bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppression of Bacterial Blight by a Bacterial Community Isolated from the Guttation Fluids of Anthuriums
Authors: Fukui R. , Fukui H. , Alvarez A. M. 
Published: December 2019

ABSTRACT

Growth and survival of
Xanthomonas campestris
pv. dieffenbachiae in guttation fluids (xylem sap exuded from leaf margins) of anthuriums were suppressed by several bacterial strains indigenous to leaves of various anthurium cultivars. Inhibition of growth was not observed in filter-sterilized guttation fluids and was restored to original levels only by reintroducing specific mixtures of bacteria into filter-sterilized guttation fluids. The inhibitory effect was related to the species in the bacterial community rather than to the total numbers of bacteria in the guttation fluids. One very effective bacterial community consisted of five species isolated from inhibitory guttation fluids of two susceptible anthurium cultivars. The individual strains in this community had no effect on the pathogen, but the mixture was inhibitory to
X. campestris
pv. dieffenbachiae in guttation fluids. The populations of the individual strains remained near the initial inoculum levels for at least 14 days. The effect of the five inhibitory strains on reducing disease in susceptible anthurium plants was tested by using a bioluminescent strain of
X. campestris
pv. dieffenbachiae to monitor the progression of disease in leaves nondestructively. Invasion of the pathogen through hydathodes at leaf margins was reduced by applying the strain mixture to the leaves. When the strain mixture was applied directly to wounds created on the leaf margins, the pathogen failed to invade through the wounds. This bacterial community has potential for biological control of anthurium blight.
Immobilization Patterns and Dynamics of Acetate-Utilizing Methanogens Immobilized in Sterile Granular Sludge in Upflow Anaerobic Sludge Blanket Reactors
Authors: Schmidt Jens Ejbye , Ahring Birgitte Kjær 
Published: December 2019

ABSTRACT

Sterile granular sludge was inoculated with either
Methanosarcina mazeii
S-6,
Methanosaeta concilii
GP-6, or both species in acetate-fed upflow anaerobic sludge blanket (UASB) reactors to investigate the immobilization patterns and dynamics of aceticlastic methanogens in granular sludge. After several months of reactor operation, the methanogens were immobilized, either separately or together. The fastest immobilization was observed in the reactor containing
M. mazeii
S-6. The highest effluent concentration of acetate was observed in the reactor with only
M. mazeii
S-6 immobilized, while the lowest effluent concentration of acetate was observed in the reactor where both types of methanogens were immobilized together. No changes were observed in the kinetic parameters (

K
s

and μ
max
) of immobilized
M. concilii
GP-6 or
M. mazeii
S-6 compared with suspended cultures, indicating that immobilization does not affect the growth kinetics of these methanogens. An enzyme-linked immunosorbent assay using polyclonal antibodies against either
M. concilii
GP-6 or
M. mazeii
S-6 showed significant variations in the two methanogenic populations in the different reactors. Polyclonal antibodies were further used to study the spatial distribution of the two methanogens.
M. concilii
GP-6 was immobilized only on existing support material without any specific pattern.
M. mazeii
S-6, however, showed a different immobilization pattern: large clumps were formed when the concentration of acetate was high, but where the acetate concentration was low this strain was immobilized on support material as single cells or small clumps. The data clearly show that the two aceticlastic methanogens immobilize differently in UASB systems, depending on the conditions found throughout the UASB reactor.
Physiological Characterization of Viable-but-Nonculturable
Campylobacter jejuni
Cells
Authors: Tholozan J. L. , Cappelier J. M. , Tissier J. P. , Delattre G. , Federighi M. 
Published: December 2019

