bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of a Generalized Transducing Phage of Poly-(gamma)-Glutamic Acid-Producing Bacillus subtilis and Its Application for Analysis of Tn917-LTV1 Insertional Mutants Defective in Poly-(gamma)-Glutamic Acid Production
Authors: Nagai T , Itoh Y
Published: January 2020

A generalized transducing phage, (phi)BN100, was isolated from a Bacillus subtilis (natto) strain producing poly-(gamma)-glutamic acid ((gamma)PGA). Transduction frequencies for a given marker ranged from 3.8 x 10(sup-8) to 1.6 x 10(sup-6) per phage particle. The genome size of the phage was approximately 42 kb. (phi)BN100 was used successfully to identify bona fide Tn917-LTV1 transpositional mutants defective in (gamma)PGA production.
Importance of laccase in vegetative growth of pleurotus Florida
Authors: Das N , Sengupta S , Mukherjee M
Published: January 2020

Mycelial culture of Pleurotus florida produced highest extracellular laccase in optimum growth medium. At least two laccases (L(inf1) and L(inf2)) were shown to be present in the culture filtrate. Low-laccase-yielding mutants with impaired L(inf2) activity had poor mycelial growth and could not form fruit body, whereas the revertants from the same mutants were similar to the parent in mycelial growth and fruit body formation.
Cry9Ca1 Toxin, a Bacillus thuringiensis Insecticidal Crystal Protein with High Activity against the Spruce Budworm (Choristoneura fumiferana)
Authors: Van Frankenhuyzen K , Gringorten L , Gauthier D
Published: January 2020

The Cry9Ca1 toxin from Bacillus thuringiensis was significantly more toxic to spruce budworm (Choristoneura fumiferana) than the Cry1Ab6, Cry1Ba1, Cry1Ca2, Cry1Da1, Cry1Ea1, and Cry1Fa2 toxins. It displayed high activity against silkworm (Bombyx mori) but was not toxic to black army cutworm (Actebia fennica) or gypsy moth (Lymantria dispar). The Cry9Ca1 is the most effective spruce budworm toxin known to date and may offer promise for control and resistance management of that species.
Reduction of hexavalent uranium from organic complexes by sulfate- and iron-reducing bacteria
Authors: Ganesh R , Robinson K G , Reed G D , Sayler G S
Published: January 2020

The influence of organic-hexavalent-uranium [U(VI)] complexation on U(VI) reduction by a sulfate-reducing bacterium (Desulfovibrio desulfuricans) and an iron-reducing bacterium (Shewanella alga) was evaluated. Four aliphatic ligands (acetate, malonate, oxalate, and citrate) and an aromatic ligand (tiron [4,5-dihydroxy-1,3-benzene disulfonic acid]) were used to study complexed-uranium bioavailability. The trends in uranium reduction varied with the nature and the amount of U(VI)-organic complex formed and the type of bacteria present. D. desulfuricans rapidly reduced uranium from a monodentate aliphatic (acetate) complex. However, reduction from multidentate aliphatic complexes (malonate, oxalate, and citrate) was slower. A decrease in the amount of organic-U(VI) complex in solution significantly increased the rate of reduction. S. alga reduced uranium more rapidly from multidentate aliphatic complexes than from monodentate aliphatic complexes. The rate of reduction decreased with a decrease in the amount of multidentate complexes present. Uranium from an aromatic (tiron) complex was readily available for reduction by D. desulfuricans, while an insignificant level of U(VI) from the tiron complex was reduced by S. alga. These results indicate that selection of bacteria for rapid uranium reduction will depend on the organic composition of waste streams.
Detection of low levels of enteric viruses in metropolitan and airplane sewage
Authors: Shieh Y S , Baric R S , Sobsey M D
Published: January 2020

To detect less prevalent viruses, such as wild-type polioviruses in sewage from a highly immunized community, a method was developed to efficiently recover viruses and remove PCR inhibitors. The method consisted of initial separation of solids from liquid, followed by solvent extractions, polyethylene glycol precipitations, Sephadex G-200 chromatography, and guanidinium isothiocyanate (GIT) extraction. To elute viruses from the separated solids, 0.5 M threonine (pH 7.5) was as efficient as 3% beef extract but conferred no PCR inhibition. In samples that were concentrated approximately 1,000-fold, 21% of the initially seeded viruses were recovered. When poliovirus type 3 (PV3) Sabin strain at low levels and PV1 LSc strain at high levels were seeded in raw sewage, PV3 was specifically detected in the final sample concentrates at sensitivities of 14 PFU by direct PCR and 0.7 PFU by GIT extraction-PCR. While applying the method to international airplane sewage, which contains high levels of solids as well as commercial sanitizers, 44% (7 of 16) of the samples were found to harbor enteroviruses by both cell culture infectivity and pan-enterovirus PCR analyses. Nucleotide sequencing of the PCR products revealed that multiple enterovirus genotypes were amplified from each final sewage concentrate, whereas the fewer virus genotypes detected by cell culture infectivity were probably the better growing strains. By this method, we demonstrated that air travel may contribute to the intercontinental dissemination of enteric pathogens.
Regulation of the Synthesis and Activity of Ammonia Monooxygenase in Nitrosomonas europaea by Altering pH To Affect NH(inf3) Availability
Authors: Stein L Y , Arp D J , Hyman M R
Published: January 2020

