bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Nutrient Addition and Environmental Factors on Prophage Induction in Natural Populations of Marine
Synechococcus
Species
Authors: McDaniel L. , Paul J. H. 
Published: February 2005

ABSTRACT

A series of experiments were conducted with samples collected in both Tampa Bay and the Gulf of Mexico to assess the impact of nutrient addition on cyanophage induction in natural populations of
Synechococcus
sp. The samples were virus reduced to decrease the background level of cyanophage and then either left untreated or amended with nitrate, ammonium, urea, or phosphate. Replicate samples were treated with mitomycin C to stimulate cyanophage induction. In five of the nine total experiments performed, cyanophage induction was present in the non-nutrient-amended control samples. Stimulation of cyanophage induction in response to nutrient addition (phosphate) occurred in only one Tampa Bay sample. Nutrient additions caused a decrease in lytic (or control) phage production in three of three offshore stations, in one of three estuarine experiments, and in a lysogenic marine
Synechococcus
in culture. These results suggest that the process of cyanophage induction as an assay of
Synechococcus
lysogeny was not inorganically nutrient limited, at least in the samples examined. More importantly, it was observed that the level of cyanophage induction (cyanophage milliliter
−1
) was inversely correlated to
Synechococcus
and cyanophage abundance. Thus, the intensity of the prophage induction response is defined by ambient population size and cyanophage abundance. This corroborates prior observations that lysogeny in
Synechococcus
is favored during times of low host abundance.
Role of the
bga1
-Encoded Extracellular β-Galactosidase of
Hypocrea jecorina
in Cellulase Induction by Lactose
Authors: Seiboth Bernhard , Hartl Lukas , Salovuori Noora , Lanthaler Karin , Robson Geoff D. , Vehmaanperä Jari , Penttilä Merja E. , Kubicek Christian P. 
Published: February 2005

ABSTRACT

Lactose is the only soluble and economically feasible carbon source for the production of cellulases or heterologous proteins regulated by cellulase expression signals by
Hypocrea jecorina
(
Trichoderma reesei
). We investigated the role of the major β-galactosidase of
H. jecorina
in lactose metabolism and cellulase induction. A genomic copy of the
bga1
gene was cloned, and this copy encodes a 1,023-amino-acid protein with a 20-amino-acid signal sequence. This protein has a molecular mass of 109.3 kDa, belongs to glycosyl hydrolase family 35, and is the major extracellular β-galactosidase during growth on lactose. Its transcript was abundant during growth on
l
-arabinose and
l
-arabinitol but was much less common when the organism was grown on lactose,
d
-galactose, galactitol,
d
-xylose, and xylitol. Δ
bga1
strains grow more slowly and accumulate less biomass on lactose, but the cellobiohydrolase I and II gene expression and the final cellulase yields were comparable to those of the parental strain. Overexpression of
bga1
under the control of the pyruvate kinase promoter reduced the lag phase, increased growth on lactose, and limited transcription of cellobiohydrolases. We detected an additional extracellular β-galactosidase activity that was not encoded by
bga1
but no intracellular β-galactosidase activity. In conclusion, cellulase production on lactose occurs when β-galactosidase activity levels are low but decreases as the β-galactosidase activities increase. The data indicate that
bga1
-encoded β-galactosidase activity is a critical factor for cellulase production on lactose.
Comparison of Ileum Microflora of Pigs Fed Corn-, Wheat-, or Barley-Based Diets by Chaperonin-60 Sequencing and Quantitative PCR
Authors: Hill Janet E. , Hemmingsen Sean M. , Goldade Blair G. , Dumonceaux Tim J. , Klassen Jonathan , Zijlstra Ruurd T. , Goh Swee Han , Van Kessel Andrew G. 
Published: February 2005

