bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonization of Wheat Roots by an Exopolysaccharide-Producing
Pantoea agglomerans
Strain and Its Effect on Rhizosphere Soil Aggregation
Authors: Amellal N. , Burtin G. , Bartoli F. , Heulin T. 
Published: December 2019

ABSTRACT

The effect of bacterial secretion of an exopolysaccharide (EPS) on rhizosphere soil physical properties was investigated by inoculating strain NAS206, which was isolated from the rhizosphere of wheat (
Triticum durum
L.) growing in a Moroccan vertisol and was identified as
Pantoea aglomerans
. Phenotypic identification of this strain with the Biotype-100 system was confirmed by amplified ribosomal DNA restriction analysis. After inoculation of wheat seedlings with strain NAS206, colonization increased at the rhizoplane and in root-adhering soil (RAS) but not in bulk soil. Colonization further increased under relatively dry conditions (20% soil water content; matric potential, −0.55 MPa). By means of genetic fingerprinting using enterobacterial repetitive intergenic consensus PCR, we were able to verify that colonies counted as strain NAS206 on agar plates descended from inoculated strain NAS206. The intense colonization of the wheat rhizosphere by these EPS-producing bacteria was associated with significant soil aggregation, as shown by increased ratios of RAS dry mass to root tissue (RT) dry mass (RAS/RT) and the improved water stability of adhering soil aggregates. The maximum effect of strain NAS206 on both the RAS/RT ratio and aggregate stability was measured at 24% average soil water content (matric potential, −0.20 MPa). Inoculated strain NAS206 improved RAS macroporosity (pore diameter, 10 to 30 μm) compared to the noninoculated control, particularly when the soil was nearly water saturated (matric potential, −0.05 MPa). Our results suggest that
P. agglomerans
NAS206 can play an important role in the regulation of the water content (excess or deficit) of the rhizosphere of wheat by improving soil aggregation.
Phenotypic and Phylogenetic Characterization of Ruminal Tannin-Tolerant Bacteria
Authors: Nelson Karen E. , Thonney Michael L. , Woolston Tina K. , Zinder Stephen H. , Pell Alice N. 
Published: December 2019

ABSTRACT

The 16S rRNA sequences and selected phenotypic characteristics were determined for six recently isolated bacteria that can tolerate high levels of hydrolyzable and condensed tannins. Bacteria were isolated from the ruminal contents of animals in different geographic locations, including Sardinian sheep (
Ovis aries
), Honduran and Colombian goats (
Capra hircus
), white-tail deer (
Odocoileus virginianus
) from upstate New York, and Rocky Mountain elk (
Cervus elaphus nelsoni
) from Oregon. Nearly complete sequences of the small-subunit rRNA genes, which were obtained by PCR amplification, cloning, and sequencing, were used for phylogenetic characterization. Comparisons of the 16S rRNA of the six isolates showed that four of the isolates were members of the genus
Streptococcus
and were most closely related to ruminal strains of
Streptococcus bovis
and the recently described organism
Streptococcus gallolyticus
. One of the other isolates, a gram-positive rod, clustered with the clostridia in the low-G+C-content group of gram-positive bacteria. The sixth isolate, a gram-negative rod, was a member of the family
Enterobacteriaceae
in the gamma subdivision of the class
Proteobacteria
. None of the 16S rRNA sequences of the tannin-tolerant bacteria examined was identical to the sequence of any previously described microorganism or to the sequence of any of the other organisms examined in this study. Three phylogenetically distinct groups of ruminal bacteria were isolated from four species of ruminants in Europe, North America, and South America. The presence of tannin-tolerant bacteria is not restricted by climate, geography, or host animal, although attempts to isolate tannin-tolerant bacteria from cows on low-tannin diets failed.
Comparison ofPaenibacillus azotofixansStrains Isolated from Rhizoplane, Rhizosphere, and Non-Root-Associated Soil from Maize Planted in Two Different Brazilian Soils
Authors: Seldin Lucy , Rosado Alexandre Soares , da Cruz Davi William , Nobrega Alberto , van Elsas Jan Dirk , Paiva Edilson 
Published: December 2019

