bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of Anaerobic Microorganisms Involved in Long-Chain Fatty Acid Degradation in Methanogenic Sludges as Revealed by RNA-Based Stable Isotope Probing
Authors: Hatamoto Masashi , Imachi Hiroyuki , Yashiro Yuto , Ohashi Akiyoshi , Harada Hideki 
Published: May 2007

ABSTRACT

Long-chain fatty acid (LCFA) degradation is a key step in methanogenic treatment of wastes/wastewaters containing high concentrations of lipids. However, despite the importance of LCFA-degrading bacteria, their natural diversity is little explored due to the limited availability of isolate information and the lack of appropriate molecular markers. We therefore investigated these microbes by using RNA-based stable isotope probing. We incubated four methanogenic sludges (mesophilic sludges MP and MBF and thermophilic sludges TP and JET) with
13
C-labeled palmitate (1 mM) as a substrate. After 8 to 19 days of incubation, we could detect
13
C-labeled bacterial rRNA. A density-resolved terminal restriction fragment length polymorphism fingerprinting analysis showed distinct bacterial populations in
13
C-labeled and unlabeled rRNA fractions. The bacterial populations in the
13
C-labeled rRNA fractions were identified by cloning and sequencing of reverse-transcribed 16S rRNA. Diverse phylogenetic bacterial sequences were retrieved, including those of members of the family
Syntrophaceae
, clone cluster MST belonging to the class
Deltaproteobacteria
,
Clostridium
clusters III and IV, phylum
Bacteroidetes
, phylum
Spirochaetes
, and family
Syntrophomonadaceae
. Although
Syntrophomonadaceae
species are considered to be the major fatty acid-degrading syntrophic microorganisms under methanogenic conditions, they were detected in only two of the clone libraries. These results suggest that phylogenetically diverse bacterial groups were active in situ in the degradation of LCFA under methanogenic conditions.
Quantitative Evaluation of the Impact of Bather Density on Levels of Human-Virulent Microsporidian Spores in Recreational Water
Authors: Graczyk Thaddeus K. , Sunderland Deirdre , Tamang Leena , Shields Timothy M. , Lucy Frances E. , Breysse Patrick N. 
Published: May 2007

ABSTRACT

Microsporidial gastroenteritis, a serious disease of immunocompromised people, can have a waterborne etiology. During summer months, samples of recreational bathing waters were tested weekly for human-virulent microsporidian spores and water quality parameters in association with high and low bather numbers during weekends and weekdays, respectively.
Enterocytozoon bieneusi
spores were detected in 59% of weekend (
n
= 27) and 30% of weekday (
n
= 33) samples, and
Encephalitozoon intestinalis
spores were concomitant in a single weekend sample; the overall prevalence was 43%. The numbers of bathers, water turbidity levels, prevalences of spore-positive samples, and concentrations of spores were significantly higher for weekend than for weekday samples;
P
values were <0.001, <0.04, <0.03, and <0.04, respectively. Water turbidity and the concentration of waterborne spores were significantly correlated with bather density, with
P
values of <0.001 and <0.01, respectively. As all water samples were collected on days deemed acceptable for bathing by fecal bacterial standards, this study reinforces the scientific doubt about the reliability of bacterial indicators in predicting human waterborne pathogens. The study provides evidence that bathing in public waters can result in exposure to potentially viable microsporidian spores and that body contact recreation in potable water can play a role in the epidemiology of microsporidiosis. The study indicates that resuspension of bottom sediments by bathers resulted in elevated turbidity values and implies that the microbial load from both sediments and bathers can act as nonpoint sources for the contamination of recreational waters with
Enterocytozoon bieneusi
spores. Both these mechanisms can be considered for implementation in predictive models for contamination with microsporidian spores.
Specific Detection and Real-Time PCR Quantification of Potentially Mycophagous Bacteria Belonging to the Genus
Collimonas
in Different Soil Ecosystems
Authors: Höppener-Ogawa Sachie , Leveau Johan H. J. , Smant Wiecher , van Veen Johannes A. , de Boer Wietse 
Published: May 2007

