bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Gammaproteobacteria Associated with Blood-Feeding Leeches and a Broad Phylogenetic Analysis of Leech Endosymbionts
Authors: Perkins Susan L. , Budinoff Rebecca B. , Siddall Mark E. 
Published: September 2005

ABSTRACT

Many monophagous animals have coevolutionary relationships with bacteria that provide unavailable nutrients to the host. Frequently, these microbial partners are vertically inherited and reside in specialized structures or tissues. Here we report three new lineages of bacterial symbionts of blood-feeding leeches, one from the giant Amazonian leech,
Haementeria ghilianii
, and two others from
Placobdelloides
species. These hosts each possess a different mycetome or esophageal organ morphology where the bacterial cells are located. DNA sequencing of the bacterial 16S rRNA genes and fluorescent in situ hybridization placed these symbionts in two separate clades in the class
Gammaproteobacteria
. We also conducted a broad phylogenetic analysis of the herein-reported DNA sequences as well as others from bacterial symbionts reported elsewhere in the literature, including alphaproteobacterial symbionts from the leech genus
Placobdella
as well as
Aeromonas veronii
from the medicinal leech,
Hirudo medicinalis
, and a
Rickettsia
sp. detected in
Hemiclepsis marginata
. Combined, these results indicate that blood-feeding leeches have forged bacterial partnerships at least five times during their evolutionary history.
Extensive Diversity of Ionizing-Radiation-Resistant Bacteria Recovered from Sonoran Desert Soil and Description of Nine New Species of the GenusDeinococcusObtained from a Single Soil Sample
Authors: Rainey Fred A. , Ray Keren , Ferreira Margarida , Gatz Bridget Z. , Nobre M. Fernanda , Bagaley Danielle , Rash Brian A. , Park Mie-Jung , Earl Ashlee M. , Shank Nicole C. , Small Alanna M. , Henk Margaret C. , Battista John R. , Kämpfer Peter , da Costa Milton S. 
Published: September 2005

ABSTRACTThe ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a60Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the generaDeinococcus,Geodermatophilus, andHymenobacterwere still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiation-resistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60Deinococcusstrains, the characterization of which revealed nine novel species of this genus.
Identification of Genes Induced in
Listeria monocytogenes
during Growth and Attachment to Cut Cabbage, Using Differential Display
Authors: Palumbo Jeffrey D. , Kaneko Aya , Nguyen Kimanh D. , Gorski Lisa 
Published: September 2005

ABSTRACT

The food-borne pathogen
Listeria monocytogenes
is a ubiquitous soil bacterium with the potential to contaminate fresh produce during cultivation and postharvest processing. In order to identify potential mechanisms by which
L. monocytogenes
may successfully attach to and colonize fresh produce, gene expression in
L. monocytogenes
cells inoculated onto fresh-cut cabbage was compared to gene expression in cells grown under control conditions. Differential display of reverse transcriptase PCR fragments amplified with a set of 81 arbitrary primers allowed the isolation and identification of 32
L. monocytogenes
gene fragments that were observed to be more highly expressed under cabbage-associated conditions. Genes involved in carbohydrate, amino acid, and nucleic acid metabolism, motility and cell division, and transport were identified, as were a number of open reading frames (ORFs) encoding putative proteins with no known functions. Site-directed mutations in two ORFs encoding potential cell surface-associated proteins and a third ORF encoding a putative regulatory protein had no effect on the mutants' capacity to attach to fresh-cut cabbage. Although this study did not show clearly the impact of the differentially expressed genes on growth on cabbage, it is a first step in identifying some of the genetic factors that are potentially involved.
Impact of Phages on Two-Species Bacterial Communities
Authors: Harcombe W. R. , Bull J. J. 
Published: September 2005

