bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth on Urea Can Trigger Death and Peroxidation of the Cyanobacterium
Synechococcus
sp. Strain PCC 7002
Authors: Sakamoto Toshio , Delgaizo Victoria B. , Bryant Donald A. 
Published: December 2019

ABSTRACT

Laboratory conditions have been identified that cause the rapid death of cultures of cyanobacteria producing urease. Once the death phase had initiated in the stationary growth phase, cells were rapidly bleached of all pigmentation. Null mutations in the
ureC
gene, encoding the alpha subunit of urease, were constructed, and these mutants were no longer sensitive to growth in the presence of urea. High levels of peroxides, including lipid peroxides, were detected in the bleaching cells. Exogenously added polyunsaturated fatty acids triggered a similar death response. Vitamin E suppressed the formation of peroxides and delayed the onset of cell bleaching. The results suggest that these cyanobacterial cells undergo a metabolic imbalance that ultimately leads to oxidative stress and lipid peroxide formation. These observations may provide insights into the mechanism of sudden cyanobacterial bloom disappearance in nature.
Flow Cytometry Detection of Infectious Rotaviruses in Environmental and Clinical Samples
Authors: Abad F. Xavier , Pintó Rosa M. , Bosch Albert 
Published: December 2019

ABSTRACT

A method for the detection of infectious human rotaviruses based on infection of CaCo-2 cells and detection of infected cells by indirect immunofluorescence and flow cytometry (IIF-FC) has been developed. The technique was validated by performing a seminested reverse transcription-PCR assay with sorted cell populations. The efficiency of the procedure has been compared with that of the standard method of infection of MA104 cells and ulterior detection by IIF and optical microscopy (IIF-OM) and with that of infection of MA104 cells and detection by IIF-FC. The limit of sensitivity for the detection of the cell-adapted strain Ito
r
P13, expressed as the most probable number of cytopathogenic units, was established as 200 and 2 for MA104 and CaCo-2 cells, respectively, by the IIF-FC method. The ratio of infectious virus particles to total virus particles for a wild-type rotavirus was determined to be 1/2 × 10
6
and 1/2 × 10
4
for IIF-OM with MA104 cells and IIF-FC with CaCo-2 cells, respectively. The use of IIF-FC with CaCo-2 cells was tested with fecal and water samples and proved to be more effective than the standard procedure for rotavirus detection.
Differentiation of
Lactobacillus
Species by Molecular Typing
Authors: Zhong Wei , Millsap Kevin , Bialkowska-Hobrzanska Hanna , Reid Gregor 
Published: December 2019

ABSTRACT

A total of 64 type, reference, clinical, health food, and stock isolates of microaerophilic
Lactobacillus
species were examined by restriction fragment length polymorphisms. Of particular interest were members of six of the eight species most commonly recovered from the vaginas of healthy premenopausal women, namely,
Lactobacillus jensenii
,
L. casei
,
L. rhamnosus
,
L. acidophilus
,
L. plantarum
, and
L. fermentum
. Six main groupings were identified on the basis of ribotyping. This technique was able to classify fresh isolates to the species level. In the case of the ribotype A grouping for
L. rhamnosus
, differences between strains were evident by chromosome typing (chromotyping). Many isolates did not possess plasmids. Six
L. rhamnosus
strains isolated from four different health food products appeared to be identical to
L. rhamnosus
ATCC 21052. The molecular typing system is useful for identifying and differentiating
Lactobacillus
isolates. Studies of strains of potential importance to the urogenital flora should include molecular characterization as a means of comparing genetic traits with those of strains whose characteristics associated with colonization and antagonism against pathogens have been defined.
A Two-Component Monooxygenase Catalyzes Both the Hydroxylation of
p
-Nitrophenol and the Oxidative Release of Nitrite from 4-Nitrocatechol in
Bacillus sphaericus
JS905
Authors: Kadiyala Venkateswarlu , Spain Jim C. 
Published: December 2019