ABSTRACT

Campylobacter jejuni
is a pathogenic, microaerophilic, gram-negative, mesophilic bacterium. Three strains isolated from humans with enteric campylobacteriosis were able to survive at high population levels (10
7
cells ml
−1
) as viable-but-nonculturable (VBNC) forms in microcosm water. The VBNC forms of the three
C. jejuni
strains were enumerated and characterized by using 5-cyano-2,3-ditolyl tetrazolium chloride–4′,6-diamino-2-phenylindole staining. Cellular volume, adenylate energy charge, internal pH, intracellular potassium concentration, and membrane potential values were determined in stationary-phase cell suspensions after 48 h of culture on Columbia agar and after 1 to 30 days of incubation in microcosm water and compared. A notable increase in cell volume was observed with the VBNC state; the average cell volumes were 1.73 μl mg of protein
−1
for the culturable form and 10.96 μl mg of protein
−1
after 30 days of incubation in microcosm water. Both the internal potassium content and the membrane potential were significantly lower in the VBNC state than in the culturable state. Culturable cells were able to maintain a difference of 0.6 to 0.9 pH unit between the internal and external pH values; with VBNC cells this difference decreased progressively with time of incubation in microcosm water. Measurements of the cellular adenylate nucleotide concentrations revealed that the cells had a low adenylate energy charge (0.66 to 0.26) after 1 day of incubation in microcosm water, and AMP was the only nucleotide detected in the three strains after 30 days of incubation in microcosm water.
Randomly Amplified Polymorphic DNA Analysis of Clinical and Environmental Isolates of
Vibrio vulnificus
and Other
Vibrio
Species
Authors: Warner Jennifer M. , Oliver James D. 
Published: December 2019

ABSTRACT

Vibrio vulnificus
is an estuarine bacterium that is capable of causing a rapidly fatal infection in humans. A randomly amplified polymorphic DNA (RAPD) PCR protocol was developed for use in detecting
V. vulnificus
, as well as other members of the genus
Vibrio
. The resulting RAPD profiles were analyzed by using RFLPScan software. This RAPD method clearly differentiated between members of the genus
Vibrio
and between isolates of
V. vulnificus
. Each
V. vulnificus
strain produced a unique band pattern, indicating that the members of this species are genetically quite heterogeneous. All of the vibrios were found to have amplification products whose sizes were within four common molecular weight ranges, while the
V. vulnificus
strains had an additional two molecular weight range bands in common. All of the
V. vulnificus
strains isolated from clinical specimens produced an additional band that was only occasionally found in environmental strains; this suggests that, as is the case with the Kanagawa hemolysin of
Vibrio parahaemolyticus
, the presence of this band may be correlated with the ability of a strain to produce an infection in humans. In addition, band pattern differences were observed between encapsulated and nonencapsulated isogenic morphotypes of the same strain of
V. vulnificus
.
Identification of a Novel Group of Bacteria in Sludge from a Deteriorated Biological Phosphorus Removal Reactor
Authors: Nielsen Alex T. , Liu Wen-Tso , Filipe Carlos , Grady Leslie , Molin Søren , Stahl David A. 
Published: December 2019

ABSTRACT

The microbial diversity of a deteriorated biological phosphorus removal reactor was investigated by methods not requiring direct cultivation. The reactor was fed with media containing acetate and high levels of phosphate (P/C weight ratio, 8:100) but failed to completely remove phosphate in the effluent and showed very limited biological phosphorus removal activity. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA was used to investigate the bacterial diversity. Up to 11 DGGE bands representing at least 11 different sequence types were observed; DNA from the 6 most dominant of these bands was further isolated and sequenced. Comparative phylogenetic analysis of the partial 16S rRNA sequences suggested that one sequence type was affiliated with the alpha subclass of the
Proteobacteria
, one was associated with the
Legionella
group of the gamma subclass of the
Proteobacteria
, and the remaining four formed a novel group of the gamma subclass of the
Proteobacteria
with no close relationship to any previously described species. The novel group represented approximately 75% of the PCR-amplified DNA, based on the DGGE band intensities. Two oligonucleotide rRNA probes for this novel group were designed and used in a whole-cell hybridization analysis to investigate the abundance of this novel group in situ. The bacteria were coccoid and 3 to 4 μm in diameter and represented approximately 35% of the total population, suggesting a relatively close agreement with the results obtained by the PCR-based DGGE method. Further, based on electron microscopy and standard staining microscopic analysis, this novel group was able to accumulate granule inclusions, possibly consisting of polyhydroxyalkanoate, inside the cells.
In Situ Identification of Cyanobacteria with Horseradish Peroxidase-Labeled, rRNA-Targeted Oligonucleotide Probes
Authors: Schönhuber Wilhelm , Zarda Boris , Eix Stella , Rippka Rosmarie , Herdman Michael , Ludwig Wolfgang , Amann Rudolf 
Published: December 2019

