bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments
Authors: Shi Y. , Zwolinski M. D. , Schreiber M. E. , Bahr J. M. , Sewell G. W. , Hickey W. J. 
Published: December 2019

ABSTRACT

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly
Bacteria
;
Eucarya
and
Archaea
were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-
Proteobacteria
(B+G), 31 to 35% α-
Proteobacteria
(ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly
Bacteria
(83 to 101%) and lacked detectable
Archaea
but differed in that a small fraction (2 to 8%) of
Eucarya
was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the
Bacteria
community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems.
Anaerobic Dehalogenation of Hydroxylated Polychlorinated Biphenyls by
Desulfitobacterium dehalogenans
Authors: Wiegel Juergen , Zhang Xiaoming , Wu Qingzhong 
Published: December 2019

ABSTRACT

Ten years after reports on the existence of anaerobic dehalogenation of polychlorinated biphenyls (PCBs) in sediment slurries, we report here on the rapid reductive dehalogenation of
para
-hydroxylated PCBs (HO-PCBs), the excreted main metabolites of PCB in mammals, which can exhibit estrogenic and antiestrogenic activities in humans. The anaerobic bacterium
Desulfitobacterium dehalogenans
completely dehalogenates all flanking chlorines (chlorines in
ortho
position to the
para
-hydroxyl group) from congeners such as 3,3′,5,5′-tetrachloro-4,4′-dihydroxybiphenyl.
Microbial Degradation of Octamethylcyclotetrasiloxane
Authors: Grümping R. , Michalke K. , Hirner A. V. , Hensel R. 
Published: December 2019

ABSTRACT
The microbial degradation of low-molecular-weight polydimethylsiloxanes was investigated through laboratory experiments. Octamethylcyclotetrasiloxane was found to be biodegraded under anaerobic conditions in composted sewage sludge, as monitored by the occurrence of the main polydimethylsiloxane degradation product, dimethylsilanediol, compared to that found in experiments with sterilized control samples.
High-Resolution Genotyping of
Campylobacter
Strains Isolated from Poultry and Humans with Amplified Fragment Length Polymorphism Fingerprinting
Authors: Duim Birgitta , Wassenaar Trudy M. , Rigter Alan , Wagenaar Jaap 
Published: December 2019

ABSTRACT

For epidemiological studies of
Campylobacter
infections, molecular typing methods that can differentiate campylobacters at the strain level are needed. In this study we used a recently developed genotyping method, amplified fragment length polymorphism (AFLP), which is based on selective amplification of restriction fragments of chromosomal DNA, for genetic typing of
Campylobacter jejuni
and
Campylobacter coli
strains derived from humans and poultry. We developed an automated AFLP fingerprinting method in which restriction endonucleases
Hin
dIII and
Hha
I were used in combination with one set of selective PCR primers. This method resulted in evenly distributed band patterns for amplified fragments ranging from 50 to 500 bp long. The discriminatory power of AFLP was assessed with a
C. jejuni
strain, an isogenic flagellin mutant, and distinct
C. jejuni
strains having known pulsed-field gel electrophoresis and
fla
PCR-restriction fragment length polymorphism genotypes. Unrelated
C. jejuni
strains produced heterogeneous patterns, whereas genetically related strains produced similar AFLP patterns. Twenty-five
Campylobacter
strains obtained from poultry farms in The Netherlands grouped in three
C. jejuni
clusters that were separate from a
C. coli
cluster. The band patterns of 10
C. jejuni
strains isolated from humans were heterogeneous, and most of these strains grouped with poultry strains. Our results show that AFLP analysis can distinguish genetically unrelated strains from genetically related strains of
Campylobacter
species. However, desirable genetically related strains can be differentiated by using other genotyping methods. We concluded that automated AFLP analysis is an attractive tool which can be used as a primary method for subtyping large numbers of
Campylobacter
strains and is extremely useful for epidemiological investigations.
Lethality of a Heat- and Phosphate-Catalyzed Glucose By-Product to
Escherichia coli
O157:H7 and Partial Protection Conferred by the
rpoS
Regulon
Authors: Byrd Jeffrey J. , Cheville Ann M. , Bose Jeffrey L. , Kaspar Charles W. 
Published: December 2019

