bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Organization and Localization of the
pufLM
Genes of the Photosynthesis Reaction Center in Phylogenetically Diverse Marine
Alphaproteobacteria
Authors: Pradella Silke , Allgaier Martin , Hoch Christa , Päuker Orsola , Stackebrandt Erko , Wagner-Döbler Irene 
Published: June 2004

ABSTRACT

Genome organization, plasmid content and localization of the
pufLM
genes of the photosynthesis reaction center were studied by pulsed-field gel electrophoresis (PFGE) in marine phototrophic
Alphaproteobacteria
. Both anaerobic phototrophs (
Rhodobacter veldkampii
and
Rhodobacter sphaeroides
) and strictly aerobic anoxygenic phototrophs from the
Roseobacter
-
Sulfitobacter
-
Silicibacter
clade (
Roseivivax halodurans
,
Roseobacter litoralis
,
Staleya guttiformis
,
Roseovarius tolerans
, and five new strains isolated from dinoflagellate cultures) were investigated. The complete genome size was estimated for
R. litoralis
DSM6996
T
to be 4,704 kb, including three linear plasmids. All strains contained extrachromosomal elements of various conformations (linear or circular) and lengths (between 4.35 and 368 kb). In strain DFL-12, a member of a putative new genus isolated from a culture of the toxic dinoflagellate
Prorocentrum lima
, seven linear plasmids were found, together comprising 860 kb of genetic information. Hybridization with probes against the
pufLM
genes of the photosynthesis gene cluster after Southern transfer of the genomic DNAs showed these genes to be located on a linear plasmid of 91 kb in
R. litoralis
and on a linear plasmid of 120 kb in
S. guttiformis
, theoretically allowing their horizontal transfer. In all other strains, the
pufLM
genes were detected on the bacterial chromosome. The large number and significant size of the linear plasmids found especially in isolates from dinoflagellates might account for the metabolic versatility and presumed symbiotic association with eukaryotic hosts in these bacteria.
Dimethylsulfoniopropionate Metabolism by
Pfiesteria
-Associated
Roseobacter
spp
Authors: Miller Todd R. , Belas Robert 
Published: June 2004

ABSTRACT

The
Roseobacter
clade of marine bacteria is often found associated with dinoflagellates, one of the major producers of dimethylsulfoniopropionate (DMSP). In this study, we tested the hypothesis that
Roseobacter
species have developed a physiological relationship with DMSP-producing dinoflagellates mediated by the metabolism of DMSP. DMSP was measured in
Pfiesteria
and
Pfiesteria
-like (
Cryptoperidiniopsis
) dinoflagellates, and the identities and metabolic potentials of the associated
Roseobacter
species to degrade DMSP were determined. Both
Pfiesteria piscicida
and
Pfiesteria shumwayae
produce DMSP with an average intracellular concentration of 3.8 μM. Cultures of
P. piscicida
or
Cryptoperidiniopsis
sp. that included both the dinoflagellates and their associated bacteria rapidly catabolized 200 μM DMSP (within 30 h), and the rate of catabolism was much higher for
P. piscicida
cultures than for
P. shumwayae
cultures. The community of bacteria from
P. piscicida
and
Cryptoperidiniopsis
cultures degraded DMSP with the production of dimethylsulfide (DMS) and acrylate, followed by 3-methylmercaptopropionate (MMPA) and methanethiol (MeSH). Four DMSP-degrading bacteria were isolated from the
P. piscicida
cultures and found to be taxonomically related to
Roseobacter
species. All four isolates produced MMPA from DMSP. Two of the strains also produced MeSH and DMS, indicating that they are capable of utilizing both the lyase and demethylation pathways. The diverse metabolism of DMSP by the dinoflagellate-associated
Roseobacter
spp. offers evidence consistent with a hypothesis that these bacteria benefit from association with DMSP-producing dinoflagellates.
Biomass Content Governs Fermentation Rate in Nitrogen-Deficient Wine Musts
Authors: Varela Cristian , Pizarro Francisco , Agosin Eduardo 
Published: June 2004

