bluuebunny/crossref_metadata_2025_split huggingface dataset:
AnagrQuorum Sensing System That Regulates Granulose Formation and Sporulation in Clostridium acetobutylicum
Authors: Steiner Elisabeth , Scott Jamie , Minton Nigel P. , Winzer Klaus 
Published: December 2011

ABSTRACTThe Gram-positive, anaerobic, endospore-forming bacteriumClostridium acetobutylicumhas considerable biotechnological potential due to its ability to produce solvents as fermentation products, in particular the biofuel butanol. Its genome contains a putativeagrlocus,agrBDCA, known in staphylococci to constitute a cyclic peptide-based quorum sensing system. In staphylococci,agrBDis required for the generation of a peptide signal that, upon extracellular accumulation, is sensed by anagrCA-encoded two-component system. Using ClosTron technology,agrB,agrC, andagrAmutants ofC. acetobutylicumATCC 824 were generated and phenotypically characterized. Mutants and wild type displayed similar growth kinetics and no apparent differences in solvent formation under the conditions tested. However, the number of heat-resistant endospores formed by the mutants in liquid culture was reduced by about one order of magnitude. On agar-solidified medium, spore formation was more strongly affected, particularly inagrAandagrCmutants. Similarly, accumulation of the starch-like storage compound granulose was almost undetectable in colonies ofagrB,agrA, andagrCmutants. Importantly, these defects could be genetically complemented, demonstrating that they were directly linked toagrinactivation. A diffusible factor produced byagrBD-expressing strains was found to restore granulose and spore formation in theagrBmutant. Furthermore, a synthetic cyclic peptide, designed on the basis of theC. acetobutylicumAgrD sequence, was also capable of complementing the defects of theagrBmutant when added exogenously to the culture. Together, these findings support the hypothesis thatagr-dependent quorum sensing is involved in the regulation of sporulation and granulose formation inC. acetobutylicum.
Transcriptional Analysis of a Dehalococcoides-Containing Microbial Consortium Reveals Prophage Activation
Authors: Waller Alison S. , Hug Laura A. , Mo Kaiguo , Radford Devon R. , Maxwell Karen L. , Edwards Elizabeth A. 
Published: December 2011

ABSTRACT

Chlorinated solvents are among the most prevalent groundwater contaminants in the industrialized world. Biodegradation with
Dehalococcoides
-containing mixed cultures is an effective remediation technology. To elucidate transcribed genes in a
Dehalococcoides
-containing mixed culture, a shotgun metagenome microarray was created and used to investigate gene transcription during vinyl chloride (VC) dechlorination and during starvation (no chlorinated compounds) by a microbial enrichment culture called KB-1. In both treatment conditions, methanol was amended as an electron donor. Subsequently, spots were sequenced that contained the genes most differentially transcribed between the VC-degrading and methanol-only conditions, as well as spots with the highest intensities. Sequencing revealed that during VC degradation
Dehalococcoides
genes involved in transcription, translation, metabolic energy generation, and amino acid and lipid metabolism and transport were overrepresented in the transcripts compared to the average
Dehalococcoides
genome. KB-1
rdh
A14
(
vcrA
) was the only reductive dehalogenase homologous (RDH) gene with higher transcript levels during VC degradation, while multiple RDH genes had higher transcript levels in the absence of VC. Numerous hypothetical genes from
Dehalococcoides
also had higher transcript levels in methanol-only treatments, indicating that many uncharacterized proteins are involved in cell maintenance in the absence of chlorinated substrates. In addition, microarray results prompted biological experiments confirming that electron acceptor limiting conditions activated a
Dehalococcoides
prophage. Transcripts from
Spirochaetes
,
Chloroflexi
,
Geobacter
, and methanogens demonstrate the importance of non-
Dehalococcoides
organisms to the culture, and sequencing of identified shotgun clones of interest provided information for follow-on targeted studies.
Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site
Authors: Green Stefan J. , Prakash Om , Jasrotia Puja , Overholt Will A. , Cardenas Erick , Hubbard Daniela , Tiedje James M. , Watson David B. , Schadt Christopher W. , Brooks Scott C. , Kostka Joel E. 
Published: December 2011

ABSTRACT

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus
Rhodanobacter
(class
Gammaproteobacteria
) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of
Rhodanobacter
bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.
Dead or Alive: Deformed Wing Virus and Varroa destructor Reduce the Life Span of Winter Honeybees
Authors: Dainat Benjamin , Evans Jay D. , Chen Yan Ping , Gauthier Laurent , Neumann Peter 
Published: December 2011