The obligately ammonia-oxidizing bacterium Nitrosomonas europaea was incubated in medium containing 50 mM ammonium. Changes in the concentration of nitrite, the pH, and the NH(inf4)(sup+)- and NH(inf2)OH-dependent O(inf2) uptake activities of the cell suspension were monitored. The NH(inf4)(sup+)-dependent O(inf2) uptake activity doubled over the first 3 h of incubation and then slowly returned to its original level over the following 5 h. The extent of stimulation of NH(inf4)(sup+)-dependent O(inf2) uptake activity was decreased by lowering the initial pH of the medium. Radiolabeling studies demonstrated that the stimulation of NH(inf4)(sup+)-dependent O(inf2) uptake activity involved de novo synthesis of several polypeptides. Under O(inf2)-limited conditions, the stimulated NH(inf4)(sup+)-dependent O(inf2) uptake activity was stabilized. Rapid, controlled, and predictable changes in this activity could be caused by acidification of the medium in the absence of ammonia oxidation. These results indicate that the NH(inf4)(sup+)-dependent O(inf2) uptake activity in N. europaea is strongly regulated in response to NH(inf3) concentration.
Production of poly(3-hydroxybutyrate) by fed-batch culture of filamentation-suppressed recombinant Escherichia coli
Authors: Wang F , Lee S Y
Published: January 2020

Recombinant Escherichia coli XL1-Blue harboring a high-copy-number plasmid containing the Alcaligenes eutrophus polyhydroxyalkanoate synthesis genes could efficiently synthesize poly(3-hydroxybutyrate) (PHB) in a complex medium containing yeast extract and tryptone but not in a defined medium. One of the reasons for the reduced PHB production in a defined medium was thought to be severe filamentation of cells in this medium. By overexpressing an essential cell division protein, FtsZ, in recombinant E. coli producing PHB, filamentation could be suppressed and PHB could be efficiently produced in a defined medium. A high PHB concentration of 149 g/liter, with high productivity of 3.4 g of PHB/liter/h, could be obtained by the pH-stat fed-batch culture of the filamentation-suppressed recombinant E. coli in a defined medium. It was also found that insufficient oxygen supply at a dissolved oxygen concentration (DOC) of 1 to 3% of air saturation during active PHB synthesis phase did not negatively affect PHB production. By growing cells to the concentration of 110 g/liter and then controlling the DOC in the range of 1 to 3% of air saturation, a PHB concentration of 157 g/liter and PHB productivity of 3.2 g of PHB/liter/h were obtained. For the scale-up studies, fed-batch culture was carried out in a 50-liter stirred tank fermentor, in which the DOC decreased to zero when cell concentration reached 50 g/liter. However, a relatively high PHB concentration of 101 g/liter and PHB productivity of 2.8 g of PHB/liter/h could still be obtained, which demonstrated the possibility of industrial production of PHB in a defined medium by employing the filamentation-suppressed recombinant E. coli.
Two anaerobic polychlorinated biphenyl-dehalogenating enrichments that exhibit different para-dechlorination specificities
Authors: Wu Q , Wiegel J
Published: January 2020

Two anaerobic polychlorinated biphenyl (PCB)-dechlorinating enrichments with distinct substrate specificities were obtained: a 2,3,4,6-tetrachlorobiphenyl (2346-CB) para-dechlorinating enrichment derived from Aroclor 1260-contaminated Woods Pond (Lenox, Mass.) sediment and a 2,4,6-trichlorobiphenyl (246-CB) unflanked para-dechlorinating enrichment derived from PCB-free Sandy Creek Nature Center (Athens, Ga.) sediment. The enrichments have been successfully transferred to autoclaved soil slurries over 20 times by using 300 to 350 microM 2346-CB or 246-CB. Both enrichments required soil for successful transfer of dechlorination activity. The 2346-CB enrichment para dehalogenated, in the absence or presence of 2346-CB, only 4 of 25 tested para halogen-containing congeners: 234-CB, 2345-CB, 2346-CB, and 2,4,6-tribromobiphenyl (246-BrB). In the presence of 246-CB, the 246-CB enrichment para dehalogenated 23 of the 25 tested congeners. However, only three congeners (34-CB, 2346-CB, and 246-BrB) were dehalogenated in the absence of 246-CB, indicating that these specific congeners initiate dehalogenation in this enrichment culture. The addition of the 2346-CB (para)-dechlorinating enrichment did not further stimulate the 2346-CB-primed dechlorination of the Aroclor 1260 residue in Woods Pond sediment samples. Compared to the addition of the primer 246-CB or the 246-CB unflanked para-dechlorinating enrichment alone, the addition of both 246-CB (300 microM) and the 246-CB enrichment stimulated the unflanked para dechlorination of the Aroclor 1260 residue in Woods Pond sediments. These results indicate that the two enrichments contain different PCB-dechlorinating organisms, each with high substrate specificities. Furthermore, bioaugmentation with the enrichment alone did not stimulate the desired dechlorination in PCB-contaminated Woods Pond sediment.
Mutational analysis of pcpA and its role in pentachlorophenol degradation by Sphingomonas (Flavobacterium) chlorophenolica ATCC 39723
Authors: Chanama S , Crawford R L
Published: January 2020

