bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissimilatory Reduction of Fe(III) and Other Electron Acceptors by a
Thermus
Isolate
Authors: Kieft T. L. , Fredrickson J. K. , Onstott T. C. , Gorby Y. A. , Kostandarithes H. M. , Bailey T. J. , Kennedy D. W. , Li S. W. , Plymale A. E. , Spadoni C. M. , Gray M. S. 
Published: December 2019

ABSTRACT

A thermophilic bacterium that can use O
2
, NO
3
−
, Fe(III), and S
0
as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus
Thermus
, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of
Thermus
strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(III) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth.
Thermus
strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities (0.5 mM) of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of
Thermus
strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduced in the presence of either lactate or H
2
. Both strains were also able to mineralize NTA to CO
2
and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by
Thermus
strains SA-01 and NMX2 A.1 is approximately 65°C; their optimum pH is 6.5 to 7.0. This is the first report of a
Thermus
sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S.
Morphological and Compositional Changes in a Planktonic Bacterial Community in Response to Enhanced Protozoan Grazing
Authors: Jürgens Klaus , Pernthaler Jakob , Schalla Sven , Amann Rudolf 
Published: December 2019

ABSTRACTWe analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rRNA-targeted oligonucleotide probes. Enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceranDaphnia magna. The removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-resistant morphotypes. These were mainly different types of filamentous bacteria which correlated in biomass with the population development of heterotrophic nanoflagellates (HNF). Small bacterial rods and cocci, which showed increased proportion after removal ofDaphniaand doubling times of 6 to 11 h, belonged nearly exclusively to the beta subdivision of the classProteobacteriaand theCytophaga-Flavobacteriumcluster. The majority of this newly produced bacterial biomass was rapidly consumed by HNF. In contrast, the proportion of bacteria belonging to the gamma and alpha subdivisions of theProteobacteriaincreased throughout the experiment. The alpha subdivision consisted mainly of rods that were 3 to 6 μm in length, which probably exceeded the size range of bacteria edible by protozoa. Initially, these organisms accounted for less than 1% of total bacteria, but after 72 h they became the predominant group of the bacterial assemblage. Other types of grazing-resistant, filamentous bacteria were also found within the beta subdivision ofProteobacteriaand theCytophaga-Flavobacteriumcluster. We conclude that the predation regimen is a major structuring force for the bacterial community composition in this system. Protozoan grazing resulted in shifts of the morphological as well as the taxonomic composition of the bacterial assemblage. Grazing-resistant filamentous bacteria can develop within different phylogenetic groups of bacteria, and formerly underepresented taxa might become a dominant group when protozoan predation is the major selective pressure.
Kinetics of Sulfate and Hydrogen Uptake by the Thermophilic Sulfate-Reducing Bacteria
Thermodesulfobacterium
sp. Strain JSP and
Thermodesulfovibrio
sp. Strain R1Ha3
Authors: Sonne-Hansen Jacob , Westermann Peter , Ahring Birgitte K. 
Published: December 2019

ABSTRACT

Half-saturation constants (

K
m

), maximum uptake rates (
V
max
), and threshold concentrations for sulfate and hydrogen were determined for two thermophilic sulfate-reducing bacteria (SRB) in an incubation system without headspace.

K
m

values determined for the thermophilic SRB were similar to the constants described for mesophilic SRB isolated from environments with low sulfate concentrations.
In Situ Analysis of Phototrophic Sulfur Bacteria in the Chemocline of Meromictic Lake Cadagno (Switzerland)
Authors: Tonolla Mauro , Demarta Antonella , Peduzzi Raffaele , Hahn Dittmar 
Published: December 2019

ABSTRACT

Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) revealed the presence of a diverse number of phototrophic sulfur bacteria. Sequences resembled those of rRNA of type strains
Chromatium okenii
DSM169 and
Amoebobacter purpureus
DSM4197, as well as those of four bacteria forming a tight cluster with
A. purpureus
DSM4197 and
Lamprocystis roseopersicina
DSM229. In situ hybridization with fluorescent (Cy3 labeled) oligonucleotide probes indicated that all large-celled phototrophic sulfur bacteria in the chemocline of Lake Cadagno were represented by
C. okenii
DSM169, while small-celled phototrophic sulfur bacteria consisted of four major populations with different distribution profiles in the chemocline indicating different ecophysiological adaptations.
Steady-State Nitrogen Isotope Effects of N
2
and N
2
O Production in
Paracoccus denitrificans
Authors: Barford Carol C. , Montoya Joseph P. , Altabet Mark A. , Mitchell Ralph 
Published: December 2019

