bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosensor Determination of the Microscale Distribution of Nitrate, Nitrate Assimilation, Nitrification, and Denitrification in a Diatom-Inhabited Freshwater Sediment
Authors: Lorenzen Jan , Larsen Lars Hauer , Kjær Thomas , Revsbech Niels-Peter 
Published: December 2019

ABSTRACT

High-resolution NO
3
−
profiles in freshwater sediment covered with benthic diatoms were obtained with a new microscale NO
3
−
biosensor characterized by absence of interference from chemical species other than NO
2
−
and N
2
O. Analysis of the microprofiles obtained indicated no nitrification during darkness, high rates of nitrification and a tight coupling between nitrification and denitrification during illumination, and substantial rates of NO
3
−
assimilation during illumination. Nitrification during darkness could be induced by purging the bulk water with O
2
gas, indicating that the stimulatory effect on nitrification by illumination was caused by algal production of O
2
. NH
4
+
addition did not stimulate nitrification during darkness when O
2
was restricted to the upper 1-mm layer, and there was thus a low nitrification potential in the permanently oxic top 1 mm of the sediment.
Initial Transformations in the Biodegradation of Benzothiazoles by
Rhodococcus
Isolates
Authors: De Wever Helene , Vereecken Karen , Stolz Andreas , Verachtert Hubert 
Published: December 2019

ABSTRACT

Benzothiazole-2-sulfonate (BTSO
3
) is one of the side products occurring in 2-mercaptobenzothiazole (MBT) production wastewater. We are the first to isolate an axenic culture capable of BTSO
3
degradation. The isolate was identified as a
Rhodococcus erythropolis
strain and also degraded 2-hydroxybenzothiazole (OBT) and benzothiazole (BT), but not MBT, which was found to inhibit the biodegradation of OBT, BT, and BTSO
3
. In anaerobic resting cell assays, BTSO
3
was transformed into OBT in stoichiometric amounts. Under aerobic conditions, OBT was observed as an intermediate in BT breakdown and an unknown compound transiently accumulated in several assays. This product was identified as a dihydroxybenzothiazole. Benzothiazole degradation pathways seem to converge into OBT, which is then transformed further into the dihydroxy derivative.
A New Intermediate in the Mineralization of 3,4-Dichloroaniline by the White Rot Fungus
Phanerochaete chrysosporium
Authors: Sandermann Heinrich , Heller Werner , Hertkorn Norbert , Hoque Enamul , Pieper Dietmar , Winkler Reinhard 
Published: December 2019

ABSTRACT

Phanerochaete chrysosporium
ATCC 34541 has been reported to be unable to mineralize 3,4-dichloroaniline (DCA). However, high mineralization is now shown to occur when a fermentation temperature of 37° and gassing with oxygen are used. Mineralization did not correlate with lignin peroxidase activity. The latter was high under C limitation and low under N limitation, whereas the reverse was true for mineralization. The kinetics of DCA metabolism was studied in low-N and low-C and C- and N-rich culture media by metabolite analysis and
14
CO
2
determination. In all cases, DCA disappeared within 2 days, and a novel highly polar conjugate termed DCAX accumulated in the growth medium. This metabolite was a dead-end product under C and N enrichment. In oxygenated low-C medium and in much higher yield in oxygenated low-N medium, DCAX was converted to DCA-succinimide and then mineralized. DCAX was purified by high-performance liquid chromatography and identified as
N
-(3,4-dichlorophenyl)-α-ketoglutaryl-δ-amide by high-performance liquid chromatography and mass spectroscopy, gas chromatography and mass spectroscopy, and nuclear magnetic resonance spectroscopy. The formation of conjugate intermediates is proposed to facilitate mineralization because the sensitive amino group of DCA needs protection so that ring cleavage rather than oligomerization can occur.
Identification and Characterization of
Leuconostoc carnosum
, Associated with Production and Spoilage of Vacuum-Packaged, Sliced, Cooked Ham
Authors: Björkroth K. J. , Vandamme P. , Korkeala H. J. 
Published: December 2019

