bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composition of Soil Microbial Communities Enriched on a Mixture of Aromatic Hydrocarbons
Authors: Greene E. Anne , Kay Jason G. , Jaber Karim , Stehmeier Les G. , Voordouw Gerrit 
Published: July 2002

ABSTRACT

Soil contaminated with C5+, which contained benzene (45%, wt/wt), dicyclopentadiene (DCPD) plus cyclopentadiene (together 20%), toluene (6%), styrene (3%), xylenes (2%), naphthalene (2%), and smaller quantities of other compounds, served as the source for isolation of 55 genomically distinct bacteria (standards). Use of benzene as a substrate by these bacteria was most widespread (31 of 44 standards tested), followed by toluene (23 of 44), xylenes (14 of 44), styrene (10 of 44), and naphthalene (10 of 44). Master filters containing denatured genomic DNAs of all 55 standards were used to analyze the community compositions of C5+ enrichment cultures by reverse sample genome probing (RSGP). The communities enriched from three contaminated soils were similar to those enriched from three uncontaminated soils from the same site. The compositions of these communities were time dependent and showed a succession of
Pseudomonas
and
Rhodococcus
spp. before convergence on a composition dominated by
Alcaligenes
spp. The dominant community members detected by RSGP were capable of benzene degradation at all stages of succession. The enrichments effectively degraded all C5+ components except DCPD. Overall, degradation of individual C5+ hydrocarbons followed first-order kinetics, with the highest rates of removal for benzene.
Characterization of the Protocatechuic Acid Catabolic Gene Cluster from
Streptomyces
sp. Strain 2065
Authors: Iwagami Sakura G. , Yang Keqian , Davies Julian 
Published: July 2002

ABSTRACT

Protocatechuate 3,4-dioxygenase (EC
1.13.11.3
) catalyzes the ring cleavage step in the catabolism of aromatic compounds through the protocatechuate branch of the β-ketoadipate pathway. A protocatechuate 3,4-dioxygenase was purified from
Streptomyces
sp. strain 2065 grown in
p
-hydroxybenzoate, and the N-terminal sequences of the β- and α-subunits were obtained. PCR amplification was used for the cloning of the corresponding genes, and DNA sequencing of the flanking regions showed that the
pcaGH
genes belonged to a 6.5-kb protocatechuate catabolic gene cluster; at least seven genes in the order
pcaIJFHGBL
appear to be transcribed unidirectionally. Analysis of the cluster revealed the presence of a
pcaL
homologue which encodes a fused γ-carboxymuconolactone decarboxylase/β-ketoadipate enol-lactone hydrolase previously identified in the
pca
gene cluster from
Rhodococcus opacus
1CP. The
pcaIJ
genes encoded proteins with a striking similarity to succinyl-coenzyme A (CoA):3-oxoacid CoA transferases of eukaryotes and contained an indel which is strikingly similar between high-G+C gram-positive bacteria and eukaryotes.
Genetic Diversity among
Arthrobacter
Species Collected across a Heterogeneous Series of Terrestrial Deep-Subsurface Sediments as Determined on the Basis of 16S rRNA and
recA
Gene Sequences
Authors: van Waasbergen Lorraine G. , Balkwill David L. , Crocker Fiona H. , Bjornstad Bruce N. , Miller Robert V. 
Published: July 2002

ABSTRACT

This study was undertaken in an effort to understand how the population structure of bacteria within terrestrial deep-subsurface environments correlates with the physical and chemical structure of their environment. Phylogenetic analysis was performed on strains of
Arthrobacter
that were collected from various depths, which included a number of different sedimentary units from the Yakima Barricade borehole at the U.S. Department of Energy's Hanford site, Washington, in August 1992. At the same time that bacteria were isolated, detailed information on the physical, chemical, and microbiological characteristics of the sediments was collected. Phylogenetic trees were prepared from the 39 deep-subsurface
Arthrobacter
isolates (as well as 17 related type strains) based on 16S rRNA and
recA
gene sequences. Analyses based on each gene independently were in general agreement. These analyses showed that, for all but one of the strata (sedimentary layers characterized by their own unifying lithologic composition), the deep-subsurface isolates from the same stratum are largely monophyletic. Notably, the layers for which this is true were composed of impermeable sediments. This suggests that the populations within each of these strata have remained isolated under constant, uniform conditions, which have selected for a particular dominant genotype in each stratum. Conversely, the few strains isolated from a gravel-rich layer appeared along several lineages. This suggests that the higher-permeability gravel decreases the degree of isolation of this population (through greater groundwater flow), creating fluctuations in environmental conditions or allowing migration, such that a dominant population has not been established. No correlation was seen between the relationship of the strains and any particular chemical or physical characteristics of the sediments. Thus, this work suggests that within sedimentary deep-subsurface environments, permeability of the deposits plays a major role in determining the genetic structure of resident bacterial populations.
Phylogenetic Diversity of Bacteria Associated with the Marine Sponge
Rhopaloeides odorabile
Authors: Webster Nicole S. , Wilson Kate J. , Blackall Linda L. , Hill Russell T. 
Published: July 2002