ABSTRACT

Nitrogen stable-isotope compositions (δ
15
N) can help track denitrification and N
2
O production in the environment, as can knowledge of the isotopic discrimination, or isotope effect, inherent to denitrification. However, the isotope effects associated with denitrification as a function of dissolved-oxygen concentration and their influence on the isotopic composition of N
2
O are not known. We developed a simple steady-state reactor to allow the measurement of denitrification isotope effects in
Paracoccus denitrificans
. With [dO
2
] between 0 and 1.2 μM, the N stable-isotope effects of NO
3
−
and N
2
O reduction were constant at 28.6‰ ± 1.9‰ and 12.9‰ ± 2.6‰, respectively (mean ± standard error,
n
= 5). This estimate of the isotope effect of N
2
O reduction is the first in an axenic denitrifying culture and places the δ
15
N of denitrification-produced N
2
O midway between those of the nitrogenous oxide substrates and the product N
2
in steady-state systems. Application of both isotope effects to N
2
O cycling studies is discussed.
Effectiveness of Chemometric Techniques in Discrimination of
Lactobacillus helveticus
Biotypes from Natural Dairy Starter Cultures on the Basis of Phenotypic Characteristics
Authors: Gatti Monica , Contarini Giovanna , Neviani Erasmo 
Published: December 2019

ABSTRACT

Lactobacillus helveticus
is the dominant organism in natural starter cultures used for the production of typical Italian cheeses. In this study, 74
L. helveticus
strains, isolated from grana and provolone cheese natural whey starters, were distinguished with respect to their origin by using both cell wall protein profiles and chemometric evaluation of some phenotypic parameters, such as the ability to acidify cultures and the presence of nonspecific proteolytic and peptidase activities. Cell wall protein patterns allowed
L. helveticus
strains to be distinguished with respect to their source of isolation. Among the different phenotypes studied, no single specific parameter permitted the two groups of strains to be separated. A good discrimination between the two groups of
L. helveticus
species was obtained by multivariate statistical techniques, which permitted the extraction of all of the discriminating information retained in the phenotypic activities. Associations between strain phenotype expression and dairy environmental ecosystem source are discussed.
Cloning and Nucleotide Sequence Analysis of
gyrB
of
Bacillus cereus
,
B. thuringiensis
,
B. mycoides
, and
B. anthracis
and Their Application to the Detection of
B. cereus
in Rice
Authors: Yamada Shoichi , Ohashi Eiji , Agata Norio , Venkateswaran Kasthuri 
Published: December 2019

ABSTRACT

As 16S rRNA sequence analysis has proven inadequate for the differentiation of
Bacillus cereus
from closely related species, we employed the gyrase B gene (
gyrB
) as a molecular diagnostic marker. The
gyrB
genes of
B. cereus
JCM 2152
T
,
Bacillus thuringiensis
IAM 12077
T
,
Bacillus mycoides
ATCC 6462
T
, and
Bacillus anthracis
Pasteur #2H were cloned and sequenced. Oligonucleotide PCR primer sets were designed from within
gyrB
sequences of the respective bacteria for the specific amplification and differentiation of
B. cereus
,
B. thuringiensis
, and
B. anthracis
. The results from the amplification of
gyrB
sequences correlated well with results obtained with the 16S rDNA-based hybridization study but not with the results of their phenotypic characterization. Some of the reference strains of both
B. cereus
(three serovars) and
B. thuringiensis
(two serovars) were not positive in PCR amplification assays with
gyrB
primers. However, complete sequencing of 1.2-kb
gyrB
fragments of these reference strains showed that these serovars had, in fact, lower homology than their originally designated species. We developed and tested a procedure for the specific detection of the target organism in boiled rice that entailed 15 h of preenrichment followed by PCR amplification of the
B. cereus
-specific fragment. This method enabled us to detect an initial inoculum of 0.24 CFU of
B. cereus
cells per g of boiled rice food homogenate without extracting DNA. However, a simple two-step filtration step is required to remove PCR inhibitory substances.
Surface-Grafted, Environmentally Sensitive Polymers for Biofilm Release
Authors: Ista Linnea K. , Pérez-Luna Víctor H. , López Gabriel P. 
Published: December 2019

