bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functionally Redundant Cellobiose-Degrading Soil Bacteria Respond Differentially to Oxygen
Authors: Schellenberger Stefanie , Drake Harold L. , Kolb Steffen 
Published: July 2011

ABSTRACT

The availability of oxygen (O
2
) in aerated (i.e., water-unsaturated) soils affects the metabolic activities of aerobic and anaerobic soil prokaryotes that degrade plant-derived saccharides. Fluctuating availabilities of O
2
were imposed on agricultural soil slurries supplemented with cellobiose. Slurries were subjected to oxic conditions (48 h), followed by an anoxic period (120 h) and a final oxic period (24 h). Redox potential was stable at 500 mV during oxic periods but decreased rapidly (within 10 h) under anoxic conditions to −330 mV. The consumption of cellobiose occurred without apparent delay at all redox potentials. The metabolic activities of seven previously identified saccharolytic family-level taxa of the investigated soil were measured with newly designed quantitative PCR assays targeting the 16S rRNA. Four taxa responded to the experimental conditions. The amounts of rRNAs of
Micrococcaceae
and
Cellulomonadaceae
(
Actinobacteria
) increased under oxic conditions. In contrast, the RNA contents of
Clostridiaceae
(cluster I,
Firmicutes
) and two uncultured family-level-taxa, i.e., “Cellu” and “Sphingo” (both
Bacteroidetes
) increased under anoxic conditions. That the degradation of cellobiose was independent of the availability of O
2
and that redox potentials decreased in response to anaerobic activities indicated that the degradation of cellobiose was linked to functionally redundant cellobiose-degrading taxa capable of altering redox conditions.
Possible Overestimation of Surface Disinfection Efficiency by Assessment Methods Based on Liquid Sampling Procedures as Demonstrated by
In Situ
Quantification of Spore Viability
Authors: Grand I. , Bellon-Fontaine M.-N. , Herry J.-M. , Hilaire D. , Moriconi F.-X. , Naïtali M. 
Published: July 2011

ABSTRACT

The standard test methods used to assess the efficiency of a disinfectant applied to surfaces are often based on counting the microbial survivors sampled in a liquid, but total cell removal from surfaces is seldom achieved. One might therefore wonder whether evaluations of microbial survivors in liquid-sampled cells are representative of the levels of survivors in whole populations. The present study was thus designed to determine the “damaged/undamaged” status induced by a peracetic acid disinfection for
Bacillus atrophaeus
spores deposited on glass coupons directly on this substrate and to compare it to the status of spores collected in liquid by a sampling procedure. The method utilized to assess the viability of both surface-associated and liquid-sampled spores included fluorescence labeling with a combination of Syto 61 and Chemchrome V6 dyes and quantifications by analyzing the images acquired by confocal laser scanning microscopy. The principal result of the study was that the viability of spores sampled in the liquid was found to be poorer than that of surface-associated spores. For example, after 2 min of peracetic acid disinfection, less than 17% ± 5% of viable cells were detected among liquid-sampled cells compared to 79% ± 5% or 47% ± 4%, respectively, when the viability was evaluated on the surface after or without the sampling procedure. Moreover, assessments of the survivors collected in the liquid phase, evaluated using the microscopic method and standard plate counts, were well correlated. Evaluations based on the determination of survivors among the liquid-sampled cells can thus overestimate the efficiency of surface disinfection procedures.
Heavy-Machinery Traffic Impacts Methane Emissions as Well as Methanogen Abundance and Community Structure in Oxic Forest Soils
Authors: Frey Beat , Niklaus Pascal A. , Kremer Johann , Lüscher Peter , Zimmermann Stephan 
Published: July 2011

ABSTRACT

Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH
4
consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (
mcrA
) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting
mcrA
sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most
mcrA
gene sequences were mostly similar to known sequences from wetlands. The majority of
mcrA
gene sequences belonged either to the order
Methanosarcinales
or
Methanomicrobiales
, whereas both sites were dominated by members of the families
Methanomicrobiaceae
Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.
Biochemical Characterization and Relative Expression Levels of Multiple Carbohydrate Esterases of the Xylanolytic Rumen Bacterium Prevotella ruminicola 23 Grown on an Ester-Enriched Substrate
Authors: Kabel Mirjam A. , Yeoman Carl J. , Han Yejun , Dodd Dylan , Abbas Charles A. , de Bont Jan A. M. , Morrison Mark , Cann Isaac K. O. , Mackie Roderick I. 
Published: July 2011