ABSTRACT

Bacteria that metabolize
p
-nitrophenol (PNP) oxidize the substrate to 3-ketoadipic acid via either hydroquinone or 1,2,4-trihydroxybenzene (THB); however, initial steps in the pathway for PNP biodegradation via THB are unclear. The product of initial hydroxylation of PNP could be either 4-nitrocatechol or 4-nitroresorcinol. Here we describe the complete pathway for aerobic PNP degradation by
Bacillus sphaericus
JS905 that was isolated by selective enrichment from an agricultural soil in India. Washed cells of PNP-grown JS905 released nitrite in stoichiometric amounts from PNP and 4-nitrocatechol. Experiments with extracts obtained from PNP-grown cells revealed that the initial reaction is a hydroxylation of PNP to yield 4-nitrocatechol. 4-Nitrocatechol is subsequently oxidized to THB with the concomitant removal of the nitro group as nitrite. The enzyme that catalyzed the two sequential monooxygenations of PNP was partially purified and separated into two components by anion-exchange chromatography and size exclusion chromatography. Both components were required for NADH-dependent oxidative release of nitrite from PNP or 4-nitrocatechol. One of the components was identified as a reductase based on its ability to catalyze the NAD(P)H-dependent reduction of 2,6-dichlorophenolindophenol and nitroblue tetrazolium. Nitrite release from either PNP or 4-nitrocatechol was inhibited by the flavoprotein inhibitor methimazole. Our results indicate that the two monooxygenations of PNP to THB are catalyzed by a single two-component enzyme system comprising a flavoprotein reductase and an oxygenase.
Glutamate Biosynthesis in
Lactococcus lactis
subsp.
lactis
NCDO 2118
Authors: Lapujade P. , Cocaign-Bousquet M. , Loubiere P. 
Published: December 2019

ABSTRACT

Unlike other lactic acid bacteria,
Lactococcus lactis
subsp.
lactis
NCDO 2118 was able to grow in a medium lacking glutamate and the amino acids of the glutamate family. Growth in such a medium proceeded after a lag phase of about 2 days and with a reduced growth rate (0.11 h
−1
) compared to that in the reference medium containing glutamate (0.16 h
−1
). The enzymatic studies showed that a phosphoenolpyruvate carboxylase activity was present, while the malic enzyme and the enzymes of the glyoxylic shunt were not detected. As in most anaerobic bacteria, no α-ketoglutarate dehydrogenase activity could be detected, and the citric acid cycle was restricted to a reductive pathway leading to succinate formation and an oxidative branch enabling the synthesis of α-ketoglutarate. The metabolic bottleneck responsible for the limited growth rate was located in this latter pathway. As regards the synthesis of glutamate from α-ketoglutarate, no glutamate dehydrogenase was detected. While the glutamate synthase-glutamine synthetase system was detected at a low level, high transaminase activity was measured. The conversion of α-ketoglutarate to glutamate by the transaminase, the reverse of the normal physiological direction, operated with different amino acids as nitrogen donor. All of the enzymes assayed were shown to be constitutive.
Increase in Endogenous and Exogenous Cyclic AMP Levels Inhibits Sclerotial Development in
Sclerotinia sclerotiorum
Authors: Rollins Jeffrey A. , Dickman Martin B. 
Published: December 2019

ABSTRACT

Growth and development of a wild-type
Sclerotinia sclerotiorum
isolate were examined in the presence of various pharmacological compounds to investigate signal transduction pathways that influence the development of sclerotia. Compounds known to increase endogenous cyclic AMP (cAMP) levels in other organisms by inhibiting phosphodiesterase activity (caffeine and 3-isobutyl-1-methyl xanthine) or by activating adenylate cyclase (NaF) reduced or eliminated sclerotial development in
S. sclerotiorum
. Growth in the presence of 5 mM caffeine correlated with increased levels of endogenous cAMP in mycelia. In addition, incorporation of cAMP into the growth medium decreased or eliminated the production of sclerotia in a concentration-dependent manner and increased the accumulation of oxalic acid. Inhibition of sclerotial development was cAMP specific, as exogenous cyclic GMP, AMP, and ATP did not influence sclerotial development. Transfer of developing cultures to cAMP-containing medium at successive time points demonstrated that cAMP inhibits development prior to or during sclerotial initiation. Together, these results indicate that cAMP plays a role in the early transition between mycelial growth and sclerotial development.
Biodegradation of Variable-Chain-Length Alkanes at Low Temperatures by a Psychrotrophic
Rhodococcus
sp
Authors: Whyte Lyle G. , Hawari Jalal , Zhou Edward , Bourbonnière Luc , Inniss William E. , Greer Charles W. 
Published: December 2019

