bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Characterization of a Novel Single-Stranded RNA Virus Infectious to a Marine Fungoid Protist,
Schizochytrium
sp. (Thraustochytriaceae, Labyrinthulea)
Authors: Takao Yoshitake , Nagasaki Keizo , Mise Kazuyuki , Okuno Tetsuro , Honda Daiske 
Published: August 2005

ABSTRACT

Thraustochytrids are cosmopolitan osmoheterotrophic microorganisms that play important roles as decomposers, producers of polyunsaturated fatty acids, and pathogens of mollusks, especially in coastal ecosystems. SssRNAV, a novel single-stranded RNA (ssRNA) virus infecting the marine fungoid protist
Schizochytrium
sp. (Labyrinthulea, Thraustochytriaceae) was isolated from the coastal water of Kobe Harbor, Japan, in July 2000, and its basic characteristics were examined. The virus particle is icosahedral, lacks a tail, and is ca. 25 nm in diameter. SssRNAV formed crystalline arrays and random assemblies within the cytoplasm of host cells, and it was also concentrated along the intracellular membrane structures. By means of one-step growth experiments, the lytic cycle and the burst size were estimated to be <8 h and 5.8 × 10
3
to 6.4 × 10
4
infectious units per host cell, respectively. SssRNAV had a single molecule of ssRNA that was approximately 10.2 kb long, three major proteins (37, 34, and 32 kDa), and two minor proteins (80 and 18 kDa). Although SssRNAV was considered to have some similarities with invertebrate viruses belonging to the family
Dicistroviridae
based on its partial nucleotide sequence, further genomic analysis is required to determine the detailed classification and nomenclature of SssRNAV. Our results indicate that viral infection is one of the significant factors controlling the dynamics of thraustochytrids and provide new insights into understanding the ecology of these organisms.
Low Intraspecific Diversity in a
Polynucleobacter
Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond
Authors: Hahn Martin W. , Pöckl Matthias , Wu Qinglong L. 
Published: August 2005

ABSTRACT

Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a
Polynucleobacter
subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the
Polynucleobacter
cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a
Polynucleobacter
population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.
Structure and Topology of Microbial Communities in the Major Gut Compartments ofMelolontha melolonthaLarvae (Coleoptera: Scarabaeidae)
Authors: Egert Markus , Stingl Ulrich , Dyhrberg Bruun Lars , Pommerenke Bianca , Brune Andreas , Friedrich Michael W. 
Published: August 2005

ABSTRACTPhysicochemical gut conditions and the composition and topology of the intestinal microbiota in the major gut compartments of the root-feeding larva of the European cockchafer (Melolontha melolontha) were studied. Axial and radial profiles of pH, O2, H2, and redox potential were measured with microsensors. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes in midgut samples of individual larvae revealed a simple but variable and probably nonspecific community structure. In contrast, the T-RFLP profiles of the hindgut samples were more diverse but highly similar, especially in the wall fraction, indicating the presence of a gut-specific community involved in digestion. While high acetate concentrations in the midgut and hindgut (34 and 15 mM) corroborated the presence of microbial fermentation in both compartments, methanogenesis was confined to the hindgut.Methanobrevibacterspp. were the only methanogens detected and were restricted to this compartment. Bacterial 16S rRNA gene clone libraries of the hindgut were dominated by clones related to theClostridiales. Clones related to theActinobacteria,Bacillales,Lactobacillales, and γ-Proteobacteriawere restricted to the lumen, whereas clones related to the β- and δ-Proteobacteriawere found only on the hindgut wall. Results of PCR-based analyses and fluorescence in situ hybridization of whole cells with group-specific oligonucleotide probes documented thatDesulfovibrio-related bacteria comprise 10 to 15% of the bacterial community at the hindgut wall. The restriction of the sulfate-reducer-specific adenosine-5′-phosphosulfate reductase geneapsAto DNA extracts of the hindgut wall in larvae from four other populations in Europe suggested that sulfate reducers generally colonize this habitat.
Mycosubtilin Overproduction by
Bacillus subtilis
BBG100 Enhances the Organism's Antagonistic and Biocontrol Activities
Authors: Leclère Valérie , Béchet Max , Adam Akram , Guez Jean-Sébastien , Wathelet Bernard , Ongena Marc , Thonart Philippe , Gancel Frédérique , Chollet-Imbert Marlène , Jacques Philippe 
Published: August 2005

