bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phototrophs in High-Iron-Concentration Microbial Mats: Physiological Ecology of Phototrophs in an Iron-Depositing Hot Spring
Authors: Pierson B. K. , Parenteau M. N. , Griffin B. M. 
Published: December 2019

ABSTRACTAt Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [14C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.
Biodegradation of Free Phytol by Bacterial Communities Isolated from Marine Sediments under Aerobic and Denitrifying Conditions
Authors: Rontani Jean-François , Bonin Patricia C. , Volkman John K. 
Published: December 2019

ABSTRACT

Biodegradation of (
E
)-phytol [3,7,11,15-tetramethylhexadec-2(
E
)-en-1-ol] by two bacterial communities isolated from recent marine sediments under aerobic and denitrifying conditions was studied at 20°C. This isoprenoid alcohol is metabolized efficiently by these two bacterial communities via 6,10,14-trimethylpentadecan-2-one and (
E
)-phytenic acid. The first step in both aerobic and anaerobic bacterial degradation of (
E
)-phytol involves the transient production of (
E
)-phytenal, which in turn can be abiotically converted to 6,10,14-trimethylpentadecan-2-one. Most of the isoprenoid metabolites identified in vitro could be detected in a fresh sediment core collected at the same site as the sediments used for the incubations. Since (
E
)-phytenal is less sensitive to abiotic degradation at the temperature of the sediments (15°C), the major part of (
E
)-phytol appeared to be biodegraded in situ via (
E
)-phytenic acid. (
Z
)- and (
E
)-phytenic acids are present in particularly large quantities in the upper section of the core, and their concentrations quickly decrease with depth in the core. This degradation (which takes place without significant production of phytanic acid) is attributed to the involvement of alternating β-decarboxymethylation and β-oxidation reaction sequences induced by denitrifiers. Despite the low nitrate concentration of marine sediments, denitrifying bacteria seem to play a significant role in the mineralization of (
E
)-phytol.
Determining Sources of Fecal Pollution in a Rural Virginia Watershed with Antibiotic Resistance Patterns in Fecal Streptococci
Authors: Hagedorn Charles , Robinson Sandra L. , Filtz Jennifer R. , Grubbs Sarah M. , Angier Theresa A. , Reneau Raymond B. 
Published: December 2019

ABSTRACT
Nonpoint sources of pollution that contribute fecal bacteria to surface waters have proven difficult to identify. Knowledge of pollution sources could aid in restoration of the water quality, reduce the amounts of nutrients leaving watersheds, and reduce the danger of infectious disease resulting from exposure to contaminated waters. Patterns of antibiotic resistance in fecal streptococci were analyzed by discriminant and cluster analysis and used to identify sources of fecal pollution in a rural Virginia watershed. A database consisting of patterns from 7,058 fecal streptococcus isolates was first established from known human, livestock, and wildlife sources in Montgomery County, Va. Correct fecal streptococcus source identification averaged 87% for the entire database and ranged from 84% for deer isolates to 93% for human isolates. To field test the method and the database, a watershed improvement project (Page Brook) in Clarke County, Va., was initiated in 1996. Comparison of 892 known-source isolates from that watershed against the database resulted in an average correct classification rate of 88%. Combining all animal isolates increased correct classification rates to ≥95% for separations between animal and human sources. Stream samples from three collection sites were highly contaminated, and fecal streptococci from these sites were classified as being predominantly from cattle (>78% of isolates), with small proportions from waterfowl, deer, and unidentified sources (≈7% each). Based on these results, cattle access to the stream was restricted by installation of fencing and in-pasture watering stations. Fecal coliforms were reduced at the three sites by an average of 94%, from prefencing average populations of 15,900 per 100 ml to postfencing average populations of 960 per 100 ml. After fencing, <45% of fecal streptococcus isolates were classified as being from cattle. These results demonstrate that antibiotic resistance profiles in fecal streptococci can be used to reliably determine sources of fecal pollution, and water quality improvements can occur when efforts to address the identified sources are made.
Estimation of Methanogen Biomass by Quantitation of Coenzyme M
Authors: Elias Dwayne A. , Krumholz Lee R. , Tanner Ralph S. , Suflita Joseph M. 
Published: December 2019

