bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Viable-but-Nonculturable State Induced by Abiotic Stress in the Biocontrol Agent
Pseudomonas fluorescens
CHA0 Does Not Promote Strain Persistence in Soil
Authors: Mascher Fabio , Hase Carsten , Moënne-Loccoz Yvan , Défago Geneviève 
Published: July 2002

ABSTRACT

The effects of oxygen limitation, low redox potential, and high NaCl stress for 7 days in vitro on the rifampin-resistant biocontrol inoculant
Pseudomonas fluorescens
CHA0-Rif and its subsequent persistence in natural soil for 54 days were investigated. Throughout the experiment, the strain was monitored using total cell counts (immunofluorescence microscopy), Kogure's direct viable counts, and colony counts (on rifampin-containing plates). Under in vitro conditions, viable-but-nonculturable (VBNC) cells of CHA0-Rif were obtained when the strain was exposed to a combination of low redox potential (230 mV) and oxygen limitation. This mimics a situation observed in the field, where VBNC cells of the strain were found in the waterlogged soil layer above the plow pan. Here, VBNC cells were also observed in vitro when CHA0-Rif was subjected to high NaCl levels (i.e., NaCl at 1.5 M but not 0.7 M). In all treatments, cell numbers remained close to the inoculum level for the first 12 days after inoculation of soil, regardless of the cell enumeration method used, but decreased afterwards. At the last two samplings in soil, VBNC cells of CHA0-Rif were found in all treatments except the one in which log-phase cells had been used. In the two treatments that generated high numbers of VBNC cells in vitro, VBNC cells did not display enhanced persistence compared with culturable cells once introduced into soil, which suggests that this VBNC state did not represent a physiological strategy to improve survival under adverse conditions.
Differential Damage in Bacterial Cells by Microwave Radiation on the Basis of Cell Wall Structure
Authors: Woo Im-Sun , Rhee In-Koo , Park Heui-Dong 
Published: July 2002

ABSTRACT

Microwave radiation in
Escherichia coli
and
Bacillus subtilis
cell suspensions resulted in a dramatic reduction of the viable counts as well as increases in the amounts of DNA and protein released from the cells according to the increase of the final temperature of the cell suspensions. However, no significant reduction of cell density was observed in either cell suspension. It is believed that this is due to the fact that most of the bacterial cells inactivated by microwave radiation remained unlysed. Scanning electron microscopy of the microwave-heated cells revealed severe damage on the surface of most
E. coli
cells, yet there was no significant change observed in the
B. subtilis
cells. Microwave-injured
E. coli
cells were easily lysed in the presence of sodium dodecyl sulfate (SDS), yet
B. subtilis
cells were resistant to SDS.
Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System
Authors: Whiteley Andrew S. , Bailey Mark J. 
Published: July 2002

ABSTRACT

The structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. Rapid community fingerprinting by PCR-based denaturing gradient gel electrophoresis (DGGE) of 16S rDNA indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclusively within the Vitox biological reactor. Whole-cell targeting by fluorescent in situ hybridization with specific oligonucleotides (directed to the α, β and γ subclasses of the class
Proteobacteria
[α-, β-, and γ-
Proteobacteria
, respectively], the
Cytophaga-Flavobacterium
group, and the
Pseudomonas
group) tended to mirror gross changes in bacterial community composition when compared with DGGE community fingerprinting. At the whole-cell level, the treatment compartments were numerically dominated by cells assigned to the
Cytophaga-Flavobacterium
group and to the γ-
Proteobacteria
. The α subclass
Proteobacteria
were of low relative abundance throughout the treatment system whilst the β subclass of the
Proteobacteria
exhibited local dominance in several of the processing compartments. Quantitative image analyses of cellular fluorescence was used as an indicator of physiological state within the populations probed with rDNA. For cells hybridized with EUB338, the mean fluorescence per cell decreased with increasing phenolic concentration, indicating the strong influence of the primary pollutant upon cellular rRNA content. The γ subclass of the
Proteobacteria
had a ribosome content which correlated positively with total phenolics and thiocyanate. While members of the
Cytophaga-Flavobacterium
group were numerically dominant in the processing system, their abundance and ribosome content data for individual populations did not correlate with any of the measured chemical parameters. The potential importance of the γ-
Proteobacteria
and the
Cytophaga-Flavobacteria
during this bioremediation process was highlighted.
Antibiosis between Ruminal Bacteria and Ruminal Fungi
Authors: Dehority Burk A. , Tirabasso Patricia A. 
Published: July 2002