ABSTRACT

A
Bacillus subtilis
derivative was obtained from strain ATCC 6633 by replacement of the native promoter of the mycosubtilin operon by a constitutive promoter originating from the replication gene
repU
of the
Staphylococcus aureus
plasmid pUB110. The recombinant strain, designated BBG100, produced up to 15-fold more mycosubtilin than the wild type produced. The overproducing phenotype was related to enhancement of the antagonistic activities against several yeasts and pathogenic fungi. Hemolytic activities were also clearly increased in the modified strain. Mass spectrometry analyses of enriched mycosubtilin extracts showed similar patterns of lipopeptides for BBG100 and the wild type. Interestingly, these analyses also revealed a new form of mycosubtilin which was more easily detected in the BBG100 sample. When tested for its biocontrol potential, wild-type strain ATCC 6633 was almost ineffective for reducing a
Pythium
infection of tomato seedlings. However, treatment of seeds with the BBG100 overproducing strain resulted in a marked increase in the germination rate of seeds. This protective effect afforded by mycosubtilin overproduction was also visualized by the significantly greater fresh weight of emerging seedlings treated with BBG100 compared to controls or seedlings inoculated with the wild-type strain.
16S rRNA Sequences and Differences in Bacteria Isolated from the Muztag Ata Glacier at Increasing Depths
Authors: Xiang Shurong , Yao Tandong , An Lizhe , Xu Bingliang , Wang Junxia 
Published: August 2005

ABSTRACT

Small subunit 16S rRNA sequences, growth temperatures, and phylogenetic relationships have been established for 129 bacterial isolates
recovered under aerobic growth conditions from different regions of a 22-m ice core from the Muztag Ata Mountain glacier on the Pamirs
Plateau (China). Only 11% were psychrophiles (grew at 2°C or −2°C up to ∼20°C), although the
majority (82%) were psychrotolerant (grew at 2°C or −2°C up to 37°C). The majority of the isolates
had 16S rRNA sequences similar to previously determined sequences, ranging from 85% to 100% identical to database sequences. Based on
their 16S rRNA sequences, 42.6% of the isolates were high-G+C (HGC) gram-positive bacteria, 23.3% wereγ
-
Proteobacteria
, 14.7% were α-
Proteobacteria
, 14.7% were
Flavobacteria
,
and 4.7% were low-G+C (LGC) gram-positive bacteria. There were clear differences in the depth distribution, with
Proteobacteria
, HGC/
Cytophaga
-
Flavobacterium
-
Bacteroides
(CFB),
Proteobacteria
, LGC/CFB/HGC,
Cryobacterium psychrophilum
, HGC/CFB,
Proteobacteria
/HGC/CFB, and
HGC/CFB being the predominant isolates from ice that originated from 2.7 to 3.8, 6.2, 7.5, 8.3, 9.0, 9.7, 12.5, and 15.3 m below
the surface, respectively. This layered distribution of bacterial isolates presumably reflects both differences in bacteria inhabiting
the glacier's surface, differences in bacteria deposited serendipitously on the glacier's surface by wind and snowfall, and
nutrient availability within the ice.
Diurnal Variation of Cell Proliferation in Three Bacterial Taxa from Coastal North Sea Waters
Authors: Pernthaler Annelie , Pernthaler Jakob 
Published: August 2005

ABSTRACT

Pulse-labeling with bromodeoxyuridine (BrdU) in combination with fluorescence in situ hybridization was applied to quantify the percentage of proliferating cells in coastal North Sea waters. In order to assess diurnal variability, we sampled eight or nine times, respectively, within 3 consecutive days at two seasons. Bacteria affiliated with the
Roseobacter
, SAR86, and NOR5 lineages constituted on average 19% ± 3%, 8% ± 2%, and 6% ± 1% of all cells in May 2002 and 17% ± 3%, 10% ± 2%, and 11% ± 3% in August. The relative abundances of the three populations either remained stable, or they changed very gradually during the observation periods. On average, 38 and 39% of all
Bacteria
exhibited DNA de novo synthesis in May and August, respectively. The fractions of proliferating cells in bacteria of the SAR86 (May, 59%; August, 72%) and the
Roseobacter
(48 and 53%) lineages were significantly above the community average. A substantial cell proliferation of population NOR5 (34%) was only encountered in August, concomitant with a dinoflagellate bloom. Significant short-term fluctuations of DNA-synthesizing cells were observed in
Roseobacter
during May and in NOR5 during August, hinting at a pronounced (temporal or spatial) mesoscale patchiness of growth rates in these populations. Since the BrdU proliferation assay is susceptible to misinterpretation, we also modeled the expected number of labeled cells at increasing BrdU incubation times in a slowly growing bacterial population. We suggest that the absence of visible DNA synthesis in marine bacterioplankton cells after DNA pulse-labeling must not be interpreted as an indication of cell “inactivity.”
Statistical Analyses: Possible Reasons for Unreliability of Source Tracking Efforts
Authors: Lasalde Clarivel , Rodríguez Roberto , Toranzos Gary A. 
Published: August 2005

