bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the Importance of Similarity in Carbon Source Utilization Profiles between the Biological Control Agent and the Pathogen in Biological Control of Bacterial Speck of Tomato
Authors: Ji Pingsheng , Wilson Mark 
Published: August 2002

ABSTRACTBacterial speck of tomato, caused byPseudomonas syringaepv. tomato, was used to determine whether similarity in carbon source utilization between a preemptive biological control agent and the pathogen was significant in determining the ability of the bacterium to suppress disease. Similarity in carbon source utilization was quantified as the ratio of the number of tomato carbon sources utilized in vitro by the biological control agent to the number of tomato carbon sources utilized in vitro by the target pathogen (the niche overlap index [NOI]). Suppression of the disease was quantified as the percent reduction in disease severity compared to the pathogen-only control when nonpathogenic bacteria were applied to foliage 48 h prior to the pathogen. In the collection of 36 nonpathogenic bacterial strains, there was a significant (P< 0.01), but weak (r2= 0.25), correlation between reduction in disease severity and similarity in carbon source utilization, suggesting that similarity in carbon source use was significant in determining ability to suppress disease. The relationship was investigated further using catabolic mutants ofP. syringaestrain TLP2, an effective biological control agent of speck. Catabolic mutants exhibited lower levels of similarity (NOI = 0.07 to 0.90) than did wild-type TLP2 (NOI = 0.93). With these catabolic mutants there was a significant (P< 0.01), and stronger (r2= 0.42), correlation between reduction in disease severity and similarity in carbon source utilization. This suggests that similarity in carbon source utilization was a more important component of biological control ability for the catabolic mutants than for the nonpathogenic bacteria. Together, these studies indicate that suppression of bacterial speck of tomato was correlated with nutritional similarity between the pathogenic and nonpathogenic bacteria and suggest that preemptive utilization of carbon sources was probably involved in the biological control of the disease by both the naturally occurring nonpathogenic bacteria and the catabolic mutants.
Characterization of a Novel Fructosyltransferase from
Lactobacillus reuteri
That Synthesizes High-Molecular-Weight Inulin and Inulin Oligosaccharides
Authors: van Hijum S. A. F. T. , van Geel-Schutten G. H. , Rahaoui H. , van der Maarel M. J. E. C. , Dijkhuizen L. 
Published: August 2002

ABSTRACT

Fructosyltransferase (FTF) enzymes produce fructose polymers (fructans) from sucrose. Here, we report the isolation and characterization of an FTF-encoding gene from
Lactobacillus reuteri
strain 121. A C-terminally truncated version of the
ftf
gene was successfully expressed in
Escherichia coli
. When incubated with sucrose, the purified recombinant FTF enzyme produced large amounts of fructo-oligosaccharides (FOS) with β-(2
→
1)-linked fructosyl units, plus a high-molecular-weight fructan polymer (>10
7
) with β-(2
→
1) linkages (an inulin). FOS, but not inulin, was found in supernatants of
L. reuteri
strain 121 cultures grown on medium containing sucrose. Bacterial inulin production has been reported for only
Streptococcus mutans
strains. FOS production has been reported for a few bacterial strains. This paper reports the first-time isolation and molecular characterization of (i) a
Lactobacillus ftf
gene, (ii) an inulosucrase associated with a generally regarded as safe bacterium, (iii) an FTF enzyme synthesizing both a high molecular weight inulin and FOS, and (iv) an FTF protein containing a cell wall-anchoring LPXTG motif. The biological relevance and potential health benefits of an inulosucrase associated with an
L. reuteri
strain remain to be established.
In Situ Determination of the Intracellular pH ofLactococcus lactisandLactobacillus plantarumduring Pressure Treatment
Authors: Molina-Gutierrez Adriana , Stippl Volker , Delgado Antonio , Gänzle Michael G. , Vogel Rudi F. 
Published: August 2002

