bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arbitrarily Primed PCR To Type
Vibrio
spp. Pathogenic for Shrimp
Authors: Goarant Cyrille , Merien Fabrice , Berthe Franck , Mermoud Isabelle , Perolat Philippe 
Published: December 2019

ABSTRACT

A molecular typing study on
Vibrio
strains implicated in shrimp disease outbreaks in New Caledonia and Japan was conducted by using AP-PCR (arbitrarily primed PCR). It allowed rapid identification of isolates at the genospecies level and studies of infraspecific population structures of epidemiological interest. Clusters identified within the species
Vibrio penaeicida
were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km. Other subclusters of New Caledonian
V. penaeicida
isolates could be identified, but it was not possible to link those differences to accurate epidemiological features. This contribution of AP-PCR to the study of vibriosis in penaeid shrimps demonstrates its high discriminating power and the relevance of the epidemiological information provided. This approach would contribute to better knowledge of the ecology of
Vibrio
spp. and their implication in shrimp disease in aquaculture.
Heat Resistance of Native and Demineralized Spores of
Bacillus subtilis
Sporulated at Different Temperatures
Authors: Palop Alfredo , Sala Francisco J. , Condón Santiago 
Published: December 2019

ABSTRACT

Demineralization reduced heat resistance of
B. subtilis
spores, but the pattern and magnitude of the reduction depended on sporulation temperature and on heating menstruum pH. The differences in heat resistance of native spores caused by sporulation temperature almost disappeared after demineralization. Demineralized spores were still susceptible to the heat-sensitizing effect of acidic pH.
Contrasting Effects of a Nonionic Surfactant on the Biotransformation of Polycyclic Aromatic Hydrocarbons to
cis
-Dihydrodiols by Soil Bacteria
Authors: Allen Christopher C. R. , Boyd Derek R. , Hempenstall Francis , Larkin Michael J. , Sharma Narain D. 
Published: December 2019

ABSTRACT

The biotransformation of the polycyclic aromatic hydrocarbons (PAHs) naphthalene and phenanthrene was investigated by using two dioxygenase-expressing bacteria,
Pseudomonas
sp. strain 9816/11 and
Sphingomonas yanoikuyae
B8/36, under conditions which facilitate mass-transfer limited substrate oxidation. Both of these strains are mutants that accumulate
cis
-dihydrodiol metabolites under the reaction conditions used. The effects of the nonpolar solvent 2,2,4,4,6,8,8-heptamethylnonane (HMN) and the nonionic surfactant Triton X-100 on the rate of accumulation of these metabolites were determined. HMN increased the rate of accumulation of metabolites for both microorganisms, with both substrates. The enhancement effect was most noticeable with phenanthrene, which has a lower aqueous solubility than naphthalene. Triton X-100 increased the rate of oxidation of the PAHs with strain 9816/11 with the effect being most noticeable when phenanthrene was used as a substrate. However, the surfactant inhibited the biotransformation of both naphthalene and phenanthrene with strain B8/36 under the same conditions. The observation that a nonionic surfactant could have such contrasting effects on PAH oxidation by different bacteria, which are known to be important for the degradation of these compounds in the environment, may explain why previous research on the application of the surfactants to PAH bioremediation has yielded inconclusive results. The surfactant inhibited growth of the wild-type strain
S. yanoikuyae
B1 on aromatic compounds but did not inhibit B8/36 dioxygenase enzyme activity in vitro.
Relationship between Glycosyl Hydrolase Inventory and Growth Physiology of the Hyperthermophile
Pyrococcus furiosus
on Carbohydrate-Based Media
Authors: Driskill Lance E. , Kusy Kevin , Bauer Michael W. , Kelly Robert M. 
Published: December 2019

