bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sulfidogenesis from 2-Aminoethanesulfonate (Taurine) Fermentation by a Morphologically Unusual Sulfate-Reducing Bacterium,Desulforhopalus singaporensissp. nov
Authors: Lie Thomas J. , Clawson Michael L. , Godchaux Walter , Leadbetter Edward R. 
Published: December 2019

ABSTRACTA pure culture of an obligately anaerobic marine bacterium was obtained from an anaerobic enrichment culture in which taurine (2-aminoethanesulfonate) was the sole source of carbon, energy, and nitrogen. Taurine fermentation resulted in acetate, ammonia, and sulfide as end products. Other sulfonates, including 2-hydroxyethanesulfonate (isethionate) and cysteate (alanine-3-sulfonate), were not fermented. When malate was the sole source of carbon and energy, the bacterium reduced sulfate, sulfite, thiosulfate, or nitrate (reduced to ammonia) but did not use fumarate or dimethyl sulfoxide as a terminal electron acceptor for growth. Taurine-grown cells had significantly lower adenylylphosphosulfate reductase activities than sulfate-grown cells had, which was consistent with the notion that sulfate was not released as a result of oxidative C-S bond cleavage and then assimilated. The nameDesulforhopalus singaporensisis proposed for this sulfate-reducing bacterium, which is morphologically unusual compared to the previously described sulfate-reducing bacteria by virtue of the spinae present on the rod-shaped, gram-negative, nonmotile cells; endospore formation was not discerned, nor was desulfoviridin detected. Granules of poly-β-hydroxybutyrate were abundant in taurine-grown cells. This organism shares with the other member of the genusDesulforhopaluswhich has been described a unique 13-base deletion in the 16S ribosomal DNA. It differs in several ways from a recently described endospore-forming anaerobe (K. Denger, H. Laue, and A. M. Cook, Arch. Microbiol. 168:297–301, 1997) that reportedly produces thiosulfate but not sulfide from taurine fermentation.D. singaporensisthus appears to be the first example of an organism which exhibits sulfidogenesis during taurine fermentation. Implications for sulfonate sulfur in the sulfur cycle are discussed.
Identification of the
yqhE
and
yafB
Genes Encoding Two 2,5-Diketo-
d
-Gluconate Reductases in
Escherichia coli
Authors: Yum Do-Young , Lee Bong-Yong , Pan Jae-Gu 
Published: December 2019

ABSTRACT

The identification of a gene (
yiaE
) encoding 2-ketoaldonate reductase (2KR) in our previous work led to the hypothesis that
Escherichia coli
has other ketogluconate reductases including 2,5-diketo-
d
-gluconate reductase (25DKGR) and to study of the related ketogluconate metabolism. By using the deduced amino acid sequences of 5-diketo-
d
-gluconate reductase (5KDGR) of
Gluconobacter oxydans
and 25DKGR of
Corynebacterium
sp., protein databases were screened to detect homologous proteins. Among the proteins of
E. coli
, an oxidoreductase encoded by
yjgU
and having 56% similarity to 5KDGR of
G. oxydans
and two hypothetical oxidoreductases encoded by
yqhE
and
yafB
and having 49.8 and 42% similarity, respectively, to 25DKGR of
Corynebacterium
sp. were detected. Recently, the
yjgU
gene was identified as encoding 5KDGR and renamed
idnO
(C. Bausch, N. Peekhaus, C. Utz, T. Blais, E. Murray, T. Lowary, and T. Conway, J. Bacteriol. 180:3704–3710, 1998). The pathways involved in the metabolism of ketogluconate by
E. coli
have been predicted by biochemical analysis of purified enzymes and chemical analysis of the pathway intermediates. The gene products of
yqhE
and
yafB
were identified as 25DKGR-A, and 25DKGR-B, respectively, catalyzing the reduction of 25KDG to 2-keto-
l
-gulonate (2KLG). The native 25DKGR-A, 25DKGR-B, and 5KDGR had apparent molecular weights of about 30,000, 30,000, and 54,000, respectively. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels, all three enzymes showed protein bands with a molecular weight of about 29,000, which indicated that 25DKGR-A, 25DKGR-B, and 5KDGR may exist as monomeric, monomeric, and dimeric proteins, respectively. The optimum pHs for reduction were 7.5, 7.0, and 8.0, respectively. The 5KDGR was active with NADH, whereas 25DKGR-A and 25DKGR-B were active with NADPH as a preferred electron donor. 25DKG can be converted to 5KDG by 2KR, which is then reduced to
d
-gluconate by 5KDGR. The pathways were compared with those of
Erwinia
sp. and
Corynebacterium
sp. A BLAST search of published and incomplete microbial genome sequences revealed that the ketogluconate reductases and their related metabolism may be widespread in many species.
Factors Influencing Expression ofluxCDABEandnahGenes inPseudomonas putidaRB1353(NAH7, pUTK9) in Dynamic Systems
Authors: Neilson Julia W. , Pierce Shelley A. , Maier Raina M. 
Published: December 2019

