| [an important mission for microbiologists in the new century-cultivation of the unculturable microorganisms]. | the present review summarizes the recent advances in cultivating the so-called recalcitrant microorganisms in various natural environments. firstly, the use of new electron donors and acceptors reveals a list of unique and previously unrecognized physiotypes (table 1), and the growth supporting reactions include oxidation of phosphite, arsenite, soil humic substances, benzene, fe (ii) and aryl-halides. the novel pure cultures obtained include: desulfatogenum phosphitoxidans, lithochemotrophic ar ... | 2004 | 15973982 |
| changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor. | high levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the y-12 national security complex in oak ridge, tn. a field-scale denitrifying fluidized bed reactor (fbr) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. after inoculation, biofilms developed on the granular activated carbon particles. changes in the bacterial community of the fbr were evaluated with clone libraries (n = 500 partial sequences ... | 2006 | 16292532 |
| bacterial community succession in natural river biofilm assemblages. | temporal bacterial community changes in river biofilms were studied using 16s rrna gene-based polymerase chain reaction-denaturing gradient gel electrophoresis (dgge) followed by sequence analysis. naturally occurring biofilms were sampled in 2001 during an undisturbed 7-month low-water period in the river garonne (sw france). during the sampling period epilithic biomass exhibited a particular pattern: two 3-month periods of accumulation that resulted in two peaks in summer and fall, each at abo ... | 2005 | 16341639 |
| anaerobic degradation of benzene, toluene, ethylbenzene, and xylene compounds by dechloromonas strain rcb. | dechloromonas strain rcb has been shown to be capable of anaerobic degradation of benzene coupled to nitrate reduction. as a continuation of these studies, the metabolic versatility and hydrocarbon biodegradative capability of this organism were investigated. the results of these revealed that in addition to nitrate, strain rcb could alternatively degrade benzene both aerobically and anaerobically with perchlorate or chlorate [(per)chlorate] as a suitable electron acceptor. furthermore, with nit ... | 2005 | 16332859 |
| dechloromonas hortensis sp. nov. and strain ask-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain gr-1. | recent studies on the occurrence of (per)chlorate-reducing bacteria have resulted in the characterization of strains capable of dissimilatory (per)chlorate reduction. phylogenetic analysis has shown that these bacteria are members of the proteobacteria. strains have been isolated from polluted and pristine sites, but only strains from polluted sites have been characterized in detail and deposited in culture collections. herein we describe the isolation and characterization of perchlorate-reducin ... | 2005 | 16166710 |
| population diversity in model potable water biofilms receiving chlorine or chloramine residual. | most water utilities use chlorine or chloramine to produce potable water. these disinfecting agents react with water to produce residual oxidants within a water distribution system (wds) to control bacterial growth. while monochloramine is considered more stable than chlorine, little is known about the effect it has on wds biofilms. community structure of 10-week old wds biofilms exposed to disinfectants was assessed after developing model biofilms from unamended distribution water. four biofilm ... | 2005 | 16522541 |
| identification, characterization, and classification of genes encoding perchlorate reductase. | the reduction of perchlorate to chlorite, the first enzymatic step in the bacterial reduction of perchlorate, is catalyzed by perchlorate reductase. the genes encoding perchlorate reductase (pcrabcd) in two dechloromonas species were characterized. sequence analysis of the pcrab gene products revealed similarity to alpha- and beta-subunits of microbial nitrate reductase, selenate reductase, dimethyl sulfide dehydrogenase, ethylbenzene dehydrogenase, and chlorate reductase, all of which are type ... | 2005 | 16030201 |
| hydroxylation and carboxylation--two crucial steps of anaerobic benzene degradation by dechloromonas strain rcb. | benzene is a highly toxic industrial compound that is essential to the production of various chemicals, drugs, and fuel oils. due to its toxicity and carcinogenicity, much recent attention has been focused on benzene biodegradation, especially in the absence of molecular oxygen. however, the mechanism by which anaerobic benzene biodegradation occurs is still unclear. this is because until the recent isolation of dechloromonas strains jj and rcb no organism that anaerobically degraded benzene was ... | 2005 | 16151134 |
| molecular assessment of inoculated and indigenous bacteria in biofilms from a pilot-scale perchlorate-reducing bioreactor. | bioremediation of perchlorate-contaminated groundwater can occur via bacterial reduction of perchlorate to chloride. although perchlorate reduction has been demonstrated in bacterial pure cultures, little is known about the efficacy of using perchlorate-reducing bacteria as inoculants for bioremediation in the field. a pilot-scale, fixed-bed bioreactor containing plastic support medium was used to treat perchlorate-contaminated groundwater at a site in southern california. the bioreactor was ino ... | 2005 | 16003477 |
| enzymes responsible for chlorate reduction by pseudomonas sp. are different from those used for perchlorate reduction by azospira sp. | pseudomonas sp. pda is an unusual bacterium due to its ability to respire using chlorate under aerobic conditions. the chlorate reductase produced by pda was shown to be intrinsically different from the enzyme responsible for chlorate and perchlorate [(per)chlorate] reduction produced by azospira sp. kj based on subunit composition and other enzyme properties. the perchlorate reductase from strain kj appeared to have two subunits (100 and 40 kda) while the chlorate reductase from pda had three s ... | 2005 | 15927421 |