ABSTRACT

A by-product of glucose produced during sterilization (121°C, 15 lb/in
2
, 15 min) at neutral pH and in the presence of phosphate (i.e., phosphate-buffered saline) was bactericidal to
Escherichia coli
O157:H7 (ATCC 43895). Other six-carbon (fructose and galactose) and five-carbon (arabinose, ribose, and xylose) reducing sugars also produced a toxic by-product under the same conditions. Fructose and the five-carbon sugars yielded the most bactericidal activity. Glucose concentrations of 1% (wt/vol) resulted in a 99.9% decline in the CFU of stationary-phase cells per milliliter in 2 days at 25°C. An
rpoS
mutant (pRR10::
rpoS
) of strain 43895 (FRIK 816-3) was significantly (
P
< 0.001) more sensitive to the glucose-phosphate by-product than the parent strain, as glucose concentrations from 0.05 to 0.25% resulted in a 2- to 3-log
10
reduction in CFU per milliliter in 2 days at 25°C. Likewise, log-phase cells of the wild-type strain, 43895, were significantly more sensitive (
P
< 0.001) to the glucose-phosphate by-product than were stationary-phase cells, which is consistent with the stability of
rpoS
and the regulation of
rpoS
-regulated genes. The bactericidal effect of the glucose-phosphate by-product was reduced when strains ATCC 43895 and FRIK 816-3 were incubated at a low temperature (4°C). Also, growth in glucose-free medium (i.e., nutrient broth) did not alleviate the sensitivity to the glucose-phosphate by-product and excludes the possibility of substrate-accelerated death as the cause of the bactericidal effect observed. The glucose-phosphate by-product was also bactericidal to
Salmonella typhimurium
,
Shigella dysenteriae
, and a
Klebsiella
sp. Attempts to identify the glucose-phosphate by-product were unsuccessful. These studies demonstrate the production of a glucose-phosphate by-product bactericidal to
E. coli
O157:H7 and the protective effects afforded by
rpoS
-regulated gene products. Additionally, the detection of sublethally injured bacteria may be compromised by the presence of this by-product in recovery media.
Vertical Distribution of Methanogens in the Anoxic Sediment of Rotsee (Switzerland)
Authors: Zepp Falz K. , Holliger C. , Großkopf R. , Liesack W. , Nozhevnikova A. N. , Müller B. , Wehrli B. , Hahn D. 
Published: December 2019

ABSTRACTAnoxic sediments from Rotsee (Switzerland) were analyzed for the presence and diversity of methanogens by using molecular tools and for methanogenic activity by using radiotracer techniques, in addition to the measurement of chemical profiles. After PCR-assisted sequence retrieval of the 16S rRNA genes (16S rDNA) from the anoxic sediment of Rotsee, cloning, and sequencing, a phylogenetic analysis identified two clusters of sequences and four separated clones. The sequences in cluster 1 grouped with those ofMethanosaetaspp., whereas the sequences in cluster 2 comprised the methanogenic endosymbiont ofPlagiopyla nasuta. Discriminative oligonucleotide probes were constructed against both clusters and two of the separated clones. These probes were used subsequently for the analysis of indigenous methanogens in a core of the sediment, in addition to domain-specific probes against members of the domainsBacteriaandArchaeaand the fluorescent stain 4′,6-diamidino-2-phenylindole (DAPI), by fluorescent in situ hybridization. After DAPI staining, the highest microbial density was obtained in the upper sediment layer; this density decreased with depth from (1.01 ± 0.25) × 1010to (2.62 ± 0.58) × 1010cells per g of sediment (dry weight). This zone corresponded to that of highest metabolic activity, as indicated by the ammonia, alkalinity, and pH profiles, whereas the methane profile was constant. Probes Eub338 and Arch915 detected on average 16 and 6% of the DAPI-stained cells as members of the domainsBacteriaandArchaea, respectively. Probe Rotcl1 identified on average 4% of the DAPI-stained cells asMethanosaetaspp., which were present throughout the whole core. In contrast, probe Rotcl2 identified only 0.7% of the DAPI-stained cells as relatives of the methanogenic endosymbiont ofP. nasuta, which was present exclusively in the upper 2 cm of the sediment. Probes Rotp13 and Rotp17 did not detect any cells. The spatial distribution of the two methanogenic populations corresponded well to the methane production rates determined by incubation with either [14C]acetate or [14C]bicarbonate. Methanogenesis from acetate accounted for almost all of the total methane production, which concurs with the predominance of acetoclasticMethanosaetaspp. that represented on average 91% of the archaeal population. Significant hydrogenotrophic methanogenesis was found only in the organically enriched upper 2 cm of the sediment, where the probably hydrogenotrophic relatives of the methanogenic endosymbiont ofP. nasuta, accounting on average for 7% of the archaeal population, were also detected.
Use of Antibacterial Agents To Elucidate the Etiology of Juvenile Oyster Disease (JOD) in
Crassostrea virginica
and Numerical Dominance of an α-Proteobacterium in JOD-Affected Animals
Authors: Boettcher Katherine J. , Barber Bruce J. , Singer John T. 
Published: December 2019

