bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dimethylsulfoniopropionate and Methanethiol Are Important Precursors of Methionine and Protein-Sulfur in Marine Bacterioplankton
Authors: Kiene Ronald P. , Linn Laura J. , González José , Moran Mary Ann , Bruton Jody A. 
Published: December 2019

ABSTRACTOrganic sulfur compounds are present in all aquatic systems, but their use as sources of sulfur for bacteria is generally not considered important because of the high sulfate concentrations in natural waters. This study investigated whether dimethylsulfoniopropionate (DMSP), an algal osmolyte that is abundant and rapidly cycled in seawater, is used as a source of sulfur by bacterioplankton. Natural populations of bacterioplankton from subtropical and temperate marine waters rapidly incorporated 15 to 40% of the sulfur from tracer-level additions of [35S]DMSP into a macromolecule fraction. Tests with proteinase K and chloramphenicol showed that the sulfur from DMSP was incorporated into proteins, and analysis of protein hydrolysis products by high-pressure liquid chromatography showed that methionine was the major labeled amino acid produced from [35S]DMSP. Bacterial strains isolated from coastal seawater and belonging to the α-subdivision of the divisionProteobacteriaincorporated DMSP sulfur into protein only if they were capable of degrading DMSP to methanethiol (MeSH), whereas MeSH was rapidly incorporated into macromolecules by all tested strains and by natural bacterioplankton. These findings indicate that the demethylation/demethiolation pathway of DMSP degradation is important for sulfur assimilation and that MeSH is a key intermediate in the pathway leading to protein sulfur. Incorporation of sulfur from DMSP and MeSH by natural populations was inhibited by nanomolar levels of other reduced sulfur compounds including sulfide, methionine, homocysteine, cysteine, and cystathionine. In addition, propargylglycine and vinylglycine were potent inhibitors of incorporation of sulfur from DMSP and MeSH, suggesting involvement of the enzyme cystathionine γ-synthetase in sulfur assimilation by natural populations. Experiments with [methyl-3H]MeSH and [35S]MeSH showed that the entire methiol group of MeSH was efficiently incorporated into methionine, a reaction consistent with activity of cystathionine γ-synthetase. Field data from the Gulf of Mexico indicated that natural turnover of DMSP supplied a major fraction of the sulfur required for bacterial growth in surface waters. Our study highlights a remarkable adaptation by marine bacteria: they exploit nanomolar levels of reduced sulfur in apparent preference to sulfate, which is present at 106- to 107-fold higher concentrations.
Diversity in Butane Monooxygenases among Butane-Grown Bacteria
Authors: Hamamura Natsuko , Storfa Ryan T. , Semprini Lewis , Arp Daniel J. 
Published: December 2019

ABSTRACT

Butane monooxygenases of butane-grown
Pseudomonas butanovora
,
Mycobacterium vaccae
JOB5, and an environmental isolate, CF8, were compared at the physiological level. The presence of butane monooxygenases in these bacteria was indicated by the following results. (i) O
2
was required for butane degradation. (ii) 1-Butanol was produced during butane degradation. (iii) Acetylene inhibited both butane oxidation and 1-butanol production. The responses to the known monooxygenase inactivator, ethylene, and inhibitor, allyl thiourea (ATU), discriminated butane degradation among the three bacteria. Ethylene irreversibly inactivated butane oxidation by
P. butanovora
but not by
M. vaccae
or CF8. In contrast, butane oxidation by only CF8 was strongly inhibited by ATU. In all three strains of butane-grown bacteria, specific polypeptides were labeled in the presence of [
14
C]acetylene. The [
14
C]acetylene labeling patterns were different among the three bacteria. Exposure of lactate-grown CF8 and
P. butanovora
and glucose-grown
M. vaccae
to butane induced butane oxidation activity as well as the specific acetylene-binding polypeptides. Ammonia was oxidized by all three bacteria.
P. butanovora
oxidized ammonia to hydroxylamine, while CF8 and
M. vaccae
produced nitrite. All three bacteria oxidized ethylene to ethylene oxide. Methane oxidation was not detected by any of the bacteria. The results indicate the presence of three distinct butane monooxygenases in butane-grown
P. butanovora
,
M. vaccae
, and CF8.
Sulfonates as Terminal Electron Acceptors for Growth of Sulfite-Reducing Bacteria (Desulfitobacteriumspp.) and Sulfate-Reducing Bacteria: Effects of Inhibitors of Sulfidogenesis
Authors: Lie Thomas J. , Godchaux Walter , Leadbetter Edward R. 
Published: December 2019

