bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Reduction of Nitrate and Selenate by Cell Suspensions of Selenium-Respiring Bacteria
Authors: Oremland Ronald S. , Blum Jodi Switzer , Bindi Allana Burns , Dowdle Philip R. , Herbel Mitchell , Stolz John F. 
Published: December 2019

ABSTRACTWashed-cell suspensions ofSulfurospirillum barnesiireduced selenate [Se(VI)] when cells were cultured with nitrate, thiosulfate, arsenate, or fumarate as the electron acceptor. When the concentration of the electron donor was limiting, Se(VI) reduction in whole cells was approximately fourfold greater in Se(VI)-grown cells than was observed in nitrate-grown cells; correspondingly, nitrate reduction was ∼11-fold higher in nitrate-grown cells than in Se(VI)-grown cells. However, a simultaneous reduction of nitrate and Se(VI) was observed in both cases. At nonlimiting electron donor concentrations, nitrate-grown cells suspended with equimolar nitrate and selenate achieved a complete reductive removal of nitrogen and selenium oxyanions, with the bulk of nitrate reduction preceding that of selenate reduction. Chloramphenicol did not inhibit these reductions. The Se(VI)-respiring haloalkaliphileBacillus arsenicoselenatisgave similar results, but its Se(VI) reductase was not constitutive in nitrate-grown cells. No reduction of Se(VI) was noted forBacillus selenitireducens, which respires selenite. The results of kinetic experiments with cell membrane preparations ofS. barnesiisuggest the presence of constitutive selenate and nitrate reduction, as well as an inducible, high-affinity nitrate reductase in nitrate-grown cells which also has a low affinity for selenate. The simultaneous reduction of micromolar Se(VI) in the presence of millimolar nitrate indicates that these organisms may have a functional use in bioremediating nitrate-rich, seleniferous agricultural wastewaters. Results with75Se-selenate tracer show that these organisms can lower ambient Se(VI) concentrations to levels in compliance with new regulations proposed for release of selenium oxyanions into the environment.
Identification of Phytoplankton from Flow Cytometry Data by Using Radial Basis Function Neural Networks
Authors: Wilkins M. F. , Boddy Lynne , Morris C. W. , Jonker R. R. 
Published: December 2019

ABSTRACT
We describe here the application of a type of artificial neural network, the Gaussian radial basis function (RBF) network, in the identification of a large number of phytoplankton strains from their 11-dimensional flow cytometric characteristics measured by the European Optical Plankton Analyser instrument. The effect of network parameters on optimization is examined. Optimized RBF networks recognized 34 species of marine and freshwater phytoplankton with 91.5% success overall. The relative importance of each measured parameter in discriminating these data and the behavior of RBF networks in response to data from “novel” species (species not present in the training data) were analyzed.
Pelagic-Benthic Coupling of Nucleic Acids in an Abyssal Location of the Northeastern Atlantic Ocean
Authors: Dell’Anno A. , Fabiano M. , Mei M. L. , Danovaro R. 
Published: December 2019

ABSTRACT

Spatial and temporal changes in sedimentary nucleic acid concentrations in an abyssal locality of the northeastern Atlantic Ocean were investigated in relation to fluxes of nucleic acids produced in the photic layer. Sediment trap material, collected between 1996 and 1998 at depths of 1,000, 3,000, and 4,700 m, and sediment samples were analyzed for DNA and RNA content. Nucleic acid concentrations in the sediments were very high and displayed significant temporal changes, whereas mesoscale variability was low. DNA and RNA concentrations generally displayed opposite temporal patterns, which are likely to be dependent on the nature and characteristics of DNA and RNA molecules. Nucleic acid fluxes were high and displayed clear seasonal changes apparently coupled with seasonal pulses of primary production. However, while median values of DNA fluxes were relatively similar in all sediment traps, median values of RNA fluxes almost doubled from the 1,000- to the 4,700-m depth, suggesting differences in the metabolic activity of microbes associated with sinking particles. Significant relationships between DNA concentrations in the sediments and DNA fluxes and between RNA concentrations and RNA fluxes, indicating the presence of a clear pelagic-benthic coupling of particulate nucleic acids, were observed. The benthic system investigated was not steady state since we estimated that, from September 1996 to October 1998, nucleic acid concentration in the sediments decreased by about 165 mg of DNA m
−2
. Vertical profiles revealed a significant decrease in DNA concentration with depth in the sediments, reaching an asymptotic value of about 5 μg g
−1
. This DNA fraction constitutes a pool of potentially refractory DNA (accounting for 16 to 40% of the total DNA pool) that might be buried in the sediments.
Effects of Combined Shear and Thermal Forces on Destruction of
Microbacterium lacticum
Authors: Bulut S. , Waites W. M. , Mitchell J. R. 
Published: December 2019

