bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergistic Degradation of Linuron by a Bacterial Consortium and Isolation of a Single Linuron-Degrading
Variovorax
Strain
Authors: Dejonghe Winnie , Berteloot Ellen , Goris Johan , Boon Nico , Crul Katrien , Maertens Siska , Höfte Monica , De Vos Paul , Verstraete Willy , Top Eva M. 
Published: March 2003

ABSTRACT

The bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16S rRNA gene pool, isolation and identification of strains, and biodegradation assays. Three strains,
Variovorax
sp. strain WDL1,
Delftia acidovorans
WDL34, and
Pseudomonas
sp. strain WDL5, were isolated directly from the linuron-degrading culture. In addition, subculture of this enrichment culture on potential intermediates in the degradation pathway of linuron (i.e.,
N
,
O
-dimethylhydroxylamine and 3-chloroaniline) resulted in the isolation of, respectively,
Hyphomicrobium sulfonivorans
WDL6 and
Comamonas testosteroni
WDL7. Of these five strains, only
Variovorax
sp. strain WDL1 was able to use linuron as the sole source of C, N, and energy. WDL1 first converted linuron to 3,4-dichloroaniline (3,4-DCA), which transiently accumulated in the medium but was subsequently degraded. To the best of our knowledge, this is the first report of a strain that degrades linuron further than the aromatic intermediates. Interestingly, the rate of linuron degradation by strain WDL1 was lower than that for the consortium, but was clearly increased when WDL1 was coinoculated with each of the other four strains.
D. acidovorans
WDL34 and
C. testosteroni
WDL7 were found to be responsible for degradation of the intermediate 3,4-DCA, and
H. sulfonivorans
WDL6 was the only strain able to degrade
N
,
O
-dimethylhydroxylamine. The role of
Pseudomonas
sp. strain WDL5 needs to be further elucidated. The degradation of linuron can thus be performed by a single isolate,
Variovorax
sp. strain WDL1, but is stimulated by a synergistic interaction with the other strains isolated from the same linuron-degrading culture.
2,4,6-Trinitrotoluene Reduction by an Fe-Only Hydrogenase in
Clostridium acetobutylicum
Authors: Watrous Mary M. , Clark Sandra , Kutty Razia , Huang Shouqin , Rudolph Frederick B. , Hughes Joseph B. , Bennett George N. 
Published: March 2003

ABSTRACT

The role of hydrogenase on the reduction of 2,4,6-trinitrotoluene (TNT) in
Clostridium acetobutylicum
was evaluated. An Fe-only hydrogenase was isolated and identified by using TNT reduction activity as the selection basis. The formation of hydroxylamino intermediates by the purified enzyme corresponded to expected products for this reaction, and saturation kinetics were determined with a

K
m

of 152 μM. Comparisons between the wild type and a mutant strain lacking the region encoding an alternative Fe-Ni hydrogenase determined that Fe-Ni hydrogenase activity did not significantly contribute to TNT reduction. Hydrogenase expression levels were altered in various strains, allowing study of the role of the enzyme in TNT reduction rates. The level of hydrogenase activity in a cell system correlated (
R
2
= 0.89) with the organism's ability to reduce TNT. A strain that overexpressed the hydrogenase activity resulted in maintained TNT reduction during late growth phases, which it is not typically observed in wild type strains. Strains exhibiting underexpression of hydrogenase produced slower TNT rates of reduction correlating with the determined level of expression. The isolated Fe-only hydrogenase is the primary catalyst for reducing TNT nitro substituents to the corresponding hydroxylamines in
C. acetobutylicum
in whole-cell systems. A mechanism for the reaction is proposed. Due to the prevalence of hydrogenase in soil microbes, this research may enhance the understanding of nitroaromatic compound transformation by common microbial communities.
Electricity Production byGeobacter sulfurreducensAttached to Electrodes
Authors: Bond Daniel R. , Lovley Derek R. 
Published: March 2003