ABSTRACT

Molecular techniques were employed to document the microbial diversity associated with the marine sponge
Rhopaloeides odorabile
. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the
Actinobacteria
, low-G+C gram-positive bacteria, the β- and γ-subdivisions of the
Proteobacteria
,
Cytophaga/Flavobacterium
, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in
R. odorabile.
High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge.
Fluorescent Acid-Fast Microscopy for Measuring Phagocytosis of
Mycobacterium avium
,
Mycobacterium intracellulare
, and
Mycobacterium scrofulaceum
by
Tetrahymena pyriformis
and Their Intracellular Growth
Authors: Strahl Eileen D. , Gillaspy Glenda E. , Falkinham Joseph O. 
Published: July 2002

ABSTRACT

Fluorescent acid-fast microscopy (FAM) was used to enumerate intracellular
Mycobacterium avium
,
Mycobacterium intracellulare
, and
Mycobacterium scrofulaceum
in the ciliated phagocytic protozoan
Tetrahymena pyriformis
. There was a linear relationship between FAM and colony counts of
M. avium
cells both from cultures and within protozoa. The Ziehl-Neelsen acid-fast stain could not be used to enumerate intracellular mycobacteria because uninfected protozoa contained acid-fast, bacterium-like particles. Starved, 7-day-old cultures of
T. pyriformis
transferred into fresh medium readily phagocytized
M. avium
,
M. intracellulare
, and
M. scrofulaceum
. Phagocytosis was rapid and reached a maximum in 30 min.
M. avium
,
M. intracellulare
, and
M. scrofulaceum
grew within
T. pyriformis
, increasing by factors of 4- to 40-fold after 5 days at 30°C. Intracellular
M. avium
numbers remained constant over a 25-day period of growth (by transfer) of
T. pyriformis
. Intracellular
M. avium
cells also survived protozoan encystment and germination. The growth and viability of
T. pyriformis
were not affected by mycobacterial infection. The results suggest that free-living phagocytic protozoa may be natural hosts and reservoirs for
M. avium
,
M. intracellulare
, and
M. scrofulaceum
.
Signature Lipids and Stable Carbon Isotope Analyses of Octopus Spring Hyperthermophilic Communities Compared with Those of
Aquificales
Representatives
Authors: Jahnke Linda L. , Eder Wolfgang , Huber Robert , Hope Janet M. , Hinrichs Kai-Uwe , Hayes John M. , Des Marais David J. , Cady Sherry L. , Summons Roger E. 
Published: July 2002