Sphingomonas (Flavobacterium) chlorophenolica ATCC 39723 degrades pentachlorophenol (PCP) through a catabolic pathway encoded by multiple genes. One gene required for PCP degradation is pcpA, which encodes information for a 30-kDa polypeptide, PcpA, found in the periplasm of the bacterium. The biological role of PcpA has remained unknown. We disrupted pcpA by replacing it with a defective copy through homologous recombination. The pcpA recombinant, mutant strains accumulated 2,6-dichlorohydroquinone (2,6-DiCH) as a metabolite of PCP. This work confirms that pcpA is essential for degradation of PCP by S. chlorophenolica ATCC 39723 and suggests that it encodes a protein involved in hydrolytic dehalogenation of 2,6-DiCH, an already established primary metabolite of the PCP catabolic pathway.
Analysis of mer Gene Subclasses within Bacterial Communities in Soils and Sediments Resolved by Fluorescent-PCR-Restriction Fragment Length Polymorphism Profiling
Authors: Bruce K D
Published: January 2020

Bacterial mer (mercury resistance) gene subclasses in mercury-polluted and pristine natural environments have been profiled by Fluorescent-PCR-restriction fragment length polymorphism (FluRFLP). For FluRFLP, PCR products were amplified from individual mer operons in mercury-resistant bacteria and from DNA isolated directly from bacteria in soil and sediment samples. The primers used to amplify DNA were designed from consensus sequences of the major subclasses of archetypal gram-negative mer operons within Tn501, Tn21, pDU1358, and pKLH2. Two independent PCRs were used to amplify two regions of different lengths (merRT(Delta)P [ca. 1 kb] and merR [ca. 0.4 kb]) starting at the same position in merR. The oligonucleotide primer common to both reactions (FluRX) was labelled at the 5(prm1) end with green (TET) fluorescent dye. Analysis of the mer sequences within databases indicated that the major subclasses could be differentiated on the basis of the length from FluRX to the first FokI restriction endonuclease site. The amplified PCR products were digested with FokI restriction endonuclease, with the restriction digest fragments resolved on an automated DNA sequencing machine which detected only those bands labelled with the fluorescent dye. For each of the individual mer operon sources examined, this single peak (in bases) position was observed in separate digests of either amplified region. These peak positions were as predicted on the basis of DNA sequence. mer PCR products amplified from DNA extracted directly from soil and sediment bacteria were studied in order to determine the profiles of the major mer subclasses present in each natural environment. In addition to peaks of the expected sizes, extra peaks were observed which were not predicted on the basis of DNA sequence. Those appearing in the restriction endonuclease digests of both study regions were presumed to be novel mer types. Genetic heterogeneity within and between mercury-polluted and pristine sites has been studied by this technique. Profiles generated were highly similar for samples taken within the same soil type. The profiles, however, changed markedly on crossing from one soil type to another, with gradients of the different groupings of mer genes identified.
Regulation of the Phosphate Stress Response in Rhizobium meliloti by PhoB
Authors: Al-Niemi T S , Summers M L , Elkins J G , Kahn M L , McDermott T R
Published: January 2020

Alkaline phosphatase activity and phosphate transport rates in Rhizobium meliloti increased significantly when medium phosphate levels decreased to approximately 10 (mu)M. Both responses were abolished in a Tn5:: phoB mutant, but the mutant could be complemented by a plasmid that contained cloned R. meliloti phoB. The PhoB(sup-) mutant had a normal symbiosis phenotype under growth conditions that supplied either limiting or nonlimiting levels of phosphate to the host plant Medicago sativa, suggesting that induction of genes by PhoB was not required for normal symbiotic function.
Mycotoxin production by fusarium species isolated from bananas
Authors: Jimenez M , Huerta T , Mateo R
Published: January 2020

The ability of Fusarium species isolated from bananas to produce mycotoxins was studied with 66 isolates of the following species: F. semitectum var. majus (8 isolates), F. camptoceras (3 isolates), a Fusarium sp. (3 isolates), F. moniliforme (16 isolates), F. proliferatum (9 isolates), F. subglutinans (3 isolates), F. solani (3 isolates), F. oxysporum (5 isolates), F. graminearum (7 isolates), F. dimerum (3 isolates), F. acuminatum (3 isolates), and F. equiseti (3 isolates). All isolates were cultured on autoclaved corn grains. Their toxicity to Artemia salina L. larvae was examined. Some of the toxic effects observed arose from the production of known mycotoxins that were determined by thin-layer chromatography, gas chromatography, or high-performance liquid chromatography. All F. camptoceras and Fusarium sp. isolates proved toxic to A. salina larvae; however, no specific toxic metabolites could be identified. This was also the case with eight isolates of F. moniliforme and three of F. proliferatum. The following mycotoxins were encountered in the corn culture extracts: fumonisin B(inf1) (40 to 2,900 (mu)g/g), fumonisin B(inf2) (150 to 320 (mu)g/g), moniliformin (10 to 1,670 (mu)g/g), zearalenone (5 to 470 (mu)g/g), (alpha)-zearalenol (5 to 10 (mu)g/g), deoxynivalenol (8 to 35 (mu)g/g), 3-acetyldeoxynivalenol (5 to 10 (mu)g/g), neosolaniol (50 to 180 (mu)g/g), and T-2 tetraol (5 to 15 (mu)g/g). Based on the results, additional compounds produced by the fungal isolates may play prominent roles in the toxic effects on larvae observed. This is the first reported study on the mycotoxin-producing abilities of Fusarium species that contaminate bananas.
Acid adaptation sensitizes Salmonella typhimurium to hypochlorous acid
Authors: Leyer G J , Johnson E A
Published: January 2020