ABSTRACT

Cellulose digestion, bacterial numbers, and fungal numbers were monitored over time in vitro by using a purified cellulose medium with and without antibiotics (penicillin and streptomycin). All fermentations were inoculated with a 1:10 dilution of whole rumen contents (WRC). Without antibiotics, cellulose digestion was higher (
P
< 0.01) at 24, 30, 48, and 72 h; fungi had almost disappeared by 24 h, while bacterial concentrations increased over 100-fold in 24 h and then decreased gradually up to 72 h. In those fermentations with added antibiotics, fungal concentrations increased 4-fold by 30 h and up to 42-fold at 72 h; bacterial concentrations were markedly reduced by 24 h and remained low through 72 h. Similar results were obtained with ground alfalfa as a substrate. In further studies, the in vitro fermentation of purified cellulose without antibiotics was stopped after 18 to 20 h, and the microbial population was killed by autoclaving. Antibiotics were added to half of the tubes, and all tubes were reinoculated with WRC. After 72 h, extensive cellulose digestion had occurred in those tubes without antibiotics, as compared to very low cellulose digestion with added antibiotics. The extent of this inhibition was found to increase in proportion to the length of the initial fermentation period, suggesting the production of a heat-stable inhibitory factor or factors. The inhibitory activity was present in rumen fluid, could be extracted from lyophilized rumen fluid (LRF) with water, and was stable in response to proteolytic enzymes. In addition, the water-extracted residue of LRF was found to contain growth factor activity for rumen fungi in vitro.
Culturability and In Situ Abundance of Pelagic Bacteria from the North Sea
Authors: Eilers Heike , Pernthaler Jakob , Glöckner Frank Oliver , Amann Rudolf 
Published: July 2002

ABSTRACT

The culturability of abundant members of the domain
Bacteria
in North Sea bacterioplankton was investigated by a combination of various cultivation strategies and cultivation-independent 16S rRNA-based techniques. We retrieved 16S rRNA gene (rDNA) clones from environmental DNAs and determined the in situ abundance of different groups and genera by fluorescence in situ hybridization (FISH). A culture collection of 145 strains was established by plating on oligotrophic medium. Isolates were screened by FISH, amplified ribosomal DNA restriction analysis (ARDRA), and sequencing of representative 16S rDNAs. The majority of isolates were members of the genera
Pseudoalteromonas
,
Alteromonas
, and
Vibrio
. Despite being readily culturable, they constituted only a minor fraction of the bacterioplankton community. They were not detected in the 16S rDNA library, and FISH indicated rare (<1% of total cell counts) occurrence as large, rRNA-rich, particle-associated bacteria. Conversely, abundant members of the
Cytophaga-Flavobacteria
and gamma proteobacterial SAR86 clusters, identified by FISH as 17 to 30% and up to 10% of total cells in the North Sea bacterioplankton, respectively, were cultured rarely or not at all. Whereas SAR86-affiliated clones dominated the 16S rDNA library (44 of 53 clones), no clone affiliated to the
Cytophaga-Flavobacterum
cluster was retrieved. The only readily culturable abundant group of marine bacteria was related to the genus
Roseobacter
. The group made up 10% of the total cells in the summer, and the corresponding sequences were also present in our clone library. Rarefaction analysis of the ARDRA patterns of all of the isolates suggested that the total culturable diversity by our method was high and still not covered by the numbers of isolated strains but was almost saturated for the gamma proteobacteria. This predicts a limit to the isolation of unculturable marine bacteria, particularly the gamma-proteobacterial SAR86 cluster, as long as no new techniques for isolation are available and thus contrasts with more optimistic accounts of the culturability of marine bacterioplankton.
Colonization of Corn,
Zea mays
, by the Entomopathogenic Fungus
Beauveria bassiana
Authors: Wagner Bruce L. , Lewis Leslie C. 
Published: July 2002

ABSTRACT

Light and electron microscopy were used to describe the mode of penetration by the entomopathogenic fungus
Beauveria bassiana
(Balsamo) Vuillemin into corn,
Zea mays
L. After inoculation with a foliar spray of conidia, germinating hyphae grew randomly across the leaf surface. Often a germ tube formed from a conidium and elongated only a short distance before terminating its growth. Not all developing hyphae on the leaf surface penetrated the cuticle. However, when penetration did occur, the penetration site(s) was randomly located, indicating that
B. bassiana
does not require specific topographic signals at an appropriate entry site as do some phytopathogenic fungi. Long hyphal structures were observed to follow the leaf apoplast in any direction from the point of penetration. A few hyphae were observed within xylem elements. Because vascular bundles are interconnected throughout the corn plant, this may explain how
B. bassiana
travels within the plant and ultimately provides overall insecticidal protection. Virulency bioassays demonstrate that
B. bassiana
does not lose virulence toward the European corn borer,
Ostrinia nubilalis
(Hübner), once it colonizes corn. This endophytic relationship between an entomopathogenic fungus and a plant suggests possibilities for biological control, including the use of indigenous fungal inocula as insecticides.
Microbial Community Dynamics during Production of the Mexican Fermented Maize Dough Pozol
Authors: ben Omar Nabil , Ampe Frédéric 
Published: July 2002

