bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat
Authors: McSpadden Gardener Brian B. , Weller David M. 
Published: July 2002

ABSTRACT

Take-all, caused by
Gaeumannomyces
graminis
var.
tritici
, is one of the most important fungal diseases of wheat worldwide. Knowing that microbe-based suppression of the disease occurs in monoculture wheat fields following severe outbreaks of take-all, we analyzed the changes in rhizosphere bacterial communities following infection by the take-all pathogen. Several bacterial populations were more abundant on diseased plants than on healthy plants, as indicated by higher counts on a
Pseudomonas
-selective medium and a higher fluorescence signal in terminal restriction fragment length polymorphism analyses of amplified 16S ribosomal DNA (rDNA). Amplified rDNA restriction analysis (ARDRA) of the most abundant cultured populations showed a shift in dominance from
Pseudomonas
to
Chryseobacterium
species in the rhizosphere of diseased plants. Fluorescence-tagged ARDRA of uncultured rhizosphere washes revealed an increase in ribotypes corresponding to several bacterial genera, including those subsequently identified by partial 16S sequencing as belonging to species of alpha-, beta-, and gamma-proteobacteria, sphingobacteria, and flavobacteria. The functional significance of some of these populations was investigated in vitro. Of those isolated, only a small subset of the most abundant
Pseudomonas
spp. and a
phlD

+

Pseudomonas
sp. showed any significant ability to inhibit
G.
graminis
var.
tritici
directly. When cultured strains were mixed with the inhibitory
phlD

+

Pseudomonas
strain, the
Chryseobacterium
isolates showed the least capacity to inhibit this antagonist of the pathogen, indicating that increases in
Chryseobacterium
populations may facilitate the suppression of take-all by 2,4-diacetylphloroglucinol-producing
phlD

+

pseudomonads.
Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes for Ecological Studies of Methanotrophic Bacteria
Authors: Gulledge Jay , Ahmad Azeem , Steudler Paul A. , Pomerantz William J. , Cavanaugh Colleen M. 
Published: July 2002

ABSTRACT

Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family
Methylocystaceae
(type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family,
Methylocystis
and
Methylosinus
, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family
Methylococcaceae
(type I/X methanotrophs). The remaining probes target members of individual genera of the
Methylococcaceae
, including
Methylobacter
,
Methylomonas
,
Methylomicrobium
,
Methylococcus
, and
Methylocaldum
. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus
Methylosarcina
gen. nov. are covered by a probe that otherwise targets only members of the closely related genus
Methylomicrobium
. None of the probes covers strains of the newly proposed genera
Methylocella
and “
Methylothermus
,” which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57°C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.
Fluorescent Amplified Fragment Length Polymorphism Analysis of Norwegian
Bacillus cereus
and
Bacillus thuringiensis
Soil Isolates
Authors: Ticknor Lawrence O. , Kolstø Anne-Brit , Hill Karen K. , Keim Paul , Laker Miriam T. , Tonks Melinda , Jackson Paul J. 
Published: July 2002

ABSTRACT

We examined 154 Norwegian
B. cereus
and
B. thuringiensis
soil isolates (collected from five different locations), 8
B. cereus
and 2
B. thuringiensis
reference strains, and 2
Bacillus anthracis
strains by using fluorescent amplified fragment length polymorphism (AFLP). We employed a novel fragment identification approach based on a hierarchical agglomerative clustering routine that identifies fragments in an automated fashion. No method is free of error, and we identified the major sources so that experiments can be designed to minimize its effect. Phylogenetic analysis of the fluorescent AFLP results reveals five genetic groups in these group 1 bacilli. The ATCC reference strains were restricted to two of the genetic groups, clearly not representative of the diversity in these bacteria. Both
B. anthracis
strains analyzed were closely related and affiliated with a
B. cereus
milk isolate (ATCC 4342) and a
B. cereus
human pathogenic strain (periodontitis). Across the entire study, pathogenic strains, including
B. anthracis
, were more closely related to one another than to the environmental isolates. Eight strains representing the five distinct phylogenetic clusters were further analyzed by comparison of their 16S rRNA gene sequences to confirm the phylogenetic status of these groups. This analysis was consistent with the AFLP analysis, although of much lower resolution. The innovation of automated genotype analysis by using a replicated and statistical approach to fragment identification will allow very large sample analyses in the future.
Assessing the Diversity of Marine Bacterial β-Glucosidases by Capillary Electrophoresis Zymography
Authors: Arrieta Jesús M. , Herndl Gerhard J. 
Published: July 2002

