bluuebunny/crossref_metadata_2025_split huggingface dataset:
New and Fast Method To Quantify Respiration Rates of Bacterial and Plankton Communities in Freshwater Ecosystems by Using Optical Oxygen Sensor Spots
Authors: Warkentin Mareike , Freese Heike M. , Karsten Ulf , Schumann Rhena 
Published: September 2007

ABSTRACT

A new method of respiration rate measurement based on oxygen luminescence quenching in sensor spots was evaluated for the first time for aquatic bacterial communities. The commonly used Winkler and Clark electrode methods to quantify oxygen concentration both require long incubation times, and the latter additionally causes signal drift due to oxygen consumption at the cathode. The sensor spots proved to be advantageous over those methods in terms of precise and quick oxygen measurements in natural bacterial communities, guaranteeing a respiration rate estimate during a time interval short enough to neglect variations in organism composition, abundance, and activity. Furthermore, no signal drift occurs during measurements, and respiration rate measurements are reliable even at low temperatures and low oxygen consumption rates. Both a natural bacterioplankton sample and a bacterial isolate from a eutrophic river were evaluated in order to optimize the new method for aquatic microorganisms. A minimum abundance of 2.2 × 10
6
respiring cells ml
−1
of a bacterial isolate was sufficient to obtain a distinct oxygen depletion signal within 20 min at 20°C with the new oxygen sensor spot method. Thus, a culture of a bacterial isolate from a eutrophic river (OW 144; 20 × 10
6
respiring bacteria ml
−1
) decreased the oxygen saturation about 8% within 20 min. The natural bacterioplankton sample respired 2.8% from initially 94% oxygen-saturated water in 30 min. During the growth season in 2005, the planktonic community of a eutrophic river consumed between 0.7 and 15.6 μmol O
2
liter
−1
h
−1
. The contribution of bacterial respiration to the total plankton community oxygen consumption varied seasonally between 11 and 100%.
Impact of pH on Lactate Formation and Utilization by Human Fecal Microbial Communities
Authors: Belenguer Alvaro , Duncan Sylvia H. , Holtrop Grietje , Anderson Susan E. , Lobley Gerald E. , Flint Harry J. 
Published: September 2007

ABSTRACTThe human intestine harbors both lactate-producing and lactate-utilizing bacteria. Lactate is normally present at <3 mmol liter−1in stool samples from healthy adults, but concentrations up to 100 mmol liter−1have been reported in gut disorders such as ulcerative colitis. The effect of different initial pH values (5.2, 5.9, and 6.4) upon lactate metabolism was studied with fecal inocula from healthy volunteers, in incubations performed with the addition ofdl-lactate, a mixture of polysaccharides (mainly starch), or both. Propionate and butyrate formation occurred at pH 6.4; both were curtailed at pH 5.2, while propionate but not butyrate formation was inhibited at pH 5.9. With the polysaccharide mix, lactate accumulation occurred only at pH 5.2, but lactate production, estimated usingl-[U-13C]lactate, occurred at all three pH values. Lactate was completely utilized within 24 h at pH 5.9 and 6.4 but not at pH 5.2. At pH 5.9, more butyrate than propionate was formed froml-[U-13C]lactate in the presence of polysaccharides, but propionate, formed mostly by the acrylate pathway, was the predominant product with lactate alone. Fluorescent in situ hybridization demonstrated that populations ofBifidobacteriumspp., major lactate producers, increased approximately 10-fold in incubations with polysaccharides. Populations ofEubacterium hallii, a lactate-utilizing butyrate-producing bacterium, increased 100-fold at pH 5.9 and 6.4. These experiments suggest that lactate is rapidly converted to acetate, butyrate, and propionate by the human intestinal microbiota at pH values as low as 5.9, but at pH 5.2 reduced utilization occurs while production is maintained, resulting in lactate accumulation.
Respiratory Succession and Community Succession of Bacterioplankton in Seasonally Anoxic Estuarine Waters
Authors: Crump Byron C. , Peranteau Cherie , Beckingham Barbara , Cornwell Jeffrey C. 
Published: September 2007

