bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cytochrome
c
Maturation Operon Is Involved in Manganese Oxidation in
Pseudomonas putida
GB-1
Authors: de Vrind J. P. M. , Brouwers G. J. , Corstjens P. L. A. M. , den Dulk J. , de Vrind-de Jong E. W. 
Published: December 2019

ABSTRACT

A
Pseudomonas putida
strain, strain GB-1, oxidizes Mn
2+
to Mn oxide in the early stationary growth phase. It also secretes a siderophore (identified as pyoverdine) when it is subjected to iron limitation. After transposon (Tn
5
) mutagenesis several classes of mutants with differences in Mn
2+
oxidation and/or secretion of the Mn
2+
-oxidizing activity were identified. Preliminary analysis of the Tn
5
insertion site in one of the nonoxidizing mutants suggested that a multicopper oxidase-related enzyme is involved in Mn
2+
oxidation. The insertion site in another mutant was preliminarily identified as a gene involved in the general protein secretion pathway. Two mutants defective in Mn
2+
-oxidizing activity also secreted porphyrins into the medium and appeared to be derepressed for pyoverdine production. These strains were chosen for detailed analysis. Both mutants were shown to contain Tn
5
insertions in the
ccmF
gene, which is part of the cytochrome
c
maturation operon. They were cytochrome oxidase negative and did not contain
c
-type cytochromes. Complementation with part of the
ccm
operon isolated from the wild type restored the phenotype of the parent strain. These results indicate that a functional
ccm
operon is required for Mn
2+
oxidation in
P. putida
GB-1. A possible relationship between porphyrin secretion resulting from the
ccm
mutation and stimulation of pyoverdine production is discussed.
Application of Molecular Biological Techniques to a Seasonal Study of Ammonia Oxidation in a Eutrophic Freshwater Lake
Authors: Hastings Richard C. , Saunders Jon R. , Hall Grahame H. , Pickup Roger W. , McCarthy Alan J. 
Published: December 2019

ABSTRACT

The autotrophic ammonia-oxidizing bacteria in a eutrophic freshwater lake were studied over a 12-month period. Numbers of ammonia oxidisers in the lakewater were small throughout the year, and tangential-flow concentration was required to obtain meaningful estimates of most probable numbers. Sediments from littoral and profundal sites supported comparatively large populations of these bacteria, and the nitrification potential was high, particularly in summer samples from the littoral sediment surface. In enrichment cultures, lakewater samples nitrified at low (0.67 mM) ammonium concentrations only whereas sediment samples exhibited nitrification at high (12.5 mM) ammonium concentrations also. Enrichments at low ammonium concentration did not nitrify when inoculated into high-ammonium medium, but the converse was not true. This suggests that the water column contains a population of ammonia oxidizers that is sensitive to high ammonium concentrations. The observation of nitrification at high ammonium concentration by isolates from some winter lakewater samples, identified as nitrosospiras by 16S rRNA probing, is consistent with the hypothesis that sediment ammonia oxidizers enter the water column at overturn. With only one exception, nested PCR amplification enabled the detection of
Nitrosospira
16S rDNA in all samples, but
Nitrosomonas
(
N. europaea-eutropha
lineage) 16S rDNA was never obtained. However, the latter were part of the sediment and water column communities, because their 16S rRNA could be detected by specific oligonucleotide probing of enrichment cultures. Furthermore, a specific PCR amplification regime for the
Nitrosomonas europaea
ammonia monooxygenase gene (
amoA
) yielded positive results when applied directly to sediment and lakewater samples. Patterns of
Nitrosospira
and
Nitrosomonas
detection by 16S rRNA oligonucleotide probing of sediment enrichment cultures were complex, but lakewater enrichments at low ammonium concentration were positive for nitrosomonads and not nitrosospiras. Analysis of enrichment cultures has therefore provided evidence for the existence of subpopulations within the lake ammonia-oxidizing community distinguishable on the basis of ammonium tolerance and possibly showing a seasonal distribution between the sediment and water column.
Enhanced Utilization of Phosphonate and Phosphite by
Klebsiella aerogenes
Authors: Imazu Kazuya , Tanaka Shotaro , Kuroda Akio , Anbe Yuki , Kato Junichi , Ohtake Hisao 
Published: December 2019