| dechloromonas denitrificans sp. nov., flavobacterium denitrificans sp. nov., paenibacillus anaericanus sp. nov. and paenibacillus terrae strain mh72, n2o-producing bacteria isolated from the gut of the earthworm aporrectodea caliginosa. | earthworms emit nitrous oxide (n(2)o) via the activity of bacteria in their gut. four n(2)o-producing facultative aerobes, ed1(t), ed5(t), mh21(t) and mh72, were isolated from the gut of the earthworm aporrectodea caliginosa. the isolates produced n(2)o under conditions that simulated the microenvironment of the earthworm gut. ed1(t) and ed5(t) were gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to n(2)) and contained membranous c-type cytochr ... | 2005 | 15879265 |
| 16s rrna gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "rhodocyclales". | for simultaneous identification of members of the betaproteobacterial order "rhodocyclales" in environmental samples, a 16s rrna gene-targeted oligonucleotide microarray (rhc-phylochip) consisting of 79 probes was developed. probe design was based on phylogenetic analysis of available 16s rrna sequences from all cultured and as yet uncultured members of the "rhodocyclales." the multiple nested probe set was evaluated for microarray hybridization with 16s rrna gene pcr amplicons from 29 reference ... | 2005 | 15746340 |
| isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria. | recent studies have shown that perchlorate (clo(4) (-)) can be degraded by some pure-culture and mixed-culture bacteria with the addition of hydrogen. this paper describes the isolation of two hydrogen-utilizing perchlorate-degrading bacteria capable of using inorganic carbon for growth. these autotrophic bacteria are within the genus dechloromonas and are the first dechloromonas species that are microaerophilic and incapable of growth at atmospheric oxygen concentrations. dechloromonas sp. jds5 ... | 2004 | 15834721 |
| comparison of the microbial population dynamics and phylogenetic characterization of a canoxis reactor and a uasb reactor degrading trichloroethene. | to understand the microbial ecology underlying trichloethene (tce) degradation in a coupled anaerobic/aerobic single stage (canoxis) reactor oxygenated with hydrogen peroxide (h2o2) and in an upflow anaerobic sludge bed (uasb) reactor. | 2005 | 15659198 |
| a third lineage with two-piece tmrna. | tmrna combines trna and mrna properties and helps bacteria to cope with stalled ribosomes. its termini normally pair in the trna domain, closing the mrna portion into a looping domain. a striking variation is a two-piece form that effectively breaks open the mrna domain loop, resulting from independent gene permutation events in alphaproteobacteria and cyanobacteria. convergent evolution to a similar form in separate bacterial lineages suggests that loop-opening benefits tmrna function. this arg ... | 2004 | 15326226 |
| anaerobic benzene biodegradation--a new era. | benzene is biodegraded in the absence of oxygen under a variety of terminal electron-accepting conditions. however, the mechanism by which anaerobic benzene degradation occurs is unclear. phenol and benzoate have been consistently detected as intermediates of anaerobic benzene degradation, suggesting that the hydroxylation of benzene to phenol is one of the initial steps in anaerobic benzene degradation. the conversion of phenol to benzoate could then occur by the carboxylation of phenol to form ... | 2002 | 12558180 |
| physiological and molecular characterization of anaerobic benzene-degrading mixed cultures. | nine distinct anaerobic benzene-degrading cultures were enriched from sediment samples from four different sites. these cultures used nitrate, sulphate or co2 as electron acceptors. the shortest doubling times were observed in nitrate-reducing cultures, although cell yield was lowest in these cultures. the highest substrate concentration utilized and maximum absolute rates of benzene degraded (in micro m day-1) were observed in methanogenic cultures. the microbial compositions of a methanogenic ... | 2003 | 12558592 |
| sequencing and transcriptional analysis of the chlorite dismutase gene of dechloromonas agitata and its use as a metabolic probe. | the dismutation of chlorite into chloride and o(2) represents a central step in the reductive pathway of perchlorate that is common to all dissimilatory perchlorate-reducing bacteria and is mediated by a single enzyme, chlorite dismutase. the chlorite dismutase gene cld was isolated and sequenced from the perchlorate-reducing bacterium dechloromonas agitata strain ckb. sequence analysis identified an open reading frame of 834 bp that would encode a mature protein with an n-terminal sequence iden ... | 2002 | 12324326 |
| perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium. | water treatment technologies are needed that can remove perchlorate from drinking water without introducing organic chemicals that stimulate bacterial growth in water distribution systems. hydrogen is an ideal energy source for bacterial degradation of perchlorate as it leaves no organic residue and is sparingly soluble. we describe here the isolation of a perchlorate-respiring, hydrogen-oxidizing bacterium (dechloromonas sp. strain hz) that grows with carbon dioxide as sole carbon source. strai ... | 2002 | 12366751 |
| perchlorate-reducing microorganisms isolated from contaminated sites. | an extensive microcosm survey of perchlorate-contaminated sites was undertaken to assess the ability of indigenous microorganisms to degrade perchlorate. samples from 12 contaminated sites and from one pristine location were analysed. perchlorate was degraded to below detection limit in all electron donor-amended microcosms. perchlorate-reducing microorganisms (prms) were numerous at most of these sites. sixteen distinct prms were isolated that were phylogenetically related to either dechloromon ... | 2004 | 15049925 |