ABSTRACT
We have combined the culture-independent methods of high-throughput sequencing of chaperonin-60 PCR product libraries and quantitative PCR to profile and quantify the small-intestinal microflora of pigs fed diets based on corn, wheat, or barley. A total of 2,751 chaperonin-60 PCR product clones produced from samples of ileum digesta were examined. The majority (81%) of these clones contained sequences independently recovered from all three libraries; 372 different nucleotide sequences were identified, but only 14% of the 372 different sequences were recovered from all three libraries. Taxonomic assignments of the library sequences were made by comparison to a reference database of chaperonin-60 sequences combined with phylogenetic analysis. The taxa identified are consistent with previous reports of pig ileum microflora. Frequencies of each sequence in each library were calculated to identify taxa that varied in frequency between the corn, barley, and wheat libraries. The chaperonin-60 sequence inventory was used as a basis for designing PCR primer sets for taxon-specific quantitative PCR. Results of quantitative PCR analysis of ileum digesta confirmed the relative abundances of targeted taxa identified with the library sequencing approach. The results of this study indicate that chaperonin-60 clone libraries can be valid profiles of complex microbial communities and can be used as the basis for producing quantitative PCR assays to measure the abundance of taxa of interest during experimentally induced or natural changes in a community.
Metabolism of Bismuth Subsalicylate and Intracellular Accumulation of Bismuth by
Fusarium
sp. Strain BI
Authors: Dodge Anthony G. , Wackett Lawrence P. 
Published: February 2005

ABSTRACT

Enrichment cultures were conducted using bismuth subsalicylate as the sole source of carbon and activated sludge as the inoculum. A pure culture was obtained and identified as a
Fusarium
sp. based on spore morphology and partial sequences of 18S rRNA, translation elongation factor 1-α, and β-tubulin genes. The isolate, named
Fusarium
sp. strain BI, grew to equivalent densities when using salicylate or bismuth subsalicylate as carbon sources. Bismuth nitrate at concentrations of up to 200 μM did not limit growth of this organism on glucose. The concentration of soluble bismuth in suspensions of bismuth subsalicylate decreased during growth of
Fusarium
sp. strain BI. Transmission electron microscopy and energy-dispersive spectroscopy revealed that the accumulated bismuth was localized in phosphorus-rich granules distributed in the cytoplasm and vacuoles. Long-chain polyphosphates were extracted from fresh biomass grown on bismuth subsalicylate, and inductively coupled plasma optical emission spectrometry showed that these fractions also contained high concentrations of bismuth. Enzyme activity assays of crude extracts of
Fusarium
sp. strain BI showed that salicylate hydroxylase and catechol 1,2-dioxygenase were induced during growth on salicylate, indicating that this organism degrades salicylate by conversion of salicylate to catechol, followed by
ortho
cleavage of the aromatic ring. Catechol 2,3-dioxygenase activity was not detected.
Fusarium
sp. strain BI grew with several other aromatic acids as carbon sources: benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, gentisate,
d
-mandelate,
l
-phenylalanine,
l
-tyrosine, phenylacetate, 3-hydroxyphenylacetate, 4-hydroxyphenylacetate, and phenylpropionate.
Detection and Discrimination of
Cryptosporidium parvum
and
C. hominis
in Water Samples by Immunomagnetic Separation-PCR
Authors: Ochiai Yoshitsugu , Takada Chieko , Hosaka Mitsugu 
Published: February 2005

ABSTRACT

Cryptosporidium parvum
and
C. hominis
have been the cause of large and serious outbreaks of waterborne cryptosporidiosis. A specific and sensitive recovery-detection method is required for control of this pathogen in drinking water. In the present study, nested PCR-restriction fragment length polymorphism (RFLP), which targets the divergent
Cpgp40/15
gene, was developed. This nested PCR detected only the gene derived from
C. parvum
and
C. hominis
strains, and RFLP was able to discriminate between the PCR products from
C. parvum
and
C. hominis
. To evaluate the sensitivity of nested PCR,
C. parvum
oocysts inoculated in water samples of two different turbidities were recovered by immunomagnetic separation (IMS) and detected by nested PCR and fluorescent antibody assay (FA). Genetic detection by nested PCR and oocyst number confirmed by FA were compared, and the results suggested that detection by nested PCR depends on the confirmed oocyst number and that nested PCR in combination with IMS has the ability to detect a single oocyst in a water sample. We applied an agitation procedure with river water solids to which oocysts were added to evaluate the recovery and detection by the procedure in environmental samples and found some decrease in the rate of detection by IMS.
Unique Kinetic Properties of Phenol-Degrading
Variovorax
Strains Responsible for Efficient Trichloroethylene Degradation in a Chemostat Enrichment Culture
Authors: Futamata Hiroyuki , Nagano Yayoi , Watanabe Kazuya , Hiraishi Akira 
Published: February 2005