Acid adaptation of Salmonella typhimurium at a pH of 5.0 to 5.8 for one to two cell doublings resulted in marked sensitization of the pathogen to halogen-based sanitizers including chlorine (hypochlorous acid) and iodine. Acid-adapted S. typhimurium was more resistant to an anionic acid sanitizer than was its nonadapted counterpart. A nonselective plating medium of tryptose phosphate agar plus 1% pyruvate was used throughout the study to help recover chemically stressed cells. Mechanisms of HOCl-mediated inactivation of acid-adapted and nonadapted salmonellae were investigated. Hypochlorous acid oxidized a higher percentage of cell surface sulfhydryl groups in acid-adapted cells than in nonadapted cells, and sulfhydryl oxidation was correlated with cell inactivation. HOCl caused severe metabolic disruptions in acid-adapted and nonadapted S. typhimurium, such as respiratory loss and inability to restore the adenylate energy charge from a nutrient-starved state. Sensitization of S. typhimurium to hypochlorous acid by acid adaptation also involved increased permeability of the cell surface because nonadapted cells treated with EDTA became sensitized. The results of this study establish that acid-adapted S. typhimurium cells are highly sensitized to HOCl oxidation and that inactivation by HOCl involves changes in membrane permeability, inability to maintain or restore energy charge, and probably oxidation of essential cellular components. This study provides a basis for improved practical technologies to inactivate Salmonella and implies that acid pretreatment of food plant environments may increase the efficacy of halogen sanitizers.
Listeria monocytogenes Scott A transports glucose by high-affinity and low-affinity glucose transport systems
Authors: Parker C , Hutkins R W
Published: January 2020

Listeria monocytogenes transported glucose by a high-affinity phosphoenolpyruvate-dependent phosphotransferase system and a low-affinity proton motive force-mediated system. The low-affinity system (Km = 2.9 mM) was inhibited by 2-deoxyglucose and 6-deoxyglucose, whereas the high-affinity system (Km = 0.11 mM) was inhibited by 2-deoxyglucose and mannose but not 6-deoxyglucose. Cells and vesicles artificially energized with valinomycin transported glucose or 2-deoxyglucose at rates greater than those of de-energized cells, indicating that a membrane potential could drive uptake by the low-affinity system.
Monocentric and polycentric anaerobic fungi produce structurally related cellulases and xylanases
Authors: Li X L , Chen H , Ljungdahl L G
Published: January 2020

Cellulase and xylanase cDNAs were isolated from a cDNA library of the polycentric anaerobic fungus Orpinomyces sp. strain PC-2 constructed in Escherichia coli. The cellulase cDNA (celB) was 1.8 kb long with an open reading frame (ORF) coding for a polypeptide of 471 amino acids, and the xylanase cDNA (xynA) was 1.2 kb long with an ORF encoding a polypeptide of 362 amino acids. Single transcripts of 1.9 kb for celB and 1.5 kb for xynA were detected in total RNA of Orpinomyces grown on Avicel. Genomic DNA regions coding for CelA and XynA were devoid of introns. The enzymes were highly homologous (80 to 85% identity) to the corresponding enzymes of the monocentric anaerobic fungus Neocallimastix patriciarum and, like those, contained in addition to a catalytic domain, a noncatalytic repeated peptide domain (NCRPD). The Orpinomyces xylanase contained one catalytic domain and thus differed from the Neocallimastix xylanase, which had two similar catalytic domains (H. J. Gilbert, G. P. Hazlewood, J. I. Lauie, C. G. Orpin, and G. P. Xue, Mol. Microbiol. 6:2065-2072, 1992). Two peptides corresponding to the catalytic domain and the NCRPD of XynA were synthesized, and antibodies against them were raised and affinity column purified. The antibodies against the catalytic domain peptide reacted specifically with the xylanases of Orpinomyces and Neocallimastix, while the antibodies against the NCRPD reacted with many (at least eight) extracellular proteins of Orpinomyces and Neocallimastix, suggesting that the NCRPD is present in a number of polypeptides.
Novel group within the kingdom Crenarchaeota from boreal forest soil
Authors: Jurgens G , Lindström K , Saano A
Published: January 2020

We report here the results of phylogenetic analysis of archaeal 16S rRNA gene sequences amplified by PCR with Archaea-specific primers with mixed-population DNA extracted directly from forest soil used as a template. Nucleotide signature and phylogenetic analyses show that the sequences obtained belong to the domain Archaea and form a new cluster. Its phylogenetic position suggests that sequences are from a previously undescribed terrestrial group within the kingdom Crenarchaeota.
Manganese-Dependent Cleavage of Nonphenolic Lignin Structures by Ceriporiopsis subvermispora in the Absence of Lignin Peroxidase
Authors: Jensen K A , Bao W , Kawai S , Srebotnik E , Hammel K E
Published: January 2020

Vol. 62, no. 10, p. 3684, column 2, line 16: "Tri(methylsilyl)" should read "Tri(trimethylsilyl)." Line 17: "Di(methylsilyl)" should read "Di(trimethylsilyl)." Line 20: "Tri(methylsilyl)" should read "Trimethylsilyl." Page 3686, column 1, reference 12: The journal should be Dokl. Akad. Nauk Belarusi. [This corrects the article on p. 3679 in vol. 62.].
Recovery of a strain of Clostridium botulinum producing both neurotoxin A and neurotoxin B from canned macrobiotic food
Authors: Franciosa G , Fenicia L , Pourshaban M , Aureli P
Published: January 2020

