bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Membrane Fatty Acid Composition of
Pediococcus
sp. Strain NRRL B-2354 in Response to Growth Conditions and Its Effect on Thermal Resistance
Authors: Annous Bassam A. , Kozempel Michael F. , Kurantz Michael J. 
Published: December 2019

ABSTRACT

Membrane fatty acid composition and thermal resistance (
D
value) of
Pediococcus
sp. were determined for mid-exponential-phase (ME) and stationary-phase (ST) cells grown in tryptic soy broth (TSB) and tryptone-glucose-yeast extract (TGY) at 28 and 37°C. As the cells entered the stationary phase of growth, the unsaturated fatty acid, C

18:1
n
11c

, produced during the exponential phase of growth was converted to its cyclic form, C
19:0 Δ9c
. This shift in membrane fatty acid composition was accompanied by an increase in the
D
values of this bacterium. Data from this study suggest that the membrane fatty acid composition of
Pediococcus
sp. is dependent on the growth conditions and that membrane fatty acid composition plays a critical role in thermal resistance. Thermal inactivation curves of
Pediococcus
sp. cells grown in TGY at 28°C indicated the presence of a cell population that is heterogeneous in thermal resistance. The growth of this bacterium in TGY at 37°C and in TSB at 28 and 37°C resulted in cell populations that were uniform in thermal resistance with a lag time for thermal inactivation. Thermal inactivation curves of ME and ST cultures were similar. The data presented here suggest that the cell population’s uniformity of thermal inactivation is independent of the growth phase of the culture.
Identification and Sequencing of β-Myrcene Catabolism Genes from
Pseudomonas
sp. Strain M1
Authors: Iurescia Sandra , Marconi Andrea M. , Tofani Daniela , Gambacorta Augusto , Paternò Annalisa , Devirgiliis Chiara , van der Werf Mariët J. , Zennaro Elisabetta 
Published: December 2019

ABSTRACT

The M1 strain, able to grow on β-myrcene as the sole carbon and energy source, was isolated by an enrichment culture and identified as a
Pseudomonas
sp. One β-myrcene-negative mutant, called N22, obtained by transposon mutagenesis, accumulated (
E
)-2-methyl-6-methylen-2,7-octadien-1-ol (or myrcen-8-ol) as a unique β-myrcene biotransformation product. This compound was identified by gas chromatography-mass spectrometry. We cloned and sequenced the DNA regions flanking the transposon and used these fragments to identify the M1 genomic library clones containing the wild-type copy of the interrupted gene. One of the selected cosmids, containing a 22-kb genomic insert, was able to complement the N22 mutant for growth on β-myrcene. A 5,370-bp-long sequence spanning the region interrupted by the transposon in the mutant was determined. We identified four open reading frames, named
myrA
,
myrB
,
myrC
, and
myrD
, which can potentially code for an aldehyde dehydrogenase, an alcohol dehydrogenase, an acyl-coenzyme A (CoA) synthetase, and an enoyl-CoA hydratase, respectively.
myrA
,
myrB
, and
myrC
are likely organized in an operon, since they are separated by only 19 and 36 nucleotides (nt), respectively, and no promoter-like sequences have been found in these regions. The
myrD
gene starts 224 nt upstream of
myrA
and is divergently transcribed. The
myrB
sequence was found to be completely identical to the one flanking the transposon in the mutant. Therefore, we could ascertain that the transposon had been inserted inside the
myrB
gene, in complete agreement with the accumulation of (
E
)-2-methyl-6-methylen-2,7-octadien-1-ol by the mutant. Based on sequence and biotransformation data, we propose a pathway for β-myrcene catabolism in
Pseudomonas
sp. strain M1.
Characterization and Identification of
Pediococcus
Species Isolated from Forage Crops and Their Application for Silage Preparation
Authors: Cai Yimin , Kumai Sumio , Ogawa Masuhiro , Benno Yoshimi , Nakase Takashi 
Published: December 2019