ABSTRACT

Utilization of a range of carbohydrates for growth by the hyperthermophile
Pyrococcus furiosus
was investigated by examining the spectrum of glycosyl hydrolases produced by this microorganism and the thermal labilities of various saccharides. Previously,
P. furiosus
had been found to grow in batch cultures on several α-linked carbohydrates and cellobiose but not on glucose or other β-linked sugars. Although
P. furiosus
was not able to grow on any nonglucan carbohydrate or any form of cellulose in this study (growth on oat spelt arabinoxylan was attributed to glucan contamination of this substrate), significant growth at 98°C occurred on β-1,3- and β-1,3–β-1,4-linked glucans. Oligosaccharides generated by digestion with a recombinant laminarinase derived from
P. furiosus
were the compounds that were most effective in stimulating growth of the microorganism. In several cases, periodic addition of β-glucan substrates to fed-batch cultures limited adverse thermochemical modifications of the carbohydrates (i.e., Maillard reactions and caramelization) and led to significant increases (as much as two- to threefold) in the cell yields. While glucose had only a marginally positive effect on growth in batch culture, the final cell densities nearly tripled when glucose was added by the fed-batch procedure. Nonenzymatic browning reactions were found to be significant at 98°C for saccharides with degrees of polymerization (DP) ranging from 1 to 6; glucose was the most labile compound on a mass basis and the least labile compound on a molar basis. This suggests that for DP of 2 or greater protection of the nonreducing monosaccharide component may be a factor in substrate availability. For
P. furiosus
, carbohydrate utilization patterns were found to reflect the distribution of the glycosyl hydrolases which are known to be produced by this microorganism.
Growth Characteristics of
Heterosigma akashiwo
Virus and Its Possible Use as a Microbiological Agent for Red Tide Control
Authors: Nagasaki Keizo , Tarutani Kenji , Yamaguchi Mineo 
Published: December 2019

ABSTRACT

The growth characteristics of
Heterosigma akashiwo
virus clone 01 (HaV01) were examined by performing a one-step growth experiment. The virus had a latent period of 30 to 33 h and a burst size of 7.7 × 10
2
lysis-causing units in an infected cell. Transmission electron microscopy showed that the virus particles formed on the peripheries of viroplasms, as observed in a natural
H. akashiwo
cell. Inoculation of HaV01 into a mixed algal culture containing four phytoplankton species,
H. akashiwo
H93616
,
Chattonella antiqua
(a member of the family Raphidophyceae),
Heterocapsa triquetra
(a member of the family Dinophyceae), and
Ditylum brightwellii
(a member of the family Bacillariophyceae), resulted in selective growth inhibition of
H. akashiwo
. Inoculation of HaV01 and
H. akashiwo
H93616
into a natural seawater sample produced similar results. However, a natural
H. akashiwo
red tide sample did not exhibit any conspicuous sensitivity to HaV01, presumably because of the great diversity of the host species with respect to virus infection. The growth characteristics of the lytic virus infecting the noxious harmful algal bloom-causing alga were considered, and the possibility of using this virus as a microbiological agent against
H. akashiwo
red tides is discussed.
Purification and Characterization of Gentisate 1,2-Dioxygenases from
Pseudomonas alcaligenes
NCIB 9867 and
Pseudomonas putida
NCIB 9869
Authors: Feng Yongmei , Khoo Hoon Eng , Poh Chit Laa 
Published: December 2019

ABSTRACT

Two 3-hydroxybenzoate-inducible gentisate 1,2-dioxygenases were purified to homogeneity from
Pseudomonas alcaligenes
NCIB 9867 (P25X) and
Pseudomonas putida
NCIB 9869 (P35X), respectively. The estimated molecular mass of the purified P25X gentisate 1,2-dioxygenase was 154 kDa, with a subunit mass of 39 kDa. Its structure is deduced to be a tetramer. The pI of this enzyme was established to be 4.8 to 5.0. The subunit mass of P35X gentisate 1,2-dioxygenase was 41 kDa, and this enzyme was deduced to exist as a dimer, with a native molecular mass of about 82 kDa. The pI of P35X gentisate 1,2-dioxygenase was around 4.6 to 4.8. Both of the gentisate 1,2-dioxygenases exhibited typical saturation kinetics and had apparent