ABSTRACT

Elevated winter losses of managed honeybee colonies are a major concern, but the underlying mechanisms remain controversial. Among the suspects are the parasitic mite
Varroa destructor
, the microsporidian
Nosema ceranae
, and associated viruses. Here we hypothesize that pathogens reduce the life expectancy of winter bees, thereby constituting a proximate mechanism for colony losses. A monitoring of colonies was performed over 6 months in Switzerland from summer 2007 to winter 2007/2008. Individual dead workers were collected daily and quantitatively analyzed for deformed wing virus (DWV), acute bee paralysis virus (ABPV),
N. ceranae
, and expression levels of the
vitellogenin
gene as a biomarker for honeybee longevity. Workers from colonies that failed to survive winter had a reduced life span beginning in late fall, were more likely to be infected with DWV, and had higher DWV loads. Colony levels of infection with the parasitic mite
Varroa destructor
and individual infections with DWV were also associated with reduced honeybee life expectancy. In sharp contrast, the level of
N. ceranae
infection was not correlated with longevity. In addition,
vitellogenin
gene expression was significantly positively correlated with ABPV and
N. ceranae
loads. The findings strongly suggest that
V. destructor
and DWV (but neither
N. ceranae
nor ABPV) reduce the life span of winter bees, thereby constituting a parsimonious possible mechanism for honeybee colony losses.
Anaerobic Degradation of 4-Methylbenzoate by a Newly Isolated Denitrifying Bacterium, Strain pMbN1
Authors: Lahme Sven , Harder Jens , Rabus Ralf 
Published: December 2011

ABSTRACT

A novel alphaproteobacterium isolated from freshwater sediments, strain pMbN1, degrades 4-methylbenzoate to CO
2
under nitrate-reducing conditions. While strain pMbN1 utilizes several benzoate derivatives and other polar aromatic compounds, it cannot degrade
p
-xylene or other hydrocarbons. Based on 16S rRNA gene sequence analysis, strain pMbN1 is affiliated with the genus
Magnetospirillum
.
Calcite Biomineralization by Bacterial Isolates from the Recently Discovered Pristine Karstic Herrenberg Cave
Authors: Rusznyák Anna , Akob Denise M. , Nietzsche Sándor , Eusterhues Karin , Totsche Kai Uwe , Neu Thomas R. , Frosch Torsten , Popp Jürgen , Keiner Robert , Geletneky Jörn , Katzschmann Lutz , Schulze Ernst-Detlef , Küsel Kirsten 
Published: December 2011

ABSTRACT

Karstic caves represent one of the most important subterranean carbon storages on Earth and provide windows into the subsurface. The recent discovery of the Herrenberg Cave, Germany, gave us the opportunity to investigate the diversity and potential role of bacteria in carbonate mineral formation. Calcite was the only mineral observed by Raman spectroscopy to precipitate as stalactites from seepage water. Bacterial cells were found on the surface and interior of stalactites by confocal laser scanning microscopy. Proteobacteria dominated the microbial communities inhabiting stalactites, representing more than 70% of total 16S rRNA gene clones. Proteobacteria formed 22 to 34% of the detected communities in fluvial sediments, and a large fraction of these bacteria were also metabolically active. A total of 9 isolates, belonging to the genera
Arthrobacter
,
Flavobacterium
,
Pseudomonas
,
Rhodococcus
,
Serratia
, and
Stenotrophomonas
, grew on alkaline carbonate-precipitating medium. Two cultures with the most intense precipitate formation,
Arthrobacter sulfonivorans
and
Rhodococcus globerulus
, grew as aggregates, produced extracellular polymeric substances (EPS), and formed mixtures of calcite, vaterite, and monohydrocalcite.
R. globerulus
formed idiomorphous crystals with rhombohedral morphology, whereas
A. sulfonivorans
formed xenomorphous globular crystals, evidence for taxon-specific crystal morphologies. The results of this study highlighted the importance of combining various techniques in order to understand the geomicrobiology of karstic caves, but further studies are needed to determine whether the mineralogical biosignatures found in nutrient-rich media can also be found in oligotrophic caves.
Listeria monocytogenes Mutants with Altered Growth Phenotypes at Refrigeration Temperature and High Salt Concentrations
Authors: Burall Laurel S. , Laksanalamai Pongpan , Datta Atin R. 
Published: December 2011