ABSTRACT

The molecular and isotopic compositions of lipid biomarkers of cultured
Aquificales
genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from Octopus Spring.
Thermocrinis ruber
,
Thermocrinis
sp. strain HI 11/12,
Hydrogenobacter
thermophilus
TK-6,
Aquifex pyrophilus
, and
Aquifex aeolicus
all contained glycerol-ether phospholipids as well as acyl glycerides. The
n
-C
20:1
and
cy
-C
21
fatty acids dominated all of the
Aquificales
, while the alkyl glycerol ethers were mainly C
18:0
. These
Aquificales
biomarkers were major constituents of the lipid extracts of two Octopus Spring samples, a biofilm associated with the siliceous vent walls, and the well-known pink streamer community (PSC). Both the biofilm and the PSC contained mono- and dialkyl glycerol ethers in which C
18
and C
20
alkyl groups were prevalent. Phospholipid fatty acids included both the
Aquificales n
-C
20:1
and
cy
-C
21
, plus a series of
iso
-branched fatty acids (
i
-C
15:0
to
i
-C
21:0
), indicating an additional bacterial component. Biomass and lipids from the PSC were depleted in
13
C relative to source water CO
2
by 10.9 and 17.2‰, respectively. The C
20–21
fatty acids of the PSC were less depleted than the
iso
-branched fatty acids, 18.4 and 22.6‰, respectively. The biomass of
T. ruber
grown on CO
2
was depleted in
13
C by only 3.3‰ relative to C source. In contrast, biomass was depleted by 19.7‰ when formate was the C source. Independent of carbon source,
T. ruber
lipids were heavier than biomass (+1.3‰). The depletion in the C
20–21
fatty acids from the PSC indicates that
Thermocrinis
biomass must be similarly depleted and too light to be explained by growth on CO
2
. Accordingly,
Thermocrinis
in the PSC is likely to have utilized formate, presumably generated in the spring source region.
Effect of Solar UV-B Radiation on a Phyllosphere Bacterial Community
Authors: Jacobs Janette L. , Sundin George W. 
Published: July 2002

ABSTRACT

The effect of solar UV-B radiation on the population dynamics and composition of the culturable bacterial community from peanut (
Arachis
hypogeae
L.) was examined in field studies using plants grown under UV-B−transmitting (UV-B+) or UV-B−excluding (UV-B−) plastic filters. Our data demonstrate that solar UV-B selection alters phyllosphere bacterial community composition and that UV tolerance is a prevalent phenotype late in the season. The total bacterial population size was not affected by either UV-B treatment. However, isolates from the UV-B+ plots (
n
= 368) were significantly more UV tolerant than those from the UV-B− (
n
= 363) plots. UV sensitivity was determined as the minimal inhibitory dose of UV that resulted in an inhibition of growth compared to the growth of a nonirradiated control. The difference in minimal inhibitory doses among bacterial isolates from UV-B+ and UV-B− treatments was mainly partitioned among nonpigmented isolates, with pigmented isolates as a group being characterized as UV tolerant. A large increase in UV tolerance was observed within isolate groups collected late (89 and 96 days after planting) in the season. Identification of 200 late-season isolates indicated that the predominant UV-tolerant members of this group were
Bacillus
coagulans
,
Clavibacter
michiganensis
, and
Curtobacterium
flaccumfaciens
. We selected
C
.
michiganensis
as a model UV-tolerant epiphyte to study if cell survival on UV-irradiated peanut leaves was increased relative to UV survival in vitro. The results showed an enhancement in the survival of
C
.
michiganensis
G7.1, especially following high UV-C doses (300 and 375 J m
−2
), that was evident between 24 and 96 h after inoculation. A dramatic increase in the in planta/in vitro survival ratio was observed over the entire 96-h experiment period for
C
.
michiganensis
T5.1.
Differential Synthesis of Peritoxins and Precursors by Pathogenic Strains of the Fungus
Periconia circinata
Authors: Churchill Alice C. L. , Dunkle Larry D. , Silbert Walter , Kennedy Kevin J. , Macko Vlado 
Published: July 2002

ABSTRACT

Pathogenic strains of the soilborne fungus
Periconia circinata
produce peritoxins with host-selective toxicity against susceptible genotypes of sorghum. The peritoxins are low-molecular-weight, hybrid molecules consisting of a peptide and a chlorinated polyketide. Culture fluids from pathogenic, toxin-producing (Tox
+
) and nonpathogenic, non-toxin-producing (Tox
−
) strains were analyzed directly by gradient high-performance liquid chromatography (HPLC) with photodiode array detection and HPLC-mass spectrometry to detect intermediates and final products of the biosynthetic pathway. This approach allowed us to compare the metabolite profiles of Tox
+
and Tox
−
strains. Peritoxins A and B and the biologically inactive intermediates,
N
-3-(
E
-pentenyl)-glutaroyl-aspartate, circinatin, and 7-chlorocircinatin, were detected only in culture fluids of the Tox
+
strains. The latter two compounds were produced consistently by Tox
+
strains regardless of the amount of peritoxins produced under various culture conditions. In summary, none of the known peritoxin-related metabolites were detected in Tox
−
strains, which suggests that these strains may lack one or more functional genes required for peritoxin biosynthesis.
Production of Capsular Polysaccharide of
Streptococcus pneumoniae
Type 14 and Its Purification by Affinity Chromatography
Authors: Suárez Norma , Fraguas Laura Franco , Texeira Esther , Massaldi Hugo , Batista-Viera Francisco , Ferreira Fernando 
Published: July 2002