ABSTRACTPaenibacillus azotofixansis a nitrogen-fixing bacterium often found in soil and in the rhizospheres of different grasses. In this study, two Brazilian clay soils were planted with cross-hybrid maize (BR-201) and four stages of plant growth were analyzed to characterize theP. azotofixanspopulations present in the rhizoplanes, rhizospheres, and non-root-associated soils (herein called nonrhizospheres). A total of 106 strains were isolated and identified asP. azotofixanswith an API 50CH kit, by classical biochemical tests, and via the use of specific primers based on the 16S rRNA gene in PCRs. To compare the isolated strains, phenotypic characteristics were determined and three different probes were used in hybridization experiments: twonifprobes and one probe comprising a 0.58-kb fragment cloned from theP. azotofixansC3L4 genome. These results were used to construct a dendrogram, in which two main clusters could be observed. One cluster contained exclusively strains from Várzea soil, and the other contained the majority of strains from Cerrado soil. The 60 strains from Várzea soil and the 46 strains from Cerrado soil were further analyzed with REP and BOX primers, respectively. Based on the patterns obtained, it was possible to identify 21 different groups among strains from Várzea soil and 4 different groups among strains from Cerrado soil. These different patterns were tested by multivariate analysis of variance, and differences in the populations ofP. azotofixansduring the four stages of plant growth were demonstrated. Moreover, strains isolated from the rhizoplanes, rhizospheres, and nonrhizospheres of maize planted in Cerrado and Várzea soils were shown to be statistically different; the diversity ofP. azotofixansstrains was affected by the soil type.
Occurrence of Fusaproliferin and Beauvericin in
Fusarium
-Contaminated Livestock Feed in Iowa
Authors: Munkvold Gary , Stahr H. M. , Logrieco Antonio , Moretti Antonio , Ritieni Alberto 
Published: December 2019

ABSTRACT

Fusarium
fungal contaminants and related mycotoxins were investigated in eight maize feed samples submitted to the Iowa State University Veterinary Diagnostic Laboratory.
Fusarium moniliforme
,
F. proliferatum
, and
F. subglutinans
were isolated from seven, eight, and five samples, respectively. These strains belonged to mating populations A, D, and E of the teleomorph
Gibberella fujikuroi
. Fusaproliferin was detected at concentrations of 0.1 to 30 μg/g in four samples, and beauvericin was detected (0.1 to 3.0 μg/g) in five samples. Fumonisins were detected in all eight samples (1.1 to 14 μg/g). Ten of 11 strains of
F. proliferatum
and all 12 strains of
F. subglutinans
isolated from the samples produced fusaproliferin in culture on whole maize kernels (4 to 350 and 100 to 1,000 μg/g, respectively). Nine
F. proliferatum
strains also produced beauvericin in culture (85 to 350 μg/g), but none of the
F. subglutinans
strains produced beauvericin. Fumonisin B
1
was produced by all nine
F. moniliforme
strains (50 to 2,000 μg/g) and by 10 of the
F. proliferatum
strains (1,000 to 2,000 μg/g). This is the first report of the natural occurrence of fusaproliferin outside Italy and of the natural occurrence of beauvericin in North America.
Purification and Characterization of an NAD-Malic Enzyme from
Bradyrhizobium japonicum
A1017
Authors: Chen Fan , Okabe Youichi , Osano Kaoru , Tajima Shigeyuki 
Published: December 2019