ABSTRACTBioluminescent reporter organisms have been successfully exploited as analytical tools for in situ determination of bioavailable levels of contaminants in static environmental samples. Continued characterization and development of such reporter systems is needed to extend the application of these bioreporters to in situ monitoring of degradation in dynamic environmental systems. In this study, the naphthalene-degrading,luxbioreporter bacteriumPseudomonas putidaRB1353 was used to evaluate the relative influences of cell growth stage, cell density, substrate concentration, oxygen tension, and background carbon substrates on both the magnitude of the light response and the rate of salicylate disappearance. The effect of these variables on the lag time required to obtain maximum luminescence and degradation was also monitored. Strong correlations were observed between the first three factors and both the magnitude and induction time of luminescence and degradation rate. The maximum luminescence response to nonspecific background carbon substrates (soil extract broth or Luria broth) was 50% lower than that generated in response to 1 mg of sodium salicylate liter−1. Oxygen tension was evaluated over the range of 0.5 to 40 mg liter−1, with parallel inhibition to luminescence and degradation rate (20 mg of sodium salicylate liter−1) observed at 1.5 mg liter−1and below and no effect observed above 5 mg liter−1. Oxygen tensions from 2 to 4 mg liter−1influenced the magnitude of luminescence but not the salicylate degradation rate. The results suggest that factors causing parallel shifts in the magnitude of both luminescence and degradation rate were influencing regulation of thenahoperon promoters. For factors that cause nonparallel shifts, other regulatory mechanisms are explored. This study demonstrates thatluxreporter bacteria can be used to monitor both substrate concentration and metabolic response in dynamic systems. However, eachluxreporter system and application will require characterization and calibration.
Microbial Population Changes during Bioremediation of an Experimental Oil Spill
Authors: MacNaughton Sarah J. , Stephen John R. , Venosa Albert D. , Davis Gregory A. , Chang Yun-Juan , White David C. 
Published: December 2019

ABSTRACT

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and
Flexibacter-Cytophaga-Bacteroides
phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.
Soil Bacterial Community Shift Correlated with Change from Forest to Pasture Vegetation in a Tropical Soil
Authors: Nüsslein Klaus , Tiedje James M. 
Published: December 2019

ABSTRACT

The change in vegetative cover of a Hawaiian soil from forest to pasture led to significant changes in the composition of the soil bacterial community. DNAs were extracted from both soil habitats and compared for the abundance of guanine-plus-cytosine (G+C) content, by analysis of abundance of phylotypes of small-subunit ribosomal DNA (SSU rDNA) amplified from fractions with 63 and 35% G+C contents, and by phylogenetic analysis of the dominant rDNA clones in the 63% G+C content fraction. All three methods showed differences between the forest and pasture habitats, providing evidence that vegetation had a strong influence on microbial community composition at three levels of taxon resolution. The forest soil DNA had a peak in G+C content of 61%, while the DNA of the pasture soil had a peak in G+C content of 67%. None of the dominant phylotypes found in the forest soil were detected in the pasture soil. For the 63% G+C fraction SSU rDNA sequence analysis of the three most dominant members revealed that their phyla changed from
Fibrobacter
and
Syntrophomonas
assemblages in the forest soil to
Burkholderia
and
Rhizobium–Agrobacterium
assemblages in the pasture soil.
Sporogenic Effect of Polyunsaturated Fatty Acids on Development of
Aspergillus
spp
Authors: Calvo Ana M. , Hinze Lori L. , Gardner Harold W. , Keller Nancy P. 
Published: December 2019