ABSTRACT

A twin-screw extruder and a rotational rheometer were used to generate shear forces in concentrated gelatin inoculated with a heat-resistant isolate of a vegetative bacterial species,
Microbacterium lacticum
. Shear forces in the extruder were mainly controlled by varying the water feed rate. The water content of the extrudates changed between 19 and 45% (wet weight basis). Higher shear forces generated at low water contents and the calculated die wall shear stress correlated strongly with bacterial destruction. No surviving microorganisms could be detected at the highest wall shear stress of 409 kPa, giving log reduction of 5.3 (minimum detection level, 2 × 10
4
CFU/sample). The mean residence time of the microorganism in the extruder was 49 to 58 s, and the maximum temperature measured in the end of the die was 73°C. The
D
75°C
of the microorganism in gelatin at 65% water content was 20 min. It is concluded that the physical forces generated in the reverse screw element and the extruder die rather than heat played a major part in cell destruction. In a rotational rheometer, after shearing of a mix of microorganisms with gelatin at 65% (wt/wt) moisture content for 4 min at a shear stress of 2.8 kPa and a temperature of 75°C, the number of surviving microorganisms in the sheared sample was 5.2 × 10
6
CFU/g of sample compared with 1.4 × 10
8
CFU/g of sample in the nonsheared control. The relative effectiveness of physical forces in the killing of bacteria and destruction of starch granules is discussed.
Significance of Size and Nucleic Acid Content Heterogeneity as Measured by Flow Cytometry in Natural Planktonic Bacteria
Authors: Gasol Josep M. , Zweifel Ulla Li , Peters Francesc , Fuhrman Jed A. , Hagström Åke 
Published: December 2019

ABSTRACT

Total bacterial abundances estimated with different epifluorescence microscopy methods (4′,6-diamidino-2-phenylindole [DAPI], SYBR Green, and Live/Dead) and with flow cytometry (Syto13) showed good correspondence throughout two microcosm experiments with coastal Mediterranean water. In the Syto13-stained samples we could differentiate bacteria with apparent high DNA (HDNA) content and bacteria with apparent low DNA (LDNA) content. HDNA bacteria, “live” bacteria (determined as such with the Molecular Probes Live/Dead
Bac
Light bacterial viability kit), and nucleoid-containing bacteria (NuCC) comprised similar fractions of the total bacterial community. Similarly, LDNA bacteria and “dead” bacteria (determined with the kit) comprised a similar fraction of the total bacterial community in one of the experiments. The rates of change of each type of bacteria during the microcosm experiments were also positively correlated between methods. In various experiments where predator pressure on bacteria had been reduced, we detected growth of the HDNA bacteria without concomitant growth of the LDNA bacteria, such that the percentage contribution of HDNA bacteria to total bacterial numbers (%HDNA) increased. This indicates that the HDNA bacteria are the dynamic members of the bacterial assemblage. Given how quickly and easily the numbers of HDNA and LDNA bacteria can be obtained, and given the similarity to the numbers of “live” cells and NuCC, the %HDNA is suggested as a reference value for the percentage of actively growing bacteria in marine planktonic environments.
Hydrogen Profiles and Localization of Methanogenic Activities in the Highly Compartmentalized Hindgut of Soil-Feeding Higher Termites (
Cubitermes
spp.)
Authors: Schmitt-Wagner Dirk , Brune Andreas 
Published: December 2019