ABSTRACT

An NAD-malic enzyme was purified to homogeneity from
Bradyrhizobium japonicum
A1017, and its molecular characteristics were surveyed. The enzyme exhibited native and subunit molecular masses of 388 and 85 kDa, respectively, suggesting that it exists as a homotetramer, and was activated by metabolic intermediates in glycolysis. The role of the enzyme in bacteroids’ carbon metabolism is discussed.
Balance of Activities of Alcohol Acetyltransferase and Esterase in
Saccharomyces cerevisiae
Is Important for Production of Isoamyl Acetate
Authors: Fukuda Kiyoshi , Yamamoto Nagi , Kiyokawa Yoshifumi , Yanagiuchi Toshiyasu , Wakai Yoshinori , Kitamoto Katsuhiko , Inoue Yoshiharu , Kimura Akira 
Published: December 2019

ABSTRACT

Isoamyl acetate is synthesized from isoamyl alcohol and acetyl coenzyme A by alcohol acetyltransferase (AATFase) in
Saccharomyces cerevisiae
and is hydrolyzed by esterases at the same time. We hypothesized that the balance of both enzyme activities was important for optimum production of isoamyl acetate in sake brewing. To test this hypothesis, we constructed yeast strains with different numbers of copies of the AATFase gene (
ATF1
) and the isoamyl acetate-hydrolyzing esterase gene (
IAH1
) and used these strains in small-scale sake brewing. Fermentation profiles as well as components of the resulting sake were largely alike; however, the amount of isoamyl acetate in the sake increased with an increasing ratio of AATFase/Iah1p esterase activity. Therefore, we conclude that the balance of these two enzyme activities is important for isoamyl acetate accumulation in sake mash.
Persistence of PCR-Detectable
Bacteroides distasonis
from Human Feces in River Water
Authors: Kreader Carol A. 
Published: December 2019

ABSTRACT

To evaluate the persistence of PCR-detectable
Bacteroides distasonis
in surface water, whole human feces were dispersed into water from the Ohio River and incubated in flasks in the laboratory or in diffusion chambers in situ. Duplicate samples were taken daily, and material that pelleted at 16,000 ×
g
was assayed by PCR. Persistence of PCR-detectable DNA from this anaerobe depended upon temperature and predation, two of the factors shown by others to influence the survival of aerobic bacteria detected by culture.
B. distasonis
was detected by PCR for at least 2 weeks at 4°C but for only 4 to 5 days at 14°C, 1 to 2 days at 24°C, and 1 day at 30°C. In filtered water or in the presence of cycloheximide, a eukaryotic inhibitor, persistence at 24°C was extended by at least a week.
Survival of
Enterococcus faecalis
in an Oligotrophic Microcosm: Changes in Morphology, Development of General Stress Resistance, and Analysis of Protein Synthesis
Authors: Hartke Axel , Giard Jean-Christophe , Laplace Jean-Marie , Auffray Yanick 
Published: December 2019

ABSTRACT

The ability of
Enterococcus faecalis
to metabolically adapt to an oligotrophic environment has been analyzed.
E. faecalis
is able to survive for prolonged periods under conditions of complete starvation established by incubation in tap water. During incubation in this microcosm, cells developed a rippled cell surface with irregular shapes. Exponentially growing cells survived to the same extent as cells starved for glucose prior to exposure to the multiple nutrient deficient stress. Chloramphenicol treatment during incubation in tap water led to a rapid decline in plate counts for exponentially growing cells but showed progressively reduced influence on stationary-phase cells harvested after different times of glucose starvation. During incubation in the oligotrophic environment, cells from the exponential-growth phase and early-stationary phase became progressively more resistant to other environmental stresses (heat [62°C], acid [pH 3.3], UV
254 nm
light [180 J/m
2
], and sodium hypochlorite [0.05%]) until they reached a maximum of survival characteristic for each treatment. In contrast, cells starved of glucose for 24 h did not become more resistant to the different treatments during incubation in tap water. Our combined data suggest that energy starvation induces a response similar to that triggered by oligotrophy. Analysis of protein synthesis by two-dimensional gel electrophoresis revealed the enhanced synthesis of 51 proteins which were induced in the oligotrophic environment. A comparison of these oligotrophy-inducible proteins with the 42 glucose starvation-induced polypeptides (J. C. Giard, A. Hartke, S. Flahaut, P. Boutibonnes, and Y. Auffray, Res. Microbiol. 148:27–35, 1997) showed that 16 are common between the two different starvation conditions. These proteins and the corresponding genes seem to play a key role in the observed phenomena of long-term survival and development of general stress resistance of starved cultures of
E. faecalis
.
Threonine Aldolase Overexpression plus Threonine Supplementation Enhanced Riboflavin Production in
Ashbya gossypii
Authors: Monschau Nicole , Sahm Hermann , Stahmann K.-Peter 
Published: December 2019