K
m

s of 92 and 143 μM for gentisate, respectively. Broad substrate specificities were exhibited towards alkyl and halogenated gentisate analogs. Both enzymes had similar kinetic turnover characteristics for gentisate, with
k
cat
/

K
m

values of 44.08 × 10
4
s
−1
M
−1
for the P25X enzyme and 39.34 × 10
4
s
−1
M
−1
for the P35X enzyme. Higher
k
cat
/

K
m

values were expressed by both enzymes against the substituted gentisates. Significant differences were observed between the N-terminal sequences of the first 23 amino acid residues of the P25X and P35X gentisate 1,2-dioxygenases. The P25X gentisate 1,2-dioxygenase was stable between pH 5.0 and 7.5, with the optimal pH around 8.0. The P35X enzyme showed a pH stability range between 7.0 and 9.0, and the optimum pH was also 8.0. The optimal temperature for both P25X and P35X gentisate 1,2-dioxygenases was around 50°C, but the P35X enzyme was more heat stable than that from P25X. Both enzymes were strongly stimulated by 0.1 mM Fe
2+
but were completely inhibited by the presence of 5 mM Cu
2+
. Partial inhibition of both enzymes was also observed with 5 mM Mn
2+
, Zn
2+
, and EDTA.
Molecular Characterization of the Genes
pcaG
and
pcaH
, Encoding Protocatechuate 3,4-Dioxygenase, Which Are Essential for Vanillin Catabolism in
Pseudomonas
sp. Strain HR199
Authors: Overhage Jörg , Kresse Andreas U. , Priefert Horst , Sommer Horst , Krammer Gerhard , Rabenhorst Jürgen , Steinbüchel Alexander 
Published: December 2019

ABSTRACT

Pseudomonas
sp. strain HR199 is able to utilize eugenol (4-allyl-2-methoxyphenol), vanillin (4-hydroxy-3-methoxybenzaldehyde), or protocatechuate as the sole carbon source for growth. Mutants of this strain which were impaired in the catabolism of vanillin but retained the ability to utilize eugenol or protocatechuate were obtained after nitrosoguanidine mutagenesis. One mutant (SK6169) was used as recipient of a
Pseudomonas
sp. strain HR199 genomic library in cosmid pVK100, and phenotypic complementation was achieved with a 5.8-kbp
Eco
RI fragment (E58). The amino acid sequences deduced from two corresponding open reading frames (ORF) identified on E58 revealed high degrees of homology to
pcaG
and
pcaH
, encoding the two subunits of protocatechuate 3,4-dioxygenase. Three additional ORF most probably encoded a 4-hydroxybenzoate 3-hydroxylase (PobA) and two putative regulatory proteins, which exhibited homology to PcaQ of
Agrobacterium tumefaciens
and PobR of
Pseudomonas aeruginosa
, respectively. Since mutant SK6169 was also complemented by a subfragment of E58 that harbored only
pcaH
, this mutant was most probably lacking a functional β subunit of the protocatechuate 3,4-dioxygenase. Since this mutant was still able to grow on protocatechuate and lacked protocatechuate 4,5-dioxygenase and protocatechuate 2,3-dioxygenase, the degradation had to be catalyzed by different enzymes. Two other mutants (SK6184 and SK6190), which were also impaired in the catabolism of vanillin, were not complemented by fragment E58. Since these mutants accumulated 3-carboxy muconolactone during cultivation on eugenol, they most probably exhibited a defect in a step of the catabolic pathway following the
ortho
cleavage. Moreover, in these mutants cyclization of 3-carboxymuconic acid seems to occur by a
syn
absolute stereochemical course, which is normally only observed for
cis
,
cis
-muconate lactonization in pseudomonads. In conclusion, vanillin is degraded through the
ortho
-cleavage pathway in
Pseudomonas
sp. strain HR199 whereas protocatechuate could also be metabolized via a different pathway in the mutants.
Molecular Differentiation of
Renibacterium salmoninarum
Isolates from Worldwide Locations
Authors: Grayson Thomas H. , Cooper Lynne F. , Atienzar Franck A. , Knowles Mark R. , Gilpin Martyn L. 
Published: December 2019