ABSTRACT

The dynamics of the microbial community responsible for the traditional fermentation of maize in the production of Mexican pozol was investigated by using a polyphasic approach combining (i) microbial enumerations with culture media, (ii) denaturing gradient gel electrophoresis (DGGE) fingerprinting of total community DNA with bacterial and eukaryotic primers and sequencing of partial 16S ribosomal DNA (rDNA) genes, (iii) quantification of rRNAs from dominant microbial taxa by using phylogenetic oligonucleotide probes, and (iv) analysis of sugars and fermentation products. A
Streptococcus
species dominated the fermentation and accounted for between 25 and 75% of the total flora throughout the process. Results also showed that the initial epiphytic aerobic microflora was replaced in the first 2 days by heterofermentative lactic acid bacteria (LAB), including a close relative of
Lactobacillus fermentum
, producing lactic acid and ethanol; this heterolactic flora was then progressively replaced by homofermentative LAB (mainly close relatives of
L. plantarum
,
L. casei
, and
L. delbrueckii
) which continued acidification of the maize dough. At the same time, a very diverse community of yeasts and fungi developed, mainly at the periphery of the dough. The analysis of the DGGE patterns obtained with bacterial and eukaryotic primers targeting the 16S and 18S rDNA genes clearly demonstrated that there was a major shift in the community structure after 24 h and that high biodiversity—according to the Shannon-Weaver index—was maintained throughout the process. These results proved that a relatively high number of species, at least six to eight, are needed to perform this traditional lactic acid fermentation. The presence of
Bifidobacterium
,
Enterococcus
, and enterobacteria suggests a fecal origin of some important pozol microorganisms. Overall, the results obtained with different culture-dependent or -independent techniques clearly confirmed the importance of developing a polyphasic approach to study the ecology of fermented foods.
Modeling Reduction of Uranium U(VI) under Variable Sulfate Concentrations by Sulfate-Reducing Bacteria
Authors: Spear John R. , Figueroa Linda A. , Honeyman Bruce D. 
Published: July 2002

ABSTRACT

The kinetics for the reduction of sulfate alone and for concurrent uranium [U(VI)] and sulfate reduction, by mixed and pure cultures of sulfate-reducing bacteria (SRB) at 21 ± 3°C were studied. The mixed culture contained the SRB
Desulfovibrio vulgaris
along with a
Clostridium
sp. determined via 16S ribosomal DNA analysis. The pure culture was
Desulfovibrio desulfuricans
(ATCC 7757). A zero-order model best fit the data for the reduction of sulfate from 0.1 to 10 mM. A lag time occurred below cell concentrations of 0.1 mg (dry weight) of cells/ml. For the mixed culture, average values for the maximum specific reaction rate,
V
max
, ranged from 2.4 ± 0.2 μmol of sulfate/mg (dry weight) of SRB · h
−1
) at 0.25 mM sulfate to 5.0 ± 1.1 μmol of sulfate/mg (dry weight) of SRB · h
−1
at 10 mM sulfate (average cell concentration, 0.52 mg [dry weight]/ml). For the pure culture,
V
max
was 1.6 ± 0.2 μmol of sulfate/mg (dry weight) of SRB · h
−1
at 1 mM sulfate (0.29 mg [dry weight] of cells/ml). When both electron acceptors were present, sulfate reduction remained zero order for both cultures, while uranium reduction was first order, with rate constants of 0.071 ± 0.003 mg (dry weight) of cells/ml · min
−1
for the mixed culture and 0.137 ± 0.016 mg (dry weight) of cells/ml · min
−1
(U
0
= 1 mM) for the
D. desulfuricans
culture. Both cultures exhibited a faster rate of uranium reduction in the presence of sulfate and no lag time until the onset of U reduction in contrast to U alone. This kinetics information can be used to design an SRB-dominated biotreatment scheme for the removal of U(VI) from an aqueous source.
Production of Angiotensin-I-Converting-Enzyme-Inhibitory Peptides in Fermented Milks Started by
Lactobacillus delbrueckii
subsp.
bulgaricus
SS1 and
Lactococcus lactis
subsp.
cremoris
FT4
Authors: Gobbetti M. , Ferranti P. , Smacchi E. , Goffredi F. , Addeo F. 
Published: July 2002