ABSTRACTHydrostatic pressure may affect the intracellular pH of microorganisms by (i) enhancing the dissociation of weak organic acids and (ii) increasing the permeability of the cytoplasmic membrane and inactivation of enzymes required for pH homeostasis. The internal pHs ofLactococcus lactisandLactobacillus plantarumduring and after pressure treatment at 200 and 300 MPa and at pH values ranging from 4.0 to 6.5 were determined. Pressure treatment at 200 MPa for up to 20 min did not reduce the viability of either strain at pH 6.5. Pressure treatment at pH 6.5 and 300 MPa reduced viable cell counts ofLactococcus lactisandLactobacillus plantarumby 5 log after 20 and 120 min, respectively. Pressure inactivation was faster at pH 5 or 4. At ambient pressure, both strains maintained a transmembrane pH gradient of 1 pH unit at neutral pH and about 2 pH units at pH 4.0. During pressure treatment at 200 and 300 MPa, the internal pH ofL. lactiswas decreased to the value of the extracellular pH during compression. The same result was observed during treatment ofLactobacillus plantarumat 300 MPa.Lactobacillus plantarumwas unable to restore the internal pH after a compression-decompression cycle at 300 MPa and pH 6.5.Lactococcus lactislost the ability to restore its internal pH after 20 and 4 min of pressure treatment at 200 and 300 MPa, respectively. As a consequence, pressure-mediated stress reactions and cell death may be considered secondary effects promoted by pH and other environmental conditions.
Characterization of the 5-Carboxyvanillate Decarboxylase Gene and Its Role in Lignin-Related Biphenyl Catabolism in
Sphingomonas paucimobilis
SYK-6
Authors: Peng Xue , Masai Eiji , Kitayama Hirotaka , Harada Kyo , Katayama Yoshihiro , Fukuda Masao 
Published: August 2002

ABSTRACT

Sphingomonas paucimobilis
SYK-6 degrades a lignin-related biphenyl compound, 5,5′-dehydrodivanillate (DDVA), to 5-carboxyvanillate (5CVA) by the enzyme reactions catalyzed by the DDVA
O
-demethylase (LigX), the ring cleavage oxygenase (LigZ), and the
meta
-cleavage compound hydrolase (LigY). In this study we examined the degradation step of 5CVA. 5CVA was transformed to vanillate,
O
-demethylated, and further degraded via the protocatechuate 4,5-cleavage pathway by this strain. A cosmid clone which conferred the 5CVA degradation activity to a host strain was isolated. In the 7.0-kb
Eco
RI fragment of the cosmid we found a 1,002-bp open reading frame responsible for the conversion of 5CVA to vanillate, and we designated it
ligW
. The gene product of
ligW
(LigW) catalyzed the decarboxylation of 5CVA to produce vanillate along with the specific incorporation of deuterium from deuterium oxide, indicating that LigW is a nonoxidative decarboxylase of 5CVA. LigW did not require any metal ions or cofactors for its activity. The decarboxylase activity was specific to 5CVA. Inhibition experiments with 5CVA analogs suggested that two carboxyl groups oriented
meta
to each other in 5CVA are important to the substrate recognition by LigW. Gene walking analysis indicated that the
ligW
gene was located on the 18-kb DNA region with other DDVA catabolic genes, including
ligZ
,
ligY
, and
ligX
.
Cloning and Characterization of the Ferulic Acid Catabolic Genes of
Sphingomonas paucimobilis
SYK-6
Authors: Masai Eiji , Harada Kyo , Peng Xue , Kitayama Hirotaka , Katayama Yoshihiro , Fukuda Masao 
Published: August 2002

ABSTRACT

Sphingomonas paucimobilis
SYK-6 degrades ferulic acid to vanillin, and it is further metabolized through the protocatechuate 4,5-cleavage pathway. We obtained a Tn
5
mutant of SYK-6, FA2, which was able to grow on vanillic acid but not on ferulic acid. A cosmid which complemented the growth deficiency of FA2 on ferulic acid was isolated. The 5.2-kb
Bam
HI-
Eco
RI fragment in this cosmid conferred the transformation activity of ferulic acid to vanillin on
Escherichia coli
host cells. A sequencing analysis revealed the genes
ferB
and
ferA
in this fragment; these genes consist of 852- and 2,127-bp open reading frames, respectively. The deduced amino acid sequence of
ferB
showed 40 to 48% identity with that of the feruloyl-coenzyme A (CoA) hydratase/lyase genes of
Pseudomonas
and
Amycolatopsis
ferulic acid degraders. On the other hand, the deduced amino acid sequence of
ferA
showed no significant similarity to the feruloyl-CoA synthetase genes of other ferulic acid degraders. However, the deduced amino acid sequence of
ferA
did show 31% identity with pimeloyl-CoA synthetase of
Pseudomonas mendocina
35, which has been classified as a new superfamily of acyl-CoA synthetase (ADP forming) with succinyl-CoA synthetase (L. B. Sánchez, M. Y. Galperin, and M. Müller, J. Biol. Chem. 275:5794-5803, 2000). On the basis of the enzyme activity of
E. coli
carrying each of these genes,
ferA
and
ferB
were shown to encode a feruloyl-CoA synthetase and feruloyl-CoA hydratase/lyase, respectively.
p
-coumaric acid, caffeic acid, and sinapinic acid were converted to their corresponding benzaldehyde derivatives by the cell extract containing FerA and FerB, thereby indicating their broad substrate specificities. We found a
ferB
homolog,
ferB2
, upstream of a 5-carboxyvanillic acid decarboxylase gene (
ligW
) involved in the degradation of 5,5′-dehydrodivanillic acid. The deduced amino acid sequence of
ferB2
showed 49% identity with
ferB
, and its gene product showed feruloyl-CoA hydratase/lyase activity with a substrate specificity similar to that of FerB. Insertional inactivation of each
fer
gene in
S. paucimobilis
SYK-6 suggested that the
ferA
gene is essential and that
ferB
and
ferB2
genes are involved in ferulic acid degradation.
Environmental Factors That Control Microbial Perchlorate Reduction
Authors: Chaudhuri Swades K. , O'Connor Susan M. , Gustavson Ruth L. , Achenbach Laurie A. , Coates John D. 
Published: August 2002