ABSTRACT

Klebsiella aerogenes
ATCC 9621 was able to utilize phosphonates (P
n
), including aminoethylphosphonate, ethylphosphonate, methylphosphonate (MP
n
), and phosphonoacetate, and inorganic phosphite (P
t
) as sole sources of phosphorus (P). The products of the
phn
gene cluster were absolutely required for P
n
breakdown and P
t
oxidation to inorganic phosphate (P
i
) in this organism. To determine if
K. aerogenes
ATCC 9621 could be engineered to enhance the utilization of P
n
and P
t
, a multicopy plasmid, pBI05, which carried the entire
phn
gene cluster, was introduced into this strain. Despite the increased dosage of the
phn
genes,
K. aerogenes
ATCC 9621(pBI05) could utilize only up to 1.1-fold more P
n
and P
t
than did the control strain with the parent vector alone. These results suggested that P
i
, which was generated from P
n
and P
t
, might limit further utilization of these P compounds. Consequently, to convert the resulting P
i
to polyphosphate (polyP), the plasmid pKP28, which carried the
K. aerogenes ppk
gene (which encodes polyP kinase), was introduced into
K. aerogenes
ATCC 9621(pBI05). Overexpression of the
ppk
gene in
K. aerogenes
ATCC 9621(pBI05, pKP28) resulted in a 2.5-fold increase in P
t
utilization over that of the control strain. This recombinant strain also accumulated approximately sixfold more P than did the control strain when the cells were grown with MP
n
as a sole source of P.
Xanthan Lyase of
Bacillus
sp. Strain GL1 Liberates Pyruvylated Mannose from Xanthan Side Chains
Authors: Hashimoto Wataru , Miki Hikaru , Tsuchiya Noriaki , Nankai Hirokazu , Murata Kousaku 
Published: December 2019

ABSTRACT

When the bacterium
Bacillus
sp. strain GL1 was grown in a medium containing xanthan as the carbon source, the viscosity of the medium decreased in association with growth, showing that the bacterium had xanthan-depolymerizing enzymes. One of the xanthan-depolymerizing enzymes (xanthan lyase) was present in the medium and was found to be induced by xanthan. The xanthan lyase purified from the culture fluid was a monomer with a molecular mass of 75 kDa, and was most active at pH 5.5 and 50°C. The enzyme was highly specific for xanthan and produced pyruvylated mannose. The result indicates that the enzyme cleaved the linkage between the terminal pyruvylated mannosyl and glucuronyl residues in the side chain of xanthan.
Genetic Characterization of
Pseudomonas syringae
pv. syringae Strains from Stone Fruits in California
Authors: Little E. L. , Bostock R. M. , Kirkpatrick B. C. 
Published: December 2019

ABSTRACT

Strains of
Pseudomonas syringae
pv. syringae were isolated from healthy and diseased stone fruit tissues sampled from 43 orchard sites in California in 1995 and 1996. These strains, together with
P. syringae
strains from other hosts and pathovars, were tested for pathogenicity and the presence of the
syrB
and
syrC
genes and were genetically characterized by using enterobacterial repetitive intergenic consensus (ERIC) primers and PCR. All 89 strains of
P. syringae
pv. syringae tested were moderately to highly pathogenic on Lovell peach seedlings regardless of the host of origin, while strains of other pathovars exhibited low or no pathogenicity. The 19 strains of
P. syringae
pv. syringae examined by restriction fragment length polymorphism analysis contained the
syrB
and
syrC
genes, whereas no hybridization occurred with 4 strains of other
P. syringae
pathovars. The
P. syringae
pv. syringae strains from stone fruit, except for a strain from New Zealand, generated ERIC genomic fingerprints which shared four fragments of similar mobility. Of the
P. syringae
pv. syringae strains tested from other hosts, only strains from rose, kiwi, and pear generated genomic fingerprints that had the same four fragments as the stone fruit strains. Analysis of the ERIC fingerprints from
P. syringae
pv. syringae strains showed that the strains isolated from stone fruits formed a distinct cluster separate from most of the strains isolated from other hosts. These results provide evidence of host specialization within the diverse pathovar
P. syringae
pv. syringae.
Characterization of Genes Involved in Biosynthesis of a Novel Antibiotic from
Burkholderia cepacia
BC11 and Their Role in Biological Control of
Rhizoctonia solani
Authors: Kang Yaowei , Carlson Russell , Tharpe Wendy , Schell Mark A. 
Published: December 2019

