bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth of
Dehalobacter
and
Dehalococcoides
spp. during Degradation of Chlorinated Ethanes
Authors: Grostern Ariel , Edwards Elizabeth A. 
Published: January 2006

ABSTRACT

Mixed anaerobic microbial subcultures enriched from a multilayered aquifer at a former chlorinated solvent disposal facility in West Louisiana were examined to determine the organism(s) involved in the dechlorination of the toxic compounds 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA) to ethene. Sequences phylogenetically related to
Dehalobacter
and
Dehalococcoides
, two genera of anaerobic bacteria that are known to respire with chlorinated ethenes, were detected through cloning of bacterial 16S rRNA genes. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments after starvation and subsequent reamendment of culture with 1,2-DCA showed that the
Dehalobacter
sp. grew during the dichloroelimination of 1,2-DCA to ethene, implicating this organism in degradation of 1,2-DCA in these cultures. Species-specific real-time quantitative PCR was further used to monitor proliferation of
Dehalobacter
and
Dehalococcoides
during the degradation of chlorinated ethanes and showed that in fact both microorganisms grew simultaneously during the degradation of 1,2-DCA. Conversely,
Dehalobacter
grew during the dichloroelimination of 1,1,2-TCA to vinyl chloride (VC) but not during the subsequent reductive dechlorination of VC to ethene, whereas
Dehalococcoides
grew only during the reductive dechlorination of VC but not during the dichloroelimination of 1,1,2-TCA. This demonstrated that in mixed cultures containing multiple dechlorinating microorganisms, these organisms can have either competitive or complementary dechlorination activities, depending on the chloro-organic substrate.
Effects of Endogenous Substrates on Adaptation of Anaerobic Microbial Communities to 3-Chlorobenzoate
Authors: Becker Jennifer G. , Berardesco Gina , Rittmann Bruce E. , Stahl David A. 
Published: January 2006

ABSTRACT
Lengthy adaptation periods in laboratory studies evaluating the potential for contaminant biodegradation in natural or engineered environments may indicate that the native microbial communities are not metabolizing the contaminants in situ. In this study, we characterized the adaptation period preceding the biodegradation of 3-chlorobenzoate in anaerobic communities derived from lake sediment and wastewater sludge digesters. The importance of alternative mechanisms of adaptation of the anaerobic communities to 3-chlorobenzoate was evaluated by monitoring the concentrations of metabolic substrates and products as well as the levels of total small subunit (SSU) rRNA and SSU rRNA from populations thought to be important in 3-chlorobenzoate mineralization. The anaerobic environments from which the 3-chlorobenzoate-degrading communities were derived contained different levels of endogenous substrates. Increasing methane levels in the digester and sediment communities and decreasing chemical oxygen demand concentrations in the sediment community during the adaptation periods revealed that endogenous substrates were preferentially utilized relative to 3-chlorobenzoate. Methane and chemical oxygen demand concentrations leveled off concomitantly with the onset of 3-chlorobenzoate biodegradation, suggesting that depletion of the preferentially degraded endogenous substrates stimulated 3-chlorobenzoate metabolism. Consistent with these observations, adaptation to 3-chlorobenzoate occurred more rapidly in digester samples that were depleted of endogenous substrates compared to samples that contained high levels of these biodegradable compounds. Other potential adaptation mechanisms, e.g., genetic change or selective population enrichment, appeared to be less important based on the reproducibility and relative lengths of the adaptation events, trends in the SSU rRNA levels, and/or amplification of SSU rRNA genes from key populations.
Involvement of Cyclopropane Fatty Acids in the Response of
Pseudomonas putida
KT2440 to Freeze-Drying
Authors: Muñoz-Rojas Jesús , Bernal Patricia , Duque Estrella , Godoy Patricia , Segura Ana , Ramos Juan-Luis 
Published: January 2006

