bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Linoleic Acid Concentration on Conjugated Linoleic Acid Production by
Butyrivibrio fibrisolvens
A38
Authors: Kim Young Jun , Liu Rui Hai , Bond Daniel R. , Russell James B. 
Published: July 2002

ABSTRACT

Butyrivibrio fibrisolvens
A38 inocula were inhibited by as little as 15 μM linoleic acid (LA), but growing cultures tolerated 10-fold more LA before growth was inhibited. Growing cultures did not produce significant amounts of
cis
-9,
trans
-11 conjugated linoleic acid (CLA) until the LA concentration was high enough to inhibit biohydrogenation, growth was inhibited, and lysis was enhanced. Washed-cell suspensions that were incubated anaerobically with 350 μM LA converted most of the LA to hydrogenated products, and little CLA was detected. When the washed-cell suspensions were incubated aerobically, biohydrogenation was inhibited, CLA production was at least twofold greater, and CLA persisted. The LA isomerase reaction was very rapid, but the LA isomerase did not recycle like a normal enzyme to catalyze more substrate. Cells that were preincubated with CLA lost their ability to produce more CLA from LA, and the CLA accumulation was directly proportional (
r
2
= 0.98) to the initial cell density. Growing cells were as sensitive to CLA as LA, the LA isomerase and reductases of biohydrogenation were linked, and free CLA was not released. Because growing cultures of
B. fibrisolvens
A38 did not produce significant amounts of CLA until the LA concentration was high, biohydrogenation was arrested, and the cell density had declined, the flow of CLA from the rumen may be due to LA-dependent bacterial inactivation, death, or lysis.
Detection on Surfaces and in Caco-2 Cells of
Campylobacter jejuni
Cells Transformed with New
gfp, yfp
, and
cfp
Marker Plasmids
Authors: Miller William G. , Bates Anne H. , Horn Sharon T. , Brandl Maria T. , Wachtel Marian R. , Mandrell Robert E. 
Published: July 2002

ABSTRACT

We have developed two sets of
Campylobacter
shuttle vectors containing either the
gfp
(green fluorescent protein),
yfp
(yellow fluorescent protein), or
cfp
(cyan fluorescent protein) reporter gene. In one set, the reporter gene is fused to a consensus
Campylobacter
promoter sequence (P
c
). The other set contains a pUC18 multicloning site upstream of the reporter gene, allowing the construction of transcriptional fusions using known promoters or random genomic fragments.
C. jejuni
cells transformed with the P
c
fusion plasmids are strongly fluorescent and easily visualized on chicken skin, on plant tissue, and within infected Caco-2 cells. In each
C. jejuni
strain tested, these plasmids were maintained over several passages in the absence of antibiotic selection. Also, in many
C. jejuni
strains, >91% of the cells transformed with the P
c
fusion plasmids remained fluorescent after several days. Experiments with yellow fluorescent and cyan fluorescent
C. jejuni
transformants suggest that aggregates containing two or more strains of
C. jejuni
may be present in an enrichment broth culture. Colonies arising from these aggregates would be heterologous in nature; therefore, isolation of a pure culture of
C. jejuni
, by selecting single colonies, from an environmental sample may not always yield a single strain.
Molecular and Phenotypic Characterization of
Pseudomonas
spp. Isolated from Milk
Authors: Wiedmann Martin , Weilmeier Denise , Dineen Sean S. , Ralyea Robert , Boor Kathryn J. 
Published: July 2002

ABSTRACT

Putative
Pseudomonas
spp. isolated predominantly from raw and processed milk were characterized by automated ribotyping and by biochemical reactions. Isolates were biochemically profiled using the Biolog system and API 20 NE and by determining the production of proteases, lipases, and lecithinases for each isolate. Isolates grouped into five coherent clusters, predominated by the species
P. putida
(cluster A),
P. fluorescens
(cluster B),
P. fragi
(as identified by Biolog) or
P. fluorescens
(as identified by API 20 NE) (cluster C),
P. fragi
(as identified by Biolog) or
P. putida
(as identified by API 20 NE) (cluster D), and
P. fluorescens
(cluster E). Isolates within each cluster also displayed similar enzyme activities. Isolates in clusters A, C, and D were generally negative for all three enzyme activities; isolates in cluster B were predominantly positive for all three enzyme activities; and isolates in cluster E were negative for lecithinase but predominantly positive for protease and lipase activities. Thus, only isolates from clusters B and E produced enzyme activities associated with dairy product flavor defects. Thirty-eight ribogroups were differentiated among the 70 isolates. Ribotyping was highly discriminatory for dairy
Pseudomonas
isolates, with a Simpson's index of discrimination of 0.955. Isolates of the same ribotype were never classified into different clusters, and ribotypes within a given cluster generally showed similar ribotype patterns; thus, specific ribotype fragments may be useful markers for tracking the sources of pseudomonads in dairy production systems. Our results suggest that ribogroups are generally homogeneous with respect to nomenspecies and biovars, confirming the identification potential of ribotyping for
Pseudomonas
spp.
Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis
Authors: Dunbar John , Ticknor Lawrence O. , Kuske Cheryl R. 
Published: July 2002