ABSTRACT

Anoxia occurs in bottom waters of stratified estuaries when respiratory consumption of oxygen, primarily by bacteria, outpaces atmospheric and photosynthetic reoxygenation. Once water becomes anoxic, bacterioplankton must change their metabolism to some form of anaerobic respiration. Analysis of redox chemistry in water samples spanning the oxycline of Chesapeake Bay during the summer of 2004 suggested that there was a succession of respiratory metabolism following the loss of oxygen. Bacterial community doubling time, calculated from bacterial abundance (direct counts) and production (anaerobic leucine incorporation), ranged from 0.36 to 0.75 day and was always much shorter than estimates of the time that the bottom water was anoxic (18 to 44 days), indicating that there was adequate time for bacterial community composition to shift in response to changing redox conditions. However, community composition (as determined by PCR-denaturing gradient gel electrophoresis analysis of 16S rRNA genes) in anoxic waters was very similar to that in surface waters in June when nitrate respiration was apparent in the water column and only partially shifted away from the composition of the surface community after nitrate was depleted. Anoxic water communities did not change dramatically until August, when sulfate respiration appeared to dominate. Surface water populations that remained dominant in anoxic waters were
Synechococcus
sp.,
Gammaproteobacteria
in the SAR86 clade, and
Alphaproteobacteria
relatives of
Pelagibacter ubique
, including a putative estuarine-specific
Pelagibacter
cluster. Populations that developed in anoxic water were most similar (<92% similarity) to uncultivated
Firmicutes
, uncultivated
Bacteroidetes, Gammaproteobacteria
in the genus
Thioalcalovibrio
, and the uncultivated SAR406 cluster. These results indicate that typical estuarine bacterioplankton switch to anaerobic metabolism under anoxic conditions but are ultimately replaced by different organisms under sulfidic conditions.
Low-Load Compression Testing: a Novel Way of Measuring Biofilm Thickness
Authors: Paramonova Ekaterina , de Jong Ed D. , Krom Bastiaan P. , van der Mei Henny C. , Busscher Henk J. , Sharma Prashant K. 
Published: September 2007

ABSTRACT
Biofilms are complex and dynamic communities of microorganisms that are studied in many fields due to their abundance and economic impact. Biofilm thickness is an important parameter in biofilm characterization. Current methods of measuring biofilm thicknesses have several limitations, including application, availability, and costs. Here, we present low-load compression testing (LLCT) as a new method for measuring biofilm thickness. With LLCT, biofilm thicknesses are measured during compression by inducing small loads, up to 5 Pa, corresponding to 0.1% deformation, making LLCT essentially a nondestructive technique. Comparison of the thicknesses of various bacterial and yeasts biofilms obtained by LLCT and by using confocal laser scanning microscopy (CLSM) resulted in the conclusion that CLSM underestimates the biofilm thickness due to poor penetration of different fluorescent dyes, especially through the thicker biofilms, whereas LLCT does not suffer from this thickness limitation.
Detection ofSalmonellaspp. in Retail Raw Food Samples from Vietnam and Characterization of Their Antibiotic Resistance
Authors: Van Thi Thu Hao , Moutafis George , Istivan Taghrid , Tran Linh Thuoc , Coloe Peter J. 
Published: September 2007

ABSTRACTA study was conducted to examine the levels ofSalmonellaspp. contamination in raw food samples, including chicken, beef, pork, and shellfish, from Vietnam and to determine their antibiotic resistance characteristics. A total of 180 samples were collected and examined for the presence ofSalmonellaspp., yielding 91Salmonellaisolates. Sixty-one percent of meat and 18% of shellfish samples were contaminated withSalmonellaspp. Susceptibility of all isolates to a variety of antimicrobial agents was tested, and resistance to tetracycline, ampicillin/amoxicillin, nalidixic acid, sulfafurazole, and streptomycin was found in 40.7%, 22.0%, 18.7%, 16.5%, and 14.3% of the isolates, respectively. Resistance to enrofloxacin, trimethoprim, chloramphenicol, kanamycin, and gentamicin was also detected (8.8 to 2.2%). About half (50.5%) of the isolates were resistant to at least one antibiotic, and multiresistantSalmonellaisolates, resistant to at least three different classes of antibiotics, were isolated from all food types. One isolate from chicken (serovar Albany) contained a variant of theSalmonellagenomic island 1 antibiotic resistance gene cluster. The results show that antibiotic resistance inSalmonellaspp. in raw food samples from Vietnam is significant.
Transcriptomics-Based Identification of Novel Factors Enhancing Heterologous Protein Secretion in Yeasts
Authors: Gasser Brigitte , Sauer Michael , Maurer Michael , Stadlmayr Gerhard , Mattanovich Diethard 
Published: September 2007