ABSTRACTPrevious studies have suggested that members of theGeobacteraceaecan use electrodes as electron acceptors for anaerobic respiration. In order to better understand this electron transfer process for energy production,Geobacter sulfurreducenswas inoculated into chambers in which a graphite electrode served as the sole electron acceptor and acetate or hydrogen was the electron donor. The electron-accepting electrodes were maintained at oxidizing potentials by connecting them to similar electrodes in oxygenated medium (fuel cells) or to potentiostats that poised electrodes at +0.2 V versus an Ag/AgCl reference electrode (poised potential). When a small inoculum ofG. sulfurreducenswas introduced into electrode-containing chambers, electrical current production was dependent upon oxidation of acetate to carbon dioxide and increased exponentially, indicating for the first time that electrode reduction supported the growth of this organism. When the medium was replaced with an anaerobic buffer lacking nutrients required for growth, acetate-dependent electrical current production was unaffected and cells attached to these electrodes continued to generate electrical current for weeks. This represents the first report of microbial electricity production solely by cells attached to an electrode. Electrode-attached cells completely oxidized acetate to levels below detection (<10 μM), and hydrogen was metabolized to a threshold of 3 Pa. The rates of electron transfer to electrodes (0.21 to 1.2 μmol of electrons/mg of protein/min) were similar to those observed for respiration with Fe(III) citrate as the electron acceptor (Eo′ =+0.37 V). The production of current in microbial fuel cell (65 mA/m2of electrode surface) or poised-potential (163 to 1,143 mA/m2) mode was greater than what has been reported for other microbial systems, even those that employed higher cell densities and electron-shuttling compounds. Since acetate was completely oxidized, the efficiency of conversion of organic electron donor to electricity was significantly higher than in previously described microbial fuel cells. These results suggest that the effectiveness of microbial fuel cells can be increased with organisms such asG. sulfurreducensthat can attach to electrodes and remain viable for long periods of time while completely oxidizing organic substrates with quantitative transfer of electrons to an electrode.
Evaluation of Potential Indicators of Viral Contamination in Shellfish and Their Applicability to Diverse Geographical Areas
Authors: Formiga-Cruz M. , Allard A. K. , Conden-Hansson A.-C. , Henshilwood K. , Hernroth B. E. , Jofre J. , Lees D. N. , Lucena F. , Papapetropoulou M. , Rangdale R. E. , Tsibouxi A. , Vantarakis A. , Girones R. 
Published: March 2003

ABSTRACT

The distribution of the concentration of potential indicators of fecal viral pollution in shellfish was analyzed under diverse conditions over 18 months in diverse geographical areas. These microorganisms have been evaluated in relation to contamination by human viral pathogens detected in parallel in the analyzed shellfish samples. Thus, significant shellfish-growing areas from diverse countries in the north and south of Europe (Greece, Spain, Sweden, and the United Kingdom) were defined and studied by analyzing different physicochemical parameters in the water and the levels of
Escherichia coli
, F-specific RNA bacteriophages, and phages infecting
Bacteroides fragilis
strain RYC2056 in the shellfish produced, before and after depuration treatments. A total of 475 shellfish samples were studied, and the results were statistically analyzed. According to statistical analysis, the presence of human viruses seems to be related to the presence of all potential indicators in the heavily contaminated areas, where
E. coli
would probably be suitable as a fecal indicator. The F-RNA phages, which are present in higher numbers in Northern Europe, seem to be significantly related to the presence of viral contamination in shellfish, with a very weak predictive value for hepatitis A virus, human adenovirus, and enterovirus and a stronger one for Norwalk-like virus. However, it is important to note that shellfish produced in A or clean B areas can sporadically contain human viruses even in the absence of
E. coli
or F-RNA phages. The data presented here will be useful in defining microbiological parameters for improving the sanitary control of shellfish consumed raw or barely cooked.
Prokaryotic Homologs of the Eukaryotic 3-Hydroxyanthranilate 3,4-Dioxygenase and 2-Amino-3-Carboxymuconate-6-Semialdehyde Decarboxylase in the 2-Nitrobenzoate Degradation Pathway ofPseudomonas fluorescensStrain KU-7
Authors: Muraki Takamichi , Taki Masami , Hasegawa Yoshie , Iwaki Hiroaki , Lau Peter C. K. 
Published: March 2003