ABSTRACT

Pseudomonas putida
KT2440, a saprophytic soil bacterium that colonizes the plant root, is a suitable microorganism for the removal of pollutants and a stable host for foreign genes used in biotransformation processes. Because of its potential use in agriculture and industry, we investigated the conditions for the optimal preservation of the strain and its derivatives for long-term storage. The highest survival rates were achieved with cells that had reached the stationary phase and which had been subjected to freeze-drying in the presence of disaccharides (trehalose, maltose, and lactose) as lyoprotectants. Using fluorescence polarization techniques, we show that cell membranes of KT2440 were more rigid in the stationary phase than in the exponential phase of growth. This is consistent with the fact that cells grown in the stationary phase exhibited a higher proportion of C
17:cyclopropane
as a fatty acid than cells in the exponential phase. Mutants for the
cfaB
gene, which encodes the main C
17:cyclopropane
synthase, and for the
cfaA
gene, which encodes a minor C
17:cyclopropane
synthase, were constructed. These mutants were more sensitive to freeze-drying than wild-type cells, particularly the mutant with a knockout in the
cfaB
gene that produced less than 2% of the amount of C
17:cyclopropane
produced by the parental strain.
Real-Time Fluorogenic Reverse Transcription-PCR Assays for Detection of Bacteriophage MS2
Authors: O'Connell Kevin P. , Bucher Jennifer R. , Anderson Patricia E. , Cao Cheng J. , Khan Akbar S. , Gostomski Mark V. , Valdes James J. 
Published: January 2006

ABSTRACT
Bacteriophage MS2 is used in place of pathogenic viruses in a wide variety of studies that range from testing of compounds for disinfecting surfaces to studying environmental transport and fate of pathogenic viruses in groundwater. MS2 is also used as a pathogen simulant in the research, development, and testing (including open air tests) of methods, systems, and devices for the detection of pathogens in both the battlefield and homeland defense settings. PCR is often used as either an integral part of such detection systems or as a reference method to assess the sensitivity and specificity of microbial detection. To facilitate the detection of MS2 by PCR, we describe here a set of real-time fluorogenic reverse transcription-PCR assays. The sensitivity of the assays (performed with primer pairs and corresponding dye-labeled probes) ranged from 0.4 to 40 fg of MS2 genomic RNA (200 to 20,000 genome equivalents). We also demonstrate the usefulness of the primer pairs in assays without dye-labeled probe that included the DNA-binding dye SYBR green. None of the assays gave false-positive results when tested against 400 pg of several non-MS2 nucleic acid targets.
Molecular Analysis of an Inactive Aflatoxin Biosynthesis Gene Cluster in
Aspergillus oryzae
RIB Strains
Authors: Tominaga Mihoko , Lee Yun-Hae , Hayashi Risa , Suzuki Yuji , Yamada Osamu , Sakamoto Kazutoshi , Gotoh Kuniyasu , Akita Osamu 
Published: January 2006

ABSTRACT

To help assess the potential for aflatoxin production by
Aspergillus oryzae
, the structure of an aflatoxin biosynthesis gene homolog cluster in
A. oryzae
RIB 40 was analyzed. Although most genes in the corresponding cluster exhibited from 97 to 99% similarity to those of
Aspergillus flavus
, three genes shared 93% similarity or less. A 257-bp deletion in the
aflT
region, a frameshift mutation in
norA
, and a base pair substitution in
verA
were found in
A. oryzae
RIB 40. In the
aflR
promoter, two substitutions were found in one of the three putative AreA binding sites and in the FacB binding site. PCR primers were designed to amplify homologs of
aflT
,
nor-1
,
aflR
,
norA
,
avnA
,
verB
, and
vbs
and were used to detect these genes in 210
A. oryzae
strains. Based on the PCR results, the
A. oryzae
RIB strains were classified into three groups, although most of them fell into two of the groups. Group 1, in which amplification of all seven genes was confirmed, contained 122 RIB strains (58.1% of examined strains), including RIB 40. Seventy-seven strains (36.7%) belonged to group 2, characterized by having only
vbs
,
verB
, and
avnA
in half of the cluster. Although slight expression of
aflR
was detected by reverse transcription-PCR in some group 1 strains, including RIB 40, other genes (
avnA
,
vbs
,
verB
, and
omtA
) related to aflatoxin production were not detected.
aflR
was not detected in group 2 strains by Southern analysis.
Deep Desulfurization of Diesel Oil and Crude Oils by a Newly Isolated
Rhodococcus erythropolis
Strain
Authors: Yu Bo , Xu Ping , Shi Quan , Ma Cuiqing 
Published: January 2006

