bluuebunny/crossref_metadata_2025_split huggingface dataset:
Niche-Partitioning of
Prochlorococcus
Populations in a Stratified Water Column in the Eastern North Atlantic Ocean
Authors: West Nyree J. , Scanlan David J. 
Published: December 2019

ABSTRACT

The in situ community structure of
Prochlorococcus
populations in the eastern North Atlantic Ocean was examined by analysis of
Prochlorococcus
16S rDNA sequences with three independent approaches: cloning and sequencing, hybridization to specific oligonucleotide probes, and denaturing gradient gel electrophoresis (DGGE). The hybridization of high-light (HL) and low-light (LL)
Prochlorococcus
genotype-specific probes to two depth profiles of PCR-amplified 16S rDNA sequences revealed that in these two stratified water columns, an obvious niche-partitioning of
Prochlorococcus
genotypes occurred. In each water column a shift from the HL to the LL genotype was observed, a transition correlating with the depth of the surface mixed layer (SML). Only the HL genotype was found in the SML in each water column, whereas the LL genotype was distributed below the SML. The range of in situ irradiance to which each genotype was subjected within these distinct niches was consistent with growth irradiance studies of cultured HL- and LL-adapted
Prochlorococcus
strains. DGGE analysis and the sequencing of
Prochlorococcus
16S rDNA clones were in full agreement with the genotype-specific oligonucleotide probe hybridization data. These observations of a partitioning of
Prochlorococcus
genotypes in a stratified water column provide a genetic basis for the dim and bright
Prochlorococcus
populations observed in flow cytometric signatures in several oceanic provinces.
Vibrios Associated with
Litopenaeus vannamei
Larvae, Postlarvae, Broodstock, and Hatchery Probionts
Authors: Vandenberghe Johan , Verdonck Linda , Robles-Arozarena Rocio , Rivera Gabriel , Bolland Annick , Balladares Marcos , Gomez-Gil Bruno , Calderon Jorge , Sorgeloos Patrick , Swings Jean 
Published: December 2019

ABSTRACT

Several bacteriological surveys were performed from 1994 to 1996 at different
Litopenaeus vannamei
hatcheries (in Ecuador) and shrimp farms (in Mexico). Samples were taken from routine productions of healthy and diseased
L. vannamei
larvae, postlarvae, and their culture environment and from healthy and diseased juveniles and broodstock. In Ecuador, the dominant bacterial flora associated with shrimp larvae showing symptoms of zoea 2 syndrome, mysis mold syndrome, and bolitas syndrome has been determined. Strains were characterized by Biolog metabolic fingerprinting and identified by comparison to a database of 850
Vibrio
type and reference strains. A selection of strains was further genotypically fine typed by AFLP.
Vibrio alginolyticus
is predominantly present in all larval stages and is associated with healthy nauplius and zoea stages. AFLP genetic fingerprinting shows high genetic heterogeneity among
V. alginolyticus
strains, and the results suggest that putative probiotic and pathogenic strains each have specific genotypes.
V. alginolyticus
was found to be associated with larvae with the zoea 2 syndrome and the mysis mold syndrome, while different
Vibrio
species (
V. alginolyticus
and
V. harveyi
) are associated with the bolitas syndrome.
V. harveyi
is associated with diseased postlarvae, juveniles, and broodstock. The identities of the strains identified as
V. harveyi
by the Biolog system could not be unambiguously confirmed by AFLP genomic fingerprinting.
Vibrio
strain STD3-988 and one unidentified strain (STD3-959) are suspected pathogens of only juvenile and adult stages.
V. parahaemolyticus
,
Photobacterium damselae
, and
V. mimicus
are associated with juvenile and adult stages.
Analysis of Fungal Diversity in the Wheat Rhizosphere by Sequencing of Cloned PCR-Amplified Genes Encoding 18S rRNA and Temperature Gradient Gel Electrophoresis
Authors: Smit Eric , Leeflang Paula , Glandorf Boet , Dirk van Elsas Jan , Wernars Karel 
Published: December 2019