ABSTRACT

Controlling bacterial biofouling is desirable for almost every human enterprise in which solid surfaces are introduced into nonsterile aqueous environments. One approach that is used to decrease contamination of manufactured devices by microorganisms is using materials that easily slough off accumulated material (i.e., fouling release surfaces). The compounds currently used for this purpose rely on low surface energy to inhibit strong attachment of organisms. In this study, we examined the possible use of environmentally responsive (or “smart”) polymers as a new class of fouling release agents; a surface-grafted thermally responsive polymer, poly(
N
-isopropylacrylamide) (PNIPAAM), was used as a model compound. PNIPAAM is known to have a lower critical solubility temperature of ∼32°C (i.e., it is insoluble in water at temperatures above 32°C and is soluble at temperatures below 32°C). Under experimental conditions, >90% of cultured microorganisms (
Staphylococcus epidermidis
,
Halomonas marina
) and naturally occurring marine microorganisms that attached to grafted PNIPAAM surfaces during 2-, 18-, 36-, and 72-h incubations were removed when the hydration state of the polymer was changed from a wettability that was favorable for attachment to a wettability that was less favorable. Of particular significance is the observation that an organism known to attach in the greatest numbers to hydrophobic substrata (i.e.,
H. marina
) was removed when transition of PNIPAAM to a more hydrated state occurred, whereas an organism that attaches in the greatest numbers to hydrophilic substrata (i.e.,
S. epidermidis
) was removed when the opposite transition occurred. Neither solvated nor desolvated PNIPAAM exhibited intrinsic fouling release properties, indicating that the phase transition was the important factor in removal of organisms. Based on our observations of the behavior of this model system, we suggest that environmentally responsive polymers represent a new approach for controlling biofouling release.
Detection of Small Numbers ofCampylobacter jejuniandCampylobacter coliCells in Environmental Water, Sewage, and Food Samples by a Seminested PCR Assay
Authors: Waage Astrid S. , Vardund Traute , Lund Vidar , Kapperud Georg 
Published: December 2019

ABSTRACTA rapid and sensitive assay was developed for detection of small numbers ofCampylobacter jejuniandCampylobacter colicells in environmental water, sewage, and food samples. Water and sewage samples were filtered, and the filters were enriched overnight in a nonselective medium. The enrichment cultures were prepared for PCR by a rapid and simple procedure consisting of centrifugation, proteinase K treatment, and boiling. A seminested PCR based on specific amplification of the intergenic sequence between the twoCampylobacterflagellin genes,flaAandflaB, was performed, and the PCR products were visualized by agarose gel electrophoresis. The assay allowed us to detect 3 to 15 CFU ofC. jejuniper 100 ml in water samples containing a background flora consisting of up to 8,700 heterotrophic organisms per ml and 10,000 CFU of coliform bacteria per 100 ml. Dilution of the enriched cultures 1:10 with sterile broth prior to the PCR was sometimes necessary to obtain positive results. The assay was also conducted with food samples analyzed with or without overnight enrichment. As few as ≤3 CFU per g of food could be detected with samples subjected to overnight enrichment, while variable results were obtained for samples analyzed without prior enrichment. This rapid and sensitive nested PCR assay provides a useful tool for specific detection ofC. jejuniorC. coliin drinking water, as well as environmental water, sewage, and food samples containing high levels of background organisms.
Effects of Surfactant Mixtures, Including Corexit 9527, on Bacterial Oxidation of Acetate and Alkanes in Crude Oil
Authors: Bruheim Per , Bredholt Harald , Eimhjellen Kjell 
Published: December 2019