A rare strain of Clostridium botulinum subtype Ab was isolated from a canned macrobiotic food suspected of being linked to a fatal case of food-borne botulism. The strain was recovered and identified by conventional methods modified by the inclusion of a PCR assay (G. Franciosa, J.L. Ferreira, and C.L. Hatheway, J. Clin. Microbiol. 32:1911-1917, 1994). The titers of neurotoxins produced by the strain were evaluated by a mouse bioassay.
Purification and Characterization of a Proteasome from the Hyperthermophilic Archaeon Pyrococcus furiosus
Authors: Bauer M W , Bauer S H , Kelly R M
Published: January 2020

A 640-kDa proteasome consisting of (alpha) (25-kDa) and (beta) (22-kDa) subunits, and with a temperature optimum of 95(deg)C, was purified from crude cell extracts of a hyperthermophilic archaeon, Pyrococcus furiosus. Although this is the fourth member of the kingdom Euryarchaeota (and the first hyperthermophile) found to contain a proteasome, none has been identified among the members of the kingdom Crenarchaeota.
Lignin Peroxidase Isozymes from Phanerochaete chrysosporium Can Be Enzymatically Dephosphorylated
Authors: Rothschild N , Hadar Y , Dosoretz C G
Published: January 2020

The extracellular lignin peroxidase (LIP) protein profile of the fungus Phanerochaete chrysosporium, grown in nonimmersed liquid culture under conditions of excess nitrogen, changed markedly with culture age. At peak LIP activity (day 4), the heme-protein profile in the extracellular fluid, analyzed by anion-exchange high-pressure liquid chromatography, was characterized by a predominance of the LIP isozymes H1 and H2, small amounts of H6 and H8, and other minor peaks, designated Ha and Hb. On day 5, the level of H1 increased and it became the dominant isozyme, with a corresponding decrease in the level of H2. Moreover, the relative levels of H6 and H8 decreased with corresponding increases in Ha and Hb levels. This change in LIP profile occurred extracellularly and resulted from the enzymatic dephosphorylation of LIP isozymes. An enzymatic fraction responsible for LIP isozyme dephosphorylation, termed LIP dephosphorylating (LpD) fraction, was partially purified from the culture fluid. Incubation of the LpD fraction with (sup32)P-labeled H2, H6, H8, and H10 isozymes separated from nitrogen-limited cultures resulted in the formation of the dephosphorylated isozymes H1, Ha, Hb, and Hc, respectively. Dephosphorylation did not significantly change the catalytic properties of the LIP isozymes with veratryl alcohol as a substrate. LIP dephosphorylation is therefore suggested to be a posttranslational modification process catalyzed extracellularly by the LpD activity.
Dechlorination of Atrazine by a Rhizobium sp. Isolate
Authors: Bouquard C , Ouazzani J , Prome J , Michel-Briand Y , Plesiat P
Published: January 2020

A Rhizobium sp. strain, named PATR, was isolated from an agricultural soil and found to actively degrade the herbicide atrazine. Incubation of PATR in a basal liquid medium containing 30 mg of atrazine liter(sup-1) resulted in the rapid consumption of the herbicide and the accumulation of hydroxyatrazine as the only metabolite detected after 8 days of culture. Experiments performed with ring-labeled [(sup14)C]atrazine indicated no mineralization. The enzyme responsible for the hydroxylation of atrazine was partially purified and found to consist of four 50-kDa subunits. Its synthesis in PATR was constitutive. This new atrazine hydrolase demonstrated 92% sequence identity through a 24-amino-acid fragment with atrazine chlorohydrolase AtzA produced by Pseudomonas sp. strain ADP.
Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample
Authors: Suzuki M T , Rappé M S , Haimberger Z W , Winfield H , Adair N , Ströbel J , Giovannoni S J
Published: January 2020

Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the gamma subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched a novel rDNA clone related to the gamma subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases.
Plasmid-mediated mineralization of carbofuran by Sphingomonas sp. strain CF06
Authors: Feng X , Ou L T , Ogram A
Published: January 2020

A bacterial strain (CF06) that mineralized both the carbonyl group and the aromatic ring of the insecticide carbofuran and that is capable of using carbofuran as a sole source of carbon and nitrogen was isolated from a soil in Washington state. Phospholipid fatty acid and 16S rRNA sequencing analysis indicate that CF06 is a Sphingomonas sp. CF06 contains five plasmids, at least some of which are required for metabolism of carbofuran. Loss of the plasmids induced by growth at 42 degrees C resulted in the inability of the cured strain to grow on carbofuran as a sole source of carbon. Introduction of the plasmids confers on Pseudomonas fluorescens M480R the ability to use carbofuran as a sole source of carbon for growth and energy. Of the five plasmids, four are rich in insertion sequence elements and contain large regions of overlap. Rearrangements, deletions, and loss of individual plasmids that resulted in the loss of the carbofuran-degrading phenotype were observed following introduction of Tn5.
Organic solvent tolerance and antibiotic resistance increased by overexpression of marA in Escherichia coli
Authors: Asako H , Nakajima H , Kobayashi K , Kobayashi M , Aono R
Published: January 2020