ABSTRACT

The ability of terminal restriction fragment (T-RFLP or TRF) profiles of 16S rRNA genes to provide useful information about the relative diversity of complex microbial communities was investigated by comparison with other methods. Four soil communities representing two pinyon rhizosphere and two between-tree (interspace) soil environments were compared by analysis of 16S rRNA gene clone libraries and culture collections (Dunbar et al., Appl. Environ. Microbiol. 65:1662–1669, 1998) and by analysis of 16S rDNA TRF profiles of community DNA. The TRF method was able to differentiate the four communities in a manner consistent with previous comparisons of the communities by analysis of 16S rDNA clone libraries. TRF profiles were not useful for calculating and comparing traditional community richness or evenness values among the four soil environments. Statistics calculated from
Rsa
I,
Hha
I,
Hae
III, and
Msp
I profiles of each community were inconsistent, and the combined data were not significantly different between samples. The detection sensitivity of the method was tested. In standard PCRs, a seeded population comprising 0.1 to 1% of the total community could be detected. The combined results demonstrate that TRF analysis is an excellent method for rapidly comparing the relationships between bacterial communities in environmental samples. However, for highly complex communities, the method appears unable to provide classical measures of relative community diversity.
Physiological and Chemical Investigations into Microbial Degradation of Synthetic Poly(
cis
-1,4-isoprene)
Authors: Bode Helge B. , Zeeck Axel , Plückhahn Kirsten , Jendrossek Dieter 
Published: July 2002

ABSTRACT

Streptomyces coelicolor
1A and
Pseudomonas citronellolis
were able to degrade synthetic high-molecular-weight poly(
cis
-1,4-isoprene) and vulcanized natural rubber. Growth on the polymers was poor but significantly greater than that of the nondegrading strain
Streptomyces lividans
1326 (control). Measurement of the molecular weight distribution of the polymer before and after degradation showed a time-dependent increase in low-molecular-weight polymer molecules for
S. coelicolor
1A and
P. citronellolis
, whereas the molecular weight distribution for the control (
S. lividans
1326) remained almost constant. Three degradation products were isolated from the culture fluid of
S. coelicolor
1A grown on vulcanized rubber and were identified as (
6Z
)-2,6-dimethyl-10-oxo-undec-6-enoic acid, (
5Z
)-6-methyl-undec-5-ene-2,9-dione, and (
5Z
,
9Z
)-6,10-dimethyl-pentadec-5,9-diene-2,13-dione. An oxidative pathway from poly(
cis
-1,4-isoprene) to methyl-branched diketones is proposed. It includes (i) oxidation of an aldehyde intermediate to a carboxylic acid, (ii) one cycle of β-oxidation, (iii) oxidation of the conjugated double bond resulting in a β-keto acid, and (iv) decarboxylation.
Microbial Activity in Aquatic Environments Measured by Dimethyl Sulfoxide Reduction and Intercomparison with Commonly Used Methods
Authors: Griebler Christian , Slezak Doris 
Published: July 2002