| role of citrobacter amalonaticus and citrobacter farmeri in dissimilatory perchlorate reduction. | the article deals with the novel physiological function of dissimilatory perchlorate reduction by strains jb101 and jb109 isolated from a laboratory-enriched mixed consortium originating from a sewage treatment facility. the biochemical and physiological data of the strains showed good correspondence with members of the family enterobacteriaceae. the partial 16s rdna sequence of the strains jb101 and jb109 had similarity of 99.8% to citrobacter amalonaticus and 98% to citrobacter farmeri, respec ... | 2004 | 15069667 |
| environmental factors that control microbial perchlorate reduction. | as part of a study to elucidate the environmental parameters that control microbial perchlorate respiration, we investigated the reduction of perchlorate by the dissimilatory perchlorate reducer dechlorosoma suillum under a diverse set of environmental conditions. our results demonstrated that perchlorate reduction by d. suillum only occurred under anaerobic conditions in the presence of perchlorate and was dependent on the presence of molybdenum. perchlorate reduction was dependent on the prese ... | 2002 | 12200296 |
| universal immunoprobe for (per)chlorate-reducing bacteria. | recent studies in our lab have demonstrated the ubiquity and diversity of microorganisms which couple growth to the reduction of chlorate or perchlorate [(per)chlorate] under anaerobic conditions. we identified two taxonomic groups, the dechloromonas and the dechlorosoma groups, which represent the dominant (per)chlorate-reducing bacteria (clrb) in the environment. as part of these studies we demonstrated that chlorite dismutation is a central step in the reductive pathway of (per)chlorate that ... | 2002 | 12039773 |
| insights and inferences about integron evolution from genomic data. | integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign dna. these are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. here, we provide a systematic analysis of the distribution and diversity of integron inti genes and integron-containing bacteria. | 2008 | 18513439 |
| quadricoccus australiensis gen. nov., sp. nov., a beta-proteobacterium from activated sludge biomass. | a gram-negative coccus, designated strain ben 117t, was obtained in axenic culture by micromanipulation from an australian activated sludge biomass sample, which had been subjected to chlorination in order to alleviate problems associated with foaming and bulking. this isolate was a strict aerobe and grew in axenic culture, also appearing in biomass samples as cocci or clusters of cocci in tetrads, thus resembling the morphotype 'g-bacteria' seen commonly in activated sludge samples. strain ben ... | 2002 | 11858148 |
| characterization of denitrifying phosphate-accumulating organisms cultivated under different electron acceptor conditions using polymerase chain reaction-denaturing gradient gel electrophoresis assay. | to investigate the characteristics and the microbial diversity of denitrifying phosphate-accumulating organisms (dnpaos) that are capable of conducting enhanced biological phosphorus removal (ebpr) using nitrate as electron acceptor, three sequencing batch reactors were operated under three different electron acceptor conditions, i.e., only oxygen, oxygen together with nitrate and only nitrate. based on the chemical analysis concerning the biochemical transformation of each reactor, it was found ... | 2002 | 11827346 |
| anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of dechloromonas. | benzene contamination is a significant problem. it is used in a wide range of manufacturing processes and is a primary component of petroleum-based fuels. benzene is a hydrocarbon that is soluble, mobile, toxic and stable, especially in ground and surface waters. it is poorly biodegraded in the absence of oxygen. however, anaerobic benzene biodegradation has been documented under various conditions. although benzene biomineralization has been demonstrated with nitrate, fe(iii), sulphate or co2 a ... | 2001 | 11429602 |
| dechloromonas agitata gen. nov., sp. nov. and dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per)chlorate-reducing bacteria and their phylogenetic position. | previous studies on the ubiquity and diversity of microbial (per)chlorate reduction resulted in the isolation of 20 new strains of dissimilatory (per)chlorate-reducing bacteria. phylogenetic analysis revealed that all of the isolates were members of the proteobacteria with representatives in the alpha-, beta- and gamma-subclasses. the majority of the new isolates were located in the beta-subclass and were closely related to each other and to the phototrophic rhodocyclus species. here an in-depth ... | 2001 | 11321099 |
| anaerobic redox cycling of iron by freshwater sediment microorganisms. | the potential for microbially mediated anaerobic redox cycling of iron (fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. most probable number enumerations revealed the presence of significant populations of fe(iii)-reducing (approximately 10(8) cells ml(-1)) and fe(ii)-oxidizing, nitrate-reducing organisms (approximately 10(5) cells ml(-1)) in the freshwater sediment used to inoculate the enrichment cultures. nitrate reduction commenced imm ... | 2006 | 16343326 |
| stimulation and molecular characterization of bacterial perchlorate degradation by plant-produced electron donors. | root homogenate from poplar trees (populus deltoides x nigra dn34, imperial carolina) stimulated perchlorate degradation in microcosms of soil and water samples collected at a perchlorate contaminated site, the longhorn army ammunition plant (lhaap), located outside karnack, texas. direct use of root products by perchlorate-degrading bacteria was shown for the first time as six pureculture bacteria isolated from lhaap perchlorate-degrading microcosms degraded perchlorate when given root products ... | 2006 | 16433366 |
| nitrous oxide reductase genes (nosz) of denitrifying microbial populations in soil and the earthworm gut are phylogenetically similar. | earthworms emit nitrous oxide (n2o) and dinitrogen (n2). it has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (m. a. horn, a. schramm, and h. l. drake, appl. environ. microbiol. 69:1662-1669, 2003). this hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. to test this hypothesis, t ... | 2006 | 16461644 |