ABSTRACT

Riboflavin production in the filamentous fungus
Ashbya gossypii
is limited by glycine, an early precursor required for purine synthesis. We report an improvement of riboflavin production in this fungus by overexpression of the glycine biosynthetic enzyme threonine aldolase. The
GLY1
gene encoding the threonine aldolase of
A. gossypii
was isolated by heterologous complementation of the glycine-auxotrophic
Saccharomyces cerevisiae
strain YM13 with a genomic library from
A. gossypii
. The deduced amino acid sequence of
GLY1
showed 88% similarity to threonine aldolase from
S. cerevisiae
. In the presence of the
GLY1
gene, 25 mU of threonine aldolase specific activity mg
−1
was detectable in crude extracts of
S. cerevisiae
YM13. Disruption of
GLY1
led to a complete loss of threonine aldolase activity in
A. gossypii
crude extracts, but growth of and riboflavin production by the knockout mutant were not affected. This indicated a minor role of the enzyme in glycine biosynthesis of
A. gossypii
. However, overexpression of
GLY1
under the control of the constitutive
TEF
promoter and terminator led to a 10-fold increase of threonine aldolase specific activity in crude extracts along with a 9-fold increase of riboflavin production when the medium was supplemented with threonine. This strong enhancement, which could not be achieved by supplementation with glycine alone, was attributed to an almost quantitative uptake of threonine and its intracellular conversion into glycine. This became evident by a subsequent partial efflux of the glycine formed.
Low-Concentration Kinetics of Atmospheric CH
4
Oxidation in Soil and Mechanism of NH
4
+
Inhibition
Authors: Gulledge Jay , Schimel Joshua P. 
Published: December 2019

ABSTRACT

NH
4
+
inhibition kinetics for CH
4
oxidation were examined at near-atmospheric CH
4
concentrations in three upland forest soils. Whether NH
4
+
-independent salt effects could be neutralized by adding nonammoniacal salts to control samples in lieu of deionized water was also investigated. Because the levels of exchangeable endogenous NH
4
+
were very low in the three soils, desorption of endogenous NH
4
+
was not a significant factor in this study. The

K
m(app)

values for water-treated controls were 9.8, 22, and 57 nM for temperate pine, temperate hardwood, and birch taiga soils, respectively. At CH
4
concentrations of ≤15 μl liter
−1
, oxidation followed first-order kinetics in the fine-textured taiga soil, whereas the coarse-textured temperate soils exhibited Michaelis-Menten kinetics. Compared to water controls, the

K
m(app)

values in the temperate soils increased in the presence of NH
4
+
salts, whereas the
V

max(
app
)

values decreased substantially, indicating that there was a mixture of competitive and noncompetitive inhibition mechanisms for whole NH
4
+
salts. Compared to the corresponding K
+
salt controls, the