ABSTRACTThis study demonstrates the ability ofDesulfitobacteriumspp. to utilize aliphatic sulfonates as terminal electron acceptors (TEA) for growth. Isethionate (2-hydroxyethanesulfonate) reduction byDesulfitobacterium hafnienseresulted in acetate as well as sulfide accumulation in accordance with the expectation that the carbon portion of isethionate was oxidized to acetate and the sulfur was reduced to sulfide. The presence of a polypeptide, approximately 97 kDa, was evident in isethionate-grown cells ofDesulfitobacterium hafniense,Desulfitobacteriumsp. strain PCE 1, and the two sulfate-reducing bacteria (SRB)—Desulfovibrio desulfuricansIC1 (T. J. Lie, J. R. Leadbetter, and E. R. Leadbetter, Geomicrobiol. J. 15:135–149, 1998) andDesulfomicrobium norvegicum; this polypeptide was not detected when these bacteria were grown on TEA other than isethionate, suggesting involvement in its metabolism. The sulfate analogs molybdate and tungstate, effective in inhibiting sulfate reduction by SRB, were examined for their effects on sulfonate reduction. Molybdate effectively inhibited sulfonate reduction by strain IC1 and selectively inhibited isethionate (but not cysteate) reduction byDesulfitobacterium dehalogenansandDesulfitobacteriumsp. strain PCE 1.Desulfitobacterium hafniense, however, grew with both isethionate and cysteate in the presence of molybdate. In contrast, tungstate only partially inhibited sulfonate reduction by both SRB andDesulfitobacteriumspp. Similarly, another inhibitor of sulfate reduction, 1,8-dihydroxyanthraquinone, effectively inhibited sulfate reduction by SRB but only partially inhibited sulfonate reduction by both SRB andDesulfitobacterium hafniense.
Bacterial Production ofd-Erythroascorbic Acid andl-Ascorbic Acid through Functional Expression ofSaccharomyces cerevisiaed-Arabinono-1,4-Lactone Oxidase inEscherichia coli
Authors: Lee Byung-Hoon , Huh Won-Ki , Kim Seong-Tae , Lee Jung-Shin , Kang Sa-Ouk 
Published: December 2019

ABSTRACTd-Arabinono-1,4-lactone oxidase, which catalyzes the terminal step in the biosynthesis ofd-erythroascorbic acid inSaccharomyces cerevisiae, was functionally expressed inEscherichia coliinherently lacking the enzyme. The recombinantE. colistrain expressing the enzyme could overproduced-erythroascorbic acid andl-ascorbic acid when supplied withd-arabinono-1,4-lactone andl-galactono-1,4-lactone, respectively.
Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples
Authors: Miller D. N. , Bryant J. E. , Madsen E. L. , Ghiorse W. C. 
Published: December 2019

ABSTRACTWe compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption methods (bead mill homogenization and freeze-thaw lysis), and lysozyme digestion were evaluated based on the yield and molecular size of the recovered DNA. Pairwise comparisons of the nine extraction procedures revealed that bead mill homogenization with SDS combined with either chloroform or phenol optimized both the amount of DNA extracted and the molecular size of the DNA (maximum size, 16 to 20 kb). Neither lysozyme digestion before SDS treatment nor guanidine isothiocyanate treatment nor addition of Chelex 100 resin improved the DNA yields. Bead mill homogenization in a lysis mixture containing chloroform, SDS, NaCl, and phosphate-Tris buffer (pH 8) was found to be the best physical lysis technique when DNA yield and cell lysis efficiency were used as criteria. The bead mill homogenization conditions were also optimized for speed and duration with two different homogenizers. Recovery of high-molecular-weight DNA was greatest when we used lower speeds and shorter times (30 to 120 s). We evaluated four different DNA purification methods (silica-based DNA binding, agarose gel electrophoresis, ammonium acetate precipitation, and Sephadex G-200 gel filtration) for DNA recovery and removal of PCR inhibitors from crude extracts. Sephadex G-200 spin column purification was found to be the best method for removing PCR-inhibiting substances while minimizing DNA loss during purification. Our results indicate that for these types of samples, optimum DNA recovery requires brief, low-speed bead mill homogenization in the presence of a phosphate-buffered SDS-chloroform mixture, followed by Sephadex G-200 column purification.
Selection of a Highly Monensin-Resistant
Prevotella bryantii
Subpopulation with Altered Outer Membrane Characteristics
Authors: Callaway Todd R. , Russell James B. 
Published: December 2019

ABSTRACT

Prevotella bryantii
cultures treated with monensin grew more slowly than untreated cultures, but only if the monensin concentration was greater than 1 μM. Cultures that were repeatedly transferred (eight transfers or 25 doublings) with monensin always grew rapidly, even at a 10 μM concentration. The amount of monensin needed to facilitate half-maximal potassium depletion (