ABSTRACT

It has been shown that the coexistence of methanogenesis and reductive acetogenesis in the hindgut of the wood-feeding termite
Reticulitermes flavipes
is based largely on the radial distribution of the respective microbial populations and relatively high hydrogen partial pressures in the gut lumen. Using Clark-type microelectrodes, we showed that the situation in
Cubitermes orthognathus
and other soil-feeding members of the subfamily Termitinae is different and much more complex. All major compartments of agarose-embedded hindguts were anoxic at the gut center, and high H
2
partial pressures (1 to 10 kPa) in the alkaline anterior region rendered the mixed segment and the third proctodeal segment (P3) significant sources of H
2
. Posterior to the P3 segment, however, H
2
concentrations were generally below the detection limit (<100 Pa). All hindgut compartments turned into efficient hydrogen sinks when external H
2
was supplied, but methane was formed mainly in the P3/4a and P4b compartments, and in the latter only when H
2
or formate was added. Addition of H
2
to the gas headspace stimulated CH
4
emission of living termites, indicating that endogenous H
2
production limits methanogenesis also in vivo. At the low H
2
partial pressures in the posterior hindgut, methanogens would most likely outcompete homoacetogens for this electron donor. This might explain the apparent predominance of methanogenesis over reductive acetogenesis in the hindgut of soil-feeding termites, although the presence of homoacetogens in the anterior, highly alkaline region cannot yet be excluded. In addition, the direct contact of anterior and posterior hindgut compartments in situ permits a cross-epithelial transfer of H
2
or formate, which would not only fuel methanogenesis in these compartments, but would also create favorable microniches for reductive acetogenesis. In situ rates and spatial distribution of H
2
-dependent acetogenic activities are addressed in a companion paper (A. Tholen and A. Brune, Appl. Environ. Microbiol. 65:4497–4505, 1999).
Diversity and Abundance of Bolidophyceae (Heterokonta) in Two Oceanic Regions
Authors: Guillou Laure , Moon-Van Der Staay Seung-Yeo , Claustre Herve , Partensky Frederic , Vaulot Daniel 
Published: December 2019

ABSTRACT

The diversity and abundance of the Bolidophyceae (Heterokonta), a newly described picoplanktonic algal class which is a sister group to the diatoms, was assessed in the equatorial Pacific Ocean and in the Mediterranean Sea by culture isolation, molecular biology techniques, and pigment analyses. Eight strains of Bolidophyceae were isolated in culture from different mesotrophic and oligotrophic areas. The corresponding small subunit (SSU) rRNA gene sequences allowed us to design two probes specific for the Bolidophyceae. These probes have been used in natural samples (i) to selectively amplify and detect Bolidophyceae sequences and (ii) to quantify the relative abundance of Bolidophyceae within the picoeukaryote community. Sequences available to date indicate that the class Bolidophyceae comprises at least three different clades, two corresponding to the previously described species
Bolidomonas pacifica
and
Bolidomonas mediterranea
and the third one corresponding to a subspecies of
B. pacifica
. Amplification of the SSU rRNA gene from natural samples with universal primers and hybridization using a
Bolidomonas
-specific probe followed by a eukaryote-specific probe allowed us to estimate the contribution of the Bolidophyceae to the eukaryotic DNA in both Pacific and Mediterranean waters to be lower than 1%. Similarly, high-performance liquid chromatography analyses of fucoxanthin, the major carotenoid present in Bolidophyceae, indicated that less than 4% of the total chlorophyll
a
in the picoplanktonic fraction in the equatorial Pacific was due to Bolidophyceae. Consequently, although strains of Bolidophyceae have been isolated from samples collected at several stations, this new class seems to have been a minor component of the natural picoeukaryotic populations in the ecosystems investigated, at least during the periods sampled.
Mechanisms of Action of Carvacrol on the Food-Borne Pathogen
Bacillus cereus
Authors: Ultee A. , Kets E. P. W. , Smid E. J. 
Published: December 2019

ABSTRACT

Carvacrol, a naturally occurring compound mainly present in the essential oil fraction of oregano and thyme, was studied for its effect on bioenergetic parameters of vegetative cells of the food-borne pathogen
Bacillus cereus
. Incubation for 30 min in the presence of 1 to 3 mM carvacrol reduced the viable cell numbers exponentially. Carvacrol (2 mM) significantly depleted the intracellular ATP pool to values close to 0 within 7 min. No proportional increase of the extracellular ATP pool was observed. Depletion of the internal ATP pool was associated with a change of the membrane potential (Δψ). At concentrations of 0.01 mM carvacrol and above, a significant reduction of Δψ was observed, leading to full dissipation of Δψ at concentrations of 0.15 mM and higher. Finally, an increase of the permeability of the cytoplasmic membrane for protons and potassium ions was observed (at 0.25 and 1 mM carvacrol, respectively). From this study, it could be concluded that carvacrol interacts with the membranes of
B. cereus
by changing its permeability for cations like H
+
and K
+
. The dissipation of ion gradients leads to impairment of essential processes in the cell and finally to cell death.
Distribution of Sulfate-Reducing and Methanogenic Bacteria in Anaerobic Aggregates Determined by Microsensor and Molecular Analyses
Authors: Santegoeds Cecilia M. , Damgaard Lars Riis , Hesselink Gijs , Zopfi Jakob , Lens Piet , Muyzer Gerard , de Beer Dirk 
Published: December 2019