ABSTRACT

Genetic manipulation of fluorescent pseudomonads has provided major insight into their production of antifungal molecules and their role in biological control of plant disease.
Burkholderia cepacia
also produces antifungal activities, but its biological control activity is much less well characterized, in part due to difficulties in applying genetic tools. Here we report genetic and biochemical characterization of a soil isolate of
B. cepacia
relating to its production of an unusual antibiotic that is very active against a variety of soil fungi. Purification and preliminary structural analyses suggest that this antibiotic (called AFC-BC11) is a novel lipopeptide associated largely with the cell membrane. Analysis of conditions for optimal production of AFC-BC11 indicated stringent environmental regulation of its synthesis. Furthermore, we show that production of AFC-BC11 is largely responsible for the ability of
B. cepacia
BC11 to effectively control the damping-off of cotton caused by the fungal pathogen
Rhizoctonia solani
in a gnotobiotic system. Using Tn
5
mutagenesis, we identified, cloned, and characterized a region of the genome of strain BC11 that is required for production of this antifungal metabolite. DNA sequence analysis suggested that this region encodes proteins directly involved in the production of a nonribosomally synthesized lipopeptide.
Isolation and Identification of
Helicobacter
spp. from Canine and Feline Gastric Mucosa
Authors: Jalava Katri , On Stephen L. W. , Vandamme Peter A. R. , Happonen Irmeli , Sukura Antti , Hänninen Marja-Liisa 
Published: December 2019

ABSTRACT

It is known that virtually all healthy adult dogs and cats harbor spiral helicobacters in their gastric mucosa. Three species,
Helicobacter felis
,
Helicobacter bizzozeronii
, and
Helicobacter salomonis
have been isolated in vitro from the gastric mucosa of these animals. The aims of this study were to evaluate the efficacy of an isolation method for canine and feline gastric helicobacters that has been developed at the University of Helsinki; to estimate the prevalence and distribution of these taxa in the samples examined; and to assess the efficacy and validity of an extensive set of standardized conventional phenotypic tests, whole-cell protein profiling, and ultrastructural analysis in identifying the different species isolated from canine and feline gastric mucosa. We cultured 95 and 22 gastric mucosal biopsies from dogs and cats, respectively. Twenty-one
H. bizzozeronii
strains, 8
H. felis
strains, 8
H. salomonis
strains, 3 mixed cultures, 2 “
Flexispira rappini
”-like organisms, and 3 as yet uncharacterized strains were isolated from the dogs, and 3
H. felis
strains were isolated from the cats. The methods used here yielded
Helicobacter
isolation rates of 51% from dogs and 13.6% from cats, which exceed those reported previously. The main difficulties were primary isolation, mixed cultures, and identification to the species level. In the species identification, a detailed morphological examination was found to yield important phenotypic characteristics. A large panel of biochemical and tolerance tests did not clearly differentiate the closely related species
H. bizzozeronii
,
H. felis
, and
H. salomonis
. Highly standardized whole-cell protein profiling was shown to be an excellent method for species identification. Improvements in culture conditions for these bacteria are still needed, especially for cats. A genetic identification method not requiring culture is needed for future studies of these very fastidious helicobacters, as the clinical significance and ecology of these species within the gastric mucosa of the domestic carnivores remain largely unknown.
Resistance to Tellurite as a Selection Marker for Genetic Manipulations of
Pseudomonas
Strains
Authors: Sanchez-Romero Juan M. , Diaz-Orejas Ramon , De Lorenzo Victor 
Published: December 2019

ABSTRACT

Resistance to the toxic compound potassium tellurite (Tel
r
) has been employed as a selection marker built into a set of transposon vectors and broad-host-range plasmids tailored for genetic manipulations of
Pseudomonas
strains potentially destined for environmental release. In this study, the activated Tel
r
determinants encoded by the cryptic
telAB
genes of plasmid RK2 were produced, along with the associated
kilA
gene, as DNA cassettes compatible with cognate vectors. In one case, the Tel
r
determinants were assembled between the I and O ends of a suicide delivery vector for mini-Tn
5
transposons. In another case, the
kilA
and
telAB
genes were combined with a minimal replicon derived from a variant of
Pseudomonas
plasmid pPS10, which is able to replicate in a variety of gram-negative hosts and is endowed with a modular collection of cloning and expression assets. Either in the plasmid or in the transposon vector, the Tel
r
marker was combined with a 12-kb DNA segment of plasmid pWW0 of
Pseudomonas putida
mt-2 encoding the upper TOL pathway enzymes. This allowed construction of antibiotic resistance-free but selectable
P. putida
strains with the ability to grow on toluene as the sole carbon source through an
ortho
-cleavage catabolic pathway.
Synthesis of Glycine Betaine from Exogenous Choline in the Moderately Halophilic Bacterium
Halomonas elongata
Authors: Cánovas David , Vargas Carmen , Csonka Laszlo N. , Ventosa Antonio , Nieto Joaquín J. 
Published: December 2019

