bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light-Mediated Nitrite Accumulation during Denitrification by
Pseudomonas
sp. Strain JR12
Authors: Barak Yoram , Tal Yossi , van Rijn Jaap 
Published: December 2019

ABSTRACT

The effect of light on the denitrifying characteristics of a nonphotosynthetic denitrifier,
Pseudomonas
sp. strain JR12, was examined. Already at low light intensities, nitrite accumulated as a result of light inhibition of nitrite but not of nitrate reduction rates. Exposure of this bacterium to light caused a photooxidation of cytochrome
c
, an intermediate electron carrier in its respiratory pathway. Photoinhibition of nitrite reduction was reversible, as nitrite reduction rates returned to preillumination levels when light-exposed cells were returned to dark conditions. Antimycin A reversed the inhibitory effect of light on nitrite reduction by preventing a reversed electron flow. Aerobic respiration by this bacterium was not affected by light.
Cloning and Sequencing of the
Sphingomonas
(
Pseudomonas
)
paucimobilis
Gene Essential for the O Demethylation of Vanillate and Syringate
Authors: Nishikawa Seiji , Sonoki Tomonori , Kasahara Tatsuhide , Obi Takahiro , Kubota Shoko , Kawai Shinya , Morohoshi Noriyuki , Katayama Yoshihiro 
Published: December 2019

ABSTRACT

Sphingomonas
(
Pseudomonas
)
paucimobilis
SYK-6 is able to grow on 5,5′-dehydrodivanillic acid (DDVA), syringate, vanillate, and other dimeric model compounds of lignin as a sole carbon source. Nitrosoguanidine mutagenesis of
S. paucimobilis
SYK-6 was performed, and two mutants with altered DDVA degradation pathways were isolated. The mutant strain NT-1 could not degrade DDVA, but could degrade syringate, vanillate, and 2,2′,3′-trihydroxy-3-methoxy-5,5′-dicarboxybiphenyl (OH-DDVA). Strain DC-49 could slowly assimilate DDVA, but could degrade neither vanillate nor syringate, although it could degrade protocatechuate and 3-
O
-methylgallate. A complementing DNA fragment of strain DC-49 was isolated from the cosmid library of strain SYK-6. The minimum DNA fragment complementing DC-49 was determined to be the 1.8-kbp insert of pKEX2.0. Sequencing analysis showed an open reading frame of 1,671 bp in this fragment, and a similarity search indicated that the deduced amino acid sequence of this open reading frame had significant similarity (60%) to the formyltetrahydrofolate synthetase of
Clostridium thermoaceticum.
Transcription of
ppk
from
Acinetobacter
sp. Strain ADP1, Encoding a Putative Polyphosphate Kinase, Is Induced by Phosphate Starvation
Authors: Geißdörfer Walter , Ratajczak Andreas , Hillen Wolfgang 
Published: December 2019

ABSTRACT

Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP. We cloned the
ppk
gene (2,073 bp) from
Acinetobacter
sp. strain ADP1; this gene encodes a putative polypeptide of 78.6 kDa with extensive homology to polyphosphate kinase from
Escherichia coli
and other bacteria. Chromosomal disruption of
ppk
by inserting a transcriptionally fused
lacZ
does not affect growth under conditions of phosphate limitation or excess. β-Galactosidase activity expressed from the single-copy
ppk
::
lacZ
fusion is induced 5- to 15-fold by phosphate starvation. An increased amount of
ppk
transcript (2.2 kb) was detected when cells were grown at a limiting phosphate concentration. Primer extension analysis revealed a regulated promoter located upstream of a second, constitutive promoter. Potential similarities of this regulation with the effects of PhoB and PhoR of
E. coli
are discussed.
Biochemical and Genetic Characterization of an Extracellular Protease from
Pseudomonas fluorescens
CY091
Authors: Liao Ching-Hsing , McCallus Daniel E. 
Published: December 2019