ABSTRACT

Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363–370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 ± 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 ± 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(
N
)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass.
Polyphosphates in Intraradical and Extraradical Hyphae of an Arbuscular Mycorrhizal Fungus,
Gigaspora margarita
Authors: Solaiman M. Zakaria , Ezawa Tatsuhiro , Kojima Tomoko , Saito Masanori 
Published: December 2019

ABSTRACT

The amount of polyphosphate in the intraradical and extraradical hyphae of
Gigaspora margarita
was estimated from successive extractions with trichloroacetic acid (TCA), EDTA, and phenol-chloroform (PC). In the intraradical hyphae, most of the polyphosphate was present in TCA- and EDTA-soluble (short-chain and long-chain) fractions, whereas most of the polyphosphate in the extraradical hyphae was present in EDTA- and PC-soluble (long-chain and granular) fractions.
Enzymatic Function of the Nor-1 Protein in Aflatoxin Biosynthesis in
Aspergillus parasiticus
Authors: Zhou Renqing , Linz John E. 
Published: December 2019

ABSTRACT

The
nor-1
gene is involved in aflatoxin biosynthesis in
Aspergillus parasiticus
and was predicted to encode a norsolorinic acid ketoreductase. Recombinant Nor-1 expressed in
Escherichia coli
converted the 1′ keto group of norsolorinic acid to the 1′ hydroxyl group of averantin in crude
E. coli
cell extracts in the presence of NADPH. The results confirm that Nor-1 functions as a ketoreductase in vitro.
Effect of O-Side-Chain-Lipopolysaccharide Chemistry on Metal Binding
Authors: Langley S. , Beveridge T. J. 
Published: December 2019

ABSTRACT

Pseudomonas aeruginosa
PAO1 produces two chemically distinct types of lipopolysaccharides (LPSs), termed A-band LPS and B-band LPS. The A-band O-side chain is electroneutral at physiological pH, while the B-band O-side chain contains numerous negatively charged sites due to the presence of uronic acid residues in the repeat unit structure. Strain PAO1 (A
+
B
+
) and three isogenic LPS mutants (A
+
B
−
, A
−
B
+
, and A
−
B
−
) were studied to determine the contribution of the O-side-chain portion of LPS to metal binding by the surfaces of gram-negative cells. Transmission electron microscopy with energy-dispersive X-ray spectroscopy was used to locate and analyze sites of metal deposition, while atomic absorption spectrophotometry and inductively coupled plasma-mass spectrometry were used to perform bulk quantitation of bound metal. The results indicated that cells of all of the strains caused the precipitation of gold as intracellular, elemental crystals with a
d
-spacing of 2.43 Å. This type of precipitation has not been reported previously for gram-negative cells and suggests that in the organisms studied gold binding is not a surface-mediated event. All four strains bound similar amounts of copper (0.213 to 0.222 μmol/mg [dry weight] of cells) at the cell surface, suggesting that the major surface metal-binding sites reside in portions of the LPS which are common to all strains (perhaps the phosphoryl groups in the core-lipid A region). However, significant differences were observed in the abilities of strains dps89 (A
−
B
+
) and AK1401 (A
+
B
−
) to bind iron and lanthanum, respectively. Strain dps89 caused the precipitation of iron (1.623 μmol/mg [dry weight] of cells) as an amorphous mineral phase (possibly iron hydroxide) on the cell surface, while strain AK1401 nucleated precipitation of lanthanum (0.229 μmol/mg [dry weight] of cells) as apiculate, surface-associated crystals. Neither iron nor lanthanum precipitates were observed on the cells of other strains, which suggests that the combination of A-band LPS and B-band LPS produced by a cell may result in a cell surface which promotes the formation of metal-rich precipitates. We therefore propose that the negatively charged sites located in the O-side chains are not directly responsible for the binding of metallic ions; however, the B-band LPS molecule as a whole may contribute to overall cell surface properties which favor the precipitation of distinct metal-rich mineral phases.
Hydrolysis of Pork Muscle Sarcoplasmic Proteins by
Lactobacillus curvatus
and
Lactobacillus sake
Authors: Fadda Silvina , Sanz Yolanda , Vignolo Graciela , Aristoy M.-Concepción , Oliver Guillermo , Toldrá Fidel 
Published: December 2019