| community structure and function in a h(2)-based membrane biofilm reactor capable of bioreduction of selenate and chromate. | two different h(2)-based, denitrifying membrane-biofilm reactors (mbfrs) initially reduced se(vi) or cr(vi) stably to se(0) or cr(iii). when the oxidized contaminants in the influent were switched, each new oxidized contaminant was reduced immediately, and its reduction soon was approximately the same or greater than it had been in its original mbfr. the precipitation of reduced selenium and chromium in the biofilm was verified by scanning electron microscopy and energy dispersive x-ray analysis ... | 2006 | 16673108 |
| isolation and characterization of dechlorospirillum anomalous strain jb116 from a sewage treatment plant. | the dissimilatory perchlorate reducers mainly belong to two monophyletic groups, viz. dechloromonas and azospira in the beta subclass of proteobacteria. the present study describes isolation and genetic characterization of dechlorospirillum anomalous strain jb116 that belongs to alpha subclass of proteobacteria. the strain jb116 was isolated under facultative anaerobic conditions on a growth medium containing sodium perchlorate and sodium acetate as electron (e(-)) acceptor and e(-) donor, respe ... | 2008 | 16782316 |
| ghp, a new c-type green heme protein from halochromatium salexigens and other proteobacteria. | we have isolated a minor soluble green-colored heme protein (ghp) from the purple sulfur bacterium, halochromatium salexigens, which contains a c-type heme. a similar protein has also been observed in the purple bacteria allochromatium vinosum and rhodopseudomonas cryptolactis. this protein has wavelength maxima at 355, 420, and 540 nm and remains unchanged upon addition of sodium dithionite or potassium ferricyanide, indicating either an unusually low or high redox potential, respectively. the ... | 2006 | 16817906 |
| stability in a denitrifying fluidized bed reactor. | this study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. the perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. in the absence of perturbations, nitrate removal was stable and consistently greater ... | 2006 | 16874554 |
| supplementing bacillus sp. rs1 with dechloromonas sp. hz for enhancing selenate reduction in agricultural drainage water. | cost and efficiency are two important factors considered in the remediation of se-contaminated agricultural drainage water through bacterial reduction of soluble se(vi) to insoluble se(0). bacillus sp. rs1 isolated from rice straw was assessed for its ability to use inexpensive molasses to reduce se(vi) in agricultural drainage water containing no3- levels of 0, 50, 100, 250, and 500 mg/l. the results showed that se(vi) (1000 microg/l) was almost entirely reduced to se(iv) (62.7%) and se(0) (36. ... | 2007 | 17140639 |
| kinetics of a hydrogen-oxidizing, perchlorate-reducing bacterium. | this paper provides the first kinetic parameters for a hydrogen-oxidizing perchlorate-reducing bacterium (pcrb), dechloromonas sp. pc1. the qmax for perchlorate and chlorate were 3.1 and 6.3 mg/mgdw-day, respectively. the k for perchlorate was 0.14 mg/l, an order of magnitude lower than reported for other pcrb. the yields y on perchlorate and chlorate were 0.23 and 0.22 mgdw/mg, respectively, and the decay constant b was 0.055/day. the growth-threshold, smin, for perchlorate was 14 microg/l, sug ... | 2006 | 16938337 |
| identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing. | stable-isotope probing (sip) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. a sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [(13)c]acetate or [(13)c]methanol as the main carbon source and nitrate as the electron acceptor. we analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon ... | 2006 | 16897304 |
| respiratory transformation of nitrous oxide (n2o) to dinitrogen by bacteria and archaea. | n2o is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. it is an obligatory inorganic metabolite of denitrifying bacteria, and some production of n2o is also found in nitrifying and methanotrophic bacteria. we focus this review on the respiratory aspect of n2o transformation catalysed by the multicopper enzyme nitrous oxide reductase (n2or) that provides the bacterial cell with an electron sink for anaerobic growth. t ... | 2007 | 17027372 |
| ecology of the microbial community removing phosphate from wastewater under continuously aerobic conditions in a sequencing batch reactor. | all activated sludge systems for removing phosphate microbiologically are configured so the biomass is cycled continuously through alternating anaerobic and aerobic zones. this paper describes a novel aerobic process capable of decreasing the amount of phosphate from 10 to 12 mg p liter(-1) to less than 0.1 mg p liter(-1) (when expressed as phosphorus) over an extended period from two wastewaters with low chemical oxygen demand. one wastewater was synthetic, and the other was a clarified effluen ... | 2007 | 17293509 |
| electrochemical stimulation of microbial perchlorate reduction. | as part of our studies into the diversity of dissimilatory perchlorate reducing bacteria (dprb) we investigated the reduction of perchlorate in the cathodic chamber of a bioelectrical reactor (ber). our results demonstrated that washed cells of dechloromonas and azospira species readily reduced 90 mg l(-1) perchlorate in the ber with 2,6-anthraquinone disulfonate (aqds) as a mediator. no perchlorate was reduced in the absence of cells or aqds, or in an open-circuit control. similar results were ... | 2007 | 17396669 |
| perchlorate reduction by autotrophic bacteria attached to zerovalent iron in a flow-through reactor. | biological reduction of perchlorate by autotrophic microorganisms attached to zerovalent iron (zvi) was studied in flow-through columns. the effects of ph, flow rate, and influent perchlorate and nitrate concentrations on perchlorate reduction were investigated. excellent perchlorate removal performance (> or = 99%) was achieved at empty bed residence times (ebrts) ranging from 0.3 to 63 h and an influent perchlorate concentration of 40-600 microg l(-1). at the longest liquid residence times, wh ... | 2007 | 17328214 |