ABSTRACT

Pseudomonas fluorescens
CY091 cultures produce an extracellular protease with an estimated molecular mass of 50 kDa. Production of this enzyme (designated AprX) was observed in media containing CaCl
2
or SrCl
2
but not in media containing ZnCl
2
, MgCl
2
, or MnCl
2
. The requirement of Ca
2+
(or Sr
2+
) for enzyme production was concentration dependent, and the optimal concentration for production was determined to be 0.35 mM. Following ammonium sulfate precipitation and ion-exchange chromatography, the AprX in the culture supernatant was purified to near electrophoretic homogeneity. Over 20% of the enzyme activity was retained in the AprX sample which had been heated in boiling water for 10 min, indicating that the enzyme is highly resistant to heat inactivation. The enzyme activity was almost completely inhibited in the presence of 1 mM 1,10-phenanthroline, but only 30% of the activity was inhibited in the presence of 1 mM EGTA. The gene encoding AprX was cloned from the genome of
P. fluorescens
CY091 by isolating cosmid clones capable of restoring the protease production in a nonproteolytic mutant of strain CY091. The genomic region of strain CY091 containing the
aprX
gene was located within a 7.3-kb DNA fragment. Analysis of the complete nucleotide sequence of this 7.3-kb fragment revealed the presence of a cluster of genes required for the production of extracellular AprX in
P. fluorescens
and
Escherichia coli
. The AprX protein showed 50 to 60% identity in amino acid sequence to the related proteases produced by
Pseudomonas aeruginosa
and
Erwinia chrysanthemi
. Two conserved sequence domains possibly associated with Ca
2+
and Zn
2+
binding were identified. Immediately adjacent to the
aprX
structural gene, a gene (
inh
) encoding a putative protease inhibitor and three genes (
aprD
,
aprE
, and
aprF
), possibly required for the transport of AprX, were also identified. The organization of the gene cluster involved in the synthesis and secretion of AprX in
P. fluorescens
CY091 appears to be somewhat different from that previously demonstrated in
P. aeruginosa
and
E. chrysanthemi.
Acidophilic Methanotrophic Communities from
Sphagnum
Peat Bogs
Authors: Dedysh Svetlana N. , Panikov Nicolai S. , Tiedje James M. 
Published: December 2019

ABSTRACT

Highly enriched methanotrophic communities (>25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. The enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20°C), and pH values of 3 to 6. Enriched communities contained a mixture of rod-shaped bacteria arranged in aggregates with a minor contribution of
Hyphomicrobium
-like cells. The growth stoichiometry of isolates was characteristic of methanotrophic bacteria (CH
4
/O
2
/CO
2
=1:1.1:0.59), with an average apparent yield of 0.41 ± 0.03 g of biomass C/g of CH
4
-C. DNA from each enrichment yielded a PCR product of the expected size with primers for both
mmoX
and
mmoY
genes of soluble methane monooxygenase. Two types of sequences were obtained for PCR-amplified fragments of
mmoX
. One of them exhibited high identity to the
mmoX
protein of the
Methylocystis-Methylosinus
group, whereas the other showed an equal level of divergence from both the
Methylosinus-Methylocystis
group and
Methylococcus capsulatus
(Bath) and formed a distinct branch. The pH optimum for growth and for CH
4
uptake was 4.5 to 5.5, which is very similar to that for the optimum CH
4
uptake observed in the original peat samples. These methanotrophs are moderate acidophiles rather than acidotolerant organisms, since their growth rate and methane uptake were much lower at neutral pH. The growth of the methanotrophic community was enhanced by using media with a very low salt content (20 to 200 mg/liter), more typical of their natural environment. All four enriched communities grew on N-free medium.
Bacterial Community Dynamics during Start-Up of a Trickle-Bed Bioreactor Degrading Aromatic Compounds
Authors: Stoffels Marion , Amann Rudolf , Ludwig Wolfgang , Hekmat Dariusch , Schleifer Karl-Heinz 
Published: December 2019

ABSTRACT

This study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (Solvesso100). The starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a car painting facility as the inoculum and Solvesso100 as the sole carbon source. The bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotides. Two significant shifts in the bacterial community structure could be demonstrated. The original inoculum from the wastewater of the car factory was rich in proteobacteria of the alpha and beta subclasses, while the final fermentor enrichment was dominated by bacteria closely related to
Pseudomonas putida
or
Pseudomonas mendocina
, which both belong to the gamma subclass of the class
Proteobacteria
. A second significant shift was observed when the fermentor culture was transferred as inoculum to the trickle-bed bioreactor. The community structure in the bioreactor gradually returned to a higher complexity, with the dominance of beta and alpha subclass proteobacteria, whereas the gamma subclass proteobacteria sharply declined. Obviously, the preceded pollutant adaptant did not lead to a significant enrichment of bacteria that finally dominated in the trickle-bed bioreactor. In the course of experiments, three new 16S as well as 23S rRNA-targeted probes for beta subclass proteobacteria were designed, probe SUBU1237 for the genera
Burkholderia
and
Sutterella
, probe ALBO34a for the genera
Alcaligenes
and
Bordetella
, and probe Bcv13b for
Burkholderia cepacia
and
Burkholderia vietnamiensis
. Bacteria hybridizing with the probe Bcv13b represented the main Solvesso100-degrading population in the reactor.
Self-Transmissible Mercury Resistance Plasmids with Gene-Mobilizing Capacity in Soil Bacterial Populations: Influence of Wheat Roots and Mercury Addition
Authors: Smit Eric , Wolters Anneke , van Elsas Jan Dirk 
Published: December 2019