We previously reported that overexpression of the soxS or robA gene causes in several Escherichia coli strains the acquisition of higher organic solvent tolerance and also increased resistance to a number of antibiotics (H. Nakajima, K. Kobayashi, M. Kobayashi, H. Asako, and R. Aono, Appl. Environ. Microbiol. 61:2302-2307, 1995). Most E. coli strains cannot grow in the presence of cyclohexane. We isolated the marRAB genes from a Kohara lambda phage clone and cyclohexane-tolerant mutant strain OST3408. We found a substitution of serine for arginine at position 73 in the coding region of marR of OST3408 and designated the gene marR08. Our genetic analysis revealed that marR08 is responsible for the cyclohexane-tolerant phenotype. We observed that the marA gene on high-copy-number plasmids increased the organic solvent tolerance of E. coli strains. Furthermore, exposure of E. coli cells to salicylate, which activates the mar regulon genes, also raised organic solvent tolerance. Overexpression of the marA, soxS, or robA gene increased resistance to numerous antibiotics but not to hydrophilic aminoglycosides.
A Three-Component Enzyme System Catalyzes the O Demethylation of the Herbicide Dicamba in Pseudomonas maltophilia DI-6
Authors: Wang X , Li B , Herman P L , Weeks D P
Published: January 2020

An enzyme activity which converts dicamba (2-methoxy-3,6-dichlorobenzoic acid) to 3,6-dichlorosalicylic acid in vitro has been detected in cell lysates of Pseudomonas maltophilia DI-6. Phenyl-Sepharose column chromatography of a partially purified lysate resulted in the separation of this enzyme into three separate protein components tentatively identified as an oxygenase, a ferredoxin, and a reductase. The activity of dicamba O-demethylase was dependent on oxygen and required NADH and Mg(sup2+).
Effect of Bacillus thuringiensis toxins on the membrane potential of lepidopteran insect midgut cells
Authors: Peyronnet O , Vachon V , Brousseau R , Baines D , Schwartz J L , Laprade R
Published: January 2020

To test whether the ability of Bacillus thuringiensis toxins to form pores in the midgut epithelial cell membrane of susceptible insects correlates with their in vivo toxicity, we measured the effects of different toxins on the electrical potential of the apical membrane of freshly isolated midguts from gypsy moth (Lymantria dispar) and silkworm (Bombyx mori) larvae. In the absence of toxin, the membrane potential, measured with a conventional glass microelectrode, was stable for up to 30 min. It was sensitive to the K+ concentration and the oxygenation of the external medium. Addition of toxins to which L. dispar is highly [CryIA(a) and CryIA(b)] or only slightly [CryIA(c) and CryIC] sensitive caused a rapid, irreversible, and dose-dependent depolarization of the membrane. CryIF, whose toxicity towards L. dispar is unknown, and CryIE, which is at best poorly active in vivo, were also active in vitro. In contrast, CryIB and CryIIIA, a coleopteran-specific toxin, had no significant effect. The basolateral-membrane potential was unaffected by CryIA(a) or CryIC when the toxin was applied to the basal side of the epithelium. In B. mori midguts, the apical-membrane potential was abolished by CryIA(a), to which silkworm larvae are susceptible, but CryIA(b) and CryIA(c); to which they are resistant, had no detectable effect. Although the technique discriminated between active and inactive toxins, the concentration required to produce a given effect varied much less extensively than the sensitivity of gypsy moth larvae, suggesting that additional factors influence the toxins' level of toxicity in vivo.
Manipulation of independent synthesis and degradation of polyphosphate in Escherichia coli for investigation of phosphate secretion from the cell
Authors: Van Dien S J , Keyhani S , Yang C , Keasling J D
Published: January 2020

The genes involved in polyphosphate metabolism in Escherichia coli were cloned behind different inducible promoters on separate plasmids. The gene coding for polyphosphate kinase (PPK), the enzyme responsible for polyphosphate synthesis, was placed behind the Ptac promoter. Polyphosphatase, a polyphosphate depolymerase, was similarly expressed by using the arabinose-inducible PBAD promoter. The ability of cells containing these constructs to produce active enzymes only when induced was confirmed by polyphosphate extraction, enzyme assays, and RNA analysis. The inducer concentrations giving optimal expression of each enzyme were determined. Experiments were performed in which ppk was induced early in growth, overproducing PPK and allowing large amounts of polyphosphate to accumulate (80 mumol in phosphate monomer units per g of dry cell weight). The ppx gene was subsequently induced, and polyphosphate was degraded to inorganic phosphate. Approximately half of this polyphosphate was depleted in 210 min. The phosphate released from polyphosphate allowed the growth of phosphate-starved cells and was secreted into the medium, leading to a down-regulation of the phosphate-starvation response. In addition, the steady-state polyphosphate level was precisely controlled by manipulating the degree of ppx induction. The polyphosphate content varied from 98 to 12 mumol in phosphate monomer units per g of dry cell weight as the arabinose concentration was increased from 0 to 0.02% by weight.
Manure Enhances Plasmid Mobilization and Survival of Pseudomonas putida Introduced into Field Soil
Authors: Gotz A , Smalla K
Published: January 2020