K
m(app)

values for NH
4
+
salts increased substantially, whereas the
V

max
(app)

values remained virtually unchanged, indicating that NH
4
+
acted by competitive inhibition. Nonammoniacal salts caused inhibition to increase with increasing CH
4
concentrations in all three soils. In the birch taiga soil, this trend occurred with both NH
4
+
and K
+
salts, and the slope of the increase was not affected by the addition of NH
4
+
. Hence, the increase in inhibition resulted from an NH
4
+
-independent mechanism. These results show that NH
4
+
inhibition of atmospheric CH
4
oxidation resulted from enzymatic substrate competition and that additional inhibition that was not competitive resulted from a general salt effect that was independent of NH
4
+
.
Rice Hull Ash and Silicic Acid as Adsorbents for Concentration of Bacteriocins
Authors: Janes M. E. , Nannapaneni R. , Proctor A. , Johnson M. G. 
Published: December 2019

ABSTRACT

A model procedure has been developed for the rapid extraction of five bacteriocins (nisin, pediocin RS2, leucocin BC2, lactocin GI3, and enterocin CS1) from concentrated freeze-dried crude culture supernatants by adsorption onto acid or alkaline rice hull ash (RHA) or silicic acid (SA). Bacteriocins were adsorbed onto RHA or SA by a pH-dependent method and desorbed by decreasing the pH to 2.5 or 3.0 and heating at 90°C for 5 min. The maximum adsorption and optimal pH range for different bacteriocins were as follows: nisin, 97% at pH 7.0; lactocin GI3, 94% at pH 6.0; pediocin RS2, 97% at pH 8.0 to 9.0; leucocin BC2, 88% at pH 9.0; and enterocin CS1, 94% at pH 5.0. The desorption level of lactocin GI3 or enterocin CS1 from the surfaces of both RHA and SA was 94%, while the desorption level of pediocin RS2 and leucocin BC2 was 50% or less. Nisin was desorbed readily from SA (91%) but not from RHA (50% or less). The adsorption of bacteriocins onto RHA and SA increased with the increasing concentration of bacteriocins. Analysis of the desorbed bacteriocins after dialysis and sodium dodecyl sulfate–16% polyacrylamide gel electrophoresis showed a single band that gave a single inhibition zone when overlaid with
Lactobacillus plantarum
for detection of lactocin GI3, enterocin CS1, and nisin. RHA appears useful for extraction, concentration, and partial purification of the five bacteriocins.
Accumulation of α-Keto Acids as Essential Components in Cyanide Assimilation by
Pseudomonas fluorescens
NCIMB 11764
Authors: Kunz Daniel A. , Chen Jui-Lin , Pan Guangliang 
Published: December 2019

ABSTRACT

Pyruvate (Pyr) and α-ketoglutarate (αKg) accumulated when cells of
Pseudomonas fluorescens
NCIMB 11764 were cultivated on growth-limiting amounts of ammonia or cyanide and were shown to be responsible for the nonenzymatic removal of cyanide from culture fluids as previously reported (J.-L. Chen and D. A. Kunz, FEMS Microbiol. Lett. 156:61–67, 1997). The accumulation of keto acids in the medium paralleled the increase in cyanide-removing activity, with maximal activity (760 μmol of cyanide removed min
−1
ml of culture fluid
−1
) being recovered after 72 h of cultivation, at which time the keto acid concentration was 23 mM. The reaction products that formed between the biologically formed keto acids and cyanide were unambiguously identified as the corresponding cyanohydrins by
13
C nuclear magnetic resonance spectroscopy. Both the Pyr and α-Kg cyanohydrins were further metabolized by cell extracts and served also as nitrogenous growth substrates. Radiotracer experiments showed that CO
2
(and NH
3
) were formed as enzymatic conversion products, with the keto acid being regenerated as a coproduct. Evidence that the enzyme responsible for cyanohydrin conversion is cyanide oxygenase, which was shown previously to be required for cyanide utilization, is based on results showing that (i) conversion occurred only when extracts were induced for the enzyme, (ii) conversion was oxygen and reduced-pyridine nucleotide dependent, and (iii) a mutant strain defective in the enzyme was unable to grow when it was provided with the cyanohydrins as a growth substrate. Pyr and αKg were further shown to protect cells from cyanide poisoning, and excretion of the two was directly linked to utilization of cyanide as a growth substrate. The results provide the basis for a new mechanism of cyanide detoxification and assimilation in which keto acids play an essential role.
A Small, Dilute-Cytoplasm, High-Affinity, Novel Bacterium Isolated by Extinction Culture and Having Kinetic Constants Compatible with Growth at Ambient Concentrations of Dissolved Nutrients in Seawater
Authors: Button D. K. , Robertson Betsy R. , Lepp Paul W. , Schmidt Thomas M. 
Published: December 2019