ABSTRACTA new method to determine microbial (bacterial and fungal) activity in various freshwater habitats is described. Based on microbial reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), our DMSO reduction method allows measurement of the respiratory activity in interstitial water, as well as in the water column. DMSO is added to water samples at a concentration (0.75% [vol/vol] or 106 mM) high enough to compete with other naturally occurring electron acceptors, as determined with oxygen and nitrate, without stimulating or inhibiting microbial activity. Addition of NaN3, KCN, and formaldehyde, as well as autoclaving, inhibited the production of DMS, which proves that the reduction of DMSO is a biotic process. DMSO reduction is readily detectable via the formation of DMS even at low microbial activities. All water samples showed significant DMSO reduction over several hours. Microbially reduced DMSO is recovered in the form of DMS from water samples by a purge and trap system and is quantified by gas chromatography and detection with a flame photometric detector. The DMSO reduction method was compared with other methods commonly used for assessment of microbial activity. DMSO reduction activity correlated well with bacterial production in predator-free batch cultures. Cell-production-specific DMSO reduction rates did not differ significantly in batch cultures with different nutrient regimes but were different in different growth phases. Overall, a cell-production-specific DMSO reduction rate of 1.26 × 10−17± 0.12 × 10−17mol of DMS per produced cell (mean ± standard error;R2= 0.78) was calculated. We suggest that the relationship of DMSO reduction rates to thymidine and leucine incorporation is linear (theR2values ranged from 0.783 to 0.944), whereas there is an exponential relationship between DMSO reduction rates and glucose uptake, as well as incorporation (theR2values ranged from 0.821 to 0.931). Based on our results, we conclude that the DMSO reduction method is a nonradioactive alternative to other methods commonly used to assess microbial activity.
Isolation and Characterization of Five
Erwinia amylovora
Bacteriophages and Assessment of Phage Resistance in Strains of
Erwinia amylovora
Authors: Schnabel Elise L. , Jones Alan L. 
Published: July 2002

ABSTRACT

Phages able to infect the fire blight pathogen
Erwinia amylovora
were isolated from apple, pear, and raspberry tissues and from soil samples collected at sites displaying fire blight symptoms. Among a collection of 50 phage isolates, 5 distinct phages, including relatives of the previously described phages φEa1 and φEa7 and 3 novel phages named φEa100, φEa125, and φEa116C, were identified based on differences in genome size and restriction fragment pattern. φEa1, the phage distributed most widely, had an approximately 46-kb genome which exhibited some restriction site variability between isolates. Phages φEa100, φEa7, and φEa125 each had genomes of approximately 35 kb and could be distinguished by their
Eco
RI restriction fragment patterns. φEa116C contained an approximately 75-kb genome. φEa1, φEa7, φEa100, φEa125, and φEa116C were able to infect 39, 36, 16, 20, and 40, respectively, of 40
E. amylovora
strains isolated from apple orchards in Michigan and 8, 12, 10, 10, and 12, respectively, of 12
E. amylovora
strains isolated from raspberry fields (
Rubus
spp.) in Michigan. Only 22 of 52 strains were sensitive to all five phages, and 23 strains exhibited resistance to more than one phage. φEa116C was more effective than the other phages at lysing
E. amylovora
strain Ea110 in liquid culture, reducing the final titer of Ea110 by >95% when added at a ratio of 1 PFU per 10 CFU and by 58 to 90% at 1 PFU per 10
5
CFU.
Bacteria
and
Archaea
Physically Associated with Gulf of Mexico Gas Hydrates
Authors: Lanoil Brian D. , Sassen Roger , La Duc Myron T. , Sweet Stephen T. , Nealson Kenneth H. 
Published: July 2002

ABSTRACT

Although there is significant interest in the potential interactions of microbes with gas hydrate, no direct physical association between them has been demonstrated. We examined several intact samples of naturally occurring gas hydrate from the Gulf of Mexico for evidence of microbes. All samples were collected from anaerobic hemipelagic mud within the gas hydrate stability zone, at water depths in the ca. 540- to 2,000-m range. The δ
13
C of hydrate-bound methane varied from −45.1‰ Peedee belemnite (PDB) to −74.7‰ PDB, reflecting different gas origins. Stable isotope composition data indicated microbial consumption of methane or propane in some of the samples. Evidence of the presence of microbes was initially determined by 4,6-diamidino 2-phenylindole dihydrochloride (DAPI) total direct counts of hydrate-associated sediments (mean = 1.5 × 10
9
cells g
−1
) and gas hydrate (mean = 1.0 × 10
6
cells ml
−1
). Small-subunit rRNA phylogenetic characterization was performed to assess the composition of the microbial community in one gas hydrate sample (AT425) that had no detectable associated sediment and showed evidence of microbial methane consumption.
Bacteria
were moderately diverse within AT425 and were dominated by gene sequences related to several groups of
Proteobacteria
, as well as
Actinobacteria
and low-G + C
Firmicutes
. In contrast, there was low diversity of
Archaea
, nearly all of which were related to methanogenic
Archaea
, with the majority specifically related to
Methanosaeta
spp. The results of this study suggest that there is a direct association between microbes and gas hydrate, a finding that may have significance for hydrocarbon flux into the Gulf of Mexico and for life in extreme environments.
Sorption of Fe (Hydr)Oxides to the Surface of
Shewanella putrefaciens
: Cell-Bound Fine-Grained Minerals Are Not Always Formed De Novo
Authors: Glasauer S. , Langley S. , Beveridge T. J. 
Published: July 2002

