Abstract:
:Phylogenetic and "fingerprinting" analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing approximately 5,000 sequences from a single soil sample (i.e., a closed site-specific library was used to create PCR primers for use at this site). These primers were initially tested in silico prior to empirical testing by PCR amplification of known target sequences and of controls based on disparate phylogenetic groups. Although all primers were highly specific according to the in silico analysis, the empirical analyses clearly exhibited a high degree of nonspecificity for many of the phyla or classes, while other primers proved to be highly specific. These findings suggest that significant care must be taken when interpreting studies whose results were obtained with target specific primers that were not adequately validated, especially where population densities or dynamics have been inferred from the data. Further, we suggest that the reliability of quantification of specific target abundance using 16S rRNA-based quantitative PCR is case specific and must be determined through rigorous empirical testing rather than solely in silico.
journal_name
Appl Environ Microbioljournal_title
Applied and environmental microbiologyauthors
Morales SE,Holben WEdoi
10.1128/AEM.02166-08subject
Has Abstractpub_date
2009-05-01 00:00:00pages
2677-83issue
9eissn
0099-2240issn
1098-5336pii
AEM.02166-08journal_volume
75pub_type
杂志文章abstract::A glycosyltransferase, involved in the synthesis of cyclic maltosylmaltose [CMM; cyclo-{-->6)-alpha-D-Glcp(1-->4)-alpha-D-Glcp(1-->6)-alpha-D-Glcp(1-->4)-alpha-D-Glcp(1-->}] from starch, was purified to homogeneity from the culture supernatant of Arthrobacter globiformis M6. The CMM-forming enzyme had a molecular mass...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.72.2.1065-1071.2006
更新日期:2006-02-01 00:00:00
abstract::It is now possible to obtain accurate total counts of the bacteria of natural waters with the use of acridine orange staining and epifluorescence microscopy. This approach can be coupled to highly sensitive measurements of heterotrophic activity using radioisotopes. To accomplish this, three variations of a "specific ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.36.2.297-305.1978
更新日期:1978-08-01 00:00:00
abstract::A set of 22 phages of Listeria species (listeriaphages) (21 temperate and 1 virulent) were compared on the basis of morphology and protein composition. All 22 phages had icosahedral heads and exhibited either contractile or noncontractile tails. They represented two different morphotypes. Twenty phages belonged to the...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.58.1.296-302.1992
更新日期:1992-01-01 00:00:00
abstract::Flow cytometry was used to enumerate and characterize bacteria from a sand column microcosm simulating aquifer conditions. Pure cultures of a species of Bacillus isolated from subsurface sediments or Bacillus megaterium were first evaluated to identify these organisms' characteristic histograms. Counting was then carr...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.62.12.4580-4586.1996
更新日期:1996-12-01 00:00:00
abstract::Sterol demethylation inhibitor (DMI) fungicides are widely used to control fungi pathogenic to humans and plants. Resistance to DMIs is mediated either through alterations in the structure of the target enzyme CYP51 (encoding 14alpha-demethylase), through increased expression of the CYP51 gene, or through increased ex...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.72.4.2581-2585.2006
更新日期:2006-04-01 00:00:00
abstract::Thymidine incorporation by the microbial community on standing dead leaves of Spartina alterniflora did not obey many of the assumptions inherent in the use of the technique in planktonic systems. Incorporation rates of [methly-H]thymidine were nonsaturable over a wide concentration range (10 to 10 nM). Owing to metab...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.52.5.1206-1208.1986
更新日期:1986-11-01 00:00:00
abstract::For decades, untreated sewage flowing northward from Tijuana, Mexico, via the Tijuana River has adversely affected the water quality of the recreational beaches of San Diego, California. We used quantitative reverse transcription-PCR to measure the levels of hepatitis A virus (HAV) and enteroviruses in coastal waters ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01024-06
更新日期:2006-12-01 00:00:00
abstract::Laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. While laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. Here, we report the purification and characterization of a laccase (...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01757-09
