bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Analysis of Phenoxyalkanoic Acid Degradation in
Sphingomonas herbicidovorans
MH
Authors: Müller Tina A. , Byrde Steven M. , Werlen Christoph , van der Meer Jan Roelof , Kohler Hans-Peter E. 
Published: October 2004

ABSTRACT

Phenoxyalkanoic acid degradation is well studied in
Beta
- and
Gammaproteobacteria
, but the genetic background has not been elucidated so far in
Alphaproteobacteria
. We report the isolation of several genes involved in dichlor- and mecoprop degradation from the alphaproteobacterium
Sphingomonas herbicidovorans
MH and propose that the degradation proceeds analogously to that previously reported for 2,4-dichlorophenoxyacetic acid (2,4-D). Two genes for α-ketoglutarate-dependent dioxygenases,
sdpA
MH
and
rdpA
MH
, were found, both of which were adjacent to sequences with potential insertion elements. Furthermore, a gene for a dichlorophenol hydroxylase (
tfdB
), a putative regulatory gene (
cadR
), two genes for dichlorocatechol 1,2-dioxygenases (
dccA
I/II
), two for dienelactone hydrolases (
dccD
I/II
), part of a gene for maleylacetate reductase (
dccE
), and one gene for a potential phenoxyalkanoic acid permease were isolated. In contrast to other 2,4-D degraders, the
sdp
,
rdp
, and
dcc
genes were scattered over the genome and their expression was not tightly regulated. No coherent pattern was derived on the possible origin of the
sdp
,
rdp
, and
dcc
pathway genes.
rdpA
MH
was 99% identical to
rdpA
MC1
, an (
R
)-dichlorprop/α-ketoglutarate dioxygenase from
Delftia acidovorans
MC1, which is evidence for a recent gene exchange between
Alpha
- and
Betaproteobacteria
. Conversely, DccA
I
and DccA
II
did not group within the known chlorocatechol 1,2-dioxygenases, but formed a separate branch in clustering analysis. This suggests a different reservoir and reduced transfer for the genes of the modified
ortho
-cleavage pathway in
Alphaproteobacteria
compared with the ones in
Beta
- and
Gammaproteobacteria
.
Production ofl-Ascorbic Acid by Metabolically EngineeredSaccharomyces cerevisiaeandZygosaccharomyces bailii
Authors: Sauer Michael , Branduardi Paola , Valli Minoska , Porro Danilo 
Published: October 2004

ABSTRACTYeasts do not possess an endogenous biochemical pathway for the synthesis of vitamin C. However, incubated withl-galactose,l-galactono-1,4-lactone, orl-gulono-1,4-lactone intermediates from the plant or animal pathway leading tol-ascorbic acid,Saccharomyces cerevisiaeandZygosaccharomyces bailiicells accumulate the vitamin intracellularly. Overexpression of theS. cerevisiaeenzymesd-arabinose dehydrogenase andd-arabinono-1,4-lactone oxidase enhances this ability significantly. In fact, the respective recombinant yeast strains even gain the capability to accumulate the vitamin in the culture medium. An even better result is obtainable by expression of the plant enzymel-galactose dehydrogenase fromArabidopsis thaliana. Budding yeast cells overexpressing the endogenousd-arabinono-1,4-lactone oxidase as well asl-galactose dehydrogenase are capable of producing about 100 mg ofl-ascorbic acid liter−1, converting 40% (wt/vol) of the starting compoundl-galactose.
Involvement of Linear Plasmids in Aerobic Biodegradation of Vinyl Chloride
Authors: Danko Anthony S. , Luo Meizhong , Bagwell Christopher E. , Brigmon Robin L. , Freedman David L. 
Published: October 2004

