bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Transcriptional Activator (ChnR) and a 6-Oxohexanoate Dehydrogenase (ChnE) in the Cyclohexanol Catabolic Pathway in
Acinetobacter
sp. Strain NCIMB 9871 and Localization of the Genes That Encode Them
Authors: Iwaki Hiroaki , Hasegawa Yoshie , Teraoka Masahiro , Tokuyama Tai , Bergeron Hélène , Lau Peter C. K. 
Published: December 2019

ABSTRACT

We identified
chnR
, a gene encoding an AraC-XylS type of transcriptional activator that regulates the expression of
chnB
, the structural gene for cyclohexanone monooxygenase (CHMO) in
Acinetobacter
sp. strain NCIMB 9871. The gene sequence of
chnE
, which encodes an NADP
+
-linked 6-oxohexanoate dehydrogenase, the enzyme catalyzing the fifth step of cyclohexanol degradation, was also determined. The gene arrangement is
chnB-chnE-chnR
. The predicted molecular masses of the three polypeptides were verified by radiolabeling by using the T7 expression system. Inducible expression of cloned
chnB
in
Escherichia coli
depended upon the presence of
chnR
. A transcriptional
chnB
::
lacZ
fusion experiment revealed that cyclohexanone induces
chnB
expression in
E. coli
, in which a 22-fold increase in activity was observed.
Genotypic Diversity among
Brevibacillus laterosporus
Strains
Authors: Zahner Viviane , Rabinovitch Leon , Suffys Phylip , Momen Hooman 
Published: December 2019

ABSTRACT

In comparison with other entomopathogenic
Bacillus
species, the genome of
Brevibacillus laterosporus
is poorly characterized. The aim of this study was to examine genetic variability in
B. laterosporus
by using a range of typing methodologies. Strains of
B. laterosporus
were examined for variation in 13 chromosomal genes encoding enzymes by multilocus enzyme electrophoresis. Optimal conditions of pulsed-field gel electrophoresis and randomly amplified polymorphic DNA were established that allowed analysis of the genome of
B. laterosporus
. None of these techniques allowed the identification of a convenient molecular marker for entomopathogenic strains, although one specific primer amplified only DNA from almost all mosquitocidal strains.
Disruption of
TRI101
, the Gene Encoding Trichothecene 3-
O
-Acetyltransferase, from
Fusarium sporotrichioides
Authors: McCormick Susan P. , Alexander Nancy J. , Trapp Susan E. , Hohn Thomas M. 
Published: December 2019

ABSTRACT

We screened a
Fusarium sporotrichioides
NRRL 3299 cDNA expression library in a toxin-sensitive
Saccharomyces cerevisiae
strain lacking a functional
PDR5
gene. Fourteen yeast transformants were identified as resistant to the trichothecene 4,15-diacetoxyscirpenol, and each carried a cDNA encoding the trichothecene 3-
O
-acetyltransferase that is the
F. sporotrichioides
homolog of the
Fusarium graminearum TRI101
gene. Mutants of
F. sporotrichioides
NRRL 3299 produced by disruption of
TRI101
were altered in their abilities to synthesize T-2 toxin and accumulated isotrichodermol and small amounts of 3,15-didecalonectrin and 3-decalonectrin, trichothecenes that are not observed in cultures of the parent strain. Our results indicate that TRI101 converts isotrichodermol to isotrichodermin and is required for the biosynthesis of T-2 toxin.
Osmoprotection ofEscherichia coliby Peptone Is Mediated by the Uptake and Accumulation of Free Proline but Not of Proline-Containing Peptides
Authors: Amezaga Maria-Rosario , Booth Ian R. 
Published: December 2019