更新日期:2010-02-01 00:00:00
abstract::Lyophilizatin of 13 cyanobacterial cultures belonging to seven genera was attempted in a variety of suspending substances. All organisms survived lyophilization when suspended in lamb serum. Some of the organisms could be successfully lyophilized in horse serum, beef serum, fetal bovine serum, or human ascites fluid. ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.32.6.777-780.1976
更新日期:1976-12-01 00:00:00
abstract::Recombinant plasmid pM25 containing the celE gene of Clostridium thermocellum, which codes for an enzymatically active endoglucanase, was transformed into Lactobacillus plantarum by electroporation. Strains harboring pM25 expressed thermostable endoglucanase, which was found predominantly in the culture medium. Two ot...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.55.8.2095-2097.1989
更新日期:1989-08-01 00:00:00
abstract::Xanthomonas citri subsp. citri is the causal agent of citrus canker, which has a significant impact on citrus production. In this study, we characterized the galU gene of X. citri subsp. citri. Two galU mutants (F6 and D12) were identified in an X. citri subsp. citri EZ-Tn5
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02897-09
更新日期:2010-04-01 00:00:00
abstract::Despite the importance of human noroviruses (NoVs) in public health, little information concerning the effectiveness of ozone against NoVs is available. We determined the efficacy of ozone disinfection using murine norovirus (MNV) as a surrogate of human NoV. MNV in ozone demand-free buffer was exposed to a predetermi...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01955-09
更新日期:2010-02-01 00:00:00
abstract::Saccharomyces cerevisiae killer strains secrete a protein toxin active on nonkiller strains of the same (or other) yeast species. Different killer toxins, K1, K2, K28, and Klus, have been described. Each toxin is encoded by a medium-size (1.5- to 2.3-kb) M double-stranded RNA (dsRNA) located in the cytoplasm. M dsRNAs...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02991-16
更新日期:2017-02-01 00:00:00
abstract::Growth on 3-chlorobenzoate was found to induce the enzymes of the protocatechuate meta ring fission pathway in Alcaligenes sp. strain BR60. The chlorobenzoate catabolic genes, designated cba, were localized to a 3.7-kb NotI-EcoRI fragment within the nonrepeated region of the composite transposon Tn5271. The cba genes ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.59.11.3625-3633.1993
更新日期:1993-11-01 00:00:00
abstract::Helix alpha 4 of Bacillus thuringiensis Cry toxins is thought to play a critical role in the toxins' mode of action. Accordingly, single-site substitutions of many Cry1Aa helix alpha 4 amino acid residues have previously been shown to cause substantial reductions in the protein's pore-forming activity. Changes in prot...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01930-08
更新日期:2009-01-01 00:00:00
abstract::Fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization with 16S rRNA-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine Arctic sediment (Svalbard). FISH resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. U...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.67.1.387-395.2001
更新日期:2001-01-01 00:00:00
abstract::The nutristat, a substrate concentration-controlled continuous culture, was used to grow pentachlorophenol (PCP)-degrading microorganisms. The PCP concentration control system consisted of on-line measurement of the PCP concentration in the culture vessel with a tangential filter and a flowthrough spectrophotometer. W...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.59.10.3373-3377.1993
更新日期:1993-10-01 00:00:00
abstract::Growth of the Pseudomonas mendocina ymp strain on insoluble ferrihydrite is enhanced by exogenous reductants with concurrent increase in soluble iron concentrations. This shows that exogenous reductants play a substantial role in the overall microbial iron bioavailability. The exogenous reductants may work together wi...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02586-06
更新日期:2007-05-01 00:00:00
abstract::Symbioses with gut microorganisms provides a means by which terrestrial herbivores are able to obtain energy. These microorganisms ferment cell wall materials of plants to short-chain fatty acids (SCFA), which are then absorbed and used by the host animal. Many marine herbivorous fishes contain SCFA (predominantly ace...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.68.3.1374-1380.2002
更新日期:2002-03-01 00:00:00