ABSTRACT

Lactobacillus curvatus
CECT 904 and
Lactobacillus sake
CECT 4808 were selected on the basis of their proteolytic activities against synthetic substrates. Further, the effects of whole cells, cell extracts, and a combination of both enzymatic sources on muscle sarcoplasmic proteins were determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and reverse-phase high-performance liquid chromatography analyses. Strains of both species displayed proteinase activities on five sarcoplasmic proteins. The inoculation of whole cells caused a degradation of peptides, whereas the addition of cell extracts resulted in the generation of both hydrophilic and hydrophobic peptides. This phenomenon was remarkably more pronounced when
L. curvatus
was involved. Whole cells also consumed a great amount of free amino acids, while the addition of intracellular enzymes contributed to their generation.
L. sake
accounted for a greater release of free amino acids. In general, cell viability and also proteolytic events were promoted when cell suspensions were provided with cell extracts as an extra source of enzymes.
Functional Analyses of the Promoters in the Lantibiotic Mutacin II Biosynthetic Locus in
Streptococcus mutans
Authors: Qi Fengxia , Chen Ping , Caufield Page W. 
Published: December 2019

ABSTRACT

The lantibiotic bacteriocin mutacin II is produced by the group II
Streptococcus mutans
. The mutacin II biosynthetic locus consists of seven genes,
mutR
, -
A
, -
M
, -
T
, -
F
, -
E
, and -
G
, organized as two operons. The
mutAMTFEG
operon is transcribed from the
mutA
promoter 55 bp upstream of the translation start codon for MutA, while the
mutR
promoter is 76 bp upstream of the
mutR
structural gene. Expression of the
mutA
promoter is regulated by the components of the growth medium, while the
mutR
promoter activity does not seem to be affected by these conditions. Inactivation of
mutR
abolishes transcription of the
mutA
operon but does not affect its own promoter activity. The expressions of both
mutA
and
mutR
promoters are independent of the growth stage, while the production of mutacin II is only elevated at the early stationary phase. Taken together, these results suggest that expression of the mutacin operon is regulated by a complex system involving transcriptional and posttranscriptional or posttranslational controls.
Purification and Properties of a Xylan-Binding Endoxylanase from Alkaliphilic
Bacillus
sp. Strain K-1
Authors: Ratanakhanokchai Khanok , Kyu Khin Lay , Tanticharoen Morakot 
Published: December 2019

ABSTRACT

An alkaliphilic bacterium,
Bacillus
sp. strain K-1, produces extracellular xylanolytic enzymes such as xylanases, β-xylosidase, arabinofuranosidase, and acetyl esterase when grown in xylan medium. One of the extracellular xylanases that is stable in an alkaline state was purified to homogeneity by affinity adsorption-desorption on insoluble xylan. The enzyme bound to insoluble xylan but not to crystalline cellulose. The molecular mass of the purified xylan-binding xylanase was estimated to be approximately 23 kDa. The enzyme was stable at alkaline pHs up to 12. The optimum temperature and optimum pH of the enzyme activity were 60°C and 5.5, respectively. Metal ions such as Fe
2+
, Ca
2+
, and Mg
2+
greatly increased the xylanase activity, whereas Mn
2+
strongly inhibited it. We also demonstrated that the enzyme could hydrolyze the raw lignocellulosic substances effectively. The enzymatic products of xylan hydrolysis were a series of short-chain xylooligosaccharides, indicating that the enzyme was an endoxylanase.
Estimating Bacterial Growth Parameters by Means of Detection Times
Authors: Baranyi József , Pin Carmen 
Published: December 2019