ABSTRACT

As part of a study to elucidate the environmental parameters that control microbial perchlorate respiration, we investigated the reduction of perchlorate by the dissimilatory perchlorate reducer
Dechlorosoma suillum
under a diverse set of environmental conditions. Our results demonstrated that perchlorate reduction by
D. suillum
only occurred under anaerobic conditions in the presence of perchlorate and was dependent on the presence of molybdenum. Perchlorate reduction was dependent on the presence of the enzyme chlorite dismutase, which was induced during metabolism of perchlorate. Anaerobic conditions alone were not enough to induce expression of this enzyme. Dissolved oxygen concentrations less than 2 mg liter
−1
were enough to inhibit perchlorate reduction by
D. suillum
. Similarly to oxygen, nitrate also regulated chlorite dismutase expression and repressed perchlorate reduction by
D. suillum.
Perchlorate-grown cultures of
D. suillum
preferentially reduced nitrate in media with equimolar amounts of perchlorate and nitrate. In contrast, an extended (40 h) lag phase was observed if a similar nitrate-perchlorate medium was inoculated with a nitrate-grown culture. Perchlorate reduction commenced only when nitrate was completely removed in either of these experiments. In contrast to
D. suillum
, nitrate had no inhibitory effects on perchlorate reduction by the perchlorate reducer
Dechloromonas agitata
strain CKB. Nitrate was reduced to nitrite concomitant with perchlorate reduction to chloride. These studies demonstrate that microbial respiration of perchlorate is significantly affected by environmental conditions and perchlorate reduction is directly dependent on bioavailable molybdenum and the presence or absence of competing electron acceptors. A microbial treatment strategy can achieve and maintain perchlorate concentrations below the recommended regulatory level, but only in environments in which the variables described above can be controlled.
Molecular Evidence for a Uniform Microbial Community in Sponges from Different Oceans
Authors: Hentschel Ute , Hopke Jörn , Horn Matthias , Friedrich Anja B. , Wagner Michael , Hacker Jörg , Moore Bradley S. 
Published: August 2002

ABSTRACT

Sponges (class Porifera) are evolutionarily ancient metazoans that populate the tropical oceans in great abundances but also occur in temperate regions and even in freshwater. Sponges contain large numbers of bacteria that are embedded within the animal matrix. The phylogeny of these bacteria and the evolutionary age of the interaction are virtually unknown. In order to provide insights into the species richness of the microbial community of sponges, we performed a comprehensive diversity survey based on 190 sponge-derived 16S ribosomal DNA (rDNA) sequences. The sponges
Aplysina aerophoba
and
Theonella swinhoei
were chosen for construction of the bacterial 16S rDNA library because they are taxonomically distantly related and they populate nonoverlapping geographic regions. In both sponges, a uniform microbial community was discovered whose phylogenetic signature is distinctly different from that of marine plankton or marine sediments. Altogether 14 monophyletic, sponge-specific sequence clusters were identified that belong to at least seven different bacterial divisions. By definition, the sequences of each cluster are more closely related to each other than to a sequence from nonsponge sources. These monophyletic clusters comprise 70% of all publicly available sponge-derived 16S rDNA sequences, reflecting the generality of the observed phenomenon. This shared microbial fraction represents the smallest common denominator of the sponges investigated in this study. Bacteria that are exclusively found in certain host species or that occur only transiently would have been missed. A picture emerges where sponges can be viewed as highly concentrated reservoirs of so far uncultured and elusive marine microorganisms.
Effect of Modified Atmosphere Composition on the Metabolism of Glucose byBrochothrix thermosphacta
Authors: Pin Carmen , García de Fernando Gonzalo D. , Ordóñez Juan A. 
Published: August 2002