ABSTRACT

We describe a rapid and efficient method for producing the capsular polysaccharide of
Streptococcus pneumoniae
by fermentation on tryptic soy broth and purification of this compound by using immobilized soybean lectin as an affinity adsorbent. In principle, the same strategy can be used to produce purified capsular polysaccharides from other streptococcal serotypes by selecting the appropriate lectin adsorbents.
Rapid Method of Determining Factors Limiting Bacterial Growth in Soil
Authors: Aldén L. , Demoling F. , Bååth E. 
Published: July 2002

ABSTRACT
A technique to determine which nutrients limit bacterial growth in soil was developed. The method was based on measuring the thymidine incorporation rate of bacteria after the addition of C, N, and P in different combinations to soil samples. First, the thymidine incorporation method was tested in two different soils: an agricultural soil and a forest humus soil. Carbon (as glucose) was found to be the limiting substance for bacterial growth in both of these soils. The effect of adding different amounts of nutrients was studied, and tests were performed to determine whether the additions affected the soil pH and subsequent bacterial activity. The incubation time required to detect bacterial growth after adding substrate to the soil was also evaluated. Second, the method was used in experiments in which three different size fractions of straw (1 to 2, 0.25 to 1, and <0.25 mm) were mixed into the agricultural soil in order to induce N limitation for bacterial growth. When the straw fraction was small enough (<0.25 mm), N became the limiting nutrient for bacterial growth after about 3 weeks. After the addition of the larger straw fractions (1 to 2 and 0.25 to 1 mm), the soil bacteria were C limited throughout the incubation period (10 weeks), although an increase in the thymidine incorporation rate after the addition of C and N together compared with adding them separately was seen in the sample containing the size fraction from 0.25 to 1 mm. Third, soils from high-pH, limestone-rich areas were examined. P limitation was observed in one of these soils, while tendencies toward P limitation were seen in some of the other soils.
Yeast Population Dynamics during the Fermentation and Biological Aging of Sherry Wines
Authors: Esteve-Zarzoso B. , Peris-Torán M. J. , Garcı́a-Maiquez E. , Uruburu F. , Querol A. 
Published: July 2002

ABSTRACTMolecular and physiological analyses were used to study the evolution of the yeast population, from alcoholic fermentation to biological aging in the process of “fino” sherry wine making. The four races of “flor”Saccharomyces cerevisiae (beticus, cheresiensis, montuliensis, androuxii) exhibited identical restriction patterns for the region spanning the internal transcribed spacers 1 and 2 (ITS-1 and ITS-2) and the 5.8S rRNA gene, but this pattern was different, from those exhibited by non-florS. cerevisiaestrains. This flor-specific pattern was detected only after wines were fortified, never during alcoholic fermentation, and all the strains isolated from the velum exhibited the typical flor yeast pattern. By restriction fragment length polymorphism of mitochondrial DNA and karyotyping, we showed that (i) the native strain is better adapted to fermentation conditions than commercial strains; (ii) two different populations ofS. cerevisiaestrains are involved in the process of elaboration, of fino sherry wine, one of which is responsible for must fermentation and the other, for wine aging; and (iii) one strain was dominant in the flor population integrating the velum from sherry wines produced in González Byass wineries, although other authors have described a succession of races of florS. cerevisiaeduring wine aging. Analyzing all these results together, we conclude that yeast population dynamics during biological aging is a complex phenomenon and differences between yeast populations from different wineries can be observed.
Dissimilatory Nitrite Reductase Genes from Autotrophic Ammonia-Oxidizing Bacteria
Authors: Casciotti Karen L. , Ward Bess B. 
Published: July 2002

