bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abundance of Dioxygenase Genes Similar to
Ralstonia
sp. Strain U2
nagAc
Is Correlated with Naphthalene Concentrations in Coal Tar-Contaminated Freshwater Sediments
Authors: Dionisi Hebe M. , Chewning Christopher S. , Morgan Katherine H. , Menn Fu-Min , Easter James P. , Sayler Gary S. 
Published: July 2004

ABSTRACT

We designed a real-time PCR assay able to recognize dioxygenase large-subunit gene sequences with more than 90% similarity to the
Ralstonia
sp. strain U2
nagAc
gene (
nagAc
-like gene sequences) in order to study the importance of organisms carrying these genes in the biodegradation of naphthalene. Sequencing of PCR products indicated that this real-time PCR assay was specific and able to detect a variety of
nagAc
-like gene sequences. One to 100 ng of contaminated-sediment total DNA in 25-μl reaction mixtures produced an amplification efficiency of 0.97 without evident PCR inhibition. The assay was applied to surficial freshwater sediment samples obtained in or in close proximity to a coal tar-contaminated Superfund site. Naphthalene concentrations in the analyzed samples varied between 0.18 and 106 mg/kg of dry weight sediment. The assay for
nagAc
-like sequences indicated the presence of (4.1 ± 0.7) × 10
3
to (2.9 ± 0.3) × 10
5
copies of
nagAc
-like dioxygenase genes per μg of DNA extracted from sediment samples. These values corresponded to (1.2 ± 0.6) × 10
5
to (5.4 ± 0.4) × 10
7
copies of this target per g of dry weight sediment when losses of DNA during extraction were taken into account. There was a positive correlation between naphthalene concentrations and
nagAc
-like gene copies per microgram of DNA (
r
= 0.89) and per gram of dry weight sediment (
r
= 0.77). These results provide evidence of the ecological significance of organisms carrying
nagAc
-like genes in the biodegradation of naphthalene.
Effect of Pyocyanin on a Crude-Oil-Degrading Microbial Community
Authors: Norman R. Sean , Moeller Peter , McDonald Thomas J. , Morris Pamela J. 
Published: July 2004

ABSTRACT

Pseudomonas aeruginosa
is an
n
-alkane degrader that is frequently isolated from petroleum-contaminated sites and produces factors that enhance its competitiveness and survival in many environments. In this study, one such factor, pyocyanin, has been detected in an oil-degrading culture containing
P. aeruginosa
and is a redox-active compound capable of inhibiting microbial growth. To examine the effects of pyocyanin further, an oil-degrading culture was grown with and without 9.5 μM pyocyanin and microbial community structure and oil degradation were monitored for 50 days. Denaturing gradient gel electrophoresis (DGGE) analysis of cultures revealed a decrease in the microbial community diversity in the pyocyanin-amended cultures compared to that of the unamended cultures. Two members of the microbial community in pure culture exhibited intermediate and high sensitivities to pyocyanin corresponding to intermediate and low levels of activity for the antioxidant enzymes catalase and superoxide dismutase, respectively. Another member of the community that remained constant in the DGGE gels over the 50-day culture incubation period exhibited no sensitivity to pyocyanin, corresponding to a high level of catalase and superoxide dismutase when examined in pure culture. Pyocyanin also affected the overall degradation of the crude oil. At 50 days, the culture without pyocyanin had decreased polycyclic aromatic hydrocarbons compared to the pyocyanin-amended culture, with a specific reduction in the degradation of dibenzothiophenes, naphthalenes, and C
29
and C
30
hopanes. This study demonstrated that pyocyanin influenced the diversity of the microbial community and suggests the importance of understanding how interspecies interactions influence the degradation capability of a microbial community.
Multivariate Analyses of
Burkholderia
Species in Soil: Effect of Crop and Land Use History
Authors: Salles Joana Falcão , van Veen Johannes Antonius , van Elsas Jan Dirk 
Published: July 2004

