bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-Field Spatial Variability in the Degradation of the Phenyl-Urea Herbicide Isoproturon Is the Result of Interactions between Degradative
Sphingomonas
spp. and Soil pH
Authors: Bending Gary D. , Lincoln Suzanne D. , Sørensen Sebastian R. , Morgan J. Alun W. , Aamand Jens , Walker Allan 
Published: February 2003

ABSTRACT

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the
Sphingomonas
group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the
Sphingomonas
group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading
Sphingomonas
sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of
Sphingomonas
spp. could largely account for the spatial variation of IPU degradation rates across the field.
Microbial Community Composition Affects Soil Fungistasis
Authors: de Boer Wietse , Verheggen Patrick , Klein Gunnewiek Paulien J. A. , Kowalchuk George A. , van Veen Johannes A. 
Published: February 2003

ABSTRACT

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi
Chaetomium globosum
,
Fusarium culmorum
,
Fusarium oxysporum
, and
Trichoderma harzianum
to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.
Computer Simulation of
Clostridium botulinum
Strain 56A Behavior at Low Spore Concentrations
Authors: Zhao L. , Montville T. J. , Schaffner D. W. 
Published: February 2003

ABSTRACT

It is generally assumed that spore behavior is independent of spore concentration, but recently published mathematical models indicate that this is not the case. A Monte Carlo simulation was employed in this study to further examine the independence assumption by evaluating the inherent variance in spore germination data. All simulations were carried out with @Risk software. A total of 500 to 4,000 iterations were needed for each simulation to reach convergence. Lag time and doubling time from a higher inoculum concentration were used to simulate the time to detection (TTD) at a lower inoculum concentration under otherwise identical environmental conditions. The point summaries of the simulated and observed TTDs were recorded for the 26 simulations, with kinetic data at the target inoculum concentration. The ratios of the median (

R
m

= median
obs
/median
sim
) and 90% range (

R
r

= 90% range
obs
/90% range
sim
) were calculated. Most

R
m

and

R
r

values were greater than one, indicating that the simulated TTDs were smaller and more homogeneous than the observed ones.

R
r

values departed farther from one than

R
m

values. Ratios obtained when simulating 1 spore with 10,000 spores deviated the farthest from one. Neither ratio was significantly different from the other when simulating 1 spore with 100 spores or simulating 100 spores with 10,000 spores. When kinetic data were not available, the percent positive observed at the 95th percentile of the simulated TTDs was obtained. These simulation results confirmed that the assumption of independence between spores is not valid.
Production by
Clostridium acetobutylicum
ATCC 824 of CelG, a Cellulosomal Glycoside Hydrolase Belonging to Family 9
Authors: López-Contreras Ana M. , Martens Aernout A. , Szijarto Nora , Mooibroek Hans , Claassen Pieternel A. M. , van der Oost John , de Vos Willem M. 
Published: February 2003

ABSTRACT

The genome sequence of
Clostridium acetobutylicum
ATCC 824, a noncellulolytic solvent-producing strain, predicts the production of various proteins with domains typical for cellulosomal subunits. Most of the genes coding for these proteins are grouped in a cluster similar to that found in cellulolytic clostridial species, such as
Clostridium cellulovorans
. CAC0916, one of the open reading frames present in the putative cellulosome gene cluster, codes for CelG, a putative endoglucanase belonging to family 9, and it was cloned and overexpressed in
Escherichia coli
. The overproduced CelG protein was purified by making use of its high affinity for cellulose and was characterized. The biochemical properties of the purified CelG were comparable to those of other known enzymes belonging to the same family. Expression of CelG by
C. acetobutylicum
grown on different substrates was studied by Western blotting by using antibodies raised against the purified
E. coli
-produced protein. Whereas the antibodies cross-reacted with CelG-like proteins secreted by cellobiose- or cellulose-grown
C. cellulovorans
cultures, CelG was not detectable in extracellular medium from
C. acetobutylicum
grown on cellobiose or glucose. However, notably, when lichenan-grown cultures were used, several bands corresponding to CelG or CelG-like proteins were present, and there was significantly increased extracellular endoglucanase activity.
Rhizobium etli
and
Rhizobium gallicum
Nodulate Common Bean (
Phaseolus vulgaris
) in a Traditionally Managed Milpa Plot in Mexico: Population Genetics and Biogeographic Implications
Authors: Silva Claudia , Vinuesa Pablo , Eguiarte Luis E. , Martínez-Romero Esperanza , Souza Valeria 
Published: February 2003