ABSTRACT

Listeria monocytogenes
can survive and grow in refrigerated temperatures and high-salt environments. In an effort to better understand the associated mechanisms, a library of ∼ 5,200 transposon mutants of LS411, a food isolate from the Jalisco cheese outbreak, were screened for their ability to grow in brain heart infusion (BHI) broth at 5°C or in the presence of 7% NaCl and two mutants with altered growth profiles were identified. The LS522 mutant has a transposon insertion between
secA2
and
iap
and showed a significant reduction in growth in BHI broth at 5°C and in the presence of 7% NaCl. Reverse transcriptase quantitative PCR (RT-qPCR) revealed a substantial reduction in the expression of
iap
. Additionally, a hypothetical gene (
met
), containing a putative
S
-adenosylmethionine-dependent methyltransferase domain, downstream of
iap
had downregulated expression. In-frame deletion mutants of
iap
and
met
were created in LS411. The LS560 (LS411
Δiap
) mutant showed reduced growth at 5°C and in the presence of 7% salt, confirming its role in cold and salt growth attenuation. Surprisingly, the LS655 (LS411 Δ
met
) mutant showed slightly increased growth during refrigeration, though no alteration was seen in salt growth relative to the wild-type strain. The LS527 mutant, containing an insertion 36 bp upstream of the
gbu
operon, showed reduced expression of the
gbu
transcript by RT-qPCR and also showed growth reduction at 5°C and in the presence of 7% salt. This attenuation was severely exacerbated when the mutant was grown under the combined stresses. Analysis of the
gbu
operon deletion mutant showed decreased growth in 7% salt and refrigeration, supporting the previously characterized role for this gene in cold and salt adaptation. These studies indicate the potential for an intricate relationship between environmental stress regulation and virulence in
L. monocytogenes
.
Characteristics of Spoilage-Associated Secondary Cucumber Fermentation
Authors: Franco Wendy , Pérez-Díaz Ilenys M. , Johanningsmeier Suzanne D. , McFeeters Roger F. 
Published: December 2011

ABSTRACT

Secondary fermentations during the bulk storage of fermented cucumbers can result in spoilage that causes a total loss of the fermented product, at an estimated cost of $6,000 to $15,000 per affected tank. Previous research has suggested that such fermentations are the result of microbiological utilization of lactic acid and the formation of acetic, butyric, and propionic acids. The objectives of this study were to characterize the chemical and environmental conditions associated with secondary cucumber fermentations and to isolate and characterize potential causative microorganisms. Both commercial spoilage samples and laboratory-reproduced secondary fermentations were evaluated. Potential causative agents were isolated based on morphological characteristics. Two yeasts,
Pichia manshurica
and
Issatchenkia occidentalis
, were identified and detected most commonly concomitantly with lactic acid utilization. In the presence of oxygen, yeast metabolic activities lead to lactic acid degradation, a small decline in the redox potential (E
h
, Ag/AgCl, 3 M KCl) of the fermentation brines, and an increase in pH to levels at which bacteria other than the lactic acid bacteria responsible for the primary fermentation can grow and produce acetic, butyric, and propionic acids. Inhibition of these yeasts by allyl isothiocyanate (AITC) resulted in stabilization of the fermented medium, while the absence of the preservative resulted in the disappearance of lactic and acetic acids in a model system. Additionally, three Gram-positive bacteria,
Lactobacillus buchneri
, a
Clostridium
sp., and
Pediococcus ethanolidurans
, were identified as potentially relevant to different stages of the secondary fermentation. The unique opportunity to study commercial spoilage samples generated a better understanding of the microbiota and environmental conditions associated with secondary cucumber fermentations.
Validating Thermal Inactivation of Salmonella spp. in Fresh and Aged Chicken Litter
Authors: Kim Jinkyung , Diao Junshu , Shepherd Marion W. , Singh Randhir , Heringa Spencer D. , Gong Chao , Jiang Xiuping 
Published: December 2011

ABSTRACT

Our results revealed that a 7-log reduction of
Salmonella
can be achieved by exposing fresh chicken litter for 80.5 to 100.8, 78.4 to 93.1, and 44.1 to 63 min at 70, 75, and 80°C, respectively, depending on initial moisture contents. However, the aged chicken litter requires more heat treatment.
Identification of an Enzyme System for Daidzein-to-Equol Conversion in Slackia sp. Strain NATTS
Authors: Tsuji Hirokazu , Moriyama Kaoru , Nomoto Koji , Akaza Hideyuki 
Published: December 2011

