Publications

theoretical simulation of the spectroscopy and dynamics of a red copper protein.	the electronic absorption, circular dichroism and x-ray absorption spectroscopy of the red copper protein nitrosocyanin is simulated with classical molecular dynamics simulations in conjunction with time-dependent density functional theory (tddft) and multireference configuration interaction (mrci) calculations on the active site, with the remainder of the protein and solvent included via point charges. in the molecular dynamics simulations of the oxidised form of the protein an exogenous water ...	2011	21322477
fate of nitrogen-fixing bacteria in crude oil contaminated wetland ultisol.	the effect of crude oil on the growth of legumes (calopogonium muconoides and centrosema pubescens) and fate of nitrogen-fixing bacteria in wetland ultisol was investigated using standard cultural techniques. the results revealed observable effects of oil on soil physico-chemistry, plant growth and nodulation as well as on densities of heterotrophic, hydrocarbonoclastic and nitrogen fixing bacteria. the effects however varied with different levels (0.5%, 1%, 5%, 10%, 15% and 20%) of pollution. a ...	2011	21755289
[analysis of the changes of microbial community structure on bio-carrier of recirculating aquaculture systems (ras)].	in order to study the variation of microbial community structure and the mechanism of denitrification on bio-carrier in recirculating aquaculture systems (ras) during the periods of bio-film formation and operation the systems, traditional microbiological methods were applied to count the quantity of heterotrophic bacteria, ammonia oxidize bacteria and nitrite oxidize bacteria. the amplified products of variable v3 region of bacterial 16s rdna were separated by using denaturing gradient gel elec ...	2011	21404692
nitrifying bacterial community structure of a full-scale integrated fixed-film activated sludge process as investigated by pyrosequencing.	nitrifying bacterial community structures of suspended and attached biomasses in a full-scale integrated fixed-film activated sludge process were investigated by analyzing 16s rrna gene sequences obtained from pyrosequencing. the suspended biomass had a higher number of ammoniaoxidizing bacterial sequences (0.8% of total sequences) than the attached biomass (0.07%), although most of the sequences were within the nitrosomonas oligotropha lineage in both biomasses. nitrospira-like nitrite-oxidizin ...	2011	21464601
a specific inorganic triphosphatase from nitrosomonas europaea: structure and catalytic mechanism.	the cyth superfamily of proteins is named after its two founding members, the cyab adenylyl cyclase from aeromonas hydrophila and the human 25-kda thiamine triphosphatase. because these proteins often form a closed +¦-barrel, they are also referred to as "triphosphate tunnel metalloenzymes" (ttm). functionally, they are characterized by their ability to bind triphosphorylated substrates and divalent metal ions. these proteins exist in most organisms and catalyze different reactions, depending on ...	2011	21840996
investigation of nitrogen converters in membrane bioreactor.	in this study, the activity and diversity of nitrogen converters, ammonia-oxidizing bacteria (aob) and nitrite-oxidizing bacteria (nob), ammonia-oxidizing archaea (aoa) and anammox bacteria in a pilot-scale membrane bioreactor (mbr) were investigated and monitored using amoa and 16s rdna-based molecular tools. the pilot-scale mbr (100 m(3)/day) was located inside the full-scale pasakoy advanced wastewater treatment plant (wwtp), and operated for approximately 5 months without sludge purge. durin ...	2011	21469010
elemental profiling of single bacterial cells as a function of copper exposure and growth phase.	the elemental composition of single cells of nitrosomonas europaea 19718 was studied via synchrotron x-ray fluorescence microscopy (xfm) as a function of inhibition by divalent copper (cu(ii)) and batch growth phase. based on xfm, the intracellular cu concentrations in exponential phase cultures of n. europaea exposed to cu(ii) were statistically higher than in stationary phase cultures at the 95% confidence interval (+¦ôçè=ôçè0.05). however, the impact of cu inferred from specific oxygen uptake ...	2011	21698126
effects of nitrite on ammonia-oxidizing activity and gene regulation in three ammonia-oxidizing bacteria.	nitrite is the highly toxic end product of ammonia oxidation that accumulates in the absence of a nitrite-consuming process and is inhibitory to nitrifying and other bacteria. the effects of nitrite on ammonia oxidation rates and regulation of a common gene set were compared in three ammonia-oxidizing bacteria (aob) to determine whether responses to this toxic metabolite were uniform. mid-exponential-phase cells of nitrosomonas europaea atcc 19718, nitrosospira multiformis atcc 25196, and nitros ...	2011	21470297
bacterial community structure of a full-scale biofilter treating pig house exhaust air.	biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. quantitative fluorescence in situ hybridization (fish) and 16s rrna gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter consisting of two consecutive compartments (front and back filter). the analysis revealed a highly specialized bacterial community of limited diversity, dominated by a few groups of betaproteobacteria (e ...	2011	21514081
investigating nitrosomonas europaea stress biomarkers in batch, continuous culture, and biofilm reactors.	the understanding of nitrification inhibition in ammonia oxidizing bacteria (aob) by priority pollutants and emerging contaminants is critical in managing the nitrogen cycle to preserve current water supplies, one of the national academy of engineers grand challenges in engineering for the twenty-first century. nitrosomonas europaea is an excellent model aob for nitrification inhibition experimentation due to its well-defined nh(3) metabolism and the availability of a wide range of physiological ...	2011	21514466