ABSTRACT

Two fermented milks containing angiotensin-I-converting-enzyme (ACE)-inhibitory peptides were produced by using selected
Lactobacillus delbrueckii
subsp.
bulgaricus
SS1 and
L. lactis
subsp.
cremoris
FT4. The pH 4.6-soluble nitrogen fraction of the two fermented milks was fractionated by reversed-phase fast-protein liquid chromatography. The fractions which showed the highest ACE-inhibitory indexes were further purified, and the related peptides were sequenced by tandem fast atom bombardment-mass spectrometry. The most inhibitory fractions of the milk fermented by
L. delbrueckii
subsp.
bulgaricus
SS1 contained the sequences of β-casein (β-CN) fragment 6-14 (f6-14), f7-14, f73-82, f74-82, and f75-82. Those from the milk fermented by
L. lactis
subsp.
cremoris
FT4 contained the sequences of β-CN f7-14, f47-52, and f169-175 and κ-CN f155-160 and f152-160. Most of these sequences had features in common with other ACE-inhibitory peptides reported in the literature. In particular, the β-CN f47-52 sequence had high homology with that of angiotensin-II. Some of these peptides were chemically synthesized. The 50% inhibitory concentrations (IC
50
s) of the crude purified fractions containing the peptide mixture were very low (8.0 to 11.2 mg/liter). When the synthesized peptides were used individually, the ACE-inhibitory activity was confirmed but the IC
50
s increased considerably. A strengthened inhibitory effect of the peptide mixtures with respect to the activity of individual peptides was presumed. Once generated, the inhibitory peptides were resistant to further proteolysis either during dairy processing or by trypsin and chymotrypsin.
Engineering Hydrogen Sulfide Production and Cadmium Removal by Expression of the Thiosulfate Reductase Gene (
phsABC
) from
Salmonella enterica
Serovar Typhimurium in
Escherichia coli
Authors: Bang Sang-Weon , Clark Douglas S. , Keasling Jay D. 
Published: July 2002

ABSTRACT

The thiosulfate reductase gene (
phsABC
) from
Salmonella enterica
serovar Typhimurium was expressed in
Escherichia coli
to overproduce hydrogen sulfide from thiosulfate for heavy metal removal (or precipitation). A 5.1-kb DNA fragment containing
phsABC
was inserted into the pMB1-based, high-copy, isopropyl-β-
d
-thiogalactopyranoside-inducible expression vector pTrc99A and the RK2-based, medium-copy,
m
-toluate-inducible expression vector pJB866, resulting in plasmids pSB74 and pSB77. A 3.7-kb DNA fragment, excluding putative promoter and regulatory regions, was inserted into the same vectors, making plasmids pSB103 and pSB107.
E. coli
DH5α strains harboring the
phsABC
constructs showed higher thiosulfate reductase activity and produced significantly more sulfide than the control strains under both aerobic and anaerobic conditions. Among the four
phsABC
constructs,
E. coli
DH5α (pSB74) produced thiosulfate reductase at the highest level and removed the most cadmium from solution under anaerobic conditions: 98% of all concentrations up to 150 μM and 91% of 200 μM. In contrast, a negative control did not produce any measurable sulfide and removed very little cadmium from solution. Energy-dispersive X-ray spectroscopy revealed that the metal removed from solution precipitated as a complex of cadmium and sulfur, most likely cadmium sulfide.
Identification and Characteristics of a Novel
Burkholderia
Strain with Broad-Spectrum Antimicrobial Activity
Authors: Cain Cody C. , Henry Alexis T. , Waldo Robert H. , Casida Lester J. , Falkinham Joseph O. 
Published: July 2002

ABSTRACT

A
Burkholderia
strain isolated from soil is capable of inhibiting the growth of bacteria, plant-pathogenic fungi, pathogenic yeasts, and protozoa. Inhibition does not involve cell contact or the presence of living cells, suggesting that at least a substantial portion of the antimicrobial activity is due to the excretion of extracellular compounds.
Lactobacillus coryniformis
subsp.
coryniformis
Strain Si3 Produces a Broad-Spectrum Proteinaceous Antifungal Compound
Authors: Magnusson Jesper , Schnürer Johan 
Published: July 2002