ABSTRACT

Pediococcus
species isolated from forage crops were characterized, and their application to silage preparation was studied. Most isolates were distributed on forage crops at low frequency. These isolates could be divided into three (A, B, and C) groups by their sugar fermentation patterns. Strains LA 3, LA 35, and LS 5 are representative isolates from groups A, B, and C, respectively. Strains LA 3 and LA 35 had intragroup DNA homology values above 93.6%, showing that they belong to the species
Pediococcus acidilactici
. Strain LS 5 belonged to
Pediococcus pentosaceus
on the basis of DNA-DNA relatedness. All three of these strains and strain SL 1 (
Lactobacillus casei
, isolated from a commercial inoculant) were used as additives to alfalfa and Italian ryegrass silage preparation at two temperatures (25 and 48°C). When stored at 25°C, all of the inoculated silages were well preserved and exhibited significantly (
P
< 0.05) reduced fermentation losses compared to that of their control in alfalfa and Italian ryegrass silages. When stored at 48°C, silages inoculated with strains LA 3 and LA 35 were also well preserved, with a significantly (
P
< 0.05) lower pH, butyric acid and ammonia-nitrogen content, gas production, and dry matter loss and significantly (
P
< 0.05) higher lactate content than the control, but silages inoculated with LS 5 and SL 1 were of poor quality.
P. acidilactici
LA 3 and LA 35 are considered suitable as potential silage inoculants.
Microbial Utilization of Electrically Reduced Neutral Red as the Sole Electron Donor for Growth and Metabolite Production
Authors: Park D. H. , Laivenieks M. , Guettler M. V. , Jain M. K. , Zeikus J. G. 
Published: December 2019

ABSTRACT

Electrically reduced neutral red (NR) served as the sole source of reducing power for growth and metabolism of pure and mixed cultures of H
2
-consuming bacteria in a novel electrochemical bioreactor system. NR was continuously reduced by the cathodic potential (−1.5 V) generated from an electric current (0.3 to 1.0 mA), and it was subsequently oxidized by
Actinobacillus succinogenes
or by mixed methanogenic cultures. The
A. succinogenes
mutant strain FZ-6 did not grow on fumarate alone unless electrically reduced NR or hydrogen was present as the electron donor for succinate production. The mutant strain, unlike the wild type, lacked pyruvate formate lyase and formate dehydrogenase. Electrically reduced NR also replaced hydrogen as the sole electron donor source for growth and production of methane from CO
2
. These results show that both pure and mixed cultures can function as electrochemical devices when electrically generated reducing power can be used to drive metabolism. The potential utility of utilizing electrical reducing power in enhancing industrial fermentations or biotransformation processes is discussed.
16S rRNA Gene Sequence Analysis of
Photobacterium damselae
and Nested PCR Method for Rapid Detection of the Causative Agent of Fish Pasteurellosis
Authors: Osorio Carlos R. , Collins Matthew D. , Toranzo Alicia E. , Barja Juan L. , Romalde Jesús L. 
Published: December 2019

ABSTRACT

The causative agent of fish pasteurellosis, the organism formerly known as
Pasteurella piscicida
, has been reclassified as
Photobacterium damselae
subsp.
piscicida
on the basis of 16S rRNA gene sequence comparisons and chromosomal DNA-DNA hybridization data; thus, this organism belongs to the same species as
Photobacterium damselae
subsp.
damselae
(formerly
Vibrio damselae
). Since reassignment of
P. damselae
subsp.
piscicida
was based on only two strains, one objective of the present work was to confirm the taxonomic position of this fish pathogen by sequencing the 16S rRNA genes of 26 strains having different geographic and host origins. In addition, a nested PCR protocol for detection of
P. damselae
based on 16S rRNA was developed. This PCR protocol was validated by testing 35 target and 24 nontarget pure cultures, and the detection limits obtained ranged from 1 pg to 10 fg of DNA (200 to 20 cells). A similar level of sensitivity was observed when the PCR protocol was applied to fish tissues spiked with bacteria. The PCR approach described in this paper allows detection of the pathogen in mixed plate cultures obtained from asymptomatic fish suspected to be carriers of
P. damselae
subsp.
piscicida
, in which growth of this bacterium cannot be visualized. Our results indicate that the selective primers which we designed represent a powerful tool for sensitive and specific detection of fish pasteurellosis.
Physiological Adaptations Involved in Alkane Assimilation at a Low Temperature by
Rhodococcus
sp. Strain Q15
Authors: Whyte L. G. , Slagman S. J. , Pietrantonio F. , Bourbonnière L. , Koval S. F. , Lawrence J. R. , Inniss W. E. , Greer C. W. 
Published: December 2019