ABSTRACT
We developed a new numerical method to estimate bacterial growth parameters by means of detection times generated by different initial counts. The observed detection times are subjected to a transformation involving the (unknown) maximum specific growth rate and the (known) ratios between the different inoculum sizes and the constant detectable level of counts. We present an analysis of variance (ANOVA) protocol based on a theoretical result according to which, if the specific rate used for the transformation is correct, the transformed values are scattered around the same mean irrespective of the original inoculum sizes. That mean, termed the physiological state of the inoculum,α̂, and the maximum specific growth rate, μ, can be estimated by minimizing the variance ratio of the ANOVA procedure. The lag time of the population can be calculated as λ = −ln α̂/μ; i.e. the lag is inversely proportional to the maximum specific growth rate and depends on the initial physiological state of the population. The more accurately the cell number at the detection level is known, the better the estimate for the variance of the lag times of the individual cells.
Lethal Effect ofRickettsia rickettsiion Its Tick Vector (Dermacentor andersoni)
Authors: Niebylski Mark L. , Peacock Mort G. , Schwan Tom G. 
Published: December 2019

ABSTRACTRickettsia rickettsii, the causative agent of Rocky Mountain spotted fever, was lethal for the majority of experimentally and transovarially infected Rocky Mountain wood ticks (Dermacentor andersoni). Overall, 94.1% of nymphs infected as larvae by feeding on rickettsemic guinea pigs died during the molt into adults and 88.3% of adult female ticks infected as nymphs died prior to feeding. In contrast, only 2.8% of uninfected larvae failed to develop into adults over two generations. Infected female ticks incubated at 4°C had a lower mortality (80.9%) than did those held at 21°C (96.8%). Rickettsiae were vertically transmitted to 39.0% of offspring, and significantly fewer larvae developed from infected ticks. The lethal effect ofR. rickettsiimay explain the low prevalence of infected ticks in nature and affect its enzootic maintenance.
High-Level Formation of Active
Pseudomonas cepacia
Lipase after Heterologous Expression of the Encoding Gene and Its Modified Chaperone in
Escherichia coli
and Rapid In Vitro Refolding
Authors: Quyen Dinh Thi , Schmidt-Dannert Claudia , Schmid Rolf D. 
Published: December 2019

ABSTRACT

The lipase from
Pseudomonas cepacia
ATCC 21808 (recently reclassified as
Burkholderia cepacia
) is widely used by organic chemists for enantioselective synthesis and is manufactured from recombinant
P. cepacia
harboring on a plasmid the clustered genes for lipase and its chaperone. High levels of expression of inactive lipase (40%) in
Escherichia coli
were achieved with pCYTEXP1 under the control of the strong, temperature-inducible λP
RL
promoter. However, no overexpression of the lipase chaperone was achieved in
E. coli
. Thus, chemical refolding of inactive lipase in the absence of its chaperone yielded only 25 U/mg, compared to 3,470 U of the purified lipase secreted by recombinant
P. cepacia
per mg. Sequence analysis of the chaperone revealed a high GC content (>90%) in the 5′ region of the gene and the presence of a putative membrane anchor at the N terminus. Hence, the 5′ region of the gene was replaced by a synthetic fragment, and the putative membrane anchor was removed by deletion of the first 34 or 70 N-terminal amino acids. Only truncation of the gene led to overexpression of the chaperone (up to 60%) in
E. coli
. With this chaperone, it was possible to obtain for the first time in a simple refolding procedure a highly active
Pseudomonas
lipase (classes I and II) expressed in
E. coli
with a specific activity of up to 4,850 U/mg and a yield of 314,000 U/g of
E. coli
wet cells.
Evaluation of Immunomagnetic Separation for Recovery of Infectious
Cryptosporidium parvum
Oocysts from Environmental Samples
Authors: Rochelle Paul A. , De Leon Ricardo , Johnson Anne , Stewart Mic H. , Wolfe Roy L. 
Published: December 2019