ABSTRACT

Aspergillus
spp. are frequently occurring seed-colonizing fungi that complete their disease cycles through the development of asexual spores, which function as inocula, and through the formation of cleistothecia and sclerotia. We found that development of all three of these structures in
Aspergillus nidulans
,
Aspergillus flavus
, and
Aspergillus parasiticus
is affected by linoleic acid and light. The specific morphological effects of linoleic acid include induction of precocious and increased asexual spore development in
A. flavus
and
A. parasiticus
strains and altered sclerotium production in some
A. flavus
strains in which sclerotium production decreases in the light but increases in the dark. In
A. nidulans
, both asexual spore production and sexual spore production were altered by linoleic acid. Spore development was induced in all three species by hydroperoxylinoleic acids, which are linoleic acid derivatives that are produced during fungal colonization of seeds. The sporogenic effects of these linoleic compounds on
A. nidulans
are similar to the sporogenic effects of
A. nidulans
psi factor, an endogenous mixture of hydroxylinoleic acid moieties. Light treatments also significantly increased asexual spore production in all three species. The sporogenic effects of light, linoleic acid, and linoleic acid derivatives on
A. nidulans
required an intact
veA
gene. The sporogenic effects of light and linoleic acid on
Aspergillus
spp., as well as members of other fungal genera, suggest that these factors may be significant environmental signals for fungal development.
Transformation of Sulfur Compounds by an Abundant Lineage of Marine Bacteria in the α-Subclass of the Class
Proteobacteria
Authors: González José M. , Kiene Ronald P. , Moran Mary Ann 
Published: December 2019

ABSTRACT

Members of a group of marine bacteria that is numerically important in coastal seawater and sediments were characterized with respect to their ability to transform organic and inorganic sulfur compounds. Fifteen strains representing the
Roseobacter
group (a phylogenetic cluster of marine bacteria in the α-subclass of the class
Proteobacteria
) were isolated from seawater, primarily from the southeastern United States. Although more than one-half of the isolates were obtained without any selection for sulfur metabolism, all of the isolates were able to degrade the sulfur-containing osmolyte dimethyl sulfoniopropionate (DMSP) with production of dimethyl sulfide (DMS). Five isolates also degraded DMSP with production of methanethiol, indicating that both cleavage and demethylation pathways for DMSP occurred in the same organism, which is unusual. Five isolates were able to reduce dimethyl sulfoxide to DMS, and several isolates also degraded DMS and methanethiol. Sulfite oxygenase activity and methanesulfonic acid oxygenase activity were also present in some of the isolates. The ability to incorporate the reduced sulfur in DMSP and methanethiol into cellular material was studied with one of the isolates. A group-specific 16S rRNA probe indicated that the relative abundance of uncultured bacteria in the
Roseobacter
group increased in seawater enriched with DMSP or DMS. Because this group typically accounts for >10% of the 16S ribosomal DNA pool in coastal seawater and sediments of the southern United States, clues about its potential biogeochemical role are of particular interest. Studies of culturable representatives suggested that the group could mediate a number of steps in the cycling of both organic and inorganic forms of sulfur in marine environments.
Nitrification and Autotrophic Nitrifying Bacteria in a Hydrocarbon-Polluted Soil
Authors: Deni Jamal , Penninckx Michel J. 
Published: December 2019

