bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut-Associated Denitrification and In Vivo Emission of Nitrous Oxide by the Earthworm Families Megascolecidae and Lumbricidae in New Zealand
Authors: Wüst Pia K. , Horn Marcus A. , Henderson Gemma , Janssen Peter H. , Rehm Bernd H. A. , Drake Harold L. 
Published: April 2009

ABSTRACTPrevious studies have documented the capacity of European earthworms belonging to the family Lumbricidae to emit the greenhouse gas nitrous oxide (N2O), an activity attributed primarily to the activation of ingested soil denitrifiers. To extend the information base to earthworms in the Southern Hemisphere, four species of earthworms in New Zealand were examined for gut-associated denitrification.Lumbricus rubellusandAporrectodea rosea(introduced species of Lumbricidae) emitted N2O, whereas emission of N2O byOctolasion cyaneum(an introduced species of Lumbricidae) and emission of N2O byOctochaetus multiporus(a native species of Megascolecidae) were variable and negligible, respectively. Exposing earthworms to nitrite or nitrate and acetylene significantly increased the amount of N2O emitted, implicating denitrification as the primary source of N2O and indicating that earthworms emitted dinitrogen (N2) in addition to N2O. The alimentary canal displayed a high capacity to produce N2O when it was supplemented with nitrite, and alimentary canal contents contained large amounts of carbohydrates and organic acids indicative of fermentation (e.g., succinate, acetate, and formate) that could serve as sources of reductant for denitrification.nosZencodes a portion of the terminal oxidoreductase used in denitrification. ThenosZsequences detected in the alimentary canals ofL. rubellusandO. multiporuswere similar to those retrieved from soil and were distantly related to sequences of uncultured soil bacteria and genera common in soils (i.e.,Bradyrhizobium,Azospirillum,Rhodopseudomonas,Rhodospirillum,Pseudomonas,Oligotropha, andSinorhizobium). These findings (i) suggest that the capacity to emit N2O and N2is a general trait of earthworms and not geographically restricted, (ii) indicate that species belonging to different earthworm families (i.e., Megascolecidae and Lumbricidae) may not have equal capacities to emit N2O, and (iii) also corroborate previous findings that link this capacity to denitrification in the alimentary canal.
Metabolic Engineering of
Saccharomyces cerevisiae
for Production of Novel Cyanophycins with an Extended Range of Constituent Amino Acids
Authors: Steinle Anna , Bergander Klaus , Steinbüchel Alexander 
Published: April 2009

ABSTRACT

Cyanophycin (multi-
l
-arginyl-poly-
l
-aspartic acid; also known as cyanophycin grana peptide [CGP]) is a putative precursor for numerous biodegradable technically used chemicals. Therefore, the biosynthesis and production of the polymer in recombinant organisms is of special interest. The synthesis of cyanophycin derivatives consisting of a wider range of constituents would broaden the applications of this polymer. We applied recombinant
Saccharomyces cerevisiae
strains defective in arginine metabolism and expressing the cyanophycin synthetase of
Synechocystis
sp. strain PCC 6308 in order to synthesize CGP with citrulline and ornithine as constituents. Strains defective in arginine degradation (Car1 and Car2) accumulated up to 4% (wt/wt) CGP, whereas strains defective in arginine synthesis (Arg1, Arg3, and Arg4) accumulated up to 15.3% (wt/wt) of CGP, which is more than twofold higher than the previously content reported in yeast and the highest content ever reported in eukaryotes. Characterization of the isolated polymers by different analytical methods indicated that CGP synthesized by strain Arg1 (with argininosuccinate synthetase deleted) consisted of up to 20 mol% of citrulline, whereas CGP from strain Arg3 (with ornithine carbamoyltransferase deleted) consisted of up to 8 mol% of ornithine, and CGP isolated from strain Arg4 (with argininosuccinate lyase deleted) consisted of up to 16 mol% lysine. Cultivation experiments indicated that the incorporation of citrulline or ornithine is enhanced by the addition of low amounts of arginine (2 mM) and also by the addition of ornithine or citrulline (10 to 40 mM), respectively, to the medium.
Campylobacter
Colonization of the Turkey Intestine in the Context of Microbial Community Development
Authors: Scupham Alexandra J. 
Published: April 2009