ABSTRACTMixtures of nonionic and anionic surfactants, including Corexit 9527, were tested to determine their effects on bacterial oxidation of acetate and alkanes in crude oil by cells pregrown on these substrates. Corexit 9527 inhibited oxidation of the alkanes in crude oil byAcinetobacter calcoaceticusATCC 31012, while Span 80, a Corexit 9527 constituent, markedly increased the oil oxidation rate. Another Corexit 9527 constituent, the negatively charged dioctyl sulfosuccinate (AOT), strongly reduced the oxidation rate. The combination of Span 80 and AOT increased the rate, but not as much as Span 80 alone increased it, which tentatively explained the negative effect of Corexit 9527. The results of acetate uptake and oxidation experiments indicated that the nonionic surfactants interacted with the acetate uptake system while the anionic surfactant interacted with the oxidation system of the bacteria. The overall effect of Corexit 9527 on alkane oxidation byA. calcoaceticusATCC 31012 thus seems to be the sum of the independent effects of the individual surfactants in the surfactant mixture. WhenRhodococcussp. strain 094 was used, the alkane oxidation rate decreased to almost zero in the presence of a mixture of Tergitol 15-S-7 and AOT even though the Tergitol 15-S-7 surfactant increased the alkane oxidation rate and AOT did not affect it. This indicated that there was synergism between the two surfactants rather than an additive effect like that observed forA. calcoaceticusATCC 31012.
Analysis and Dynamics of the Chromosomal Complements of Wild Sparkling-Wine Yeast Strains
Authors: Nadal Dolors , Carro David , Fernández-Larrea Juan , Piña Benjamin 
Published: December 2019

ABSTRACTWe isolatedSaccharomyces cerevisiaeyeast strains that are able to carry out the second fermentation of sparkling wine from spontaneously fermenting musts in El Penedès (Spain) by specifically designed selection protocols. All of them (26 strains) showed one of two very similar mitochondrial DNA (mtDNA) restriction patterns, whereas their karyotypes differed. These strains showed high rates of karyotype instability, which were dependent on both the medium and the strain, during vegetative growth. In all cases, the mtDNA restriction pattern was conserved in strains kept under the same conditions. Analysis of different repetitive sequences in their genomes suggested that ribosomal DNA repeats play an important role in the changes in size observed in chromosome XII, whereas SUC genes or Ty elements did not show amplification or transposition processes that could be related to rearrangements of the chromosomes showing these sequences. Karyotype changes also occurred in monosporidic diploid derivatives. We propose that these changes originated mainly from ectopic recombination between repeated sequences interspersed in the genome. None of the rearranged karyotypes provided a selective advantage strong enough to allow the strains to displace the parental strains. The nature and frequency of these changes suggest that they may play an important role in the establishment and maintenance of the genetic diversity observed inS. cerevisiaewild populations.
Isolation and Characterization of a Second Subunit of Molecular Chaperonin from
Pyrococcus kodakaraensis
KOD1: Analysis of an ATPase-Deficient Mutant Enzyme
Authors: Izumi Michi , Fujiwara Shinsuke , Takagi Masahiro , Kanaya Shigenori , Imanaka Tadayuki 
Published: December 2019

ABSTRACT

The
cpkA
gene encoding a second (α) subunit of archaeal chaperonin from
Pyrococcus kodakaraensis
KOD1 was cloned, sequenced, and expressed in
Escherichia coli
. Recombinant CpkA was studied for chaperonin functions in comparison with CpkB (β subunit). The effect on decreasing the insoluble form of proteins was examined by coexpressing CpkA or CpkB with CobQ (cobyric acid synthase from
P. kodakaraensis
) in
E. coli
. The results indicate that both CpkA and CpkB effectively decrease the amount of the insoluble form of CobQ. Both CpkA and CpkB possessed the same ATPase activity as other bacterial and eukaryal chaperonins. The ATPase-deficient mutant proteins CpkA-D95K and CpkB-D95K were constructed by changing conserved Asp
95
to Lys. Effect of the mutation on the ATPase activity and CobQ solubilization was examined. Neither mutant exhibited ATPase activity in vitro. Nevertheless, they decreased the amount of the insoluble form of CobQ by coexpression as did wild-type CpkA and CpkB. These results implied that both CpkA and CpkB could assist protein folding for nascent protein in
E. coli
without requiring energy from ATP hydrolysis.
Contribution of Methanotrophic and Nitrifying Bacteria to CH
4
and NH
4
+
Oxidation in the Rhizosphere of Rice Plants as Determined by New Methods of Discrimination
Authors: Bodelier Paul L. E. , Frenzel Peter 
Published: December 2019