ABSTRACT

The assessment of
Burkholderia
diversity in agricultural areas is important considering the potential use of this genus for agronomic and environmental applications. Therefore, the aim of this work was to ascertain how plant species and land use management drive the diversity of the genus
Burkholderia
. In a greenhouse experiment, different crops, i.e., maize, oat, barley, and grass, were planted in pots containing soils with different land use histories, i.e., maize monoculture, crop rotation, and permanent grassland, for three consecutive growth cycles. The diversity of
Burkholderia
spp. in the rhizosphere soil was assessed by genus-specific PCR-denaturing gradient gel electrophoresis (DGGE) and analyzed by canonical correspondence analysis (CCA). CCA ordination plots showed that previous land use was the main factor affecting the composition of the
Burkholderia
community. Although most variation in the
Burkholderia
community structure was observed between the permanent grassland and agricultural areas, differences between the crop rotation and maize monoculture groups were also observed. Plant species affected
Burkholderia
community structure to a lesser extent than did land use history. Similarities were observed between
Burkholderia
populations associated with maize and grass, on the one hand, and between those associated with barley and oat, on the other hand. Additionally, CCA ordination plots demonstrated that these two groups (maize/grass versus barley/oat) had a negative correlation. The identification of bands from the DGGE patterns demonstrated that the species correlated with the environmental variables were mainly affiliated with
Burkholderia
species that are commonly isolated from soil, in particular
Burkholderia glathei
,
B. caledonica
,
B. hospita
, and
B. caribiensis
.
Effect of High-Pressure-Induced Ice I-to-Ice III Phase Transitions on Inactivation of
Listeria innocua
in Frozen Suspension
Authors: Luscher C. , Balasa A. , Fröhling A. , Ananta E. , Knorr D. 
Published: July 2004

ABSTRACT

The inactivation of
Listeria innocua
BGA 3532 at subzero temperatures and pressures up to 400 MPa in buffer solution was studied to examine the impact of high-pressure treatments on bacteria in frozen matrices. The state of aggregation of water was taken into account. The inactivation was progressing rapidly during pressure holding under liquid conditions, whereas in the ice phases, extended pressure holding times had comparatively little effect. The transient phase change of ice I to other ice polymorphs (ice II or ice III) during pressure cycles above 200 MPa resulted in an inactivation of about 3 log cycles, probably due to the mechanical stress associated with the phase transition. This effect was independent of the applied pressure holding time. Flow cytometric analyses supported the assumption of different mechanisms of inactivation of
L. innocua
in the liquid phase and ice I (large fraction of sublethally damaged cells due to pressure inactivation) in contrast to cells subjected to ice I-to-ice III phase transitions (complete inactivation due to cell rupture). Possible applications of high-pressure-induced phase transitions include cell disintegration for the recovery of intracellular components and inactivation of microorganisms in frozen food.
Evaluation of a Strategy for
Toxoplasma gondii
Oocyst Detection in Water
Authors: Villena Isabelle , Aubert Dominique , Gomis Philippe , Ferté Hubert , Inglard Jean-Christophe , Denis-Bisiaux Hélène , Dondon Julie-Muriel , Pisano Eric , Ortis Naïma , Pinon Jean-Michel 
Published: July 2004

ABSTRACT

Several recent outbreaks of toxoplasmosis were related to drinking water. We propose a strategy for
Toxoplasma
oocyst detection as part of an approach to detecting multiple waterborne parasites, including
Giardia
and
Cryptosporidium
spp., by the U.S. Environmental Protection Agency method with the same sample. Water samples are filtered to recover
Toxoplasma
oocysts and purified on a sucrose density gradient. Detection is based on PCR and mouse inoculation (bioassay) to determine the presence and infectivity of recovered oocysts. In an experimental seeding assay with 100 liters of deionized water, a parasite density of 1 oocyst/liter was successfully detected by PCR in 60% of cases and a density of 10 oocysts/liter was detected in 100% of cases. The sensitivity of the PCR assay varied from less than 10 to more than 1000 oocysts/liter, depending on the sample source. PCR was always more sensitive than mouse inoculation. This detection strategy was then applied to 139 environmental water samples collected over a 20-month period. Fifty-three samples contained PCR inhibitors, which were overcome in 39 cases by bovine serum albumin addition. Among 125 interpretable samples, we detected
Toxoplasma
DNA in 10 cases (8%). None of the samples were positive by mouse inoculation. This strategy efficiently detects
Toxoplasma
oocysts in water and may be suitable as a public health sentinel method.
Effect of Dilution Rate on Metabolic Pathway Shift between Aceticlastic and Nonaceticlastic Methanogenesis in Chemostat Cultivation
Authors: Shigematsu Toru , Tang Yueqin , Kobayashi Tsutomu , Kawaguchi Hiromi , Morimura Shigeru , Kida Kenji 
Published: July 2004