ABSTRACT

Pseudomonas putida
strain AJ and
Ochrobactrum
strain TD were isolated from hazardous waste sites based on their ability to use vinyl chloride (VC) as the sole source of carbon and energy under aerobic conditions. Strains AJ and TD also use ethene and ethylene oxide as growth substrates. Strain AJ contained a linear megaplasmid (approximately 260 kb) when grown on VC or ethene, but it contained no circular plasmids. While strain AJ was growing on ethylene oxide, it was observed to contain a 100-kb linear plasmid, and its ability to use VC as a substrate was retained. The linear plasmids in strain AJ were cured, and the ability of strain AJ to consume VC, ethene, and ethylene oxide was lost following growth on a rich substrate (Luria-Bertani broth) through at least three transfers. Strain TD contained three linear plasmids, ranging in size from approximately 90 kb to 320 kb, when growing on VC or ethene. As with strain AJ, the linear plasmids in strain TD were cured following growth on Luria-Bertani broth and its ability to consume VC and ethene was lost. Further analysis of these linear plasmids may help reveal the pathway for VC biodegradation in strains AJ and TD and explain why this process occurs at many but not all sites where groundwater is contaminated with chloroethenes. Metabolism of VC and ethene by strains AJ and TD is initiated by an alkene monooxygenase. Their yields during growth on VC (0.15 to 0.20 mg of total suspended solids per mg of VC) are similar to the yields reported for other isolates (i.e.,
Mycobacterium
sp.,
Nocardioides
sp., and
Pseudomonas
sp.).
Comparison of Compositions and Metabolic Activities of Fecal Microbiotas in Young Adults and in Antibiotic-Treated and Non-Antibiotic-Treated Elderly Subjects
Authors: Woodmansey Emma J. , McMurdo Marion E. T. , Macfarlane George T. , Macfarlane Sandra 
Published: October 2004

ABSTRACT

The colonic microbiota mediates many cellular and molecular events in the host that are important to health. These processes can be affected in the elderly, because in some individuals, the composition and metabolic activities of the microbiota change with age. Detailed characterizations of the major groups of fecal bacteria in healthy young adults, in healthy elderly people, and in hospitalized elderly patients receiving antibiotics were made in this study, together with measurements of their metabolic activities, by analysis of fecal organic acid and ammonia concentrations. The results showed that total anaerobe numbers remained relatively constant in old people; however, individual bacterial genera changed markedly with age. Reductions in numbers of bacteroides and bifidobacteria in both elderly groups were accompanied by reduced species diversity. Bifidobacterial populations in particular showed marked variations in the dominant species, with
Bifidobacterium angulatum
and
Bifidobacterium adolescentis
being frequently isolated from the elderly and
Bifidobacterium longum
,
Bifidobacterium catenulatum
,
Bifidobacterium boum
, and
Bifidobacterium infantis
being detected only from the healthy young volunteers. Reductions in amylolytic activities of bacterial isolates in healthy elderly subjects and reduced short-chain fatty acid concentrations supported these findings, since bifidobacteria and bacteroides are important saccharolytic groups in the colon. Conversely, higher numbers of proteolytic bacteria were observed with feces samples from the antibiotic-treated elderly group, which were also associated with increased proteolytic species diversity (fusobacteria, clostridia, and propionibacteria). Other differences in the intestinal ecosystem in elderly subjects were observed, with alterations in the dominant clostridial species in combination with greater numbers of facultative anaerobes.
Discrimination of Modes of Action of Antifungal Substances by Use of Metabolic Footprinting
Authors: Allen Jess , Davey Hazel M. , Broadhurst David , Rowland Jem J. , Oliver Stephen G. , Kell Douglas B. 
Published: October 2004

ABSTRACT

Diploid cells of
Saccharomyces cerevisiae
were grown under controlled conditions with a Bioscreen instrument, which permitted the essentially continuous registration of their growth via optical density measurements. Some cultures were exposed to concentrations of a number of antifungal substances with different targets or modes of action (sterol biosynthesis, respiratory chain, amino acid synthesis, and the uncoupler). Culture supernatants were taken and analyzed for their “metabolic footprints” by using direct-injection mass spectrometry. Discriminant function analysis and hierarchical cluster analysis allowed these antifungal compounds to be distinguished and classified according to their modes of action. Genetic programming, a rule-evolving machine learning strategy, allowed respiratory inhibitors to be discriminated from others by using just two masses. Metabolic footprinting thus represents a rapid, convenient, and information-rich method for classifying the modes of action of antifungal substances.
“CandidatusHepatoplasma crinochetorum,” a New, Stalk-Forming Lineage ofMollicutesColonizing the Midgut Glands of a Terrestrial Isopod
Authors: Wang Yongjie , Stingl Ulrich , Anton-Erxleben Friederike , Geisler Sabine , Brune Andreas , Zimmer Martin 
Published: October 2004

