bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detritus-Dependent Development of the Microbial Community in an Experimental System: Qualitative Analysis by Denaturing Gradient Gel Electrophoresis
Authors: van Hannen Erik J. , Mooij Wolf , van Agterveld Miranda P. , Gons Herman J. , Laanbroek Hendrikus J. 
Published: December 2019

ABSTRACT

Correlations between the biomass of phytoplankton and the biomass of bacteria and between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the “microbial loop.” To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga
Ankistrodesmus falcatus
or the cyanobacterium
Oscillatoria limnetica
in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities, the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined.
Structures and Properties of Gellan Polymers Produced bySphingomonas paucimobilisATCC 31461 from Lactose Compared with Those Produced from Glucose and from Cheese Whey
Authors: Fialho Arsénio M. , Martins Lígia O. , Donval Marie-Lucie , Leitão Jorge H. , Ridout Michael J. , Jay Andrew J. , Morris Victor J. , Sá-Correia Isabel 
Published: December 2019

ABSTRACTThe dairy industry produces large quantities of whey as a by-product of cheese production and is increasingly looking for new ways to utilize this waste product. Gellan gum is reliably produced bySphingomonas paucimobilisin growth media containing lactose, a significant component of cheese whey, as a carbon source. We studied and compared polysaccharide biosynthesis byS. paucimobilisATCC 31461 in media containing glucose, lactose (5 to 30 g/liter), and sweet cheese whey. We found that altering the growth medium can markedly affect the polysaccharide yield, acyl substitution level, polymer rheological properties, and susceptibility to degradation. Depression of gellan production from lactose compared with gellan production from glucose (approximately 30%) did not appear to occur at the level of synthesis of sugar nucleotides, which are the donors of monomers used for biosynthesis of the repetitive tetrasaccharide unit of gellan. The lactose-derived biopolymer had the highest total acyl content; the glucose- and whey-derived gellans had similar total acyl contents but differed markedly in their acetate and glycerate levels. Rheological studies revealed how the functionality of a gellan polysaccharide is affected by changes in the acyl substitution.
Degradation of Chlorobenzenes at Nanomolar Concentrations by
Burkholderia
sp. Strain PS14 in Liquid Cultures and in Soil
Authors: Rapp Peter , Timmis Kenneth N. 
Published: December 2019

ABSTRACT

The utilization of 1,2,4,5-tetrachloro-, 1,2,4-trichloro-, the three isomeric dichlorobenzenes and fructose as the sole carbon and energy sources at nanomolar concentrations was studied in batch experiments with
Burkholderia
sp. strain PS14. In liquid culture, all chlorobenzenes were metabolized within 1 h from their initial concentration of 500 nM to below their detection limits of 0.5 nM for 1,2,4,5-tetrachloro- and 1,2,4-trichlorobenzene and 7.5 nM for the three dichlorobenzene isomers, with 63% mineralization of the tetra- and trichloroisomers. Fructose at the same initial concentration was, in contrast, metabolized over a 4-h incubation period down to a residual concentration of approximately 125 nM with 38% mineralization during this time. In soil microcosms,
Burkholderia
sp. strain PS14 metabolized tetrachlorobenzene present at 64.8 ppb and trichlorobenzene present at 54.4 ppb over a 72-h incubation period to below the detection limits of 0.108 and 0.09 ppb, respectively, with approximately 80% mineralization. A high sorptive capacity of
Burkholderia
sp. strain PS14 for 1,2,4,5-tetrachlorobenzene was found at very low cell density. The results demonstrate that
Burkholderia
sp. strain PS14 exhibits a very high affinity for chlorobenzenes at nanomolar concentrations.
High-Level Production of Heterologous Protein by Engineered Yeasts Grown in Cottage Cheese Whey
Authors: Maullu Carlo , Lampis Giorgio , Desogus Alessandra , Ingianni Angela , Rossolini Gian Maria , Pompei Raffaello 
Published: December 2019