ABSTRACT

Acetate conversion pathways of methanogenic consortia in acetate-fed chemostats at dilution rates of 0.025 and 0.6 day
−1
were investigated by using
13
C-labeled acetates, followed by gas chromatography-mass spectrometry (GC-MS) analysis of the CH
4
and CO
2
produced. Nonaceticlastic syntrophic oxidation by acetate-oxidizing syntrophs and hydrogenotrophic methanogens was suggested to occupy a primary pathway (approximately 62 to 90%) in total methanogenesis at the low dilution rate. In contrast, aceticlastic cleavage of acetate by aceticlastic methanogens was suggested to occupy a primary pathway (approximately 95 to 99%) in total methanogenesis at the high dilution rate. Phylogenetic analyses of transcripts of the methyl coenzyme M reductase gene (
mcrA
) confirmed that a significant number of transcripts of the genera
Methanoculleus
(hydrogenotrophic methanogens) and
Methanosarcina
(aceticlastic methanogens) were present in the chemostats at the low and high dilution rates, respectively. The
mcrA
transcripts of the genus
Methanosaeta
(aceticlastic methanogens), which dominated the population in a previous study (T. Shigematsu, Y. Tang, H. Kawaguchi, K. Ninomiya, J. Kijima, T. Kobayashi, S. Morimura, and K. Kida, J. Biosci. Bioeng.
96:
547-558, 2003), were poorly detected at both dilution rates due to the limited coverage of the primers used. These results demonstrated that the dilution rate could cause a shift in the primary pathway of acetate conversion to methane in acetate-fed chemostats.
Mineralization of Individual Congeners of Linear Alkylbenzenesulfonate by Defined Pairs of Heterotrophic Bacteria
Authors: Schleheck David , Knepper Thomas P. , Fischer Karin , Cook Alasdair M. 
Published: July 2004

ABSTRACTParvibaculum lavamentivoransDS-1Tutilized the commercial surfactant linear alkylbenzenesulfonate (LAS) (20 congeners with C10to C13side chains) as a carbon and energy source by shortening the side chain, and sulfophenylcarboxylates (SPCs) and similar compounds (e.g., α,β-unsaturated SPCs [SPC-2Hs]) were excreted with quantitative recovery of the sulfophenyl moiety. 2-(4-Sulfophenyl)decane (2-C10-LAS) was converted largely to 3-(4-sulfophenyl)butyrate (3-C4-SPC), as were 2-C12-LAS and 2-C14-LAS; the other products were 5-C6-SPC (SPC+2C) and 3-C4-SPC-2H. 2-C11-LAS was converted largely to 4-C5-SPC with the corresponding SPC+2C and SPC-2H; similarly, 3-C12-LAS yielded 4-C6-SPC with the corresponding SPC+2C and SPC-2H. This pattern of products confirmed that LAS is degraded by ω-oxygenation and chain shortening through β-oxidation. At least nine major SPCs were formed from commercial LAS. The novel isolatesComamonas testosteroniSPB-2 and KF-1 utilized 3-C4-SPC;Delftia acidovoransSPH-1 utilized 4-C6-SPC enantioselectively. The substrate-dependent oxygen uptake of whole cells of strain SPB-2 indicated that there was inducible oxygenation of 3-C4-SPC and of 4-sulfophenol in whole cells of the strains ofC. testosteroniduring growth with 3-C4-SPC or 4-sulfophenol. The degradative pathways apparently involved 4-sulfocatechol and 4-sulfocatechol 1,2-dioxygenase. Strain SPB-2 and strain DS-1Tgrew together in LAS-salts medium, and only seven of the nine major SPCs were recovered. Strain SPB-2 utilized 3-C4-SPC, 3-C5-SPC, and 3-C4-SPC-2H. Strain SPH-1 grew together with strain DS-1Tin LAS-salts medium, and a different set of seven major SPCs was recovered. Strain SPH-1 utilized 4-C6-SPC, 4-C5-SPC, 4-C6-SPC-2H, and 4-C5-SPC-2H. A three-member community consisting of strains DS-1T, SPB-2, and SPH-1 utilized four major SPCs. We inferred that this community mineralized the major SPCs derived from 8 of the 20 LAS congeners.
Light Dependence of [3H]Leucine Incorporation in the Oligotrophic North Pacific Ocean
Authors: Church Matthew J. , Ducklow Hugh W. , Karl David M. 
Published: July 2004