ABSTRACT

The stability of the genetic structure of rhizobial populations nodulating
Phaseolus vulgaris
cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial
rrs
,
glnII
,
nifH
, and
nodB
sequences), along with host range experiments, placed the isolates examined in
Rhizobium etli
bv. phaseoli and
Rhizobium gallicum
bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the
R. etli
and
R. gallicum
populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis,
nifH
copy number determination, and host range experiments. Plasmid profiles and
nifH
hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an
R. gallicum
bv. gallicum population nodulating common bean in America are discussed.
Characterization of Chitinase Genes from an Alkaliphilic Actinomycete,
Nocardiopsis prasina
OPC-131
Authors: Tsujibo Hiroshi , Kubota Takahiro , Yamamoto Mitsugu , Miyamoto Katsushiro , Inamori Yoshihiko 
Published: February 2003

ABSTRACT

An alkaliphilic actinomycete,
Nocardiopsis
prasina
OPC-131, secretes chitinases, ChiA, ChiB, and ChiBΔ, in the presence of chitin. The genes encoding ChiA and ChiB were cloned and sequenced. The open reading frame (ORF) of
chiA
encoded a protein of 336 amino acids with a calculated molecular mass of 35,257 Da. ChiA consisted of only a catalytic domain and showed a significant homology with family 18 chitinases. The
chiB
ORF encoded a protein of 296 amino acids with a calculated molecular mass of 31,500 Da. ChiB is a modular enzyme consisting of a chitin-binding domain type 3 (ChtBD type 3) and a catalytic domain. The catalytic domain of ChiB showed significant similarity to
Streptomyces
family 19 chitinases. ChiBΔ was the truncated form of ChiB lacking ChtBD type 3. Expression plasmids coding for ChiA, ChiB, and ChiBΔ were constructed to investigate the biochemical properties of these recombinant proteins. These enzymes showed pHs and temperature optima similar to those of native enzymes. ChiB showed more efficient hydrolysis of chitin and stronger antifungal activity than ChiBΔ, indicating that the ChtBD type 3 of ChiB plays an important role in the efficient hydrolysis of chitin and in antifungal activity. Furthermore, the finding of family 19 chitinase in
N.
prasina
OPC-131 suggests that family 19 chitinases are distributed widely in actinomycetes other than the genus
Streptomyces
.
Heat and Osmotic Stress Responses of Probiotic
Lactobacillus rhamnosus
HN001 (DR20) in Relation to Viability after Drying
Authors: Prasad Jaya , McJarrow Paul , Gopal Pramod 
Published: February 2003

ABSTRACT

The viability of lactic acid bacteria in frozen, freeze-dried, and air-dried forms is of significant commercial interest to both the dairy and food industries. In this study we observed that when prestressed with either heat (50°C) or salt (0.6 M NaCl),
Lactobacillus rhamnosus
HN001 (also known as DR20) showed significant (
P
< 0.05) improvement in viability compared with the nonstressed control culture after storage at 30°C in the dried form. To investigate the mechanisms underlying this stress-related viability improvement in
L. rhamnosus
HN001, we analyzed protein synthesis in cultures subjected to different growth stages and stress conditions, using two-dimensional gel electrophoresis and N-terminal sequencing. Several proteins were up- or down-regulated after either heat or osmotic shock treatments. Eleven proteins were positively identified, including the classical heat shock proteins GroEL and DnaK and the glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, lactate dehydrogenase, enolase, phosphoglycerate kinase, and triose phosphate isomerase, as well as tagatose 1,6-diphosphate aldolase of the tagatose pathway. The phosphocarrier protein HPr (histidine-containing proteins) was up-regulated in cultures after the log phase irrespective of the stress treatments used. The relative synthesis of an ABC transport-related protein was also up-regulated after shock treatments. Carbohydrate analysis of cytoplasmic contents showed higher levels (20 ± 3 μg/mg of protein) in cell extracts (CFEs) derived from osmotically stressed cells than in the unstressed control (15 ± 3 μg/mg of protein). Liquid chromatography of these crude carbohydrate extracts showed significantly different profiles. Electrospray mass spectrometry analysis of CFEs revealed, in addition to normal mono-, di-, tri-, and tetrasaccharides, the presence of saccharides modified with glycerol.
Desulfonation and Degradation of the Disulfodiphenylethercarboxylates from Linear Alkyldiphenyletherdisulfonate Surfactants
Authors: Schleheck David , Lechner Melanie , Schönenberger René , Suter Marc J.-F. , Cook Alasdair M. 
Published: February 2003