ABSTRACTA long history of experimental work has shown that addition of bacteriophages to a monoculture of bacteria leads to only a temporary depression of bacterial levels. Resistant bacteria usually become abundant, despite reduced growth rates relative to those of phage-sensitive bacteria. This restoration of high bacterial density occurs even if the phages evolve to overcome bacterial resistance. We believe that the generality of this result may be limited to monocultures, in which the resistant bacteria do not face competition from bacterial species unaffected by the phage. As a simple case, we investigated the impact of phages attacking one species in a two-species culture of bacteria. In the absence of phages,Escherichia coliB andSalmonella entericaserovar Typhimurium were stably maintained during daily serial passage in glucose minimal medium (M9). When either of twoE. coli-specific phages (T7 or T5) was added to the mixed culture,E. colibecame extinct or was maintained at densities that were orders of magnitude lower than those before phage introduction, even though theE. colidensities with phage reached high levels whenSalmonellawas absent. In contrast, the addition of a phage that attacked onlySalmonella(SP6) led to transient decreases in the bacterial number whetherE. coliwas absent or present. These results suggest that phages can sometimes, although not always, provide long-term suppression of target bacteria.
Inhibition of NO
3
−
and NO
2
−
Reduction by Microbial Fe(III) Reduction: Evidence of a Reaction between NO
2
−
and Cell Surface-Bound Fe
2+
Authors: Coby Aaron J. , Picardal Flynn W. 
Published: September 2005

ABSTRACT

A recent study (D. C. Cooper, F. W. Picardal, A. Schimmelmann, and A. J. Coby, Appl. Environ. Microbiol. 69:3517-3525, 2003) has shown that NO
3
−
and NO
2
−
(NO
x
−
) reduction by
Shewanella putrefaciens
200 is inhibited in the presence of goethite. The hypothetical mechanism offered to explain this finding involved the formation of a Fe(III) (hydr)oxide coating on the cell via the surface-catalyzed, abiotic reaction between Fe
2+
and NO
2
−
. This coating could then inhibit reduction of NO
x
−
by physically blocking transport into the cell. Although the data in the previous study were consistent with such an explanation, the hypothesis was largely speculative. In the current work, this hypothesis was tested and its environmental significance explored through a number of experiments. The inhibition of ∼3 mM NO
3
−
reduction was observed during reduction of a variety of Fe(III) (hydr)oxides, including goethite, hematite, and an iron-bearing, natural sediment. Inhibition of oxygen and fumarate reduction was observed following treatment of cells with Fe
2+
and NO
2
−
, demonstrating that utilization of other soluble electron acceptors could also be inhibited. Previous adsorption of Fe
2+
onto
Paracoccus denitrificans
inhibited NO
x
−
reduction, showing that Fe(II) can reduce rates of soluble electron acceptor utilization by non-iron-reducing bacteria. NO
2
−
was chemically reduced to N
2
O by goethite or cell-sorbed Fe
2+
, but not at appreciable rates by aqueous Fe
2+
. Transmission and scanning electron microscopy showed an electron-dense, Fe-enriched coating on cells treated with Fe
2+
and NO
2
−
. The formation and effects of such coatings underscore the complexity of the biogeochemical reactions that occur in the subsurface.
Resistance of Marine Bacterioneuston to Solar Radiation
Authors: Agogué Hélène , Joux Fabien , Obernosterer Ingrid , Lebaron Philippe 
Published: September 2005