ABSTRACT

A set of mercury resistance plasmids was obtained from wheat rhizosphere soil amended or not amended with mercuric chloride via exogenous plasmid isolation by using
Pseudomonas fluorescens
R2f,
Pseudomonas putida
UWC1, and
Enterobacter cloacae
BE1 as recipient strains. The isolation frequencies were highest from soil amended with high levels of mercury, and the isolation frequencies from unamended soil were low. With
P. putida
UWC1 as the recipient, the isolation frequency was significantly enhanced in wheat rhizosphere compared to bulk soil. Twenty transconjugants were analyzed per recipient strain. All of the transconjugants contained plasmids which were between 40 and 50 kb long. Eight selected plasmids were distributed among five groups, as shown by restriction digestion coupled with a similarity matrix analysis. However, all of the plasmids formed a tight group, as judged by hybridization with two whole-plasmid probes and comparisons with other plasmids in dot blot hybridization analyses. The results of replicon typing and broad-host-range incompatibility (Inc) group-specific PCR suggested that the plasmid isolates were not related to any previously described Inc group. Although resistance to copper, resistance to streptomycin, and/or resistance to chloramphenicol was found in several plasmids, catabolic sequences were generally not identified. One plasmid, pEC10, transferred into a variety of bacteria belonging to the β and γ subdivisions of the class
Proteobacteria
and mobilized as well as retromobilized the IncQ plasmid pSUP104. A PCR method for detection of pEC10-like replicons was used, in conjunction with other methods, to monitor pEC10-homologous sequences in mercury-polluted and unpolluted soils. The presence of mercury enhanced the prevalence of pEC10-like replicons in soil and rhizosphere bacterial populations.
PCR for Detection of
Shigella
spp. in Mayonnaise
Authors: Villalobo Eduardo , Torres Antonio 
Published: December 2019

ABSTRACT

The use of PCR to amplify a specific
virA
gene fragment serves as a highly specific and sensitive method to detect virulent bacteria of the genus
Shigella
and enteroinvasive
Escherichia coli
. Amplification of a 215-bp DNA band was obtained by using isolated genomic DNA of
Shigella
, individual cells of
Shigella dysenteriae
, and mayonnaise contaminated with
S. dysenteriae
. Moreover, a multiplex PCR with specific (
virA
) and bacterium-restricted (16S ribosomal DNA) primers generated an amplification product of approximately 755 bp for all bacteria tested and an additional 215-bp product for
Shigella
and enteroinvasive
E. coli.
Grazing of a
Tetrahymena
sp. on Adhered Bacteria in Percolated Columns Monitored by In Situ Hybridization with Fluorescent Oligonucleotide Probes
Authors: Eisenmann Heinrich , Harms Hauke , Meckenstock Rainer , Meyer Elisabeth I. , Zehnder Alexander J. B. 
Published: December 2019

ABSTRACT

Predation of attached
Pseudomonas putida
mt2 by the small ciliate
Tetrahymena
sp. was investigated with a percolated column system. Grazing rates were examined under static and dynamic conditions and were compared to grazing rates in batch systems containing suspended prey. The prey densities were 2 × 10
8
bacteria per ml of pore space and 2 × 10
8
bacteria per ml of suspension, respectively. Postingestion in situ hybridization of bacteria with fluorescent oligonucleotide probes was used to quantify ingestion. During 30 min, a grazing rate of 1,382 ± 1,029 bacteria individual
−1
h
−1
was obtained with suspended prey; this was twice the grazing rate observed with attached bacteria under static conditions. Continuous percolation at a flow rate of 73 cm h
−1
further decreased the grazing rate to about 25% of the grazing rate observed with suspended prey. A considerable proportion of the protozoans fed on neither suspended bacteria nor attached bacteria. The transport of ciliates through the columns was monitored at the same time that predation was monitored. Less than 20% of the protozoans passed through the columns without being retained. Most of these organisms ingested no bacteria, whereas the retained protozoans grazed more efficiently. Retardation of ciliate transport was greater in columns containing attached bacteria than in bacterium-free columns. We propose that the correlation between grazing activity and retardation of transport is a consequence of the interaction between active predators and attached bacteria.
Characterization of the
rrnB
Operon of the Plant Pathogen
Rhodococcus fascians
and Targeted Integrations of Exogenous Genes at
rrn
Loci
Authors: Pisabarro Agustín , Correia António , Martín Juan F. 
Published: December 2019