ABSTRACTProblematic fermentations are common in the wine industry. Assimilable nitrogen deficiency is the most prevalent cause of sluggish fermentations and can reduce fermentation rates significantly. A lack of nitrogen diminishes a yeast's metabolic activity, as well as the biomass yield, although it has not been clear which of these two interdependent factors is more significant in sluggish fermentations. Under winemaking conditions with different initial nitrogen concentrations, metabolic flux analysis was used to isolate the effects. We quantified yeast physiology and identified key metabolic fluxes. We also performed cell concentration experiments to establish how biomass yield affects the fermentation rate. Intracellular analysis showed that trehalose accumulation, which is highly correlated with ethanol production, could be responsible for sustaining cell viability in nitrogen-poor musts independent of the initial assimilable nitrogen content. Other than the higher initial maintenance costs in sluggish fermentations, the main difference between normal and sluggish fermentations was that the metabolic flux distributions in nitrogen-deficient cultures revealed that the specific sugar uptake rate was substantially lower. The results of cell concentration experiments, however, showed that in spite of lower sugar uptake, adding biomass from sluggish cultures not only reduced the time to finish a problematic fermentation but also was less likely to affect the quality of the resulting wine as it did not alter the chemistry of the must.
Evolutionary Relationships of Primary Prokaryotic Endosymbionts of Whiteflies and Their Hosts
Authors: Thao MyLo Ly , Baumann Paul 
Published: June 2004

ABSTRACTWhiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are plant sap-sucking insects that harbor prokaryotic primary endosymbionts (P-endosymbionts) within specialized cells located in their body cavity. Four-kilobase DNA fragments containing 16S-23S ribosomal DNA (rDNA) were amplified from the P-endosymbiont of 24 whiteflies from 22 different species of 2 whitefly subfamilies. In addition, 3-kb DNA fragments containing mitochondrialcytB,nd1, and large-subunit rDNA (LrDNA) were amplified from 17 whitefly species. Comparisons of the P-endosymbiont (16S-23S rDNA) and host (cytB-nd1-LrDNA) phylogenetic trees indicated overall congruence consistent with a single infection of a whitefly ancestor with a bacterium and subsequent cospeciation (cocladogenesis) of the host and the P-endosymbiont. On the basis of both the P-endosymbiont and host trees, the whiteflies could be subdivided into at least five clusters. The major subdivision was between the subfamiliesAleyrodinaeandAleurodicinae. Unlike the P-endosymbionts of may other insects, the P-endosymbionts of whiteflies were related toPseudomonasand possibly to the P-endosymbionts of psyllids. The lineage consisting of the P-endosymbionts of whiteflies is given the designation “CandidatusPortiera” gen. nov., with a single species, “CandidatusPortiera aleyrodidarum” sp. nov.
Cloning, Sequencing, and Characterization of a Heat- and Alkali-Stable Type I Pullulanase from
Anaerobranca gottschalkii
Authors: Bertoldo Costanzo , Armbrecht Martin , Becker Fiona , Schäfer Thomas , Antranikian Garabed , Liebl Wolfgang 
Published: June 2004

ABSTRACT

The gene encoding a type I pullulanase was identified from the genome sequence of the anaerobic thermoalkaliphilic bacterium
Anaerobranca gottschalkii
. In addition, the homologous gene was isolated from a gene library of
Anaerobranca horikoshii
and sequenced. The proteins encoded by these two genes showed 39% amino acid sequence identity to the pullulanases from the thermophilic anaerobic bacteria
Fervidobacterium pennivorans
and
Thermotoga maritima
. The pullulanase gene from
A. gottschalkii
(encoding 865 amino acids with a predicted molecular mass of 98 kDa) was cloned and expressed in
Escherichia coli
strain BL21(DE3) so that the protein did not have the signal peptide. Accordingly, the molecular mass of the purified recombinant pullulanase (rPulAg) was 96 kDa. Pullulan hydrolysis activity was optimal at pH 8.0 and 70°C, and under these physicochemical conditions the half-life of rPulAg was 22 h. By using an alternative expression strategy in
E. coli
Tuner(DE3)(pLysS), the pullulanase gene from
A. gottschalkii
, including its signal peptide-encoding sequence, was cloned. In this case, the purified recombinant enzyme was a truncated 70-kDa form (rPulAg′). The N-terminal sequence of purified rPulAg′ was found 252 amino acids downstream from the start site, presumably indicating that there was alternative translation initiation or N-terminal protease cleavage by
E. coli
. Interestingly, most of the physicochemical properties of rPulAg′ were identical to those of rPulAg. Both enzymes degraded pullulan via an endo-type mechanism, yielding maltotriose as the final product, and hydrolytic activity was also detected with amylopectin, starch, β-limited dextrins, and glycogen but not with amylose. This substrate specificity is typical of type I pullulanases. rPulAg was inhibited by cyclodextrins, whereas addition of mono- or bivalent cations did not have a stimulating effect. In addition, rPulAg′ was stable in the presence of 0.5% sodium dodecyl sulfate, 20% Tween, and 50% Triton X-100. The pullulanase from
A. gottschalkii
is the first thermoalkalistable type I pullulanase that has been described.
Identification of Sigma Factor σB-Controlled Genes and Their Impact on Acid Stress, High Hydrostatic Pressure, and Freeze Survival inListeria monocytogenesEGD-e
Authors: Wemekamp-Kamphuis Henrike H. , Wouters Jeroen A. , de Leeuw Patrick P. L. A. , Hain Torsten , Chakraborty Trinad , Abee Tjakko 
Published: June 2004