ABSTRACTThe 2-nitrobenzoic acid degradation pathway ofPseudomonas fluorescensstrain KU-7 proceeds via a novel 3-hydroxyanthranilate intermediate. In this study, we cloned and sequenced a 19-kb DNA locus of strain KU-7 that encompasses the 3-hydroxyanthranilatemeta-cleavage pathway genes. The gene cluster, designatednbaEXHJIGFCDR,is organized tightly and in the same direction. ThenbaCandnbaDgene products were found to be novel homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase, respectively. The NbaC enzyme carries out the oxidation of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate-6-semialdehyde, while the NbaD enzyme catalyzes the decarboxylation of the latter compound to 2-aminomuconate-6-semialdehyde. The NbaC and NbaD proteins were overexpressed inEscherichia coliand characterized. The substrate specificity of the 23.8-kDa NbaC protein was found to be restricted to 3-hydroxyanthranilate. InE. coli, this enzyme oxidizes 3-hydroxyanthranilate with a specific activity of 8 U/mg of protein. Site-directed mutagenesis experiments revealed the essential role of two conserved histidine residues (His52 and His96) in the NbaC sequence. The NbaC activity is also dependent on the presence of Fe2+but is inhibited by other metal ions, such as Zn2+, Cu2+, and Cd2+. The NbaD protein was overproduced as a 38.7-kDa protein, and its specific activity towards 2-amino-3-carboxymuconate-6-semialdehyde was 195 U/mg of protein. Further processing of 2-aminomuconate-6-semialdehyde to pyruvic acid and acetyl coenzyme A was predicted to proceed via the activities of NbaE, NbaF, NbaG, NbaH, NbaI, and NbaJ. The predicted amino acid sequences of these proteins are highly homologous to those of the corresponding proteins involved in the metabolism of 2-aminophenol (e.g., AmnCDEFGH inPseudomonassp. strain AP-3). The NbaR-encoding gene is predicted to have a regulatory function of the LysR family type. The function of the product of the small open reading frame, NbaX, like the homologous sequences in the nitrobenzene or 2-aminophenol metabolic pathway, remains elusive.
Bacterial rRNA Genes Associated with Soil Suppressiveness against the Plant-Parasitic Nematode
Heterodera schachtii
Authors: Yin Bei , Valinsky Lea , Gao Xuebiao , Becker J. Ole , Borneman James 
Published: March 2003

ABSTRACT

The goal of this study was to identify bacteria involved in soil suppressiveness against the plant-parasitic nematode
Heterodera schachtii
. Since
H. schachtii
cysts isolated from the suppressive soil can transfer this beneficial property to nonsuppressive soils, analysis of the cyst-associated microorganisms should lead to the identification of the causal organisms. Our experimental approach was to identify bacterial rRNA genes (rDNA) associated with
H. schachtii
cysts obtained from soil mixtures with various levels of suppressiveness. We hypothesized that we would be able to identify bacteria involved in the suppressiveness by correlating population shifts with differing levels of suppressiveness. Soil treatments containing different amounts of suppressive and fumigation-induced nonsuppressive soils exhibited various levels of suppressiveness after two nematode generations. The 10%-suppressive-soil treatment contained numbers of eggs per gram of soil similar to those of the 100%-suppressive-soil treatment, indicating that the suppressive factor(s) had been transferred. Bacterial rDNA associated with
H. schachtii
cysts were identified using a culture-independent method termed oligonucleotide fingerprinting of rRNA genes. Bacteria from five major taxonomic groups (
Actinobacteria
,
Cytophaga-Flexibacter-Bacteroides
, α-
Proteobacteria
, β-
Proteobacteria
, and γ-
Proteobacteria
) were identified. Three bacterial rDNA groups contained clones that were more prevalent in the highly suppressive soil treatments than in the less suppressive treatments, indicating a potential involvement in the
H. schachtii
suppressiveness. When these three groups were examined with specific PCR analyses performed on
H. schachtii
cysts that developed in soils treated with three biocidal compounds, only one bacterial rDNA group with moderate to high sequence identity to rDNA from several
Rhizobium
species and uncultured α-proteobacterial clones was consistently associated with the highly suppressive treatments. A quantitative PCR analysis confirmed the association of this
Rhizobium
-like rDNA group with the
H. schachtii
suppressiveness.
Conidial Hydrophobins ofAspergillus fumigatus
Authors: Paris Sophie , Debeaupuis Jean-Paul , Crameri Reto , Carey Marilyn , Charlès Franck , Prévost Marie Christine , Schmitt Christine , Philippe Bruno , Latgé Jean Paul 
Published: March 2003