ABSTRACTThe effect of meat peptone type I (Sigma) on the growth ofEscherichia colicells under hyperosmotic stress has been investigated. Peptone is a complex mixture of peptides with a small content of free amino acids, which resembles nutrients found in natural environments. Our data showed that peptone enhances the growth ofE. colicells in high-osmolarity medium to levels higher than those achieved with the main compatible solute in bacteria, glycine betaine. The mechanism of osmoprotection by peptone comprises the uptake and accumulation of the compatible solute, proline. The main role of the peptides contained in peptone is the provision of nutrients rather than the intracellular accumulation of osmolytes. In contrast toListeria monocytogenes(M. R. Amezaga, I. Davidson, D. McLaggan, A. Verheul, T. Abee, and I. R. Booth, Microbiology 141:41–49, 1995),E. colidoes not accumulate exogenous peptides for osmoprotection and peptides containing proline do not lead to the accumulation of proline as a compatible solute. In late-logarithmic-phase cultures ofE. coligrowing at high osmolarity plus peptone, proline becomes the limiting factor for growth, and the intracellular pools of proline are not maintained. This is a consequence of the low concentration of free proline in peptone, the catabolism of proline byE. coli, and the inability ofE. colito utilize proline-containing peptides as a source of compatible solutes. Our data highlight the role that natural components in food such as peptides play in undermining food preservation regimes, such as high osmolarity, and also that the specific mechanisms of osmoprotection by these compounds differ according to the organism.
Effects of Pulsed Electric Fields on Inactivation Kinetics of
Listeria innocua
Authors: Wouters Patrick C. , Dutreux Nicole , Smelt Jan P. P. M. , Lelieveld Huub L. M. 
Published: December 2019

ABSTRACT

The effects of pulsed electric field (PEF) treatment and processing factors on the inactivation kinetics of
Listeria innocua
NCTC 11289 were investigated by using a pilot plant PEF unit with a flow rate of 200 liters/h. The electric field strength, pulse length, number of pulses, and inlet temperature were the most significant process factors influencing the inactivation kinetics. Product factors (pH and conductivity) also influenced the inactivation kinetics. In phosphate buffer at pH 4.0 and 0.5 S/m at 40°C, a 3.0-V/μm PEF treatment at an inlet temperature of 40°C resulted in ≥6.3 log inactivation of strain NCTC 11289 at 49.5°C. A synergistic effect between temperature and PEF inactivation was also observed. The inactivation obtained with PEF was compared to the inactivation obtained with heat. We found that heat inactivation was less effective than PEF inactivation under similar time and temperature conditions.
L. innocua
cells which were incubated for a prolonged time in the stationary phase were more resistant to the PEF treatment, indicating that the physiological state of the microorganism plays a role in inactivation by PEF. Sublethal injury of cells was observed after PEF treatment, and the injury was more severe when the level of treatment was increased. Overall, our results indicate that it may be possible to use PEF in future applications in order to produce safe products.
Molecular Analysis of the Microbial Diversity Present in the Colonic Wall, Colonic Lumen, and Cecal Lumen of a Pig
Authors: Pryde Susan E. , Richardson Anthony J. , Stewart Colin S. , Flint Harry J. 
Published: December 2019

ABSTRACT

Random clones of 16S ribosomal DNA gene sequences were isolated after PCR amplification with eubacterial primers from total genomic DNA recovered from samples of the colonic lumen, colonic wall, and cecal lumen from a pig. Sequences were also obtained for cultures isolated anaerobically from the same colonic-wall sample. Phylogenetic analysis showed that many sequences were related to those of
Lactobacillus
or
Streptococcus
spp. or fell into clusters IX, XIVa, and XI of gram-positive bacteria. In addition, 59% of randomly cloned sequences showed less than 95% similarity to database entries or sequences from cultivated organisms. Cultivation bias is also suggested by the fact that the majority of isolates (54%) recovered from the colon wall by culturing were related to
Lactobacillus
and
Streptococcus
, whereas this group accounted for only one-third of the sequence variation for the same sample from random cloning. The remaining cultured isolates were mainly
Selenomonas
related. A higher proportion of
Lactobacillus reuteri
-related sequences than of
Lactobacillus acidophilus
- and
Lactobacillus amylovorus
-related sequences were present in the colonic-wall sample. Since the majority of bacterial ribosomal sequences recovered from the colon wall are less than 95% related to known organisms, the roles of many of the predominant wall-associated bacteria remain to be defined.
Linking Toluene Degradation with Specific Microbial Populations in Soil
Authors: Hanson Jessica R. , Macalady Jennifer L. , Harris David , Scow Kate M. 
Published: December 2019