ABSTRACT

Leuconostoc carnosum
was shown to be the specific spoilage organism in vacuum-packaged, sliced, cooked ham showing spoilage during 3 weeks of shelf life. Identification of the specific spoilage organism was done by use of phenotypic data and
Cla
I,
Eco
RI, and
Hin
dIII reference strain ribopatterns. One hundred
L. carnosum
isolates associated with the production and spoilage of the ham were further characterized by pulsed-field gel electrophoresis (PFGE), together with some meat-associated
Leuconostoc
species:
L. citreum
,
L. gelidum
,
L. mesenteroides
subsp.
dextranicum
, and
L. mesenteroides
subsp.
mesenteroides. Apa
I and
Sma
I digests divided the industrial
L. carnosum
strains into 25 different PFGE types,
Apa
I and
Sma
I types being consistent. Only one specific PFGE type was associated with the spoiled packages. This type also was detected in air and raw-meat mass samples. The spoilage strain did not produce bacteriocins. Only seven isolates belonging to three different PFGE types produced bacteriocins. Similarity analysis of the industrial
L. carnosum
strains revealed a homogeneous cluster which could be divided into eight subclusters consisting of strains having at most three-fragment differences. The
L. carnosum
cluster was clearly distinguished from the other meat-associated leuconostoc clusters, with the exception of the
L. carnosum
type strain. Ribotyping can be very helpful in the identification of
L. carnosum
, but its discriminatory power is too weak for strain characterization. PFGE provides good discrimination for studies dealing with the properties of homogeneous
L. carnosum
strains.
PCR-Based DNA Amplification and Presumptive Detection ofEscherichia coliO157:H7 with an Internal Fluorogenic Probe and the 5′ Nuclease (TaqMan) Assay
Authors: Oberst R. D. , Hays M. P. , Bohra L. K. , Phebus R. K. , Yamashiro C. T. , Paszko-Kolva C. , Flood S. J. A. , Sargeant J. M. , Gillespie J. R. 
Published: December 2019

ABSTRACTPresumptive identification ofEscherichia coliO157:H7 is possible in an individual, nonmultiplexed PCR if the reaction targets the enterohemorrhagicE. coli(EHEC)eaeAgene. In this report, we describe the development and evaluation of the sensitivity and specificity of a PCR-based 5′ nuclease assay for presumptively detectingE. coliO157:H7 DNA. The specificity of theeaeA-based 5′ nuclease assay system was sufficient to correctly identify allE. coliO157:H7 strains evaluated, mirroring the previously described specificity of the PCR primers. The SZ-primed,eaeA-targeted 5′ nuclease detection assay was capable of rapid, semiautomated, presumptive detection ofE. coliO157:H7 when ≥103CFU/ml was present in modified tryptic soy broth (mTSB) or modifiedE. colibroth and when ≥104CFU/ml was present in ground beef-mTSB mixtures. Incorporating an immunomagnetic separation (IMS) step, followed by a secondary enrichment culturing step and DNA recovery with a QIAamp tissue kit (Qiagen), improved the detection threshold to ≥102CFU/ml. Surprisingly, immediately after IMS, the sensitivity of culturing on sorbitol MacConkey agar containing cefeximine and tellurite (CT-SMAC) was such that identifiable colonies were demonstrated only when ≥104CFU/ml was present in the sample. Several factors that might be involved in creating these false-negative CT-SMAC culture results are discussed. The SZ-primed,eaeA-targeted 5′ nuclease detection system demonstrated that it can be integrated readily into standard culturing procedures and that the assay can be useful as a rapid, automatable process for the presumptive identification ofE. coliO157:H7 in ground beef and potentially in other food and environmental samples.
Genetic Relatedness among Environmental, Clinical, and Diseased-Eel
Vibrio vulnificus
Isolates from Different Geographic Regions by Ribotyping and Randomly Amplified Polymorphic DNA PCR
Authors: Arias Covadonga R. , Pujalte María Jesús , Garay Esperanza , Aznar Rosa 
Published: December 2019