ABSTRACT

Like bacteria, fungi play an important role in the soil ecosystem. As only a small fraction of the fungi present in soil can be cultured, conventional microbiological techniques yield only limited information on the composition and dynamics of fungal communities in soil. DNA-based methods do not depend on the culturability of microorganisms, and therefore they offer an attractive alternative for the study of complex fungal community structures. For this purpose, we designed various PCR primers that allow the specific amplification of fungal 18S-ribosomal-DNA (rDNA) sequences, even in the presence of nonfungal 18S rDNA. DNA was extracted from the wheat rhizosphere, and 18S rDNA gene banks were constructed in
Escherichia coli
by cloning PCR products generated with primer pairs EF4-EF3 (1.4 kb) and EF4-fung5 (0.5 kb). Fragments of 0.5 kb from the cloned inserts were sequenced and compared to known rDNA sequences. Sequences from all major fungal taxa were amplified by using both primer pairs. As predicted by computer analysis, primer pair EF4-EF3 appeared slightly biased to amplify
Basidiomycota
and
Zygomycota
, whereas EF4-fung5 amplified mainly
Ascomycota
. The 61 clones that were sequenced matched the sequences of 24 different species in the Ribosomal Database Project (RDP) database. Similarity values ranged from 0.676 to 1. Temperature gradient gel electrophoresis (TGGE) analysis of the fungal community in the wheat rhizosphere of a microcosm experiment was carried out after amplification of total DNA with both primer pairs. This resulted in reproducible, distinctive fingerprints, confirming the difference in amplification specificity. Clear banding patterns were obtained with soil and rhizosphere samples by using both primer sets in combination. By comparing the electrophoretic mobility of community fingerprint bands to that of the bands obtained with separate clones, some could be tentatively identified. While 18S-rDNA sequences do not always provide the taxonomic resolution to identify fungal species and strains, they do provide information on the diversity and dynamics of groups of related species in environmental samples with sufficient resolution to produce discrete bands which can be separated by TGGE. This combination of 18S-rDNA PCR amplification and TGGE community analysis should allow study of the diversity, composition, and dynamics of the fungal community in bulk soil and in the rhizosphere.
Characterization of the Binding Protein-Dependent Cellobiose and Cellotriose Transport System of the Cellulose Degrader
Streptomyces reticuli
Authors: Schlösser Andreas , Jantos Jens , Hackmann Karl , Schrempf Hildgund 
Published: December 2019

ABSTRACT

Streptomyces reticuli
has an inducible ATP-dependent uptake system specific for cellobiose and cellotriose. By reversed genetics a gene cluster encoding components of a binding protein-dependent cellobiose and cellotriose ABC transporter was cloned and sequenced. The deduced gene products comprise a regulatory protein (CebR), a cellobiose binding lipoprotein (CebE), two integral membrane proteins (CebF and CebG), and the NH
2
-terminal part of an intracellular β-glucosidase (BglC). The gene for the ATP binding protein MsiK is not linked to the
ceb
operon. We have shown earlier that MsiK is part of two different ABC transport systems, one for maltose and one for cellobiose and cellotriose, in
S. reticuli
and
Streptomyces lividans
. Transcription of polycistronic
cebEFG
and
bglC
mRNAs is induced by cellobiose, whereas the
cebR
gene is transcribed independently. Immunological experiments showed that CebE is synthesized during growth with cellobiose and that MsiK is produced in the presence of several sugars at high or moderate levels. The described ABC transporter is the first one of its kind and is the only specific cellobiose/cellotriose uptake system of
S. reticuli
, since insertional inactivation of the
cebE
gene prevents high-affinity uptake of cellobiose.
Comparison of Fungal Laccases and Redox Mediators in Oxidation of a Nonphenolic Lignin Model Compound
Authors: Li Kaichang , Xu Feng , Eriksson Karl-Erik L. 
Published: December 2019

ABSTRACTSeveral fungal laccases have been compared for the oxidation of a nonphenolic lignin dimer, 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propan-1,3-diol (I), and a phenolic lignin model compound, phenol red, in the presence of the redox mediators 1-hydroxybenzotriazole (1-HBT) or violuric acid. The oxidation rates of dimer I by the laccases were in the following order:Trametes villosalaccase (TvL) >Pycnoporus cinnabarinuslaccase (PcL) >Botrytis cinerealaccase (BcL) >Myceliophthora thermophilalaccase (MtL) in the presence of either 1-HBT or violuric acid. The order is the same if the laccases are used at the same molar concentration or added to the same activity (with ABTS [2,2′-azinobis (3-ethylbenzothiazoline-6-sulfonic acid)] as a substrate). During the oxidation of dimer I, both 1-HBT and violuric acid were to some extent consumed. Their consumption rates also follow the above order of laccases, i.e., TvL > PcL > BcL > MtL. Violuric acid allowed TvL and PcL to oxidize dimer I much faster than 1-HBT, while BcL and violuric acid oxidized dimer I more slowly than BcL and 1-HBT. The oxidation rate of dimer I is dependent upon bothkcatand the stability of the laccase. Both 1-HBT and violuric acid inactivated the laccases, violuric acid to a greater extent than 1-HBT. The presence of dimer I or phenol red in the reaction mixture slowed down this inactivation. The inactivation is mainly due to the reaction of the redox mediator free radical with the laccases. We did not find any relationship between the carbohydrate content of the laccases and their inactivation. When the redox potential of the laccases is in the range of 750 to 800 mV, i.e., above that of the redox mediator, it does not affectkcatand the oxidation rate of dimer I.
Mapping of Sugar and Amino Acid Availability in Soil around Roots with Bacterial Sensors of Sucrose and Tryptophan
Authors: Jaeger C. H. , Lindow S. E. , Miller W. , Clark E. , Firestone M. K. 
Published: December 2019