ABSTRACT

The soil-isolated strain XP was identified as
Rhodococcus erythropolis. R. erythropolis
XP could efficiently desulfurize benzonaphthothiophene, a complicated model sulfur compound that exists in crude oil. The desulfurization product of benzonaphthothiophene was identified as α-hydroxy-β-phenyl-naphthalene. Resting cells could desulfurize diesel oil (total organic sulfur, 259 ppm) after hydrodesulfurization. The sulfur content of diesel oil was reduced by 94.5% by using the resting cell biocatalyst for 24 h at 30°C. Biodesulfurization of crude oils was also investigated. After 72 h of treatment at 30°C, 62.3% of the total sulfur content in Fushun crude oil (initial total sulfur content, 3,210 ppm) and 47.2% of that in Sudanese crude oil (initial total sulfur, 1,237 ppm) were removed. Gas chromatography with pulsed-flame photometric detector analysis was used to evaluate the effect of
R. erythropolis
XP treatment on the sulfur content in Fushun crude oil, and it was shown that most organic sulfur compounds were eliminated after biodesulfurization.
Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre
Authors: Cottrell Matthew T. , Mannino Antonio , Kirchman David L. 
Published: January 2006

ABSTRACT

The abundance of aerobic anoxygenic phototrophic (AAP) bacteria, cyanobacteria, and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific Gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic Ocean but only 5% or less in the Pacific Ocean. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than that of
Prochlorococcus
spp. and 10-fold higher than that of
Synechococcus
spp. In contrast,
Prochlorococcus
spp. outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP bacterial genera (
Erythrobacter
and
Roseobacter
spp.). Concentrations of bacteriochlorophyll
a
(BChl
a
) were low (∼1%) compared to those of chlorophyll
a
in the North Atlantic. Although the BChl
a
content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll
a
content of
Prochlorococcus
, the pigment content of AAP bacteria approached that of
Prochlorococcus
in shelf break water. Our results suggest that AAP bacteria can be quite abundant in some oceanic regimes and that their distribution in the water column is consistent with phototrophy.
Presence and Growth of Naturalized
Escherichia coli
in Temperate Soils from Lake Superior Watersheds
Authors: Ishii Satoshi , Ksoll Winfried B. , Hicks Randall E. , Sadowsky Michael J. 
Published: January 2006

ABSTRACT

The presence of
Escherichia coli
in water is used as an indicator of fecal contamination, but recent reports indicate that soil populations can also be detected in tropical, subtropical, and some temperate environments. In this study, we report that viable
E. coli
populations were repeatedly isolated from northern temperate soils in three Lake Superior watersheds from October 2003 to October 2004. Seasonal variation in the population density of soilborne
E. coli
was observed; the greatest cell densities, up to 3 × 10
3
CFU/g soil, were found in the summer to fall (June to October), and the lowest numbers, ≤1 CFU/g soil, occurred during the winter to spring months (February to May). Horizontal, fluorophore-enhanced repetitive extragenic palindromic PCR (HFERP) DNA fingerprint analyses indicated that identical soilborne
E. coli
genotypes, those with ≥92% similarity values, overwintered in frozen soil and were present over time. Soilborne
E. coli
strains had HFERP DNA fingerprints that were unique to specific soils and locations, suggesting that these
E. coli
strains became naturalized, autochthonous members of the soil microbial community. In laboratory studies, naturalized
E. coli
strains had the ability to grow and replicate to high cell densities, up to 4.2 × 10
5
CFU/g soil, in nonsterile soils when incubated at 30 or 37°C and survived longer than 1 month when soil temperatures were ≤25°C. To our knowledge, this is the first report of the growth of naturalized
E. coli
in nonsterile, nonamended soils. The presence of significant populations of naturalized populations of
E. coli
in temperate soils may confound the use of this bacterium as an indicator of fecal contamination.
Involvement of NarK1 and NarK2 Proteins in Transport of Nitrate and Nitrite in the Denitrifying Bacterium
Pseudomonas aeruginosa
PAO1
Authors: Sharma Vandana , Noriega Chris E. , Rowe John J. 
Published: January 2006