ABSTRACTThe gene encoding the alternative sigma factor σBinListeria monocytogenesis induced upon exposure of cells to several stresses. In this study, we investigated the impact of asigBnull mutation on the survival ofL. monocytogenesEGD-e at low pH, during high-hydrostatic-pressure treatment, and during freezing. The survival of ΔsigBmutant exponential-phase cells at pH 2.5 was 10,000-fold lower than the survival of EGD-e wild-type cells. Moreover, the ΔsigBmutant failed to show an acid tolerance response. Upon preexposure for 1 h to pH 4.5, the survival at pH 2.5 was 100,000-fold lower for the ΔsigBmutant than for the wild type. The glutamate decarboxylase (GAD) acid resistance system is important in survival and adaptation ofL. monocytogenesin acidic conditions. The σBdependence of thegadgenes (gadA,gadB,gadC,gadD, andgadE) was analyzed in silico. Putative σB-dependent promoter sites were found upstream of thegadCBoperon (encoding a glutamate/γ-aminobutyrate antiporter and a glutamate decarboxylase, respectively) and thelmo2434gene (gadD, encoding a putative glutamate decarboxylase). Reverse transcriptase PCR revealed that expression of thegadCBoperon and expression ofgadDare indeed σBdependent. In addition, a proteomics approach was used to analyze the protein expression profiles upon acid exposure. Although the GAD proteins were not recovered, nine proteins accumulated in the wild type but not in the ΔsigBstrain. These proteins included Pfk, GalE, ClpP, and Lmo1580. Exposure to pH 4.5, in order to preload cells with active σBand consequently with σB-dependent general stress proteins, also provided considerable protection against high-hydrostatic-pressure treatment and freezing. The combined data argue that the expression of σB-dependent genes providesL. monocytogeneswith nonspecific multiple-stress resistance that may be relevant for survival in the natural environment as well as during food processing.
Syntrophic-Methanogenic Associations along a Nutrient Gradient in the Florida Everglades
Authors: Chauhan Ashvini , Ogram Andrew , Reddy K. R. 
Published: June 2004

ABSTRACT

Nutrient runoff from the Everglades Agricultural Area resulted in a well-documented gradient of phosphorus concentrations in soil and water, with concomitant ecosystem-level changes, in the northern Florida Everglades. It was recently reported that sulfate-reducing prokaryote assemblage composition, numbers, and activities are dependent on position along the gradient (H. Castro, K. R. Reddy, and A. Ogram, Appl. Environ. Microbiol.
68:
6129-6137, 2002). The present study utilized a combination of culture- and non-culture-based approaches to study differences in composition of assemblages of syntrophic and methanogenic microbial communities in eutrophic, transition, and oligotrophic areas along the phosphorus gradient. Methanogenesis rates were much higher in eutrophic and transition regions, and sequence analysis of 16S rRNA gene clone libraries constructed from samples taken from these regions revealed differences in composition and activities of syntroph-methanogen consortia. Methanogens from eutrophic and transition regions were almost exclusively composed of hydrogenotrophic methanogens, with approximately 10,000-fold-greater most probable numbers of hydrogenotrophs than of acetotrophs. Most cultivable strains from eutrophic and transition regions clustered within novel lineages. In non-culture-based studies to enrich syntrophs, most bacterial and archaeal clones were either members of novel lineages or closely related to uncultivated environmental clones. Novel cultivable
Methanosaeta
sp. and fatty acid-oxidizing bacteria related to the genera
Syntrophomonas
and
Syntrophobacter
were observed in microcosms containing soil from eutrophic regions, and different lines of evidence indicated the existence of novel syntrophic association in eutrophic regions.
Detection and Quantification of Airborne Conidia of
Fusarium circinatum
, the Causal Agent of Pine Pitch Canker, from Two California Sites by Using a Real-Time PCR Approach Combined with a Simple Spore Trapping Method
Authors: Schweigkofler Wolfgang , O'Donnell Kerry , Garbelotto Matteo 
Published: June 2004