ABSTRACT

Renibacterium salmoninarum
is a genospecies that is an obligate pathogen of salmonid fish and is capable of intracellular survival. Conventional typing systems have failed to differentiate isolates of
R. salmoninarum
. We used two methods to assess the extent of molecular variation which was present in isolates from different geographic locations. In one analysis we investigated possible polymorphisms in a specific region of the genome, the intergenic spacer (ITS) region between the 16S and 23S rRNA genes. In the other analysis we analyzed differences throughout the genome by using randomly amplified polymorphic DNA (RAPD). We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples. The results showed that the 16S-23S ribosomal DNA spacer region of
R. salmoninarum
is highly conserved and suggested that only a single copy of the rRNA operon is present in this slowly growing pathogen. DNA sequencing of the spacer region showed that it was the same length in all 14 isolates examined, and the same nucleotide sequence, sequevar 1, was obtained for 11 of these isolates. Two other sequevars were found. No tRNA genes were found. We found that RAPD analysis allows reproducible differentiation between isolates of
R. salmoninarum
obtained from different hosts and different geographic regions. By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences.
Effect of Phenylurea Herbicides on Soil Microbial Communities Estimated by Analysis of 16S rRNA Gene Fingerprints and Community-Level Physiological Profiles
Authors: el Fantroussi Saïd , Verschuere Laurent , Verstraete Willy , Top Eva M. 
Published: December 2019

ABSTRACT
The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.
Anaerobic Oxidation of o -Xylene, m -Xylene, and Homologous Alkylbenzenes by New Types of Sulfate-Reducing Bacteria
Authors: Harms Gerda , Zengler Karsten , Rabus Ralf , Aeckersberg Frank , Minz Dror , Rosselló-Mora Ramon , Widdel Friedrich 
Published: December 2019

ABSTRACT

Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with
o
-xylene and
m
-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the δ subclass of the class
Proteobacteria
. Strain oXyS1 showed the highest similarities to
Desulfobacterium cetonicum
and
Desulfosarcina variabilis
(similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being
Desulfococcus multivorans
(similarity value, 86.9%). Complete mineralization of
o
-xylene and
m
-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene,
o
-ethyltoluene, benzoate, and
o
-methylbenzoate in addition to
o
-xylene. Strain mXyS1 oxidized toluene,
m
-ethyltoluene,
m
-isoproyltoluene, benzoate, and
m
-methylbenzoate in addition to
m
-xylene. Strain oXyS1 did not utilize
m
-alkyltoluenes, whereas strain mXyS1 did not utilize
o
-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide.
Fungal Degradation of Lipophilic Extractives in
Eucalyptus globulus
Wood
Authors: Gutiérrez Ana , del Río José C. , Martínez María Jesús , Martínez Angel T. 
Published: December 2019

ABSTRACT

Solid-state fermentation of eucalypt wood with several fungal strains was investigated as a possible biological pretreatment for decreasing the content of compounds responsible for pitch deposition during Cl
2
-free manufacture of paper pulp. First, different pitch deposits were characterized by gas chromatography (GC) and GC-mass spectrometry (MS). The chemical species identified arose from lipophilic wood extractives that survived the pulping and bleaching processes. Second, a detailed GC-MS analysis of the lipophilic fraction after fungal treatment of wood was carried out, and different degradation patterns were observed. The results showed that some basidiomycetes that decreased the lipophilic fraction also released significant amounts of polar extractives, which were identified by thermochemolysis as originating from lignin depolymerization. Therefore, the abilities of fungi to control pitch should be evaluated after analysis of compounds involved in deposit formation and not simply by estimating the decrease in the total extractive content. In this way,
Phlebia radiata
,
Funalia trogii
,
Bjerkandera adusta
, and
Poria subvermispora
strains were identified as the most promising organisms for pitch biocontrol, since they degraded 75 to 100% of both free and esterified sterols, as well as other lipophilic components of the eucalypt wood extractives.
Ophiostoma piliferum
, a fungus used commercially for pitch control, hydrolyzed the sterol esters and triglycerides, but it did not appear to be suitable for eucalypt wood treatment because it increased the content of free sitosterol, a major compound in pitch deposits.
Homofermentative Production of
d
- or
l
-Lactate in Metabolically Engineered
Escherichia coli
RR1
Authors: Chang Dong-Eun , Jung Heung-Chae , Rhee Joon-Shick , Pan Jae-Gu 
Published: December 2019