ABSTRACT

Two commercial immunomagnetic separation (IMS) kits for
Cryptosporidium
were compared for recovery of oocysts from environmental samples. Oocyst recovery efficiencies with the Dynal and Crypto-Scan kits ranged from 62 to 100% and 34 to 74%, respectively, for seeded environmental water concentrates (turbidity of 210 to 11,480 nephelometric turbidity units). Recovery efficiencies were dependent on the mechanism of agitation during the magnetic capture procedure. An assay combining in vitro cell culture and reverse transcriptase PCR demonstrated that oocysts recovered by IMS retained their infectivity.
Biodiversity of
Lactococcus garvieae
Strains Isolated from Fish in Europe, Asia, and Australia
Authors: Eldar Avi , Goria Mariella , Ghittino Claudio , Zlotkin Amir , Bercovier Herve 
Published: December 2019

ABSTRACT

Lactococcus garvieae
(junior synonym,
Enterococcus seriolicida
) is a major pathogen of fish, producing fatal septicemia among fish species living in very diverse environments. The phenotypic traits of
L. garvieae
strains collected from three different continents (Asia, Europe, and Australia) indicated phenotypic heterogeneity. On the basis of the acidification of
d
-tagatose and sucrose, three biotypes were defined. DNA relatedness values and a specific PCR assay showed that all the biotypes belonged to the same genospecies,
L. garvieae
. All of the
L. garvieae
strains were serotyped as Lancefield group N. Ribotyping proved that one clone was found both in Japan, where it probably originated, and in Italy, where it was probably imported. PCR of environmental samples did not reveal the source of the contamination of the fish in Italy. Specific clones (ribotypes) were found in outbreaks in Spain and in Italy. The
L. garvieae
reference strain, isolated in the United Kingdom from a cow, belonged to a unique ribotype.
L. garvieae
is a rising zoonotic agent. The biotyping scheme, the ribotyping analysis, and the PCR assay described in this work allowed the proper identification of
L. garvieae
and the description of the origin and of the source of contamination of strains involved in outbreaks or in sporadic cases.
In Vivo Fluxes in the Ammonium-Assimilatory Pathways in
Corynebacterium glutamicum
Studied by
15
N Nuclear Magnetic Resonance
Authors: Tesch M. , de Graaf A. A. , Sahm H. 
Published: December 2019

ABSTRACT

Glutamate dehydrogenase (GDH) and glutamine synthetase (GS)–glutamine 2-oxoglutarate-aminotransferase (GOGAT) represent the two main pathways of ammonium assimilation in
Corynebacterium glutamicum
. In this study, the ammonium assimilating fluxes in vivo in the wild-type ATCC 13032 strain and its GDH mutant were quantitated in continuous cultures. To do this, the incorporation of
15
N label from [
15
N]ammonium in glutamate and glutamine was monitored with a time resolution of about 10 min with in vivo
15
N nuclear magnetic resonance (NMR) used in combination with a recently developed high-cell-density membrane-cyclone NMR bioreactor system. The data were used to tune a standard differential equation model of ammonium assimilation that comprised ammonia transmembrane diffusion, GDH, GS, GOGAT, and glutamine amidotransferases, as well as the anabolic incorporation of glutamate and glutamine into biomass. The results provided a detailed picture of the fluxes involved in ammonium assimilation in the two different
C. glutamicum
strains in vivo. In both strains, transmembrane equilibration of 100 mM [
15
N]ammonium took less than 2 min. In the wild type, an unexpectedly high fraction of 28% of the NH
4
+
was assimilated via the GS reaction in glutamine, while 72% were assimilated by the reversible GDH reaction via glutamate. GOGAT was inactive. The analysis identified glutamine as an important nitrogen donor in amidotransferase reactions. The experimentally determined amount of 28% of nitrogen assimilated via glutamine is close to a theoretical 21% calculated from the high peptidoglycan content of
C. glutamicum
. In the GDH mutant, glutamate was exclusively synthesized over the GS/GOGAT pathway. Its level was threefold reduced compared to the wild type.