ABSTRACT

Since 1988, juvenile oyster disease (JOD) has resulted in high seasonal losses of cultured Eastern oysters (
Crassostrea virginica
) in the Northeast. Although the cause of JOD remains unknown, most evidence is consistent with either a bacterial or a protistan etiology. For the purpose of discerning between these hypotheses, the antibacterial antibiotics norfloxacin and sulfadimethoxine-ormetoprim (Romet-B) were tested for the ability to delay the onset of JOD mortality and/or reduce the JOD mortality of cultured juvenile
C. virginica
. Hatchery-produced
C. virginica
seed were exposed in triplicate groups of 3,000 animals each to either norfloxacin, sulfadimethoxine-ormetoprim, or filter-sterilized seawater (FSSW) and deployed in floating trays on the Damariscotta River of Maine on 17 July 1997. Each week thereafter, a subset of animals from each group was reexposed to the assigned treatment. Repeated immersion in either a sulfadimethoxine-ormetoprim or a norfloxacin solution resulted in a delay in the onset of JOD mortality in treated animals and reduced weekly mortality rates. Weekly treatments with either norfloxacin or sulfadimethoxine-ormetoprim also resulted in a statistically significant reduction in cumulative mortality (55 and 67% respectively) compared to animals treated weekly with FSSW (81%) or those that had received only a single treatment with either norfloxacin, sulfadimethoxine-ormetoprim, or FSSW (77, 84, and 82%, respectively). Bacteriological analyses revealed a numerically dominant bacterium in those animals with obvious signs of JOD. Sequence analysis of the 16S rRNA gene from these bacteria indicates that they are a previously undescribed species of marine α-proteobacteria.
Characterization of
Pseudomonas aeruginosa
Bacteriophage UNL-1, a Bacterial Virus with a Novel UV-A-Inducible DNA Damage Reactivation Phenotype
Authors: Shaffer Julie J. , Jacobsen Lisa M. , Schrader John O. , Lee Kit W. , Martin Eugene L. , Kokjohn Tyler A. 
Published: December 2019

ABSTRACT

UNL-1, a lytic virus of
Pseudomonas aeruginosa
, was observed to express a novel inducible DNA damage reactivation activity in UV-A-irradiated
P. aeruginosa
host cells. The expression of bacteriophage reactivation was quantified in hosts exposed to either UV-C or UV-A radiation. While reactivation of UV-C-damaged UNL-1 was not inducible in UV-C-irradiated host cells, an approximately 13-fold induction was observed in UV-A-irradiated host cells. When host cells were exposed to sunlight, reactivation of damaged UNL-1 virus increased eightfold. The UV-A induction of UNL-1 DNA damage reactivation was supported in hosts lacking
recA
gene function. This report is the first description of a
recA
-independent, UV-inducible virus DNA damage repair system. Our findings suggest that a combination of both host and virus DNA repair processes contribute to the persistence and sustained replication of some bacterial viruses in aquatic environments.
Enhancement of Solubilization and Biodegradation of Polyaromatic Hydrocarbons by the Bioemulsifier Alasan
Authors: Barkay T. , Navon-Venezia S. , Ron E. Z. , Rosenberg E. 
Published: December 2019