ABSTRACT

Earlier work showed that the biodegradation of a commercial linear monoalkyldiphenyletherdisulfonate surfactant as a carbon source for microbial growth leads to the quantitative formation of corresponding disulfodiphenylether carboxylates (DSDPECs), which were not degraded. α-Proteobacterium strain DS-1 (DSM 13023) catalyzes these reactions. These DSDPECs have now been characterized by high-pressure liquid chromatography coupled via an electrospray interface to a mass spectrometer. DSDPECs were a complex mixture of compounds which indicated catabolism via ω-oxygenation and β-oxidation. DSDPECs were subject to quantitative desulfonation in bacterial cultures in which they served as sole sulfur sources for bacterial growth. On average, one sulfonate group per DSDPEC species was removed, and the organism responsible for this desulfonation was isolated and identified as
Rhodococcus opacus
ISO-5. The products were largely monosulfodiphenylether carboxylate-phenols (MSDPEC-phenols). MSDPEC-phenols were subject to extensive dissimilation by bacteria from activated sludge.
Phylogenetic Diversity of Nitrogenase (
nifH
) Genes in Deep-Sea and Hydrothermal Vent Environments of the Juan de Fuca Ridge
Authors: Mehta Mausmi P. , Butterfield David A. , Baross John A. 
Published: February 2003

ABSTRACT

The subseafloor microbial habitat associated with typical unsedimented mid-ocean-ridge hydrothermal vent ecosystems may be limited by the availability of fixed nitrogen, inferred by the low ammonium and nitrate concentrations measured in diffuse hydrothermal fluid. Dissolved N
2
gas, the largest reservoir of nitrogen in the ocean, is abundant in deep-sea and hydrothermal vent fluid. In order to test the hypothesis that biological nitrogen fixation plays an important role in nitrogen cycling in the subseafloor associated with unsedimented hydrothermal vents, degenerate PCR primers were designed to amplify the nitrogenase iron protein gene
nifH
from hydrothermal vent fluid. A total of 120
nifH
sequences were obtained from four samples: a nitrogen-poor diffuse vent named marker 33 on Axial Volcano, sampled twice over a period of 1 year as its temperature decreased; a nitrogen-rich diffuse vent near Puffer on Endeavour Segment; and deep seawater with no detectable hydrothermal plume signal. Subseafloor
nifH
genes from marker 33 and Puffer are related to anaerobic clostridia and sulfate reducers. Other
nifH
genes unique to the vent samples include proteobacteria and divergent
Archaea
. All of the
nifH
genes from the deep-seawater sample are most closely related to the thermophilic, anaerobic archaeon
Methanococcus thermolithotrophicus
(77 to 83% amino acid similarity). These results provide the first genetic evidence of potential nitrogen fixers in hydrothermal vent environments and indicate that at least two sources contribute to the diverse assemblage of
nifH
genes detected in hydrothermal vent fluid:
nifH
genes from an anaerobic, hot subseafloor and
nifH
genes from cold, oxygenated deep seawater.
Comparison of Method 1623 and Cell Culture-PCR for Detection of
Cryptosporidium
spp. in Source Waters
Authors: LeChevallier Mark W. , Di Giovanni George D. , Clancy Jennifer L. , Bukhari Zia , Bukhari Shan , Rosen Jeffrey S. , Sobrinho Jose , Frey Michelle M. 
Published: February 2003

ABSTRACT

Analysis of
Cryptosporidium
occurrence in six watersheds by method 1623 and the integrated cell culture-PCR (CC-PCR) technique provided an opportunity to evaluate these two methods. The average recovery efficiencies were 58.5% for the CC-PCR technique and 72% for method 1623, but the values were not significantly different (
P
= 0.06).
Cryptosporidium
oocysts were detected in 60 of 593 samples (10.1%) by method 1623. Infectious oocysts were detected in 22 of 560 samples (3.9%) by the CC-PCR technique. There was 87% agreement between the total numbers of samples positive as determined by method 1623 and CC-PCR for four of the sites. The other two sites had 16.3 and 24% correspondence between the methods. Infectious oocysts were detected in all of the watersheds. Overall, approximately 37% of the
Cryptosporidium
oocysts detected by the immunofluorescence method were viable and infectious. DNA sequence analysis of the
Cryptosporidium
parvum
isolates detected by CC-PCR showed the presence of both the bovine and human genotypes. More than 90% of the
C. parvum
isolates were identified as having the bovine or bovine-like genotype. The estimates of the concentrations of infectious
Cryptosporidium
and the resulting daily and annual risks of infection compared well for the two methods. The results suggest that most surface water systems would require, on average, a 3-log reduction in source water
Cryptosporidium
levels to meet potable water goals.
Characterization of a Thermostable
d
-Stereospecific Alanine Amidase from
Brevibacillus borstelensis
BCS-1
Authors: Baek Dae Heoun , Kwon Seok-Joon , Hong Seung-Pyo , Kwak Mi-Sun , Lee Mi-Hwa , Song Jae Jun , Lee Seung-Goo , Yoon Ki-Hong , Sung Moon-Hee 
Published: February 2003