ABSTRACT

Dilutions of raw seawater produced a bacterial isolate capable of extended growth in unamended seawater. Its 2.9-Mb genome size and 40-fg dry mass were similar to values for many naturally occurring aquatic organotrophs, but water and DNA comprised a large portion of this small chemoheterotroph, as compared to
Escherichia coli
. The isolate used only a few aromatic hydrocarbons and acetate, and glucose and amino acid incorporation were entirely absent, although many membrane and cytoplasmic proteins were inducible; it was named
Cycloclasticus oligotrophus
. A general rate equation that incorporates saturation phenomena into specific affinity theory is derived. It is used to relate the kinetic constants for substrate uptake by the isolate to its cellular proteins. The affinity constant

K
A

for toluene was low at 1.3 μg/liter under optimal conditions, similar to those measured in seawater, and the low value was ascribed to an unknown slow step such as limitation by a cytoplasmic enzyme;

K
A

increased with increasing specific affinities. Specific affinities,

a°
s

, were protocol sensitive, but under optimal conditions were 47.4 liters/mg of cells/h, the highest reported in the literature and a value sufficient for growth in seawater at concentrations sometimes found. Few rRNA operons, few cytoplasmic proteins, a small genome size, and a small cell size, coupled with a high

a°
s

and a low solids content and the ability to grow without intentionally added substrate, are consistent with the isolation of a marine bacterium with properties typical of the bulk of those present.
Sequence Polymorphism in the β-Tubulin Gene Reveals Heterogeneous and Variable Population Structures in
Cryptosporidium parvum
Authors: Widmer Giovanni , Tchack Laurie , Chappell Cynthia L. , Tzipori Saul 
Published: December 2019

ABSTRACT

Restriction fragment length polymorphism (RFLP) analysis of isolates of
Cryptosporidium parvum
has revealed two subgroups, termed H and C. The limited resolution of the RFLP method precludes an in-depth study of the genetic structure of
C. parvum
populations. Published
C. parvum
restriction polymorphisms lie within protein-coding regions known to be more homogeneous than noncoding sequences. To better assess the degrees of heterogeneity between and within
C. parvum
isolates, sequence polymorphism in the β-tubulin intron, the only
C. parvum
intron described to date, was investigated. In contrast to the two genotypes distinguished by multilocus RFLP, several alleles were detected by sequence and RFLP analysis of the β-tubulin intron and adjacent exon 2. Isolates carrying different β-tubulin alleles were found. Significantly, one of the β-tubulin alleles present in two geographically unrelated isolates combined features of C- and H-type isolates, suggesting that it might have arisen from a recombination event. A comparison of multiple samples of a calf-propagated laboratory isolate showed that the ratio of different β-tubulin alleles fluctuated during serial passage.
In Situ Detection of an Uncultured Predominant Bacillus in Dutch Grassland Soils
Authors: Felske Andreas , Akkermans Antoon D. L. , De Vos Willem M. 
Published: December 2019

ABSTRACT

Uncultured predominant
Bacillus
ribotype DA001 in Dutch Drentse A grassland soils, as revealed by its 16S rRNA sequence, was detected in soil by fluorescent whole-cell in situ hybridization. A prominent rod-shaped cell type was identified in bacterial suspensions prepared from soil by a multiple 16S rRNA probing approach.