ABSTRACT

Alasan, a high-molecular-weight bioemulsifier complex of an anionic polysaccharide and proteins that is produced by
Acinetobacter radioresistens
KA53 (S. Navon-Venezia, Z. Zosim, A. Gottlieb, R. Legmann, S. Carmeli, E. Z. Ron, and E. Rosenberg, Appl. Environ. Microbiol. 61:3240–3244, 1995), enhanced the aqueous solubility and biodegradation rates of polyaromatic hydrocarbons (PAHs). In the presence of 500 μg of alasan ml
−1
, the apparent aqueous solubilities of phenanthrene, fluoranthene, and pyrene were increased 6.6-, 25.7-, and 19.8-fold, respectively. Physicochemical characterization of the solubilization activity suggested that alasan solubilizes PAHs by a physical interaction, most likely of a hydrophobic nature, and that this interaction is slowly reversible. Moreover, the increase in apparent aqueous solubility of PAHs does not depend on the conformation of alasan and is not affected by the formation of multimolecular aggregates of alasan above its saturation concentration. The presence of alasan more than doubled the rate of [
14
C]fluoranthene mineralization and significantly increased the rate of [
14
C]phenanthrene mineralization by
Sphingomonas paucimobilis
EPA505. The results suggest that alasan-enhanced solubility of hydrophobic compounds has potential applications in bioremediation.
Development of a Self-Cloning System for
Actinomadura verrucosospora
and Identification of Polyketide Synthase Genes Essential for Production of the Angucyclic Antibiotic Pradimicin
Authors: Dairi Tohru , Hamano Yoshimitsu , Furumai Tamotsu , Oki Toshikazu 
Published: December 2019

ABSTRACT

A self-cloning system for
Actinomadura verrucosospora
, a producer of the angucyclic antibiotic pradimicin A (PRM A), has been developed. The system is based on reproducible and reliable protoplasting and regeneration conditions for
A. verrucosospora
and a novel plasmid vector that consists of a replicon from a newly found
Actinomadura
plasmid and a selectable marker cloned from the
Actinomadura
strain. The system has an efficiency of more than 10
5
CFU/microgram of DNA. Using this system, we have cloned and identified the polyketide synthase (PKS) genes essential for PRM A biosynthesis from
A. verrucosospora
. Nucleotide sequence analysis of the 3.5-kb
Sal
I-
Sph
I fragment showed that ketosynthase subunits (open reading frame 1 [ORF1] and ORF2) of the essential PKS genes have strong similarities (59 to 89%) to those for angucyclic antibiotic biosynthesis.
Occurrence, Diversity, and Pathogenicity of Halophilic
Vibrio
spp. and Non-O1
Vibrio cholerae
from Estuarine Waters along the Italian Adriatic Coast
Authors: Barbieri Elena , Falzano Loredana , Fiorentini Carla , Pianetti Anna , Baffone Wally , Fabbri Alessia , Matarrese Paola , Casiere Annarita , Katouli Mohammad , Kühn Inger , Möllby Roland , Bruscolini Francesca , Donelli Gianfranco 
Published: December 2019