ABSTRACT

Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with
13
C isotope tracer analysis to measure the community’s response to addition of 35 μg of [
13
C]toluene ml of soil solution
−1
. After 119 h of incubation with toluene, 96% of the incorporated
13
C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total
13
C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [
13
C]glucose. Our study showed that coupling
13
C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil.
Partitioning Effects during Terminal Carbon and Electron Flow in Sediments of a Low-Salinity Meltwater Pond near Bratina Island, McMurdo Ice Shelf, Antarctica
Authors: Mountfort Douglas O. , Kaspar Heinrich F. , Downes Malcolm , Asher Rodney A. 
Published: December 2019

ABSTRACTA study of anaerobic sediments below cyanobacterial mats of a low-salinity meltwater pond called Orange Pond on the McMurdo Ice Shelf at temperatures simulating those in the summer season (<5°C) revealed that both sulfate reduction and methane production were important terminal anaerobic processes. Addition of [2-14C]acetate to sediment samples resulted in the passage of label mainly to CO2. Acetate addition (0 to 27 mM) had little effect on methanogenesis (a 1.1-fold increase), and while the rate of acetate dissimilation was greater than the rate of methane production (6.4 nmol cm−3h−1compared to 2.5 to 6 nmol cm−3h−1), the portion of methane production attributed to acetate cleavage was <2%. Substantial increases in the methane production rate were observed with H2(2.4-fold), and H2uptake was totally accounted for by methane production under physiological conditions. Formate also stimulated methane production (twofold), presumably through H2release mediated through hydrogen lyase. Addition of sulfate up to 50-fold the natural levels in the sediment (interstitial concentration, ∼0.3 mM) did not substantially inhibit methanogenesis, but the process was inhibited by 50-fold chloride (36 mM). No net rate of methane oxidation was observed when sediments were incubated anaerobically, and denitrification rates were substantially lower than rates for sulfate reduction and methanogenesis. The results indicate that carbon flow from acetate is coupled mainly to sulfate reduction and that methane is largely generated from H2and CO2where chloride, but not sulfate, has a modulating role. Rates of methanogenesis at in situ temperatures were four- to fivefold less than maximal rates found at 20°C.
Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization
Authors: DeLong Edward F. , Taylor Lance Trent , Marsh Terence L. , Preston Christina M. 
Published: December 2019

ABSTRACT

Fluorescent in situ hybridization (FISH) using rRNA-specific oligonucleotide probes has emerged as a popular technique for identifying individual microbial cells. In natural samples, however, the signal derived from fluor-labeled oligonucleotide probes often is undetectable above background fluorescence in many cells. To circumvent this difficulty, we applied fluorochrome-labeled polyribonucleotide probes to identify and enumerate marine planktonic archaea and bacteria. The approach greatly enhanced the sensitivity and applicability of FISH with seawater samples, allowing confident identification and enumeration of planktonic cells to ocean depths of 3,400 m. Quantitative whole-cell hybridization experiments using these probes accounted for 90 to 100% of the total 4′,6-diamidino-2-phenylindole (DAPI)-stained cells in most samples. As predicted in a previous study (R. Massana, A. E. Murray, C. M. Preston, and E. F. DeLong, Appl. Environ. Microbiol. 63:50–56, 1997), group I and II marine archaea predominate in different zones in the water column, with maximal cell densities of 10
5
/ml. The high cell densities of archaea, extending from surface waters to abyssal depths, suggest that they represent a large and significant fraction of the total picoplankton biomass in coastal ocean waters. The data also show that the vast majority of planktonic prokaryotes contain significant numbers of ribosomes, rendering them easily detectable with polyribonucleotide probes. These results imply that the majority of planktonic cells visualized by DAPI do not represent lysed cells or “ghosts,” as was suggested in a previous report.
Molecular Characterization of a Toluene-Degrading Methanogenic Consortium
Authors: Ficker Monica , Krastel Kirsten , Orlicky Stephen , Edwards Elizabeth 
Published: December 2019