| microbial ecology of a perchlorate-reducing, hydrogen-based membrane biofilm reactor. | the hydrogen-based membrane biofilm reactor (mbfr) has been shown to reduce perchlorate to below 4 microg/l, but little is known about the microbial ecology of this or other hydrogen-based reactors, especially when influent perchlorate concentrations are much lower than the influent oxygen and nitrate concentrations. dissimilatory (per)chlorate-reducing bacteria (pcrb) can use oxygen as an electron acceptor, and most can also use nitrate. since oxygen and nitrate can be reduced concurrently with ... | 2008 | 17915282 |
| arsenic sequestration by nitrate respiring microbial communities in urban lake sediments. | changes in microbial community composition and activity were related to geochemical conditions favoring arsenic sequestration in sediments collected from the urban, arsenic-contaminated upper mystic lake. after amendment with nitrate, >94% total soluble arsenic is sequestered by fe(iii)-(oxy)hydroxides generated in live sediments. of this sequestered arsenic, >75% existed as as(iii), indicating as redox state alone is not responsible for changes in mobility. arsenic sequestration was concurrent ... | 2007 | 17935754 |
| change of sludge consortium in response to sequential adaptation to benzene, toluene, and o-xylene. | activated sludge was sequentially adapted to benzene, toluene, and o-xylene (btx) to study the effects on the change of microbial community. sludge adapted to btx separately degraded each by various rates in the following order; toluene>o-xylene>benzene. degradation rates were increased after exposure to repeated spikes of substrates. eleven different kinds of sludge were prepared by the combination of btx sequential adaptations. clustering analyses (jaccard, dice, pearson, and cosine product co ... | 2007 | 18092460 |
| identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by rna-based stable isotope probing. | the halogenated compound tetrachloroethene (perchloroethene, pce) is a persistent contaminant of aquifers, soils and sediments. although a number of microorganisms are known to reductively dechlorinate pce by dehalorespiration, their diversity and community structure especially in pristine environments remain elusive. in this study, we report on the detection of a novel group of dehalorespiring bacteria that reductively dechlorinate pce to cis-dichloroethene by rna-based stable isotope probing. ... | 2008 | 18211265 |
| functional diversity and electron donor dependence of microbial populations capable of u(vi) reduction in radionuclide-contaminated subsurface sediments. | in order to elucidate the potential mechanisms of u(vi) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. a polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. the addition of ethanol and gluc ... | 2008 | 18378664 |
| structure and function of the microbial community in a full-scale enhanced biological phosphorus removal plant. | the structure and function of the microbial community in a full-scale enhanced biological phosphorus removal wastewater treatment plant (wwtp; skagen) were investigated using the full-cycle rrna approach, combined with ecophysiological studies. a total of 87 16s rrna gene sequences were retrieved, and 78 operational taxonomic units were identified. novel oligonucleotide probes were designed, and quantitative fluorescence in situ hybridization revealed that six hitherto undescribed probe-defined ... | 2007 | 18048920 |
| pha-accumulating microorganisms in full-scale wastewater treatment plants. | a study was conducted to clarify phylogenetic affiliations of polyhydroxyalkanoate (pha)-accumulating microorganisms in full-scale activated sludge processes. activated sludge samples obtained from three full-scale activated sludge processes were aerobically incubated with excess acetate to increase their pha content. the buoyant density separation method was applied to selectively collect pha-accumulating cells, which were then analysed by the group-level fish and the pcr-dgge-sequencing method ... | 2008 | 18653931 |
| biogeochemical processes in ethanol stimulated uranium-contaminated subsurface sediments. | a laboratory incubation experiment was conducted with uranium-contaminated subsurface sediment to assess the geochemical and microbial community response to ethanol amendment. a classical sequence of terminal electron-accepting processes (teaps) was observed in ethanol-amended slurries, with no3- reduction, fe(iii) reduction, so4(2-) reduction, and ch4 production proceeding in sequence until all of the added 13c-ethanol (9 mm) was consumed. approximately 60% of the u(vi) content of the sediment ... | 2008 | 18605559 |
| proteomic detection of proteins involved in perchlorate and chlorate metabolism. | mass spectrometry and a time-course cell lysis method were used to study proteins involved in perchlorate and chlorate metabolism in pure bacterial cultures and environmental samples. the bacterial cultures used included dechlorosoma sp. kj, dechloromonas hortensis, pseudomonas chloritidismutans ask-1, and pseudomonas stutzeri. the environmental samples included an anaerobic sludge enrichment culture from a sewage treatment plant, a sample of a biomass-covered activated carbon matrix from a bior ... | 2009 | 19199051 |
| periplasmic c cytochromes and chlorate reduction in ideonella dechloratans. | the aim of this study was to clarify the pathway of electron transfer between the inner membrane components and the periplasmic chlorate reductase. several soluble c-type cytochromes were found in the periplasm. the optical difference spectrum of dithionite-reduced periplasmic extract shows that at least one of these components is capable of acting as an electron donor to the enzyme chlorate reductase. the cytochromes were partially separated, and the fractions were analyzed by uv/visible spectr ... | 2009 | 19233956 |