ABSTRACT

The role of choline in osmoprotection in the moderate halophile
Halomonas elongata
has been examined. Transport and conversion of choline to betaine began immediately after addition of choline to the growth medium. Intracellular accumulation of betaine synthesized from choline was salt dependent up to 2.5 M NaCl. Oxidation of choline was enhanced at 2.0 M NaCl in the presence or absence of externally provided betaine. This indicates that the NaCl concentration in the growth medium has major effects on the choline-betaine pathway of
H. elongata
.
Automated Confocal Laser Scanning Microscopy and Semiautomated Image Processing for Analysis of Biofilms
Authors: Kuehn Martin , Hausner Martina , Bungartz Hans-Joachim , Wagner Michael , Wilderer Peter A. , Wuertz Stefan 
Published: December 2019

ABSTRACT

The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study,
Pseudomonas fluorescens
or a green fluorescent protein-expressing
Escherichia coli
strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.
Analysis of the Bacteriolytic Enzymes of the Autolytic
Lactococcus lactis
subsp.
cremoris
Strain AM2 by Renaturing Polyacrylamide Gel Electrophoresis: Identification of a Prophage-Encoded Enzyme
Authors: Lepeuple Anne-Sophie , Van Gemert Ellis , Chapot-Chartier Marie-Pierre 
Published: December 2019

ABSTRACT

Lactococcus lactis
subsp.
cremoris
AM2 was previously shown to lyse early and extensively during cheese ripening (M.-P. Chapot-Chartier, C. Deniel, M. Rousseau, L. Vassal, and J.-C. Gripon, Int. Dairy J. 4:251–269, 1994). We analyzed the bacteriolytic activities of autolytic strain AM2 by using renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis performed with two different substrates in the gel,
Micrococcus lysodeikticus
and
L. lactis
autoclaved cells. Several lytic activities were detected in
L. lactis
AM2; a major lytic activity, designated A2 (46 kDa), was found only with the
L. lactis
cell substrate. This activity appears to be different from major peptidoglycan hydrolase AcmA characterized previously (G. Buist, J. Kok, K. J. Leenhouts, M. Dabrowska, G. Venema, and A. J. Haandrickman, J. Bacteriol. 177:1554–1563, 1995), which has a similar molecular mass. The two enzymes differ in substrate specificity as well as in sensitivity to pH and different chemical compounds.
L. lactis
AM2 is lysogenic and mitomycin C inducible. Enzyme A2 was shown to be inducible by mitomycin C and to be prophage encoded. It was identified as an enzyme similar to the lysin encoded by lactococcal small isometric temperate bacteriophages. A prophage-cured derivative of
L. lactis
AM2 was obtained, and this isolate exhibited different autolytic properties than AM2. After prolonged incubation in the stationary phase after growth on M17 medium, the extent of lysis of an AM2 culture was 60%, whereas over the same period there was almost no lysis in a prophage-cured derivative strain culture. These results suggest that the prophage lytic system is involved in the strain AM2 lysis observed in liquid medium and that it could also be involved in the lysis observed during cheese ripening.
Ethylene Removal by a Biofilter with Immobilized Bacteria
Authors: Elsgaard Lars 
Published: December 2019