ABSTRACT

Pinus radiata
(Monterey pine), a tree native to coastal California and Mexico, is widely planted worldwide for timber production. A major threat to Monterey pine plantations is the fungal disease pine pitch canker, caused by
Fusarium circinatum
(
Hypocreales
). We present a novel trapping approach using filter paper in combination with a rapid molecular method to detect the presence of inoculum in the air. The assay is also useful for diagnosing the presence of the pathogen on plants. The test is based on the
F. circinatum
specific primer pair CIRC1A-CIRC4A, which amplifies a 360-bp DNA fragment in the intergenic spacer region of the nuclear ribosomal operon. Real-time PCR was used to calculate the number of fungal spores present in each reaction mixture by comparing the threshold cycle (Ct) of unknown spore samples to the Ct values of standards with known amounts of
F. circinatum
spores. The filter paper method allows prolonged and more sensitive spore sampling in the field compared to traditional traps using petri dishes filled with selective medium. A field test at two sites in coastal California infested with pine pitch canker was carried out during the summer and fall of 2002. Spore counts were in the range of ca. 1 × 10
3
to ca. 7 × 10
5
/m
2
, with the highest spore counts in the fall, suggesting a seasonal fluctuation.
Specific 12β-Hydroxylation of Cinobufagin by Filamentous Fungi
Authors: Ye Min , Qu Guiqin , Guo Hongzhu , Guo Dean 
Published: June 2004

ABSTRACTBiotransformation of natural products has great potential for producing new drugs and could provide in vitro models of mammalian metabolism. Microbial transformation of the cytotoxic steroid cinobufagin was investigated. Cinobufagin could be specifically hydroxylated at the 12β-position by the fungusAlternaria alternata. Six products from a scaled-up fermentation were obtained by silica gel column chromatography and reversed-phase liquid chromatography and were identified as 12β-hydroxyl cinobufagin, 12β-hydroxyl desacetylcinobufagin, 3-oxo-12β-hydroxyl cinobufagin, 3-oxo-12β-hydroxyl desacetylcinobufagin, 12-oxo-cinobufagin, and 3-oxo-12α-hydroxyl cinobufagin. The last five products are new compounds. 12β-Hydroxylation of cinobufagin byA. alternatais a fast catalytic reaction and was complete within 8 h of growth with the substrate. This reaction was followed by dehydrogenation of the 3-hydroxyl group and then deacetylation at C-16. Hydroxylation at C-12β also was the first step in the metabolism of cinobufagin by a variety of fungal strains. In vitro cytotoxicity assays suggest that 12β-hydroxyl cinobufagin and 3-oxo-12α-hydroxyl cinobufagin exhibit somewhat decreased but still significant cytotoxic activities. The 12β-hydroxylated bufadienolides produced by microbial transformation are difficult to obtain by chemical synthesis.
Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (
Picea mariana
) Seedlings Grown in a Nursery
Authors: Filion M. , Hamelin R. C. , Bernier L. , St-Arnaud M. 
Published: June 2004

ABSTRACT

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (
Picea mariana
) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased
P. mariana
seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of
Acidobacteria
,
Gammaproteobacteria
, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of
Actinobacteria
, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.
Modeling the Rate of Attachment of
Listeria monocytogenes
,
Pantoea agglomerans
, and
Pseudomonas fluorescens
to, and the Probability of Their Detachment from, Potato Tissue at 10°C
Authors: Garrood M. J. , Wilson P. D. G. , Brocklehurst T. F. 
Published: June 2004