ABSTRACT

Cottage cheese whey is a cheese industry by-product still rich in proteins and lactose. Its recycling is seldom cost-effective. In this work we show that the lactose-utilizing yeast
Kluyveromyces lactis
, engineered for production of recombinant human lysozyme, can be grown in cottage cheese whey, resulting in high-level production of the heterologous protein (125 μg/ml).
Development of Primers to O-Antigen Biosynthesis Genes for Specific Detection of
Escherichia coli
O157 by PCR
Authors: Maurer John J. , Schmidt Denise , Petrosko Patricia , Sanchez Susan , Bolton Lance , Lee Margie D. 
Published: December 2019

ABSTRACT

The chemical composition of each O-antigen subunit in gram-negative bacteria is a reflection of the unique DNA sequences within each
rfb
operon. By characterizing DNA sequences contained with each
rfb
operon, a diagnostic serotype-specific probe to
Escherichia coli
O serotypes that are commonly associated with bacterial infections can be generated. Recently, from an
E. coli
O157:H7 cosmid library, O-antigen-positive cosmids were identified with O157-specific antisera. By using the cosmid DNAs as probes, several DNA fragments which were unique to
E. coli
O157 serotypes were identified by Southern analysis. Several of these DNA fragments were subcloned from O157-antigen-positive cosmids and served as DNA probes in Southern analysis. One DNA fragment within plasmid pDS306 which was specific for
E. coli
O157 serotypes was identified by Southern analysis. The DNA sequence for this plasmid revealed homology to two
rfb
genes, the first of which encodes a GDP-mannose dehydratase. These
rfb
genes were similar to O-antigen biosynthesis genes in
Vibrio cholerae
and
Yersinia enterocolitica
serotype O:8. An oligonucleotide primer pair was designed to amplify a 420-bp DNA fragment from
E. coli
O157 serotypes. The PCR test was specific for
E. coli
O157 serotypes. PCR detected as few as 10 cells with the O157-specific
rfb
oligonucleotide primers. Coupled with current enrichment protocols, O157 serotyping by PCR will provide a rapid, specific, and sensitive method for identifying
E. coli
O157.
Reductive Dechlorination of Chlorinated Ethenes and 1,2-Dichloroethane by “
Dehalococcoides ethenogenes
” 195
Authors: Maymó-Gatell Xavier , Anguish Timothy , Zinder Stephen H. 
Published: December 2019

ABSTRACT

“
Dehalococcoides ethenogenes
” 195 can reductively dechlorinate tetrachloroethene (PCE) completely to ethene (ETH). When PCE-grown strain 195 was transferred (2% [vol/vol] inoculum) into growth medium amended with trichloroethene (TCE),
cis
-dichloroethene (DCE), 1,1-DCE, or 1,2-dichloroethane (DCA) as an electron acceptor, these chlorinated compounds were consumed at increasing rates over time, which indicated that growth occurred. Moreover, the number of cells increased when TCE, 1,1-DCE, or DCA was present. PCE, TCE, 1,1-DCE, and
cis
-DCE were converted mainly to vinyl chloride (VC) and then to ETH, while DCA was converted to ca. 99% ETH and 1% VC.
cis
-DCE was used at lower rates than PCE, TCE, 1,1-DCE, or DCA was used. When PCE-grown cultures were transferred to media containing VC or
trans
-DCE, products accumulated slowly, and there was no increase in the rate, which indicated that these two compounds did not support growth. When the intermediates in PCE dechlorination by strain 195 were monitored, TCE was detected first, followed by
cis
-DCE. After a lag, VC, 1,1-DCE, and
trans
-DCE accumulated, which is consistent with the hypothesis that
cis
-DCE is the precursor of these compounds. Both
cis
-DCE and 1,1-DCE were eventually consumed, and both of these compounds could be considered intermediates in PCE dechlorination, whereas the small amount of
trans
-DCE that was produced persisted. Cultures grown on TCE, 1,1-DCE, or DCA could immediately dechlorinate PCE, which indicated that PCE reductive dehalogenase activity was constitutive when these electron acceptors were used.
Evidence for Involvement of Gut-Associated Denitrifying Bacteria in Emission of Nitrous Oxide (N2O) by Earthworms Obtained from Garden and Forest Soils
Authors: Matthies Carola , Grießhammer Anja , Schmittroth Martina , Drake Harold L. 
Published: December 2019