ABSTRACTThe influence of irradiance on bacterial incorporation of [3H]leucine was evaluated at Station ALOHA in the oligotrophic North Pacific subtropical gyre. Six experiments were conducted on three cruises to Station ALOHA to examine how [3H]leucine incorporation varied as a function of irradiance. Two experiments were also conducted to assess the photoautotrophic response to irradiance (based on photosynthetic uptake of [14C]bicarbonate) in both the upper and lower photic zones. Rates of [3H]leucine incorporation responded to irradiance in a photosynthesis-like manner, increasing sharply at low light and then saturating and sometimes declining with increasing light intensity. The influence of irradiance on bacterial growth was evaluated in both the well-lit (5 to 25 m) and dimly lit regions of the upper ocean (75 to 100 m) to determine whether the bacterial response to irradiance differed along the depth-dependent light gradient of the photic zone. [3H]leucine incorporation rates were analyzed with a photosynthesis-irradiance model for a quantitative description of the relationships between [3H]leucine incorporation and irradiance. Maximum rates of [3H]leucine incorporation in the upper photic zone increased 48 to 92% relative to those of dark-incubated samples, with [3H]leucine incorporation saturating at light intensities between 58 and 363 μmol of quanta m−2s−1. Rates of [3H]leucine incorporation in the deep photic zone were photostimulated 53 to 114% and were susceptible to photoinhibition, with rates declining at light intensities of >100 μmol of quanta m−2s−1. The results of these experiments revealed that sunlight directly influences bacterial growth in this open-ocean ecosystem.
Populations Implicated in Anaerobic Reductive Dechlorination of 1,2-Dichloropropane in Highly Enriched Bacterial Communities
Authors: Ritalahti Kirsti M. , Löffler Frank E. 
Published: July 2004

ABSTRACT

1,2-Dichloropropane (1,2-D), a widespread groundwater contaminant, can be reductively dechlorinated to propene by anaerobic bacteria. To shed light on the populations involved in the detoxification process, a comprehensive 16S rRNA gene-based bacterial community analysis of two enrichment cultures derived from geographically distinct locations was performed. Analysis of terminal restriction fragments, amplicons obtained with dechlorinator-specific PCR primers, and enumeration with quantitative real-time PCR as well as screening clone libraries all implied that
Dehalococcoides
populations were involved in 1,2-D dechlorination in both enrichment cultures. Physiological traits (e.g., dechlorination in the presence of ampicillin and a requirement for hydrogen as the electron donor) supported the involvement of
Dehalococcoides
populations in the dechlorination process. These findings expand the spectrum of chloroorganic compounds used by
Dehalococcoides
species as growth-supporting electron acceptors. The combined molecular approach allowed a comparison between different 16S rRNA gene-based approaches for the detection of
Dehalococcoides
populations.
Effects of Seeding Procedures and Water Quality on Recovery of
Cryptosporidium
Oocysts from Stream Water by Using U.S. Environmental Protection Agency Method 1623
Authors: Francy Donna S. , Simmons Otto D. , Ware Michael W. , Granger Emma J. , Sobsey Mark D. , Schaefer Frank W. 
Published: July 2004