ABSTRACTThe surface ofAspergillus fumigatusconidia, the first structure recognized by the host immune system, is covered by rodlets. We report that this outer cell wall layer contains two hydrophobins, RodAp and RodBp, which are found as highly insoluble complexes. TheRODAgene was previously characterized, and ΔrodAconidia do not display a rodlet layer (N. Thau, M. Monod, B. Crestani, C. Rolland, G. Tronchin, J. P. Latgé, and S. Paris, Infect. Immun. 62:4380-4388, 1994). TheRODBgene was cloned and disrupted. RodBp was highly homologous to RodAp and different from DewAp ofA. nidulans. ΔrodBconidia had a rodlet layer similar to that of the wild-type conidia. Therefore, unlike RodAp, RodBp is not required for rodlet formation. The surface of ΔrodAconidia is granular; in contrast, an amorphous layer is present at the surface of the conidia of the ΔrodAΔrodBdouble mutant. These data show that RodBp plays a role in the structure of the conidial cell wall. Moreover, rodletless mutants are more sensitive to killing by alveolar macrophages, suggesting that RodAp or the rodlet structure is involved in the resistance to host cells.
Identification and Characterization of Two Novel Clostridial Bacteriocins, Circularin A and Closticin 574
Authors: Kemperman Robèr , Kuipers Anneke , Karsens Harma , Nauta Arjen , Kuipers Oscar , Kok Jan 
Published: March 2003

ABSTRACTTwo novel antibacterial peptides of clostridial species were purified, N-terminally sequenced, and characterized. Moreover, their structural genes were identified. Closticin 574 is an 82-amino-acid bacteriocin produced byClostridium tyrobutyricumADRIAT 932. The supernatant of the producing strain showed a high level of activity against the indicator strainC. tyrobutyricum. The protein is synthesized as a preproprotein that is possibly secreted via the general secretion pathway, after which it is hydrolyzed at an Asp-Pro site. Circularin A is produced byClostridium beijerinckiiATCC 25752 as a prepeptide of 72 amino acids. Cleavage of the prepeptide between the third leucine and fourth valine residues followed by a head-to-tail ligation between the N and C termini creates a circular antimicrobial peptide of 69 amino acids. The unusually small circularin A leader peptide of three amino acids is cleaved off in this process. The supernatant ofC. beijerinckiiATCC 25752 showed a broad antibacterial activity range.
Transcriptional Cross-Regulation of the Catechol and Protocatechuate Branches of the β-Ketoadipate Pathway Contributes to Carbon Source-Dependent Expression of the
Acinetobacter
sp. Strain ADP1
pobA
Gene
Authors: Brzostowicz Patricia C. , Reams Andrew B. , Clark Todd J. , Neidle Ellen L. 
Published: March 2003

ABSTRACT

Transcriptional control of carbon source preferences by
Acinetobacter
sp. strain ADP1 was assessed with a
pobA
::
lacZ
fusion during growth on alternative substrates. The
pobA
-encoded enzyme catalyzes the first step in the degradation of 4-hydroxybenzoate, a compound consumed rapidly as a sole carbon source. If additional aromatic carbon sources are available, 4-hydroxybenzoate consumption is inhibited by unknown mechanisms. As reported here, during growth on aromatic substrates,
pobA
was not expressed despite the presence of 4-hydroxybenzoate, an inducer that normally causes the PobR regulator to activate
pobA
transcription. Growth on organic acids such as succinate, fumarate, and acetate allowed higher levels of
pobA
expression. In each case,
pobA
expression increased at the end of the exponential growth phase. Complex transcriptional regulation controlled 4-hydroxybenzoate catabolism in multisubstrate environments. Additional studies focused on the wild-type preference for benzoate consumption prior to 4-hydroxybenzoate consumption. These compounds are degraded via the catechol and protocatechuate branches of the β-ketoadipate pathway, respectively. Here, mutants were characterized that degraded benzoate and 4-hydroxybenzoate concurrently. These mutants lacked the BenM and CatM transcriptional regulators that normally activate genes for benzoate catabolism. A model is presented in which BenM and CatM prevent
pobA
expression indirectly during growth on benzoate. These regulators may affect
pobA
expression by lowering the PcaK-mediated uptake of 4-hydroxybenzoate. Consistent with this model, BenM and CatM bound in vitro to an operator-promoter fragment controlling the expression of several
pca
genes, including
pcaK
. These studies provide the first direct evidence of transcriptional cross-regulation between the distinct but analogous branches of the β-ketoadipate pathway.
Tri1Encodes the Cytochrome P450 Monooxygenase for C-8 Hydroxylation during Trichothecene Biosynthesis inFusarium sporotrichioidesand Resides Upstream of Another NewTriGene
Authors: Meek Isaac B. , Peplow Andrew W. , Ake, Charles , Phillips T. D. , Beremand Marian N. 
Published: March 2003