ABSTRACT

Analyses for the presence of indicator organisms provide information on the microbiological quality of water. Indicator organisms recommended by the United States Environmental Protection Agency for monitoring the microbiological quality of water include
Escherichia coli
, a thermotolerant coliform found in the feces of warm-blooded animals. These bacteria can also be isolated from environmental sources such as the recreational and pristine waters of tropical rain forests in the absence of fecal contamination. In the present study,
E. coli
isolates were compared to
E. coli
K12 (ATCC 29425) by restriction fragment length polymorphism using pulsed-field gel electrophoresis. Theoretically, genomic DNA patterns generated by PFGE are highly specific for the different isolates of an organism and can be used to identify variability between environmental and fecal isolates. Our results indicate a different band pattern for almost every one of the
E. coli
isolates analyzed. Cluster analysis did not show any relations between isolates and their source of origin. Only the discriminant function analysis grouped the samples with the source of origin. The discrepancy observed between the cluster analysis and discriminant function analysis relies on their mathematical basis. Our validation analyses indicate the presence of an artifact (i.e., grouping of environmental versus fecal samples as a product of the statistical analyses used and not as a result of separation in terms of source of origin) in the classification results; therefore, the large genetic heterogeneity observed in these
E. coli
populations makes the grouping of isolates by source rather difficult, if not impossible.
Regiospecificity of Two Multicomponent Monooxygenases from
Pseudomonas stutzeri
OX1: Molecular Basis for Catabolic Adaptation of This Microorganism to Methylated Aromatic Compounds
Authors: Cafaro Valeria , Notomista Eugenio , Capasso Paola , Di Donato Alberto 
Published: August 2005

ABSTRACT

The pathways for degradation of aromatic hydrocarbons are constantly modified by a variety of genetic mechanisms. Genetic studies carried out with
Pseudomonas stutzeri
OX1 suggested that the
tou
operon coding for toluene
o
-xylene monooxygenase (ToMO) was recently recruited into a preexisting pathway that already possessed the
ph
operon coding for phenol hydroxylase (PH). This apparently resulted in a redundancy of enzymatic activities, because both enzymes are able to hydroxylate (methyl)benzenes to (methyl)catechols via the intermediate production of (methyl)phenols. We investigated the kinetics and regioselectivity of toluene and
o
-xylene oxidation using
Escherichia coli
cells expressing ToMO and PH complexes. Our data indicate that in the recombinant system the enzymes act sequentially and that their catalytic efficiency and regioselectivity optimize the degradation of toluene and
o
-xylene, both of which are growth substrates. The main product of toluene oxidation by ToMO is
p
-cresol, the best substrate for PH, which catalyzes its transformation to 4-methylcatechol. The sequential action of the two enzymes on
o
-xylene leads, via the intermediate 3,4-dimethylphenol, to the exclusive production of 3,4-dimethylcatechol, the only dimethylcatechol isomer that can serve as a carbon and energy source after further metabolic processing. Moreover, our data strongly support a metabolic explanation for the acquisition of the ToMO operon by
P. stutzeri
OX1. It is possible that using the two enzymes in a concerted fashion confers on the strain a selective advantage based on the ability of the microorganism to optimize the efficiency of the use of nonhydroxylated aromatic hydrocarbons, such as benzene, toluene, and
o
-xylene.
Single-Nucleotide Polymorphism Phylotyping of
Escherichia coli
Authors: Hommais Florence , Pereira Sabrina , Acquaviva Cécile , Escobar-Páramo Patricia , Denamur Erick 
Published: August 2005

ABSTRACT

We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30
Escherichia coli
strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes,
trpA
,
trpB
,
putP
,
icdA
, and
polB
, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different
E. coli
pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical
E. coli
isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different
E. coli
strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.
Characterization of Colony Morphology Variants Isolated from
Pseudomonas aeruginosa
Biofilms
Authors: Kirisits Mary Jo , Prost Lynne , Starkey Melissa , Parsek Matthew R. 
Published: August 2005