ABSTRACT

Patterns of microbial community dynamics in the turkey intestine were examined. Every week of the 18-week production cycle, cecal bacterial communities and
Campylobacter
loads were examined from five birds for each of two flocks. Molecular fingerprinting via the automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) of the cecal samples revealed that microbial communities changed in a time-dependent manner, and during both trials they developed via transition through three phases during the production cycle. A core component of the microbiota consisting of 11
Bacteroidetes
types was present throughout both trials. In contrast, constant succession was detected in the
Clostridiales
populations until week 10 or 11, with few shared sequences between the flocks. Changes in
Campylobacter jejuni
and
Campylobacter coli
loads were correlated to, but not dependent on, the two acute transitions delimiting the three developmental phases.
CO
2
Production as an Indicator of Biofilm Metabolism
Authors: Kroukamp Otini , Wolfaardt Gideon M. 
Published: April 2009

ABSTRACT

Biofilms are important in aquatic nutrient cycling and microbial proliferation. In these structures, nutrients like carbon are channeled into the production of extracellular polymeric substances or cell division; both are vital for microbial survival and propagation. The aim of this study was to assess carbon channeling into cellular or noncellular fractions in biofilms. Growing in tubular reactors, biofilms of our model strain
Pseudomonas
sp. strain CT07 produced cells to the planktonic phase from the early stages of biofilm development, reaching pseudo steady state with a consistent yield of ∼10
7
cells·cm
−2
·h
−1
within 72 h. Total direct counts and image analysis showed that most of the converted carbon occurred in the noncellular fraction, with the released and sessile cells accounting for <10% and <2% of inflowing carbon, respectively. A CO
2
evolution measurement system (CEMS) that monitored CO
2
in the gas phase was developed to perform a complete carbon balance across the biofilm. The measurement system was able to determine whole-biofilm CO
2
production rates in real time and showed that gaseous CO
2
production accounted for 25% of inflowing carbon. In addition, the CEMS made it possible to measure biofilm response to changing environmental conditions; changes in temperature or inflowing carbon concentration were followed by a rapid response in biofilm metabolism and the establishment of new steady-state conditions.
Escherichia coli
and
Salmonella enterica
Are Protected against Acetic Acid, but Not Hydrochloric Acid, by Hypertonicity
Authors: Chapman B. , Ross T. 
Published: April 2009

ABSTRACT

Chapman et al. (B. Chapman, N. Jensen, T Ross, and M. B. Cole, Appl. Environ. Microbiol. 72:5165-5172, 2006) demonstrated that an increased NaCl concentration prolongs survival of
Escherichia coli
O157 SERL 2 in a broth model simulating the aqueous phase of a food dressing or sauce containing acetic acid. We examined the responses of five other
E. coli
strains and four
Salmonella enterica
strains to increasing concentrations of NaCl under conditions of lethal acidity and observed that the average “lag” time prior to inactivation decreases in the presence of hydrochloric acid but not in the presence of acetic acid. For
E. coli
in the presence of acetic acid, the lag time increased with increasing NaCl concentrations up to 2 to 4% at pH 4.0, up to 4 to 6% at pH 3.8, and up to 4 to 7% (wt/wt of water) NaCl at pH 3.6.
Salmonella
was inactivated more rapidly by combined acetic acid and NaCl stresses than
E. coli
, but increasing NaCl concentrations still decreased the lag time prior to inactivation in the presence of acetic acid; at pH 4.0 up to 1 to 4% NaCl was protective, and at pH 3.8 up to 1 to 2% NaCl delayed the onset of inactivation. Sublethal injury kinetics suggest that this complex response is a balance between the lethal effects of acetic acid, against which NaCl is apparently protective, and the lethal effects of the NaCl itself. Compared against 3% NaCl, 10% (wt/wt of water) sucrose with 0.5% NaCl (which has similar osmotic potential) was found to be equally protective against adverse acetic acid conditions. We propose that hypertonicity may directly affect the rate of diffusion of acetic acid into cells and hence cell survival.
Molecular Diversification in the Quorum-Sensing System of
Vibrio cholerae
: Role of Natural Selection in the Emergence of Pandemic Strains
Authors: Talyzina Nina M. , Ingvarsson Pär K. , Zhu Jun , Wai Sun N. , Andersson Agneta 
Published: April 2009