ABSTRACT

The rate of attachment of bacteria to, and their subsequent detachment from, the cut surface of raw potato tissue was measured and modeled by using mathematical approaches that allowed detailed objective comparisons of adhesion processes under different conditions. Attachment was rapid and reached equilibrium after contact for 60 min. A new method to measure the probability of detachment was developed and modeled, revealing that the probability of detachment for
Pseudomonas fluorescens
remained unchanged for contact times between less than 5 s and 60 min.
Listeria monocytogenes
, however, was more easily removed initially, with the probability of detachment decreasing over the first 2 min of contact but remaining constant and equivalent to that for
Pseudomonas fluorescens
thereafter. For all of the bacteria tested, the number of bacteria attached after 2 min of contact was proportional to the inoculum concentration raised to the power of 0.79.
Characterization of Bacterial Communities in Feces from Healthy Elderly Volunteers and Hospitalized Elderly Patients by Using Real-Time PCR and Effects of Antibiotic Treatment on the Fecal Microbiota
Authors: Bartosch Sabine , Fite Alemu , Macfarlane George T. , McMurdo Marion E. T. 
Published: June 2004

ABSTRACTFecal bacteria were studied in healthy elderly volunteers (age, 63 to 90 years;n= 35) living in the local community, elderly hospitalized patients (age, 66 to 103;n= 38), and elderly hospitalized patients receiving antibiotic treatment (age, 65 to 100;n= 21). Group- and species-specific primer sets targeting 16S rRNA genes were used to quantitate intestinal bacteria by using DNA extracted from feces and real-time PCR. The principal difference between healthy elderly volunteers and both patient cohorts was a marked reduction in theBacteroides-Prevotellagroup following hospitalization. Reductions in bifidobacteria,Desulfovibriospp.,Clostridium clostridiiforme, andFaecalibacterium prausnitziiwere also found in the hospitalized patients. However, total 16S rRNA gene copy numbers (per gram of wet weight of feces) were generally lower in the stool samples of the two groups of hospitalized patients compared to the number in the stool samples of elderly volunteers living in the community, so the relative abundance (percentage of the group- and species-specific rRNA gene copies in relation to total bacterial rRNA gene copies) of bifidobacteria,Desulfovibriospp.,C. clostridiiforme, andF. prausnitziidid not change. Antibiotic treatment resulted in further reductions in the numbers of bacteria and their prevalence and, in some patients, complete elimination of certain bacterial communities. Conversely, the numbers of enterobacteria increased in the hospitalized patients who did not receive antibiotics, and due to profound changes in fecal microbiotas during antibiotic treatment, the opportunistic speciesEnterococcus faecalisproliferated.
Vertical Transmission of Endobacteria in the Arbuscular Mycorrhizal FungusGigaspora margaritathrough Generation of Vegetative Spores
Authors: Bianciotto V. , Genre A. , Jargeat P. , Lumini E. , Bécard G. , Bonfante P. 
Published: June 2004

ABSTRACTArbuscular mycorrhizal (AM) fungi living in symbiotic association with the roots of vascular plants have also been shown to host endocellular rod-shaped bacteria. Based on their ribosomal sequences, these endobacteria have recently been identified as a new taxon,CandidatusGlomeribacter gigasporarum. In order to investigate the cytoplasmic stability of the endobacteria in their fungal host and their transmission during AM fungal reproduction (asexual), a system based on transformed carrot roots and single-spore inocula ofGigaspora margaritawas used. Under these in vitro sterile conditions, with no risk of horizontal contamination, the propagation of endobacteria could be monitored, and it was shown, by using primers designed for both 16S and 23S ribosomal DNAs, to occur through several vegetative spore generations (SG0 to SG4). A method of confocal microscopy for quantifying the density of endobacteria in spore cytoplasm was designed and applied; endobacteria were consistently found in all of the spore generations, although their number rapidly decreased from SG0 to SG4. The study demonstrates that a vertical transmission of endobacteria takes place through the fungal vegetative generations (sporulation) of an AM fungus, indicating that active bacterial proliferation occurs in the coenocytic mycelium of the fungus, and suggests that these bacteria are obligate endocellular components of their AM fungal host.