ABSTRACT

In this study, we report the isolation of small, rough, strongly cohesive colony morphology variants from aging
Pseudomonas aeruginosa
PAO1 biofilms. Similar to many of the
P. aeruginosa
colony morphology variants previously described in the literature, these variants autoaggregate in liquid culture and hyperadhere to solid surfaces. They also exhibit increased hydrophobicity and reduced motility compared to the wild-type parent strain. Despite the similarities in appearance of our colony morphology variant isolates on solid medium, the isolates showed a range of responses in various phenotypic assays. These variants form biofilms with significant three-dimensional structure and more biomass than the wild-type parent. To further explore the nature of the variants, their transcriptional profiles were evaluated. The variants generally showed increased expression of the
psl
and
pel
loci, which have been previously implicated in the adherence of
P. aeruginosa
to solid surfaces. When a mutation in the
psl
locus was introduced into a colony morphology variant, the colony morphology was only partially affected, but hyperadherence and autoaggregation were lost. Finally, similar colony morphology variants were found in isolates from cystic fibrosis patients. These variants displayed many of the same characteristics as the laboratory variants, suggesting a link between laboratory and cystic fibrosis biofilms.
Metagenomic Analysis Reveals Diverse Polyketide Synthase Gene Clusters in Microorganisms Associated with the Marine Sponge
Discodermia dissoluta
Authors: Schirmer Andreas , Gadkari Rishali , Reeves Christopher D. , Ibrahim Fadia , DeLong Edward F. , Hutchinson C. Richard 
Published: August 2005

ABSTRACT

Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge
Discodermia dissoluta
revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up <1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of
D. dissoluta
consists mainly of
Entotheonella
spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.
Adhesion of
Vibrio cholerae
to Granular Starches
Authors: Gancz Hanan , Niderman-Meyer Orly , Broza Meir , Kashi Yechezkel , Shimoni Eyal 
Published: August 2005

ABSTRACT

Cholera is a severe diarrheal disease caused by specific serogroups of
Vibrio cholerae
that are pathogenic to humans. Cholera can become epidemic and deadly without adequate medical care. Appropriate rehydration therapy can reduce the mortality rate from as much as 50% of the affected individuals to <1%. Thus, oral rehydration therapy (ORT) is an important measure in the treatment of this disease. To further reduce the symptoms associated with cholera, improvements in oral rehydration solution (ORS) by starch incorporation were suggested. Here, we report that
V. cholerae
adheres to starch granules incorporated in ORS. Adhesion of 98% of the cells was observed within 2 min when cornstarch granules were used. Other starches showed varied adhesion rates, indicating that starch source and composition play an important role in the interaction of
V. cholerae
and starch granules. Sugars metabolized by
V. cholerae
showed a repressive effect on the adhesion process. The possible mechanisms involved are discussed. Comparing
V. cholerae
adhesion with the adhesion of other pathogens suggests the involvement of starch degradation capabilities. This adhesion to granular starch can be used to improve ORT.
Multilocus Simple Sequence Repeat Markers for Differentiating Strains and Evaluating Genetic Diversity of
Xylella fastidiosa
Authors: Lin Hong , Civerolo Edwin L. , Hu Rong , Barros Samuel , Francis Marta , Walker M. Andrew 
Published: August 2005

ABSTRACT

A genome-wide search was performed to identify simple sequence repeat (SSR) loci among the available sequence databases from four strains of
Xylella fastidiosa
(strains causing Pierce's disease, citrus variegated chlorosis, almond leaf scorch, and oleander leaf scorch). Thirty-four SSR loci were selected for SSR primer design and were validated in PCR experiments. These multilocus SSR primers, distributed across the
X. fastidiosa
genome, clearly differentiated and clustered
X. fastidiosa
strains collected from grape, almond, citrus, and oleander. They are well suited for differentiating strains and studying
X. fastidiosa
epidemiology and population genetics.
Comparison of Microcapillary Cytometry Technology and Flow Cytometry for CD4
+
and CD8
+
T-Cell Estimation
Authors: Kandathil A. J. , Kannangai R. , David S. , Nithyanandam G. , Solomon S. , Balakrishnan P. , Abraham O. C. , Subramanian S. , Rupali P. , Verghese V. P. , Pulimood S. , Sridharan G. 
Published: August 2005

ABSTRACT

An alternative technology for the estimation of T cells based on a microcapillary technique (Guava Technologies, Hayward, CA) was compared to FACSCount (Becton Dickinson, San Jose, CA). Samples from 51 human immunodeficiency virus-infected and 21 healthy individuals were tested. The correlation (
r
) of the two systems for CD4
+
T cells was 0.994, and the coefficient of variation was 6.5%, establishing equable performance between the two technologies.