ABSTRACT
Individual cyanobacterial cells are normally identified in environmental samples only on the basis of their pigmentation and morphology. However, these criteria are often insufficient for the differentiation of species. Here, a whole-cell hybridization technique is presented that uses horseradish peroxidase (HRP)-labeled, rRNA-targeted oligonucleotides for in situ identification of cyanobacteria. This indirect method, in which the probe-conferred enzyme has to be visualized in an additional step, was necessary since fluorescently monolabeled oligonucleotides were insufficient to overstain the autofluorescence of the target cells. Initially, a nonfluorescent detection assay was developed and successfully applied to cyanobacterial mats. Later, it was demonstrated that tyramide signal amplification (TSA) resulted in fluorescent signals far above the level of autofluorescence. Furthermore, TSA-based detection of HRP was more sensitive than that based on nonfluorescent substrates. Critical points of the assay, such as cell fixation and permeabilization, specificity, and sensitivity, were systematically investigated by using four oligonucleotides newly designed to target groups of cyanobacteria.
Augmentation of Killing of
Escherichia coli
O157 by Combinations of Lactate, Ethanol, and Low-pH Conditions
Authors: Jordan Sarah L. , Glover Jayne , Malcolm Laura , Thomson-Carter Fiona M. , Booth Ian R. , Park Simon F. 
Published: December 2019

ABSTRACT

The acid tolerance of
Escherichia coli
O157:H7 strains can be overcome by addition of lactate, ethanol, or a combination of the two agents. Killing can be increased by as much as 4 log units in the first 5 min of incubation at pH 3 even for the most acid-tolerant isolates. Exponential-phase, habituated, and stationary-phase cells are all sensitive to incubation with lactate and ethanol. Killing correlates with disruption of the capacity for pH homeostasis. Habituated and stationary-phase cells can partially offset the effects of the lowering of cytoplasmic pH.
Glycine Betaine: Reserve Form of Choline in
Penicillium fellutanum
in Low-Sulfate Medium
Authors: Park Yong-Il , Buszko Marian L. , Gander John E. 
Published: December 2019

ABSTRACT

In spite of choline’s importance in fungal metabolism, its sources in cytoplasm have not been fully established.
13
C nuclear magnetic resonance analysis of mycelial extracts from day-5
Penicillium fellutanum
cultures showed that, as well as choline-
O
-sulfate, intracellular glycine betaine is another reserve form of choline, depending on the availability of sulfate in the culture medium. These observations are discussed relative to the multiple roles of choline and its precursors in
P. fellutanum
.
Role of Surface Proteins in
Vibrio cholerae
Attachment to Chitin
Authors: Tarsi Renato , Pruzzo Carla 
Published: December 2019

ABSTRACT

The role of surface proteins in
Vibrio cholerae
attachment to chitin particles in vitro was studied. Treatment of
V. cholerae
O1 ATCC 14034 and ATCC 14035 with pronase E reduced the attachment of bacteria to chitin particles by 57 to 77%. A statistically significant reduction was also observed when the attachment to chitin was evaluated in the presence of homologous Sarkosyl-insoluble membrane proteins (MPs) (67 to 84%),
N
-acetylglucosamine (GlcNAc) (62%), the sugar that makes up chitin, and wheat germ agglutinin (40 to 56%), a lectin that binds GlcNAc. The soluble oligomers
N
,
N
′-diacetylchitobiose or
N
,
N
′,
N
"-triacetylchitotriose caused an inhibition of 14 to 23%. Sarkosyl-insoluble MPs able to bind chitin particles were isolated and visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; two of these peptides (molecular sizes, 36 and 53 kDa) specifically bind GlcNAc.
A Search for Ligninolytic Peroxidases in the Fungus
Pleurotus eryngii
Involving α-Keto-γ-Thiomethylbutyric Acid and Lignin Model Dimers
Authors: Caramelo Lucília , Martínez María Jesús , Martínez Ángel T. 
Published: December 2019