Improving nitrogen removal in two modified decentralized wastewater systems.	Efficient nutrient removal in decentralized wastewater treatment systems is a challenging task. To improve the removal of organic matter and nitrogen from wastewater, two types of bioreactors using membrane-aerated biofilm reactor (MABR) and microbial fuel cell (MFC) techniques were evaluated. During more than 250 days of continuous-flow reactor operation, both reactors showed consistently high chemical oxygen demand removal (>86%). At an influent ammonium-nitrogen (NH4(+)-N) concentration of 30 ...	2011	21905409
genomics for key players in the n cycle from guinea pigs to the next frontier.	while sequencing methods were available in the late 1970s, it was not until the human genome project and a significant influx of funds for such research that this technology became high throughput. the fields of microbiology and microbial ecology, among many others, have been tremendously impacted over the years, to such an extent that the determination of complete microbial genome sequences is now commonplace. given the lower costs of next-generation sequencing platforms, even small laboratorie ...	2011	21514469
genetic transformation of ammonia-oxidizing bacteria.	the study of traits of ammonia-oxidizing bacteria (aob) by genetic transformation is an approach that is facilitated by the availability of aob genome sequences. to transform an aob, a vector construct is introduced into the cells by electroporation or conjugation to effect the inactivation, complementation, or expression of a selected gene. for inactivation studies, the vector construct should contain the gene of interest with an antibiotic resistance cassette and recombine into the cell's chro ...	2011	21185445
cell-mediated deposition of porous silica on bacterial biofilms.	living hybrid materials that respond dynamically to their surrounding environment have important applications in bioreactors. silica based sol-gels represent appealing matrix materials as they form a mesoporous biocompatible glass lattice that allows for nutrient diffusion while firmly encapsulating living cells. despite progress in sol-gel cellular encapsulation technologies, current techniques typically form bulk materials and are unable to generate regular silica membranes over complex geomet ...	2011	21538338
hessian fly-associated bacteria: transmission, essentiality, and composition.	plant-feeding insects have been recently found to use microbes to manipulate host plant physiology and morphology. gall midges are one of the largest groups of insects that manipulate host plants extensively. hessian fly (hf, mayetiola destructor) is an important pest of wheat and a model system for studying gall midges. to examine the role of bacteria in parasitism, a systematic analysis of bacteria associated with hf was performed for the first time. diverse bacteria were found in different de ...	2011	21858016
dissecting iron uptake and homeostasis in nitrosomonas europaea.	the chemolithoautotroph nitrosomonas europaea oxidizes about 25 mol of nh(3) for each mole of co(2) that is converted to biomass using an array of heme and nonheme fe-containing proteins. hence mechanisms of efficient iron (fe) uptake and homeostasis are particularly important for this betaproteobacterium. among nitrifiers, n.europaea has been the most studied to date. characteristics that make n.europaea a suitable model to study fe uptake and homeostasis are as follows: (a) its sequenced genom ...	2011	21185446
liquid chromatography-mass spectrometry-based proteomics of nitrosomonas.	during the last century, the research on aerobic ammonium-oxidizing bacteria (aob) lead to many exciting physiological and biochemical discoveries. nevertheless the molecular biology of aob is not well understood. the availability of the genome sequences of several nitrosomonas species opened up new possiblities to use state of the art transcriptomic and proteomic tools to study aob. with the currect technology, thousands of proteins can be analyzed in several hours of measurement and translated ...	2011	21185449
geobacter sulfurreducens cytochrome c peroxidases: electrochemical classification of catalytic mechanisms.	bacterial cytochrome c peroxidase (ccp) enzymes are diheme redox proteins that reduce hydrogen peroxide to water. they are canonically characterized by a peroxidatic (called l, for "low reduction potential") active site heme and a secondary heme (h, for "high reduction potential") associated with electron transfer, and an enzymatic activity that exists only when the h-heme is prereduced to the fe(ii) oxidation state. the prereduction step results in a conformational change at the active site its ...	2011	21524102
[diversity of beta-proteobacterial ammonia-oxidizing bacteria and ammonia-oxidizing archaea in shrimp farm sediment].	in order to study the diversity of ammonia-oxidizing bacteria (aob) and ammonia-oxidizing archaea (aoa) in shrimp farm sediment.	2011	21465792
ammonia-oxidizing bacteria in biofilters removing trihalomethanes are related to nitrosomonas oligotropha.	ammonia-oxidizing bacteria (aob) in nitrifying biofilters degrading four regulated trihalomethanes-trichloromethane, bromodichloromethane, dibromochloromethane, and tribromomethane-were related to nitrosomonas oligotropha. n. oligotropha is associated with chloraminated drinking water systems, and its presence in the biofilters might indicate that trihalomethane tolerance is another reason that this bacterium is dominant in chloraminated systems.	2011	21278264
nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'nitrosococcus halophilus' and 'nitrosomonas mobilis'.	local associations between anammox bacteria and obligate aerobic bacteria in the genus nitrosococcus appear to be significant for ammonia oxidation in oxygen minimum zones. the literature on the genus nitrosococcus in the chromatiaceae family of purple sulfur bacteria (gammaproteobacteria, chromatiales) contains reports on four described species, nitrosococcus nitrosus, nitrosococcus oceani, 'nitrosococcus halophilus' and 'nitrosomonas mobilis', of which only n. nitrosus and n. oceani are validl ...	2011	21204874
Abundance and composition of epiphytic bacterial and archaeal ammonia oxidizers of marine red and brown macroalgae.	Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on t ...	2012	22081571