ABSTRACTA biofilter which eliminated ethylene (C2H4) from the high parts-per-million range to levels near the limit for plant hormonal activity (0.01 to 0.1 ppm) was developed. Isolated ethylene-oxidizing bacteria were immobilized on peat-soil in a biofilter (687 cm3) and subjected to an atmospheric gas flow (73.3 ml min−1) with 2 or 117 ppm of C2H4. Ethylene was eliminated to a minimum level of 0.017 ppm after operation with 2.05 ppm of C2H4for 16 days. Also, the inlet C2H4concentration of 117 ppm was reduced to <0.04 ppm. During operation with 2 and 117 ppm of C2H4, an increase in the C2H4removal rate was observed, which was attributed to proliferation of the immobilized bacteria, notably in the first 0- to 5-cm segment of the biofilter. The maximal C2H4elimination capacity of the biofilter was 21 g of C2H4m−3day−1during operation with 117 ppm of C2H4in the inlet gas. However, for the first 0- to 5-cm segment of the biofilter, an elimination capacity of 146 g of C2H4m−3day−1was calculated. Transition of the biofilter temperature from 21 to 10°C caused a 1.6-fold reduction in the C2H4removal rate, which was reversed during operation for 18 days. Batch experiments with inoculated peat-soil demonstrated that C2H4removal still occurred after storage at 2, 8, and 20°C for 2, 3, and 4 weeks. However, the C2H4removal rate decreased with increasing storage time and was reduced by ca. 50% after storage for 2 weeks at all three temperatures. The biofilter could be a suitable tool for C2H4removal in, e.g., horticultural storage facilities, since it (i) removed C2H4to 0.017 ppm, (ii) had a good operational stability, and (iii) operated efficiently at 10°C.
Biodegradation of Aromatic Hydrocarbons in an Extremely Acidic Environment
Authors: Stapleton Raymond D. , Savage Dwayne C. , Sayler Gary S. , Stacey Gary 
Published: December 2019

ABSTRACTThe potential for biodegradation of aromatic hydrocarbons was evaluated in soil samples recovered along gradients of both contaminant levels and pH values existing downstream of a long-term coal pile storage basin. pH values for areas greatly impacted by runoff from the storage basin were 2.0. Even at such a reduced pH, the indigenous microbial community was metabolically active, showing the ability to oxidize more than 40% of the parent hydrocarbons, naphthalene and toluene, to carbon dioxide and water. Treatment of the soil samples with cycloheximide inhibited mineralization of the aromatic substrates. DNA hybridization analysis indicated that whole-community nucleic acids recovered from these samples did not hybridize with genes, such asnahA,nahG,nahH,todC1C2, andtomA, that encode common enzymes from neutrophilic bacteria. Since these data suggested that the degradation of aromatic compounds may involve a microbial consortium instead of individual acidophilic bacteria, experiments using microorganisms isolated from these samples were initiated. While no defined mixed cultures were able to evolve14CO2from labeled substrates in these mineralization experiments, an undefined mixed culture including a fungus, a yeast, and several bacteria successfully metabolized approximately 27% of supplied naphthalene after 1 week. This study shows that biodegradation of aromatic hydrocarbons can occur in environments with extremely low pH values.
Purification and Characterization of a Trehalose Synthase from the Basidiomycete
Grifola frondosa
Authors: Saito Koki , Kase Toshiya , Takahashi Eiichi , Takahashi Eisaku , Horinouchi Sueharu 
Published: December 2019

ABSTRACT

A trehalose synthase (TSase) that catalyzes the synthesis of trehalose from
d
-glucose and α-
d
-glucose 1-phosphate (α-
d
-glucose 1-P) was detected in a basidiomycete,
Grifola frondosa
. TSase was purified 106-fold to homogeneity with 36% recovery by ammonium sulfate precipitation and several steps of column chromatography. The native enzyme appears to be a dimer since it has apparent molecular masses of 120 kDa, as determined by gel filtration column chromatography, and 60 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Although TSase catalyzed the phosphorolysis of trehalose to
d
-glucose and α-
d
-glucose 1-P, in addition to the synthesis of trehalose from the two substrates, the TSase equilibrium strongly favors trehalose synthesis. The optimum temperatures for phosphorolysis and synthesis of trehalose were 32.5 to 35°C and 35 to 37.5°C, respectively. The optimum pHs for these reactions were 6.5 and 6.5 to 6.8, respectively. The substrate specificity of TSase was very strict: among eight disaccharides examined, only trehalose was phosphorolyzed, and only α-
d
-glucose 1-P served as a donor substrate with
d
-glucose as the acceptor in trehalose synthesis. Two efficient enzymatic systems for the synthesis of trehalose from sucrose were identified. In system I, the α-
d
-glucose 1-P liberated by 1.05 U of sucrose phosphorylase was linked with
d
-glucose by 1.05 U of TSase, generating trehalose at the initial synthesis rate of 18 mmol/h in a final yield of 90 mol% under optimum conditions (300 mM each sucrose and glucose, 20 mM inorganic phosphate, 37.5°C, and pH 6.5). In system II, we added 1.05 U of glucose isomerase and 20 mM MgSO
4
to the reaction mixture of system I to convert fructose, a by-product of the sucrose phosphorylase reaction, into glucose. This system generated trehalose at the synthesis rate of 4.5 mmol/h in the same final yield.