ABSTRACTA toluene-degrading methanogenic consortium enriched from creosote-contaminated aquifer material was maintained on toluene as the sole carbon and energy source for 10 years. The species in the consortium were characterized by using a molecular approach. Total genomic DNA was isolated, and 16S rRNA genes were amplified by using PCR performed with kingdom-specific primers that were specific for 16S rRNA genes from either members of the kingdomBacteriaor members of the kingdomArchaea. A total of 90 eubacterial clones and 75 archaeal clones were grouped by performing a restriction fragment length polymorphism (RFLP) analysis. Six eubacterial sequences and two archaeal sequences were found in the greatest abundance (in six or more clones) based on the RFLP analysis. The relative abundance of each putative species was estimated by using fluorescent in situ hybridization (FISH), and the presence of putative species was determined qualitatively by performing slot blot hybridization with consortium DNA. Both archaeal species and two of the six eubacterial species were detected in the DNA and FISH hybridization experiments. A phylogenetic analysis of these four dominant organisms suggested that the two archaeal species are related to the generaMethanosaetaandMethanospirillum. One of the eubacterial species is related to the genusDesulfotomaculum, while the other is not related to any previously described genus. By elimination, we propose that the last organism probably initiates the attack on toluene.
Seasonal Enumeration of Fecal Coliform Bacteria from the Feces of Ring-Billed Gulls (
Larus delawarensis
) and Canada Geese (
Branta canadensis
)
Authors: Alderisio K. A. , DeLuca N. 
Published: December 2019

ABSTRACT

Water suppliers have often implicated roosting birds for fecal contamination of their surface waters. Geese and gulls have been the primary targets of this blame although literature documenting the fecal coliform content of these birds is quite limited. To determine the actual fecal coliform concentrations of these birds, fecal samples from 249 ring-billed gulls and 236 Canada geese in Westchester County, N.Y., were analyzed over a 2-year period. Results indicate that gull feces contain a greater average concentration of fecal coliform bacteria per gram (3.68 × 10
8
) than do goose feces (1.53 × 10
4
); however, average fecal sample weights of the geese were more than 15 times higher than those of the gulls.
Monitoring Methanotrophic Bacteria in Hybrid Anaerobic-Aerobic Reactors with PCR and a Catabolic Gene Probe
Authors: Miguez Carlos B. , Shen Chun F. , Bourque Denis , Guiot Serge R. , Groleau Denis 
Published: December 2019

ABSTRACTWe attempted to mimic in small upflow anaerobic sludge bed (UASB) bioreactors the metabolic association found in nature between methanogens and methanotrophs. UASB bioreactors were inoculated with pure cultures of methanotrophs, and the bioreactors were operated by using continuous low-level oxygenation in order to favor growth and/or survival of methanotrophs. Unlike the reactors in other similar studies, the hybrid anaerobic-aerobic bioreactors which we used were operated synchronously, not sequentially. Here, emphasis was placed on monitoring various methanotrophic populations by using classical methods and also a PCR amplification assay based on themmoXgene fragment of the soluble methane monooxygenase (sMMO). The following results were obtained: (i) under the conditions used,Methylosinus sporiumappeared to survive better thanMethylosinus trichosporium; (ii) the PCR method which we used could detect as few as about 2,000 sMMO gene-containing methanotrophs per g (wet weight) of granular sludge; (iii) inoculation of the bioreactors with pure cultures of methanotrophs contributed greatly to increases in the sMMO-containing population (although the sMMO-containing population decreased gradually with time, at the end of an experiment it was always at least 2 logs larger than the initial population before inoculation); (iv) in general, there was a good correlation between populations with the sMMO gene and populations that exhibited sMMO activity; and (v) inoculation with sMMO-positive cultures helped increase significantly the proportion of sMMO-positive methanotrophs in reactors, even after several weeks of operation under various regimes. At some point, anaerobic-aerobic bioreactors like those described here might be used for biodegradation of various chlorinated pollutants.
Anaerobic versus Aerobic Degradation of Dimethyl Sulfide and Methanethiol in Anoxic Freshwater Sediments
Authors: Lomans Bart P. , Op den Camp Huub J. M. , Pol Arjan , Vogels Godfried D. 
Published: December 2019

