Abstract:
:Denitrification is an alternative type of anaerobic respiration in which nitrate is reduced to gaseous products via nitrite. The key step in this process is the reduction of nitrite to nitric oxide, which is catalyzed by two structurally different but functionally equivalent forms of nitrite reductase encoded by the nirK and nirS genes. Cultivation-independent studies based on these functional marker genes showed that in the environment there was a dominance of organisms with nirK and nirS genes presumably derived from organisms that have not been cultured yet. However, the phylogenetic affiliation of these organisms has not been resolved since the ability to denitrify is widespread in phylogenetically unrelated organisms. To unravel the phylogeny of the organisms from which the nitrite reductase (nirK) genes originated, one option is to use a special variant of whole-cell hybridization termed recognition of individual genes-fluorescence in situ hybridization (RING-FISH). In RING-FISH a multiply labeled transcript polynucleotide probe is used to detect a single gene on the bacterial chromosome during FISH. Here, RING-FISH was used with laboratory cultures and environmental samples, such as activated sludge. Furthermore, probe-based cell sorting using magnetic beads could also be carried out with mixtures of pure cultures, which led to effective depletion of the nirK-negative organism but capture of the nirK-positive organism, which was demonstrated by terminal restriction fragment length polymorphism analysis based on 16S rRNA genes. The results indicate that RING-FISH coupled with probe-based cell sorting could be used with environmental samples, which could provide a means for phylogenetic classification of nirK-type denitrifiers. Thus, the results of RING-FISH could increase our understanding of the phylogeny and function of denitrifying microorganisms in the environment.
journal_name
Appl Environ Microbioljournal_title
Applied and environmental microbiologyauthors
Pratscher J,Stichternoth C,Fichtl K,Schleifer KH,Braker Gdoi
10.1128/AEM.01992-08subject
Has Abstractpub_date
2009-02-01 00:00:00pages
802-10issue
3eissn
0099-2240issn
1098-5336pii
AEM.01992-08journal_volume
75pub_type
杂志文章abstract::Cattle are a known reservoir of Shiga toxin-producing Escherichia coli. The prevalence and stability of Shiga toxin and/or Shiga toxin genes among native wild ungulates in Idaho were investigated. The frequency of both Shiga genes and toxin was similar to that reported for Idaho cattle ( approximately 19%). ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01158-08
更新日期:2009-02-01 00:00:00
abstract::We examined the bacterial communities of epilithic biofilms in 17 streams which represented a gradient ranging from relatively pristine streams to streams highly impacted by acid mine drainage (AMD). A combination of automated ribosomal intergenic spacer analysis with multivariate analysis and ordination provided a se...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00274-09
更新日期:2009-06-01 00:00:00
abstract::The microbial production of biofuels and other added-value chemicals is often limited by the intrinsic toxicity of these compounds. The phasin PhaP from the soil bacterium Azotobacter sp. strain FA8 is a polyhydroxyalkanoate granule-associated protein that protects recombinant Escherichia coli against several kinds of...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00662-17
更新日期:2017-06-30 00:00:00
abstract::The frequency of isolation of three nonhomologous chlorobenzoate catabolic genotypes (clc, cba, and fcb) was determined for 464 isolates from freshwater sediments and groundwater in the vicinity of the Hyde Park industrial landfill site in the Niagara watershed. Samples were collected from both contaminated and noncon...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.65.4.1627-1635.1999
更新日期:1999-04-01 00:00:00
abstract::Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl sho...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.70.7.4187-4192.2004
更新日期:2004-07-01 00:00:00
abstract::Mutacin 1140 belongs to the epidermin family of type AI lantibiotics. This family has a broad spectrum of activity against Gram-positive bacteria. The binding of mutacin 1140 to lipid II leads to the inhibition of cell wall synthesis. Pharmacokinetic experiments with type AI lantibiotics are generally discouraging for...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00830-18
更新日期:2018-07-17 00:00:00