ABSTRACT

A 6.0-kb
Sal
I DNA fragment containing an entire rRNA operon (
rrnB
) was cloned from a cosmid gene bank of the phytopathogenic strain
Rhodococcus fascians
D188. The nucleotide sequence of the 6-kb fragment was determined and had the organization 16S rRNA-spacer-23S rRNA-spacer-5S rRNA without tRNA-encoding genes in the spacer regions. The 5′ and 3′ ends of the mature 16S, 23S, and 5S rRNAs were determined by alignment with the
rrn
operons of
Bacillus subtilis
and other gram-positive bacteria. Four copies of the
rrn
operons were identified by hybridization with an
rrnB
probe in
R. fascians
type strain ATCC 12974 and in the virulent strain
R. fascians
D188. However, another isolate, CECT 3001 (= NRRL B15096), also classified as
R. fascians
, produced five
rrn
-hybridizing bands. An integrative vector containing a 2.5-kb DNA fragment internal to
rrnB
was constructed for targeted integration of exogenous genes at the
rrn
loci. Transformants carrying the exogenous chloramphenicol resistance gene (
cmr
) integrated in different
rrn
operons were obtained. These transformants had normal growth rates in complex medium and minimal medium and were fully stable for the integrated marker.
Effects of Ionic and Osmotic Strength on the Glucosyltransferase of
Rhizobium meliloti
Responsible for Cyclic β-(1,2)-Glucan Biosynthesis
Authors: Ingram-Smith Cheryl , Miller Karen J. 
Published: December 2019

ABSTRACT

The cyclic β-(1,2)-glucans of
Rhizobium meliloti
and
Agrobacterium tumefaciens
play an important role during hypoosmotic adaptation, and the synthesis of these compounds is osmoregulated. Glucosyltransferase, the enzyme responsible for cyclic β-(1,2)-glucan biosynthesis, is present constitutively, suggesting that osmotic regulation of the biosynthesis of these glucans occurs through modulation of enzyme activity. In this study, we examined regulation of cyclic glucan biosynthesis in vitro with membrane preparations from
R. meliloti
. The results show that ionic solutes inhibit glucan synthesis, even when they are present at low concentrations (e.g., 10 mM). In contrast, neutral solutes (glucose, sucrose, and the compatible solutes glycine betaine and trehalose) were found to stimulate glucan synthesis in vitro when they were present at high concentrations (e.g., 1 M). Furthermore, high concentrations of these neutral solutes were shown to compensate for the inhibition of glucosyltransferase activity by ionic solutes. Consistent with their ionic character, the compatible solute potassium glutamate and the osmoprotectant choline chloride inhibited glucosyltransferase activity in vitro. The results suggest that intracellular ion concentrations, intracellular osmolarity, and intracellular concentrations of nonionic compatible solutes all act as important determinants of glucosyltransferase activity in vivo. Additional experiments were performed with an
ndvA
mutant defective for transport of cyclic glucans and an
ndvB
mutant that produces a C-terminal truncated glucosyltransferase. Cyclic β-(1,2)-glucan biosynthesis, although reduced, was found to be osmoregulated in both mutants. These results reveal that NdvA and the C terminus of NdvB are not required for osmotic regulation of cyclic β-(1,2)-glucan biosynthesis.
Characterization of the Different Dextransucrase Activities Excreted in Glucose, Fructose, or Sucrose Medium by
Leuconostoc mesenteroides
NRRL B-1299
Authors: Dols Marguerite , Remaud-Simeon M. , Willemot R. M. , Vignon M. , Monsan P. 
Published: December 2019