We report a field study on plasmid mobilization in an agricultural soil. The influence of pig manure on the mobilization of the IncQ plasmid pIE723 by indigenous plasmids or by the IncP(alpha) plasmid pGP527 into the recipient Pseudomonas putida UWC1 (Rif(supr) Nal(supr)) was studied in field soil. Six plots were prepared in duplicate, three of which were treated with manure prior to inoculation of the donor and recipient strains. As a donor strain, either Escherichia coli J53(pIE723) or E. coli 600(pIE723, pGP527) was used. Putative transconjugants obtained on a selective medium were confirmed by DNA hybridization and PCR. Plasmid mobilization by indigenous mobilizing plasmids was observed on two occasions in manured soil. Manuring of soil significantly enhanced the frequency of pIE723 mobilization by pGP527, since mobilization frequencies into P. putida UWC1 were at least 10-fold higher in manured soil than in nonmanured soil. Enhanced numbers of P. putida UWC1 transconjugant and recipient colonies could be observed in manured soil throughout the 79-day field test. Transfer of pIE723 or pG527 into indigenous soil or rhizosphere bacteria could not be detected when indigenous bacteria isolated by selective cultivation were screened for the presence of these plasmids by DNA hybridization. Furthermore, the presence of IncN-, IncP-, or IncQ-specific sequences was confirmed in total community DNA extracted directly from the manured or nonmanured soil by PCR. IncW plasmids were detectable only in manured soil, indicating entry of these plasmids into soil via manure.
Cell Hydrophobicity and Sulfur Adhesion of Thiobacillus thiooxidans
Authors: Takeuchi T L , Suzuki I
Published: January 2020

Thiobacillus thiooxidans cells became more hydrophobic but less adhesive to elemental sulfur in the presence of increasing potassium phosphate concentrations. At a fixed concentration of potassium phosphate, however, there was a peak of both cell hydrophobicity and adhesion to sulfur at around pH 5. Oxidation of sulfur by the cells was affected in a complex manner by the phosphate concentration and pH, although it was inhibited by a high concentration of potassium phosphate.
Production of Clostridium bifermentans Spores as Inoculum for Bioremediation of Nitroaromatic Contaminants
Authors: Sembries S , Crawford R L
Published: January 2020

Spores of Clostridium bifermentans KMR-1 were produced for use as a microbial inoculum for bioremediation and were preserved in both liquid and dry forms. All spore formulations showed good viability and ability to biodegrade the target compound, 2,4,6-trinitrotoluene (TNT), after 4 months of storage. For low-cost bulk spore production, several medium compositions, based on soy peptone, corn steep liquor, and meat peptone, were tested and yielded 10(sup7) spores per ml. A medium pH above 7.0, a low glucose concentration, and a sufficient concentration of protein favored the sporulation of C. bifermentans KMR-1.
The effects of adding lactococcal proteinase on the growth rate of Lactococcus lactis in milk depend on the type of enzyme
Authors: Helinck S , Richard J , Juillard V
Published: January 2020

Increasing the proteolytic activity of Lactococcus lactis cultures in milk by adding the corresponding proteinase resulted in a stimulation of the growth rate regardless of the strain and the type of proteinase, demonstrating that the rate of casein degradation was responsible for the growth rate limitation of L. lactis in milk. However, the stimulation was only transient, and the reduction in growth rate in the poststimulation phase depended on the type of cell envelope proteinase. When a PI-type proteinase was added, three causes were involved in the subsequent reduction in growth rate: degradation of the added proteinase, repression of the proteolytic activity expressed by the cells, and competition for peptide uptake. When a PIII-type proteinase was added, the cessation of stimulation was due to the autoproteolysis of the added enzyme only.
Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin
Authors: Hammer P E , Hill D S , Lam S T , Van Pée K H , Ligon J M
Published: January 2020

Pyrrolnitrin is a secondary metabolite of Pseudomonas and Burkholderia sp. strains with strong antifungal activity. Production of pyrrolnitrin has been correlated with the ability of some bacteria to control plant diseases caused by fungal pathogens, including the damping-off pathogen Rhizoctonia solani. Pseudomonas fluorescens BL915 has been reported to produce pyrrolnitrin and to be an effective biocontrol agent for this pathogen. We have isolated a 32-kb genomic DNA fragment from this strain that contains genes involved in the biosynthesis of pyrrolnitrin. Marker-exchange mutagenesis of this DNA with Tn5 revealed the presence of a 6.2-kb region that contains genes required for the synthesis of pyrrolnitrin. The nucleotide sequence of the 6.2-kb region was determined and found to contain a cluster of four genes that are required for the production of pyrrolnitrin. Deletion mutations in any of the four genes resulted in a pyrrolnitrin-nonproducing phenotype. The putative coding sequences of the four individual genes were cloned by PCR and fused to the tac promoter from Escherichia coli. In each case, the appropriate tac promoter-pyrrolnitrin gene fusion was shown to complement the pyrrolnitrin-negative phenotype of the corresponding deletion mutant. Transfer of the four gene cluster to E. coli resulted in the production of pyrrolnitrin by this organism, thereby demonstrating that the four genes are sufficient for the production of this metabolite and represent all of the genes required to encode the pathway for pyrrolnitrin biosynthesis.
Epidemiological relatedness and clonal types of natural populations of Escherichia coli strains producing Shiga toxins in separate populations of cattle and sheep
Authors: Beutin L , Geier D , Zimmermann S , Aleksic S , Gillespie H A , Whittam T S
Published: January 2020