ABSTRACT

A chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (TCE)-degrading activities (H. Futamata, S. Harayama, and K. Watanabe, Appl. Environ. Microbiol.
67:
4671-4677, 2001). To identify the bacterial populations responsible for the high TCE-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. Three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.75, and 1.25 g liter
−1
day
−1
) in this study, and the TCE-degrading activities of the enrichments were measured. Among them, the enrichment at 0.75 g liter
−1
day
−1
(enrichment 0.75) expressed the highest activity. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments detected a
Variovorax
ribotype as the strongest band in enrichment 0.75; however, it was not a major ribotype in the other samples. Bacteria were isolated from enrichment 0.75 by direct plating, and their 16S rRNA genes and genes encoding the largest subunit of phenol hydroxylase (LmPHs) were analyzed. Among the bacteria isolated, several strains were affiliated with the genus
Variovorax
and were shown to have high-affinity-type LmPHs. The LmPH of the
Variovorax
strains was also detected as the major genotype in enrichment 0.75. Kinetic analyses of phenol and TCE degradation revealed, however, that these strains exhibited quite low affinity for phenol compared to other phenol-degrading bacteria, while they showed quite high specific TCE-degrading activities and relatively high affinity for TCE. Owing to these unique kinetic traits, the
Variovorax
strains can obviate competitive inhibition of TCE degradation by the primary substrate of the catabolic enzyme (i.e., phenol), contributing to the high TCE-degrading activity of the chemostat enrichments. On the basis of physiological information, mechanisms accounting for the way the
Variovorax
population overgrew the chemostat enrichment are discussed.
Adhesion-Aggregation and Inactivation of
Poliovirus 1
in Groundwater Stored in a Hydrophobic Container
Authors: Gassilloud Benoît , Gantzer Christophe 
Published: February 2005

ABSTRACT

Viral inactivation and adhesion-aggregation in water are often studied as separate phenomena. When the focus is placed on viral adhesion-aggregation, inactivation is neglected because the phenomena under investigation occur over a short period measured in days. When viral inactivation is studied, adhesion-aggregation phenomena are considered to be negligible because viral survival is traced over several days or months. In the present work, we took a global approach, examining the relative contributions of each of these processes in a complex system composed of groundwater,
Poliovirus 1
, and a hydrophobic container (polypropylene) maintained in a dark environment at 20°C. We demonstrated that infectious viral load fell off 2.8 log
10
during the first 20 days. During this time, adhesion was far from negligible because it accounted for most of the decline, 1.5 log
10
. Adhesion was undoubtedly favored by the presence of divalent ions in the groundwater. After 20 days, aggregation may also have been the cause of 0.66 to 0.92 log
10
of viral loss. Finally, viral inactivation was quantitatively the lowest phenomena because it only explained 0.38 to 0.64 log
10
of the viral loss. This study thus clearly demonstrated that estimates of viral survival in a given system must always take into account adhesion-aggregation phenomena which may be responsible for the majority of viral loss in the aqueous phase. Adhesion and aggregation are reversible processes which may lead to an underestimation of viral load in certain studies.
High Motility Reduces Grazing Mortality of Planktonic Bacteria
Authors: Matz Carsten , Jürgens Klaus 
Published: February 2005

