bluuebunny/crossref_metadata_2025 huggingface dataset:
High-Level Genotypic Variation and Antibiotic Sensitivity among
Escherichia coli
O157 Strains Isolated from Two Scottish Beef Cattle Farms
Authors: Vali Leila , Wisely Karen A. , Pearce Michael C. , Turner Esther J. , Knight Hazel I. , Smith Alastair W. , Amyes Sebastian G. B.
Published: October 2004

Escherichia coli
O157:H7 is a human pathogen that is carried and transmitted by cattle. Scotland is known to have one of the highest rates of
E. coli
O157 human infections in the world. Two hundred ninety-three isolates were obtained from naturally infected cattle and the environment on two farms in the Scottish Highlands. The isolates were typed by pulsed-field gel electrophoresis (PFGE) with XbaI restriction endonuclease enzyme, and 19 different variations in patterns were found. There was considerable genomic diversity within the
E. coli
O157 population on the two farms. The PFGE pattern of one of the observed subtypes matched exactly with that of a strain obtained from a Scottish patient with hemolytic-uremic syndrome. To examine the stability of an individual
E. coli
O157 strain, continuous subculturing of a strain was performed 110 times. No variation from the original PFGE pattern was observed. We found three indistinguishable subtypes of
E. coli
O157 on both study farms, suggesting common sources of infection. We also examined the antibiotic resistance of the isolated strains. Phenotypic studies demonstrated resistance of the strains to sulfamethoxazole (100%), chloramphenicol (3.07%), and at a lower rate, other antibiotics, indicating the preservation of antibiotic sensitivity in a rapidly changing population of
E. coli
O157.
Molecular Analysis of Geographic Patterns of Eukaryotic Diversity in Antarctic Soils
Authors: Lawley Blair , Ripley Sarah , Bridge Paul , Convey Peter
Published: October 2004

We describe the application of molecular biological techniques to estimate eukaryotic diversity (primarily fungi, algae, and protists) in Antarctic soils across a latitudinal and environmental gradient between approximately 60 and 87°S. The data were used to (i) test the hypothesis that diversity would decrease with increasing southerly latitude and environmental severity, as is generally claimed for “higher” faunal and plant groups, and (ii) investigate the level of endemicity displayed in different taxonomic groups. Only limited support was obtained for a systematic decrease in diversity with latitude, and then only at the level of a gross comparison between maritime (Antarctic Peninsula/Scotia Arc) and continental Antarctic sites. While the most southerly continental Antarctic site was three to four times less diverse than all maritime sites, there was no evidence for a trend of decreasing diversity across the entire range of the maritime Antarctic (60 to 72°S). Rather, we found the reverse pattern, with highest diversity at sites on Alexander Island (ca. 72°S), at the southern limit of the maritime Antarctic. The very limited overlap found between the eukaryotic biota of the different study sites, combined with their generally low relatedness to existing sequence databases, indicates a high level of Antarctic site isolation and possibly endemicity, a pattern not consistent with similar studies on other continents.
Enzymatic Analysis of an Amylolytic Enzyme from the Hyperthermophilic Archaeon
Pyrococcus furiosus
Reveals Its Novel Catalytic Properties as both an α-Amylase and a Cyclodextrin-Hydrolyzing Enzyme
Authors: Yang Sung-Jae , Lee Hee-Seob , Park Cheon-Seok , Kim Yong-Ro , Moon Tae-Wha , Park Kwan-Hwa
Published: October 2004

Genomic analysis of the hyperthermophilic archaeon
Pyrococcus furiosus
revealed the presence of an open reading frame (ORF PF1939) similar to the enzymes in glycoside hydrolase family 13. This amylolytic enzyme, designated PFTA (
Pyrococcus furiosus
thermostable amylase), was cloned and expressed in
Escherichia coli
. The recombinant PFTA was extremely thermostable, with an optimum temperature of 90°C. The substrate specificity of PFTA suggests that it possesses characteristics of both α-amylase and cyclodextrin-hydrolyzing enzyme. Like typical α-amylases, PFTA hydrolyzed maltooligosaccharides and starch to produce mainly maltotriose and maltotetraose. However, it could also attack and degrade pullulan and β-cyclodextrin, which are resistant to α-amylase, to primarily produce panose and maltoheptaose, respectively. Furthermore, acarbose, a potent α-amylase inhibitor, was drastically degraded by PFTA, as is typical of cyclodextrin-hydrolyzing enzymes. These results confirm that PFTA possesses novel catalytic properties characteristic of both α-amylase and cyclodextrin-hydrolyzing enzyme.
Potential Role of a Novel Psychrotolerant Member of the FamilyGeobacteraceae,Geopsychrobacter electrodiphilusgen. nov., sp. nov., in Electricity Production by a Marine Sediment Fuel Cell
Authors: Holmes Dawn E. , Nicoll Julie S. , Bond Daniel R. , Lovley Derek R.
Published: October 2004