ABSTRACT

The psychrotroph
Rhodococcus
sp. strain Q15 was examined for its ability to degrade individual
n
-alkanes and diesel fuel at low temperatures, and its alkane catabolic pathway was investigated by biochemical and genetic techniques. At 0 and 5°C, Q15 mineralized the short-chain alkanes dodecane and hexadecane to a greater extent than that observed for the long-chain alkanes octacosane and dotriacontane. Q15 utilized a broad range of aliphatics (C
10
to C
21
alkanes, branched alkanes, and a substituted cyclohexane) present in diesel fuel at 5°C. Mineralization of hexadecane at 5°C was significantly greater in both hydrocarbon-contaminated and pristine soil microcosms seeded with Q15 cells than in uninoculated control soil microcosms. The detection of hexadecane and dodecane metabolic intermediates (1-hexadecanol and 2-hexadecanol and 1-dodecanol and 2-dodecanone, respectively) by solid-phase microextraction–gas chromatography-mass spectrometry and the utilization of potential metabolic intermediates indicated that Q15 oxidizes alkanes by both the terminal oxidation pathway and the subterminal oxidation pathway. Genetic characterization by PCR and nucleotide sequence analysis indicated that Q15 possesses an aliphatic aldehyde dehydrogenase gene highly homologous to the
Rhodococcus erythropolis thcA
gene.
Rhodococcus
sp. strain Q15 possessed two large plasmids of approximately 90 and 115 kb (shown to mediate Cd resistance) which were not required for alkane mineralization, although the 90-kb plasmid enhanced mineralization of some alkanes and growth on diesel oil at both 5 and 25°C.
Distribution of
Clostridium perfringens
and Fecal Sterols in a Benthic Coastal Marine Environment Influenced by the Sewage Outfall from McMurdo Station, Antarctica
Authors: Edwards Diane D. , McFeters Gordon A. , Venkatesan M. Indira 
Published: December 2019

ABSTRACT

The spatial distribution, movement, and impact of the untreated wastewater outfall from McMurdo Station, Antarctica, were investigated under early austral summer conditions. The benthic environment was examined to determine the distribution of
Clostridium perfringens
in sediment cores and the intestinal contents of native invertebrates and fish along a transect of stations. These stations extended ca. 411 m south of the outfall. The findings revealed that the concentration of
C. perfringens
decreased with depth in the sediment and distance from the outfall. High percentages of tunicates and sea urchins were colonized with this bacterium along the transect. Coprostanol concentrations were also measured in sediment samples taken from each of the transect stations, and a similar trend was observed. These results are in agreement with the findings of previous studies performed with the water column and collectively provide evidence that the disposal of domestic wastes deserves special consideration in polar marine environments.
phnE
and
glpT
Genes Enhance Utilization of Organophosphates in
Escherichia coli
K-12
Authors: Elashvili Ilya , DeFrank Joseph J. , Culotta Valeria C. 
Published: December 2019

ABSTRACT

Wild-type
Escherichia coli
K-12 strain JA221 grows poorly on low concentrations (≤1 mM) of diisopropyl fluorophosphate and its hydrolysis product, diisopropyl phosphate (DIPP), as sole phosphorus sources. Spontaneous organophosphate utilization (OPU) mutants were isolated that efficiently utilized these alternate sources of phosphate. A genomic library was constructed from one such OPU mutant, and two genes were isolated that conferred the OPU phenotype to strain JA221 upon transformation. These genes were identified as
phnE
and
glpT
. The original OPU mutation represented
phnE
gene activation and corresponded to the same 8-bp unit deletion from the cryptic wild-type
E. coli
K-12
phnE
gene that has been shown previously to result in
phnE
activation. In comparison, sequence analysis revealed that the observed OPU phenotype conferred by the
glpT
gene was not the result of a mutation. PCR clones of
glpT
from both the mutant and the wild type were found to confer the OPU phenotype to JA221 when they were present on the high-copy-number pUC19 plasmid but not when they were present on the low-copy-number pWSK29 plasmid. This suggests that the OPU phenotype associated with the
glpT
gene is the result of amplification and overproduction of the
glpT
gene product. Both the active
phnE
and multicopy
glpT
genes facilitated effective metabolism of low concentrations of DIPP, whereas only the active
phnE
gene could confer the ability to break down a chromogenic substrate, 5-bromo-4-chloro-3-indoxyl phosphate-
p
-toluidine (X-P
i
). This result indicates that in
E. coli
, X-P
i
is transported exclusively by the Phn system, whereas DIPP (or its metabolite) may be transported by both Phn and Glp systems.
Effect of Insertion Site and Metabolic Load on the Environmental Fitness of a Genetically Modified
Pseudomonas fluorescens
Isolate
Authors: De Leij Frans A. A. M. , Thomas Catherine E. , Bailey Mark J. , Whipps John M. , Lynch James M. 
Published: December 2019