ABSTRACTThe influence of atmosphere composition on the metabolism ofBrochothrix thermosphactawas studied by analyzing the consumption of glucose and the production of ethanol, acetic and lactic acids, acetaldehyde, and diacetyl-acetoin under atmospheres containing different combinations of carbon dioxide and oxygen. When glucose was metabolized under oxygen-free atmospheres, lactic acid was one of the main end products, while under atmospheres rich in oxygen mainly acetoin-diacetyl was produced. The proportions of the total consumed glucose used for the production of acetoin (aerobic metabolism) and lactic acid (anaerobic metabolism) were used to decide whether aerobic or anaerobic metabolism predominated at a given atmosphere composition. The boundary conditions between dominantly anaerobic and aerobic metabolisms were determined by logistic regression. The metabolism of glucose byB. thermosphactawas influenced not only by the oxygen content of the atmosphere but also by the carbon dioxide content. At high CO2percentages, glucose metabolism remained anaerobic under greater oxygen contents.
Metabolic Control Analysis of Glycerol Synthesis inSaccharomyces cerevisiae
Authors: Cronwright Garth R. , Rohwer Johann M. , Prior Bernard A. 
Published: August 2002

ABSTRACTGlycerol, a major by-product of ethanol fermentation bySaccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. To gain a clearer understanding of and to quantify the extent to which parameters of the pathway affect glycerol flux inS. cerevisiae, a kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally. The model was validated by comparing experimental results on the rate of glycerol production to the rate calculated by the model. Values calculated by the model agreed well with those measured in independent experiments. The model also mimics the changes in the rate of glycerol synthesis at different phases of growth. Metabolic control analysis values calculated by the model indicate that the NAD+-dependent glycerol 3-phosphate dehydrogenase-catalyzed reaction has a flux control coefficient (Cv1J) of approximately 0.85 and exercises the majority of the control of flux through the pathway. Response coefficients of parameter metabolites indicate that flux through the pathway is most responsive to dihydroxyacetone phosphate concentration (RDHAPJ= 0.48 to 0.69), followed by ATP concentration (RATPJ= −0.21 to −0.50). Interestingly, the pathway responds weakly to NADH concentration (RNADHJ= 0.03 to 0.08). The model indicates that the best strategy to increase flux through the pathway is not to increase enzyme activity, substrate concentration, or coenzyme concentration alone but to increase all of these parameters in conjunction with each other.
Influence of Hydrodynamics and Cell Signaling on the Structure and Behavior of
Pseudomonas aeruginosa
Biofilms
Authors: Purevdorj B. , Costerton J. W. , Stoodley P. 
Published: August 2002

ABSTRACT

Biofilms were grown from wild-type (WT)
Pseudomonas aeruginosa
PAO1 and the cell signaling
lasI
mutant PAO1-JP1 under laminar and turbulent flows to investigate the relative contributions of hydrodynamics and cell signaling for biofilm formation. Various biofilm morphological parameters were quantified using Image Structure Analyzer software. Multivariate analysis demonstrated that both cell signaling and hydrodynamics significantly (
P
< 0.000) influenced biofilm structure. In turbulent flow, both biofilms formed streamlined patches, which in some cases developed ripple-like wave structures which flowed downstream along the surface of the flow cell. In laminar flow, both biofilms formed monolayers interspersed with small circular microcolonies. Ripple-like structures also formed in four out of six WT biofilms, although their velocity was approximately 10 times less than that of those that formed in the turbulent flow cells. The movement of biofilm cell clusters over solid surfaces may have important clinical implications for the dissemination of biofilm subject to fluid shear, such as that found in catheters. The ability of the cell signaling mutant to form biofilms in high shear flow demonstrates that signaling mechanisms are not required for the formation of strongly adhered biofilms. Similarity between biofilm morphologies in WT and mutant biofilms suggests that the dilution of signal molecules by mass transfer effects in faster flowing systems mollifies the dramatic influence of signal molecules on biofilm structure reported in previous studies.
Optimization of Bacteriocin Production by Batch Fermentation of
Lactobacillus plantarum
LPCO10
Authors: Leal-Sánchez M. V. , Jiménez-Díaz R. , Maldonado-Barragán A. , Garrido-Fernández A. , Ruiz-Barba J. L. 
Published: August 2002