ABSTRACT

Methanotrophic and nitrifying bacteria are both able to oxidize CH
4
as well as NH
4
+
. To date it is not possible to estimate the relative contribution of methanotrophs to nitrification and that of nitrifiers to CH
4
oxidation and thus to assess their roles in N and C cycling in soils and sediments. This study presents new options for discrimination between the activities of methanotrophs and nitrifiers, based on the competitive inhibitor CH
3
F and on recovery after inhibition with C
2
H
2
. By using rice plant soil as a model system, it was possible to selectively inactivate methanotrophs in soil slurries at a CH
4
/CH
3
F/NH
4
+
molar ratio of 0.1:1:18. This ratio of CH
3
F to NH
4
+
did not affect ammonia oxidation, but methane oxidation was inhibited completely. By using the same model system, it could be shown that after 24 h of exposure to C
2
H
2
(1,000 parts per million volume), methanotrophs recovered within 24 h while nitrifiers stayed inactive for at least 3 days. This gave an “assay window” of 48 h when only methanotrophs were active. Applying both assays to model microcosms planted with rice plants demonstrated a major contribution of methanotrophs to nitrification in the rhizosphere, while the contribution of nitrifiers to CH
4
oxidation was insignificant.
Molecular Characterization of a Phage-Encoded Resistance System in
Lactococcus lactis
Authors: McGrath Stephen , Seegers Jos F. M. L. , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: December 2019

ABSTRACT

A specific fragment of the genome of Tuc2009, a temperate lactococcal bacteriophage, was shown to contain several open reading frames, whose deduced protein products exhibited similarities to proteins known to be involved in DNA replication and modification. In this way, a putative single-stranded binding protein, replisome organizer protein, topoisomerase I, and a methylase were identified. When the genetic information coding for the putative replisome organizer protein of Tuc2009, Rep
2009
, was supplied on a high-copy-number plasmid vector, it was shown to confer a phage-encoded resistance (Per) phenotype on its lactococcal host UC509.9. The presence of this recombinant plasmid was shown to cause a marked reduction in Tuc2009 DNA replication, suggesting that the observed phage resistance was due to titration of a factor, or factors, required for Tuc2009 DNA replication. Further experiments delineated the phage resistance-conferring region to a 160-bp fragment rich in direct repeats. Gel retardation experiments, which indicated a protein-DNA interaction between this 160-bp fragment and the Rep
2009
protein, were performed. UC509.9 strains harboring plasmids with randomly mutated versions of this fragment were shown to display a variable phage resistance phenotype, depending on the position of the mutations.
Role of
Bacillus thuringiensis
Toxin Domains in Toxicity and Receptor Binding in the Diamondback Moth
Authors: Ballester V. , Granero F. , de Maagd R. A. , Bosch D. , Ménsua J. L. , Ferré J. 
Published: December 2019

ABSTRACT

The toxic fragment of
Bacillus thuringiensis
crystal proteins consists of three distinct structural domains. There is evidence that domain I is involved in pore formation and that domain II is involved in receptor binding and specificity. It has been found that, in some cases, domain III is also important in determining specificity. Furthermore, involvement of domain III in binding has also been reported recently. To investigate the role of toxin domains in the diamondback moth (
Plutella xylostella
), we used hybrid toxins with domain III substitutions among Cry1C, Cry1E, and Cry1Ab. Neither Cry1E nor G27 (a hybrid with domains I and II from Cry1E and domain III from Cry1C) was toxic, whereas Cry1C and F26 (the reciprocal hybrid) were equally toxic. H04 (a hybrid with domains I and II from Cry1Ab and domain III from Cry1C) showed toxicity that was of a similar level as that of Cry1Ab and significantly higher than that of Cry1C. Binding assays with
125
I-Cry1C showed that Cry1C and F26 competed for the same binding sites on midgut membrane vesicles, whereas Cry1E, G27, and H04 did not bind to these sites. Our results show that, in contrast to findings in other insects for the toxins and hybrids used here, toxin specificity as well as specificity of binding to membrane vesicles in the diamondback moth is mediated by domain II (and/or I) and not by domain III.