abstract::Pseudomonas fluorescens 2-79 suppresses take-all, a major root disease of wheat caused by Gaeumannomyces graminis var. tritici. The bacteria produce an antibiotic, phenazine-1-carboxylic acid (PCA), and a fluorescent pyoverdin siderophore. Previous studies have established that PCA has an important role in the biologi...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.57.11.3270-3277.1991
更新日期:1991-11-01 00:00:00
abstract::N-acylhomoserine lactones (AHLs) are signaling molecules in many quorum-sensing (QS) systems that regulate interactions between various pathogenic bacteria and their hosts. Quorum quenching by the enzymatic inactivation of AHLs holds great promise in preventing and treating infections, and several such enzymes have be...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00477-10
更新日期:2010-08-01 00:00:00
abstract::Forty-nine isolates of Butyrivibrio fibrisolvens and a single isolate of Butyrivibrio crossotus were screened for the production of inhibitors by a deferred plating procedure. Twenty-five isolates produced factors which, to various degrees, inhibited the growth of the other Butyrivibrio isolates. None of the inhibitor...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.63.2.394-402.1997
更新日期:1997-02-01 00:00:00
abstract::The biodegradation of benzene, toluene, and chlorobenzenes by Pseudomonas putida involves the initial conversion of the parent molecules to cis-dihydrodiols by dioxygenase enzyme systems. The cis-dihydrodiols are then converted to the corresponding catechols by dihydrodiol dehydrogenase enzymes. Pseudomonas sp. strain...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.54.6.1399-1404.1988
更新日期:1988-06-01 00:00:00
abstract::Cryptosporidium is a genus of waterborne protozoan parasites that causes significant gastrointestinal disease in humans. These parasites can accumulate in environmental biofilms and be subsequently released to contaminate water supplies. Natural microbial assemblages were collected each season from an eastern Pennsylv...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01804-09
更新日期:2010-02-01 00:00:00
abstract::Protoplasts of Claviceps purpurea were prepared by treatment of mycelium with a lytic mixture of snail gut enzyme and cellulase from Trichoderma viride. Such protoplasts could be efficiently lysed by Triton X-100 treatment at high osmotic pressure without Ca or Mg, allowing the release of intact vacuoles in high yield...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.47.4.710-714.1984
更新日期:1984-04-01 00:00:00
abstract::Identification and design of new cellulolytic enzymes with higher catalytic efficiency are a key factor in reducing the production cost of lignocellulosic bioalcohol. We report here identification of a novel β-glucosidase (Gluc1C) from Paenibacillus sp. strain MTCC 5639 and construction of bifunctional chimeric protei...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01386-12
更新日期:2012-10-01 00:00:00
abstract::In this article, a new mechanism influencing the transport of microorganisms through unsaturated porous media is examined, and a new method for directly visualizing bacterial behavior within a porous medium under controlled chemical and flow conditions is introduced. Resting cells of hydrophilic and relatively hydroph...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.60.2.509-516.1994
更新日期:1994-02-01 00:00:00
abstract::In this study, we examine bacterial attachment and survival on a titanium (Ti) cathode coated with various carbon nanomaterials (CNM): pristine carbon nanotubes (CNT), oxidized carbon nanotubes (O-CNT), oxidized-annealed carbon nanotubes (OA-CNT), carbon black (CB), and reduced graphene oxide (rGO). The carbon nanomat...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00582-15
更新日期:2015-07-01 00:00:00
abstract::Alkyl glycosides are attractive surfactants because of their high surface activity and good biodegradability and can be produced from renewable resources. Through enzymatic catalysis, one can obtain well-defined alkyl glycosides, something that is very difficult to do using conventional chemistry. However, there is a ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00359-13
更新日期:2013-06-01 00:00:00
abstract::The need for protozoa for the proliferation of Legionella pneumophila in aquatic habitats is still not fully understood and is even questioned by some investigators. This study shows the in vivo growth of L. pneumophila in protozoa in aquatic biofilms developing at high concentrations on plasticized polyvinyl chloride...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.70.11.6826-6833.2004
更新日期:2004-11-01 00:00:00