ABSTRACT

Because there is some controversy concerning the ligninolytic enzymes produced by
Pleurotus
species, ethylene release from α-keto-γ-thiomethylbutyric acid (KTBA), as described previously for
Phanerochaete chrysosporium
lignin peroxidase (LiP), was used to assess the oxidative power of
Pleurotus eryngii
cultures and extracellular proteins. Lignin model dimers were used to confirm the ligninolytic capabilities of enzymes isolated from liquid and solid-state fermentation (SSF) cultures. Three proteins that oxidized KTBA in the presence of veratryl alcohol and H
2
O
2
were identified (two proteins were found in liquid cultures, and one protein was found in SSF cultures). These proteins are versatile peroxidases that act on Mn
2+
, as well as on simple phenols and veratryl alcohol. The two peroxidases obtained from the liquid culture were able to degrade a nonphenolic β-O-4 dimer, yielding veratraldehyde, as well as a phenolic dimer which is not efficiently oxidized by
P. chrysosporium
peroxidases. The former reaction is characteristic of LiP. The third KTBA-oxidizing peroxidase oxidized only the phenolic dimer (in the presence of Mn
2+
). Finally, a fourth Mn
2+
-oxidizing peroxidase was identified in the SSF cultures on the basis of its ability to oxidize KTBA in the presence of Mn
2+
. This enzyme is related to the Mn-dependent peroxidase of
P. chrysosporium
because it did not exhibit activity with veratryl alcohol and Mn-independent activity with dimers. These results show that
P. eryngii
produces three types of peroxidases that have the ability to oxidize lignin but lacks a typical LiP. Similar enzymes (in terms of N-terminal sequence and catalytic properties) are produced by other
Pleurotus
species. Some structural aspects of
P. eryngii
peroxidases related to the catalytic properties are discussed.
Bacterivory Rate Estimates and Fraction of Active Bacterivores in Natural Protist Assemblages from Aquatic Systems
Authors: González Juan M. 
Published: December 2019

ABSTRACT
Unlike the fraction of active bacterioplankton, the fraction of active bacterivores (i.e., those involved in grazing) during a specified time period has not been studied yet. Fractions of protists actively involved in bacterivory were estimated assuming that the distributions of bacteria and fluorescently labeled bacteria (FLB) ingested by protists follow Poisson distributions. Estimates were compared with experimental data obtained from FLB uptake experiments. The percentages of protists with ingested FLB (experimental) and the estimates obtained from Poisson distributions were similar for both flagellates and ciliates. Thus, the fraction of protists actively grazing on natural bacteria during a given time period could be estimated. The fraction of protists with ingested bacteria depends on the incubation time and reaches a saturating value. Aquatic systems with very different characteristics were analyzed; estimates of the fraction of protists actively grazing on bacteria ranged from 7 to 100% in the studied samples. Some nanoflagellates appeared to be grazing on specific bacterial sizes. Evidence indicated that there was no discrimination for or against bacterial surrogates (i.e., FLB); also, bacteria were randomly encountered by bacterivorous protists during these short-term uptake experiments. These analyses made it possible to estimate the ingestion rates from FLB uptake experiments by counting the number of flagellates containing ingested FLB. These results represent the first reported estimates of active bacterivores in natural aquatic systems; also, a proposed protocol for estimating in situ ingestion rates by protists represents a significant improvement and simplification to the current protocol and avoids the tedious work of counting the number of ingested FLB per protist.
Reduction of Cell Lysate Viscosity during Processing of Poly(3-Hydroxyalkanoates) by Chromosomal Integration of the Staphylococcal Nuclease Gene in
Pseudomonas putida
Authors: Boynton Zhuang L. , Koon Joseph J. , Brennan Elaine M. , Clouart Jeralyn D. , Horowitz Daniel M. , Gerngross Tillman U. , Huisman Gjalt W. 
Published: December 2019

ABSTRACT

Poly(3-hydroxyalkanoates) (PHAs) are biodegradable thermoplastics which are accumulated by many bacterial species in the form of intracellular granules and which are thought to serve as reserves of carbon and energy.
Pseudomonas putida
accumulates a polyester, composed of medium-side-chain 3-hydroxyalkanoic acids, which has excellent film-forming properties. Industrial processing of PHA involves purification of the PHA granules from high-cell-density cultures. After the fermentation process, cells are lysed by homogenization and PHA granules are purified by chemical treatment and repeated washings to yield a PHA latex. Unfortunately, the liberation of chromosomal DNA during lysis causes a dramatic increase in viscosity, which is problematic in the subsequent purification steps. Reduction of the viscosity is generally achieved by the supplementation of commercially available nuclease preparations or by heat treatment; however, both procedures add substantial costs to the process. As a solution to this problem, a nuclease-encoding gene from
Staphylococcus aureus
was integrated into the genomes of several PHA producers. Staphylococcal nuclease is readily expressed in PHA-producing
Pseudomonas
strains and is directed to the periplasm, and occasionally to the culture medium, without affecting PHA production or strain stability. During downstream processing, the viscosity of the lysate from a nuclease-integrated
Pseudomonas
strain was reduced to a level similar to that observed for the wild-type strain after treatment with commercial nuclease. The nuclease gene was also functionally integrated into the chromosomes of other PHA producers, including
Ralstonia eutropha
.
Microbiological and Geochemical Characterization of Fluvially Deposited Sulfidic Mine Tailings
Authors: Wielinga Bruce , Lucy Juliette K. , Moore Johnnie N. , Seastone October F. , Gannon James E. 
Published: December 2019