ABSTRACT

Genetic relationships among 132 strains of
Vibrio vulnificus
(clinical, environmental, and diseased-eel isolates from different geographic origins, as well as seawater and shellfish isolates from the western Mediterranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with
Kpn
I and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Random amplification of DNA was performed with M13 and T3 universal primers. The comparison between ribotyping and RAPD PCR revealed an overall agreement regarding the high level of homogeneity of diseased-eel isolates in contrast to the genetic heterogeneity of Mediterranean isolates. The latter suggests the existence of autochthonous clones present in Mediterranean coastal waters. Both techniques have revealed a genetic proximity among Spanish fish farm isolates and a close relationship between four Spanish eel farm isolates and some Mediterranean isolates. Whereas the differentiation within diseased-eel isolates was only possible by ribotyping, RAPD PCR was able to differentiate phenotypically atypical isolates of
V. vulnificus
. On the basis of our results, RAPD PCR is proposed as a better technique than ribotyping for rapid typing in the routine analysis of new
V. vulnificus
isolates.
Mode of Action of Linenscin OC2 against
Listeria innocua
Authors: Boucabeille Catherine , Letellier Lucienne , Simonet Jean-Marc , Henckes Gilles 
Published: December 2019

ABSTRACT

Linenscin OC2 is a small hydrophobic substance produced by the orange cheese coryneform bacterium
Brevibacterium linens
OC2. Linenscin OC2 inhibits growth of gram-negative bacteria with an altered outer membrane permeability and gram-positive bacteria. It is also able to lyse eucaryotic cells. The mode of action of linenscin OC2 on the
Listeria innocua
cytoplasmic membrane and the effects of environmental parameters were investigated. Addition of low doses of linenscin OC2 resulted in an immediate perturbation of the permeability properties of the cytoplasmic membrane and of the bacterial energetic state. Linenscin OC2 induced a loss of cytoplasmic potassium, depolarization of the cytoplasmic membrane, complete hydrolysis of internal ATP, efflux of inorganic phosphate, and transient increase in oxygen consumption. Potassium loss occurred in the absence of a proton motive force and was severely reduced at low temperatures, presumably as a result of increased ordering of the lipid hydrocarbon chains of the cytoplasmic membrane. We propose that linenscin OC2 interacts with the cytoplasmic membrane and that the permeability changes observed at low doses reflect the formation of pore-like structures in this membrane.
Symbiotic Relationship of
Thiothrix
spp. with an Echinoderm
Authors: Brigmon Robin L. , De Ridder Chantal 
Published: December 2019

ABSTRACT

Immunoassay procedures were used to investigate the symbiotic relationship of
Thiothrix
spp. in the intestinal cecum of the spatangoid species
Echinocardium cordatum. Thiothrix
spp. were identified in nodule samples from
E. cordatum
digestive tubes based on microscopic examination, enzyme-linked immunosorbent assay, and indirect immunofluorescence.
Thiothrix
spp. protein made up as much as 84% of the total protein content of the nodules. This is the first identification of
Thiothrix
spp. internally symbiotic with marine invertebrates.
Threonine Overproduction in Yeast Strains Carrying the
HOM3-R2
Mutant Allele under the Control of Different Inducible Promoters
Authors: Farfán María-José , Aparicio Luis , Calderón Isabel L. 
Published: December 2019

ABSTRACT

The
HOM3
gene of
Saccharomyces cerevisiae
codes for aspartate kinase, which plays a crucial role in the regulation of the metabolic flux that leads to threonine biosynthesis. With the aim of obtaining yeast strains able to overproduce threonine in a controlled way, we have placed the
HOM3-R2
mutant allele, which causes expression of a feedback-insensitive enzyme, under the control of four distinctive regulatable yeast promoters, namely, P

GAL1

, P

CHA1

, P

CYC1-HSE2

, and P

GPH1

. The amino acid contents of strains bearing the different constructs were analyzed both under repression and induction conditions. Although some differences in overall threonine production were found, a maximum of around 400 nmol/mg (dry weight) was observed. Other factors, such as excretion to the medium and activity of the catabolic threonine/serine deaminase, also affect threonine accumulation. Thus, improvement of threonine productivity by yeast cells would probably require manipulation of these and other factors.
In Situ Population Dynamics of Bacterial Viruses in a Terrestrial Environment
Authors: Ashelford Kevin E. , Day Martin J. , Bailey Mark J. , Lilley Andrew K. , Fry John C. 
Published: December 2019