ABSTRACT

Using molecular techniques and microsensors for H
2
S and CH
4
, we studied the population structure of and the activity distribution in anaerobic aggregates. The aggregates originated from three different types of reactors: a methanogenic reactor, a methanogenic-sulfidogenic reactor, and a sulfidogenic reactor. Microsensor measurements in methanogenic-sulfidogenic aggregates revealed that the activity of sulfate-reducing bacteria (2 to 3 mmol of S
2−
m
−3
s
−1
or 2 × 10
−9
mmol s
−1
per aggregate) was located in a surface layer of 50 to 100 μm thick. The sulfidogenic aggregates contained a wider sulfate-reducing zone (the first 200 to 300 μm from the aggregate surface) with a higher activity (1 to 6 mmol of S
2−
m
−3
s
−1
or 7 × 10
−9
mol s
−1
per aggregate). The methanogenic aggregates did not show significant sulfate-reducing activity. Methanogenic activity in the methanogenic-sulfidogenic aggregates (1 to 2 mmol of CH
4
m
−3
s
−1
or 10
−9
mmol s
−1
per aggregate) and the methanogenic aggregates (2 to 4 mmol of CH
4
m
−3
s
−1
or 5 × 10
−9
mmol s
−1
per aggregate) was located more inward, starting at ca. 100 μm from the aggregate surface. The methanogenic activity was not affected by 10 mM sulfate during a 1-day incubation. The sulfidogenic and methanogenic activities were independent of the type of electron donor (acetate, propionate, ethanol, or H
2
), but the substrates were metabolized in different zones. The localization of the populations corresponded to the microsensor data. A distinct layered structure was found in the methanogenic-sulfidogenic aggregates, with sulfate-reducing bacteria in the outer 50 to 100 μm, methanogens in the inner part, and
Eubacteria
spp. (partly syntrophic bacteria) filling the gap between sulfate-reducing and methanogenic bacteria. In methanogenic aggregates, few sulfate-reducing bacteria were detected, while methanogens were found in the core. In the sulfidogenic aggregates, sulfate-reducing bacteria were present in the outer 300 μm, and methanogens were distributed over the inner part in clusters with syntrophic bacteria.
Biodegradation of Methyl
tert
-Butyl Ether by a Bacterial Pure Culture
Authors: Hanson Jessica R. , Ackerman Corinne E. , Scow Kate M. 
Published: December 2019

ABSTRACT

A bacterial strain, PM1, which is able to utilize methyl
tert
-butyl ether (MTBE) as its sole carbon and energy source, was isolated from a mixed microbial consortium in a compost biofilter capable of degrading MTBE. Initial linear rates of MTBE degradation by 2 × 10
6
cells ml
−1
were 0.07, 1.17, and 3.56 μg ml
−1
h
−1
for initial concentrations of 5, 50, and 500 μg MTBE ml
−1
, respectively. When incubated with 20 μg of uniformly labeled [
14
C]MTBE ml
−1
, strain PM1 converted 46% to
14
CO
2
and 19% to
14
C-labeled cells within 120 h. This yield is consistent with the measurement of protein accumulation at different MTBE concentrations from which was estimated a biomass yield of 0.18 mg of cells mg MTBE
−1
. Strain PM1 was inoculated into sediment core material collected from a contaminated groundwater plume at Port Hueneme, California, in which there was no evidence of MTBE degradation. Strain PM1 readily degraded 20 μg of MTBE ml
−1
added to the core material. The rate of MTBE removal increased with additional inputs of 20 μg of MTBE ml
−1
. These results suggest that PM1 has potential for use in the remediation of MTBE-contaminated environments.
Relationships of Bradyrhizobia from the Legumes
Apios americana
and
Desmodium glutinosum
Authors: Parker Matthew A. 
Published: December 2019