ABSTRACT

Two haplotypes of the
Vibrio cholerae
quorum-sensing system regulator
hapR
are described:
hapR1
, common among nonpandemic, non-O1, non-O139 strains, and
hapR2
, associated with pandemic O1 and O139 and epidemic O37
V. cholerae
strains. The
hapR2
has evolved under strong natural selection, implying that its fixation was influenced by conditions that led to cholera pandemics.
Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur
Authors: Raina Jean-Baptiste , Tapiolas Dianne , Willis Bette L. , Bourne David G. 
Published: April 2009

ABSTRACTMarine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coral-associated bacteria. Two coral species,Montipora aequituberculataandAcropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera,Roseobacter, Spongiobacter, Vibrio, andAlteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated withRoseobactersp. constituted 28% of theM. aequituberculatatissue libraries, while 59% of the clones from theA. milleporalibraries were affiliated with sequences related to theSpongiobactergenus.Vibriospp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under “normal” environmental conditions, they are a natural component of coral-associated communities. Genes homologous todddD, anddddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.
Quantitative Method To Determine Sporicidal Decontamination of Building Surfaces by Gaseous Fumigants, and Issues Related to Laboratory-Scale Studies
Authors: Rastogi Vipin K. , Wallace Lalena , Smith Lisa S. , Ryan Shawn P. , Martin Blair 
Published: April 2009

ABSTRACTChlorine dioxide gas and vaporous hydrogen peroxide sterilant have been used in the cleanup of building interiors contaminated with spores ofBacillus anthracis. A systematic study, in collaboration with the U.S. Environmental Protection Agency, was jointly undertaken by the U.S. Army-Edgewood Chemical Biological Center to determine the sporicidal efficacies of these two fumigants on six building structural materials: carpet, ceiling tile, unpainted cinder block, painted I-beam steel, painted wallboard, and unpainted pinewood. Critical issues related to high-throughput sample processing and spore recovery from porous and nonporous surfaces included (i) the extraction of spores from complex building materials, (ii) the effects of titer challenge levels on fumigant efficacy, and (iii) the impact of bioburden inclusion on spore recovery from surfaces and spore inactivation. Small pieces (1.3 by 1.3 cm of carpet, ceiling tile, wallboard, I-beam steel, and pinewood and 2.5 by 1.3 cm for cinder block) of the materials were inoculated with an aliquot of 50 μl containing the target number (1 × 106, 1 × 107, or 1 × 108) of avirulent spores ofB. anthracisNNR1Δ1. The aliquot was dried overnight in a biosafety cabinet, and the spores were extracted by a combination of a 10-min sonication and a 2-min vortexing using 0.5% buffered peptone water as the recovery medium. No statistically significant drop in the kill efficacies of the fumigants was observed when the spore challenge level was increased from 6 log units to 8 log units, even though a general trend toward inhibition of fumigant efficacy was evident. The organic burden (0 to 5%) in the spore inoculum resulted in a statistically significant drop in spore recovery (at the 2 or 5% level). The effect on spore killing was a function of the organic bioburden amount and the material type. In summary, a high-throughput quantitative method was developed for determining the efficacies of fumigants, and the spore recoveries from five porous materials and one nonporous material ranged between 20 and 80%.
Simultaneous Cellulose Degradation and Electricity Production by
Enterobacter cloacae
in a Microbial Fuel Cell
Authors: Rezaei Farzaneh , Xing Defeng , Wagner Rachel , Regan John M. , Richard Tom L. , Logan Bruce E. 
Published: April 2009