ABSTRACT

A total of 90 bacterial strains were isolated from the sea surface microlayer (i.e., bacterioneuston) and underlying waters (i.e., bacterioplankton) from two sites of the northwestern Mediterranean Sea. The strains were identified by sequence analysis, and growth recovery was investigated after exposure to simulated solar radiation. Bacterioneuston and bacterioplankton isolates were subjected to six different exposure times, ranging from 0.5 to 7 h of simulated noontime solar radiation. Following exposure, the growth of each isolate was monitored, and different classes of resistance were determined according to the growth pattern. Large interspecific differences among the 90 marine isolates were observed. Medium and highly resistant strains accounted for 41% and 22% of the isolates, respectively, and only 16% were sensitive strains. Resistance to solar radiation was equally distributed within the bacterioneuston and bacterioplankton. Relative contributions to the highly resistant class were 43% for γ-proteobacteria and 14% and 8% for α-proteobacteria and the
Cytophaga/Flavobacterium/Bacteroides
(CFB) group, respectively. Within the γ-proteobacteria, the
Pseudoalteromonas
and
Alteromonas
genera appeared to be highly resistant to solar radiation. The majority of the CFB group (76%) had medium resistance. Our study further provides evidence that pigmented bacteria are not more resistant to solar radiation than nonpigmented bacteria.
Survival of
Mycobacterium avium
subsp.
paratuberculosis
in Dam Water and Sediment
Authors: Whittington Richard J. , Marsh Ian B. , Reddacliff Leslie A. 
Published: September 2005

ABSTRACT

In a previous longitudinal study,
Mycobacterium avium
subsp.
paratuberculosis
survived for 55 weeks in fecal material in the shade, but for much shorter periods in exposed locations. In this experiment, the survival of the organism was studied in 250 liters of dam water and sediment in large water troughs that were placed in either a semiexposed location or in a shaded location and compared to survival in fecal material and soil in the shaded location. Survival in water and/or sediment in the shade was for up to 48 weeks compared to 36 weeks in the semiexposed location. Survival in sediment was 12 to 26 weeks longer than survival in the water column. Survival in soil and fecal material in the terrestrial environment in the shaded location was only 12 weeks. Although disturbance to sediment could not be ruled out as a factor, there was evidence of dormancy in both the water column and the sediment, since the organism could not be recovered for several months before again becoming detectable. The results suggest that water may be a significant reservoir of
M. avium
subsp.
paratuberculosis
infection. Further research on the biology of the organism in aquatic environments is warranted. Animal health authorities will need to provide appropriate advice to farmers to minimize exposure of livestock to potentially infected water sources. Survival of the organism in water destined for human consumption will need to be addressed if the organism is found to be involved in the etiology of Crohn's disease.
Enzyme-Coupled Assay for β-Xylosidase Hydrolysis of Natural Substrates
Authors: Wagschal Kurt , Franqui-Espiet Diana , Lee Charles C. , Robertson George H. , Wong Dominic W. S. 
Published: September 2005

ABSTRACT

We describe here a new enzyme-coupled assay for the quantitation of
d
-xylose using readily available enzymes that allows kinetic evaluation of hemicellulolytic enzymes using natural xylooligosaccharide substrates. Hydrogen peroxide is generated as an intermediary analyte, which allows flexibility in the choice of the chromophore or fluorophore used as the final reporter. Thus, we present
d
-xylose quantitation results for solution-phase assays performed with both the fluorescent reporter resorufin, generated from
N
-acetyl-3,7-dihydroxyphenoxazine (Amplex Red), and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), whose corresponding radical cation has an absorbance maximum at ∼400 nm. We also describe a useful solid-phase variation of the assay performed with the peroxidase substrate 3,3′-diaminobenzidine tetrahydrochloride, which produces an insoluble brown precipitate. In addition, kinetic parameters for hydrolysis of the natural substrates xylobiose and xylotriose were obtained using this assay for a glycosyl hydrolase family 39 β-xylosidase from
Thermoanaerobacterium
sp. strain JW/SL YS485 (Swiss-Prot accession no.
O30360
). At higher xylobiose substrate concentrations the enzyme showed an increase in the rate indicative of transglycosylation, while for xylotriose marked substrate inhibition was observed. At lower xylobiose concentrations
k
cat
was 2.7 ± 0.4 s
−1
,

K
m

was 3.3 ± 0.7 mM, and
k
cat
/

K
m

was 0.82 ± 0.21 mM
−1
· s
−1
. Nonlinear curve fitting to a substrate inhibition model showed that for xylotriose