ABSTRACT

We examined physiological adaptations which allow the psychrotroph
Rhodococcus
sp. strain Q15 to assimilate alkanes at a low temperature (alkanes are contaminants which are generally insoluble and/or solid at low temperatures). During growth at 5°C on hexadecane or diesel fuel, strain Q15 produced a cell surface-associated biosurfactant(s) and, compared to glucose-acetate-grown cells, exhibited increased cell surface hydrophobicity. A transmission electron microscopy examination of strain Q15 grown at 5°C revealed the presence of intracellular electron-transparent inclusions and flocs of cells connected by an extracellular polymeric substance (EPS) when cells were grown on a hydrocarbon and morphological differences between the EPS of glucose-acetate-grown and diesel fuel-grown cells. A lectin binding analysis performed by using confocal scanning laser microscopy (CSLM) showed that the EPS contained a complex mixture of glycoconjugates, depending on both the growth temperature and the carbon source. Two glycoconjugates [β-
d
-Gal-(1-3)-
d
-GlcNAc and α-
l
-fucose] were detected only on the surfaces of cells grown on diesel fuel at 5°C. Using scanning electron microscopy, we observed strain Q15 cells on the surfaces of octacosane crystals, and using CSLM, we observed strain Q15 cells covering the surfaces of diesel fuel microdroplets; these findings indicate that this organism assimilates both solid and liquid alkane substrates at a low temperature by adhering to the alkane phase. Membrane fatty acid analysis demonstrated that strain Q15 adapted to growth at a low temperature by decreasing the degree of saturation of membrane lipid fatty acids, but it did so to a lesser extent when it was grown on hydrocarbons at 5°C; these findings suggest that strain Q15 modulates membrane fluidity in response to the counteracting influences of low temperature and hydrocarbon toxicity.
Mechanism of Pyrite Dissolution in the Presence of
Thiobacillus ferrooxidans
Authors: Fowler T. A. , Holmes P. R. , Crundwell F. K. 
Published: December 2019

ABSTRACT

In spite of the environmental and commercial interests in the bacterial leaching of pyrite, two central questions have not been answered after more than 35 years of research: does
Thiobacillus ferrooxidans
enhance the rate of leaching above that achieved by ferric sulfate solutions under the same conditions, and if so, how do the bacteria affect such an enhancement? Experimental conditions of previous studies were such that the concentrations of ferric and ferrous ions changed substantially throughout the course of the experiments. This has made it difficult to interpret the data obtained from these previous works. The aim of this work was to answer these two questions by employing an experimental apparatus designed to maintain the concentrations in solution at a constant value. This was achieved by using the constant redox potential apparatus described previously (P. I. Harvey, and F. K. Crundwell, Appl. Environ. Microbiol. 63:2586–2592, 1997; T. A. Fowler, and F. K. Crundwell, Appl. Environ. Microbiol. 64:3570–3575, 1998). Experiments were conducted in both the presence and absence of
T. ferrooxidans
, maintaining the same conditions in solution. The rate of dissolution of pyrite with bacteria was higher than that without bacteria at the same concentrations of ferrous and ferric ions in solution. Analysis of the dependence of the rate of leaching on the concentration of ferric ions and on the pH, together with results obtained from electrochemical measurements, provided clear evidence that the higher rate of leaching with bacteria is due to the bacteria increasing the pH at the surface of the pyrite.
Comparative Diversity of Ammonia Oxidizer 16S rRNA Gene Sequences in Native, Tilled, and Successional Soils
Authors: Bruns Mary Ann , Stephen John R. , Kowalchuk George A. , Prosser James I. , Paul Eldor A. 
Published: December 2019

ABSTRACT

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within
Nitrosospira
cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for
Nitrosospira
cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the
Nitrosospira
cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.
Isolation and Characterization of Proteolytic Ruminal Bacteria from Sheep and Goats Fed the Tannin-Containing Shrub Legume
Calliandra calothyrsus
Authors: McSweeney Christopher S. , Palmer Brian , Bunch Rowan , Krause Denis O. 
Published: December 2019