ABSTRACT

The bacterial genus
Collimonas
has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. Here, we report the first field inventory of the occurrence and abundance of
Collimonas
in soils (
n
= 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of
Collimonas
and fungal biomass. Estimates of fungal densities were based on ergosterol measurements. Each soil was also characterized in terms of its physical and chemical properties and vegetation and management types. Culturable
Collimonas
was identified in plate-spread soil samples by its ability to clear colloidal chitin, in combination with a
Collimonas
-specific restriction fragment length polymorphism analysis of 16S rRNA PCR amplified from individual colonies. Using this approach, we found culturable collimonads only in (semi)natural grasslands. A real-time PCR assay for the specific quantification of
Collimonas
16S rRNA in total soil DNA was developed.
Collimonas
was detectable in 80% of the soil samples, with densities up to 10
5
cells g
−1
(dry weight) soil. The numbers of
Collimonas
cells per gram of soil were consistently lowest in fungus-poor arable soils and, surprisingly, also in fungus-rich organic layers of forest soils. When all soils were included, no significant correlation was observed between the number of
Collimonas
cells and ergosterol-based soil fungal biomass. Based on this result, we rejected our null hypothesis, and possible explanations for this were addressed.
Dekkera bruxellensisandLactobacillus viniForm a Stable Ethanol-Producing Consortium in a Commercial Alcohol Production Process
Authors: Passoth Volkmar , Blomqvist Johanna , Schnürer Johan 
Published: May 2007

ABSTRACTThe ethanol production process of a Swedish alcohol production plant was dominated byDekkera bruxellensisandLactobacillus vini, with a high number of lactic acid bacteria. The product quality, process productivity, and stability were high; thus,D. bruxellensisandL. vinican be regarded as commercial ethanol production organisms.
Possible Origins of CTnBST, a Conjugative Transposon Found Recently in a Human Colonic
Bacteroides
Strain
Authors: Schlesinger David J. , Shoemaker Nadja B. , Salyers Abigail A. 
Published: May 2007

ABSTRACT

A previous survey of
Bacteroides
isolates suggested that the
ermB
gene entered
Bacteroides
spp. recently. Previously,
ermB
had been found almost exclusively in gram-positive bacteria. In one
Bacteroides
strain,
ermB
was located on 100-kb conjugative transposon (CTn) CTnBST. To assess the possible origin of this CTn, we obtained the full DNA sequence of CTnBST and used this information to investigate its possible origins. Over one-half of CTnBST had high sequence identity to a putative CTn found in the genome of
Bacteroides fragilis
YCH46. This included the ends of the CTn and genes involved in integration, transfer, and excision. However, the region around the
ermB
gene contained genes that appeared to originate from gram-positive organisms. In particular, a 7-kb segment containing the
ermB
gene was 100% identical to an
ermB
region found in the genome of the gram-positive bacterium
Arcanobacterium pyogenes
. A screen of
Bacteroides
isolates whose DNA cross-hybridized with a CTnBST probe revealed that several isolates did not carry the 7-kb region, implying that the acquisition of this region may be more recent than the acquisition of the entire CTnBST element by
Bacteroides
spp. We have also identified other
Bacteroides
isolates that carry a slightly modified 7-kb region but have no other traces of CTnBST. Thus, it is possible that this 7-kb region could itself be part of a mobile element that has inserted in a
Bacteroides
CTn. Our results show that CTnBST is a hybrid element which has acquired a portion of its coding region from gram-positive bacteria but which may originally have come from
Bacteroides
spp. or some related species.
Mycorrhizal and Rhizobial Colonization of Genetically Modified and Conventional Soybeans
Authors: Powell Jeff R. , Gulden Robert H. , Hart Miranda M. , Campbell Rachel G. , Levy-Booth David J. , Dunfield Kari E. , Pauls K. Peter , Swanton Clarence J. , Trevors Jack T. , Klironomos John N. 
Published: May 2007

ABSTRACT

We grew plants of nine soybean varieties, six of which were genetically modified to express transgenic
cp4-epsps
, in the presence of
Bradyrhizobium japonicum
and arbuscular mycorrhizal fungi. Mycorrhizal colonization and nodule abundance and mass differed among soybean varieties; however, in no case was variation significantly associated with the genetic modification.
Screening of Exopolysaccharide-Producing
Lactobacillus
and
Bifidobacterium
Strains Isolated from the Human Intestinal Microbiota
Authors: Ruas-Madiedo Patricia , Moreno José Antonio , Salazar Nuria , Delgado Susana , Mayo Baltasar , Margolles Abelardo , de los Reyes-Gavilán Clara G. 
Published: May 2007