K
d

) from monensin-selected cells was 16-fold greater than “unadapted” wild-type cultures (3,200 versus 200 nM). Cells taken from continuous culture had a

K
d

of 100 nM, and these inocula could not grow in batch culture when the monensin concentration was greater than 300 nM. Continuous cultures treated with monensin nearly washed out, but the surviving cells had a

K
d

of 1,300 nM. When wild-type cells were transferred in batch culture with 10 μM monensin, the

K
d

did not reach its maximum value (3,200 nM) until after eight transfers (25 doublings).

K
d

declined when monensin was removed, and it took eight transfers to reach the control value (200 nM). The most probable number of wild-type cells was 1,000-fold lower than of the monensin-selected cells, but calculations based on relative growth advantage and

K
d

indicated that the wild-type culture had 1 to 10% highly monensin-resistant cells. Cell pellets of wild-type cultures were more difficult to disperse than were monensin-selected cells, and water-soluble phenol extracts of monensin-selected cells had 1.8-fold more anthrone-reactive material than did the wild type. Wild-type cultures that were washed in Tris buffer (pH 8.0) released little alkaline phosphatase and were agglutinated by lysozyme. Monensin-selected cultures leaked ninefold more alkaline phosphatase and were not agglutinated by lysozyme. Wild-type colonies taken from high-dilution agar roll tubes retained the lysozyme agglutination phenotype even if transferred with monensin, and monensin-selected colonies were never agglutinated. These observations indicated that wild-type
P. bryantii
cultures had a subpopulation with different outer membrane characteristics and increased monensin resistance.
Biochemical and Genetic Analyses of Ferulic Acid Catabolism in
Pseudomonas
sp. Strain HR199
Authors: Overhage Jörg , Priefert Horst , Steinbüchel Alexander 
Published: December 2019

ABSTRACT

The gene loci
fcs
, encoding feruloyl coenzyme A (feruloyl-CoA) synthetase,
ech
, encoding enoyl-CoA hydratase/aldolase, and
aat
, encoding β-ketothiolase, which are involved in the catabolism of ferulic acid and eugenol in
Pseudomonas
sp. strain HR199 (DSM7063), were localized on a DNA region covered by two
Eco
RI fragments (E230 and E94), which were recently cloned from a
Pseudomonas
sp. strain HR199 genomic library in the cosmid pVK100. The nucleotide sequences of parts of fragments E230 and E94 were determined, revealing the arrangement of the aforementioned genes. To confirm the function of the structural genes
fcs
and
ech
, they were cloned and expressed in
Escherichia coli
. Recombinant strains harboring both genes were able to transform ferulic acid to vanillin. The feruloyl-CoA synthetase and enoyl-CoA hydratase/aldolase activities of the
fcs
and
ech
gene products, respectively, were confirmed by photometric assays and by high-pressure liquid chromatography analysis. To prove the essential involvement of the
fcs
,
ech
, and
aat
genes in the catabolism of ferulic acid and eugenol in
Pseudomonas
sp. strain HR199, these genes were inactivated separately by the insertion of omega elements. The corresponding mutants
Pseudomonas
sp. strain HR
fcs
ΩGm and
Pseudomonas
sp. strain HR
ech
ΩKm were not able to grow on ferulic acid or on eugenol, whereas the mutant
Pseudomonas
sp. strain HR
aat
ΩKm exhibited a ferulic acid- and eugenol-positive phenotype like the wild type. In conclusion, the degradation pathway of eugenol via ferulic acid and the necessity of the activation of ferulic acid to the corresponding CoA ester was confirmed. The
aat
gene product was shown not to be involved in this catabolism, thus excluding a β-oxidation analogous degradation pathway for ferulic acid. Moreover, the function of the
ech
gene product as an enoyl-CoA hydratase/aldolase suggests that ferulic acid degradation in
Pseudomonas
sp. strain HR199 proceeds via a similar pathway to that recently described for
Pseudomonas fluorescens
AN103.
Flagellate Predation on a Bacterial Model Community: Interplay of Size-Selective Grazing, Specific Bacterial Cell Size, and Bacterial Community Composition
Authors: Hahn Martin W. , Höfle Manfred G. 
Published: December 2019