ABSTRACT
We propose a new method for the fast separation and detection of β-glucosidases in environmental samples. With this approach, β-glucosidases extracted from bacteria are evidenced by substrate-incorporated capillary electrophoresis (CE zymography) and their kinetic parameters can be determined by repeated injections using different substrate concentrations. Preliminary results obtained with natural bacterial communities from the coastal North Sea suggest that the diversity of β-glucosidases in the marine environment might be much higher than previously observed.
Molecular Characterization of a New Abortive Infection System (AbiU) from
Lactococcus lactis
LL51-1
Authors: Dai Gang , Su Ping , Allison Gwen E. , Geller Bruce L. , Zhu Ping , Kim Woojin S. , Dunn Noel W. 
Published: July 2002

ABSTRACT

This study reports on the identification and characterization of a novel abortive infection system, AbiU, from
Lactococcus lactis.
AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 × 10
−1
, 1.0 × 10
−2
, and 1.0 × 10
−1
, respectively.
abiU
involves two open reading frames,
abiU1
(1,772 bp) and
abiU2
(1,019 bp). Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage. AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.
Engineering Cytochrome P450 BM-3 for Oxidation of Polycyclic Aromatic Hydrocarbons
Authors: Li Qing-Shan , Ogawa Jun , Schmid Rolf D. , Shimizu Sakayu 
Published: July 2002

ABSTRACT

Cytochrome P450 BM-3, a self-sufficient P450 enzyme from
Bacillus megaterium
that catalyzes the subterminal hydroxylation of long-chain fatty acids, has been engineered into a catalyst for the oxidation of polycyclic aromatic hydrocarbons. The activities of a triplet mutant (A74G/F87V/L188Q) towards naphthalene, fluorene, acenaphthene, acenaphthylene, and 9-methylanthracene were 160, 53, 109, 287, and 22/min, respectively. Compared with the activities of the wild type towards these polycyclic aromatic hydrocarbons, those of the mutant were improved by up to 4 orders of magnitude. The coupling efficiencies of the mutant towards naphthalene, fluorene, acenaphthene, acenaphthylene, and 9-methylanthracene were 11, 26, 5.4, 15, and 3.2%, respectively, which were also improved several to hundreds fold. The high activities of the mutant towards polycyclic aromatic hydrocarbons indicate the potential of engineering P450 BM-3 for the biodegradation of these compounds in the environment.
Nitrogen Fixation Genes in an Endosymbiotic
Burkholderia
Strain
Authors: Minerdi Daniela , Fani Renato , Gallo Romina , Boarino Alessandra , Bonfante Paola 
Published: July 2002

ABSTRACT

In this paper we report the identification and characterization of a DNA region containing putative
nif
genes and belonging to a
Burkholderia
endosymbiont of the arbuscular mycorrhizal fungus
Gigaspora margarita
. A genomic library of total DNA extracted from the fungal spores was also representative of the bacterial genome and was used to investigate the prokaryotic genome. Screening of the library with
Azospirillum brasilense nifHDK
genes as the prokaryotic probes led to the identification of a 6,413-bp region. Analysis revealed three open reading frames encoding putative proteins with a very high degree of sequence similarity with the two subunits (NifD and NifK) of the component I and with component II (NifH) of nitrogenase from different diazotrophs. The three genes were arranged in an operon similar to that shown by most archaeal and bacterial diazotrophs. PCR experiments with primers designed on the
Burkholderia nifHDK
genes and Southern blot analysis demonstrate that they actually belong to the genome of the
G. margarita
endosymbiont. They offer, therefore, the first sequence for the
nif
operon described for
Burkholderia
. Reverse transcriptase PCR experiments with primers designed on the
Burkholderia nifH
and
nifD
genes and performed on total RNA extracted from spores demonstrate that the gene expression was limited to the germination phase. A phylogenetic analysis performed on the available
nifK
sequences placed the endosymbiotic
Burkholderia
close to
A. brasilense
.
Chromate Reduction by a Pseudomonad Isolated from a Site Contaminated with Chromated Copper Arsenate
Authors: McLean Jeff , Beveridge Terry J. 
Published: July 2002