ABSTRACT

Multilocus enzyme electrophoresis, partial 23S rRNA sequences, and nearly full-length 16S rRNA sequences all indicated high genetic similarity among root-nodule bacteria associated with
Apios americana
,
Desmodium glutinosum
, and
Amphicarpaea bracteata
, three common herbaceous legumes whose native geographic ranges in eastern North America overlap extensively. A total of 19 distinct multilocus genotypes (electrophoretic types [ETs]) were found among the 35
A. americana
and 33
D. glutinosum
isolates analyzed. Twelve of these ETs (representing 78% of all isolates) were either identical to ETs previously observed in
A. bracteata
populations, or differed at only one locus. Within both 23S and 16S rRNA genes, several isolates from
A. americana
and
D. glutinosum
were either identical to
A. bracteata
isolates or showed only single nucleotide differences. Growth rates and nitrogenase activities of
A. bracteata
plants inoculated with isolates from
D. glutinosum
were equivalent to levels found with native
A. bracteata
bacterial isolates, but none of the three
A. americana
isolates tested had high symbiotic effectiveness on
A. bracteata
. Phylogenetic analysis of both 23S and 16S rRNA sequences indicated that both
A. americana
and
D. glutinosum
harbored rare bacterial genotypes similar to
Bradyrhizobium japonicum
USDA 110. However, the predominant root nodule bacteria on both legumes were closely related to
Bradyrhizobium elkanii
.
Phylogenetic Diversity of Nitrogen Fixation Genes in the Symbiotic Microbial Community in the Gut of Diverse Termites
Authors: Ohkuma Moriya , Noda Satoko , Kudo Toshiaki 
Published: December 2019

ABSTRACT

Nitrogen fixation by the microorganisms in the gut of termites is one of the crucial aspects of symbiosis, since termites usually thrive on a nitrogen-poor diet. The phylogenetic diversity of the nitrogen-fixing organisms within the symbiotic community in the guts of various termite species was investigated without culturing the resident microorganisms. A portion of the dinitrogenase reductase gene (
nifH
) was directly amplified from DNA extracted from the mixed population in the termite gut. Analysis of deduced amino acid sequences of the products of the clonally isolated
nifH
genes revealed the presence of diverse
nifH
sequences in most of the individual termite species, and their constituents were considerably different among termite species. A majority of the
nifH
sequences from six lower termites, which showed significant levels of nitrogen fixation activity, could be assigned to either the anaerobic
nif
group (consisting of clostridia and sulfur reducers) or the alternative
nif
methanogen group among the
nifH
phylogenetic groups. In the case of three higher termites, which showed only low levels of nitrogen fixation activity, a large number of the sequences were assigned to the most divergent
nif
group, probably functioning in some process other than nitrogen fixation and being derived from methanogenic archaea. The
nifH
groups detected were similar within each termite family but different among the termite families, suggesting an evolutionary trend reflecting the diazotrophic habitats in the symbiotic community. Within these phylogenetic groups, the sequences from the termites formed lineages distinct from those previously recognized in studies using classical microbiological techniques, and several sequence clusters unique to termites were found. The results indicate the presence of diverse potentially nitrogen-fixing microbial assemblages in the guts of termites, and the majority of them are as yet uncharacterized.
Regulation of Exopolysaccharide Production by
Lactococcus lactis
subsp.
cremoris
by the Sugar Source
Authors: Looijesteijn Petronella J. , Boels Ingeborg C. , Kleerebezem Michiel , Hugenholtz Jeroen 
Published: December 2019

ABSTRACT

Lactococcus lactis
produced more exopolysaccharide (EPS) on glucose than on fructose as the sugar substrate, although the transcription level of the
eps
gene cluster was independent of the sugar source. A major difference between cells grown on the two substrates was the capacity to produce sugar nucleotides, the EPS precursors. However, the activities of the enzymes required for the synthesis of nucleotide sugars were not changed upon growth on different sugars. The activity of fructosebisphosphatase (FBPase) was by far the lowest of the enzymes involved in precursor formation under all conditions. FBPase catalyzes the conversion of fructose-1,6-diphosphate into fructose-6-phosphate, which is an essential step in the biosynthesis of sugar nucleotides from fructose but not from glucose. By overexpression of the
fbp
gene, which resulted in increased EPS synthesis on fructose, it was proven that the low activity of FBPase is indeed limiting not only for EPS production but also for growth on fructose as a sugar source.