ABSTRACT

A gene encoding a new thermostable
d
-stereospecific alanine amidase from the thermophile
Brevibacillus borstelensis
BCS-1 was cloned and sequenced. The molecular mass of the purified enzyme was estimated to be 199 kDa after gel filtration chromatography and about 30 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that the enzyme could be composed of a hexamer with identical subunits. The purified enzyme exhibited strong amidase activity towards
d
-amino acid-containing aromatic, aliphatic, and branched amino acid amides yet exhibited no enzyme activity towards
l
-amino acid amides,
d
-amino acid-containing peptides, and NH
2
-terminally protected amino acid amides. The optimum temperature and pH for the enzyme activity were 85°C and 9.0, respectively. The enzyme remained stable within a broad pH range from 7.0 to 10.0. The enzyme was inhibited by dithiothreitol, 2-mercaptoethanol, and EDTA yet was strongly activated by Co
2+
and Mn
2+
. The
k
cat
/

K
m

for
d
-alaninamide was measured as 544.4 ± 5.5 mM
−1
min
−1
at 50°C with 1 mM Co
2+
.
Complete Detoxification of Vinyl Chloride by an Anaerobic Enrichment Culture and Identification of the Reductively Dechlorinating Population as a
Dehalococcoides
Species
Authors: He Jianzhong , Ritalahti Kirsti M. , Aiello Michael R. , Löffler Frank E. 
Published: February 2003

ABSTRACT

A major obstacle in the implementation of the reductive dechlorination process at chloroethene-contaminated sites is the accumulation of the intermediate vinyl chloride (VC), a proven human carcinogen. To shed light on the microbiology involved in the final critical dechlorination step, a sediment-free, nonmethanogenic, VC-dechlorinating enrichment culture was derived from tetrachloroethene (PCE)-to-ethene-dechlorinating microcosms established with material from the chloroethene-contaminated Bachman Road site aquifer in Oscoda, Mich. After 40 consecutive transfers in defined, reduced mineral salts medium amended with VC, the culture lost the ability to use PCE and trichloroethene (TCE) as metabolic electron acceptors. PCE and TCE dechlorination occurred in the presence of VC, presumably in a cometabolic process. Enrichment cultures supplied with lactate or pyruvate as electron donor dechlorinated VC to ethene at rates up to 54
μ
mol liter
−1
day
−1
, and dichloroethenes (DCEs) were dechlorinated at about 50% of this rate. The half-saturation constant (

K
S

) for VC was 5.8
μ
M, which was about one-third lower than the concentrations determined for
cis
-DCE and
trans
-DCE. Similar VC dechlorination rates were observed at temperatures between 22 and 30°C, and negligible dechlorination occurred at 4 and 35°C. Reductive dechlorination in medium amended with ampicillin was strictly dependent on H
2
as electron donor. VC-dechlorinating cultures consumed H
2
to threshold concentrations of 0.12 ppm by volume. 16S rRNA gene-based tools identified a
Dehalococcoides
population, and
Dehalococcoides
-targeted quantitative real-time PCR confirmed VC-dependent growth of this population. These findings demonstrate that
Dehalococcoides
populations exist that use DCEs and VC but not PCE or TCE as metabolic electron acceptors.
PCR Assay for Identification of
Histoplasma capsulatum
Based on the Nucleotide Sequence of the M Antigen
Authors: Guedes Herbert Leonel de Matos , Guimarães Allan Jefferson , Muniz Mauro de Medeiros , Pizzini Claudia Vera , Hamilton Andrew John , Peralta José Mauro , Deepe, George S. , Zancopé-Oliveira Rosely M. 
Published: February 2003

ABSTRACT

The major diagnostic antigens of
Histoplasma capsulatum
var.
capsulatum
are the H and M antigens, pluripotent glycoproteins that elicit both humoral and T-cell-mediated immune responses. The gene encoding the M antigen has previously been sequenced, and its sequence has significant overall homology to those of the genes for fungal catalases. Regions of the M-antigen gene with little or no homology were used to design four oligonucleotide sequences for application in the PCR detection and identification of
H. capsulatum
var.
capsulatum
. The PCR correctly identified the 31
H. capsulatum
var.
capsulatum
strains isolated from human, animal, and soil specimens and 1
H. capsulatum
var.
duboisii
isolate. PCR products of 111 and 279 bp were amplified with primers Msp1F-Msp1R and Msp2F-Msp2R, respectively. No amplification product was obtained from DNA extracted from an
H. capsulatum
var.
farciminosum
isolate. The specificity of the PCR with the M-antigen-derived primers was confirmed by the total absence of amplification products when genomic DNA from
Paracoccidioides brasiliensis
,
Candida
spp.,
Sporothrix schenckii
,
Cryptococcus neoformans
,
Blastomyces dermatitidis
,
Coccidioides immitis
,
Aspergillus niger
, and
Aspergillus fumigatus
were applied in the reaction. This rapid, sensitive, and specific assay provides a way to identify typical and atypical isolates of
H. capsulatum
var.
capsulatum
.