ABSTRACT

A pseudomonad (CRB5) isolated from a decommissioned wood preservation site reduced toxic chromate [Cr(VI)] to an insoluble Cr(III) precipitate under aerobic and anaerobic conditions. CRB5 tolerated up to 520 mg of Cr(VI) liter
−1
and reduced chromate in the presence of copper and arsenate. Under anaerobic conditions it also reduced Co(III) and U(VI), partially internalizing each metal. Metal precipitates were also found on the surface of the outer membrane and (sometimes) on a capsule. The results showed that chromate reduction by CRB5 was mediated by a soluble enzyme that was largely contained in the cytoplasm but also found outside of the cells. The crude reductase activity in the soluble fraction showed a

K
m

of 23 mg liter
−1
(437 μM) and a
V
max
of 0.98 mg of Cr h
−1
mg of protein
−1
(317 nmol min
−1
mg of protein
−1
). Minor membrane-associated Cr(VI) reduction under anaerobiosis may account for anaerobic reduction of chromate under nongrowth conditions with an organic electron donor present. Chromate reduction under both aerobic and anaerobic conditions may be a detoxification strategy for the bacterium which could be exploited to bioremediate chromate-contaminated or other toxic heavy metal-contaminated environments.
Temperature-Driven Adaptation of the Bacterial Community in Peat Measured by Using Thymidine and Leucine Incorporation
Authors: Ranneklev Sissel Brit , Bååth Erland 
Published: July 2002

ABSTRACT

The temperature-driven adaptation of the bacterial community in peat was studied, by altering temperature to simulate self-heating and a subsequent return to mesophilic conditions. The technique used consisted of extracting the bacterial community from peat using homogenization-centrifugation and measuring the rates of thymidine (TdR) or leucine (Leu) incorporation by the extracted bacterial community at different temperatures. Increasing the peat incubation temperature from 25°C to 35, 45, or 55°C resulted in a selection of bacterial communities whose optimum temperatures for activity correlated to the peat incubation temperatures. Although TdR and Leu incorporations were significantly correlated, the Leu/TdR incorporation ratios were affected by temperature. Higher Leu/TdR incorporation ratios were found at higher temperatures of incubation of the extracted bacterial community. Higher Leu/TdR incorporation ratios were also found for bacteria in peat samples incubated at higher temperatures. The reappearance of the mesophilic community and disappearance of the thermophilic community when the incubation temperature of the peat was shifted down were monitored by measuring TdR incorporation at 55°C (thermophilic activity) and 25°C (mesophilic activity). Shifting the peat incubation temperature from 55 to 25°C resulted in a recovery of the mesophilic activity, with a subsequent disappearance of the thermophilic activity. The availability of substrate for bacterial growth varied over time and among different peat samples. To avoid confounding effects of substrate availability, a temperature adaptation index was calculated. This index consisted of the log
10
ratio of TdR incorporation at 55 and 25°C. The temperature index decreased linearly with time, indicating that no thermophilic activity would be detected by the TdR technique 1 month after the temperature downshift. There were no differences between the slopes of the temperature adaptation indices over time for peat samples incubated at 55°C 3 or 11 days before incubation at 25°C. Thus, different levels of bacterial activity did not affect the temperature-driven adaptation of the bacterial community.
Simultaneous Measurement of Denitrification and Nitrogen Fixation Using Isotope Pairing with Membrane Inlet Mass Spectrometry Analysis
Authors: An Soonmo , Gardner Wayne S. , Kana Todd 
Published: July 2002