ABSTRACT

The occurrence, diversity, and pathogenicity of
Vibrio
spp. were investigated in two estuaries along the Italian Adriatic coast.
Vibrio alginolyticus
was the predominant species, followed by
Vibrio parahaemolyticus
, non-O1
Vibrio cholerae
, and
Vibrio vulnificus
. By using a biochemical fingerprinting method, all isolates were grouped into nine phenotypes with similarity levels of 75 to 97.5%. The production of toxins capable of causing cytoskeleton-dependent changes was detected in a large number of
Vibrio
strains. These findings indicate a significant presence of potentially pathogenic
Vibrio
strains along the Adriatic coast.
Specificity of
Lactococcus lactis
subsp.
cremoris
SK11 Proteinase, Lactocepin III, in Low-Water-Activity, High-Salt-Concentration Humectant Systems and Its Stability Compared with That of Lactocepin I
Authors: Reid Julian R. , Coolbear Tim 
Published: December 2019

ABSTRACT

Marked changes in the specificity of hydrolysis of α
s1
-, β-, and κ-caseins by lactocepin III from
Lactococcus lactis
subsp.
cremoris
SK11 were found in humectant systems giving the equivalent water activity (a
w
) and salt concentration of cheddar cheese. Correlations were noted between certain peptides produced by the activity of lactocepin III in the humectant systems and peptides found in cheddar cheese. The stability of lactocepin III was compared with that of lactocepin I from
L. lactis
subsp.
cremoris
HP in the humectant systems at different pHs. Significant differences between the stability of each of the lactocepin types were evident. The relationship between stability and humectant type, a
w
, pH, and NaCl concentration was complex. Nevertheless, in those systems where a
w
, pH, and NaCl concentration were equivalent to those in cheddar cheese, lactocepin I was generally more stable than lactocepin III. It was concluded that differences in the specificity and/or stability of various lactocepin types are likely to persist in cheese itself and therefore potentially contribute to differences in the peptide composition of ripened cheese.
Visualization and Modelling of the Thermal Inactivation of Bacteria in a Model Food
Authors: Bellara Sanjay R. , Fryer Peter J. , McFarlane Caroline M. , Thomas Colin R. , Hocking Paul M. , Mackey Bernard M. 
Published: December 2019

ABSTRACT

A large number of incidents of food poisoning have been linked to undercooked meat products. The use of mathematical modelling to describe heat transfer within foods, combined with data describing bacterial thermal inactivation, may prove useful in developing safer food products while minimizing thermal overprocessing. To examine this approach, cylindrical agar blocks containing immobilized bacteria (
Salmonella typhimurium
and
Brochothrix thermosphacta
) were used as a model system in this study. The agar cylinders were subjected to external conduction heating by immersion in a water bath. They were then incubated, sliced open, and examined by image analysis techniques for regions of no bacterial growth. A finite-difference scheme was used to model thermal conduction and the consequent bacterial inactivation. Bacterial inactivation rates were modelled with values for the time required to reduce bacterial number by 90% (D) and the temperature increase required to reduce D by 90% taken from the literature. Model simulation results agreed well with experimental results for both bacteria, demonstrating the utility of the technique.
Identification and Characterization of a Flagellin Gene from the Endosymbiont of the Hydrothermal Vent Tubeworm
Riftia pachyptila
Authors: Millikan Deborah S. , Felbeck Horst , Stein Jeffrey L. 
Published: December 2019

ABSTRACT

The bacterial endosymbionts of the hydrothermal vent tubeworm
Riftia pachyptila
play a key role in providing their host with fixed carbon. Results of prior research suggest that the symbionts are selected from an environmental bacterial population, although a free-living form has been neither cultured from nor identified in the hydrothermal vent environment. To begin to assess the free-living potential of the symbiont, we cloned and characterized a flagellin gene from a symbiont fosmid library. The symbiont
fliC
gene has a high degree of homology with other bacterial flagellin genes in the amino- and carboxy-terminal regions, while the central region was found to be nonconserved. A sequence that was homologous to that of a consensus ς
28
RNA polymerase recognition site lay upstream of the proposed translational start site. The symbiont protein was expressed in
Escherichia coli
, and flagella were observed by electron microscopy. A 30,000-
M
r
protein subunit was identified in whole-cell extracts by Western blot analysis. These results provide the first direct evidence of a motile free-living stage of a chemoautotrophic symbiont and support the hypothesis that the symbiont of
R. pachyptila
is acquired with each new host generation.