ABSTRACT

An
Escherichia coli
library comprising 8,424 strains incorporating gene fragments of the equol-producing bacterium
Slackia
sp. strain NATTS was constructed and screened for
E. coli
strains having daidzein- and dihydrodaidzein (DHD)- metabolizing activity. We obtained 3 clones that functioned to convert daidzein to DHD and 2 clones that converted DHD to equol. We then sequenced the gene fragments inserted into plasmids contained by these 5 clones. All of the gene fragments were contiguous, encoding three open reading frames (ORF-1, -2, and -3). Analysis of
E. coli
strains containing an expression vector incorporating one of the
orf-1
,
-2
, or
-3
genes revealed that (i) the protein encoded by
orf
-
1
was involved in the conversion of
cis/trans-
tetrahydrodaidzein (
cis/trans-
THD) to equol, (ii) the protein encoded by
orf
-
2
was involved in the conversion of DHD to
cis/trans-
THD, and (iii) the protein encoded by
orf
-
3
was involved in the conversion of daidzein to DHD. ORF-1 had a primary amino acid structure similar to that of succinate dehydrogenase. ORF-2 was presumed to be an enzyme belonging to the short-chain dehydrogenase/reductase superfamily. ORF-3 was predicted to have 42% identity to the daidzein reductase of
Lactococcus
strain 20-92 and belonged to the NADH:flavin oxidoreductase family. These findings showed that the daidzein-to-equol conversion reaction in the
Slackia
sp. NATTS strain proceeds by the action of these three enzymes.
Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation
Authors: Lee Patrick K. H. , Dill Brian D. , Louie Tiffany S. , Shah Manesh , VerBerkmoes Nathan C. , Andersen Gary L. , Zinder Stephen H. , Alvarez-Cohen Lisa 
Published: December 2011

ABSTRACT

Bacteria of the genus
Dehalococcoides
play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of
Dehalococcoides ethenogenes
strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (
nif
) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the
nif
operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.
Dissimilatory Reduction of Extracellular Electron Acceptors in Anaerobic Respiration
Authors: Richter Katrin , Schicklberger Marcus , Gescher Johannes 
Published: December 2011

ABSTRACTAn extension of the respiratory chain to the cell surface is necessary to reduce extracellular electron acceptors like ferric iron or manganese oxides. In the past few years, more and more compounds were revealed to be reduced at the surface of the outer membrane of Gram-negative bacteria, and the list does not seem to have an end so far.Shewanellaas well asGeobacterstrains are model organisms to discover the biochemistry that enables the dissimilatory reduction of extracellular electron acceptors. In both cases,c-type cytochromes are essential electron-transferring proteins. They make the journey of respiratory electrons from the cytoplasmic membrane through periplasm and over the outer membrane possible. Outer membrane cytochromes have the ability to catalyze the last step of the respiratory chains. Still, recent discoveries provided evidence that they are accompanied by further factors that allow or at least facilitate extracellular reduction. This review gives a condensed overview of our current knowledge of extracellular respiration, highlights recent discoveries, and discusses critically the influence of different strategies for terminal electron transfer reactions.
Suspicion of Mycobacterium avium subsp. paratuberculosis Transmission between Cattle and Wild-Living Red Deer (Cervus elaphus) by Multitarget Genotyping
Authors: Fritsch Isabel , Luyven Gabriele , Köhler Heike , Lutz Walburga , Möbius Petra 
Published: December 2011

ABSTRACT

Multitarget genotyping of the etiologic agent
Mycobacterium avium
subsp.
paratuberculosis
is necessary for epidemiological tracing of paratuberculosis (Johne's disease). The study was undertaken to assess the informative value of different typing techniques and individual genome markers by investigation of
M. avium
subsp.
paratuberculosis
transmission between wild-living red deer and farmed cattle with known shared habitats. Fifty-three
M. avium
subsp.
paratuberculosis
type II isolates were differentiated by short sequence repeat analysis (SSR; 4 loci), mycobacterial interspersed repetitive-unit–variable-number tandem-repeat analysis (MIRU-VNTR; 8 loci), and restriction fragment length polymorphism analysis based on IS
900
(IS
900
-RFLP) using BstEII and PstI digestion. Isolates originated from free-living red deer (
Cervus elaphus
) from Eifel National Park (
n
= 13), six cattle herds living in the area of this park (
n
= 23), and five cattle herds without any contact with these red deer (
n
= 17). Data based on individual herds and genotypes verified that SSR G2 repeats did not exhibit sufficient stability for epidemiological studies. Two common SSR profiles (without G2 repeats), nine MIRU-VNTR patterns, and nine IS
900
-RFLP patterns were detected, resulting in 17 genotypes when combined. A high genetic variability was found for red deer and cattle isolates within and outside Eifel National Park, but it was revealed only by combination of different typing techniques. Results imply that within this restricted area, wild-living and farmed animals maintain a reservoir for specific
M. avium
subsp.
paratuberculosis
genotypes. No host relation of genotypes was obtained. Results suggested that four genotypes had been transmitted between and within species and that one genotype had been transmitted between cattle herds only. Use of multitarget genotyping for
M. avium
subsp.
paratuberculosis
type II strains and sufficiently stable genetic markers is essential for reliable interpretations of epidemiological studies on paratuberculosis.