ABSTRACT

We measured expression and used biochemical characterization of multiple carbohydrate esterases by the xylanolytic rumen bacterium
Prevotella ruminicola
23 grown on an ester-enriched substrate to gain insight into the carbohydrate esterase activities of this hemicellulolytic rumen bacterium. The
P. ruminicola
23 genome contains 16 genes predicted to encode carbohydrate esterase activity, and based on microarray data, four of these were upregulated >2-fold at the transcriptional level during growth on an ester-enriched oligosaccharide (XOS
FA,Ac
) from corn relative to a nonesterified fraction of corn oligosaccharides (AXOS). Four of the 16 esterases (Xyn10D-Fae1A, Axe1-6A, AxeA1, and Axe7A), including the two most highly induced esterases (Xyn10D-Fae1A and Axe1-6A), were heterologously expressed in
Escherichia coli
, purified, and biochemically characterized. All four enzymes showed the highest activity at physiologically relevant pH (6 to 7) and temperature (30 to 40°C) ranges. The
P. ruminicola
23 Xyn10D-Fae1A (a carbohydrate esterase [CE] family 1 enzyme) released ferulic acid from methylferulate, wheat bran, corn fiber, and XOS
FA,Ac
, a corn fiber-derived substrate enriched in
O
-acetyl and ferulic acid esters, but exhibited negligible activity on sugar acetates. As expected, the
P. ruminicola
Axe1-6A enzyme, which was predicted to possess two distinct esterase family domains (CE1 and CE6), released ferulic acid from the same substrates as Xyn10D-Fae1 and was also able to cleave
O
-acetyl ester bonds from various acetylated oligosaccharides (AcXOS). The
P. ruminicola
23 AxeA1, which is not assigned to a CE family, and Axe7A (CE7) were found to be acetyl esterases that had activity toward a broad range of mostly nonpolymeric acetylated substrates along with AcXOS. All enzymes were inhibited by the proximal location of other side groups like 4-
O
-methylglucuronic acid, ferulic acid, or acetyl groups. The unique diversity of carbohydrate esterases in
P. ruminicola
23 likely gives it the ability to hydrolyze substituents on the xylan backbone and enhances its capacity to efficiently degrade hemicellulose.
L
-Arabitol Is the Actual Inducer of Xylanase Expression in Hypocrea jecorina (Trichoderma reesei)
Authors: Mach-Aigner Astrid R. , Gudynaite-Savitch Loreta , Mach Robert L. 
Published: July 2011

ABSTRACT

The saprophytic fungus
Hypocrea jecorina
(anamorph,
Trichoderma reesei
) is an important native producer of hydrolytic enzymes, including xylanases. Regarding principles of sustainability, cheap and renewable raw materials, such as
d
-xylose (the backbone monomer of xylan), have been receiving increasing attention from industries. Recently, it was demonstrated that small (0.5 to 1 mM) amounts of
d
-xylose induce the highest expression of xylanase in
H. jecorina
. However, it was also reported that active metabolism of
d
-xylose is necessary for induction. In this report, we demonstrate that xylitol, the next intermediate in the pentose pathway after
d
-xylose, does not trigger transcription of xylanase-encoding genes in
H. jecorina
QM9414. The highest level of transcription of xylanolytic enzyme-encoding genes occurred in an
xdh1
(encoding a xylitol dehydrogenase) deletion strain cultured in the presence of 0.5 mM
d
-xylose, suggesting that a metabolite upstream of xylitol is the inducer. The expression levels of xylanases in an
xdh1
-
lad1
double-deletion strain were lower than that of an
xdh1
deletion strain. This observation suggested that
l
-xylulose is not an inducer and led to the hypothesis that
l
-arabitol is the actual inducer of xylanase expression. A direct comparison of transcript levels following the incubation of the
H. jecorina
parental strain with various metabolites of the pentose pathway confirmed this hypothesis. In addition, we demonstrate that
xyr1
, the activator gene, is not induced in the presence of pentose sugars and polyols, regardless of the concentration used; instead, we observed low constitutive expression of
xyr1
.
Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus
Authors: Holmes Dawn E. , Risso Carla , Smith Jessica A. , Lovley Derek R. 
Published: July 2011