Previous studies have shown that members of the familyGeobacteraceaethat attach to the anodes of sediment fuel cells are directly involved in harvesting electricity by oxidizing organic compounds to carbon dioxide and transferring the electrons to the anode. In order to learn more about this process, microorganisms from the anode surface of a marine sediment fuel cell were enriched and isolated with Fe(III) oxide. Two unique marine isolates were recovered, strains A1Tand A2. They are gram-negative, nonmotile rods, with abundantc-type cytochromes. Phylogenetic analysis of the 16S rRNA,recA,gyrB,fusA,rpoB, andnifDgenes indicated that strains A1Tand A2 represent a unique phylogenetic cluster within theGeobacteraceae. Both strains were able to grow with an electrode serving as the sole electron acceptor and transferred ca. 90% of the electrons available in their organic electron donors to the electrodes. These organisms are the first psychrotolerant members of theGeobacteraceaereported thus far and can grow at temperatures between 4 and 30°C, with an optimum temperature of 22°C. Strains A1Tand A2 can utilize a wide range of traditional electron acceptors, including all forms of soluble and insoluble Fe(III) tested, anthraquinone 2,6-disulfonate, and S0. In addition to acetate, both strains can utilize a number of other organic acids, amino acids, long-chain fatty acids, and aromatic compounds to support growth with Fe(III) nitrilotriacetic acid as an electron acceptor. The metabolism of these organisms differs in that only strain A1Tcan use acetoin, ethanol, and hydrogen as electron donors, whereas only strain A2 can use lactate, propionate, and butyrate. The nameGeopsychrobacter electrodiphilusgen. nov., sp. nov., is proposed for strains A1Tand A2, with strain A1T(ATCC BAA-880T; DSM 16401T; JCM 12469) as the type strain. Strains A1Tand A2 (ATCC BAA-770; JCM 12470) represent the first organisms recovered from anodes that can effectively couple the oxidation of organic compounds to an electrode. Thus, they may serve as important model organisms for further elucidation of the mechanisms of microbe-electrode electron transfer in sediment fuel cells.
Genetic Analysis of Phenoxyalkanoic Acid Degradation in
Sphingomonas herbicidovorans
MH
Authors: Müller Tina A. , Byrde Steven M. , Werlen Christoph , van der Meer Jan Roelof , Kohler Hans-Peter E.
Published: October 2004

Phenoxyalkanoic acid degradation is well studied in
Beta
- and
Gammaproteobacteria
, but the genetic background has not been elucidated so far in
Alphaproteobacteria
. We report the isolation of several genes involved in dichlor- and mecoprop degradation from the alphaproteobacterium
Sphingomonas herbicidovorans
MH and propose that the degradation proceeds analogously to that previously reported for 2,4-dichlorophenoxyacetic acid (2,4-D). Two genes for α-ketoglutarate-dependent dioxygenases,
sdpA
MH
and
rdpA
MH
, were found, both of which were adjacent to sequences with potential insertion elements. Furthermore, a gene for a dichlorophenol hydroxylase (
tfdB
), a putative regulatory gene (
cadR
), two genes for dichlorocatechol 1,2-dioxygenases (
dccA
I/II
), two for dienelactone hydrolases (
dccD
I/II
), part of a gene for maleylacetate reductase (
dccE
), and one gene for a potential phenoxyalkanoic acid permease were isolated. In contrast to other 2,4-D degraders, the
sdp
,
rdp
, and
dcc
genes were scattered over the genome and their expression was not tightly regulated. No coherent pattern was derived on the possible origin of the
sdp
,
rdp
, and
dcc
pathway genes.
rdpA
MH
was 99% identical to
rdpA
MC1
, an (
R
)-dichlorprop/α-ketoglutarate dioxygenase from
Delftia acidovorans
MC1, which is evidence for a recent gene exchange between
Alpha
- and
Betaproteobacteria
. Conversely, DccA
I
and DccA
II
did not group within the known chlorocatechol 1,2-dioxygenases, but formed a separate branch in clustering analysis. This suggests a different reservoir and reduced transfer for the genes of the modified
ortho
-cleavage pathway in
Alphaproteobacteria
compared with the ones in
Beta
- and
Gammaproteobacteria
.
Production ofl-Ascorbic Acid by Metabolically EngineeredSaccharomyces cerevisiaeandZygosaccharomyces bailii
Authors: Sauer Michael , Branduardi Paola , Valli Minoska , Porro Danilo
Published: October 2004

Yeasts do not possess an endogenous biochemical pathway for the synthesis of vitamin C. However, incubated withl-galactose,l-galactono-1,4-lactone, orl-gulono-1,4-lactone intermediates from the plant or animal pathway leading tol-ascorbic acid,Saccharomyces cerevisiaeandZygosaccharomyces bailiicells accumulate the vitamin intracellularly. Overexpression of theS. cerevisiaeenzymesd-arabinose dehydrogenase andd-arabinono-1,4-lactone oxidase enhances this ability significantly. In fact, the respective recombinant yeast strains even gain the capability to accumulate the vitamin in the culture medium. An even better result is obtainable by expression of the plant enzymel-galactose dehydrogenase fromArabidopsis thaliana. Budding yeast cells overexpressing the endogenousd-arabinono-1,4-lactone oxidase as well asl-galactose dehydrogenase are capable of producing about 100 mg ofl-ascorbic acid liter−1, converting 40% (wt/vol) of the starting compoundl-galactose.
Involvement of Linear Plasmids in Aerobic Biodegradation of Vinyl Chloride
Authors: Danko Anthony S. , Luo Meizhong , Bagwell Christopher E. , Brigmon Robin L. , Freedman David L.
Published: October 2004