ABSTRACT

Electricity can be directly generated by bacteria in microbial fuel cells (MFCs) from many different biodegradable substrates. When cellulose is used as the substrate, electricity generation requires a microbial community with both cellulolytic and exoelectrogenic activities. Cellulose degradation with electricity production by a pure culture has not been previously demonstrated without addition of an exogenous mediator. Using a specially designed U-tube MFC, we enriched a consortium of exoelectrogenic bacteria capable of using cellulose as the sole electron donor. After 19 dilution-to-extinction serial transfers of the consortium, 16S rRNA gene-based community analysis using denaturing gradient gel electrophoresis and band sequencing revealed that the dominant bacterium was
Enterobacter cloacae
. An isolate designated
E. cloacae
FR from the enrichment was found to be 100% identical to
E. cloacae
ATCC 13047
T
based on a partial 16S rRNA sequence. In polarization tests using the U-tube MFC and cellulose as a substrate, strain FR produced 4.9 ± 0.01 mW/m
2
, compared to 5.4 ± 0.3 mW/m
2
for strain ATCC 13047
T
. These results demonstrate for the first time that it is possible to generate electricity from cellulose using a single bacterial strain without exogenous mediators.
Effects of Long-Term Starvation on a Host Bivalve (Codakia orbicularis, Lucinidae) and Its Symbiont Population
Authors: Caro Audrey , Got Patrice , Bouvy Marc , Troussellier Marc , Gros Olivier 
Published: April 2009

ABSTRACTThe bivalveCodakia orbicularis, hosting sulfur-oxidizing gill endosymbionts, was starved (in artificial seawater filtered through a 0.22-μm-pore-size membrane) for a long-term experiment (4 months). The effects of starvation were observed using transmission electron microscopy, fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH), and flow cytometry to monitor the anatomical and physiological modifications in the gill organization of the host and in the symbiotic population housed in bacteriocytes. The abundance of the symbiotic population decreased through starvation, with a loss of one-third of the bacterial population each month, as shown by CARD-FISH. At the same time, flow cytometry revealed significant changes in the physiology of symbiotic cells, with a decrease in cell size and modifications to the nucleic acid content, while most of the symbionts maintained a high respiratory activity (measured using the 5-cyano-2,3-ditolyl tetrazolium chloride method). Progressively, the number of symbiont subpopulations was reduced, and the subsequent multigenomic state, characteristic of this symbiont in freshly collected clams, turned into one and five equivalent genome copies for the two remaining subpopulations after 3 months. Concomitant structural modifications appeared in the gill organization. Lysosymes became visible in the bacteriocytes, while large symbionts disappeared, and bacteriocytes were gradually replaced by granule cells throughout the entire lateral zone. Those data suggested that host survival under these starvation conditions was linked to symbiont digestion as the main nutritional source.
Characterization of Rhamnosidases from
Lactobacillus plantarum
and
Lactobacillus acidophilus
Authors: Beekwilder Jules , Marcozzi Daniela , Vecchi Samuele , de Vos Ric , Janssen Patrick , Francke Christof , van Hylckama Vlieg Johan , Hall Robert D. 
Published: April 2009