Two separate animal populations consisting of a herd of cattle (19 animals) and a flock of sheep (25 animals) were investigated for strains of Escherichia coli producing Shiga toxins (STEC) over a time period of 6 months. Thirty-three STEC were isolated from 63.2% of cattle and grouped into 11 serotypes and eight electrophoretic types (ETs) by multilocus enzyme analysis. In sheep, 88% of the animals excreted STEC (n = 67 isolates) belonging to 17 different serotypes and 12 different ETs. STEC from cattle and sheep differed with respect to serotype, and only 4 of the 16 ETs occurred in both animal populations. In cattle, ET14 (O116:H21) strains predominated, whereas other STEC serotypes occurred only sporadically. The predominating STEC types in sheep were ET4 (O125 strains), ET11 (O128:H2 and others), and ET14 (O146:H21). In contrast to their diversity, STEC originating from the same animal population were similar with respect to Shiga toxin (stxy genes. Almost all STEC isolated from cattle were positive for stx2 and stx2c; only one was positive for stx1. In sheep, almost all STEC isolated were positive for stx1 and stx2, whereas stx2c was not found. XbaI-digested DNAs of genetically closely related O146:H21 strains have different restriction profiles which were associated with size alterations in XbaI fragments hybridizing with stx1- and stx2-specific DNA probes. Our results indicate that stx-encoding bacteriophages might be the origin of the genetic heterogeneity in STEC from animals.
Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology
Authors: Guschin D Y , Mobarry B K , Proudnikov D , Stahl D A , Rittmann B E , Mirzabekov A D
Published: January 2020

The utility of parallel hybridization of environmental nucleic acids to many oligonucleotides immobilized in a matrix of polyacrylamide gel pads on a glass slide (oligonucleotide microchip) was evaluated. Oligonucleotides complementary to small-subunit rRNA sequences of selected microbial groups, encompassing key genera of nitrifying bacteria, were shown to selectively retain labeled target nucleic acid derived from either DNA or RNA forms of the target sequences. The utility of varying the probe concentration to normalize hybridization signals and the use of multicolor detection for simultaneous quantitation of multiple probe-target populations were demonstrated.
Bacterial viability and antibiotic susceptibility testing with SYTOX green nucleic acid stain
Authors: Roth B L , Poot M , Yue S T , Millard P J
Published: January 2020

A fluorescent nucleic acid stain that does not penetrate living cells was used to assess the integrity of the plasma membranes of bacteria. SYTOX Green nucleic acid stain is an unsymmetrical cyanine dye with three positive charges that is completely excluded from live eukaryotic and prokaryotic cells. Binding of SYTOX Green stain to nucleic acids resulted in a > 500-fold enhancement in fluorescence emission (absorption and emission maxima at 502 and 523 nm, respectively), rendering bacteria with compromised plasma membranes brightly green fluorescent. SYTOX Green stain is readily excited by the 488-nm line of the argon ion laser. The fluorescence signal from membrane-compromised bacteria labeled with SYTOX Green stain was typically > 10-fold brighter than that from intact organisms. Bacterial suspensions labeled with SYTOX Green stain emitted green fluorescence in proportion to the fraction of permeabilized cells in the population, which was quantified by microscopy, fluorometry, or flow cytometry. Flow cytometric and fluorometric approaches were used to quantify the effect of beta-lactam antibiotics on the cell membrane integrity of Escherichia coli. Detection and discrimination of live and permeabilized cells labeled with SYTOX Green stain by flow cytometry were markedly improved over those by propidium iodide-based tests. These studies showed that bacterial labeling with SYTOX Green stain is an effective alternative to conventional methods for measuring bacterial viability and antibiotic susceptibility.
Construction and characterization of Escherichia coli genetically engineered for bioremediation of Hg(2+)-contaminated environments
Authors: Chen S , Wilson D B
Published: January 2020

Escherichia coli strains were genetically engineered to express an Hg2+ transport system and metallothionein. Overexpression of a glutathione S-transferase fusion protein of Saccharomyces cerevisiae or pea metallothionein significantly increased the bioaccumulation of Hg2+ transported by MerT and MerP and protected the cells from the accumulated Hg2+. The recombinant strains have excellent properties for bioremediation of Hg(2+)-contaminated environments.
Cloning and sequence analysis of putative histidine protein kinases isolated from Lactococcus lactis MG1363
Authors: O'Connell-Motherway M , Fitzgerald G F , van Sinderen D
Published: January 2020

Eight recombinant plasmids harboring chromosomal fragments of Lactococcus lactis MG1363 were shown to phenotypically suppress a histidine protein kinase (HPK) deficiency in either of two different E. coli strains. Sequence analysis of the plasmid inserts revealed five different complete or partial open reading frames (ORFs) specifying proteins with high similarity to HPKs. One of the plasmids also harbored an additional ORF, unrelated to HPKs, with suppressing activity.
Characterization of recombinant glutamine synthetase from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1
Authors: Adul Rahman R N , Jongsareejit B , Fujiwara S , Imanaka T
Published: January 2020

The glnA gene encoding glutamine synthetase was cloned from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1, and its nucleotide sequence was determined. The glnA gene was expressed in Escherichia coli ME8459 (glnA mutant strain), and the protein was purified to homogeneity and shown to be functional in a dodecameric from (637,000 Da), exhibiting both transferase and synthetase activities. However, kinetic studies indicated that the enzyme possessed low biosynthetic activity, suggesting that the reaction was biased towards glutamate production. The optimum temperature for both activities was 60 degrees C, which was lower than the optimal growth temperature of KOD1. Recombinant KOD1 GlnA exhibited different optimum pHs depending on the reaction employed (pH 7.8 for the synthetase reaction and pH 7.2 for the transferase reaction). Of the various nucleoside triphosphates tested, GTP as well as ATP was involved in the synthetase reaction.