ABSTRACT

We investigated metabolic engineering of fermentation pathways in
Escherichia coli
for production of optically pure
d
- or
l
-lactate. Several
pta
mutant strains were examined, and a
pta
mutant of
E. coli
RR1 which was deficient in the phosphotransacetylase of the Pta-AckA pathway was found to metabolize glucose to
d
-lactate and to produce a small amount of succinate by-product under anaerobic conditions. An additional mutation in
ppc
made the mutant produce
d
-lactate like a homofermentative lactic acid bacterium. When the
pta ppc
double mutant was grown to higher biomass concentrations under aerobic conditions before it shifted to the anaerobic phase of
d
-lactate production, more than 62.2 g of
d
-lactate per liter was produced in 60 h, and the volumetric productivity was 1.04 g/liter/h. To examine whether the blocked acetate flux could be reoriented to a nonindigenous
l
-lactate pathway, an
l
-lactate dehydrogenase gene from
Lactobacillus casei
was introduced into a
pta ldhA
strain which lacked phosphotransacetylase and
d
-lactate dehydrogenase. This recombinant strain was able to metabolize glucose to
l
-lactate as the major fermentation product, and up to 45 g of
l
-lactate per liter was produced in 67 h. These results demonstrate that the central fermentation metabolism of
E. coli
can be reoriented to the production of
d
-lactate, an indigenous fermentation product, or to the production of
l
-lactate, a nonindigenous fermentation product.
Role of Calcium in Activity and Stability of the
Lactococcus lactis
Cell Envelope Proteinase
Authors: Exterkate Fred A. , Alting Arno C. 
Published: December 2019

ABSTRACT

The mature lactococcal cell envelope proteinase (CEP) consists of an N-terminal subtilisin-like proteinase domain and a large C-terminal extension of unknown function whose far end anchors the molecule in the cell envelope. Different types of CEP can be distinguished on the basis of specificity and amino acid sequence. Removal of weakly bound Ca
2+
from the native cell-bound CEP of
Lactococcus lactis
SK11 (type III specificity) is coupled with a significant reversible decrease in specific activity and a dramatic reversible reduction in thermal stability, as a result of which no activity at 25°C (pH 6.5) can be measured. The consequences of Ca
2+
removal are less dramatic for the CEP of strain Wg2 (mixed type I-type III specificity). Autoproteolytic release of CEP from cells concerns this so-called “Ca-free” form only and occurs most efficiently in the case of the Wg2 CEP. The results of a study of the relationship between the Ca
2+
concentration and the stability and activity of the cell-bound SK11 CEP at 25°C suggested that binding of at least two Ca
2+
ions occurred. Similar studies performed with hybrid CEPs constructed from SK11 and Wg2 wild-type CEPs revealed that the C-terminal extension plays a determinative role with respect to the ultimate distinct Ca
2+
dependence of the cell-bound CEP. The results are discussed in terms of predicted Ca
2+
binding sites in the subtilisin-like proteinase domain and Ca-triggered structural rearrangements that influence both the conformational stability of the enzyme and the effectiveness of the catalytic site. We argue that distinctive primary folding of the proteinase domain is guided and maintained by the large C-terminal extension.