ABSTRACT

The antifungal activity spectrum of
Lactobacillus coryniformis
subsp.
coryniformis
strain Si3 was investigated. The strain had strong inhibitory activity in dual-culture agar plate assays against the molds
Aspergillus fumigatus
,
A. nidulans
,
Penicillium roqueforti
,
Mucor hiemalis
,
Talaromyces flavus
,
Fusarium poae
,
F. graminearum
,
F. culmorum
, and
F. sporotrichoides
. A weaker activity was observed against the yeasts
Debaryomyces hansenii
,
Kluyveromyces marxianus
, and
Saccharomyces cerevisiae
. The yeasts
Rhodotorula glutinis
,
Sporobolomyces roseus
, and
Pichia anomala
were not inhibited. In liquid culture the antifungal activity paralleled growth, with maximum mold inhibition early in the stationary growth phase, but with a rapid decline in antifungal activity after 48 h. The addition of ethanol to the growth medium prevented the decline and gave an increased antifungal activity. The activity was stable during heat treatment and was retained even after autoclaving at 121°C for 15 min. Maximum activity was observed at pH values of between 3.0 and 4.5, but it decreased rapidly when pH was adjusted to a level between 4.5 and 6.0 and was lost at higher pH values. The antifungal activity was fully regained after readjustment of the pH to the initial value (pH 3.6). The activity was irreversibly lost after treatment with proteolytic enzymes (proteinase K, trypsin, and pepsin). The antifungal activity was partially purified using ion-exchange chromatography and (NH
4
)
2
SO
4
precipitation, followed by gel filtration chromatography. The active compound(s) was estimated to have a molecular mass of approximately 3 kDa. This is the first report of the production of a proteinaceous antifungal compound(s) from
L. coryniformis
subsp.
coryniformis
.
Mutation of the
ptsG
Gene Results in Increased Production of Succinate in Fermentation of Glucose by
Escherichia coli
Authors: Chatterjee Ranjini , Millard Cynthia Sanville , Champion Kathleen , Clark David P. , Donnelly Mark I. 
Published: July 2002

ABSTRACT

Escherichia coli
NZN111 is blocked in the ability to grow fermentatively on glucose but gave rise spontaneously to a mutant that had this ability. The mutant carries out a balanced fermentation of glucose to give approximately 1 mol of succinate, 0.5 mol of acetate, and 0.5 mol of ethanol per mol of glucose. The causative mutation was mapped to the
ptsG
gene, which encodes the membrane-bound, glucose-specific permease of the phosphotransferase system, protein EIICB
glc
. Replacement of the chromosomal
ptsG
gene with an insertionally inactivated form also restored growth on glucose and resulted in the same distribution of fermentation products. The physiological characteristics of the spontaneous and null mutants were consistent with loss of function of the
ptsG
gene product; the mutants possessed greatly reduced glucose phosphotransferase activity and lacked normal glucose repression. Introduction of the null mutant into strains not blocked in the ability to ferment glucose also increased succinate production in those strains. This phenomenon was widespread, occurring in different lineages of
E. coli
, including
E. coli
B.
Direct In Situ Viability Assessment of Bacteria in Probiotic Dairy Products Using Viability Staining in Conjunction with Confocal Scanning Laser Microscopy
Authors: Auty M. A. E. , Gardiner G. E. , McBrearty S. J. , O'Sullivan E. O. , Mulvihill D. M. , Collins J. K. , Fitzgerald G. F. , Stanton C. , Ross R. P. 
Published: July 2002

ABSTRACT

The viability of the human probiotic strains
Lactobacillus paracasei
NFBC 338 and
Bifidobacterium
sp. strain UCC 35612 in reconstituted skim milk was assessed by confocal scanning laser microscopy using the LIVE/DEAD
Bac
Light viability stain. The technique was rapid (<30 min) and clearly differentiated live from heat-killed bacteria. The microscopic enumeration of various proportions of viable to heat-killed bacteria was then compared with conventional plating on nutrient agar. Direct microscopic enumeration of bacteria indicated that plate counting led to an underestimation of bacterial numbers, which was most likely related to clumping. Similarly, LIVE/DEAD
Bac
Light staining yielded bacterial counts that were higher than cell numbers obtained by plate counting (CFU) in milk and fermented milk. These results indicate the value of the microscopic approach for rapid viability testing of such probiotic products. In contrast, the numbers obtained by direct microscopic counting for Cheddar cheese and spray-dried probiotic milk powder were lower than those obtained by plate counting. These results highlight the limitations of LIVE/DEAD
Bac
Light staining and the need to optimize the technique for different strain-product combinations. The minimum detection limit for in situ viability staining in conjunction with confocal scanning laser microscopy enumeration was ∼10
8
bacteria/ml (equivalent to ∼10
7
CFU/ml), based on
Bifidobacterium
sp. strain UCC 35612 counts in maximum-recovery diluent.