Pseudomonas putida
strain AJ and
Ochrobactrum
strain TD were isolated from hazardous waste sites based on their ability to use vinyl chloride (VC) as the sole source of carbon and energy under aerobic conditions. Strains AJ and TD also use ethene and ethylene oxide as growth substrates. Strain AJ contained a linear megaplasmid (approximately 260 kb) when grown on VC or ethene, but it contained no circular plasmids. While strain AJ was growing on ethylene oxide, it was observed to contain a 100-kb linear plasmid, and its ability to use VC as a substrate was retained. The linear plasmids in strain AJ were cured, and the ability of strain AJ to consume VC, ethene, and ethylene oxide was lost following growth on a rich substrate (Luria-Bertani broth) through at least three transfers. Strain TD contained three linear plasmids, ranging in size from approximately 90 kb to 320 kb, when growing on VC or ethene. As with strain AJ, the linear plasmids in strain TD were cured following growth on Luria-Bertani broth and its ability to consume VC and ethene was lost. Further analysis of these linear plasmids may help reveal the pathway for VC biodegradation in strains AJ and TD and explain why this process occurs at many but not all sites where groundwater is contaminated with chloroethenes. Metabolism of VC and ethene by strains AJ and TD is initiated by an alkene monooxygenase. Their yields during growth on VC (0.15 to 0.20 mg of total suspended solids per mg of VC) are similar to the yields reported for other isolates (i.e.,
Mycobacterium
sp.,
Nocardioides
sp., and
Pseudomonas
sp.).
Comparison of Compositions and Metabolic Activities of Fecal Microbiotas in Young Adults and in Antibiotic-Treated and Non-Antibiotic-Treated Elderly Subjects
Authors: Woodmansey Emma J. , McMurdo Marion E. T. , Macfarlane George T. , Macfarlane Sandra
Published: October 2004

The colonic microbiota mediates many cellular and molecular events in the host that are important to health. These processes can be affected in the elderly, because in some individuals, the composition and metabolic activities of the microbiota change with age. Detailed characterizations of the major groups of fecal bacteria in healthy young adults, in healthy elderly people, and in hospitalized elderly patients receiving antibiotics were made in this study, together with measurements of their metabolic activities, by analysis of fecal organic acid and ammonia concentrations. The results showed that total anaerobe numbers remained relatively constant in old people; however, individual bacterial genera changed markedly with age. Reductions in numbers of bacteroides and bifidobacteria in both elderly groups were accompanied by reduced species diversity. Bifidobacterial populations in particular showed marked variations in the dominant species, with
Bifidobacterium angulatum
and
Bifidobacterium adolescentis
being frequently isolated from the elderly and
Bifidobacterium longum
,
Bifidobacterium catenulatum
,
Bifidobacterium boum
, and
Bifidobacterium infantis
being detected only from the healthy young volunteers. Reductions in amylolytic activities of bacterial isolates in healthy elderly subjects and reduced short-chain fatty acid concentrations supported these findings, since bifidobacteria and bacteroides are important saccharolytic groups in the colon. Conversely, higher numbers of proteolytic bacteria were observed with feces samples from the antibiotic-treated elderly group, which were also associated with increased proteolytic species diversity (fusobacteria, clostridia, and propionibacteria). Other differences in the intestinal ecosystem in elderly subjects were observed, with alterations in the dominant clostridial species in combination with greater numbers of facultative anaerobes.
Discrimination of Modes of Action of Antifungal Substances by Use of Metabolic Footprinting
Authors: Allen Jess , Davey Hazel M. , Broadhurst David , Rowland Jem J. , Oliver Stephen G. , Kell Douglas B.
Published: October 2004

Diploid cells of
Saccharomyces cerevisiae
were grown under controlled conditions with a Bioscreen instrument, which permitted the essentially continuous registration of their growth via optical density measurements. Some cultures were exposed to concentrations of a number of antifungal substances with different targets or modes of action (sterol biosynthesis, respiratory chain, amino acid synthesis, and the uncoupler). Culture supernatants were taken and analyzed for their “metabolic footprints” by using direct-injection mass spectrometry. Discriminant function analysis and hierarchical cluster analysis allowed these antifungal compounds to be distinguished and classified according to their modes of action. Genetic programming, a rule-evolving machine learning strategy, allowed respiratory inhibitors to be discriminated from others by using just two masses. Metabolic footprinting thus represents a rapid, convenient, and information-rich method for classifying the modes of action of antifungal substances.
“CandidatusHepatoplasma crinochetorum,” a New, Stalk-Forming Lineage ofMollicutesColonizing the Midgut Glands of a Terrestrial Isopod
Authors: Wang Yongjie , Stingl Ulrich , Anton-Erxleben Friederike , Geisler Sabine , Brune Andreas , Zimmer Martin
Published: October 2004