ABSTRACTAnaerobic benzene oxidation coupled to the reduction of Fe(III) was studied inFerroglobus placidusin order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions.F. placidusconserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]benzene to [14C]carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism, and [14C]benzoate was produced from [14C]benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not upregulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- than in benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism ofF. placidus. This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus,F. placidusprovides a much-needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms.
Different Roles of Membrane Potentials in Electrotaxis and Chemotaxis of Dictyostelium Cells
Authors: Gao Run-chi , Zhang Xiao-dong , Sun Yao-hui , Kamimura Yoichiro , Mogilner Alex , Devreotes Peter N. , Zhao Min 
Published: July 2011

ABSTRACT

Many types of cells migrate directionally in direct current (DC) electric fields (EFs), a phenomenon termed galvanotaxis or electrotaxis. The directional sensing mechanisms responsible for this response to EFs, however, remain unknown. Exposing cells to an EF causes changes in plasma membrane potentials (
V

m

). Exploiting the ability of
Dictyostelium
cells to tolerate drastic
V

m

changes, we investigated the role of
V

m

in electrotaxis and, in parallel, in chemotaxis. We used three independent factors to control
V

m

: extracellular pH, extracellular [K
+
], and electroporation. Changes in
V

m

were monitored with microelectrode recording techniques. Depolarized
V

m

was observed under acidic (pH 5.0) and alkaline (pH 9.0) conditions as well as under higher extracellular [K
+
] conditions. Electroporation permeabilized the cell membrane and significantly reduced the
V

m

, which gradually recovered over 40 min. We then recorded the electrotactic behaviors of
Dictyostelium
cells with a defined
V

m

using these three techniques. The directionality (directedness of electrotaxis) was quantified and compared to that of chemotaxis (chemotactic index). We found that a reduced
V

m

significantly impaired electrotaxis without significantly affecting random motility or chemotaxis. We conclude that extracellular pH, [K
+
], and electroporation all significantly affected electrotaxis, which appeared to be mediated by the changes in
V

m

. The initial directional sensing mechanisms for electrotaxis therefore differ from those of chemotaxis and may be mediated by changes in resting
V

m

.
Contributions of Five Secondary Metal Uptake Systems to Metal Homeostasis of Cupriavidus metallidurans CH34
Authors: Kirsten Andreas , Herzberg Martin , Voigt Alexander , Seravalli Javier , Grass Gregor , Scherer Judith , Nies Dietrich H. 
Published: July 2011

ABSTRACT

Cupriavidus metallidurans
is adapted to high concentrations of transition metal cations and is a model system for studying metal homeostasis in difficult environments. The elemental composition of
C. metallidurans
cells cultivated under various conditions was determined, revealing the ability of the bacterium to shield homeostasis of one essential metal from the toxic action of another. The contribution of metal uptake systems to this ability was studied.
C. metallidurans
contains three CorA members of the metal inorganic transport (MIT) protein family of putative magnesium uptake systems, ZupT of the ZRT/IRT protein, or ZIP, family, and PitA, which imports metal phosphate complexes. Expression of the genes for all these transporters was regulated by zinc availability, as shown by reporter gene fusions. While expression of
zupT
was upregulated under conditions of zinc starvation, expression of the other genes was downregulated at high zinc concentrations. Only
corA
1
expression was influenced by magnesium starvation. Deletion mutants were constructed to characterize the contribution of each system to transition metal import. This identified ZupT as the main zinc uptake system under conditions of low zinc availability, CorA
1
as the main secondary magnesium uptake system, and CorA
2
and CorA
3
as backup systems for metal cation import. PitA may function as a cation-phosphate uptake system, the main supplier of divalent metal cations and phosphate in phosphate-rich environments. Thus, metal homeostasis in
C. metallidurans
is achieved by highly redundant metal uptake systems, which have only minimal cation selectivity and are in combination with efflux systems that “worry later” about surplus cations.
Genome Sequence of Mycoplasma ovipneumoniae Strain SC01
Authors: Yang Falong , Tang Cheng , Wang Yong , Zhang Huanrong , Yue Hua 
Published: July 2011