| evidence of specialized bromate-reducing bacteria in a hollow fiber membrane biofilm reactor. | bromate is a carcinogenic disinfection by-product formed from bromide during ozonation or advanced oxidation. we previously observed bromate reduction in a hydrogen-based, denitrifying hollow fiber membrane biofilm reactor (mbfr). in this research, we investigated the potential existence of specialized bromate-reducing bacteria. using denaturing gradient gel electrophoresis (dgge), we compared the microbial ecology of two denitrifying mbfrs, one amended with nitrate as the electron acceptor and ... | 2009 | 19474491 |
| behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors. | the response behavior of three dissimilatory perchlorate-reducing bacteria to different electron acceptors (nitrate, chlorate, and perchlorate) was investigated with two different assays. the observed response was species-specific, dependent on the prior growth conditions, and was inhibited by oxygen. we observed attraction toward nitrate when dechloromonas aromatica strain rcb and azospira suillum strain ps were grown with nitrate. when d. aromatica and dechloromonas agitata strain ckb were gro ... | 2009 | 19533120 |
| crystallization and preliminary x-ray diffraction of chlorite dismutase from dechloromonas aromatica rcb. | chlorite dismutase from dechloromonas aromatica rcb, a novel b-type hemoprotein that catalyzes o-o bond formation, has been crystallized. synchrotron x-ray diffraction data have been collected to 3.0 a resolution. the crystals belonged to space group p2(1)2(1)2(1), with unit-cell parameters a = 122.7, b = 202.9, c = 247.1 a. | 2009 | 19652348 |
| influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater. | the influence of ammonium availability on bacterial community structure and the physiological status of geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. ammonium concentrations varied by 2 orders of magnitude (< 4 to 400 microm) across th study site. analysis of 16s rrna sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with rhodoferax species predominating over geobacter s ... | 2009 | 19603651 |
| metabolic analysis of the soil microbe dechloromonas aromatica str. rcb: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. | initial interest in dechloromonas aromatica strain rcb arose from its ability to anaerobically degrade benzene. it is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. little physiological data has been published for this microbe. it is considered to be a free-living organism. | 2009 | 19650930 |
| identification of rice root associated nitrate, sulfate and ferric iron reducing bacteria during root decomposition. | leakage of o(2) from roots of aquatic plants supports the oxidation of ammonia to nitrate and of sulfide to sulfate in the rhizosphere, so that these electron acceptors may become available to the root microbial communities and affect their activity. we studied the composition of the bacterial community active in anoxically incubated rice roots by analysis of terminal restriction fragment length polymorphism (t-rflp) and by cloning and sequencing targeting bacterial 16s rrna. the bacterial ribos ... | 2004 | 19712368 |
| molecular characterization of microbial community in nitrate-removing activated sludge. | abstract the microbial community composition and dominant denitrifying populations in high-nitrate-removing (cr-i) and low-nitrate-removing (cr-ii) activated sludge from continuous bioreactors were investigated with most probable number (mpn) enumeration, fluorescence in situ hybridization (fish) and 16s rdna characterization. mpns of nitrate-reducing bacteria of sludge cr-i and sludge cr-ii were 2.82x10(7) and 2.69x10(4) colony-forming units ml(-1), respectively. eight denitrifying bacteria and ... | 2002 | 19709242 |
| description of the novel perchlorate-reducing bacteria dechlorobacter hydrogenophilus gen. nov., sp. nov.and propionivibrio militaris, sp. nov. | novel dissimilatory perchlorate-reducing bacteria (dprb) were isolated from enrichments conducted under conditions different from those of all previously described dprb. strain lt-1(t) was enriched using medium buffered at ph 6.6 with 2-(n-morpholino)ethanesulfonic acid (mes) and had only 95% 16s rrna gene identity with its closest relative, azonexus caeni. strain mp(t) was enriched in the cathodic chamber of a perchlorate-reducing bioelectrical reactor (ber) and together with an additional stra ... | 2010 | 19921177 |
| diversity of microbes and potential exoelectrogenic bacteria on anode surface in microbial fuel cells. | single-chamber microbial fuel cells (mfcs), inoculated with anaerobic sludge and continuously run with two kinds of organic wastewater influents, were systemically investigated. the diversity of microbes, determined by 16s rdna analysis, was analyzed on three anodes under different conditions. one anode was in a closed circuit in synthetic wastewater containing glucose. the other two anodes, in open or closed circuits, were fed effluent from an anaerobic reactor treating starch wastewater. the c ... | 2010 | 20339216 |
| how active-site protonation state influences the reactivity and ligation of the heme in chlorite dismutase. | chlorite dismutase catalyzes o(2) release from chlorite with exquisite efficiency and specificity. the spectroscopic properties, ligand binding affinities, and steady-state kinetics of chlorite dismutase from dechloromonas aromatica were examined over ph 3-11.5 to gain insight into how the protonation state of the heme environment influences dioxygen formation. an acid-base transition was observed by uv/visible and resonance raman (rr) spectroscopy with a pk(a) of 8.7, 2-3 ph units below analogo ... | 2010 | 20356038 |