abstract::A toluene-degrading methanogenic consortium enriched from creosote-contaminated aquifer material was maintained on toluene as the sole carbon and energy source for 10 years. The species in the consortium were characterized by using a molecular approach. Total genomic DNA was isolated, and 16S rRNA genes were amplified...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.65.12.5576-5585.1999
更新日期:1999-12-01 00:00:00
abstract::A separation procedure for the analysis of the enzyme components of the hyperthermophilic bacterium Thermotoga maritima involved in cellulose and xylan degradation was developed. Resolution of the enzymes was achieved by a combination of fast protein liquid chromatography anion exchange and hydrophobic interaction chr...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.61.4.1399-1407.1995
更新日期:1995-04-01 00:00:00
abstract::Thiobacillus ferrooxidans is an acidophilic organism important to metal leaching of low-grade ores. The aforementioned importance is related to the ability of the bacterium to oxidize reduced iron and sulfur, principally found in nature as pyrite (FeS2). The present study dealt with sulfide oxidation at low pH values ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.35.6.1198-1205.1978
更新日期:1978-06-01 00:00:00
abstract::The noncanonical alcohol dehydrogenase AlkJ is encoded on the alkane-metabolizing alk operon of the mesophilic bacterium Pseudomonas putida GPo1. To gain insight into the enzymology of AlkJ, we have produced the recombinant protein in Escherichia coli and purified it to homogeneity using His6 tag affinity and size exc...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.04297-13
更新日期:2014-04-01 00:00:00
abstract::[This corrects the article on p. 469 in vol. 57.]. ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.57.5.1579-1579.1991
更新日期:1991-05-01 00:00:00
abstract::We have previously reported that an acid tolerance response (ATR) can be induced in Streptococcus macedonicus cells at mid-log phase after autoacidification, transient exposure to acidic pH, or acid habituation, as well as at stationary phase. Here, we compared the transcriptional profiles of these epigenetic phenotyp...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00315-08
更新日期:2008-10-01 00:00:00
abstract::The soybean is an exotic plant introduced in Paraguay in this century; commercial cropping expanded after the 1970s. Inoculation is practiced in just 15 to 20% of the cropping areas, but root nodulation occurs in most sites where soybeans grow. Little is known about rhizobial diversity in South America, and no study h...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.66.11.5099-5103.2000
更新日期:2000-11-01 00:00:00
abstract::The biological impact of 24-h ("chronic") chromium(VI) [Cr(VI) or chromate] exposure on Shewanella oneidensis MR-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. Cells challenged aerobically with an initial chromate concentration of 0.3 mM in com...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00813-06
更新日期:2006-09-01 00:00:00
abstract::We developed a self-formed adaptor PCR (termed SEFA PCR) which can be used for chromosome walking. Most of the amplified flanking sequences were longer than 2.0 kb, and some were as long as 6.0 kb. SEFA PCR is simple and efficient and should have broad applications in the isolation of unknown sequences in complex geno...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02973-06
更新日期:2007-08-01 00:00:00
abstract::Heterologous protein production can be doubled by increasing the copy number of the corresponding heterologous gene. We constructed a host-vector system in the yeast Kluyveromyces lactis that was able to induce copy number amplification of pKD1 plasmid-based vectors upon expression of an integrated copy of the plasmid...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.65.11.4808-4813.1999
更新日期:1999-11-01 00:00:00
abstract::A method for the measurement of specific levels of gene expression that combines target mRNA and target DNA quantitation has been developed. The use of target gene dose as a normalizing factor for mRNA provides an alternative to 16S or 23S rRNA, which are unsuitable for use in the environment because of their presence...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.59.2.451-457.1993
更新日期:1993-02-01 00:00:00
abstract::Resistance to vancomycin permitted detection, in a culture of Streptococcus cremoris 290PC, of a contaminant gram-positive coccus. Morphological and physiological characteristics indicated that this bacterium was a strain of Leuconostoc sp., designated PO184. This strain contained four plasmid species, which were dist...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.48.6.1129-1133.1984