ABSTRACT

Mycoplasma ovipneumoniae
is associated with chronic nonprogressive pneumonia in both sheep and goats. Studies concerning its molecular pathogenesis, genetic analysis, and vaccine development have been hindered due to limited genomic information. Here, we announce the first complete genome sequence of this organism.
Draft Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading, Genetically Engineered Bioluminescent Bioreporter Pseudomonas fluorescens HK44
Authors: Chauhan Archana , Layton Alice C. , Williams Daniel E. , Smartt Abby E. , Ripp Steven , Karpinets Tatiana V. , Brown Steven D. , Sayler Gary S. 
Published: July 2011

ABSTRACT

Pseudomonas fluorescens
strain HK44 (DSM 6700) is a genetically engineered
lux
-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of ∼6.1 Mb of sequence indicates that 30% of the traits are unique and distributed over five genomic islands, a prophage, and two plasmids.
Genome Sequence of a Porcine Extraintestinal Pathogenic Escherichia coli Strain
Authors: Tan Chen , Xu Zhuofei , Zheng Huajun , Liu Wugang , Tang Xibiao , Shou Jin , Wu Bin , Wang Shengyue , Zhao Guo-Ping , Chen Huanchun 
Published: July 2011

ABSTRACT

Extraintestinal pathogenic
Escherichia coli
(ExPEC) is an important pathogen which can infect humans and animals and cause many diseases outside the intestine. Here, we report the first draft genome sequence of a porcine ExPEC strain, PCN033, isolated from a pig with meningitis.
Genome Sequence of Ruegeria sp. Strain KLH11, anN-Acylhomoserine Lactone-Producing Bacterium Isolated from the Marine Sponge Mycale laxissima
Authors: Zan Jindong , Fricke W. Florian , Fuqua Clay , Ravel Jacques , Hill Russell T. 
Published: July 2011

ABSTRACTRuegeriasp. strain KLH11, isolated from the marine spongeMycale laxissima, produces a complex profile ofN-acylhomoserine lactone quorum-sensing (QS) molecules. The genome sequence provides insights into the genetic potential of KLH11 to maintain complex QS systems, and this is the first genome report of a cultivated symbiont from a marine sponge.
Genome Sequence of the Rice-Pathogenic Bacterium Acidovorax avenae subsp. avenae RS-1
Authors: Xie Guan-Lin , Zhang Guo-Qing , Liu He , Lou Miao-Miao , Tian Wen-Xiao , Li Bin , Zhou Xue-Ping , Zhu Bo , Jin Gu-Lei 
Published: July 2011

ABSTRACT

Acidovorax avenae
subsp.
avenae
is a phytobacterium which is the causative agent of several plant diseases with economic significance. Here, we present the draft genome sequence of strain RS-1, which was isolated from rice shoots in a rice field in China. This strain can cause bacterial stripe of rice.
Complete Genome Sequence of Clostridium acetobutylicum DSM 1731, a Solvent-Producing Strain with Multireplicon Genome Architecture
Authors: Bao Guanhui , Wang Runjiang , Zhu Yan , Dong Hongjun , Mao Shaoming , Zhang Yanping , Chen Zugen , Li Yin , Ma Yanhe 
Published: July 2011

ABSTRACT

Clostridium acetobutylicum
is an important microorganism for solvent production. We report the complete genome sequence of
C. acetobutylicum
DSM 1731, a genome with multireplicon architecture. Comparison with the sequenced type strain
C. acetobutylicum
ATCC 824, the genome of strain DSM1731 harbors a 1.7-kb insertion and a novel 11.1-kb plasmid, which might have been acquired during evolution.
Genome Sequence of Lactobacillus ruminis SPM0211, Isolated from a Fecal Sample from a Healthy Korean
Authors: Lee Sunghee , Cho Yong-Joon , Lee Anne Hayoung , Chun Jongsik , Ha Nam-Joo , Ko GwangPyo 
Published: July 2011