ABSTRACT

Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of
Lactobacillus plantarum
, two putative rhamnosidase genes (
ram1
Lp
and
ram2
Lp
) were identified, while in
Lactobacillus acidophilus
, one rhamnosidase gene was found (
ramA
La
). Gene products from all three genes were produced after introduction into
Escherichia coli
and were then tested for their enzymatic properties. Ram1
Lp
, Ram2
Lp
, and RamA
La
were able to efficiently hydrolyze rutin and other rutinosides, while RamA
La
was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of
Lactobacillus
rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1
Lp
and RamA
La
enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1
Lp
for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium
Lactococcus lactis
. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into
L. lactis
appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes.
Organoselenium Coating on Cellulose Inhibits the Formation of Biofilms byPseudomonas aeruginosaandStaphylococcus aureus
Authors: Tran Phat L. , Hammond Adrienne A. , Mosley Thomas , Cortez Janette , Gray Tracy , Colmer-Hamood Jane A. , Shashtri Mayank , Spallholz Julian E. , Hamood Abdul N. , Reid Ted W. 
Published: April 2009

ABSTRACTAmong the most difficult bacterial infections encountered in treating patients are wound infections, which may occur in burn victims, patients with traumatic wounds, necrotic lesions in people with diabetes, and patients with surgical wounds. Within a wound, infecting bacteria frequently develop biofilms. Many current wound dressings are impregnated with antimicrobial agents, such as silver or antibiotics. Diffusion of the agent(s) from the dressing may damage or destroy nearby healthy tissue as well as compromise the effectiveness of the dressing. In contrast, the antimicrobial agent selenium can be covalently attached to the surfaces of a dressing, prolonging its effectiveness. We examined the effectiveness of an organoselenium coating on cellulose discs in inhibitingPseudomonas aeruginosaandStaphylococcus aureusbiofilm formation. Colony biofilm assays revealed that cellulose discs coated with organoselenium completely inhibitedP. aeruginosaandS. aureusbiofilm formation. Scanning electron microscopy of the cellulose discs confirmed these results. Additionally, the coating on the cellulose discs was stable and effective after a week of incubation in phosphate-buffered saline. These results demonstrate that 0.2% selenium in a coating on cellulose discs effectively inhibits bacterial attachment and biofilm formation and that, unlike other antimicrobial agents, longer periods of exposure to an aqueous environment do not compromise the effectiveness of the coating.
Diversity and Morphology of Members of the Phylum “
Synergistetes
” in Periodontal Health and Disease
Authors: Vartoukian S. R. , Palmer R. M. , Wade W. G. 
Published: April 2009

ABSTRACT

Members of the phylum “
Synergistetes
” have frequently been detected in the human oral cavity at sites of dental disease, but they have rarely been detected in studies of oral health. Only two oral “
Synergistetes
” taxa are cultivable. The aims of this study were to investigate the diversity of “
Synergistetes
” in the oral cavity, to establish whether “
Synergistetes
” taxa are more strongly associated with periodontitis than with oral health, and to visualize unculturable “
Synergistetes
” in situ. Sixty samples (saliva, dental plaque, and mucosal swabs) were collected from five subjects with periodontitis and five periodontally healthy controls. Using phylum-specific 16S rRNA gene primers, “
Synergistetes
” were identified by PCR, cloning, and sequencing of 48 clones per PCR-positive sample. Subgingival plaque samples were labeled with probes targeting rRNA of unculturable oral “
Synergistetes
” using fluorescent in situ hybridization (FISH). Analysis of 1,664 clones revealed 12 “
Synergistetes
” operational taxonomic units (OTUs) at the 99% sequence identity level, 5 of which were novel. “
Synergistetes
” OTU 4.2 was found in significantly more subjects with periodontitis than controls (
P
= 0.048) and was more abundant in subgingival plaque at diseased sites than at healthy sites in subjects with periodontitis (
P
= 0.019) or controls (
P
= 0.019). FISH analysis revealed that unculturable oral “
Synergistetes
” cells were large curved bacilli. The human oral cavity harbors a diverse population of “
Synergistetes.
” “
Synergistetes
” OTU 4.2 is associated with periodontitis and may have a pathogenic role.