ABSTRACT

Using phenotypic approaches, we have detected that 17% of human intestinal
Lactobacillus
and
Bifidobacterium
strains could be exopolysaccharide (EPS) producers. However, PCR techniques showed that only 7% harbored genes related to the synthesis of heteropolysaccharides. This is the first work to screen the human intestinal ecosystem for the detection of EPS-producing strains.
Simple and Rapid F+ Coliphage Culture, Latex Agglutination, and Typing Assay To Detect and Source Track Fecal Contamination
Authors: Love David C. , Sobsey Mark D. 
Published: May 2007

ABSTRACTSimple, rapid, and reliable fecal indicator tests are needed to better monitor and manage ambient waters and treated waters and wastes. Antibody-coated polymeric bead agglutination assays can fulfill these needs and are inexpensive and portable for nonlaboratory settings, and their reagents can be stored at ambient temperatures for months. The goal of this study was to develop, optimize, and validate a rapid microbial water quality monitoring assay using F+ coliphage culture, latex agglutination, and typing (CLAT) to detect F+ coliphage groups with antibody-coated particles. Rapid (180 min) F+ coliphage culture gave comparable results to those with the 16- to 24-h culture time used in EPA method 1601 and was amenable to CLAT assay detection. CLAT was performed on a cardboard card by mixing a drop of coliphage enrichment culture with a drop of antibody-coated polymeric beads as the detection reagent. Visual agglutination or clumping of positive samples occurred in <60 seconds. The CLAT assay had sensitivities of 96.4% (185/192 samples) and 98.2% (161/164 samples) and specificities of 100% (34/34 samples) and 97.7% (129/132 samples) for F+ RNA and DNA coliphages, respectively. CLAT successfully classified F+ RNA coliphages into serogroups typically obtained from human (groups II and III) and animal (groups I and IV) fecal sources, in similar proportions to those obtained with a nucleic acid hybridization assay. This novel group-specific antibody-based particle agglutination technique for rapid and simple detection and grouping of F+ coliphages provides a new and improved tool for monitoring the microbiological quality of drinking, recreational, shellfishing, and other waters.
Comparison of Aerobic Methanotrophic Communities in Littoral and Profundal Sediments of Lake Constance by a Molecular Approach
Authors: Rahalkar Monali , Schink Bernhard 
Published: May 2007

ABSTRACT

Analysis of
pmoA
and 16S rRNA gene clone libraries of methanotrophic bacteria in Lake Constance revealed an overall dominance of type I methanotrophs in both littoral and profundal sediments. The sediments exhibited minor differences in their methanotrophic community structures. Type X methanotrophs made up a significant part of the clone libraries only in the profundal sediment and were also found only there as a prominent peak by T-RFLP analyses.
Inhibition of
Escherichia coli
Biofilm Formation by Self-Assembled Monolayers of Functional Alkanethiols on Gold
Authors: Hou Shuyu , Burton Erik A. , Simon Karen A. , Blodgett Dustin , Luk Yan-Yeung , Ren Dacheng 
Published: May 2007