ABSTRACTUncultivated bacteria that densely colonize the midgut glands (hepatopancreas) of the terrestrial isopodPorcellio scaber(Crustacea: Isopoda) were identified by cloning and sequencing of their 16S rRNA genes. Phylogenetic analysis revealed that these symbionts represent a novel lineage of theMollicutesand are only distantly related (<82% sequence identity) to members of theMycoplasmatalesandEntomoplasmatales. Fluorescence in situ hybridization with a specific oligonucleotide probe confirmed that the amplified 16S rRNA gene sequences indeed originated from a homogeneous population of symbionts intimately associated with the epithelial surface of the hepatopancreas. The same probe also detected morphotypically identical symbionts in other crinochete isopods. Scanning and transmission electron microscopy revealed uniform spherical bacterial cells without a cell wall, sometimes interacting with the microvilli of the brush border by means of stalk-like cytoplasmic appendages, which also appeared to be involved in cell division through budding. Based on the isolated phylogenetic position and unique cytological properties, the provisional name “CandidatusHepatoplasma crinochetorum” is proposed for this new taxon ofMollicutescolonizing the hepatopancreas ofP. scaber.
Characterization of the
groEL
and
groES
Loci in
Bifidobacterium breve
UCC 2003: Genetic, Transcriptional, and Phylogenetic Analyses
Authors: Ventura Marco , Canchaya Carlos , Zink Ralf , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: October 2004

ABSTRACT

The bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes, including the GroEL and GroES proteins. The
groES
and
groEL
genes are highly conserved among eubacteria and are typically arranged as an operon. Genome analysis of
Bifidobacterium breve
UCC 2003 revealed that the
groES
and
groEL
genes are located in different chromosomal regions. The heat inducibility of the
groEL
and
groES
genes of
B. breve
UCC 2003 was verified by slot blot analysis. Northern blot analyses showed that the
cspA
gene is cotranscribed with the
groEL
gene, while the
groES
gene is transcribed as a monocistronic unit. The transcription initiation sites of these two mRNAs were determined by primer extension. Sequence and transcriptional analyses of the region flanking the
groEL
and
groES
genes of various bifidobacteria revealed similar
groEL
-
cspA
and
groES
gene units, suggesting a novel genetic organization of these chaperones. Phylogenetic analysis of the available bifidobacterial
groES
and
groEL
genes suggested that these genes evolved differently. Discrepancies in the phylogenetic positioning of
groES
-based trees make this gene an unreliable molecular marker. On the other hand, the bifidobacterial
groEL
gene sequences can be used as an alternative to current methods for tracing
Bifidobacterium
species, particularly because they allow a high level of discrimination between closely related species of this genus.
Flow Sorting of Marine Bacterioplankton after Fluorescence In Situ Hybridization
Authors: Sekar Raju , Fuchs Bernhard M. , Amann Rudolf , Pernthaler Jakob 
Published: October 2004

ABSTRACT

We describe an approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (CARD-FISH). In a sample from spring 2003 >90% of the cells were detected by CARD-FISH with a bacterial probe (EUB338). Approximately 30% of the microbial assemblage was affiliated with the
Cytophaga-Flavobacterium
lineage of the
Bacteroidetes
(CFB group) (probe CF319a), and almost 10% was targeted by a probe for the β-proteobacteria (probe BET42a). A protocol was optimized to detach cells hybridized with EUB338, BET42a, and CF319a from membrane filters (recovery rate, 70%) and to sort the cells by flow cytometry. The purity of sorted cells was >95%. 16S rRNA gene clone libraries were constructed from hybridized and sorted cells (S-EUB, S-BET, and S-CF libraries) and from unhybridized and unsorted cells (UNHYB library). Sequences related to the CFB group were significantly more frequent in the S-CF library (66%) than in the UNHYB library (13%). No enrichment of β-proteobacterial sequence types was found in the S-BET library, but novel sequences related to
Nitrosospira
were found exclusively in this library. These bacteria, together with members of marine clade OM43, represented >90% of the β-proteobacteria in the water sample, as determined by CARD-FISH with specific probes. This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats.
Synchronous Effects of Temperature, Hydrostatic Pressure, and Salinity on Growth, Phospholipid Profiles, and Protein Patterns of Four
Halomonas
Species Isolated from Deep-Sea Hydrothermal-Vent and Sea Surface Environments
Authors: Kaye Jonathan Z. , Baross John A. 
Published: October 2004