| endophytic bacterial diversity in roots of phragmites australis in constructed beijing cuihu wetland (china). | the community structure and diversity of endophytic bacteria in reed (phragmites australis) roots growing in the beijing cuihu wetland, china was investigated using the 16s rrna library technique. primers 799f and 1492r were used to amplify the specific bacterial 16s rrna fragments successfully and construct the clone library. in total, 166 individual sequences were verified by colony pcr and used to assess the diversity of endophytic bacteria in reed roots. phylogenetic analysis revealed that 7 ... | 2010 | 20528944 |
| anaerobic oxidation of arsenite linked to chlorate reduction. | microorganisms play a significant role in the speciation and mobility of arsenic in the environment. in this study, the oxidation of arsenite [as(iii)] to arsenate [as(v)] linked to chlorate (clo₃⁻) reduction was shown to be catalyzed by sludge samples, enrichment cultures (ecs), and pure cultures incubated under anaerobic conditions. no activity was observed in treatments lacking inoculum or with heat-killed sludge, or in controls lacking clo₃⁻. the as(iii) oxidation was linked to the complete ... | 2010 | 20729322 |
| structural features promoting dioxygen production by dechloromonas aromatica chlorite dismutase. | chlorite dismutase (cld) is a heme enzyme capable of rapidly and selectively decomposing chlorite (clo(2) (-)) to cl(-) and o(2). the ability of cld to promote o(2) formation from clo(2) (-) is unusual. heme enzymes generally utilize clo(2) (-) as an oxidant for reactions such as oxygen atom transfer to, or halogenation of, a second substrate. the x-ray crystal structure of dechloromonas aromatica cld co-crystallized with the substrate analogue nitrite (no(2) (-)) was determined to investigate f ... | 2010 | 20386942 |
| microbial treatment of high-strength perchlorate wastewater. | to treat wastewater containing high concentrations of perchlorate, a perchlorate reducing-bacterial consortium was obtained by enrichment culture grown on high-strength perchlorate (1200 mg l(-1)) feed medium, and was characterized in a sequence batch reactor (sbr) over a long-time operation. the consortium removed perchlorate in the sbr with high reduction rates (35-90 mg l(-1)h(-1)) and stable removal efficiency over 200-day operations. the maximum specific perchlorate reduction rate (qmax), h ... | 2010 | 20869238 |
| optimization of polyhydroxybutyrate (phb) production by excess activated sludge and microbial community analysis. | in this study, a high value-added and biodegradable thermoplastic, polyhydroxybutyrate (phb), was produced by excess activated sludge. the effects of the nutritional condition, aeration mode, sodium acetate concentration and initial ph value on phb accumulation in the activated sludge were investigated. the maximum phb content and phb yield of 67.0% (dry cell weight) and 0.740gcodgcod(-1) (cod: chemical oxygen demand), respectively, were attained by the sludge in the presence of 6.0gl(-1) sodium ... | 2010 | 20970922 |
| composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (lake geneva, switzerland). | the aim of this study was to compare the composition of bacterial and archaeal communities in contaminated sediments (vidy bay) with uncontaminated sediments (ouchy area) of lake geneva using 16s rrna clone libraries. sediments of both sites were analysed for physicochemical characteristics including porewater composition, organic carbon, and heavy metals. results show high concentrations of contaminants in sediments from vidy. particularly, high contents of fresh organic matter and nutrients le ... | 2010 | 21145090 |
| changes in the structure and function of microbial communities in drinking water treatment bioreactors upon addition of phosphorus. | phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (bac) reactors operated for perchlorate and nitrate removal from contaminated groundwater. the two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. improvement in reactor performance with respect to perchlorate and nitrate removal started within ... | 2010 | 20889793 |
| peptide biomarkers as evidence of perchlorate biodegradation. | perchlorate is a known health hazard for humans, fish, and other species. therefore, it is important to assess the response of an ecosystem exposed to perchlorate contamination. the data reported here show that a liquid chromatography-mass spectrometry-based proteomics approach for the detection of perchlorate-reducing enzymes can be used to measure the ability of microorganisms to degrade perchlorate, including determining the current perchlorate degradation status. signature peptides derived f ... | 2010 | 21115710 |
| aerobic reduction of perchlorate by bacteria isolated in kerala, south india. | possibility of perchlorate reduction by microbes raises hope for an eco-friendly mode of degradation of this toxic rocket fuel. this study reports 3 isolates (a1, a2 and a3) capable of molybdenum-independent degradation of perchlorate under aerobic conditions. the rate of degradation was the highest when perchlorate concentration was 17 mm, and then 3.2 mm, 4.7 mm and 4.1 mm of perchlorate was reduced by isolates a1, a2 and a3 (respectively) after 72 h at 28 degrees c under aerobic conditions. p ... | 2008 | 19029691 |
| quantitative rrna-targeted solution-based hybridization assay using peptide nucleic acid molecular beacons. | the potential of a solution-based hybridization assay using peptide nucleic acid (pna) molecular beacon (mb) probes to quantify 16s rrna of specific populations in rna extracts of environmental samples was evaluated by designing pna mb probes for the genera dechloromonas and dechlorosoma. in a kinetic study with 16s rrna from pure cultures, the hybridization of pna mb to target 16s rrna exhibited a higher final hybridization signal and a lower apparent rate constant than the hybridizations to no ... | 2008 | 18820054 |
| purification and characterization of the soluble cytochrome c capable to deliver electrons to chlorate reductase in ideonella dechloratans. | the electron donor for periplasmic chlorate reductase of ideonella dechloratans has been suggested to be a soluble cytochrome c [smedja bäcklund et al., 2009, appl environ microbiol75: 2439-2445]. we describe here the purification of the 9 kda periplasmic cytochrome c, denoted cytochrome c-id1, and demonstrate its ability to serve as electron donor for purified chlorate reductase. the reaction rate was found to be linearly dependent on the cytochrome c concentration in the range 0.6-4 μm. a rout ... | 2011 | 21623897 |