ABSTRACT

Lactobacillus ruminis
SPM0211 is a potential probiotic strain that shows antimicrobial activity against emerging pathogens. Here we present the draft genomic sequence of
L. ruminis
SPM0211, isolated from a fecal sample from a healthy Korean and describe both the common and unique features of this strain.
Complete Genome Sequences of the Chemolithoautotrophic Oligotropha carboxidovorans Strains OM4 and OM5
Authors: Volland Sonja , Rachinger Michael , Strittmatter Axel , Daniel Rolf , Gottschalk Gerhard , Meyer Ortwin 
Published: July 2011

ABSTRACT

We report on genome sequencing of
Oligotropha carboxidovorans
strain OM4 and resequencing of strain OM5. The genomes of both are composed of one chromosome and two plasmids. The presence of two plasmids in the OM5 genome is inconsistent with the previously published sequence, for which only one plasmid was described (D. Paul, S. Bridges, S. Burgess, Y. Dandass, and M. Lawrence, BMC Genomics 11:511, 2010).
Complete Genome Sequence of Bifidobacterium longum subsp. longum KACC 91563
Authors: Ham Jun-Sang , Lee Taeheon , Byun Mi-Jeong , Lee Kyung-Tae , Kim Min-Kyung , Han Gi-Sung , Jeong Seok-Geun , Oh Mi-Hwa , Kim Dong-Hun , Kim Heebal 
Published: July 2011

ABSTRACT

Bifidobacterium longum
strains predominate in the colonic microbiota of breast-fed infants. Here we report the complete genome sequence of
B. longum
subsp.
longum
KACC 91563, isolated from feces of neonates. A single circular chromosome of 2,385,301 bp contains 1,980 protein-coding genes, 56 tRNA genes, and 3 rRNA operons.
Genome Sequence of Lactobacillus johnsonii PF01, Isolated from Piglet Feces
Authors: Lee Je Hee , Chae Jong Pyo , Lee Ji Yoon , Lim Jong-Sung , Kim Geun-Bae , Ham Jun-Sang , Chun Jongsik , Kang Dae-Kyung 
Published: July 2011

ABSTRACT

Lactobacillus johnsonii
PF01, an autochthonous bacterium of the gastrointestinal tract, was isolated from a fecal sample from a piglet. The strain adhered specifically to the duodenal and jejunal epithelial cells of the piglet and had high bile resistance activity. Here we report the genomic sequence of
L. johnsonii
PF01.
Expression of phosphoinositide-specific phospholipase C isoforms in human umbilical vein endothelial cells
Authors: Lo Vasco V R , Pacini L , Di Raimo T , D'arcangelo D , Businaro R 
Published: July 2011

AimsThe signalling system of phosphoinositides (PIs) is involved in a number of cell and tissue functions including membrane trafficking, ion channel activity, cell cycle, apoptosis, differentiation and cell and tissue polarity. Recently, a role in cell migration was hypothesised for PI and related molecules including the phosphoinositide-specific phospholipases C (PI-PLCs), main players in PI signalling. The expression of PI-PLCs is tissue-specific and evidence suggests that it varies under different conditions such as tumour progression or cell activation. In order to obtain a complete picture, the expression of all PI-PLC isoforms was analysed in human endothelial cells (EC).MethodsUsing molecular biology methods (RT-PCR), the expression of PI-PLC isoforms was analysed in human umbilical vein endothelial cells (HUVEC), a widely used experimental model for human EC.ResultsAll the PI-PLC isoforms except PI-PLC β1, PI-PLC ɛ and PI-PLC ζ were expressed in HUVEC.ConclusionsThe growing interest in the complex cascade of events occurring in angiogenesis will provide useful insights for therapeutic strategies. The expression of PI-PLC isoforms in HUVEC is a useful tool for further studies directed to understanding their role in angiogenesis. However, although HUVEC represent a widely used experimental model for human macrovascular EC, limitations remain in that they cannot fully represent the metabolic properties and interactions of the EC distributed in the entire organism.