ABSTRACT

We developed a technique to map the availability of sugars and amino acids along live roots in an intact soil-root matrix with native microbial soil flora and fauna present. It will allow us to study interactions between root exudates and soil microorganisms at the fine spatial scale necessary to evaluate mechanisms of nitrogen cycling in the rhizosphere.
Erwinia herbicola
299R harboring a promoterless ice nucleation reporter gene, driven by either of two nutrient-responsive promoters, was used as a biosensor. Strain 299RTice exhibits tryptophan-dependent ice nucleation activity, while strain 299R(p61RYice) expresses ice nucleation activity proportional to sucrose concentration in its environment. Both biosensors exhibited up to 100-fold differences in ice nucleation activity in response to varying substrate abundance in culture. The biosensors were introduced into the rhizosphere of the annual grass
Avena barbata
and, as a control, into bulk soil. Neither strain exhibited significant ice nucleation activity in the bulk soil. Both tryptophan and sucrose were detected in the rhizosphere, but they showed different spatial patterns. Tryptophan was apparently most abundant in soil around roots 12 to 16 cm from the tip, while sucrose was most abundant in soil near the root tip. The largest numbers of bacteria (determined by acridine orange staining and direct microscopy) occurred near root sections with the highest apparent sucrose or tryptophan exudation. High sucrose availability at the root tip is consistent with leakage of photosynthate from immature, rapidly growing root tissues, while tryptophan loss from older root sections may result from lateral root perforation of the root epidermis.
Reduction of Technetium by
Desulfovibrio desulfuricans
: Biocatalyst Characterization and Use in a Flowthrough Bioreactor
Authors: Lloyd J. R. , Ridley J. , Khizniak T. , Lyalikova N. N. , Macaskie L. E. 
Published: December 2019

ABSTRACT

Resting cells of
Desulfovibrio desulfuricans
coupled the oxidation of a range of electron donors to Tc(VII) reduction. The reduced technetium was precipitated as an insoluble low-valence oxide. The optimum electron donor for the biotransformation was hydrogen, although rapid rates of reduction were also supported when formate or pyruvate was supplied to the cells. Technetium reduction was less efficient when the growth substrates lactate and ethanol were supplied as electron donors, while glycerol, succinate, acetate, and methanol supported negligible reduction. Enzyme activity was stable for several weeks and was insensitive to oxygen. Transmission electron microscopy showed that the radionuclide was precipitated at the periphery of the cell. Cells poisoned with Cu(II), which is selective for periplasmic but not cytoplasmic hydrogenases, were unable to reduce Tc(VII), a result consistent with the involvement of a periplasmic hydrogenase in Tc(VII) reduction. Resting cells, immobilized in a flowthrough membrane bioreactor and supplied with Tc(VII)-supplemented solution, accumulated substantial quantities of the radionuclide when formate was supplied as the electron donor, indicating the potential of this organism as a biocatalyst to treat Tc-contaminated wastewaters.
The Quiescent-Cell Expression System for Protein Synthesis in
Escherichia coli
Authors: Rowe Duncan C. D. , Summers David K. 
Published: December 2019

ABSTRACT

The quiescent-cell expression system is a radical alternative to conventional fermentation for protein overproduction in
Escherichia coli
. It is dependent on the controlled overexpression of a small RNA called Rcd in
hns
mutant strains to generate nongrowing, quiescent cells which are not nutrient limited. Quiescent cells no longer produce biomass and have their metabolic resources channelled toward the expression of plasmid-based genes. The biosynthetic capacity of the system is demonstrated by its ability to express chloramphenicol acetyltransferase to more than 40% of total cell protein. Quiescent cells may provide an ideal environment for the expression of toxic as well as benign proteins.
Modulation of Lipid Metabolism and Spiramycin Biosynthesis in
Streptomyces ambofaciens
Unstable Mutants
Authors: Schauner Catherine , Dary Annie , Lebrihi Ahmed , Leblond Pierre , Decaris Bernard , Germain Pierre 
Published: December 2019

