTUs derived from barcoded pyrosequencing reads provide the necessary resolution and discrimination to be useful as a next generation platform for microbial source tracking studies.

Lack of evidence for the role of gut microbiota in PAH biodegradation by the polychaete Capitella teleta.

Capitella teleta is a marine sediment-feeding polychaete known to degrade various polycyclic aromatic hydrocarbons (PAHs) and reported to possess genes involved in PAH transformation, such as those in the P450 cytochrome superfamily. Previous research focusing on biodegradation of PAHs by C. teleta demonstrated that these worms are effective biodegraders, but overlooked the possible role of its gut microbiota in facilitating PAH metabolism. Recently, C. teleta's microbiome was characterized and found to contain several bacterial genera known to contain PAH-degrading members, including Acinetobacter, Thalassotalea, and Achromobacter. Despite this, however, no data have thus far been presented demonstrating the role of C. teleta's gut microbiota in PAH degradation. The present study was designed to more conclusively determine the presence of PAH-degrading bacteria in worm digestive tracts and to more clearly distinguish the relative roles of worm versus gut-microbial metabolism in the removal of PAH from sediment. To do this, we manipulated marine sediment microorganisms and worm gut microbiota by autoclaving and antibiotic treatment, respectively. Our results showed that no fluoranthene degradation occurred in microcosms in the absence of worms. More importantly, there was no significant difference in fluoranthene degradation between antibiotic-treated and non-treated worms. We also found no evidence of fluoranthene degradation using resting cells of gut microbes of C. teleta, and we were unable to isolate fluoranthene-degrading bacterial strains from enrichments of polychaete gut contents, despite multiple attempts. Gut microbiota in worms treated with antibiotics recovered, through bidirectional transfer, between worms and sediment after 2 weeks of microcosm incubation, and gut microbes appear to be required for the survival and growth of C. teleta. Our results build on previous studies suggesting that C. teleta itself is primarily responsible for the metabolism of fluoranthene in ingested sediment. We hypothesize that C. teleta's core microbiota, which includes members of Propionibacterium as the most abundant genus, likely aid worms in obtaining key nutrients (e.g., vitamins) from its sediment diet.

Absence of Escherichia coli phylogenetic group B2 strains in humans and domesticated animals from Jeonnam Province, Republic of Korea.

Multiplex PCR analyses of DNAs from genotypically unique Escherichia coli strains isolated from the feces of 138 humans and 376 domesticated animals from Jeonnam Province, South Korea, performed using primers specific for the chuA and yjaA genes and an unknown DNA fragment, TSPE4.C2, indicated that none of the strains belonged to E. coli phylogenetic group B2. In contrast, phylogenetic group B2 strains were detected in about 17% (8 of 48) of isolates from feces of 24 wild geese and in 3% (3 of 96) of isolates obtained from the Yeongsan River in Jeonnam Province, South Korea. The distribution of E. coli strains in phylogenetic groups A, B1, and D varied depending on the host examined, and there was no apparent seasonal variation in the distribution of strains in phylogenetic groups among the Yeongsan River isolates. The distribution of four virulence genes (eaeA, hlyA, stx(1), and stx(2)) in isolates was also examined by using multiplex PCR. Virulence genes were detected in about 5% (38 of 707) of the total group of unique strains examined, with 24, 13, 13, and 9 strains containing hlyA, eaeA, stx(2), and stx(1), respectively. The virulence genes were most frequently present in phylogenetic group B1 strains isolated from beef cattle. Taken together, results of these studies indicate that E. coli strains in phylogenetic group B2 were rarely found in humans and domesticated animals in Jeonnam Province, South Korea, and that the majority of strains containing virulence genes belonged to phylogenetic group B1 and were isolated from beef cattle. Results of this study also suggest that the relationship between the presence and types of virulence genes and phylogenetic groupings may differ among geographically distinct E. coli populations.

Denitrifying Bacteria Active in Woodchip Bioreactors at Low-Temperature Conditions.

Woodchip bioreactor technology removes nitrate from agricultural subsurface drainage by using denitrifying microorganisms. Although woodchip bioreactors have demonstrated success in many field locations, low water temperature can significantly limit bioreactor efficiency and performance. To improve bioreactor performance, it is important to identify the microbes responsible for nitrate removal at low temperature conditions. Therefore, in this study, we identified and characterized denitrifiers active at low-temperature conditions by using culture-independent and -dependent approaches. By comparative 16S rRNA (gene) analysis and culture isolation technique, Pseudomonas spp., Polaromonas spp., and Cellulomonas spp. were identified as being important bacteria responsible for denitrification in woodchip bioreactor microcosms at relatively low temperature conditions (15°C). Genome analysis of Cellulomonas sp. strain WB94 confirmed the presence of nitrite reductase gene nirK. Transcription levels of this nirK were significantly higher in the denitrifying microcosms than in the non-denitrifying microcosms. Strain WB94 was also capable of degrading cellulose and other complex polysaccharides. Taken together, our results suggest that Cellulomonas sp. denitrifiers could degrade woodchips to provide carbon source and electron donors to themselves and other denitrifiers in woodchip bioreactors at low-temperature conditions. By inoculating these denitrifiers (i.e., bioaugmentation), it might be possible to increase the nitrate removal rate of woodchip bioreactors at low-temperature conditions.

Complete Genome Sequence of Klebsiella quasipneumoniae Strain S05, a Fouling-Causing Bacterium Isolated from a Membrane Bioreactor.

We report here the complete genome sequence of Klebsiella quasipneumoniae strain S05, a bacterium capable of producing membrane fouling-causing soluble substances and capable of respiring on oxygen, nitrate, and an anodic electrode. The genomic information of strain S05 should help predict metabolic pathways associated with these unique biological properties of this bacterium.