ABSTRACT

Optimization of bacteriocin production by
Lactobacillus plantarum
LPCO10 was explored by an integral statistical approach. In a prospective series of experiments, glucose and NaCl concentrations in the culture medium, inoculum size, aeration of the culture, and growth temperature were statistically combined using an experimental 2
3
5-2
fractional factorial two-level design and tested for their influence on maximal bacteriocin production by
L. plantarum
LPCO10. After the values for the less-influential variables were fixed, NaCl concentration, inoculum size, and temperature were selected to study their optimal relationship for maximal bacteriocin production. This was achieved by a new experimental 3
2
3-1
fractional factorial three-level design which was subsequently used to build response surfaces and analyzed for both linear and quadratic effects. Results obtained indicated that the best conditions for bacteriocin production were shown with temperatures ranging from 22 to 27°C, salt concentration from 2.3 to 2.5%, and
L. plantarum
LPCO10 inoculum size ranging from 10
7.3
to 10
7.4
CFU/ml, fixing the initial glucose concentration at 2%, with no aeration of the culture. Under these optimal conditions, about 3.2 × 10
4
times more bacteriocin per liter of culture medium was obtained than that used to initially purify plantaricin S from
L. plantarum
LPCO10 to homogeneity. These results indicated the importance of this study in obtaining maximal production of bacteriocins from
L. plantarum
LPCO10 so that bacteriocins can be used as preservatives in canned foods.
Molecular Evolution of Aromatic Polyketides and Comparative Sequence Analysis of Polyketide Ketosynthase and 16S Ribosomal DNA Genes from Various
Streptomyces
Species
Authors: Metsä-Ketelä Mikko , Halo Laura , Munukka Eveliina , Hakala Juha , Mäntsälä Pekka , Ylihonko Kristiina 
Published: August 2002

ABSTRACT
A 613-bp fragment of an essential ketosynthase gene from the biosynthetic pathway of aromatic polyketide antibiotics was sequenced from 99 actinomycetes isolated from soil. Phylogenetic analysis showed that the isolates clustered into clades that correspond to the various classes of aromatic polyketides. Additionally, sequencing of a 120-bp fragment from the γ-variable region of 16S ribosomal DNA (rDNA) and subsequent comparative sequence analysis revealed incongruity between the ketosynthase and 16S rDNA phylogenetic trees, which strongly suggests that there has been horizontal transfer of aromatic polyketide biosynthesis genes. The results show that the ketosynthase tree could be used for DNA fingerprinting of secondary metabolites and for screening interesting aromatic polyketide biosynthesis genes. Furthermore, the movement of the ketosynthase genes suggests that traditional marker molecules like 16S rDNA give misleading information about the biosynthesis potential of aromatic polyketides, and thus only molecules that are directly involved in the biosynthesis of secondary metabolites can be used to gain information about the biodiversity of antibiotic production in different actinomycetes.
Soil-Atmosphere CO Exchanges and Microbial Biogeochemistry of CO Transformations in a Brazilian Agricultural Ecosystem
Authors: King Gary M. , Hungria M. 
Published: August 2002

ABSTRACT

Although anthropogenic land use has major impacts on the exchange of soil and atmosphere gas in general, relatively little is known about its impacts on carbon monoxide. We compared soil-atmosphere CO exchanges as a function of land use, crop type, and tillage treatment on an experimental farm in Parãna, Brazil, that is representative of regionally important agricultural ecosystems. Our results showed that cultivated soils consumed CO at rates between 3 and 6 mg of CO m
−2
day
−1
, with no statistically significant effect of tillage method or crop. However, CO exchange for a pasture soil was near zero, and an unmanaged woodlot emitted CO at a rate of 9 mg of CO m
−2
day
−1
. Neither nitrite, aluminum sulfate, nor methyl fluoride additions affected CO consumption by tilled or untilled soils from soybean plots, indicating that CO oxidation did not depend on ammonia oxidizers and that CO oxidation patterns differed in part from patterns reported for forest soils. The apparent

K
m

for CO uptake, 5 to 11 ppm, was similar to values reported for temperate forest soils;
V
max
values, approximately 1 μg of CO g (dry weight)
−1
h
−1
, were comparable for woodlot and cultivated soils in spite of the fact that the latter consumed CO under ambient conditions. Short-term (24-h) exposure to elevated levels of CO (10% CO) partially inhibited uptake at lower concentrations (i.e., 100 ppm), suggesting that the sensitivity to CO of microbial populations that are active in situ differs from that of known carboxydotrophs. Soil-free soybean and corn roots consumed CO when they were incubated with 100-ppm concentrations and produced CO when they were incubated with ambient concentrations. These results document for the first time a role for cultivated plant roots in the dynamics of CO in an agricultural ecosystem.