ABSTRACT
In vitro ammonia-oxidizing bacteria are capable of oxidizing hydrocarbons incompletely. This transformation is accompanied by competitive inhibition of ammonia monooxygenase, the first key enzyme in nitrification. The effect of hydrocarbon pollution on soil nitrification was examined in situ. In a microcosm study, adding diesel fuel hydrocarbon to an uncontaminated soil (agricultural unfertilized soil) treated with ammonium sulfate dramatically reduced the amount of KCl-extractable nitrate but stimulated ammonium consumption. In a soil with long history of pollution that was treated with ammonium sulfate, 90% of the ammonium was transformed into nitrate after 3 weeks of incubation. Nitrate production was twofold higher in the contaminated soil than in the agricultural soil to which hydrocarbon was not added. To assess if ammonia-oxidizing bacteria acquired resistance to inhibition by hydrocarbon, the contaminated soil was reexposed to diesel fuel. Ammonium consumption was not affected, but nitrate production was 30% lower than nitrate production in the absence of hydrocarbon. The apparent reduction in nitrification resulted from immobilization of ammonium by hydrocarbon-stimulated microbial activity. These results indicated that the hydrocarbon inhibited nitrification in the noncontaminated soil (agricultural soil) and that ammonia-oxidizing bacteria in the polluted soil acquired resistance to inhibition by the hydrocarbon, possibly by increasing the affinity of nitrifying bacteria for ammonium in the soil.
Development and Field Performance of a Broad-Spectrum Nonviable Asporogenic Recombinant Strain of
Bacillus thuringiensis
with Greater Potency and UV Resistance
Authors: Sanchis Vincent , Gohar Michel , Chaufaux Josette , Arantes Olivia , Meier Alain , Agaisse Hervé , Cayley Jane , Lereclus Didier 
Published: December 2019

ABSTRACT

The main problems with
Bacillus thuringiensis
products for pest control are their often narrow activity spectrum, high sensitivity to UV degradation, and low cost effectiveness (high potency required). We constructed a sporulation-deficient SigK
−
B. thuringiensis
strain that expressed a chimeric
cry1C/Ab
gene, the product of which had high activity against various lepidopteran pests, including
Spodoptera littoralis
(Egyptian cotton leaf worm) and
Spodoptera exigua
(lesser [beet] armyworm), which are not readily controlled by other Cry δ-endotoxins. The SigK
−
host strain carried the
cry1Ac
gene, the product of which is highly active against the larvae of the major pests
Ostrinia nubilalis
(European corn borer) and
Heliothis virescens
(tobacco budworm). This new strain had greater potency and a broader activity spectrum than the parent strain. The crystals produced by the asporogenic strain remained encapsulated within the cells, which protected them from UV degradation. The
cry1C/Ab
gene was introduced into the
B. thuringiensis
host via a site-specific recombination vector so that unwanted DNA was eliminated. Therefore, the final construct contained no sequences of non-
B. thuringiensis
origin. As the recombinant strain is a mutant blocked at late sporulation, it does not produce viable spores and therefore cannot compete with wild-type
B. thuringiensis
strains in the environment. It is thus a very safe biopesticide. In field trials, this new recombinant strain protected cabbage and broccoli against a pest complex under natural infestation conditions.
Identification of an ATP-Driven, Osmoregulated Glycine Betaine Transport System in
Listeria monocytogenes
Authors: Ko Rinkei , Smith Linda Tombras 
Published: December 2019

ABSTRACT

The ability of the gram-positive, food-borne pathogen
Listeria monocytogenes
to tolerate environments of elevated osmolarity and reduced temperature is due in part to the transport and accumulation of the osmolyte glycine betaine. Previously we showed that glycine betaine transport was the result of Na
+
-glycine betaine symport. In this report, we identify a second glycine betaine transporter from
L. monocytogenes
which is osmotically activated but does not require a high concentration of Na
+
for activity. By using a pool of Tn
917
-LTV3 mutants, a salt- and chill-sensitive mutant which was also found to be impaired in its ability to transport glycine betaine was isolated. DNA sequence analysis of the region flanking the site of transposon insertion revealed three open reading frames homologous to
opuA
from
Bacillus subtilis
and
proU
from
Escherichia coli
, both of which encode glycine betaine transport systems that belong to the superfamily of ATP-dependent transporters. The three open reading frames are closely spaced, suggesting that they are arranged in an operon. Moreover, a region upstream from the first reading frame was found to be homologous to the promoter regions of both
opuA
and
proU
. One unusual feature not shared with these other two systems is that the start codons for two of the open reading frames in
L. monocytogenes
appear to be TTG. That glycine betaine uptake is nearly eliminated in the mutant strain when it is assayed in the absence of Na
+
is an indication that only the ATP-dependent transporter and the Na
+
-glycine betaine symporter occur in
L. monocytogenes
.
Oxygen-Sensing Reporter Strain of
Pseudomonas fluorescens
for Monitoring the Distribution of Low-Oxygen Habitats in Soil
Authors: Højberg Ole , Schnider Ursula , Winteler Harald V. , Sørensen Jan , Haas Dieter 
Published: December 2019