ABSTRACT

The influence of grazing by the bacterivorous nanoflagellate
Ochromonas
sp. strain DS on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. A bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day
−1
when nongrazed) and low substrate concentration (9 mg liter
−1
). Before and after the introduction of the predator, the bacterial community composition was studied by in situ techniques (immunofluorescence microscopy and fluorescent in situ hybridization), as well as by cultivation on agar media. The cell sizes of nonspecifically stained and immunofluorescently labeled bacteria were measured by image analysis. Grazing by the flagellate caused a bidirectional change in the morphological structure of the community. Medium-size bacterial cells, which dominated the nongrazed community, were largely replaced by smaller cells, as well as by cells contained in large multicellular flocs. Cell morphological changes were combined with community taxonomic changes. After introduction of the flagellate, the dominating strains with medium-size cells were largely replaced by single-celled strains with smaller cells on the one hand and, on the other hand, by
Pseudomonas
sp. strain MWH1, which formed the large, floc-like forms. We assume that size-selective grazing was the major force controlling both the morphological and the taxonomic structures of the model community.
Microbial Desulfurization of Alkylated Dibenzothiophenes from a Hydrodesulfurized Middle Distillate by
Rhodococcus erythropolis
I-19
Authors: Folsom B. R. , Schieche D. R. , DiGrazia P. M. , Werner J. , Palmer S. 
Published: December 2019

ABSTRACT

Rhodococcus erythropolis
I-19, containing multiple copies of key
dsz
genes, was used to desulfurize alkylated dibenzothiophenes (Cx-DBTs) found in a hydrodesulfurized middle-distillate petroleum (MD 1850). Initial desulfurization rates of dibenzothiophene (DBT) and MD 1850 by I-19 were 5.0 and 2.5 μmol g dry cell weight
−1
min
−1
, more than 25-fold higher than that for wild-type bacteria. According to sulfur K-edge X-ray absorption near-edge structure (XANES) analysis, thiophenic compounds accounted for >95% of the total sulfur found in MD 1850, predominantly Cx-DBTs and alkylated benzothiophenes. Extensive biodesulfurization resulted in a 67% reduction of total sulfur from 1,850 to 615 ppm S. XANES analysis of the 615-ppm material gave a sulfur distribution of 75% thiophenes, 11% sulfides, 2% sulfoxides, and 12% sulfones. I-19 preferentially desulfurized DBT and C1-DBTs, followed by the more highly alkylated Cx-DBTs. Shifting zero- to first-order (first-order) desulfurization rate kinetics were observed when MD 1850 was diluted with hexadecane. Apparent saturation rate constant (
K
0
) and half-saturation rate constant (
K
1
) values were calculated to be 2.8 μmol g dry cell weight
−1
min
−1
and 130 ppm, respectively. However, partial biocatalytic reduction of MD 1850 sulfur concentration followed by determination of initial rates with fresh biocatalyst led to a sigmoidal kinetic behavior. A competitive-substrate model suggested that the apparent
K
1
values for each group of Cx-DBTs increased with increasing alkylation. Overall desulfurization rate kinetics with I-19 were affected by the concentration and distribution of Cx-DBTs according to the number and/or lengths of alkyl groups attached to the basic ring structure.
The
ald
Gene, Encoding a Coenzyme A-Acylating Aldehyde Dehydrogenase, Distinguishes
Clostridium beijerinckii
and Two Other Solvent-Producing Clostridia from
Clostridium acetobutylicum
Authors: Toth Julianna , Ismaiel Adnan A. , Chen Jiann-Shin 
Published: December 2019