ABSTRACT

Four strains of euryhaline bacteria belonging to the genus
Halomonas
were tested for their response to a range of temperatures (2, 13, and 30°C), hydrostatic pressures (0.1, 7.5, 15, 25, 35, 45, and 55 MPa), and salinities (4, 11, and 17% total salts). The isolates were psychrotolerant, halophilic to moderately halophilic, and piezotolerant, growing fastest at 30°C, 0.1 MPa, and 4% total salts. Little or no growth occurred at the highest hydrostatic pressures tested, an effect that was more pronounced with decreasing temperatures. Growth curves suggested that the
Halomonas
strains tested would grow well in cool to warm hydrothermal-vent and associated subseafloor habitats, but poorly or not at all under cold deep-sea conditions. The intermediate salinity tested enhanced growth under certain high-hydrostatic-pressure and low-temperature conditions, highlighting a synergistic effect on growth for these combined stresses. Phospholipid profiles obtained at 30°C indicated that hydrostatic pressure exerted the dominant control on the degree of lipid saturation, although elevated salinity slightly mitigated the increased degree of lipid unsaturation caused by increased hydrostatic pressure. Profiles of cytosolic and membrane proteins of
Halomonas axialensis
and
H. hydrothermalis
performed at 30°C under various salinities and hydrostatic pressure conditions indicated several hydrostatic pressure and salinity effects, including proteins whose expression was induced by either an elevated salinity or hydrostatic pressure, but not by a combination of the two. The interplay between salinity and hydrostatic pressure on microbial growth and physiology suggests that adaptations to hydrostatic pressure and possibly other stresses may partially explain the euryhaline phenotype of members of the genus
Halomonas
living in deep-sea environments.
Nonlegumes, Legumes, and Root Nodules Harbor Different Arbuscular Mycorrhizal Fungal Communities
Authors: Scheublin Tanja R. , Ridgway Karyn P. , Young J. Peter W. , van der Heijden Marcel G. A. 
Published: October 2004

ABSTRACT

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing
Rhizobium
bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).
Metabolically Active Eukaryotic Communities in Extremely Acidic Mine Drainage
Authors: Baker Brett J. , Lutz Michelle A. , Dawson Scott C. , Bond Philip L. , Banfield Jillian F. 
Published: October 2004

ABSTRACT

Acid mine drainage (AMD) microbial communities contain microbial eukaryotes (both fungi and protists) that confer a biofilm structure and impact the abundance of bacteria and archaea and the community composition via grazing and other mechanisms. Since prokaryotes impact iron oxidation rates and thus regulate AMD generation rates, it is important to analyze the fungal and protistan populations. We utilized 18S rRNA and beta-tubulin gene phylogenies and fluorescent rRNA-specific probes to characterize the eukaryotic diversity and distribution in extremely acidic (pHs 0.8 to 1.38), warm (30 to 50°C), metal-rich (up to 269 mM Fe
2+
, 16.8 mM Zn, 8.5 mM As, and 4.1 mM Cu) AMD solutions from the Richmond Mine at Iron Mountain, Calif. A
Rhodophyta
(red algae) lineage and organisms from the
Vahlkampfiidae
family were identified. The fungal 18S rRNA and tubulin gene sequences formed two distinct phylogenetic groups associated with the classes
Dothideomycetes
and
Eurotiomycetes
. Three fungal isolates that were closely related to the
Dothideomycetes
clones were obtained. We suggest the name “
Acidomyces richmondensis
” for these isolates. Since these ascomycete fungi were morphologically indistinguishable, rRNA-specific oligonucleotide probes were designed to target the
Dothideomycetes
and
Eurotiomycetes
via fluorescent in situ hybridization (FISH). FISH analyses indicated that
Eurotiomycetes
are generally more abundant than
Dothideomycetes
in all of the seven locations studied within the Richmond Mine system. This is the first study to combine the culture-independent detection of fungi with in situ detection and a demonstration of activity in an acidic environment. The results expand our understanding of the subsurface AMD microbial community structure.
Bloom of Filamentous Bacteria in a Mesotrophic Lake: Identity and Potential Controlling Mechanism
Authors: Pernthaler Jakob , Zöllner Eckart , Warnecke Falk , Jürgens Klaus 
Published: October 2004