ABSTRACTPredation by bacteriophages is thought to control bacterial numbers and facilitate gene transfer among bacteria in the biosphere. A thorough understanding of phage population dynamics is therefore necessary if their significance in natural environments is to be fully appreciated. Here we describe the in situ population dynamics of three separate phage populations predating on separate bacterial species, living on the surface of field-grown sugar beet (Beta vulgarisvar. Amethyst), as recorded over a 9-month period. The distributions of the three phage populations were different and fluctuated temporally in 1996 (peak density, ∼103PFU g−1). One of these populations, predating on the indigenous phytosphere bacteriumSerratia liquefaciensCP6, consisted of six genetically distinct DNA phages that varied in relative abundance to the extent that an apparent temporal succession was observed between the two most abundant phages, ΦCP6-1 and ΦCP6-4.
Population Dynamics of Chesapeake Bay Virioplankton: Total-Community Analysis by Pulsed-Field Gel Electrophoresis
Authors: Wommack K. Eric , Ravel Jacques , Hill Russell T. , Chun Jongsik , Colwell Rita R. 
Published: December 2019

ABSTRACT
Recognition of viruses as the most abundant component of aquatic microbial communities has stimulated investigations of the impact of viruses on bacterio- and phytoplankton host communities. From results of field studies to date, it is concluded that in most aquatic environments, a reduction in the number of bacteria on a daily basis is caused by viral infection. However, the modest amount of in situ virus-mediated mortality may be less significant than viral infection serving to maintain clonal diversity in the host communities directly, through gene transmission (i.e., transduction), and indirectly, by elimination of numerically dominant host species. If the latter mechanism for controlling community diversity prevails, then the overall structure of aquatic viral communities would be expected to change as well over short seasonal and spatial scales. To determine whether this occurs, pulsed-field gel electrophoresis (PFGE) was used to monitor the population dynamics of Chesapeake Bay virioplankton for an annual cycle (1 year). Virioplankton in water samples collected at six stations along a transect running the length of the bay were concentrated 100-fold by ultrafiltration. Viruses were further concentrated by ultracentrifugation, and the concentrated samples were embedded in agarose. PFGE analysis of virus DNA in the agarose plugs yielded several distinct bands, ranging from 50 to 300 kb. Principal-component and cluster analyses of the virus PFGE fingerprints indicated that changes in virioplankton community structure were correlated with time, geographical location, and extent of water column stratification. From the results of this study, it is concluded that, based on the dynamic nature of the Chesapeake Bay virioplankton community structure, the clonal diversity of bacterio- and phytoplankton host communities is an important component of the virus community.
Biosynthetic Pathway of Citrinin in the Filamentous Fungus
Monascus ruber
as Revealed by
13
C Nuclear Magnetic Resonance
Authors: Hajjaj Hassan , Klaébé Alain , Loret Marie O. , Goma Gérard , Blanc Philippe J. , François Jean 
Published: December 2019

ABSTRACT

Carbon isotope distribution of [
13
C]citrinin from
Monascus ruber
incubated with [
13
C]acetate revealed that the biosynthesis of the toxin originated from a tetraketide, instead of a pentaketide as has been shown for
Penicillium
and
Aspergillus
species. The production of polyketide red pigments and citrinin by
M. ruber
may therefore be regulated at the level of the tetraketide branch point.
Development of a PCR Assay for Detection of
Yersinia ruckeri
in Tissues of Inoculated and Naturally Infected Trout
Authors: Gibello A. , Blanco M. M. , Moreno M. A. , Cutuli M. T. , Domenech A. , Domínguez L. , Fernández-Garayzábal J. F. 
Published: December 2019

ABSTRACT

A PCR-based method was developed for the specific detection of
Yersinia ruckeri
in tissues of inoculated trout and naturally infected trout. No amplification products were obtained with other yersiniae, bacterial fish pathogens, or phylogenetically related bacteria (
n
= 34). The sensitivity of PCR detection was 60 to 65 bacterial cells per PCR tube, which was decreased to 10 to 20 cells by hybridization with a nonradioactive probe. The PCR assay proved to be as reliable as and faster than the conventional culture method for the detection of
Y. ruckeri
in infected trout tissues.
Halomethane:Bisulfide/Halide Ion Methyltransferase, an Unusual Corrinoid Enzyme of Environmental Significance Isolated from an Aerobic Methylotroph Using Chloromethane as the Sole Carbon Source
Authors: Coulter Catherine , Hamilton John T. G. , McRoberts W. Colin , Kulakov Leonid , Larkin Michael J. , Harper David B. 
Published: December 2019