Uncultivated bacteria that densely colonize the midgut glands (hepatopancreas) of the terrestrial isopodPorcellio scaber(Crustacea: Isopoda) were identified by cloning and sequencing of their 16S rRNA genes. Phylogenetic analysis revealed that these symbionts represent a novel lineage of theMollicutesand are only distantly related (<82% sequence identity) to members of theMycoplasmatalesandEntomoplasmatales. Fluorescence in situ hybridization with a specific oligonucleotide probe confirmed that the amplified 16S rRNA gene sequences indeed originated from a homogeneous population of symbionts intimately associated with the epithelial surface of the hepatopancreas. The same probe also detected morphotypically identical symbionts in other crinochete isopods. Scanning and transmission electron microscopy revealed uniform spherical bacterial cells without a cell wall, sometimes interacting with the microvilli of the brush border by means of stalk-like cytoplasmic appendages, which also appeared to be involved in cell division through budding. Based on the isolated phylogenetic position and unique cytological properties, the provisional name “CandidatusHepatoplasma crinochetorum” is proposed for this new taxon ofMollicutescolonizing the hepatopancreas ofP. scaber.
Characterization of the
groEL
and
groES
Loci in
Bifidobacterium breve
UCC 2003: Genetic, Transcriptional, and Phylogenetic Analyses
Authors: Ventura Marco , Canchaya Carlos , Zink Ralf , Fitzgerald Gerald F. , van Sinderen Douwe
Published: October 2004

The bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes, including the GroEL and GroES proteins. The
groES
and
groEL
genes are highly conserved among eubacteria and are typically arranged as an operon. Genome analysis of
Bifidobacterium breve
UCC 2003 revealed that the
groES
and
groEL
genes are located in different chromosomal regions. The heat inducibility of the
groEL
and
groES
genes of
B. breve
UCC 2003 was verified by slot blot analysis. Northern blot analyses showed that the
cspA
gene is cotranscribed with the
groEL
gene, while the
groES
gene is transcribed as a monocistronic unit. The transcription initiation sites of these two mRNAs were determined by primer extension. Sequence and transcriptional analyses of the region flanking the
groEL
and
groES
genes of various bifidobacteria revealed similar
groEL
-
cspA
and
groES
gene units, suggesting a novel genetic organization of these chaperones. Phylogenetic analysis of the available bifidobacterial
groES
and
groEL
genes suggested that these genes evolved differently. Discrepancies in the phylogenetic positioning of
groES
-based trees make this gene an unreliable molecular marker. On the other hand, the bifidobacterial
groEL
gene sequences can be used as an alternative to current methods for tracing
Bifidobacterium
species, particularly because they allow a high level of discrimination between closely related species of this genus.
Flow Sorting of Marine Bacterioplankton after Fluorescence In Situ Hybridization
Authors: Sekar Raju , Fuchs Bernhard M. , Amann Rudolf , Pernthaler Jakob
Published: October 2004

We describe an approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (CARD-FISH). In a sample from spring 2003 >90% of the cells were detected by CARD-FISH with a bacterial probe (EUB338). Approximately 30% of the microbial assemblage was affiliated with the
Cytophaga-Flavobacterium
lineage of the
Bacteroidetes
(CFB group) (probe CF319a), and almost 10% was targeted by a probe for the β-proteobacteria (probe BET42a). A protocol was optimized to detach cells hybridized with EUB338, BET42a, and CF319a from membrane filters (recovery rate, 70%) and to sort the cells by flow cytometry. The purity of sorted cells was >95%. 16S rRNA gene clone libraries were constructed from hybridized and sorted cells (S-EUB, S-BET, and S-CF libraries) and from unhybridized and unsorted cells (UNHYB library). Sequences related to the CFB group were significantly more frequent in the S-CF library (66%) than in the UNHYB library (13%). No enrichment of β-proteobacterial sequence types was found in the S-BET library, but novel sequences related to
Nitrosospira
were found exclusively in this library. These bacteria, together with members of marine clade OM43, represented >90% of the β-proteobacteria in the water sample, as determined by CARD-FISH with specific probes. This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats.
Synchronous Effects of Temperature, Hydrostatic Pressure, and Salinity on Growth, Phospholipid Profiles, and Protein Patterns of Four
Halomonas
Species Isolated from Deep-Sea Hydrothermal-Vent and Sea Surface Environments
Authors: Kaye Jonathan Z. , Baross John A.
Published: October 2004

Four strains of euryhaline bacteria belonging to the genus
Halomonas
were tested for their response to a range of temperatures (2, 13, and 30°C), hydrostatic pressures (0.1, 7.5, 15, 25, 35, 45, and 55 MPa), and salinities (4, 11, and 17% total salts). The isolates were psychrotolerant, halophilic to moderately halophilic, and piezotolerant, growing fastest at 30°C, 0.1 MPa, and 4% total salts. Little or no growth occurred at the highest hydrostatic pressures tested, an effect that was more pronounced with decreasing temperatures. Growth curves suggested that the
Halomonas
strains tested would grow well in cool to warm hydrothermal-vent and associated subseafloor habitats, but poorly or not at all under cold deep-sea conditions. The intermediate salinity tested enhanced growth under certain high-hydrostatic-pressure and low-temperature conditions, highlighting a synergistic effect on growth for these combined stresses. Phospholipid profiles obtained at 30°C indicated that hydrostatic pressure exerted the dominant control on the degree of lipid saturation, although elevated salinity slightly mitigated the increased degree of lipid unsaturation caused by increased hydrostatic pressure. Profiles of cytosolic and membrane proteins of
Halomonas axialensis
and
H. hydrothermalis
performed at 30°C under various salinities and hydrostatic pressure conditions indicated several hydrostatic pressure and salinity effects, including proteins whose expression was induced by either an elevated salinity or hydrostatic pressure, but not by a combination of the two. The interplay between salinity and hydrostatic pressure on microbial growth and physiology suggests that adaptations to hydrostatic pressure and possibly other stresses may partially explain the euryhaline phenotype of members of the genus
Halomonas
living in deep-sea environments.
Nonlegumes, Legumes, and Root Nodules Harbor Different Arbuscular Mycorrhizal Fungal Communities
Authors: Scheublin Tanja R. , Ridgway Karyn P. , Young J. Peter W. , van der Heijden Marcel G. A.
Published: October 2004