ABSTRACT

The coenzyme A (CoA)-acylating aldehyde dehydrogenase (ALDH) catalyzes a key reaction in the acetone- and butanol (solvent)-producing clostridia. It reduces acetyl-CoA and butyryl-CoA to the corresponding aldehydes, which are then reduced by alcohol dehydrogenase (ADH) to form ethanol and 1-butanol. The ALDH of
Clostridium beijerinckii
NRRL B593 was purified. It had no ADH activity, was NAD(H) specific, and was more active with butyraldehyde than with acetaldehyde. The N-terminal amino acid sequence of the purified ALDH was determined. The open reading frame preceding the
ctfA
gene (encoding a subunit of the solvent-forming CoA transferase) of
C. beijerinckii
NRRL B593 was identified as the structural gene (
ald
) for the ALDH. The
ald
gene encodes a polypeptide of 468 amino acid residues with a calculated
M
r
of 51,353. The position of the
ald
gene in
C. beijerinckii
NRRL B593 corresponded to that of the
aad/adhE
gene (encoding an aldehyde-alcohol dehydrogenase) of
Clostridium acetobutylicum
ATCC 824 and DSM 792. In Southern analyses, a probe derived from the
C. acetobutylicum aad/adhE
gene did not hybridize to restriction fragments of the genomic DNAs of
C. beijerinckii
and two other species of solvent-producing clostridia. In contrast, a probe derived from the
C. beijerinckii ald
gene hybridized to restriction fragments of the genomic DNA of three solvent-producing species but not to those of
C. acetobutylicum
, indicating a key difference among the solvent-producing clostridia. The amino acid sequence of the ALDH of
C. beijerinckii
NRRL B593 was most similar (41% identity) to those of the
eutE
gene products (CoA-acylating ALDHs) of
Salmonella typhimurium
and
Escherichia coli
, whereas it was about 26% identical to the ALDH domain of the aldehyde-alcohol dehydrogenases of
C. acetobutylicum
,
E. coli
,
Lactococcus lactis
, and amitochondriate protozoa. The predicted secondary structure of the
C. beijerinckii
ALDH suggests the presence of an atypical Rossmann fold for NAD
+
binding. A comparison of the proposed catalytic pockets of the CoA-dependent and CoA-independent ALDHs identified 6 amino acids that may contribute to interaction with CoA.
Comparative Phylogenetic Assignment of Environmental Sequences of Genes Encoding 16S rRNA and Numerically Abundant Culturable Bacteria from an Anoxic Rice Paddy Soil
Authors: Hengstmann Ulf , Chin Kuk-Jeong , Janssen Peter H. , Liesack Werner 
Published: December 2019

ABSTRACT

We used both cultivation and direct recovery of bacterial 16S rRNA gene (rDNA) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. Isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (K.-J. Chin, D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen, Appl. Environ. Microbiol. 65:5042–5049, 1999). Here we describe the phylogenetic positions of these strains in relation to 57 environmental 16S rDNA clone sequences. Close matches between the two data sets were obtained for isolates from the culturable populations determined by the most-probable-number counting method to be large (3 × 10
7
to 2.5 × 10
8
cells per g [dry weight] of soil). This included matches with 16S rDNA similarity values greater than 98% within distinct lineages of the division
Verrucomicrobia
(strain PB90-1) and the
Cytophaga-Flavobacterium-Bacteroides
group (strains XB45 and PB90-2), as well as matches with similarity values greater than 95% within distinct lines of descent of clostridial cluster XIVa (strain XB90) and the family
Bacillaceae
(strain SB45). In addition, close matches with similarity values greater than 95% were obtained for cloned 16S rDNA sequences and bacteria (strains DR1/8 and RPec1) isolated from the same type of rice paddy soil during previous investigations. The correspondence between culture methods and direct recovery of environmental 16S rDNA suggests that the isolates obtained are representative geno- and phenotypes of predominant bacterial groups which account for 5 to 52% of the total cells in the anoxic rice paddy soil. Furthermore, our findings clearly indicate that a dual approach results in a more objective view of the structural and functional composition of a soil bacterial community than either cultivation or direct recovery of 16S rDNA sequences alone.
Probiotics Shown To Change Bacterial Community Structure in the Avian Gastrointestinal Tract
Authors: Netherwood Trudy , Gilbert H. J. , Parker D. S. , O’Donnell A. G. 
Published: December 2019

ABSTRACT

Culturing and molecular techniques were used to monitor changes in the bacterial flora of the avian gastrointestinal (GI) tract following introduction of genetically modified (GM) and unmodified probiotics. Community hybridization of amplified 16S ribosomal DNA demonstrated that the bacterial flora of the GI tract changed significantly in response to the probiotic treatments. The changes were not detected by culturing. Although both GM and non-GM strains of
Enterococcus faecium
NCIMB 11508 changed the bacterial flora of the chicken GI tract, they did so differently. Probing the community DNA with an
Enterococcus faecalis
-specific probe showed that the relative amount of
E. faecalis
in the total eubacterial population increased in the presence of the non-GM strain and decreased in the presence of the GM probiotic compared with the results obtained with an untreated control group.
Recovery in Embryonated Eggs of Viable but Nonculturable
Campylobacter jejuni
Cells and Maintenance of Ability To Adhere to HeLa Cells after Resuscitation
Authors: Cappelier J. M. , Minet J. , Magras C. , Colwell R. R. , Federighi M. 
Published: December 2019

ABSTRACT

The existence of a viable but nonculturable (VBNC) state has been described for
Campylobacter jejuni
as it had been for a number pathogenic bacteria. Three
C. jejuni
human isolates were suspended in surface water and subsequently entered the VBNC state. After starvation for 30 days, VBNC cells were inoculated in the yolk sacs of embryonated eggs. Culturable cells were detected in a large proportion of the embryonated eggs inoculated with VBNC
C. jejuni
cells. Recovered cells kept their adhesion properties.