ABSTRACTA novel dehalogenating/transhalogenating enzyme, halomethane:bisulfide/halide ion methyltransferase, has been isolated from the facultatively methylotrophic bacterium strain CC495, which uses chloromethane (CH3Cl) as the sole carbon source. Purification of the enzyme to homogeneity was achieved in high yield by anion-exchange chromatography and gel filtration. The methyltransferase was composed of a 67-kDa protein with a corrinoid-bound cobalt atom. The purified enzyme was inactive but was activated by preincubation with 5 mM dithiothreitol and 0.5 mM CH3Cl; then it catalyzed methyl transfer from CH3Cl, CH3Br, or CH3I to the following acceptor ions (in order of decreasing efficacy): I−, HS−, Cl−, Br−, NO2−, CN−, and SCN−. Spectral analysis indicated that cobalt in the native enzyme existed as cob(II)alamin, which upon activation was reduced to the cob(I)alamin state and then was oxidized to methyl cob(III)alamin. During catalysis, the enzyme shuttles between the methyl cob(III)alamin and cob(I)alamin states, being alternately demethylated by the acceptor ion and remethylated by halomethane. Mechanistically the methyltransferase shows features in common with cobalamin-dependent methionine synthase fromEscherichia coli. However, the failure of specific inhibitors of methionine synthase such as propyl iodide, N2O, and Hg2+to affect the methyltransferase suggests significant differences. During CH3Cl degradation by strain CC495, the physiological acceptor ion for the enzyme is probably HS−, a hypothesis supported by the detection in cell extracts of methanethiol oxidase and formaldehyde dehydrogenase activities which provide a metabolic route to formate. 16S rRNA sequence analysis indicated that strain CC495 clusters withRhizobiumspp. in the alpha subdivision of theProteobacteriaand is closely related to strain IMB-1, a recently isolated CH3Br-degrading bacterium (T. L. Connell Hancock, A. M. Costello, M. E. Lidstrom, and R. S. Oremland, Appl. Environ. Microbiol. 64:2899–2905, 1998). The presence of this methyltransferase in bacterial populations in soil and sediments, if widespread, has important environmental implications.
Nitrogen Availability to
Pseudomonas fluorescens
DF57 Is Limited during Decomposition of Barley Straw in Bulk Soil and in the Barley Rhizosphere
Authors: Jensen Linda Elise , Nybroe Ole 
Published: December 2019

ABSTRACT

The availability of nitrogen to
Pseudomonas fluorescens
DF57 during straw degradation in bulk soil and in barley rhizosphere was studied by introducing a bioluminescent reporter strain (DF57-N3), responding to nitrogen limitation, to model systems of varying complexity. DF57-N3 was apparently not nitrogen limited in the natural and sterilized bulk soil used for these experiments. The soil was subsequently amended with barley straw, representing a plant residue with a high carbon-to-nitrogen ratio (between 60 and 100). In these systems the DF57-N3 population gradually developed a nitrogen limitation response during the first week of straw decomposition, but exclusively in the presence of the indigenous microbial population. This probably reflects the restricted ability of DF57 to degrade plant polymers by hydrolytic enzymes. The impact of the indigenous population on nitrogen availability to DF57-N3 was mimicked by the cellulolytic organism
Trichoderma harzianum
Rifai strain T3 when coinoculated with DF57-N3 in sterilized, straw-amended soil. Limitation occurred concomitantly with fungal cellulase production, pointing to the significance of hydrolytic activity for the mobilization of straw carbon sources, thereby increasing the nitrogen demand. Enhanced survival of DF57-N3 in natural soil after straw amendment further indicated that DF57 was cross-fed with carbon/energy sources. The natural barley rhizosphere was experienced by DF57-N3 as an environment with restricted nitrogen availability regardless of straw amendment. In the rhizosphere of plants grown in sterilized soil, nitrogen limitation was less severe, pointing to competition with indigenous microorganisms as an important determinant of the nitrogen status for DF57-N3 in this environment. Hence, these studies have demonstrated that nitrogen availability and gene expression in
Pseudomonas
is intimately linked to the structure and function of the microbial community. Further, it was demonstrated that the activities of cellulolytic microorganisms may affect the availability of energy and specific nutrients to a group of organisms deficient in hydrolytic enzyme activities.