ABSTRACT

Two transmembrane proteins were tentatively classified as NarK1 and NarK2 in the
Pseudomonas
genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in
Pseudomonas aeruginosa
. The
narK1
and
narK2
genes are located in a cluster along with the structural genes for the nitrate reductase complex. Our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex
narK1K2GHJI
constitutes an operon. Utilizing an isogenic
narK1
mutant, a
narK2
mutant, and a
narK1K2
double mutant, we explored their effect on growth under denitrifying conditions. While the Δ
narK1
::Gm mutant was only slightly affected in its ability to grow under denitrification conditions, both the Δ
narK2
::Gm and Δ
narK1K2
::Gm mutants were found to be severely restricted in nitrate-dependent, anaerobic growth. All three strains demonstrated wild-type levels of nitrate reductase activity. Nitrate uptake by whole-cell suspensions demonstrated both the
ΔnarK2
::Gm and Δ
narK1K2
::Gm mutants to have very low yet different nitrate uptake rates, while the Δ
narK1
::Gm mutant exhibited wild-type levels of nitrate uptake. Finally,
Escherichia coli narK
rescued both the Δ
narK2
::Gm and Δ
narK1K2
::Gm mutants with respect to anaerobic respiratory growth. Our results indicate that only the NarK2 protein is required as a nitrate/nitrite transporter by
Pseudomonas aeruginosa
under denitrifying conditions.
Involvement of Quinolinate Phosphoribosyl Transferase in Promotion of Potato Growth by a
Burkholderia
Strain
Authors: Wang Keri , Conn Kenneth , Lazarovits George 
Published: January 2006

ABSTRACT

Burkholderia
sp. strain PsJN stimulates root growth of potato explants compared to uninoculated controls under gnotobiotic conditions. In order to determine the mechanism by which this growth stimulation occurs, we used Tn
5
mutagenesis to produce a mutant, H41, which exhibited no growth-promoting activity but was able to colonize potato plants as well as the wild-type strain. The gene associated with the loss of growth promotion in H41 was shown to exhibit 65% identity at the amino acid level to the
nadC
gene encoding quinolinate phosphoribosyltransferase (QAPRTase) in
Ralstonia solanacearum
. Complementation of H41 with QAPRTase restored growth promotion of potato explants by this mutant. Expression of the gene identified in
Escherichia coli
yielded a protein with QAPRTase activities that catalyzed the de novo formation of nicotinic acid mononucleotide (NaMN). Two other genes involved in the same enzymatic pathway,
nadA
and
nadB
, were physically linked to
nadC
. The
nadA
gene was cotranscribed with
nadC
as an operon in wild-type strain PsJN, while the
nadB
gene was located downstream of the
nadA
-
nadC
operon. Growth promotion by H41 was fully restored by addition of NaMN to the tissue culture medium. These data suggested that QAPRTase may play a role in the signal pathway for promotion of plant growth by PsJN.
Transmission of Nephridial Bacteria of the EarthwormEisenia fetida
Authors: Davidson Seana K. , Stahl David A. 
Published: January 2006

ABSTRACTThe lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the nephridia of several earthworm species has shown that each species of worm harbors a distinct bacterial species and that the bacteria from different species form a monophyletic cluster within the genusAcidovorax, suggesting that there is a specific association resulting from radiation from a common bacterial ancestor. Previous microscopy and culture studies revealed the presence of bacteria within the egg capsules and on the surface of embryos but did not demonstrate that the bacteria within the egg capsule were the same bacteria that colonized the nephridia. We present evidence, based on curing experiments, in situ hybridizations withAcidovorax-specific probes, and 16S rRNA gene sequence analysis, that the egg capsules contain high numbers of the bacterial symbiont and that juveniles are colonized during development within the egg capsule. Studies exposing aposymbiotic hatchlings to colonized adults and their bedding material suggested that juvenile earthworms do not readily acquire bacteria from the soil after hatching but must be colonized during development by bacteria deposited in the egg capsule. Whether this is due to the developmental stage of the host or the physiological state of the symbiont remains to be investigated.
Evolutionary Dynamics ofwAu-LikeWolbachiaVariants in NeotropicalDrosophilaspp
Authors: Miller Wolfgang J. , Riegler Markus 
Published: January 2006