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing
Rhizobium
bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).
Metabolically Active Eukaryotic Communities in Extremely Acidic Mine Drainage
Authors: Baker Brett J. , Lutz Michelle A. , Dawson Scott C. , Bond Philip L. , Banfield Jillian F.
Published: October 2004

Acid mine drainage (AMD) microbial communities contain microbial eukaryotes (both fungi and protists) that confer a biofilm structure and impact the abundance of bacteria and archaea and the community composition via grazing and other mechanisms. Since prokaryotes impact iron oxidation rates and thus regulate AMD generation rates, it is important to analyze the fungal and protistan populations. We utilized 18S rRNA and beta-tubulin gene phylogenies and fluorescent rRNA-specific probes to characterize the eukaryotic diversity and distribution in extremely acidic (pHs 0.8 to 1.38), warm (30 to 50°C), metal-rich (up to 269 mM Fe
2+
, 16.8 mM Zn, 8.5 mM As, and 4.1 mM Cu) AMD solutions from the Richmond Mine at Iron Mountain, Calif. A
Rhodophyta
(red algae) lineage and organisms from the
Vahlkampfiidae
family were identified. The fungal 18S rRNA and tubulin gene sequences formed two distinct phylogenetic groups associated with the classes
Dothideomycetes
and
Eurotiomycetes
. Three fungal isolates that were closely related to the
Dothideomycetes
clones were obtained. We suggest the name “
Acidomyces richmondensis
” for these isolates. Since these ascomycete fungi were morphologically indistinguishable, rRNA-specific oligonucleotide probes were designed to target the
Dothideomycetes
and
Eurotiomycetes
via fluorescent in situ hybridization (FISH). FISH analyses indicated that
Eurotiomycetes
are generally more abundant than
Dothideomycetes
in all of the seven locations studied within the Richmond Mine system. This is the first study to combine the culture-independent detection of fungi with in situ detection and a demonstration of activity in an acidic environment. The results expand our understanding of the subsurface AMD microbial community structure.
Bloom of Filamentous Bacteria in a Mesotrophic Lake: Identity and Potential Controlling Mechanism
Authors: Pernthaler Jakob , Zöllner Eckart , Warnecke Falk , Jürgens Klaus
Published: October 2004

Ephemeral blooms of filamentous bacteria are a common phenomenon in the water column of oligo- to mesotrophic lakes. It is assumed that the appearance of such morphotypes is favored by selective predation of bacterivorous protists and that filter-feeding zooplankton plays a major role in suppressing these bacteria. The phylogenetic affiliation of the important bloom-forming filamentous bacteria in freshwaters is presently unknown. Here we report the identification of dominant members of a filamentous bacterial assemblage during a bloom of such morphotypes in a mesotrophic lake. By molecular cloning and fluorescence in situ hybridization with specific oligonucleotide probes, up to 98% of filamentous cells in lake water could be assigned to a clade of almost identical (99% similarity) 16S rRNA gene sequence types, the cosmopolitan freshwater LD2 cluster. For a period of less than 1 week, members of the LD2 clade constituted >40% of the total bacterial biomass, potentially favored by high grazing of planktivorous protists. This is probably the most pronounced case of dominance by a single bacterioplankton species ever observed in natural freshwaters. In enclosures artificially stocked with the metazoan filter feederDaphnia, bacteria related to the LD2 clade formed a significantly larger fraction of filaments than in enclosures whereDaphniahad been removed. However, in the presence of higher numbers ofDaphniaindividuals, the LD2 bacteria, like other filaments, were eventually eliminated both in enclosures and in the lake. This points at the potential importance of filter-feeding zooplankton in controlling the occurrence and species composition of filamentous bacterial morphotypes in freshwater plankton.
Intestinal Mucus Alters the Ability of Probiotic Bacteria To Bind Aflatoxin B
1
In Vitro
Authors: Gratz S. , Mykkänen H. , Ouwehand A. C. , Juvonen R. , Salminen S. , El-Nezami H.
Published: October 2004

Several probiotics are known to bind aflatoxin B
1
(AFB
1
) to their surfaces and to adhere to intestinal mucus. In this study, preincubation of two probiotic preparations with either AFB
1
or mucus reduced the subsequent surface binding of mucus and AFB
1
, respectively, in a strain-dependent manner.
Genetic Typing of Shiga Toxin 2 Variants ofEscherichia coliby PCR-Restriction Fragment Length Polymorphism Analysis
Authors: De Baets Liesbet , Van der Taelen Imme , De Filette Marina , Piérard Denis , Allison Lesley , De Greve Henri , Hernalsteens Jean-Pierre , Imberechts Hein
Published: October 2004