ABSTRACTA method for estimating denitrification and nitrogen fixation simultaneously in coastal sediments was developed. An isotope-pairing technique was applied to dissolved gas measurements with a membrane inlet mass spectrometer (MIMS). The relative fluxes of three N2gas species (28N2,29N2, and30N2) were monitored during incubation experiments after the addition of15NO3−. Formulas were developed to estimate the production (denitrification) and consumption (N2fixation) of N2gas from the fluxes of the different isotopic forms of N2. Proportions of the three isotopic forms produced from15NO3−and14NO3−agreed with expectations in a sediment slurry incubation experiment designed to optimize conditions for denitrification. Nitrogen fixation rates from an algal mat measured with intact sediment cores ranged from 32 to 390 μg-atoms of N m−2h−1. They were enhanced by light and organic matter enrichment. In this environment of high nitrogen fixation, low N2production rates due to denitrification could be separated from high N2consumption rates due to nitrogen fixation. Denitrification and nitrogen fixation rates were estimated in April 2000 on sediments from a Texas sea grass bed (Laguna Madre). Denitrification rates (average, 20 μg-atoms of N m−2h−1) were lower than nitrogen fixation rates (average, 60 μg-atoms of N m−2h−1). The developed method benefits from simple and accurate dissolved-gas measurement by the MIMS system. By adding the N2isotope capability, it was possible to do isotope-pairing experiments with the MIMS system.
Relationship of Hydrogen Bioavailability to Chromate Reduction in Aquifer Sediments
Authors: Marsh Tamara L. , McInerney Michael J. 
Published: July 2002

ABSTRACT
Biological Cr(VI) reduction was studied in anaerobic sediments from an aquifer in Norman, Okla. Microcosms containing sediment and mineral medium were amended with various electron donors to determine those most important for biological Cr(VI) reduction. Cr(VI) (about 340 μM) was reduced with endogenous substrates (no donor), or acetate was added. The addition of formate, hydrogen, and glucose stimulated Cr(VI) reduction compared with reduction in unamended controls. From these sediments, an anaerobic Cr(VI)-utilizing enrichment was obtained that was dependent upon hydrogen for both growth and Cr(VI) reduction. No methane was produced by the enrichment, which reduced about 750 μM Cr(VI) in less than six days. The dissolved hydrogen concentration was used as an indicator of the terminal electron accepting process occurring in the sediments. Microcosms with sediments, groundwater, and chromate metabolized hydrogen to a concentration below the detection limits of the mercury vapor gas chromatograph. In microcosms without chromate, the hydrogen concentration was about 8 nM, a concentration comparable to that under methanogenic conditions. When these microcosms were amended with 500 μM Cr(VI), the dissolved hydrogen concentration quickly fell below the detection limits. These results showed that the hydrogen concentration under chromate-reducing conditions became very low, as low as that reported under nitrate- and manganese-reducing conditions, a result consistent with the free energy changes for these reactions. The utilization of formate, lactate, hydrogen, and glucose as electron donors for Cr(VI) reduction indicates that increasing the availability of hydrogen results in a greater capacity for Cr(VI) reduction. This conclusion is supported by the existence of an enrichment dependent upon hydrogen for growth and Cr(VI) reduction.
Phylogenetic and Morphological Diversity of Cyanobacteria in Soil Desert Crusts from the Colorado Plateau
Authors: Garcia-Pichel Ferran , López-Cortés Alejandro , Nübel Ulrich 
Published: July 2002