ABSTRACTEarthworms (Aporrectodea caliginosa,Lumbricus rubellus, andOctolasion lacteum) obtained from nitrous oxide (N2O)-emitting garden soils emitted 0.14 to 0.87 nmol of N2O h−1g (fresh weight)−1under in vivo conditions.L. rubellusobtained from N2O-emitting forest soil also emitted N2O, which confirmed previous observations (G. R. Karsten and H. L. Drake, Appl. Environ. Microbiol. 63:1878–1882, 1997). In contrast, commercially obtainedLumbricus terrestrisdid not emit N2O; however, such worms emitted N2O when they were fed (i.e., preincubated in) garden soils.A. caliginosa,L. rubellus, andO. lacteumsubstantially increased the rates of N2O emission of garden soil columns and microcosms. Extrapolation of the data to in situ conditions indicated that N2O emission by earthworms accounted for approximately 33% of the N2O emitted by garden soils. In vivo emission of N2O by earthworms obtained from both garden and forest soils was greatly stimulated when worms were moistened with sterile solutions of nitrate or nitrite; in contrast, ammonium did not stimulate in vivo emission of N2O. In the presence of nitrate, acetylene increased the N2O emission rates of earthworms; in contrast, in the presence of nitrite, acetylene had little or no effect on emission of N2O. In vivo emission of N2O decreased by 80% when earthworms were preincubated in soil supplemented with streptomycin and tetracycline. On a fresh weight basis, the rates of N2O emission of dissected earthworm gut sections were substantially higher than the rates of N2O emission of dissected worms lacking gut sections, indicating that N2O production occurred in the gut rather than on the worm surface. In contrast to living earthworms and gut sections that produced N2O under oxic conditions (i.e., in the presence of air), fresh casts (feces) from N2O-emitting earthworms produced N2O only under anoxic conditions. Collectively, these results indicate that gut-associated denitrifying bacteria are responsible for the in vivo emission of N2O by earthworms and contribute to the N2O that is emitted from certain terrestrial ecosystems.
Microscale Distribution of Populations and Activities of
Nitrosospira
and
Nitrospira
spp. along a Macroscale Gradient in a Nitrifying Bioreactor: Quantification by In Situ Hybridization and the Use of Microsensors
Authors: Schramm Andreas , de Beer Dirk , van den Heuvel Johan C. , Ottengraf Simon , Amann Rudolf 
Published: December 2019

ABSTRACT

The change of activity and abundance of
Nitrosospira
and
Nitrospira
spp. along a bulk water gradient in a nitrifying fluidized bed reactor was analyzed by a combination of microsensor measurements and fluorescence in situ hybridization. Nitrifying bacteria were immobilized in bacterial aggregates that remained in fixed positions within the reactor column due to the flow regimen. Nitrification occurred in a narrow zone of 100 to 150 μm on the surface of these aggregates, the same layer that contained an extremely dense community of nitrifying bacteria. The central part of the aggregates was inactive, and significantly fewer nitrifiers were found there. Under conditions prevailing in the reactor, i.e., when ammonium was limiting, ammonium was completely oxidized to nitrate within the active layer of the aggregates, the rates decreasing with increasing reactor height. To analyze the nitrification potential, profiles were also recorded in aggregates subjected to a short-term incubation under elevated substrate concentrations. This led to a shift in activity from ammonium to nitrite oxidation along the reactor and correlated well with the distribution of the nitrifying population. Along the whole reactor, the numbers of ammonia-oxidizing bacteria decreased, while the numbers of nitrite-oxidizing bacteria increased. Finally, volumetric reaction rates were calculated from microprofiles and related to cell numbers of nitrifying bacteria in the active shell. Therefore, it was possible for the first time to estimate the cell-specific activity of
Nitrosospira
spp. and hitherto-uncultured
Nitrospira
-like bacteria in situ.
The MTT [3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide] Assay Is a Fast and Reliable Method for Colorimetric Determination of Fungal Cell Densities
Authors: Freimoser Florian M. , Jakob Claude A. , Aebi Markus , Tuor Urs 
Published: December 2019