ABSTRACT

An isolate of
Pseudomonas fluorescens
(SBW25) was modified with different marker genes (
lacZY
,
aph-1
, and
xylE
). These marker genes were inserted singly or in combination into two separate (1 Mbp apart) and presumably nonessential sites (-6- and Ee) on the chromosome of SBW25. This allowed the production of a range of genetically modified SBW25 variants that differed with respect to insertion site of the marker genes and metabolic burden. The environmental fitness of the different SBW25 variants was tested in soil, in the rhizosphere of wheat and pea, and on the phylloplane of wheat. Reduced environmental fitness of the different variants was mainly attributed to the extra metabolic burden of novel gene expression, whereas choice of insertion site was of little significance. Changes in environmental fitness were dependent on the environmental conditions; an environment, such as soil, with a low microbial carrying capacity had a negative effect on the environmental fitness of variants with a large metabolic load. In environments with a larger carrying capacity, such as the rhizosphere of pea, environmental fitness of variants with a large metabolic load was not significantly different from that of variants with a smaller metabolic burden.
The Gut of the Soil MicroarthropodFolsomia candida(Collembola) Is a Frequently Changeable but Selective Habitat and a Vector for Microorganisms
Authors: Thimm Torsten , Hoffmann Andrea , Borkott Heinz , Charles Munch Jean , Tebbe Christoph C. 
Published: December 2019

ABSTRACTInteraction potentials between soil microarthropods and microorganisms were investigated withFolsomia candida(Insecta, Collembola) in microcosm laboratory experiments. Microscopic analysis revealed that the volumes of the simple, rod-shaped guts of adult specimens varied with their feeding activity, from 0.7 to 11.2 nl. A dense layer of bacterial cells, associated with the peritrophic membrane, was detected in the midgut by scanning electron microscopy. Depending on the molting stage, which occurred at intervals of approximately 4 days, numbers of heterotrophic, aerobic gut bacteria changed from 4.9 × 102to 2.3 × 106CFU per specimen. A total of 11 different taxonomic bacterial groups and the filamentous fungusAcremonium charticolawere isolated from the guts of fiveF. candidaspecimens. The most abundant isolate was related toErwinia amylovora(96.2% DNA sequence similarity to its 16S rRNA gene).F. candidapreferred to feed onPseudomonas putidaand three indigenous gut isolates rather than eight different type culture strains. When luciferase reporter gene-tagged bacterial strains were pulse fed toF. candida, gut isolates were continuously shed for 8 days to several weeks butEscherichia coliHB101 was shed for only 1 day. Ratios of ingested to released bacterial cells demonstrated that populations of nonindigenous gut bacteria likeSinorhizobium melilotiL33 andE. coliHB101 were reduced by more than 4 orders of magnitude but that the population of gut isolateAlcaligenes faecalisHR4 was reduced only 500-fold. This work demonstrates thatF. candidarepresents a frequently changeable but selective habitat for bacteria in terrestrial environments and that microarthropods have to be considered factors that modify soil microbial communities.
In Situ Detection of High Levels of Horizontal Plasmid Transfer in Marine Bacterial Communities
Authors: Dahlberg Cecilia , Bergström Maria , Hermansson Malte 
Published: December 2019

ABSTRACT

Gene transfer of the conjugative plasmid pBF1 from
Pseudomonas putida
to indigenous bacteria in seawater was investigated with a detection system for gene transfer based on the green fluorescent protein (GFP) (C. Dahlberg et al., Mol. Biol. Evol. 15:385–390, 1998). pBF1 was tagged with the
gfp
gene controlled by a
lac
promoter which is down regulated in the donor cell by a chromosomal repressor (
lacI
q
). The plasmid donor cells (
Pseudomonas putida
KT2442) subsequently do not express
gfp
. Transfer to recipient strains lacking the repressor results in expression of
gfp
. The transconjugant can subsequently be detected by epifluorescence microscopy on a single-cell level. By using this method, transfer of pBF1::
gfp
and expression of the
gfp
gene were first shown to occur during nutrient-limiting conditions to several defined recipient bacteria in artificial seawater. Second, we measured transfer of pBF1 from
P. putida
to the marine bacterial community directly in seawater samples, on a single-cell level, without limiting the detection of gene transfer to the culturable fraction of bacteria. Plasmid transfer was detected on surfaces and in bulk seawater. Seawater bacteria with different morphologies were shown to receive the plasmid. Gene transfer frequencies of 2.3 × 10
−6
to 2.2 × 10
−4
transconjugants per recipient were recorded after 3 days of incubation.
Association of Marine Archaea with the Digestive Tracts of Two Marine Fish Species
Authors: van der Maarel Marc J. E. C. , Artz Rebekka R. E. , Haanstra René , Forney Larry J. 
Published: December 2019