ABSTRACT

Shewanella putrefaciens
, a gram-negative, facultative anaerobe, is active in the cycling of iron through its interaction with Fe (hydr)oxides in natural environments. Fine-grained Fe precipitates that are attached to the outer membranes of many gram-negative bacteria have most often been attributed to precipitation and growth of the mineral at the cell surface. Our study of the sorption of nonbiogenic Fe (hydr)oxides revealed, however, that large quantities of nanometer-scale ferrihydrite (hydrous ferric oxide), goethite (α-FeOOH), and hematite (α-Fe
2
O
3
) adhered to the cell surface. Attempts to separate suspensions of cells and minerals with an 80% glycerin cushion proved that the sorbed minerals were tightly attached to the bacteria. The interaction between minerals and cells resulted in the formation of mineral-cell aggregates, which increased biomass density and provided better sedimentation of mineral Fe compared to suspensions of minerals alone. Transmission electron microscopy observations of cells prepared by whole-mount, conventional embedding, and freeze-substitution methods confirmed the close association between cells and minerals and suggested that in some instances, the mineral crystals had even penetrated the outer membrane and peptidoglycan layers. Given the abundance of these mineral types in natural environments, the data suggest that not all naturally occurring cell surface-associated minerals are necessarily formed de novo on the cell wall.
Comparative Study of the Cyclization Reactions of Three Bacterial Cyclomaltodextrin Glucanotransferases
Authors: Terada Yoshinobu , Sanbe Haruyo , Takaha Takeshi , Kitahata Sumio , Koizumi Kyoko , Okada Shigetaka 
Published: July 2002

ABSTRACT

The actions of cyclomaltodextrin glucanotransferases (CGTase; EC
2.4.1.19
) from alkalophilic
Bacillus
sp. strain A2-5a (A2-5a CGTase),
Bacillus macerans
(
Bmac
CGTase), and
Bacillus stearothermophilus
(
Bste
CGTase) on amylose were investigated. All three enzymes produced large cyclic α-1,4-glucans (cycloamyloses) at the early stage of the reaction, but these were subsequently converted into smaller cycloamyloses. However, the rates of this conversion differed among the three enzymes. The product specificity of each CGTase in the cyclization reaction was determined by measuring the amount of each cycloamylose from CD6 to CD31 (CD
n
, a cycloamylose with a degree of polymerization of
n
). A2-5a CGTase produced 10 times more CD7, while
Bmac
CGTase produced 34 times more CD6 than other cycloamyloses.
Bste
CGTase produced 12 and 3 times more CD6 and CD7 than other cycloamyloses, respectively. The substrate specificities of the linearization reactions of CD6, CD7, CD8, and larger cycloamyloses (a mixture of CD22 to CD50) were investigated, and we found that CD7 and CD8 are extremely poor substrates for both hydrolytic and transglycosidic linearization (coupling) reactions while larger cycloamyloses are linearized at a much higher rate. By repeating these cyclization and linearization reactions, the larger cycloamyloses initially produced are converted into smaller cycloamyloses and finally into mainly CD6, CD7, and CD8. These three enzymes also differ in their hydrolytic activities, which seem to accelerate the conversion of larger cycloamyloses into smaller cycloamyloses.
Growth Interactions during Bacterial Colonization of Seedling Rootlets
Authors: De Bellis P. , Ercolani G. L. 
Published: July 2002