ABSTRACT

We compared the community structures of cyanobacteria in four biological desert crusts from Utah's Colorado Plateau developing on different substrata. We analyzed natural samples, cultures, and cyanobacterial filaments or colonies retrieved by micromanipulation from field samples using microscopy, denaturing gradient gel electrophoresis, and sequencing of 16S rRNA genes. While microscopic analyses apparently underestimated the biodiversity of thin filamentous cyanobacteria, molecular analyses failed to retrieve signals for otherwise conspicuous heterocystous cyanobacteria with thick sheaths. The diversity found in desert crusts was underrepresented in currently available nucleotide sequence databases, and several novel phylogenetic clusters could be identified. Morphotypes fitting the description of
Microcoleus vaginatus
Gomont, dominant in most samples, corresponded to a tight phylogenetic cluster of probable cosmopolitan distribution, which was well differentiated from other cyanobacteria traditionally classified within the same genus. A new, diverse phylogenetic cluster, named “Xeronema,” grouped a series of thin filamentous
Phormidium
-like cyanobacteria. These were also ubiquitous in our samples and probably correspond to various botanical
Phormidium
and
Schizothrix
spp., but they are phylogenetically distant from thin filamentous cyanobacteria from other environments. Significant differences in community structure were found among soil types, indicating that soil characteristics may select for specific cyanobacteria. Gypsum crusts were most deviant from the rest, while sandy, silt, and shale crusts were relatively more similar among themselves.
Oxygen Requirements of the Food Spoilage Yeast
Zygosaccharomyces bailii
in Synthetic and Complex Media
Authors: Rodrigues Fernando , Côrte-Real Manuela , Leão Cecı́lia , van Dijken Johannes P. , Pronk Jack T. 
Published: July 2002

ABSTRACT

Most yeast species can ferment sugars to ethanol, but only a few can grow in the complete absence of oxygen. Oxygen availability might, therefore, be a key parameter in spoilage of food caused by fermentative yeasts. In this study, the oxygen requirement and regulation of alcoholic fermentation were studied in batch cultures of the spoilage yeast
Zygosaccharomyces bailii
at a constant pH, pH 3.0. In aerobic, glucose-grown cultures,
Z. bailii
exhibited aerobic alcoholic fermentation similar to that of
Saccharomyces cerevisiae
and other Crabtree-positive yeasts. In anaerobic fermentor cultures grown on a synthetic medium supplemented with glucose, Tween 80, and ergosterol,
S. cerevisiae
exhibited rapid exponential growth. Growth of
Z. bailii
under these conditions was extremely slow and linear. These linear growth kinetics indicate that cell proliferation of
Z. bailii
in the anaerobic fermentors was limited by a constant, low rate of oxygen leakage into the system. Similar results were obtained with the facultatively fermentative yeast
Candida utilis
. When the same experimental setup was used for anaerobic cultivation, in complex YPD medium,
Z. bailii
exhibited exponential growth and vigorous fermentation, indicating that a nutritional requirement for anaerobic growth was met by complex-medium components. Our results demonstrate that restriction of oxygen entry into foods and beverages, which are rich in nutrients, is not a promising strategy for preventing growth and gas formation by
Z. bailii
. In contrast to the growth of
Z. bailii
, anaerobic growth of
S. cerevisiae
on complex YPD medium was much slower than growth in synthetic medium, which probably reflected the superior tolerance of the former yeast to organic acids at low pH.
Use of Long-Range Repetitive Element Polymorphism-PCR To Differentiate
Bacillus anthracis
Strains
Authors: Brumlik Michael J. , Szymajda Urszula , Zakowska Dorota , Liang Xudong , Redkar Rajendra J. , Patra Guy , Del Vecchio Vito G. 
Published: July 2002

ABSTRACT

The genome of
Bacillus anthracis
is extremely monomorphic, and thus individual strains have often proven to be recalcitrant to differentiation at the molecular level. Long-range repetitive element polymorphism-PCR (LR REP-PCR) was used to differentiate various
B. anthracis
strains. A single PCR primer derived from a repetitive DNA element was able to amplify variable segments of a bacterial genome as large as 10 kb. We were able to characterize five genetically distinct groups by examining 105
B. anthracis
strains of diverse geographical origins. All
B. anthracis
strains produced fingerprints comprising seven to eight bands, referred to as “skeleton” bands, while one to three “diagnostic” bands differentiated between
B. anthracis
strains. LR REP-PCR fingerprints of
B. anthracis
strains showed very little in common with those of other closely related species such as
B. cereus, B. thuringiensis
, and
B. mycoides
, suggesting relative heterogeneity among the non-
B. anthracis
strains. Fingerprints from transitional non-
B. anthracis
strains, which possessed the
B. anthracis
chromosomal marker Ba813, scarcely resembled those observed for any of the five distinct
B. anthracis
groups that we have identified. The LR REP-PCR method described in this report provides a simple means of differentiating
B. anthracis
strains.