更新日期:1984-12-01 00:00:00
abstract::Laboratory batch tests indicate that addition of sterile municipal sewage biosolids to clay soil from four depths increases the numbers of Escherichia coli isolates recoverable in EC-MUG broth (EC broth with 4-methylumbelliferyl-beta-glucuronide). This effect was most marked for the deeper soil layers, with increases ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.72.3.2287-2289.2006
更新日期:2006-03-01 00:00:00
abstract::Fomites are known to play a role in the transmission of pathogens. Quantitative analysis of the parameters that affect sample recovery efficiency (SRE) at the limit of detection of viruses on fomites will aid in improving quantitative microbial risk assessment (QMRA) and infection control. The variability in SRE as a ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01370-12
更新日期:2012-11-01 00:00:00
abstract::The impact of feed supplementation with bambermycin, monensin, narasin, virginiamycin, chlortetracycline, penicillin, salinomycin, and bacitracin on the distribution of Escherichia coli pathotypes in broiler chickens was investigated using an E. coli virulence DNA microarray. Among 256 E. coli isolates examined, 59 (2...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00375-09
更新日期:2009-11-01 00:00:00
abstract::The filamentous, nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 accumulates sucrose as a compatible solute against salt stress. Sucrose-phosphate synthase activity, which is responsible for the sucrose synthesis, is increased by salt stress, but the mechanism underlying the regulation of sucrose synthesis...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01501-14
更新日期:2014-09-01 00:00:00
abstract::A survey was made to detect the sensitivity of 12 yeast genera to T-2 toxin. Seventy-five yeasts isolated from various sources were tested for their susceptibility to T-2 toxin. The MIC of T-2 for these yeasts varied from 1.0 to greater than 8.0 micrograms/ml. Of the yeasts studied, Kluyveromyces fragilis showed the g...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.48.2.416-419.1984
更新日期:1984-08-01 00:00:00
abstract::Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have d...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.05531-11
更新日期:2011-11-01 00:00:00
abstract::Antimicrobial chemicals are widely applied to clean and disinfect food-contacting surfaces. However, the cellular response of bacteria to various disinfectants is unclear. In this study, the physiological and genome-wide transcriptional responses of Bacillus cereus ATCC 14579 exposed to four different disinfectants (b...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.03003-09
更新日期:2010-05-01 00:00:00
abstract::One emerging disease of grapevine in Europe is Bois noir (BN), a phytoplasmosis caused by "Candidatus Phytoplasma solani" and spread in vineyards by the planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae). Here we present the first full characterization of the bacterial community of this important disease vector co...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02121-10
更新日期:2011-02-01 00:00:00
abstract::Botulinum neurotoxin (BoNT) serotype B (BoNT/B) is one of the serotypes of BoNT that causes deadly human botulism, though it is used clinically for treatment of many neuromuscular diseases. BoNT/B is produced by Clostridium botulinum, and it is secreted along with a group of neurotoxin-associated proteins (NAPs) in th...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00731-10
更新日期:2010-10-01 00:00:00
abstract::Although several microorganisms that produce and degrade methanethiol (MT) and dimethyl sulfide (DMS) have been isolated from various habitats, little is known about the numbers of these microorganisms in situ. This study reports on the identification and quantification of microorganisms involved in the cycling of MT ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.67.3.1044-1051.2001
更新日期:2001-03-01 00:00:00
abstract::Primers obtained from gene sequences coding for heat shock proteins (HSP) were used to specifically detect enteric protozoans of the genus Giardia. The HSP primers amplified Giardia DNA or the corresponding RNA sequences obtained from lysed cysts and gave a 163-bp product. Since the presence of the product did not ind...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.63.1.324-328.1997
更新日期:1997-01-01 00:00:00
abstract::Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.72.1.628-637.2006
更新日期:2006-01-01 00:00:00