Shiga toxins Stx1 and Stx2 play a prominent role in the pathogenesis of Shiga toxin-producingEscherichia coli(STEC) infections. Several variants of thestx2gene, encoding Stx2, have been described. In this study, we developed a PCR-restriction fragment length polymorphism system for typingstx2genes of STEC strains. The typing system discriminates eight described variants and allows the identification of newstx2variants and STEC isolates carrying multiplestx2genes. A phylogenetic tree, based on the nucleotide sequences of the toxin-encoding genes, demonstrates thatstx2sequences with the same PvuII HaeIII HincII AccI type generally cluster together.
Reverse Transcription-Booster PCR for Detection of Noroviruses in Shellfish
Authors: De Medici Dario , Croci Luciana , Suffredini Elisabetta , Toti Laura
Published: October 2004

The methods commonly used for norovirus (NV) detection are based on reverse transcription-PCR (RT-PCR) followed by confirmation of the amplified sequence. To increase sensitivity, an RT-booster PCR was developed. The proposed method showed an increase in sensitivity at least 2 log units for all the NV strains tested compared with the standard RT-PCR method. Higher sensitivity was confirmed in tests on experimentally and naturally contaminated shellfish.
Genetic Identification of a Putative Vinyl Chloride Reductase in
Dehalococcoides
sp. Strain BAV1
Authors: Krajmalnik-Brown Rosa , Hölscher Tina , Thomson Ivy N. , Saunders F. Michael , Ritalahti Kirsti M. , Löffler Frank E.
Published: October 2004

Dehalococcoides
sp. strain BAV1 couples growth with the reductive dechlorination of vinyl chloride (VC) to ethene. Degenerate primers targeting conserved regions in reductive dehalogenase (RDase) genes were designed and used to PCR amplify putative RDase genes from strain BAV1. Seven unique RDase gene fragments were identified. Transcription analysis of VC-grown BAV1 cultures suggested that
bvcA
was involved in VC reductive dechlorination, and the complete sequence of
bvcA
was obtained.
bvcA
was absent in
Dehalococcoides
isolates that failed to respire VC, yet was detected in four of eight VC-respiring mixed cultures.
Blood chemistry correlates of nutritional condition, tissue damage, and stress in migrating juvenile chinook salmon (Oncorhynchus tshawytscha)
Authors: Wagner Tyler , Congleton James L
Published: October 2004

We used factor analysis to examine the correlation structure of six multivariate blood chemistry data sets for migrating hatchery and wild juvenile chinook salmon (Oncorhynchus tshawytscha). Fish were sampled (19982002) from juvenile fish bypass systems at dams or (one data set) from fish transport barges on the Snake and Columbia rivers. Analyses were performed to determine which blood chemistry analytes covaried, to facilitate interpretation of the data sets, and to provide insight into controlling physiological mechanisms. Four underlying factors were derived from the analyses: (i) a nutritional factor composed of total protein, cholesterol, calcium, and alkaline phosphatase, (ii) a tissue damage factor composed of the enzymes alanine aminotransferase, aspartate aminotransferase, and creatine kinase, (iii) a lipid metabolism factor composed of triacylglycerol lipase and triglycerides, and (iv) a stress factor composed of cortisol, glucose, Na+, and Cl. Although causal mechanisms cannot be directly inferred from our analyses, findings of published research provide tenable causal mechanisms for the observed structure. The consistency of the correlation structure among data sets suggests that composite (latent) variables may be more reliable indicators of some physiological responses than changes in individual variables.
Cumulative effects of nutrients and pH on the plankton of two mountain lakes
Authors: Lafrancois Brenda Moraska , Nydick Koren R , Johnson Brett M , Baron Jill S
Published: October 2004

We conducted enclosure experiments to examine the cumulative effects of nutrient enrichment and acidification on the plankton of two mountain lakes with differing nutrient conditions. The low-nitrate lake responded to N, N plus acid, and N plus acid plus P additions, showing four- to seven-fold increases in chlorophyll a, increased photosynthetic rate, compositional shifts toward large chlorophytes, and decreased zooplankton biomass. The high-nitrate lake responded minimally to either N or P alone but responded strongly to combined additions of N plus acid plus P, showing eightfold increases in chlorophyll a, increased cell density and photosynthetic rates, and compositional shifts toward chlorophytes and the dinoflagellate Gymnodinium. In both study lakes, changes in chlorophyll a were linked to addition of limiting nutrients regardless of pH, whereas shifts in phytoplankton species composition were apparently affected by both nutrient conditions and acidity. The most striking changes in species composition and biomass occurred in combined N plus acid plus P treatments, indicating that continued nutrient enrichment may interact with acidification to produce marked changes in the plankton of mountain lakes.
Effects of stress on plasma homeostasis, endolymph chemistry, and check formation during otolith growth in rainbow trout (Oncorhynchus mykiss)
Authors: Payan P , Pontual H De , Edeyer A , Borelli G , Boeuf G , Mayer-Gostan N
Published: October 2004