ABSTRACT

Recent studies have shown that archaea which were always thought to live under strict anoxic or extreme environmental conditions are also present in cold, oxygenated seawater, soils, the digestive tract of a holothurian deep-sea-deposit feeder, and a marine sponge. In this study, we show, by using PCR-mediated screening in other marine eukaryotes, that marine archaea are also present in the digestive tracts of flounder and grey mullet, two fish species common in the North Sea, in fecal samples of flounder, and in suspended particulate matter of the North Sea water column. No marine archaea could be detected in the digestive tracts of mussels or the fecal pellets of a copepod species. The archaeal 16S ribosomal DNA clone libraries of feces of flounder and the contents of the digestive tracts of grey mullet and flounder were dominated by group II marine archaea. The marine archaeal clones derived from flounder and grey mullet digestive tracts and feces formed a distinct cluster within the group II marine archaea, with 76.7 to 89.8% similarity to previously described group II clones. Fingerprinting of the archaeal community of flounder digestive tract contents and feces by terminal restriction fragment length polymorphism of archaeal 16S rRNA genes after restriction with
Hha
I showed a dominant fragment at 249 bp, which is likely to be derived from group II marine archaea. Clones of marine archaea that were closely related to the fish-associated marine archaea clones were obtained from suspended particulate matter of the water column at two stations in the North Sea. Terminal restriction fragment length polymorphism fingerprinting of the archaeal community present in suspended particulate matter showed the same fragment pattern as was found for the archaeal community of the flounder digestive tract contents and feces. These data demonstrate that marine archaea are present in the digestive tracts and feces of very common marine fish. It is possible that the marine archaea associated with the digestive tracts of marine fish are liberated into the water column through the feces and subsequently contribute to the marine archaeal community of suspended particulate matter.
Influence of
Lactobacillus
spp. from an Inoculant and of
Weissella
and
Leuconostoc
spp. from Forage Crops on Silage Fermentation
Authors: Cai Yimin , Benno Yoshimi , Ogawa Masuhiro , Ohmomo Sadahiro , Kumai Sumio , Nakase Takashi 
Published: December 2019

ABSTRACT

Lactobacillus
spp. from an inoculant and
Weissella
and
Leuconostoc
spp. from forage crops were characterized, and their influence on silage fermentation was studied. Forty-two lactic acid-producing cocci were obtained from forage crops and grasses. All isolates were gram-positive, catalase-negative cocci that produced gas from glucose, and produced more than 90% of their lactate in the
d
-isomer form. These isolates were divided into groups A and B by sugar fermentation patterns. Two representative strains from the two groups, FG 5 and FG 13, were assigned to the species
Weissella paramesenteroides
and
Leuconostoc pseudomesenteroides
, respectively, on the basis of DNA-DNA relatedness. Strains FG 5, FG 13, and SL 1 (
Lactobacillus casei
), isolated from a commercial inoculant, were used as additives to alfalfa and Italian ryegrass silage preparations. Lactic acid bacterium counts were higher in all additive-treated silages than in the control silage at an early stage of ensiling. During silage fermentation, inoculation with SL 1 more effectively inhibited the growth of aerobic bacteria and clostridia than inoculation with strain FG 5 or FG 13. SL 1-treated silages stored well. However, the control and FG 5- and FG 13-treated silages had a significantly (
P
< 0.05) higher pH and butyric acid and ammonia nitrogen contents and significantly (
P
< 0.05) lower lactate content than SL 1-treated silage. Compared with the control silage, SL 1 treatments reduced the proportion of
d
-(−)-lactic acid, gas production, and dry matter loss in two kinds of silage, but the FG 5 and FG 13 treatments gave similar values in alfalfa silages and higher values (
P
< 0.05) in Italian ryegrass silage. The results confirmed that heterofermentative strains of
W. paramesenteroides
FG 5 and
L. pseudomesenteroides
FG 13 did not improve silage quality and may cause some fermentation loss.