ABSTRACT
The fluvial deposition of mine tailings generated from historic mining operations near Butte, Montana, has resulted in substantial surface and shallow groundwater contamination along Silver Bow Creek. Biogeochemical processes in the sediment and underlying hyporheic zone were studied in an attempt to characterize interactions consequential to heavy-metal contamination of shallow groundwater. Sediment cores were extracted and fractionated based on sediment stratification. Subsamples of each fraction were assayed for culturable heterotrophic microbiota, specific microbial guilds involved in metal redox transformations, and both aqueous- and solid-phase geochemistry. Populations of cultivable Fe(III)-reducing bacteria were most prominent in the anoxic, circumneutral pH regions associated with a ferricrete layer or in an oxic zone high in organic carbon and soluble iron. Sulfur- and iron-oxidizing bacteria were distributed in discrete zones throughout the tailings and were often recovered from sections at and below the anoxic groundwater interface. Sulfate-reducing bacteria were also widely distributed in the cores and often occurred in zones overlapping iron and sulfur oxidizers. Sulfate-reducing bacteria were consistently recovered from oxic zones that contained high concentrations of metals in the oxidizable fraction. Altogether, these results suggest a highly varied and complex microbial ecology within a very heterogeneous geochemical environment. Such physical and biological heterogeneity has often been overlooked when remediation strategies for metal contaminated environments are formulated.
Production of Poly(3-Hydroxybutyric Acid-Co-4-Hydroxybutyric Acid) and Poly(4-Hydroxybutyric Acid) without Subsequent Degradation by
Hydrogenophaga pseudoflava
Authors: Choi Mun Hwan , Yoon Sung Chul , Lenz Robert W. 
Published: December 2019

ABSTRACT

A
Hydrogenophaga pseudoflava
strain was able to synthesize poly(3-hydroxybutyric acid-co-4-hydroxybutyric acid) [P(3HB-co-4HB)] having a high level of 4-hydroxybutyric acid monomer unit (4HB) from γ-butyrolactone. In a two-step process in which the first step involved production of cells containing a minimum amount of poly(3-hydroxybutyric acid) [P(3HB)] and the second step involved polyester accumulation from the lactone, approximately 5 to 10 mol% of the 3-hydroxybutyric acid (3HB) derived from the first-step culture was unavoidably reincorporated into the polymer in the second cultivation step. Reincorporation of the 3HB units produced from degradation of the first-step residual P(3HB) was confirmed by high-resolution
13
C nuclear magnetic resonance spectroscopy. In order to synthesize 3HB-free poly(4-hydroxybutyric acid) [P(4HB)] homopolymer, a three-stage cultivation technique was developed by adding a nitrogen addition step, which completely removed the residual P(3HB). The resulting polymer was free of 3HB. However, when the strain was grown on γ-butyrolactone as the sole carbon source in a synthesis medium, a copolyester of P(3HB-co-4HB) containing 45 mol% 3HB was produced. One-step cultivation on γ-butyrolactone required a rather long induction time (3 to 4 days). On the basis of the results of an enzymatic study performed with crude extracts, we suggest that the inability of cells to produce 3HB in the multistep culture was due to a low level of 4-hydroxybutyric acid (4HBA) dehydrogenase activity, which resulted in a low level of acetyl coenzyme A. Thus, 3HB formation from γ-butyrolactone is driven by a high level of 4HBA dehydrogenase activity induced by long exposure to γ-butyrolactone, as is the case for a one-step culture. In addition, intracellular degradation kinetics studies showed that P(3HB) in cells was completely degraded within 30 h of cultivation after being transferred to a carbon-free mineral medium containing additional ammonium sulfate, while P(3HB-co-4HB) containing 5 mol% 3HB and 95 mol% 4HB was totally inert in interactions with the intracellular depolymerases. Intracellular inertness could be a useful factor for efficient synthesis of the P(4HB) homopolymer and of 4HB-rich P(3HB-co-4HB) by the strain used in this study.