ABSTRACT

The root-colonizing bacterium
Pseudomonas fluorescens
CHA0 was used to construct an oxygen-responsive biosensor. An anaerobically inducible promoter of
Pseudomonas aeruginosa
, which depends on the FNR (fumarate and nitrate reductase regulation)-like transcriptional regulator ANR (anaerobic regulation of arginine deiminase and nitrate reductase pathways), was fused to the structural
lacZ
gene of
Escherichia coli
. By inserting the reporter fusion into the chromosomal
att
Tn
7
site of
P. fluorescens
CHA0 by using a mini-Tn
7
transposon, the reporter strain, CHA900, was obtained. Grown in glutamate-yeast extract medium in an oxystat at defined oxygen levels, the biosensor CHA900 responded to a decrease in oxygen concentration from 210 × 10
2
Pa to 2 × 10
2
Pa of O
2
by a nearly 100-fold increase in β-galactosidase activity. Half-maximal induction of the reporter occurred at about 5 × 10
2
Pa. This dose response closely resembles that found for
E. coli
promoters which are activated by the FNR protein. In a carbon-free buffer or in bulk soil, the biosensor CHA900 still responded to a decrease in oxygen concentration, although here induction was about 10 times lower and the low oxygen response was gradually lost within 3 days. Introduced into a barley-soil microcosm, the biosensor could report decreasing oxygen concentrations in the rhizosphere for a 6-day period. When the water content in the microcosm was raised from 60% to 85% of field capacity, expression of the reporter gene was elevated about twofold above a basal level after 2 days of incubation, suggesting that a water content of 85% caused mild anoxia. Increased compaction of the soil was shown to have a faster and more dramatic effect on the expression of the oxygen reporter than soil water content alone, indicating that factors other than the water-filled pore space influenced the oxygen status of the soil. These experiments illustrate the utility of the biosensor for detecting low oxygen concentrations in the rhizosphere and other soil habitats.
Bactericidal Activity of Photocatalytic TiO
2
Reaction: toward an Understanding of Its Killing Mechanism
Authors: Maness Pin-Ching , Smolinski Sharon , Blake Daniel M. , Huang Zheng , Wolfrum Edward J. , Jacoby William A. 
Published: December 2019

ABSTRACT

When titanium dioxide (TiO
2
) is irradiated with near-UV light, this semiconductor exhibits strong bactericidal activity. In this paper, we present the first evidence that the lipid peroxidation reaction is the underlying mechanism of death of
Escherichia coli
K-12 cells that are irradiated in the presence of the TiO
2
photocatalyst. Using production of malondialdehyde (MDA) as an index to assess cell membrane damage by lipid peroxidation, we observed that there was an exponential increase in the production of MDA, whose concentration reached 1.1 to 2.4 nmol · mg (dry weight) of cells
−1
after 30 min of illumination, and that the kinetics of this process paralleled cell death. Under these conditions, concomitant losses of 77 to 93% of the cell respiratory activity were also detected, as measured by both oxygen uptake and reduction of 2,3,5-triphenyltetrazolium chloride from succinate as the electron donor. The occurrence of lipid peroxidation and the simultaneous losses of both membrane-dependent respiratory activity and cell viability depended strictly on the presence of both light and TiO
2
. We concluded that TiO
2
photocatalysis promoted peroxidation of the polyunsaturated phospholipid component of the lipid membrane initially and induced major disorder in the
E. coli
cell membrane. Subsequently, essential functions that rely on intact cell membrane architecture, such as respiratory activity, were lost, and cell death was inevitable.