ABSTRACT

Efficient production of heterologous proteins with yeasts and other eukaryotic hosts is often hampered by inefficient secretion of the product. Limitation of protein secretion has been attributed to a low folding rate, and a rational solution is the overexpression of proteins supporting folding, like protein disulfide isomerase (Pdi), or the unfolded protein response transcription factor Hac1. Assuming that other protein factors which are not directly involved in protein folding may also support secretion of heterologous proteins, we set out to analyze the differential transcriptome of a
Pichia pastoris
strain overexpressing human trypsinogen versus that of a nonexpressing strain. Five hundred twenty-four genes were identified to be significantly regulated. Excluding those genes with totally divergent functions (like, e.g., core metabolism), we reduced this number to 13 genes which were upregulated in the expression strain having potential function in the secretion machinery and in stress regulation. The respective
Saccharomyces cerevisiae
homologs of these genes, including the previously characterized secretion helpers
PDI1
,
ERO1
,
SSO2
,
KAR2
/BiP, and
HAC1
as positive controls, were cloned and overexpressed in a
P. pastoris
strain expressing a human antibody Fab fragment. All genes except one showed a positive effect on Fab fragment secretion, as did the controls. Six out of these novel secretion helper factors, more precisely Bfr2 and Bmh2 (involved in protein transport), the chaperones Ssa4 and Sse1, the vacuolar ATPase subunit Cup5, and Kin2 (a protein kinase connected to exocytosis), proved their benefits for practical application in laboratory-scale production processes by increasing both specific production rates and the volumetric productivity of an antibody fragment up to 2.5-fold in fed-batch fermentations of
P. pastoris
.
Substrate Degradation Kinetics, Microbial Diversity, and Current Efficiency of Microbial Fuel Cells Supplied with Marine Plankton
Authors: Reimers Clare E. , Stecher Hilmar A. , Westall John C. , Alleau Yvan , Howell Kate A. , Soule Leslie , White Helen K. , Girguis Peter R. 
Published: September 2007

ABSTRACT

The decomposition of marine plankton in two-chamber, seawater-filled microbial fuel cells (MFCs) has been investigated and related to resulting chemical changes, electrode potentials, current efficiencies, and microbial diversity. Six experiments were run at various discharge potentials, and a seventh served as an open-circuit control. The plankton consisted of a mixture of freshly captured phytoplankton and zooplankton (0.21 to 1 mm) added at an initial batch concentration of 27.5 mmol liter
−1
particulate organic carbon (OC). After 56.7 days, between 19.6 and 22.2% of the initial OC remained, sulfate reduction coupled to OC oxidation accounted for the majority of the OC that was degraded, and current efficiencies (of the active MFCs) were between 11.3 and 15.5%. In the open-circuit control cell, anaerobic plankton decomposition (as quantified by the decrease in total OC) could be modeled by three terms: two first-order reaction rate expressions (0.79 day
−1
and 0.037 day
−1
, at 15°C) and one constant, no-reaction term (representing 10.6% of the initial OC). However, in each active MFC, decomposition rates increased during the third week, lagging just behind periods of peak electricity generation. We interpret these decomposition rate changes to have been due primarily to the metabolic activity of sulfur-reducing microorganisms at the anode, a finding consistent with the electrochemical oxidization of sulfide to elemental sulfur and the elimination of inhibitory effects of dissolved sulfide. Representative phylotypes, found to be associated with anodes, were allied with
Delta
-,
Epsilon
-, and
Gammaproteobacteria
as well as the
Flavobacterium-Cytophaga-Bacteroides
and
Fusobacteria
. Based upon these results, we posit that higher current efficiencies can be achieved by optimizing plankton-fed MFCs for direct electron transfer from organic matter to electrodes, including microbial precolonization of high-surface-area electrodes and pulsed flowthrough additions of biomass.
Damage in
Escherichia coli
Cells Treated with a Combination of High Hydrostatic Pressure and Subzero Temperature
Authors: Moussa Marwen , Perrier-Cornet Jean-Marie , Gervais Patrick 
Published: September 2007

ABSTRACT

The relationship between membrane permeability, changes in ultrastructure, and inactivation in
Escherichia coli
strain K-12TG1 cells subjected to high hydrostatic pressure treatment at room and subzero temperatures was studied. Propidium iodide staining performed before and after pressure treatment made it possible to distinguish between reversible and irreversible pressure-mediated cell membrane permeabilization. Changes in cell ultrastructure were studied using transmission electron microscopy (TEM), which showed noticeable condensation of nucleoids and aggregation of cytosolic proteins in cells fixed after decompression. A novel technique used to mix fixation reagents with the cell suspension in situ under high hydrostatic pressure (HHP) and subzero-temperature conditions made it possible to show the partial reversibility of pressure-induced nucleoid condensation. However, based on visual examination of TEM micrographs, protein aggregation did not seem to be reversible. Reversible cell membrane permeabilization was noticeable, particularly for HHP treatments at subzero temperature. A correlation between membrane permeabilization and cell inactivation was established, suggesting different mechanisms at room and subzero temperatures. We propose that the inactivation of
E. coli
cells under combined HHP and subzero temperature occurs mainly during their transiently permeabilized state, whereas HHP inactivation at room temperature is related to a balance of transient and permanent permeabilization. The correlation between TEM results and cell inactivation was not absolute. Further work is required to elucidate the effects of pressure-induced damage on nucleoids and proteins during cell inactivation.
Decarboxylation of Sorbic Acid by Spoilage Yeasts Is Associated with the
PAD1
Gene
Authors: Stratford Malcolm , Plumridge Andrew , Archer David B. 
Published: September 2007