ABSTRACT

Streptomyces ambofaciens
is prone to genetic instability involving genomic rearrangements at the extremities of the chromosomal DNA. An amplified DNA sequence (ADS205), including an open reading frame (
orfPS
), is responsible for the reversible loss of spiramycin production in the mutant strain NSA205 (ADS205
+
Spi
−
). The product of
orfPS
is homologous to polyketide synthase systems (PKSs) involved in the biosynthesis of erythromycin and rapamycin and is overexpressed in strain NSA205 compared with the parental strain RP181110. As PKSs and fatty acid synthase systems have the same precursors, we tested the possibility that overexpression of
orfPS
also affects lipid metabolism in strain NSA205. This report focuses on comparative analysis of lipids in strain RP181110, the mutant strain NSA205, and a derivative, NSA228 (ADS205
−
Spi
+
). NSA205 showed a dramatically depressed lipid content consisting predominantly of phospholipids and triacylglycerols. This lipid content was globally restored in strain NSA228, which had lost ADS205. Furthermore, strains RP181110 and NSA205 presented similar phospholipid and triacylglycerol compositions. No abnormal fatty acids were detected in NSA205.
Interactions of Saprophytic Yeasts with a
nor
Mutant of
Aspergillus flavus
Authors: Hua Sui-Sheng T. , Baker James L. , Flores-Espiritu Melanie 
Published: December 2019

ABSTRACT

The
nor
mutant of
Aspergillus flavus
has a defective norsolorinic acid reductase, and thus the aflatoxin biosynthetic pathway is blocked, resulting in the accumulation of norsolorinic acid, a bright red-orange pigment. We developed a visual agar plate assay to monitor yeast strains for their ability to inhibit aflatoxin production by visually scoring the accumulation of this pigment of the
nor
mutant. We identified yeast strains that reduced the red-orange pigment accumulation in the
nor
mutant. These yeasts also reduced aflatoxin accumulation by a toxigenic strain of
A. flavus
. These yeasts may be useful for reducing aflatoxin contamination of food commodities.
Removal of Endotoxin during Purification of Poly(3-Hydroxybutyrate) from Gram-Negative Bacteria
Authors: Lee Sang Yup , Choi Jong-il , Han Kyuboem , Song Ji Yong 
Published: December 2019

ABSTRACT

Poly(3-hydroxybutyrate) (PHB) was produced by cultivating several gram-negative bacteria, including
Ralstonia eutropha
,
Alcaligenes latus
, and recombinant
Escherichia coli
. PHB was recovered from these bacteria by two different methods, and the endotoxin levels were determined. When PHB was recovered by the chloroform extraction method, the endotoxin level was less than 10 endotoxin units (EU) per g of PHB irrespective of the bacterial strains employed and the PHB content in the cell. The NaOH digestion method, which was particularly effective for the recovery of PHB from recombinant
E. coli
, was also examined for endotoxin removal. The endotoxin level present in PHB recovered by 0.2 N NaOH digestion for 1 h at 30°C was higher than 10
4
EU/g of PHB. Increasing the digestion time or NaOH concentration reduced the endotoxin level to less than 1 EU/g of PHB. It was concluded that PHB with a low endotoxin level, which can be used for various biomedical applications, could be produced by chloroform extraction. Furthermore, PHB with a much lower endotoxin level could be produced from recombinant
E. coli
by simple NaOH digestion.
Cloning and Characterization of a
Rhizobium leguminosarum
Gene Encoding a Bacteriocin with Similarities to RTX Toxins
Authors: Oresnik Ivan J. , Twelker Sunny , Hynes Michael F. 
Published: December 2019