K
i

was 1.7 ± 0.1 mM,
k
cat
was 2.0 ± 0.1 s
−1
,

K
m

was 0.144 ± 0.011 mM, and
k
cat
/

K
m

was 14 ± 1.3 mM
−1
· s
−1
.
Overexpression of an Anti-CD3 Immunotoxin Increases Expression and Secretion of Molecular Chaperone BiP/Kar2p byPichia pastoris
Authors: Liu Yuan Yi , Woo Jung Hee , Neville David M. 
Published: September 2005

ABSTRACTWe previously reported that the secretory capacity ofPichia pastorisis limited with respect to the secretion of a 96.5-kDa bivalent anti-CD3 immunotoxin; double-copy expression generated more translation products than single-copy expression but did not increase the secretion of the immunotoxin. InSaccharomyces cerevisiaeheterologous protein secretion has been reported to increase the expression of molecular chaperones, most prominently BiP/Kar2p. We therefore investigated the relationships between immunotoxin secretion and Kar2p expression inP. pastoris. We found that expression of the immunotoxin inP. pastorisincreased the expression of Kar2p to levels that surpassed the retrieval capacity of the cell, leading to secretion of Kar2p into the medium. The level of Kar2p secretion was correlated with the copy number of the immunotoxin gene. Intracellular Kar2p was found to bind exclusively to the unprocessed immunotoxin containing the prosequence of α-factor in the endoplasmic reticulum. These results show that Kar2p is intimately involved in immunotoxin secretion inP. pastoris. The limited capacity ofP. pastoristo retain a sufficiently high level of intracellular Kar2p may be a factor restricting the production of the immunotoxin.
Temporal Patterns of Nitrogenase Gene (
nifH
) Expression in the Oligotrophic North Pacific Ocean
Authors: Church Matthew J. , Short Cindy M. , Jenkins Bethany D. , Karl David M. , Zehr Jonathan P. 
Published: September 2005

ABSTRACT

Dinitrogen (N
2
)-fixing microorganisms (diazotrophs) play important roles in ocean biogeochemistry and plankton productivity. In this study, we examined the presence and expression of specific planktonic nitrogenase genes (
nifH
) in the upper ocean (0 to 175 m) at Station ALOHA in the oligotrophic North Pacific Ocean. Clone libraries constructed from reverse-transcribed PCR-amplified mRNA revealed six unique phylotypes. Five of the
nifH
phylotypes grouped with sequences from unicellular and filamentous cyanobacteria, and one of the phylotypes clustered with γ-proteobacteria. The cyanobacterial
nifH
phylotypes retrieved included two sequence types that phylogenetically grouped with unicellular cyanobacteria (termed groups A and B), several sequences closely related (97 to 99%) to
Trichodesmium
spp. and
Katagnymene spiralis
, and two previously unreported phylotypes clustering with heterocyst-forming
nifH
cyanobacteria. Temporal patterns of
nifH
expression were evaluated using reverse-transcribed quantitative PCR amplification of
nifH
gene transcripts. The filamentous and presumed unicellular group A cyanobacterial phylotypes exhibited elevated
nifH
transcription during the day, while members of the group B (closely related to
Crocosphaera watsonii
) unicellular phylotype displayed greater
nifH
transcription at night. In situ
nifH
expression by all of the cyanobacterial phylotypes exhibited pronounced diel periodicity. The γ-proteobacterial phylotype had low transcript abundance and did not exhibit a clear diurnal periodicity in
nifH
expression. The temporal separation of
nifH
expression by the various phylotypes suggests that open ocean diazotrophic cyanobacteria have unique in situ physiological responses to daily fluctuations of light in the upper ocean.
Occurrence and Relatedness of Vancomycin-Resistant Enterococci in Animals, Humans, and the Environment in Different European Regions
Authors: Kühn Inger , Iversen Aina , Finn Maria , Greko Christina , Burman Lars G. , Blanch Anicet R. , Vilanova Xavier , Manero Albert , Taylor Huw , Caplin Jonathan , Domínguez Lucas , Herrero Inmaculada A. , Moreno Miguel A. , Möllby Roland 
Published: September 2005