ABSTRACT

The entomopathogenic fungus
Neozygites parvispora
(Entomophthorales: Zygomycetes) grows in vitro as irregularly rod-shaped hyphal bodies in a complex medium. In order to simplify the medium composition and determine growth-promoting compounds for the cultivation of this fungus, we were looking for a rapid and quantitative method to estimate the number of living cells in small volumes of liquid culture. A colorimetric method for the determination of cell densities using MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] proved to be more accurate and timesaving than conventional hemocytometer counting.
Characterization of an Acetyl Xylan Esterase from the Anaerobic Fungus
Orpinomyces
sp. Strain PC-2
Authors: Blum David L. , Li Xin-Liang , Chen Huizhong , Ljungdahl Lars G. 
Published: December 2019

ABSTRACT

A 1,067-bp cDNA, designated
axeA
, coding for an acetyl xylan esterase (AxeA) was cloned from the anaerobic rumen fungus
Orpinomyces
sp. strain PC-2. The gene had an open reading frame of 939 bp encoding a polypeptide of 313 amino acid residues with a calculated mass of 34,845 Da. An active esterase using the original start codon of the cDNA was synthesized in
Escherichia coli
. Two active forms of the esterase were purified from recombinant
E. coli
cultures. The size difference of 8 amino acids was a result of cleavages at two different sites within the signal peptide. The enzyme released acetate from several acetylated substrates, including acetylated xylan. The activity toward acetylated xylan was tripled in the presence of recombinant xylanase A from the same fungus. Using
p
-nitrophenyl acetate as a substrate, the enzyme had a

K
m

of 0.9 mM and a
V
max
of 785 μmol min
−1
mg
−1
. It had temperature and pH optima of 30°C and 9.0, respectively. AxeA had 56% amino acid identity with BnaA, an acetyl xylan esterase of
Neocallimastix patriciarum
, but the
Orpinomyces
AxeA was devoid of a noncatalytic repeated peptide domain (NCRPD) found at the carboxy terminus of the
Neocallimastix
BnaA. The NCRPD found in many glycosyl hydrolases and esterases of anaerobic fungi has been postulated to function as a docking domain for cellulase-hemicellulase complexes, similar to the dockerin of the cellulosome of
Clostridium thermocellum
. The difference in domain structures indicated that the two highly similar esterases of
Orpinomyces
and
Neocallimastix
may be differently located, the former being a free enzyme and the latter being a component of a cellulase-hemicellulase complex. Sequence data indicate that AxeA and BnaA might represent a new family of hydrolases.
Fraction of Electrons Consumed in Electron Acceptor Reduction and Hydrogen Thresholds as Indicators of Halorespiratory Physiology
Authors: Löffler Frank E. , Tiedje James M. , Sanford Robert A. 
Published: December 2019

ABSTRACTMeasurements of the hydrogen consumption threshold and the tracking of electrons transferred to the chlorinated electron acceptor (fe) reliably detected chlororespiratory physiology in both mixed cultures and pure cultures capable of using tetrachloroethene,cis-1,2-dichloroethene, vinyl chloride, 2-chlorophenol, 3-chlorobenzoate, 3-chloro-4-hydroxybenzoate, or 1,2-dichloropropane as an electron acceptor. Hydrogen was consumed to significantly lower threshold concentrations of less than 0.4 ppmv compared with the values obtained for the same cultures without a chlorinated compound as an electron acceptor. The fevalues ranged from 0.63 to 0.7, values which are in good agreement with theoretical calculations based on the thermodynamics of reductive dechlorination as the terminal electron-accepting process. In contrast, a mixed methanogenic culture that cometabolized 3-chlorophenol exhibited a significantly lower fevalue, 0.012.
Detection and Identification of Amanitins in the Wood-Rotting Fungi
Galerina fasciculata
and
Galerina helvoliceps
Authors: Muraoka Shinjiro , Fukamachi Nobuko , Mizumoto Kiyohisa , Shinozawa Takao 
Published: December 2019