ABSTRACT

When grown in glucose or fructose medium in the absence of sucrose,
Leuconostoc mesenteroides
NRRL B-1299 produces two distinct extracellular dextransucrases named glucose glucosyltransferase (GGT) and fructose glucosyltransferase (FGT). The production level of GGT and FGT is 10 to 20 times lower than that of the extracellular dextransucrase sucrose glucosyltransferase (SGT) produced on sucrose medium (traditional culture conditions). GGT and FGT were concentrated by ultrafiltration before sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. Their molecular masses were 183 and 186 kDa, respectively, differing from the 195 kDa of SGT. The structural analysis of the dextran produced from sucrose and of the oligosaccharides synthesized by acceptor reaction in the presence of maltose showed that GGT and FGT are two different enzymes not previously described for this strain. The polymer synthesized by GGT contains 30% α(1→2) linkages, while FGT catalyzes the synthesis of a linear dextran only composed of α(1→6) linkages.
Seasonal Pattern of Tomato Mosaic Tobamovirus Infection and Concentration in Red Spruce Seedlings
Authors: Bachand George D. , Castello John D. 
Published: December 2019

ABSTRACT

Tomato mosaic tobamovirus (ToMV) infects red spruce (
Picea rubens
) and causes significant changes in its growth and physiology. The mechanism of infection and the pattern of virus concentration in seedling roots and needles were investigated. One-year-old red spruce seedlings were obtained from the nursery in April and June 1995 and August 1996 and tested for ToMV using enzyme-linked immunosorbent assay (ELISA). Virus-free seedlings were divided into three treatments: control, root inoculated, and needle inoculated. Two control, five root-inoculated, and five needle-inoculated seedlings were sampled destructively at biweekly intervals for 3 months and then tested for ToMV by ELISA. ToMV was transmitted to seedlings by root but not by needle inoculation. The virus was detected in 67 to 100% of roots but in less than 7% of needles of root-inoculated seedlings. The percent infection of root-inoculated seedlings differed significantly between the April and June and between the April and August inoculation periods. Virus concentration in infected seedling roots increased initially, peaked within 4 weeks postinoculation, and steadily declined thereafter. Significant differences in ToMV concentrations in roots also were detected among inoculation periods and sampling dates. Early spring may represent the optimal time for infection of seedlings, as well as for assaying roots for ToMV.
Influence of Water Temperature and Salinity on
Vibrio vulnificus
in Northern Gulf and Atlantic Coast Oysters (
Crassostrea virginica
)
Authors: Motes M. L. , DePaola A. , Cook D. W. , Veazey J. E. , Hunsucker J. C. , Garthright W. E. , Blodgett R. J. , Chirtel S. J. 
Published: December 2019

ABSTRACT

This study investigated the temperature and salinity parameters associated with waters and oysters linked to food-borne
Vibrio vulnificus
infections.
V. vulnificus
was enumerated in oysters collected at three northern Gulf Coast sites and two Atlantic Coast sites from July 1994 through September 1995. Two of these sites, Black Bay, La., and Apalachicola Bay, Fla., are the source of the majority of the oysters implicated in
V. vulnificus
cases. Oysters in all Gulf Coast sites exhibited a similar seasonal distribution of
V. vulnificus
: a consistently large number (median concentration, 2,300 organisms [most probable number] per g of oyster meat) from May through October followed by a gradual reduction during November and December to ≤10 per g, where it remained from January through mid-March, and a sharp increase in late March and April to summer levels.
V. vulnificus
was undetectable (<3 per g) in oysters from the North and South Carolina sites for most of the year. An exception occurred when a late-summer flood caused a drop in salinity in the North Carolina estuary, apparently causing
V. vulnificus
numbers to increase briefly to Gulf Coast levels. At Gulf Coast sites,
V. vulnificus
numbers increased with water temperatures up to 26°C and were constant at higher temperatures. High
V. vulnificus
levels (>10
3
per g) were typically found in oysters from intermediate salinities (5 to 25 ppt). Smaller
V. vulnificus
numbers (<10
2
per g) were found at salinities above 28 ppt, typical of Atlantic Coast sites. On 11 occasions oysters were sampled at times and locations near the source of oysters implicated in 13
V. vulnificus
cases; the
V. vulnificus
levels and environmental parameters associated with these samples were consistent with those of other study samples collected from the Gulf Coast from April through November. These findings suggest that the hazard of
V. vulnificus
infection is not limited to brief periods of unusual abundance of
V. vulnificus
in Gulf Coast oysters or to environmental conditions that are unusual to Gulf Coast estuaries.