ABSTRACT

The spoilage yeast
Saccharomyces cerevisiae
degraded the food preservative sorbic acid (2,4-hexadienoic acid) to a volatile hydrocarbon, identified by gas chromatography mass spectrometry as 1,3-pentadiene. The gene responsible was identified as
PAD1
, previously associated with the decarboxylation of the aromatic carboxylic acids cinnamic acid, ferulic acid, and coumaric acid to styrene, 4-vinylguaiacol, and 4-vinylphenol, respectively. The loss of
PAD1
resulted in the simultaneous loss of decarboxylation activity against both sorbic and cinnamic acids. Pad1p is therefore an unusual decarboxylase capable of accepting both aromatic and aliphatic carboxylic acids as substrates. All members of the
Saccharomyces
genus (sensu stricto) were found to decarboxylate both sorbic and cinnamic acids.
PAD1
homologues and decarboxylation activity were found also in
Candida albicans, Candida dubliniensis, Debaryomyces hansenii
, and
Pichia anomala
. The decarboxylation of sorbic acid was assessed as a possible mechanism of resistance in spoilage yeasts. The decarboxylation of either sorbic or cinnamic acid was not detected for
Zygosaccharomyces, Kazachstania
(
Saccharomyces
sensu lato),
Zygotorulaspora
, or
Torulaspora
, the genera containing the most notorious spoilage yeasts. Scatter plots showed no correlation between the extent of sorbic acid decarboxylation and resistance to sorbic acid in spoilage yeasts. Inhibitory concentrations of sorbic acid were almost identical for
S. cerevisiae
wild-type and Δ
pad1
strains. We concluded that Pad1p-mediated sorbic acid decarboxylation did not constitute a significant mechanism of resistance to weak-acid preservatives by spoilage yeasts, even if the decarboxylation contributed to spoilage through the generation of unpleasant odors.
Yeast Community Structures and Dynamics in Healthy andBotrytis-Affected Grape Must Fermentations
Authors: Nisiotou Aspasia A. , Spiropoulos Apostolos E. , Nychas George-John E. 
Published: September 2007

ABSTRACTIndigenous yeast population dynamics during the fermentation of healthy andBotrytis-affected grape juice samples from two regions in Greece, Attica and Arcadia, were surveyed. Species diversity was evaluated by using restriction fragment length polymorphism and sequence analyses of the 5.8S internal transcribed spacer and the D1/D2 ribosomal DNA (rDNA) regions of cultivable yeasts. Community-level profiles were also obtained by direct analysis of fermenting samples through denaturing gradient gel electrophoresis of 26S rDNA amplicons. Both approaches revealed structural divergences in yeast communities between samples of different sanitary states or geographical origins. In all cases,Botrytisinfection severely perturbed the bioprocess of fermentation by dramatically altering species heterogeneity and succession during the time course. At the beginning and middle of fermentations,Botrytis-affected samples possessed higher levels of biodiversity than their healthy counterparts, being enriched with fermentative and/or spoilage species, such asZygosaccharomyces bailiiandIssatchenkiaspp. orKluyveromyces dobzhanskiiandKazachstaniasp. populations that have not been reported before for wine fermentations. Importantly,Botrytis-affected samples exposed discrete final species dominance. Selection was not species specific, and two different populations, i.e.,Saccharomyces cerevisiaein samples from Arcadia andZ. bailiiin samples from Attica, could be recovered at the end ofBotrytis-affected fermentations. The governing of wine fermentations byZ. bailiiis reported for the first time and could elucidate the origins and role of this particular spoilage microbe for the wine industry. This is the first survey to compare healthy andBotrytis-affected spontaneous fermentations by using both culture-based and -independent molecular methods in an attempt to further illuminate the complex yeast ecology of grape must fermentations.
New Insights into the Ligninolytic Capability of a Wood Decay Ascomycete
Authors: Shary Semarjit , Ralph Sally A. , Hammel Kenneth E. 
Published: September 2007