ABSTRACT

Tannins in forages complex with protein and reduce the availability of nitrogen to ruminants. Ruminal bacteria that ferment protein or peptides in the presence of tannins may benefit digestion of these diets. Bacteria from the rumina of sheep and goats fed
Calliandra calothyrsus
(3.6% N and 6% condensed tannin) were isolated on proteinaceous agar medium overlaid with either condensed (calliandra tannin) or hydrolyzable (tannic acid) tannin. Fifteen genotypes were identified, based on 16S ribosomal DNA-restriction fragment length polymorphism analysis, and all were proteolytic and fermented peptides to ammonia. Ten of the isolates grew to high optical density (OD) on carbohydrates (glucose, cellobiose, xylose, xylan, starch, and maltose), while the other isolates did not utilize or had low growth on these substrates. In pure culture, representative isolates were unable to ferment protein that was present in calliandra or had been complexed with tannin. One isolate, Lp1284, had high protease activity (80 U), a high specific growth rate (0.28), and a high rate of ammonia production (734 nmol/min/ml/OD unit) on Casamino Acids and Trypticase Peptone. Phylogenetic analysis of the 16S ribosomal DNA sequence showed that Lp1284 was related (97.6%) to
Clostridium botulinum
NCTC 7273. Purified plant protein and casein also supported growth of Lp1284 and were fermented to ammonia. This is the first report of a proteolytic, ammonia-hyperproducing bacterium from the rumen. In conclusion, a diverse group of proteolytic and peptidolytic bacteria were present in the rumen, but the isolates could not digest protein that was complexed with condensed tannin.
Hemolysis, Toxicity, and Randomly Amplified Polymorphic DNA Analysis of
Stachybotrys chartarum
Strains
Authors: Vesper Stephen J. , Dearborn Dorr G. , Yike Iwona , Sorenson W. G. , Haugland Richard A. 
Published: December 2019

ABSTRACT

Stachybotrys chartarum
is an indoor air, toxigenic fungus that has been associated with a number of human and veterinary health problems. Most notable among these has been a cluster of idiopathic pulmonary hemorrhage cases that were observed in the Cleveland, Ohio, area. In this study, 16 strains of
S. chartarum
isolated from case (
n
= 8) or control (
n
= 8) homes in Cleveland and 12 non-Cleveland strains from diverse geographic locations were analyzed for hemolytic activity, conidial toxicity, and randomly amplified polymorphic DNA banding patterns. In tests for hemolytic activity, strains were grown at 23°C on wet wallboard pieces for an 8-week test period. Conidia from these wallboard pieces were subcultured on sheep’s blood agar once a week over this period and examined for growth and clearing of the medium at 37 or 23°C. Five of the Cleveland strains (all from case homes) showed hemolytic activity at 37°C throughout the 8-week test compared to 3 of the non-Cleveland strains. Five of the Cleveland strains, compared to two of the non-Cleveland strains, produced highly toxic conidia (>90 μg of T2 toxin equivalents per g [wet weight] of conidia) after 10 and 30 days of growth on wet wallboard. Only 3 of the 28 strains examined both were consistently hemolytic and produced highly toxic conidia. Each of these strains was isolated from a house in Cleveland where an infant had idiopathic pulmonary hemorrhage.
Comparison of Sensitivity of Immunofluorescent Microscopy to That of a Combination of Immunofluorescent Microscopy and Immunomagnetic Separation for Detection ofCryptosporidium parvumOocysts in Adult Bovine Feces
Authors: Pereira Maria das Graças C. , Atwill Edward R. , Jones Ted 
Published: December 2019

ABSTRACTA direct immunofluorescence assay (DFA) (Merifluor; Meridian Diagnostics, Inc., Cincinnati, Ohio) was compared to an immunomagnetic separation (IMS) assay (Dynabeads; Dynal, Inc., Lake Success, N.Y.) coupled with immunofluorescent microscopy (Waterborne, Inc., New Orleans, La.) for their ability to detect low concentrations ofCryptosporidium parvumoocysts in adult bovine fecal material. IMS-DFA resulted in a 2-log-unit increase in sensitivity (10 oocysts/g) compared to DFA alone (1,000 oocysts/g). The higher sensitivity obtained with IMS-DFA resulted from testing 2 g of fecal material instead of the 13 to 19 mg of fecal material tested in the DFA; the increased sensitivity was not attributable to a higher percent recovery.
In Situ Detection of the
Clostridium botulinum
Type C
1
Toxin Gene in Wetland Sediments with a Nested PCR Assay
Authors: Williamson Judy L. , Rocke Tonie E. , Aiken Judd M. 
Published: December 2019