ABSTRACTEphemeral blooms of filamentous bacteria are a common phenomenon in the water column of oligo- to mesotrophic lakes. It is assumed that the appearance of such morphotypes is favored by selective predation of bacterivorous protists and that filter-feeding zooplankton plays a major role in suppressing these bacteria. The phylogenetic affiliation of the important bloom-forming filamentous bacteria in freshwaters is presently unknown. Here we report the identification of dominant members of a filamentous bacterial assemblage during a bloom of such morphotypes in a mesotrophic lake. By molecular cloning and fluorescence in situ hybridization with specific oligonucleotide probes, up to 98% of filamentous cells in lake water could be assigned to a clade of almost identical (99% similarity) 16S rRNA gene sequence types, the cosmopolitan freshwater LD2 cluster. For a period of less than 1 week, members of the LD2 clade constituted >40% of the total bacterial biomass, potentially favored by high grazing of planktivorous protists. This is probably the most pronounced case of dominance by a single bacterioplankton species ever observed in natural freshwaters. In enclosures artificially stocked with the metazoan filter feederDaphnia, bacteria related to the LD2 clade formed a significantly larger fraction of filaments than in enclosures whereDaphniahad been removed. However, in the presence of higher numbers ofDaphniaindividuals, the LD2 bacteria, like other filaments, were eventually eliminated both in enclosures and in the lake. This points at the potential importance of filter-feeding zooplankton in controlling the occurrence and species composition of filamentous bacterial morphotypes in freshwater plankton.
Intestinal Mucus Alters the Ability of Probiotic Bacteria To Bind Aflatoxin B
1
In Vitro
Authors: Gratz S. , Mykkänen H. , Ouwehand A. C. , Juvonen R. , Salminen S. , El-Nezami H. 
Published: October 2004

ABSTRACT

Several probiotics are known to bind aflatoxin B
1
(AFB
1
) to their surfaces and to adhere to intestinal mucus. In this study, preincubation of two probiotic preparations with either AFB
1
or mucus reduced the subsequent surface binding of mucus and AFB
1
, respectively, in a strain-dependent manner.
Genetic Typing of Shiga Toxin 2 Variants ofEscherichia coliby PCR-Restriction Fragment Length Polymorphism Analysis
Authors: De Baets Liesbet , Van der Taelen Imme , De Filette Marina , Piérard Denis , Allison Lesley , De Greve Henri , Hernalsteens Jean-Pierre , Imberechts Hein 
Published: October 2004

ABSTRACTShiga toxins Stx1 and Stx2 play a prominent role in the pathogenesis of Shiga toxin-producingEscherichia coli(STEC) infections. Several variants of thestx2gene, encoding Stx2, have been described. In this study, we developed a PCR-restriction fragment length polymorphism system for typingstx2genes of STEC strains. The typing system discriminates eight described variants and allows the identification of newstx2variants and STEC isolates carrying multiplestx2genes. A phylogenetic tree, based on the nucleotide sequences of the toxin-encoding genes, demonstrates thatstx2sequences with the same PvuII HaeIII HincII AccI type generally cluster together.
Reverse Transcription-Booster PCR for Detection of Noroviruses in Shellfish
Authors: De Medici Dario , Croci Luciana , Suffredini Elisabetta , Toti Laura 
Published: October 2004

ABSTRACT
The methods commonly used for norovirus (NV) detection are based on reverse transcription-PCR (RT-PCR) followed by confirmation of the amplified sequence. To increase sensitivity, an RT-booster PCR was developed. The proposed method showed an increase in sensitivity at least 2 log units for all the NV strains tested compared with the standard RT-PCR method. Higher sensitivity was confirmed in tests on experimentally and naturally contaminated shellfish.