ABSTRACT

The presence of a copper-containing dissimilatory nitrite reductase gene (
nirK
) was discovered in several isolates of β-subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published
nirK
sequences from denitrifying bacteria and used to amplify a 540-bp fragment of the
nirK
gene from
Nitrosomonas marina
and five additional isolates of ammonia-oxidizing bacteria. Amplification products of the expected size were cloned and sequenced. Alignment of the nucleic acid and deduced amino acid (AA) sequences shows significant similarity (62 to 75% DNA, 58 to 76% AA) between nitrite reductases present in these nitrifiers and the copper-containing nitrite reductase found in classic heterotrophic denitrifiers. While the presence of a nitrite reductase in
Nitrosomonas europaea
is known from early biochemical work, preliminary sequence data from its genome indicate a rather low similarity to the denitrifier
nirK
s. Phylogenetic analysis of the partial nitrifier
nirK
sequences indicates that the topology of the
nirK
tree corresponds to the 16S rRNA and
amoA
trees. While the role of nitrite reduction in the metabolism of nitrifying bacteria is still uncertain, these data show that the
nirK
gene is present in closely related nitrifying isolates from many oceanographic regions and suggest that
nirK
sequences retrieved from the environment may include sequences from ammonia-oxidizing bacteria.
Microarray Analysis of Microbial Virulence Factors
Authors: Chizhikov Vladimir , Rasooly Avraham , Chumakov Konstantin , Levy Dan D. 
Published: July 2002

ABSTRACT

Hybridization with oligonucleotide microchips (microarrays) was used for discrimination among strains of
Escherichia coli
and other pathogenic enteric bacteria harboring various virulence factors. Oligonucleotide microchips are miniature arrays of gene-specific oligonucleotide probes immobilized on a glass surface. The combination of this technique with the amplification of genetic material by PCR is a powerful tool for the detection of and simultaneous discrimination among food-borne human pathogens. The presence of six genes (
eaeA
,
slt-I
,
slt-II
,
fliC
,
rfbE
, and
ipaH
) encoding bacterial antigenic determinants and virulence factors of bacterial strains was monitored by multiplex PCR followed by hybridization of the denatured PCR product to the gene-specific oligonucleotides on the microchip. The assay was able to detect these virulence factors in 15
Salmonella
,
Shigella
, and
E. coli
strains. The results of the chip analysis were confirmed by hybridization of radiolabeled gene-specific probes to genomic DNA from bacterial colonies. In contrast, gel electrophoretic analysis of the multiplex PCR products used for the microarray analysis produced ambiguous results due to the presence of unexpected and uncharacterized bands. Our results suggest that microarray analysis of microbial virulence factors might be very useful for automated identification and characterization of bacterial pathogens.
Effects of Pressure-Induced Membrane Phase Transitions on Inactivation of HorA, an ATP-Dependent Multidrug Resistance Transporter, in
Lactobacillus plantarum
Authors: Ulmer H. M. , Herberhold H. , Fahsel S. , Gänzle M. G. , Winter R. , Vogel R. F. 
Published: July 2002

ABSTRACT

The effects of pressure on cultures of
Lactobacillus plantarum
were characterized by determination of the viability and activity of HorA, an ATP-binding cassette multidrug resistance transporter. Changes in the membrane composition of
L. plantarum
induced by different growth temperatures were determined. Furthermore, the effect of the growth temperature of a culture on pressure inactivation at 200 MPa was determined. Cells were characterized by plate counts on selective and nonselective agar after pressure treatment, and HorA activity was measured by ethidium bromide efflux. Fourier transform-infrared spectroscopy and Laurdan fluorescence spectroscopy provided information about the thermodynamic phase state of the cytoplasmic membrane during pressure treatment. A pressure-temperature diagram for cell membranes was established. Cells grown at 37°C and pressure treated at 15°C lost >99% of HorA activity and viable cell counts within 36 and 120 min, respectively. The membranes of these cells were in the gel phase region at ambient pressure. In contrast, cells grown at 15°C and pressure treated at 37°C lost >99% of HorA activity and viable cell counts within 4 and 8 min, respectively. The membranes of these cells were in the liquid crystalline phase region at ambient pressure. The kinetic analysis of inactivation of
L. plantarum
provided further evidence that inactivation of HorA is a crucial step during pressure-induced cell death. Comparison of the biological findings and the membrane state during pressure treatment led to the conclusion that the inactivation of cells and membrane enzymes strongly depends on the thermodynamic properties of the membrane. Pressure treatment of cells with a liquid crystalline membrane at 0.1 MPa resulted in HorA inactivation and cell death more rapid than those of cells with a gel phase membrane at 0.1 MPa.