ABSTRACT

We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated that the number of predator-prey contacts increased with bacterial swimming speed, but ingestion rates dropped at speeds of >25 μm s
−1
as a result of handling problems with highly motile cells. Comparative studies of a moderately motile strain (<25 μm s
−1
) and a highly motile strain (>45 μm s
−1
) further revealed changes in the bacterial swimming speed distribution due to speed-selective flagellate grazing. Better long-term survival of the highly motile strain was indicated by fourfold-higher bacterial numbers in the presence of grazing compared to the moderately motile strain. Putative constraints of maintaining high swimming speeds were tested at high growth rates and under starvation with the following results: (i) for two out of three strains increased growth rate resulted in larger and slower bacterial cells, and (ii) starved cells became smaller but maintained their swimming speeds. Combined data sets for bacterial swimming speed and cell size revealed highest grazing losses for moderately motile bacteria with a cell size between 0.2 and 0.4 μm
3
. Grazing mortality was lowest for cells of >0.5 μm
3
and small, highly motile bacteria. Survival efficiencies of >95% for the ultramicrobacterial isolate CP-1 (≤0.1 μm
3
, >50 μm s
−1
) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing.
Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea FishChlorophthalmus albatrossis(Aulopiformes: Chlorophthalmidae)
Authors: Dunlap Paul V. , Ast Jennifer C. 
Published: February 2005

ABSTRACTBacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the speciesPhotobacterium phosphoreum. The identification of these bacteria asP. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ ofChlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain ofP. phosphoreum, ATCC 11040T, and the type strain ofPhotobacterium iliopiscarium, ATCC 51760T. Analysis ofgyrBresolved theC. albatrossisstrains as a strongly supported clade distinct fromP. phosphoreumandP. iliopiscarium. Genomic profiling of 109 strains from the 5C. albatrossisspecimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of theluxABFEgenes. As withgyrB, analysis ofluxABFEresolved theC. albatrossisstrains as a robustly supported clade distinct fromP. phosphoreum. Furthermore, other strains of luminous bacteria reported asP. phosphoreum, i.e., NCIMB 844, from the skin ofMerluccius capensis(Merlucciidae), NZ-11D, from the light organ ofNezumia aequalis(Macrouridae), andpjapo.1.1, from the light organ ofPhysiculus japonicus(Moridae), grouped phylogenetically bygyrBandluxABFEwith theC. albatrossisstrains, not with ATCC 11040T. These results demonstrate that luminous bacteria symbiotic withC. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated thekishitaniiclade, that is related to but evolutionarily distinct fromP. phosphoreum. Members of thekishitaniiclade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.
Bacterial Degradation of Cyanide and Its Metal Complexes under Alkaline Conditions
Authors: Luque-Almagro Víctor M. , Huertas María-J. , Martínez-Luque Manuel , Moreno-Vivián Conrado , Roldán M. Dolores , García-Gil L. Jesús , Castillo Francisco , Blasco Rafael 
Published: February 2005

ABSTRACT

A bacterial strain able to use cyanide as the sole nitrogen source under alkaline conditions has been isolated. The bacterium was classified as
Pseudomonas pseudoalcaligenes
by comparison of its 16S RNA gene sequence to those of existing strains and deposited in the Colección Española de Cultivos Tipo (Spanish Type Culture Collection) as strain CECT5344. Cyanide consumption is an assimilative process, since (i) bacterial growth was concomitant and proportional to cyanide degradation and (ii) the bacterium stoichiometrically converted cyanide into ammonium in the presence of
l
-methionine-
d
,
l
-sulfoximine, a glutamine synthetase inhibitor. The bacterium was able to grow in alkaline media, up to an initial pH of 11.5, and tolerated free cyanide in concentrations of up to 30 mM, which makes it a good candidate for the biological treatment of cyanide-contaminated residues. Both acetate and
d
,
l
-malate were suitable carbon sources for cyanotrophic growth, but no growth was detected in media with cyanide as the sole carbon source. In addition to cyanide,
P. pseudoalcaligenes
CECT5344 used other nitrogen sources, namely ammonium, nitrate, cyanate, cyanoacetamide, nitroferricyanide (nitroprusside), and a variety of cyanide-metal complexes. Cyanide and ammonium were assimilated simultaneously, whereas cyanide strongly inhibited nitrate and nitrite assimilation. Cyanase activity was induced during growth with cyanide or cyanate, but not with ammonium or nitrate as the nitrogen source. This result suggests that cyanate could be an intermediate in the cyanide degradation pathway, but alternative routes cannot be excluded.
Bias in the
Listeria monocytogenes
Enrichment Procedure: Lineage 2 Strains Outcompete Lineage 1 Strains in University of Vermont Selective Enrichments
Authors: Bruhn Jesper Bartholin , Vogel Birte Fonnesbech , Gram Lone 
Published: February 2005