This is the first study in which the effects of an external stress were analysed at different levels: plasma ho meostasis, endolymph chemistry, and otolith growth. Stress was applied to rainbow trout (Oncorhynchus mykiss) by exposure to Cl2gas. In the plasma of Cl2-stressed trout, Na+and Cldecreased (70 mmol·L1) and K+increased (2.0 mmol·L1), whereas total Ca was unchanged. A slight hypercapny (+2.4 mmHg (1 mmHg = 133.322 Pa)) was observed related to a significant rise (40%) in total CO2without pH variation. In the endolymph, Na+and Clalso decreased, whereas other parameters (K+, PO43, Mg, and, peculiarly, total Ca) remained stable. The important effect provoked by Cl2stress in endolymph was an increase of proteins (factor of 2.6) and total CO2(factor of 3.1) concentrations at the proximal side of the endolymph. The stress induced a decrease in otolith growth rate and produced a discontinuity (check) in the microstructure pattern of the otolith characterized by a large D zone. The variations in the endolymph composition are discussed and we propose that they result not only from changes in plasma concentrations, but also from changes (organic and crystallization) in otolith deposition.
Genetic polymorphism and mixed-stock fisheries analysis
Authors: Kalinowski Steven T
Published: October 2004

Genetic data can be used to estimate the stock composition of mixed-stock fisheries. Designing efficient strategies for estimating mixture proportions is important, but several aspects of study design remain poorly understood, particularly the relationship between genetic polymorphism and estimation error. In this study, computer simulation was used to investigate how the following variables affect expected squared error of mixture estimates: the number of loci examined, the number of alleles at those loci, and the size of baseline data sets. This work showed that (i) loci with more alleles produced estimates of stock proportions that had a lower expected squared error than less polymorphic loci, (ii) highly polymorphic loci did not require larger samples than less polymorphic loci, and (iii) the total number of independent alleles examined is a reasonable indicator of the quality of estimates of stock proportions.
Influence of shoreline features on fish distribution in the Laurentian Great Lakes
Authors: Wei A , Chow-Fraser P , Albert D
Published: October 2004

In this paper, we used assembled fish distributions (over 9500 field observations) and correlated them with 11 categories of the Great Lakes shoreline (i.e., bedrock, bluff, coarse beach, sandy beach  dune, sandysilty bank, clay bank, low riverine  coastal plain, composite, wetland, artificial, and unclassified) to validate the appropriateness of classifying Great Lakes fishes into three species complexes (taxocenes) that account for differences in their dependence on shoreline features. A χ2 goodness-of-fit test with Bonferroni correction indicated a significant positive association between the presence of fish and three shoreline classes: wetland, sandy beach  dune, and bluff. The Dutilleul modified t test was used to quantify the correlation between wetlands and distribution of the 25 most abundant species and those of different functional groupings. Our results confirm that (i) the Great Lakes fish community utilizes certain shoreline features (especially wetlands) disproportionately to their availability, (ii) the distribution of wetland-associated taxa is influenced by wetland type (i.e., protected embayment versus open-shoreline wetland), and (iii) the preferred utilization of coastal wetlands by a majority of the fish community is consistent across geographical scales, from the local site to the entire Great Lakes shoreline.
Predicting the impact of perturbations on salmon (Oncorhynchus spp.) communities: implications for monitoring
Authors: Arkoosh M R , Johnson L , Rossignol P A , Collier T K
Published: October 2004

Twenty-six salmon (Oncorhynchus spp.) stocks from the Pacific Northwest are listed as either threatened or endangered. A number of anthropogenic factors, likely including degradation of habitat by chemical contaminant exposure, have contributed to their decline. Techniques that can assess injury or judge the efficacy of regulatory actions on the recovery of this species are needed. We strive to understand why a population is changing by examining changes in their intrinsic birth rates, death rates, and (or) growth rates. However, salmon populations are influenced by other species in the community. To address this issue, we developed a parsimonious three-trophic-level community model consisting of prey, salmon, and parasites and examined the model's response to one anthropogenic factor (contaminant exposure) using qualitative analysis. This community model may not only provide valuable insight into salmon survival but also may broaden the approaches available to elucidate direct and indirect effects. We demonstrate analytically that some community members, possibly salmon themselves, might be ambiguous or unreliable variables to monitor. We also demonstrate that other species in the community, such as parasites, may be more sensitive than salmon in monitoring the influence of anthropogenic factors such as contaminants.
Population genetic differentiation of sea lice (Lepeophtheirus salmonis) parasitic on Atlantic and Pacific salmonids: analyses of microsatellite DNA variation among wild and farmed hosts
Authors: Todd C D , Walker A M , Ritchie M G , Graves J A , Walker A F
Published: October 2004