ABSTRACTDegradation of dimethyl sulfide and methanethiol in slurries prepared from sediments of minerotrophic peatland ditches were studied under various conditions. Maximal aerobic dimethyl sulfide-degrading capacities (4.95 nmol per ml of sediment slurry · h−1), measured in bottles shaken under an air atmosphere, were 10-fold higher than the maximal anaerobic degrading capacities determined from bottles shaken under N2or H2atmosphere (0.37 and 0.32 nmol per ml of sediment slurry · h−1, respectively). Incubations under experimental conditions which mimic the in situ conditions (i.e., not shaken and with an air headspace), however, revealed that aerobic degradation of dimethyl sulfide and methanethiol in freshwater sediments is low due to oxygen limitation. Inhibition studies with bromoethanesulfonic acid and sodium tungstate demonstrated that the degradation of dimethyl sulfide and methanethiol in these incubations originated mainly from methanogenic activity. Prolonged incubation under a H2atmosphere resulted in lower dimethyl sulfide degradation rates. Kinetic analysis of the data resulted in apparentKmvalues (6 to 8 μM) for aerobic dimethyl sulfide degradation which are comparable to those reported forThiobacillusspp.,Hyphomicrobiumspp., and other methylotrophs. ApparentKmvalues determined for anaerobic degradation of dimethyl sulfide (3 to 8 μM) were of the same order of magnitude. The low apparentKmvalues obtained explain the low dimethyl sulfide and methanethiol concentrations in freshwater sediments that we reported previously. Our observations point to methanogenesis as the major mechanism of dimethyl sulfide and methanethiol consumption in freshwater sediments.
Influence of Light Intensity on Methanotrophic Bacterial Activity in Petit Saut Reservoir, French Guiana
Authors: Dumestre J. F. , Guézennec J. , Galy-Lacaux C. , Delmas R. , Richard S. , Labroue L. 
Published: December 2019

ABSTRACT

One year after impoundment in January 1994, methanotrophic bacteria in Petit Saut Reservoir (French Guiana) were active at the oxic-anoxic interface. This activity was revealed by the sudden extinction of diffusive methane emission (600 metric tons of CH
4
· day
−1
for the whole lake surface area, i.e., 360 km
2
). Lifting of inhibition was suspected. After reviewing the potential inhibitors of this physiological guild (O
2
, NH
4
+
, sulfides) and considering the similarities with nitrifiers, we suggest that sunlight influenced the methanotrophic bacteria. On the basis of phospholipid analysis, only a type II methanotrophic community was identified in the lake. Both growth and methanotrophic activity of an enriched culture, obtained in the laboratory, were largely inhibited by illumination over 150 microeinsteins · m
−2
· s
−1
. These results were confirmed on a pure culture of
Methylosinus trichosporium
OB3B. In situ conditions showed that water transparency was quite stable in 1994 and 1995 and that the oxycline moved steadily deeper until January 1995. Considering the mean illumination profile during this period, we showed that removal of methanotrophic growth inhibition could only occur below a 2-m depth. The oxycline reached this level in October 1994, allowing methanotrophic bacteria to develop and to consume the entire methane emission 4 months later.
Production of Medium-Chain-Length Poly(3-Hydroxyalkanoates) from Gluconate by RecombinantEscherichia coli
Authors: Klinke Stefan , Ren Qun , Witholt Bernard , Kessler Birgit 
Published: December 2019

ABSTRACTIt was shown recently that recombinantEscherichia coli, defective in the β-oxidation cycle and harboring a medium-chain-length (MCL) poly(3-hydroxyalkanoate) (PHA) polymerase-encoding gene ofPseudomonas, is able to produce MCL PHA from fatty acids but not from sugars or gluconate (S. Langenbach, B. H. A. Rehm, and A. Steinbüchel, FEMS Microbiol. Lett. 150:303–309, 1997; Q. Ren, Ph.D. thesis, ETH Zürich, Zürich, Switzerland, 1997). In this study, we report the formation of MCL PHA from gluconate by recombinantE. coli. By introduction of genes coding for an MCL PHA polymerase and the cytosolic thioesterase I (′thioesterase I) intoE. coliJMU193, we were able to engineer a pathway for the synthesis of MCL PHA from gluconate. We used two expression systems, i.e., thebadpromoter andalkpromoter, for the ′thioesterase I- and PHA polymerase-encoding genes, respectively, which enabled us to modulate their expression independently over a range of inducer concentrations, which resulted in a maximum MCL PHA accumulation of 2.3% of cell dry weight from gluconate. We found that the amount of PHA and the ′thioesterase I activity are directly correlated. Moreover, the polymer accumulated in the recombinantE. coliconsisted mainly of 3-hydroxyoctanoate monomers. On the basis of our data, we propose an MCL PHA biosynthesis pathway scheme for recombinantE. coliJMU193, harboring PHA polymerase and ′thioesterase I, when grown on gluconate, which involves both de novo fatty acid synthesis and β-oxidation.