| thermodynamic targeting of microbial perchlorate reduction by selective electron donors. | here we describe 2,6-anthrahydroquinone disulfonate (ah(2)ds) as a model thermodynamically 'targeting' electron donor capable of selectively stimulating respiratory processes relevant to the bioremediation of perchlorate. pure cultures of dechloromonas aromatica, dechloromonas agitata and azospira suillum, as well as uncharacterized microbial consortia, were capable of stoichiometrically reducing perchlorate to chloride upon oxidation of ah(2)ds to the corresponding quinone 2,6-anthraquinone dis ... | 2009 | 19092865 |
| impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. | adding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. recent studies have demonstrated that soil-applied biochar promotes systemic resistance of plants to several prominent foliar pathogens. one potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. the objective of this study was to assess the eff ... | 2011 | 21622786 |
| repeated anaerobic microbial redox cycling of iron. | some nitrate- and fe(iii)-reducing microorganisms are capable of oxidizing fe(ii) with nitrate as the electron acceptor. this enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during fe-n redox oscillations. we examined this phenomenon in synthetic fe(iii) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. nitrate and acetate were added at alternate inter ... | 2011 | 21742920 |
| phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants. | the activated sludge process is an essential process for treating domestic and industrial wastewaters in most wastewater treatment plants (wwtps). this process consists of a mixture of general and special microorganisms in a form of a complex enrichment population. thus, the exploration of activated sludge microbial communities is crucial to improve the performance of activated sludge process. in this study, we investigated the phylogenetic diversity and metabolic potential of activated sludge m ... | 2011 | 21780771 |
| interactions between perchlorate and nitrate reductions in the biofilm of a hydrogen-based membrane biofilm reactor. | we studied the microbial functional and structural interactions between nitrate (no(3)(-)) and perchlorate (clo(4)(-)) reductions in the hydrogen (h(2))-based membrane biofilm reactor (mbfr). when h(2) was not limiting, clo(4)(-) and no(3)(-) reductions were complete, and the mbfr's biofilm was composed mainly of bacteria from the ε- and β-proteobacteria classes, with autotrophic genera sulfuricurvum, hydrogenophaga, and dechloromonas dominating the biofilm. based on functional-gene and pyrosequ ... | 2011 | 22017212 |
| maximizing microbial degradation of perchlorate using a genetic algorithm: media optimization. | microbial communities are under constant influence of physical and chemical components in ecosystems. shifts in conditions such as ph, temperature or carbon source concentration can translate into shifts in overall ecosystem functioning. these conditions can be manipulated in a laboratory setup using evolutionary computation methods such as genetic algorithms (gas). in work described here, a ga methodology was successfully applied to define sets of environmental conditions for microbial enrichme ... | 2012 | 22079750 |
| cultivation-independent analysis of archaeal and bacterial communities of the formation water in an indian coal bed to enhance biotransformation of coal into methane. | biogenic origin of the significant proportion of coal bed methane has indicated the role of microbial communities in methanogenesis. by using cultivation-independent approach, we have analysed the archaeal and bacterial community present in the formation water of an indian coal bed at 600-700 m depth to understand their role in methanogenesis. presence of methanogens in the formation water was inferred by epifluorescence microscopy and pcr amplification of mcra gene. archaeal 16s rrna gene clone ... | 2011 | 22202965 |
| 454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. | activated sludge (as) contains highly complex microbial communities. in this study, pcr-based 454 pyrosequencing was applied to investigate the bacterial communities of as samples from 14 sewage treatment plants of asia (mainland china, hong kong, and singapore), and north america (canada and the united states). a total of 259 k effective sequences of 16s rrna gene v4 region were obtained from these as samples. these sequences revealed huge amount of operational taxonomic units (otus) in as, tha ... | 2011 | 22170428 |
| long term performance of an arsenite-oxidizing-chlorate-reducing microbial consortium in an upflow anaerobic sludge bed (uasb) bioreactor. | a chlorate (clo(3)(-)) reducing microbial consortium oxidized arsenite (as(iii)) to arsenate (as(v)) in an upflow anaerobic sludge-bed bioreactor over 550 days operation. as(iii) was converted with high conversion efficiencies (>98%) at volumetric loadings ranging from 0.45 to 1.92 mmol as/(l(reactor)d). the oxidation of as(iii) was linked to the complete reduction of clo(3)(-) to cl(-) and h(2)o, as demonstrated by a molar ratio of approximately 3.0 mol as(iii) oxidized per mole of cl(-) formed ... | 2011 | 21333531 |
| a bioassay for the detection of perchlorate in the ppb range. | a bioassay for the determination of ppb (++g-àl(-1)) concentrations of perchlorate has been developed and is described herein. the assay uses the enzyme perchlorate reductase (pr) from the perchlorate-reducing organism dechloromonas agitata in purified and partially purified forms to detect perchlorate. the redox active dye phenazine methosulfate (pms) is shown to efficiently shuttle electrons to pr from nadh. perchlorate can be determined indirectly by monitoring nadh oxidization by pr. to lowe ... | 2011 | 21384912 |