ABSTRACT

Rootlet elongation and bacterial growth on rootlets were determined after inoculation of cucumber and spinach seedlings with
Pseudomonas
strains differing in production of siderophores and HCN. Siderophore producers grew more profusely than nonproducers on both species and promoted rootlet elongation on cucumber. Coinoculation of siderophore producers and nonproducers resulted in restricted growth of the latter. The total populations of nonproducers of HCN in the presence of HCN producers were not decreased, but the tenacity of their association with the rootlet surface was altered.
Selection of Specific Endophytic Bacterial Genotypes by Plants in Response to Soil Contamination
Authors: Siciliano Steven D. , Fortin Nathalie , Mihoc Anca , Wisse Gesine , Labelle Suzanne , Beaumier Danielle , Ouellette Danielle , Roy Real , Whyte Lyle G. , Banks M. Kathy , Schwab Paul , Lee Ken , Greer Charles W. 
Published: July 2002

ABSTRACT

Plant-bacterial combinations can increase contaminant degradation in the rhizosphere, but the role played by indigenous root-associated bacteria during plant growth in contaminated soils is unclear. The purpose of this study was to determine if plants had the ability to selectively enhance the prevalence of endophytes containing pollutant catabolic genes in unrelated environments contaminated with different pollutants. At petroleum hydrocarbon contaminated sites, two genes encoding hydrocarbon degradation, alkane monooxygenase (
alkB
) and naphthalene dioxygenase (
ndoB
), were two and four times more prevalent in bacteria extracted from the root interior (endophytic) than from the bulk soil and sediment, respectively. In field sites contaminated with nitroaromatics, two genes encoding nitrotoluene degradation, 2-nitrotoluene reductase (
ntdAa
) and nitrotoluene monooxygenase (
ntnM
), were 7 to 14 times more prevalent in endophytic bacteria. The addition of petroleum to sediment doubled the prevalence of
ndoB
-positive endophytes in
Scirpus pungens
, indicating that the numbers of endophytes containing catabolic genotypes were dependent on the presence and concentration of contaminants. Similarly, the numbers of
alkB
- or
ndoB
-positive endophytes in
Festuca arundinacea
were correlated with the concentration of creosote in the soil but not with the numbers of
alkB
- or
ndoB
-positive bacteria in the bulk soil. Our results indicate that the enrichment of catabolic genotypes in the root interior is both plant and contaminant dependent.
Cloning and Expression of the Benzoate Dioxygenase Genes from
Rhodococcus
sp. Strain 19070
Authors: Haddad Sandra , Eby D. Matthew , Neidle Ellen L. 
Published: July 2002

ABSTRACT

The
bopXYZ
genes from the gram-positive bacterium
Rhodococcus
sp. strain 19070 encode a broad-substrate-specific benzoate dioxygenase. Expression of the BopXY terminal oxygenase enabled
Escherichia coli
to convert benzoate or anthranilate (2-aminobenzoate) to a nonaromatic
cis
-diol or catechol, respectively. This expression system also rapidly transformed
m
-toluate (3-methylbenzoate) to an unidentified product. In contrast, 2-chlorobenzoate was not a good substrate. The BopXYZ dioxygenase was homologous to the chromosomally encoded benzoate dioxygenase (BenABC) and the plasmid-encoded toluate dioxygenase (XylXYZ) of gram-negative acinetobacters and pseudomonads. Pulsed-field gel electrophoresis failed to identify any plasmid in
Rhodococcus
sp. strain 19070. Catechol 1,2- and 2,3-dioxygenase activity indicated that strain 19070 possesses both
meta
- and
ortho
-cleavage degradative pathways, which are associated in pseudomonads with the
xyl
and
ben
genes, respectively. Open reading frames downstream of
bopXYZ
, designated
bopL
and
bopK
, resembled genes encoding
cis
-diol dehydrogenases and benzoate transporters, respectively. The
bop
genes were in the same order as the chromosomal
ben
genes of
P. putida
PRS2000. The deduced sequences of BopXY were 50 to 60% identical to the corresponding proteins of benzoate and toluate dioxygenases. The reductase components of these latter dioxygenases, BenC and XylZ, are 201 residues shorter than the deduced BopZ sequence. As predicted from the sequence, expression of BopZ in
E. coli
yielded an approximately 60-kDa protein whose presence corresponded to increased cytochrome
c
reductase activity. While the N-terminal region of BopZ was approximately 50% identical in sequence to the entire BenC or XylZ reductases, the C terminus was unlike other known protein sequences.