ABSTRACT

Bacterial biofilms cause serious problems, such as antibiotic resistance and medical device-related infections. To further understand bacterium-surface interactions and to develop efficient control strategies, self-assembled monolayers (SAMs) of alkanethiols presenting different functional groups on gold films were analyzed to determine their resistance to biofilm formation.
Escherichia coli
was labeled with green florescence protein, and its biofilm formation on SAM-modified surfaces was monitored by confocal laser scanning microscopy. The three-dimensional structures of biofilms were analyzed with the COMSTAT software to obtain information about biofilm thickness and surface coverage. SAMs presenting methyl,
l
-gulonamide (a sugar alcohol tethered with an amide bond), and tri(ethylene glycol) (TEG) groups were tested. Among these, the TEG-terminated SAM was the most resistant to
E. coli
biofilm formation; e.g., it repressed biofilm formation by
E. coli
DH5α by 99.5% ± 0.1% for 1 day compared to the biofilm formation on a bare gold surface. When surfaces were patterned with regions consisting of methyl-terminated SAMs surrounded by TEG-terminated SAMs,
E. coli
formed biofilms only on methyl-terminated patterns. Addition of TEG as a free molecule to growth medium at concentrations of 0.1 and 1.0% also inhibited biofilm formation, while TEG at concentrations up to 1.5% did not have any noticeable effects on cell growth. The results of this study suggest that the reduction in biofilm formation on surfaces modified with TEG-terminated SAMs is a result of multiple factors, including the solvent structure at the interface, the chemorepellent nature of TEG, and the inhibitory effect of TEG on cell motility.
Biocatalytic Conversion of Avermectin to 4″-Oxo-Avermectin: Improvement of Cytochrome P450 Monooxygenase Specificity by Directed Evolution
Authors: Trefzer Axel , Jungmann Volker , Molnár István , Botejue Ajit , Buckel Dagmar , Frey Gerhard , Hill D. Steven , Jörg Mario , Ligon James M. , Mason Dylan , Moore David , Pachlatko J. Paul , Richardson Toby H. , Spangenberg Petra , Wall Mark A. , Zirkle Ross , Stege Justin T. 
Published: May 2007

ABSTRACT
Discovery of the CYP107Z subfamily of cytochrome P450 oxidases (CYPs) led to an alternative biocatalytic synthesis of 4″-oxo-avermectin, a key intermediate for the commercial production of the semisynthetic insecticide emamectin. However, under industrial process conditions, these wild-type CYPs showed lower yields due to side product formation. Molecular evolution employing GeneReassembly was used to improve the regiospecificity of these enzymes by a combination of random mutagenesis, protein structure-guided site-directed mutagenesis, and recombination of multiple natural and synthetic CYP107Z gene fragments. To assess the specificity of CYP mutants, a miniaturized, whole-cell biocatalytic reaction system that allowed high-throughput screening of large numbers of variants was developed. In an iterative process consisting of four successive rounds of GeneReassembly evolution, enzyme variants with significantly improved specificity for the production of 4″-oxo-avermectin were identified; these variants could be employed for a more economical industrial biocatalytic process to manufacture emamectin.
Multistate Evaluation of an Ultrafiltration-Based Procedure for Simultaneous Recovery of Enteric Microbes in 100-Liter Tap Water Samples
Authors: Hill Vincent R. , Kahler Amy M. , Jothikumar Narayanan , Johnson Trisha B. , Hahn Donghyun , Cromeans Theresa L. 
Published: May 2007

ABSTRACT

Ultrafiltration (UF) is increasingly being recognized as a potentially effective procedure for concentrating and recovering microbes from large volumes of water and treated wastewater. Because of their very small pore sizes, UF membranes are capable of simultaneously concentrating viruses, bacteria, and parasites based on size exclusion. In this study, a UF-based water sampling procedure was used to simultaneously recover representatives of these three microbial classes seeded into 100-liter samples of tap water collected from eight cities covering six hydrologic areas of the United States. The UF-based procedure included hollow-fiber UF as the primary step for concentrating microbes and then used membrane filtration for bacterial culture assays, immunomagnetic separation for parasite recovery and quantification, and centrifugal UF for secondary concentration of viruses. Water samples were tested for nine water quality parameters to investigate whether water quality data correlated with measured recovery efficiencies and molecular detection levels. Average total method recovery efficiencies were 71, 97, 120, 110, and 91% for φX174 bacteriophage, MS2 bacteriophage,
Enterococcus faecalis
,
Clostridium perfringens
spores, and
Cryptosporidium parvum
oocysts, respectively. Real-time PCR and reverse transcription-PCR (RT-PCR) for seeded microbes and controls indicated that tap water quality could affect the analytical performance of molecular amplification assays, although no specific water quality parameter was found to correlate with reduced PCR or RT-PCR performance.
Characterization of the Zinc-Containing Metalloprotease Encoded by
zpx
and Development of a Species-Specific Detection Method for
Enterobacter sakazakii
Authors: Kothary M. H. , McCardell B. A. , Frazar C. D. , Deer D. , Tall B. D. 
Published: May 2007