ABSTRACT

U.S. Environmental Protection Agency method 1623 is widely used to monitor source waters and drinking water supplies for
Cryptosporidium
oocysts. Matrix spikes, used to determine the effect of the environmental matrix on the method's recovery efficiency for the target organism, require the collection and analysis of two environmental samples, one for analysis of endemic oocysts and the other for analysis of recovery efficiency. A new product, ColorSeed, enables the analyst to determine recovery efficiency by using modified seeded oocysts that can be differentiated from endemic organisms in a single sample. Twenty-nine stream water samples and one untreated effluent sample from a cattle feedlot were collected in triplicate to compare modified seeding procedures to conventional seeding procedures that use viable, unmodified oocysts. Significant negative correlations were found between the average oocyst recovery and turbidity or suspended sediment; this was especially apparent in samples with turbidities greater than 100 nephelometric turbidity units and suspended sediment concentrations greater than 100 mg/liter.
Cryptosporidium
oocysts were found in 16.7% of the unseeded environmental samples, and concentrations, adjusted for recoveries, ranged from 4 to 80 oocysts per 10 liters. Determining recovery efficiency also provided data to calculate detection limits; these ranged from <2 to <215 oocysts per 10 liters. Recoveries of oocysts ranged from 2.0 to 61% for viable oocysts and from 3.0 to 59% for modified oocysts. The recoveries between the two seeding procedures were highly correlated (
r
= 0.802) and were not significantly different. Recoveries by using modified oocysts, therefore, were comparable to recoveries by using conventional seeding procedures.
Contribution of SAR11 Bacteria to Dissolved Dimethylsulfoniopropionate and Amino Acid Uptake in the North Atlantic Ocean
Authors: Malmstrom Rex R. , Kiene Ronald P. , Cottrell Matthew T. , Kirchman David L. 
Published: July 2004

ABSTRACT

SAR11 bacteria are abundant in marine environments, often accounting for 35% of total prokaryotes in the surface ocean, but little is known about their involvement in marine biogeochemical cycles. Previous studies reported that SAR11 bacteria are very small and potentially have few ribosomes, indicating that SAR11 bacteria could have low metabolic activities and could play a smaller role in the flux of dissolved organic matter than suggested by their abundance. To determine the ecological activity of SAR11 bacteria, we used a combination of microautoradiography and fluorescence in situ hybridization (Micro-FISH) to measure assimilation of
3
H-amino acids and [
35
S]dimethylsulfoniopropionate (DMSP) by SAR11 bacteria in the coastal North Atlantic Ocean and the Sargasso Sea. We found that SAR11 bacteria were often abundant in surface waters, accounting for 25% of all prokaryotes on average. SAR11 bacteria were typically as large as, if not larger than, other prokaryotes. Additionally, more than half of SAR11 bacteria assimilated dissolved amino acids and DMSP, whereas about 40% of other prokaryotes assimilated these compounds. Due to their high abundance and activity, SAR11 bacteria were responsible for about 50% of amino acid assimilation and 30% of DMSP assimilation in surface waters. The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11 bacteria outcompete other prokaryotes for these labile compounds. These data suggest that SAR11 bacteria are highly active and play a significant role in C, N, and S cycling in the ocean.
Identification of Type A, B, E, and F Botulinum Neurotoxin Genes and of Botulinum Neurotoxigenic Clostridia by Denaturing High-Performance Liquid Chromatography
Authors: Franciosa Giovanna , Pourshaban Manoocheher , De Luca Alessandro , Buccino Anna , Dallapiccola Bruno , Aureli Paolo 
Published: July 2004

ABSTRACT

Denaturing high-performance liquid chromatography (DHPLC) is a recently developed technique for rapid screening of nucleotide polymorphisms in PCR products. We used this technique for the identification of type A, B, E, and F botulinum neurotoxin genes. PCR products amplified from a conserved region of the type A, B, E, and F botulinum toxin genes from
Clostridium botulinum
, neurotoxigenic
C. butyricum
type E, and
C. baratii
type F strains were subjected to both DHPLC analysis and sequencing. Unique DHPLC peak profiles were obtained with each different type of botulinum toxin gene fragment, consistent with nucleotide differences observed in the related sequences. We then evaluated the ability of this technique to identify botulinal neurotoxigenic organisms at the genus and species level. A specific short region of the 16S rRNA gene which contains genus-specific and in some cases species-specific heterogeneity was amplified from botulinum neurotoxigenic clostridia and from different food-borne pathogens and subjected to DHPLC analysis. Different peak profiles were obtained for each genus and species, demonstrating that the technique could be a reliable alternative to sequencing for the rapid identification of food-borne pathogens, specifically of botulinal neurotoxigenic clostridia most frequently implicated in human botulism.
Molecular Analysis of Shower Curtain Biofilm Microbes
Authors: Kelley Scott T. , Theisen Ulrike , Angenent Largus T. , St. Amand Allison , Pace Norman R. 
Published: July 2004

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 shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as “soap scum,” which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the α-group of proteobacteria, mainly
Sphingomonas
spp. and
Methylobacterium
spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.