ABSTRACT

A 3-kb region containing the determinant for bacteriocin activity from
Rhizobium leguminosarum
248 was isolated and characterized by Tn
5
insertional mutagenesis and DNA sequencing. Southern hybridizations showed that this bacteriocin was encoded on the plasmid pRL1JI and that homologous loci were not found in other unrelated
R. leguminosarum
strains. Tn
5
insertional mutagenesis showed that mutations in the C-terminal half of the bacteriocin open reading frame apparently did not abolish bacteriocin activity. Analysis of the deduced amino acid sequence revealed that, similarly to RTX proteins (such as hemolysin and leukotoxin), this protein contains a characteristic nonapeptide repeated up to 18 times within the protein. In addition, a novel 19- to 25-amino-acid motif that occurred every 130 amino acids was detected. Bacteriocin bioactivity was correlated with the presence of a protein of approximately 100 kDa in the culture supernatants, and the bacteriocin bioactivity demonstrated a calcium dependence in both
R. leguminosarum
and
Sinorhizobium meliloti
. A mutant of strain 248 unable to produce this bacteriocin was found to have a statistically significant reduction in competitiveness for nodule occupancy compared to two test strains in coinoculation assays. However, this strain was unable to compete any more successfully with a third test strain, 3841, than was wild-type 248.
Indication that the Nitrogen Source Influences Both Amount and Size of Exopolysaccharides Produced by
Streptococcus thermophilus
LY03 and Modelling of the Bacterial Growth and Exopolysaccharide Production in a Complex Medium
Authors: Degeest Bart , De Vuyst Luc 
Published: December 2019

ABSTRACT

Streptococcus thermophilus
LY03 is a yogurt strain producing the same exopolysaccharide material in both milk and MRS broth. Actually, two types of exopolysaccharides are produced simultaneously. The two exopolysaccharides are identical in monomer composition (galactose and glucose in a 4:1 ratio) but differ in molecular size. Gel permeation chromatography revealed a high-molecular-mass exopolysaccharide (1.8 × 10
6
) and a low-molecular-mass exopolysaccharide (4.1 × 10
5
). Both exopolysaccharides can be isolated from the fermentation broth separately. The proportion in which they are produced is strongly dependent on the carbon/nitrogen ratio of the fermentation broth. A shift from a high-molecular-mass exopolysaccharide to a low-molecular-mass exopolysaccharide was observed with increasing initial complex nitrogen concentrations. All necessary biokinetic parameters to study the kinetics of
S. thermophilus
LY03 fermentations were obtained from a mathematical model which describes both
S. thermophilus
LY03 growth and exopolysaccharide production and degradation. The model is valid with various initial complex nitrogen concentrations and can be applied to simulate exopolysaccharide production in a milk medium.
Solubilization of Phosphates and Micronutrients by the Plant-Growth-Promoting and Biocontrol Fungus
Trichoderma harzianum
Rifai 1295-22
Authors: Altomare C. , Norvell W. A. , Björkman T. , Harman G. E. 
Published: December 2019

ABSTRACT

We investigated the capability of the plant-growth-promoting and biocontrol fungus
Trichoderma harzianum
Rifai 1295-22 (T-22) to solubilize in vitro some insoluble or sparingly soluble minerals via three possible mechanisms: acidification of the medium, production of chelating metabolites, and redox activity. T-22 was able to solubilize MnO
2
, metallic zinc, and rock phosphate (mostly calcium phosphate) in a liquid sucrose-yeast extract medium, as determined by inductively coupled plasma emission spectroscopy. Acidification was not the major mechanism of solubilization since the pH of cultures never fell below 5.0 and in cultures containing MnO
2
the pH rose from 6.8 to 7.4. Organic acids were not detected by high-performance thin-layer chromatography in the culture filtrates. Fe
2
O
3
, MnO
2
, Zn, and rock phosphate were also solubilized by cell-free culture filtrates. The chelating activity of T-22 culture filtrates was determined by a method based on measurement of the equilibrium concentration of the chrome azurol S complex in the presence of other chelating substances. A size exclusion chromatographic separation of the components of the culture filtrates indicated the presence of a complexed form of Fe but no chelation of Mn. In liquid culture,
T. harzianum
T-22 also produced diffusible metabolites capable of reducing Fe(III) and Cu(II), as determined by the formation of Fe(II)-Na
2
-bathophenanthrolinedisulfonic acid and Cu(I)-Na
2
-2,9-dimethyl-4,7-diphenyl-1,10-phenanthrolinedisulfonic acid complexes. This is the first report of the ability of a
Trichoderma
strain to solubilize insoluble or sparingly soluble minerals. This activity may explain, at least partially, the ability of T-22 to increase plant growth. Solubilization of metal oxides by
Trichoderma
involves both chelation and reduction. Both of these mechanisms also play a role in biocontrol of plant pathogens, and they may be part of a multiple-component action exerted by T-22 to achieve effective biocontrol under a variety of environmental conditions.