ABSTRACTManyFusariumspecies produce one or more agriculturally important trichothecene mycotoxins, and the relative level of toxicity of these compounds is determined by the pattern of oxygenations and acetylations or esterifications on the core trichothecene structure. Previous studies with UV-inducedFusarium sporotrichioidesNRRL 3299 trichothecene mutants defined theTri1gene and demonstrated that it was required for addition of the oxygen at the C-8 position during trichothecene biosynthesis. We have cloned and characterized theTri1gene from NRRL 3299 and found that it encodes a cytochrome P450 monooxygenase. The disruption ofTri1blocks production of C-8-oxygenated trichothecenes and leads to the accumulation of 4,15-diacetoxyscirpenol, the same phenotype observed in thetri1UV-induced mutants MB1716 and MB1370. TheTri1disruptants and thetri1UV-induced mutants do not complement one another when coinoculated, and theTri1gene sequence restores T-2 toxin production in both MB1716 and MB1370. The DNA sequence flankingTri1contains another newTrigene. Thus,Tri1encodes a C-8 hydroxylase and is located either in a new distal portion of the trichothecene gene cluster or in a second separate trichothecene gene cluster.
Respiration of
13
C-Labeled Substrates Added to Soil in the Field and Subsequent 16S rRNA Gene Analysis of
13
C-Labeled Soil DNA
Authors: Padmanabhan P. , Padmanabhan S. , DeRito C. , Gray A. , Gannon D. , Snape J. R. , Tsai C. S. , Park W. , Jeon C. , Madsen E. L. 
Published: March 2003

ABSTRACT

Our goal was to develop a field soil biodegradation assay using
13
C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived
13
C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of
13
C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for
13
CO
2
respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of
13
CO
2
emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF
6
, that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired
13
CO
2
. Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of
13
CO
2
released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of
13
C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with
13
C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of
Arthrobacter
,
Pseudomonas
,
Acinetobacter
,
Massilia
,
Flavobacterium
, and
Pedobacter
spp. for glucose;
Pseudomonas
,
Pantoea
,
Acinetobacter
,
Enterobacter
,
Stenotrophomonas
, and
Alcaligenes
spp. for phenol;
Pseudomonas
,
Acinetobacter
, and
Variovorax
spp. for naphthalene; and
Acinetobacter
,
Enterobacter
,
Stenotrophomonas
, and
Pantoea
spp. for caffeine.
Improved Anaerobic Use of Arginine by
Saccharomyces cerevisiae
Authors: Martin Olga , Brandriss Marjorie C. , Schneider Gisbert , Bakalinsky Alan T. 
Published: March 2003

ABSTRACT

Anaerobic arginine catabolism in
Saccharomyces cerevisiae
was genetically modified to allow assimilation of all four rather than just three of the nitrogen atoms in arginine. This was accomplished by bypassing normal formation of proline, an unusable nitrogen source in the absence of oxygen, and causing formation of glutamate instead. A
pro3 ure2
strain expressing a
PGK1
promoter-driven
PUT2
allele encoding Δ
1
-pyrroline-5-carboxylate dehydrogenase lacking a mitochondrial targeting sequence produced significant cytoplasmic activity, accumulated twice as much intracellular glutamate, and produced twice as much cell mass as the parent when grown anaerobically on limiting arginine as sole nitrogen source.