ABSTRACT

Wood-grown cultures of
Daldinia concentrica
oxidized a permethylated β-
14
C-labeled synthetic lignin to
14
CO
2
and also cleaved a permethylated α-
13
C-labeled synthetic lignin to give C
α
-C
β
cleavage products that were detected by
13
C nuclear magnetic resonance spectrometry. Therefore, this ascomycete resembles white-rot basidiomycetes in attacking the recalcitrant nonphenolic structures that predominate in lignin.
Direct Evidence for Production of Microcystins by
Anabaena
Strains from the Baltic Sea
Authors: Halinen Katrianna , Jokela Jouni , Fewer David P. , Wahlsten Matti , Sivonen Kaarina 
Published: September 2007

ABSTRACT

Anabaena
is a filamentous, N
2
-fixing, and morphologically diverse genus of cyanobacteria found in freshwater and brackish water environments worldwide. It contributes to the formation of toxic blooms in freshwater bodies through the production of a range of hepatotoxins or neurotoxins. In the Baltic Sea,
Anabaena
spp. form late summer blooms, together with
Nodularia spumigena
and
Aphanizomenon flos-aquae
. It has been long suspected that Baltic Sea
Anabaena
may produce microcystins. The presence of microcystins has been reported for the coastal regions of the Baltic proper, and a recent report also indicated the presence of the toxin in the open Gulf of Finland. However, at present there is no direct evidence linking Baltic Sea
Anabaena
spp. to microcystin production. Here we report on the isolation of microcystin-producing strains of the genus
Anabaena
in the open Gulf of Finland. The dominant microcystin variants produced by these strains included the highly toxic MCYST-LR as well as [
d
-Asp
3
]MCYST-LR, [
d
-Asp
3
]MCYST-HtyR, MCYST-HtyR, [
d
-Asp
3
,Dha
7
]MCYST-HtyR, and [Dha
7
]MCYST-HtyR variants. Toxic strains were isolated from the coastal Gulf of Finland as well as from the easternmost open-sea sampling station, where there were lower salinities than at other stations. This result suggests that lower salinity may favor microcystin-producing
Anabaena
strains. Furthermore, we sequenced 16S rRNA genes and found evidence for pronounced genetic heterogeneity of the microcystin-producing
Anabaena
strains. Future studies should take into account the potential presence of microcystin-producing
Anabaena
sp. in the Gulf of Finland.
Construction of p16S
lux
, a Novel Vector for Improved Bioluminescent Labeling of Gram-Negative Bacteria
Authors: Riedel Christian U. , Casey Pat G. , Mulcahy Heidi , O'Gara Fergal , Gahan Cormac G. M. , Hill Colin 
Published: September 2007

ABSTRACT
A novel vector has been constructed for the constitutive luminescent tagging of gram-negative bacteria by site-specific integration into the 16S locus of the bacterial chromosome. A number of gram-negative pathogens were successfully tagged using this vector, and the system was validated during murine infections of living animals.
Large Variabilities in Host Strain Susceptibility and Phage Host Range Govern Interactions between Lytic Marine Phages and Their
Flavobacterium
Hosts
Authors: Holmfeldt Karin , Middelboe Mathias , Nybroe Ole , Riemann Lasse 
Published: September 2007

ABSTRACT

Phages are a main mortality factor for marine bacterioplankton and are thought to regulate bacterial community composition through host-specific infection and lysis. In the present study we demonstrate for a marine phage-host assemblage that interactions are complex and that specificity and efficiency of infection and lysis are highly variable among phages infectious to strains of the same bacterial species. Twenty-three
Bacteroidetes
strains and 46 phages from Swedish and Danish coastal waters were analyzed. Based on genotypic and phenotypic analyses, 21 of the isolates could be considered strains of
Cellulophaga baltica
(
Flavobacteriaceae
). Nevertheless, all bacterial strains showed unique phage susceptibility patterns and differed by up to 6 orders of magnitude in sensitivity to the same titer of phage. The isolated phages showed pronounced variations in genome size (8 to >242 kb) and host range (infecting 1 to 20 bacterial strains). Our data indicate that marine bacterioplankton are susceptible to multiple co-occurring phages and that sensitivity towards phage infection is strain specific and exists as a continuum between highly sensitive and resistant, implying an extremely complex web of phage-host interactions. Hence, effects of phages on bacterioplankton community composition and dynamics may go undetected in studies where strain identity is not resolvable, i.e., in studies based on the phylogenetic resolution provided by 16S rRNA gene or internal transcribed spacer sequences.