ABSTRACT

More than 600 strains of wood-rotting fungi were screened for the detection of amanitins. Three strains of
Galerina fasciculata
and 18 strains of
Galerina helvoliceps
contained amanitins. These strains contained mainly α- and β-amanitins in the native fruit bodies, while α- and γ-amanitins were found in liquid-cultured mycelia. Purified amanitins were confirmed by their chromatographic profiles, spectra (UV, Fourier transform infrared, and atmospheric ionization mass), cytotoxicity for mammalian cell lines (3T3 and SiHa), and inhibitory effects on RNA polymerase II. The results revealed that the purified amanitin fractions from these species are identical to authentic amanitins and suggest that these two species must be handled as poisonous mushrooms.
Degradation of Polycarbonate by a Polyester-Degrading Strain,
Amycolatopsis
sp. Strain HT-6
Authors: Pranamuda Hardaning , Chollakup Rungsima , Tokiwa Yutaka 
Published: December 2019

ABSTRACT

Amycolatopsis
sp. strain HT-6, a poly(tetramethylene succinate) (PTMS)-degrading actinomycete, was observed to degrade poly(tetramethylene carbonate) (PTMC). In a liquid culture with 150 mg of PTMC film, 59% degradation was achieved, but with a low yield of cell growth. On the other hand, PTMS copolymerized with a small amount of PTMC, forming a copolyester carbonate (PEC) that was completely and rapidly degraded with a high yield of cell growth.
Temperature-Dependent Fermentation of
d
-Sorbitol in
Escherichia coli
O157:H7
Authors: Bouvet O. M. M. , Pernoud S. , Grimont P. A. D. 
Published: December 2019

ABSTRACT

The influence of growth temperature on the ability to ferment
d
-sorbitol was investigated in
Escherichia coli
O157:H7. It was found that O157:H7 strains have a temperature-sensitive sorbitol phenotype.
d
-Sorbitol transport and sorbitol-6-phosphate dehydrogenase activities were expressed in sorbitol-fermenting cells grown at 30°C but only at a low level at 40°C. Sorbitol-positive variants able to transport
d
-sorbitol were easily selected at 30°C from culture of Sor
−
E. coli
O157:H7 strains.
Identification of
Lactobacillus
Isolates from the Gastrointestinal Tract, Silage, and Yoghurt by 16S-23S rRNA Gene Intergenic Spacer Region Sequence Comparisons
Authors: Tannock G. W. , Tilsala-Timisjarvi A. , Rodtong S. , Ng J. , Munro K. , Alatossava T. 
Published: December 2019

ABSTRACT

Lactobacillus
isolates were identified by PCR amplification and sequencing of the region between the 16S and 23S rRNA genes (spacer region). The sequences obtained from the isolates were compared to those of reference strains held in GenBank. A similarity of 97.5% or greater was considered to provide identification. To check the reliability of the method, the V2-V3 region of the 16S rRNA gene was amplified and sequenced in the case of isolates whose spacer region sequences were less than 99% similar to that of a reference strain. Confirmation of identity was obtained in all instances. Spacer region sequencing provided rapid and accurate identification of
Lactobacillus
isolates obtained from gastrointestinal, yoghurt, and silage samples. It had an advantage over 16S V2-V3 sequence comparisons because it distinguished between isolates of
Lactobacillus casei
and
Lactobacillus rhamnosus
.
The SSSPIN study—spin in studies of spin: meta-research analysis
Authors: Bero Lisa , Chiu Kellia , Grundy Quinn 
Published: December 2019

AbstractObjectivesTo identify and calculate the prevalence of spin in studies of spin.DesignMeta-research analysis (research on research).Setting35 studies of spin in the scientific literature.Main outcome measuresSpin, categorised as: reporting practices that distort the presentation and interpretation of results, creating misleading conclusions; discordance between results and their interpretation, with presentation of favourable conclusions that are not supported by the data or results; attribution of causality when study design does not support it; and over-interpretation or inappropriate extrapolation of results.ResultsFive (14%) of 35 spin studies contained spin categorised as reporting practices that distort the presentation and interpretation of results (n=2) or categorised as over-interpretation or inappropriate extrapolation of results (n=3).ConclusionSpin occurs in research on spin. Although researchers on this topic should be sensitive to spinning their findings, our study does not undermine the need for rigorous interventions to reduce spin across various research fields.Conclusion with spinOur hypothesis that spin will be less prevalent in spin studies than in studies on other topics has been proven. Spin scholars are less likely to spin their conclusions than other researchers, and they should receive substantial resources to launch and test interventions to reduce spin and research waste in reporting.