ABSTRACT

Listeria monocytogenes
can be isolated from a range of food products and may cause food-borne outbreaks or sporadic cases of listeriosis.
L. monocytogenes
is divided into three genetic lineages and 13 serotypes. Strains of three serotypes (1/2a, 1/2b, and 4b) are associated with most human cases of listeriosis. Of these, strains of serotypes 1/2b and 4b belong to lineage 1, whereas strains of serotype 1/2a and many other strains isolated from foods belong to lineage 2.
L. monocytogenes
is isolated from foods by selective enrichment procedures and from patients by nonselective methods. The aim of the present study was to investigate if the selective enrichment procedure results in a true representation of the subtypes of
L. monocytogenes
present in a sample. Eight
L. monocytogenes
strains (four lineage 1 strains and four lineage 2 strains) and one
Listeria innocua
strain grew with identical growth rates in the nonselective medium brain heart infusion (BHI), but differed in their growth rate in the selective medium University of Vermont medium I (UVM I). When coinoculated in UVM I, some strains completely outgrew other strains. This outcome was dependent on the lineage of
L. monocytogenes
rather than the individual growth rate of the strains. When inoculated at identical cell densities in UVM I,
L. innocua
outcompeted
L. monocytogenes
lineage 1 strains but not lineage 2 strains. In addition, lineage 2
L. monocytogenes
strains outcompeted lineage 1
L. monocytogenes
strains in all combinations tested, indicating a bias in strains selected by the enrichment procedures. Bias also occurred when coinoculating two lineage 2 or lineage 1 strains; however, it did not appear to correlate with origin (clinical versus food). Identical coinoculation experiments in BHI suggested that the selective compounds in UVM I and II influenced this bias. The results of the present study demonstrate that the selective procedures used for isolation of
L. monocytogenes
may not allow a true representation of the types present in foods. Our results could have a significant impact on epidemiological studies, as lineage 1 strains, which are often isolated from clinical cases of listeriosis, may be suppressed during enrichment by other
L. monocytogenes
lineages present in a food sample.
Screening for
Bacillus
Isolates in the Broiler Gastrointestinal Tract
Authors: Barbosa Teresa M. , Serra Cláudia R. , La Ragione Roberto M. , Woodward Martin J. , Henriques Adriano O. 
Published: February 2005

ABSTRACT

Spores from a number of different
Bacillus
species are currently being used as human and animal probiotics, although their mechanisms of action remain poorly understood. Here we describe the isolation of 237 presumptive gut-associated
Bacillus
spp. isolates that were obtained by heat and ethanol treatment of fecal material from organically reared broilers followed by aerobic plating. Thirty-one representative isolates were characterized according to their morphological, physiological, and biochemical properties as well as partial 16S rRNA gene sequences and screening for the presence of plasmid DNA. The
Bacillus
species identified included
B. subtilis
,
B. pumilus
,
B. licheniformis
,
B. clausii
,
B. megaterium
,
B. firmus
, and species of the
B. cereus
group, whereas a number of our isolates could not be classified. Intrinsic properties of potential importance for survival in the gut that could be advantageous for spore-forming probiotics were further investigated for seven isolates belonging to five different species. All isolates sporulated efficiently in the laboratory, and the resulting spores were tolerant to simulated gastrointestinal tract conditions. They also exhibited antimicrobial activity against a broad spectrum of bacteria, including food spoilage and pathogenic organisms such as
Bacillus
spp.,
Clostridium perfringens
,
Staphylococcus aureus
, and
Listeria monocytogenes
. Importantly, the isolates were susceptible to most of the antibiotics tested, arguing that they would not act as donors for resistance determinants if introduced in the form of probiotic preparations. Together, our results suggest that some of the sporeformers isolated in this study have the potential to persist in or transiently associate with the complex gut ecosystem.