ABSTRACT

Enterobacter sakazakii
causes a severe form of neonatal meningitis that occurs as sporadic cases as well as outbreaks. The disease has been epidemiologically associated with consumption of reconstituted, dried infant formulas. Very little information is available regarding pathogenicity of the organism and production of virulence factors. Clinical and environmental strains were screened for production of factors which have activity against Chinese hamster ovary (CHO) cells in tissue culture. Polymyxin B lysate and sonicate preparations but not culture supernatants from the strains caused “rounding” of CHO cells. Subsequent studies showed that the CHO cell-rounding factor is a proteolytic enzyme that has activity against azocasein. The cell-bound protease was isolated by using a combination of polymyxin B lysis, followed by sonication of cells harvested from tryptone broth. The protease was purified to homogeneity by sequential ammonium sulfate precipitation, gel filtration chromatography with Sephadex G-100, hydrophobic interaction chromatography with phenyl-Sepharose CL-4B, and a second gel filtration with Sephadex G-100. In addition to activity against azocasein, the purified protease also exhibits activity against azocoll and insoluble casein but not elastin. The protease has a molecular weight of 38,000 and an isoelectric point of 4.4. It is heat labile and for maximal activity against azocasein has an optimum temperature of 37°C and a pH range of 5 to 7. Proteolytic activity is inhibited by
ortho
-phenanthroline and Zincov but is not affected by phenylmethylsulfonyl fluoride,
N
-ethylmaleimide, and trypsin inhibitors, which demonstrates that the protease is a zinc-containing metalloprotease. The metalloprotease does not hemagglutinate chicken or sheep erythrocytes. Twenty-three to 27 of the first 42 N-terminal amino acid residues of the metalloprotease are identical to proteases produced by
Serratia proteamaculans
,
Pectobacterium carotovorum
, and
Anabaena
sp. PCR analysis using primers designed from a consensus nucleotide sequence showed that 135
E. sakazakii
strains possessed the metalloprotease gene,
zpx
, and 25 non-
E. sakazakii
strains did not. The cloned
zpx
gene of strain 29544 consists of 1,026 nucleotides, and the deduced amino acid sequence of the metalloprotease has 341 amino acid residues, which corresponds to a theoretical protein size of 37,782 with a theoretical pI of 5.23. The sequence possesses three well-characterized zinc-binding and active-site motifs present in other bacterial zinc metalloproteases.
Tracking Host Sources of
Cryptosporidium
spp. in Raw Water for Improved Health Risk Assessment
Authors: Ruecker Norma J. , Braithwaite Shannon L. , Topp Edward , Edge Thomas , Lapen David R. , Wilkes Graham , Robertson Will , Medeiros Diane , Sensen Christoph W. , Neumann Norman F. 
Published: May 2007

ABSTRACT

Recent molecular evidence suggests that different species and/or genotypes of
Cryptosporidium
display strong host specificity, altering our perceptions regarding the zoonotic potential of this parasite. Molecular forensic profiling of the small-subunit rRNA gene from oocysts enumerated on microscope slides by U.S. Environmental Protection Agency method 1623 was used to identify the range and prevalence of
Cryptosporidium
species and genotypes in the South Nation watershed in Ontario, Canada. Fourteen sites within the watershed were monitored weekly for 10 weeks to assess the occurrence, molecular composition, and host sources of
Cryptosporidium
parasites impacting water within the region.
Cryptosporidium andersoni
,
Cryptosporidium
muskrat genotype II,
Cryptosporidium
cervine genotype,
C. baileyi
,
C. parvum
,
Cryptosporidium
muskrat genotype I, the
Cryptosporidium
fox genotype, genotype W1, and genotype W12 were detected in the watershed. The molecular composition of the
Cryptosporidium
parasites, supported by general land use analysis, indicated that mature cattle were likely the main source of contamination of the watershed. Deer, muskrats, voles, birds, and other wildlife species, in addition to sewage (human or agricultural) may also potentially impact water quality within the study area. Source water protection studies that use land use analysis with molecular genotyping of
Cryptosporidium
parasites may provide a more robust source-tracking tool to characterize fecal impacts in a watershed. Moreover, the information is vital for assessing environmental and human health risks posed by water contaminated with zoonotic and/or anthroponotic forms of
Cryptosporidium
.