ABSTRACT

A nested PCR was developed for detection of the
Clostridium botulinum
type C
1
toxin gene in sediments collected from wetlands where avian botulism outbreaks had or had not occurred. The C
1
toxin gene was detected in 16 of 18 sites, demonstrating both the ubiquitous distribution of
C. botulinum
type C in wetland sediments and the sensitivity of the detection assay.
Characterization of Methylglyoxal Synthase from
Clostridium acetobutylicum
ATCC 824 and Its Use in the Formation of 1,2-Propanediol
Authors: Huang Ke-xue , Rudolph Frederick B. , Bennett George N. 
Published: December 2019

ABSTRACT

A gene encoding a putative 150-amino-acid methylglyoxal synthase was identified in
Clostridium acetobutylicum
ATCC 824. The enzyme was overexpressed in
Escherichia coli
and purified. Methylglyoxal synthase has a native molecular mass of 60 kDa and an optimum pH of 7.5. The

K
m

and
V
max
values for the substrate dihydroxyacetone phosphate were 0.53 mM and 1.56 mmol min
−1
μg
−1
, respectively. When
E. coli
glycerol dehydrogenase was coexpressed with methylglyoxal synthase in
E. coli
BL21(DE3), 3.9 mM 1,2-propanediol was produced.
Determination of Total Protein Content of Bacterial Cells by SYPRO Staining and Flow Cytometry
Authors: Zubkov Mikhail V. , Fuchs Bernhard M. , Eilers Heike , Burkill Peter H. , Amann Rudolf 
Published: December 2019

ABSTRACT

An assay has been developed for measuring protein biomass of marine planktonic bacteria by flow cytometry. The method was calibrated by using five species of
Bacteria
(an
Arcobacter
sp., a
Cytophaga
sp., an
Oceanospirillum
sp., a
Pseudoalteromonas
sp., and a
Vibrio
sp.) recently isolated from seawater samples and grown in culture at different temperatures. The intensity of SYPRO-protein fluorescence of these bacteria strongly correlated with their total protein content, measured by the bicinchoninic acid method to be in the range of 60 to 330 fg of protein cell
−1
(
r
2
= 0.93,
n
= 34). According to the calibration, the mean biomass of planktonic bacteria from the North Sea in August 1998 was 24 fg of protein cell
−1
.
Characterization of Methanotrophic Bacterial Populations in Soils Showing Atmospheric Methane Uptake
Authors: Holmes Andrew J. , Roslev Peter , McDonald Ian R. , Iversen Niels , Henriksen Kaj , Murrell J. Colin 
Published: December 2019

ABSTRACT

The global methane cycle includes both terrestrial and atmospheric processes and may contribute to feedback regulation of the climate. Most oxic soils are a net sink for methane, and these soils consume approximately 20 to 60 Tg of methane per year. The soil sink for atmospheric methane is microbially mediated and sensitive to disturbance. A decrease in the capacity of this sink may have contributed to the ∼1% · year
−1
increase in the atmospheric methane level in this century. The organisms responsible for methane uptake by soils (the atmospheric methane sink) are not known, and factors that influence the activity of these organisms are poorly understood. In this study the soil methane-oxidizing population was characterized by both labelling soil microbiota with
14
CH
4
and analyzing a total soil monooxygenase gene library. Comparative analyses of [
14
C]phospholipid ester-linked fatty acid profiles performed with representative methane-oxidizing bacteria revealed that the soil sink for atmospheric methane consists of an unknown group of methanotrophic bacteria that exhibit some similarity to type II methanotrophs. An analysis of monooxygenase gene libraries from the same soil samples indicated that an unknown group of bacteria belonging to the α subclass of the class
Proteobacteria
was present; these organisms were only distantly related to extant methane-oxidizing strains. Studies on factors that affect the activity, population dynamics, and contribution to global methane flux of “atmospheric methane oxidizers” should be greatly facilitated by use of biomarkers identified in this study.