The copepod Lepeophtheirus salmonis is ectoparasitic on Atlantic and Pacific wild salmonids. It is a major pest to Atlantic salmon (Salmo salar) aquaculture and may be implicated in recent declines of certain European wild salmonid stocks. Variation at six microsatellite loci was assessed among L. salmonis from wild and farmed salmonids in Scotland, wild sea-run brown trout (Salmo trutta) in Norway, and farmed Atlantic salmon in eastern Canada. An outgroup North Pacific sample was obtained from farmed Atlantic salmon in British Columbia. No significant differentiation was found between L. salmonis from the host species or among samples from throughout the North Atlantic. This is consistent with long-distance oceanic migration of wild hosts and larval interchange between farmed and wild host stocks being sufficient to prevent genetic divergence of L. salmonis throughout the North Atlantic. These results have important management implications for both wild stock conservation and aquaculture in that genetically, L. salmonis in the North Atlantic comprises a single population: there is no evidence of isolation of populations on farmed hosts from those on wild fish. Comparison between North Pacific and North Atlantic L. salmonis populations showed significant but low differentiation (FST= 0.06).
Inferring sockeye salmon (Oncorhynchus nerka) population dynamics and water quality changes in a stained nursery lake over the past ∼500 years
Authors: Gregory-Eaves Irene , Finney Bruce P , Douglas Marianne SV , Smol John P
Published: October 2004

Historical and paleolimnological studies have demonstrated that environmental changes in the North Pacific can strongly affect sockeye salmon (Oncorhynchus nerka) abundances. Whether these marine shifts would be influential on sockeye salmon from all lake types, however, has not yet been studied. This study represents the first paleolimnological analysis of past sockeye salmon population dynamics in a stained nursery lake (Packers Lake, Alaska). We adopted a multiproxy approach to determine whether salmon-derived nutrients (inferred from δ15N) would be available for algal uptake (inferred from the diatom species responses) in this stained lake, as high concentrations of humics and iron are known to sequester phosphorus. The strong degree of coherency between δ15N and diatoms, however, suggests that salmon-derived nutrients were bioavailable and enhanced productivity. Overall, our indicators responded to changes in sockeye salmon abundances and volcanic ashfalls over the past ∼500 years. In a section of the core unaffected by tephras (AD ∼17701882), our record suggests that the number of sockeye salmon spawners fluctuated widely. Comparison of temporal shifts in inferred sockeye salmon abundances from Packers Lake with other clearwater nursery lakes reveals a broadly consistent pattern, likely influenced by past climatic changes.
Spatial and temporal variation in elemental signatures of statoliths from the Patagonian longfin squid (Loligo gahi)
Authors: Arkhipkin Alexander I , Campana Steven E , FitzGerald Jennifer , Thorrold Simon R
Published: October 2004

We quantified elemental signatures in statoliths of 718 Patagonian longfin squid (Loligo gahi) collected in the vicinity of the Falkland Islands (southwest Atlantic) and at sites on the Patagonian Shelf and coastal Peru. All squid were assigned to a spawning cohort by size, spawning condition, and back-calculated spawning date based on daily increments in statoliths. The remaining statolith was then analyzed for six elemental ratios (Mg/Ca, Mn/Ca, Sr/Ca, Cd/Ca, Ba/Ca, and Pb/Ca) using high-resolution inductively coupled plasma mass spectrometry (ICP-MS). Elemental concentrations in the statoliths were broadly similar to other biogenic aragonites. Differences in Sr/Ca ratios in statoliths among geographic locations were generally consistent with a negative correlation between Sr/Ca and temperature. Variations in statolith Cd/Ca and Ba/Ca values confirmed that during winter months, the squid were foraging deeper in the water column. Both Mg/Ca and Mn/Ca ratios in statoliths decreased with squid size, probably corresponding to a decrease in the contribution of the organic component of the statolith. Elemental signatures in the statoliths of L. gahi varied significantly geographically and between spring- and autumn-spawned cohorts, which must therefore have spent significant portions of their life histories in different environments.
Simple representation of the dynamics of biomass error propagation for stock assessment models
Authors: Walters Carl
Published: October 2004

Errors in estimates of current exploitable biomass from age-structured stock assessment models typically propagate over time as though they had been computed by using a very simple Kalman filter equation. This equation shows that persistent overestimates of biomass during stock declines are caused mainly by three factors: first-order autoregressive effects of past errors, hyperstability in relative abundance indices, and overestimates of current recruitment. Besides exposing these main causes of bias in biomass estimation, the equation can be used to develop very efficient closed-loop or management performance simulations and to provide timely biomass estimates in situations where it is not practical or economical to carry out full assessments every year.
A COMPETITION GAME WITH KNOWLEDGE ACCUMULATION AND SPILLOVERS
Authors: BISCHI GIAN-ITALO , LAMANTIA FABIO
Published: October 2004

In this paper a repeated game is proposed to model competition among firms, with profit maximizing resource allocation. The proposed model differs from the usual competition models because efforts that players exert are not seen as sunk costs, but they accumulate to form a stock of knowledge that has a cost-reducing effect. In modelling knowledge accumulation, we also consider the (knowledge) spillovers, that is, involuntary leakage of useful technological information. The game with n boundedly rational agents is modelled by a 2n-dimensional discrete dynamical system, whose state variables are the R&D efforts and the stock of accumulated knowledge of each firm involved in the competition. The model is characterized by some counteracting forces: Efforts are costly but can increase future profits; immediate expenditures of each firm can have cost-reducing effects in the long run, since accumulated knowledge can decrease both own costs and competitors' ones, because of spillover effects. In the case of two homogeneous firms we prove the existence of a unique equilibrium and its stability. Starting from these analytic results, numerical simulations are performed in order to study the effects induced by heterogeneities between the players on stability and transient dynamics, as well as the influence of the main parameters on the basins of attraction.