ABSTRACTWolbachiabacteria are common intracellular symbionts of arthropods and have been extensively studied inDrosophila. Most research focuses on two Old Word hosts,Drosophila melanogasterandDrosophila simulans, and does not take into account that some of theWolbachiaassociations in these species may have evolved only after their fast global expansion and after the exposure toWolbachiaof previously isolated habitats. Here we looked atWolbachiaof NeotropicalDrosophilaspecies. Seventy-one lines of 16 NeotropicalDrosophilaspecies sampled in different regions and at different time points were analyzed.Wolbachiais absent in lines ofDrosophila willistonicollected before the 1970s, but more recent samples are infected with a strain designatedwWil.Wolbachiais absent in all other species of the willistoni group. PolymorphicwWil-related strains were detected in some saltans group species, withD. septentriosaltansbeing coinfected with at least four variants. Based onwspandftsZsequence data,wWil ofD. willistoniis identical towAu, a strain isolated fromD. simulans, but can be discriminated when using a polymorphic minisatellite marker. In contrast towAu, which infects both germ line and somatic tissues ofD. simulans,wWil is found exclusively in the primordial germ line cells ofD. willistoniembryos. We report on a pool of closely relatedWolbachiastrains in NeotropicalDrosophilaspecies as a potential source for thewAu strain inD. simulans. Possible evolutionary scenarios reconstructing the infection history ofwAu-likeWolbachiain NeotropicalDrosophilaspecies and the Old World speciesD. simulansare discussed.
Transcriptomic and Proteomic Approach for Understanding the Molecular Basis of Adaptation of
Saccharomyces cerevisiae
to Wine Fermentation
Authors: Zuzuarregui Aurora , Monteoliva Lucía , Gil Concha , del Olmo Marcel·lí 
Published: January 2006

ABSTRACT

Throughout alcoholic fermentation,
Saccharomyces cerevisiae
cells have to cope with several stress conditions that could affect their growth and viability. In addition, the metabolic activity of yeast cells during this process leads to the production of secondary compounds that contribute to the organoleptic properties of the resulting wine. Commercial strains have been selected during the last decades for inoculation into the must to carry out the alcoholic fermentation on the basis of physiological traits, but little is known about the molecular basis of the fermentative behavior of these strains. In this work, we present the first transcriptomic and proteomic comparison between two commercial strains with different fermentative behaviors. Our results indicate that some physiological differences between the fermentative behaviors of these two strains could be related to differences in the mRNA and protein profiles. In this sense, at the level of gene expression, we have found differences related to carbohydrate metabolism, nitrogen catabolite repression, and response to stimuli, among other factors. In addition, we have detected a relative increase in the abundance of proteins involved in stress responses (the heat shock protein Hsp26p, for instance) and in fermentation (in particular, the major cytosolic aldehyde dehydrogenase Ald6p) in the strain with better behavior during vinification. Moreover, in the case of the other strain, higher levels of enzymes required for sulfur metabolism (Cys4p, Hom6p, and Met22p) are observed, which could be related to the production of particular organoleptic compounds or to detoxification processes.
Gene Targeting in the Gram-Positive Bacterium
Lactococcus lactis
, Using Various Delta Ribozymes
Authors: Fiola Karine , Perreault Jean-Pierre , Cousineau Benoit 
Published: January 2006

ABSTRACT

The
trans
-acting antigenomic delta ribozyme, isolated from the human hepatitis delta virus, was shown to be highly stable and active in vitro, as well as in mammalian cell lines. However, the stability and gene-targeting competence of this small ribozyme have not been studied previously in bacterial cells. In this paper we describe the use of two variants of the
trans
-acting antigenomic delta ribozyme targeting the abundant EF-Tu mRNA in the industrially important gram-positive bacterium
Lactococcus lactis
. These two delta ribozyme variants were expressed at significant levels and were shown to be highly stable in vivo. The half-life of the EF-Tu mRNA was slightly but consistently reduced in the presence of the classical delta ribozymes (7 to 13%). In contrast, delta ribozymes harboring a specific on/off riboswitch (SOFA-delta ribozymes) targeting the same sites on the EF-Tu mRNA considerably reduced the half-life of this mRNA (22 to 47%). The rates of catalysis of the SOFA-delta ribozymes in
L. lactis
were similar to the rates determined in vitro, showing that this new generation of delta ribozymes was highly efficient in these bacterial cells. Clearly, SOFA-delta ribozymes appear to be an ideal means for development of gene inactivation systems in bacteria.