ABSTRACTVancomycin-resistant enterococcci (VRE) in Europe are thought to have emerged partly due to the use of the glycopeptide avoparcin in animal husbandry. We compared the occurrence of VRE in geographical regions of Europe in which until 1997 large amounts of avoparcin were used (Spain, United Kingdom, and Denmark) with the occurrence of VRE in Sweden, where avoparcin was banned in 1986. We also studied the relatedness between VRE strains from different regions and habitats. In total, 2,580 samples were collected from humans, animals, and the environment (soil, sewage, recipient water). VRE resistant to 20 μg/ml vancomycin were identified in 8.2% of the samples and were found most frequently in raw and treated urban sewage samples (means, 71% and 36% of the samples, respectively), pig manure (17%), and hospital sewage (16%). The proportions of VRE-positive sewage samples were similar in Sweden, Spain, and the United Kingdom, whereas pig feces and manure were more often positive in Spain than in Sweden (30% versus 1%). Most VRE wereEnterococcus faeciumcarryingvanA, and computerized biochemical phenotyping of the isolates of different ecological origins showed a high degree of polyclonality. In conclusion, it seems that animal-associated VRE probably reflect the former use of avoparcin in animal production, whereas VRE in human-associated samples may be a result of antibiotic use in hospitals. Since there seems to be a reservoir of the resistance genes in all countries studied, precautions must be taken to limit the use of antibiotics and antibiotic-like feed additives.
Effect of Chlorine Dioxide Gas on Fungi and Mycotoxins Associated with Sick Building Syndrome
Authors: Wilson S. C. , Wu C. , Andriychuk L. A. , Martin J. M. , Brasel T. L. , Jumper C. A. , Straus D. C. 
Published: September 2005

ABSTRACT

The growth of indoor molds and their resulting products (e.g., spores and mycotoxins) can present health hazards for human beings. The efficacy of chlorine dioxide gas as a fumigation treatment for inactivating sick building syndrome-related fungi and their mycotoxins was evaluated. Filter papers (15 per organism) featuring growth of
Stachybotrys chartarum
,
Chaetomium globosum
,
Penicillium chrysogenum
, and
Cladosporium cladosporioides
were placed in gas chambers containing chlorine dioxide gas at either 500 or 1,000 ppm for 24 h.
C. globosum
was exposed to the gas both as colonies and as ascospores without asci and perithecia. After treatment, all organisms were tested for colony growth using an agar plating technique. Colonies of
S. chartarum
were also tested for toxicity using a yeast toxicity assay with a high specificity for trichothecene mycotoxins. Results showed that chlorine dioxide gas at both concentrations completely inactivated all organisms except for
C. globosum
colonies which were inactivated an average of 89%. More than 99% of ascospores of
C. globosum
were nonculturable. For all ascospore counts, mean test readings were lower than the controls (
P
< 0.001), indicating that some ascospores may also have been destroyed. Colonies of
S. chartarum
were still toxic after treatment. These data show that chlorine dioxide gas can be effective to a degree as a fumigant for the inactivation of certain fungal colonies, that the perithecia of
C. globosum
can play a slightly protective role for the ascospores and that
S. chartarum
, while affected by the fumigation treatment, still remains toxic.
Extracellular DNA in Single- and Multiple-Species Unsaturated Biofilms
Authors: Steinberger R. E. , Holden P. A. 
Published: September 2005

ABSTRACT

The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that
Pseudomonas aeruginosa
unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423, 2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for
P. aeruginosa
biofilms. Significantly more eDNA was produced in
P. aeruginosa
and
Pseudomonas putida
biofilms than in
Rhodococcus erythropolis
or
Variovorax paradoxus
biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA.