bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of copper resistance in competitive survival of Pseudomonas fluorescens in soil
Authors: Yang C H , Menge J A , Cooksey D A
Published: January 2020

A copper-resistant strain (09906) of Pseudomonas fluorescens that was isolated from a citrus grove soil is being investigated as a biological control agent for Phytophthora root rot. Since citrus grove soils in California are often contaminated with copper from many years of copper fungicide applications, the role of copper resistance in survival of strain 09906 was investigated. Three copper-sensitive Tn5 mutants were obtained with insertions in different chromosomal DNA regions. These insertions were not in the chromosomal region that hybridized with the copper resistance operon (cop) cloned from Pseudomonas syringae. A copper-sensitive mutant survived as well as the wild type in a sterile loamy sand without added copper, but with 10 and 15 micrograms of CuSO4 added per g of soil, populations of the copper-sensitive mutant were 27- and 562-fold lower, respectively, than that of the wild type after a 25-day period. In a sterilized citrus grove soil, populations of the copper-sensitive mutant and wild-type strain were similar, but in nonsterile citrus soil, populations of the copper-sensitive mutant were 112-fold lower than the wild type after 35 days. These data suggest that copper resistance genes can be important factors in persistence of P. fluorescens in soil contaminated with copper. In addition, these genes appear to play a role in competitive fitness, even in soils with a low copper content.
Comparison of conventional and reversed phage typing procedures for identification of Listeria spp
Authors: Estela L A , Sofos J N
Published: January 2020

Of 225 Listeria isolates evaluated, 199 had the same bacteriophage patterns by both the conventional (A. Audurier, A.G. Taylor, B. Carbonelle, and J. McLaughlin, Clin. Invest. Med. 7:229-232, 1984) and the new, easier to apply, "reversed" (M. J. Loessner, Appl. Environ. Microbiol. 57:882-884, 1991) phage typing procedures, 5 had different phage reactions, and the remaining 21 isolates were untypeable. Thus, the overall typeability rate was 90.7%, and 97.6% of the typeable isolates had the same phage patterns by both procedures.
Isolation of
Rhizobium meliloti nod
Gene Inducers from Alfalfa Rhizosphere Soil
Authors: León-Barrios Milagros , Dakora Felix D. , Joseph Cecillia M. , Phillips Donald A.
Published: January 2020

Methanolic extracts of alfalfa rhizosphere soil induce more
nod
gene transcription in
Rhizobium meliloti
than extracts of nonrhizosphere soil. Six peaks of
nod
-inducing activity were separated by high-performance liquid chromatography from rhizosphere soil extract, and one compound was identified by
1
H nuclear magnetic resonance, mass spectrometry, and UV-visible spectra as a formononetin-7-
O
-glycoside that activates both NodD1 and NodD2 proteins. The unanticipated presence of a glycoside in rhizosphere soil suggests either that large amounts of the glycoside were exuded by roots or that some glycosides are unexpectedly stable in soil.
p-Coumaroyl and feruloyl arabinoxylans from plant cell walls as substrates for ruminal bacteria
Authors: Akin D E , Borneman W S , Rigsby L L , Martin S A
Published: January 2020

Growth of the ruminal bacteria Ruminococcus flavefaciens FD1, Selenomonas ruminantium HD4, and Butyrivibrio fibrisolvens 49 was limited by ester-linked feruloyl and p-coumaroyl groups. The limitation of growth on phenolic acid-carbohydrate complexes varied with individual bacteria and appeared to be influenced by ability to hydrolyze carbohydrate linkages.
Modification of the Fe Protein of Nitrogenase in Natural Populations of
Trichodesmium thiebautii
Authors: Zehr Jonathan P. , Wyman Michael , Miller Veronica , Duguay Linda , Capone Douglas G.
Published: January 2020

The Fe protein of nitrogenase in the marine nonheterocystous cyanobacterium
Trichodesmium thiebautii
is interconverted between two forms, which is reminiscent of the ADP-ribosylation described in the purple bacterium
Rhodospirillum rubrum.
In natural populations of
T. thiebautii
during the day, when nitrogenase activity (NA) is present and while photosynthetic rates are high, a low-molecular-mass form of the Fe protein is present. In the late afternoon, the low-molecular-mass form is partially converted to a higher-molecular-mass form (approximately equal distribution of high- and low-molecular-mass forms of the Fe protein subunits), concurrent with cessation of NA. Some of the higher-molecular-mass form persists through the night until the very early morning, when the lower-molecular-mass form appears. New synthesis of both the Fe and MoFe proteins of nitrogenase appears to occur at this time. The higher-molecular-mass form of the Fe protein is also produced rapidly in response to artificially elevated external O
2
levels (40%) during the day.
T. thiebautii
is capable of recovery of NA in less than 1 h following exposure to 40% O
2
, which is correlated with the return of the Fe protein to the lower-molecular-mass form. Recovery from exposure to O
2
is not dependent upon protein synthesis. The modification of the Fe protein is clearly involved in regulation of NA during the diel cycle of NA in
T. thiebautii
but may also be involved in protecting the Fe protein during transient O
2
concentration increases.
Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria
Authors: Herrick J B , Madsen E L , Batt C A , Ghiorse W C
Published: January 2020

We report the amplification of bacterial genes from uninoculated surface and subsurface sediments by the polymerase chain reaction (PCR). PCR amplification of indigenous bacterial 16S ribosomal DNA genes was unsuccessful when subsurface sediment containing approximately 10(7) cells.g-1 was added directly to a PCR mixture. However, when 10 mg of sediment was inoculated with approximately 10(5) cells of Pseudomonas putida G7, the nahAc naphthalene dioxygenase gene characteristic of the P. putida G7 NAH7 plasmid was detected by PCR amplification. Southern blotting of the PCR amplification product improved sensitivity to 10(3) to 10(4) cells from samples inoculated with P. putida G7, but controls with no sediment added showed that the PCR was partially inhibited by the sediments. Lysozyme-sodium dodecyl sulfate-freeze-thaw DNA extraction was combined with gel electrophoretic partial purification in the presence of polyvinylpyrrolidone to render DNA from indigenous bacteria in surface or subsurface sediment samples amplifiable by PCR using eubacterial 16S ribosomal DNA primers. The nahAc gene could also be amplified from indigenous bacteria by using nahAc-specific primers when PCR conditions were modified by increasing Taq and primer concentrations. Restriction digests of the nahAc amplification products from surface and subsurface sediments revealed polymorphism relative to P. putida G7. The procedures for DNA extraction, purification, and PCR amplification described here demonstrate that the PCR is a potentially useful tool in studies of function- and taxon-specific DNA from indigenous microbial communities in sediment and groundwater environments.
Abundance of Virus-Sized Non-DNase-Digestible DNA (Coated DNA) in Eutrophic Seawater
Authors: Maruyama A. , Oda M. , Higashihara T.
Published: January 2020

Total DNA concentration in 0.2-μm-pore-size Nuclepore filter filtrates (<0.2-μm fraction) of Tokyo Bay water was estimated to be 9 to 19 ng/ml by an immunochemical quantification method. Almost 90% of the DNA in the <0.2-μm fraction was found in the size fractions larger than 3.0 � 10
5
Da and 0.03 μm, and most was not susceptible to DNase digestion, that is, consisted of non-DNase-digestible DNA (coated DNA). A significant amount of DNA was obtained from the <0.2-μm fraction of the seawater by three different methods: polyethylene glycol precipitation, direct ethanol precipitation, and ultrafilter concentration. Gel electrophoresis analysis of the isolated DNAs showed that they consisted mainly of coated DNAs with a similar molecular sizes (20 to 30 kb [1.3 � 10
7
to 2.0 � 10
7
Da). The abundance of the ultramicron virus-sized coated DNA in natural seawater suggests that these DNA-rich particles can be attributed to marine DNA virus assemblages and that they may be a significant phosphorus reservoir in the environment.
Production of high concentrations of ethanol from inulin by simultaneous saccharification and fermentation using Aspergillus niger and Saccharomyces cerevisiae
Authors: Ohta K , Hamada S , Nakamura T
Published: January 2020

Pure nonhydrolyzed inulin was directly converted to ethanol in a simultaneous saccharification and fermentation process. An inulinase-hyperproducing mutant, Aspergillus niger 817, was grown in a submerged culture at 30 degrees C for 5 days. The inulin-digestive liquid culture (150 ml) was supplemented with 45 g of inulin, 0.45 g of (NH4)2SO4, and 0.15 g of KH2PO4. The medium (pH 5.0) was inoculated with an ethanol-tolerant strain, Saccharomyces cerevisiae 1200, and fermentation was conducted at 30 degrees C. An additional 20 g of inulin was added to the culture after 15 h of fermentation. S. cerevisiae 1200 utilized 99% of the 65 g of inulin during the fermentation, and produced 20.4 and 21.0% (vol/vol) ethanol from chicory and dahlia inulins, respectively, within 3 days of fermentation. The maximum volumetric productivities of ethanol were 6.2 and 6.0 g/liter/h for chicory and dahlia inulins, respectively. The conversion efficiency of inulin to ethanol was 83 to 84% of the theoretical ethanol yield.
Degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) by the lignin-degrading basidiomycete Phanerochaete chrysosporium
Authors: Yadav J S , Reddy C A
Published: January 2020

Degradation of the BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes) group of organopollutants by the white-rot fungus Phanerochaete chrysosporium was studied. Our results show that the organism efficiently degrades all the BTEX components when these compounds are added either individually or as a composite mixture. Degradation was favored under nonligninolytic culture conditions in malt extract medium, in which extracellular lignin peroxidases (LIPs) and manganese-dependent peroxidases (MNPs) are not produced. The noninvolvement of LIPs and MNPs in BTEX degradation was also evident from in vitro studies using concentrated extracellular fluid containing LIPs and MNPs and from a comparison of the extents of BTEX degradation by the wild type and the per mutant, which lacks LIPs and MNPs. A substantially greater extent of degradation of all the BTEX compounds was observed in static than in shaken liquid cultures. Furthermore, the level of degradation was relatively higher at 25 than at 37 degrees C, but pH variations between 4.5 and 7.0 had little effect on the extent of degradation. Studies with uniformly ring-labeled [14C]benzene and [14C]toluene showed substantial mineralization of these compounds to 14CO2.
Cloning of the trp gene cluster from a tryptophan-hyperproducing strain of Corynebacterium glutamicum: identification of a mutation in the trp leader sequence
Authors: Herry D M , Dunican L K
Published: January 2020

Corynebacterium glutamicum ATCC 21850 produces up to 5 g of extracellular L-tryptophan per liter in broth culture and displays resistance to several synthetic analogs of aromatic amino acids. Here we report the cloning of the tryptophan biosynthesis (trp) gene cluster of this strain on a 14.5-kb BamHI fragment. Subcloning and complementation of Escherichia coli trp auxotrophs revealed that as in Brevibacterium lactofermentum, the C. glutamicum trp genes are clustered in an operon in the order trpE, trpD, trpC, trpB, trpA. The cloned fragment also confers increased resistance to the analogs 5-methyltryptophan and 6-fluorotryptophan on E. coli. The sequence of the ATCC 21850 trpE gene revealed no significant changes when compared to the trpE sequence of a wild-type strain reported previously. However, analysis of the promoter-regulatory region revealed a nonsense (TGG-to-TGA) mutation in the third of three tandem Trp codons present within a trp leader gene. Polymerase chain reaction amplification and sequencing of the corresponding region confirmed the absence of this mutation in the wild-type strain. RNA secondary-structure predictions and sequence similarities to the E. coli trp attenuator suggest that this mutation results in a constitutive antitermination response.
Conjugal Gene Transfer to Aquatic Bacteria Detected by the Generation of a New Phenotype
Authors: Barkay Tamar , Liebert Cynthia , Gillman Mark
Published: January 2020

An experimental approach based on the assembly of genes of a catabolic pathway was used to detect transconjugants in aquatic communities. Resistance to phenylmercury acetate was established in transconjugants when wide-host-range conjugal plasmids containing
merB
, the gene encoding organomercurial lyase, were transferred to strains from aquatic communities that had been acclimated to inorganic mercury and thus enriched for populations containing
merA
, the gene encoding mercuric reductase (T. Barkay, Appl. Environ. Microbiol. 53:2725-2732, 1987). Conjugation was confirmed by using the plasmids' encoded antibiotic resistance patterns and by hybridization with a eukaryotic gene. Three
merB
-conjugal plasmids, belonging to incompatibility groups W (pGTE16), P1 (pGTE26), and N (pGTE25), were prepared. Transfers by filter matings of pGTE16 and pGTE26 from
Pseudomonas aeruginosa
PA01 to indigenous strains were at efficiencies of 4.5 × 10
-2
and 4.8 × 10
-3
transconjugant per potential recipient, respectively. These efficiencies were from 1 to 2 orders of magnitude below those observed for intraspecies matings with genetically marked recipients. The third plasmid, pGTE25, was not stably maintained in
P. aeruginosa
donors, and its transfer from
Escherichia coli
donors was below the level of detection. Characterized transconjugant strains were shown to be
Pseudomonas
spp. Potential applications of the described experimental approach in the creation of bacterial populations with new catabolic capabilities in hazardous waste sites and in the detection of transfer of recombinant DNA from engineered microorganisms to indigenous bacteria are discussed.
Aspartate aminotransferase and tylosin biosynthesis in Streptomyces fradiae
Authors: Lee S H , Lee K J
Published: January 2020

Aspartate aminotransferase as well as valine dehydrogenase and threonine dehydratase was required for the biosynthesis of tylosin in Streptomyces fradiae NRRL 2702. The biosynthesis of these enzymes and tylosin production were repressed by high concentrations of ammonium ions. The change in specific tylosin production rates in batch cultures with different initial concentrations of ammonium ions showed patterns similar to those of the specific production rates of aspartate aminotransferase, valine dehydrogenase, and threonine dehydratase. Aspartate aminotransferase has been purified by acetone precipitation, DEAE-cellulose, hydroxyapatite, and preparative electrophoresis chromatographies. The purified enzyme (120 kDa) consisted of two subunits identical in molecular mass (54 kDa) and showed homogeneity, giving one band with a pI of 4.2 upon preparative isoelectric focusing. The enzyme was specific for L-aspartate in the forward reaction; the Km values were determined to be 2.7 mM for L-aspartate, 0.7 mM for 2-oxyglutarate, 12.8 mM for L-glutamate, and 0.15 mM for oxaloacetate. The enzyme was somewhat thermostable, having a maximum activity at 55 degrees C, and had a broad pH optimum that ranged from 5.5 to 8.0. The mode of action was a ping-pong-bi-bi mechanism.
Introduction and expression of the bacterial genes cysE and cysK in eukaryotic cells
Authors: Leish Z , Byrne C R , Hunt C L , Ward K A
Published: January 2020

The coding sequences of the cysE and cysK genes from Escherichia coli, which encode the enzymes of the cysteine biosynthetic pathway, namely, serine acetyltransferase (EC 2.3.1.30) and O-acetylserine sulfhydrylase (or cysteine synthase [EC 4.2.99.8]), were modified for expression in eukaryotic cells and introduced into murine L cells. A number of fusion genes comprising the cysE or cysK coding sequences joined to the promoter of the ovine metallothionein-Ia (MT-Ia) gene and various portions of the ovine growth hormone (GH) gene were prepared. Significant differences in the level of transcription were observed, depending on the amount and arrangement of the GH gene sequences used, the highest levels being obtained with the constructs MTCE10 and MTCK7, which contained only the GH 3' untranslated gene sequences. These two constructs were fused to produce the gene MTCEK1. In this single DNA sequence, each bacterial gene is under independent MT-Ia promoter control. Expression of the cysK sequence in this construct (MT-Ia promoter-cysE-3' GH sequence-MT-Ia promoter-cysK-3' GH sequence) was elevated compared with expression of the cysK gene in MTCK7. However, expression of the cysE sequence in MTCEK1 was only 40% of that of the cysE gene cloned into MTCE10. The double-promoter configuration, which enhances the expression of the second gene in MTCEK1, is proposed as a model for the modification of bacterial genes in general.
Quality control of bacterial enumeration
Authors: Donnison A M , Ross C M , Russell J M
Published: January 2020

Standard bacterial suspensions can be used to assess test method performance, via control charts, and inhibition of recovery when analyzing water samples. Variability in standard suspensions prepared from different strains and species and the use of frozen environmental samples for quality control for spore and bacteriophage analyses are also discussed.
Effects of Growth Pressure and Temperature on Fatty Acid Composition of a Barotolerant Deep-Sea Bacterium
Authors: Kamimura Kazuo , Fuse Hiroyuki , Takimura Osamu , Yamaoka Yukiho
Published: January 2020

The effects of pressure and temperature on the fatty acid composition in a barotolerant deep-sea bacterium that had branched-chain fatty acids were examined. The major fatty acids of the strain at atmospheric pressure were iso-C
15:0
, C
16:1
, iso-C
17:0
, and iso-C
17:1
. As the growth pressure increased, the proportion of unsaturated fatty acid increased because of an increase in the proportion of iso-C
17:1
. On the other hand, as the growth temperature decreased, the proportion of unsaturated fatty acid increased because of the increase in the proportion of C
16:1
and C
18:1
.
Purification, characterization, gene cloning, and sequencing of a new beta-glucosidase from Bacillus circulans subsp. alkalophilus
Authors: Paavilainen S , Hellman J , Korpela T
Published: January 2020

An intracellular beta-glucosidase was purified from cell extracts of Bacillus circulans subsp. alkalophilus by NAD affinity and high-performance anion-exchange chromatographies. The enzyme was active against a wide range of aryl-beta-glucosides and beta-linked disaccharides. The structural gene for beta-glucosidase was cloned in Escherichia coli. The beta-glucosidase gene consisted of an open reading frame of 1,350 bp encoding a protein of 450 amino acids with a calculated M(r) of 51,303. The enzyme exhibited from 45 to 66% identity with five bacterial beta-glucosidases.
Diversity within a Colony Morphotype: Implications for Ecological Research
Authors: Haldeman Dana L. , Amy Penny S.
Published: January 2020

Sets of bacterial isolates with the same colony morphologies were selected from spread plates of bacteria from deep subsurface rock samples; each set had a unique morphology. API-rapid-NFT analysis revealed that isolates within a set were the same. Fatty acid methyl ester analysis of one set of isolates clustered organisms within the same species, defining variation between isolates at the biotype (subspecies) and strain levels. Metal resistances consistently tracked with colony morphology, while antibiotic resistances were less reliable.
Effects of acetate, propionate, and butyrate on the thermophilic anaerobic degradation of propionate by methanogenic sludge and defined cultures
Authors: Van Lier J B , Grolle K C , Frijters C T , Stams A J , Lettinga G
Published: January 2020

The effects of acetate, propionate, and butyrate on the anaerobic thermophilic conversion of propionate by methanogenic sludge and by enriched propionate-oxidizing bacteria in syntrophy with Methanobacterium thermoautotrophicum delta H were studied. The methanogenic sludge was cultivated in an upflow anaerobic sludge bed (UASB) reactor fed with propionate (35 mM) as the sole substrate for a period of 80 days. Propionate degradation was shown to be severely inhibited by the addition of 50 mM acetate to the influent of the UASB reactor. The inhibitory effect remained even when the acetate concentration in the effluent was below the level of detection. Recovery of propionate oxidation occurred only when acetate was omitted from the influent medium. Propionate degradation by the methanogenic sludge in the UASB reactor was not affected by the addition of an equimolar concentration (35 mM) of butyrate to the influent. However, butyrate had a strong inhibitory effect on the growth of the propionate-oxidizing enrichment culture. In that case, the conversion of propionate was almost completely inhibited at a butyrate concentration of 10 mM. However, addition of a butyrate-oxidizing enrichment culture abolished the inhibitory effect, and propionate oxidation was even stimulated. All experiments were conducted at pH 7.0 to 7.7. The thermophilic syntrophic culture showed a sensitivity to acetate and propionate similar to that of mesophilic cultures described in the literature. Additions of butyrate or acetate to the propionate medium had no effect on the hydrogen partial pressure in the biogas of an UASB reactor, nor was the hydrogen partial pressure in propionate-degrading cultures affected by the two acids.(ABSTRACT TRUNCATED AT 250 WORDS)
Biodegradation and biotransformation of groundwater pollutant mixtures by Mycobacterium vaccae
Authors: Burback B L , Perry J J
Published: January 2020

Mycobacterium vaccae can catabolize a number of major groundwater pollutants. When added singly, acetone, cyclohexane, styrene, benzene, ethylbenzene, propylbenzene, dioxane, and 1,2-dichloroethylene can be catabolized by M. vaccae. Catabolism of a number of these chemicals was monitored by gas-chromatographic analysis. Gas-chromatographic analysis indicated that the products of benzene degradation are phenol and hydroquinone. The products of chlorobenzene and ethylbenzene degradation are 4-chlorophenol and 4-ethylphenol. The extent that some compounds were catabolized when present as mixtures was also investigated. When toluene and benzene were present concomitantly, toluene was catabolized and benzene oxidation was delayed. Although toluene promoted the degradation of styrene, a lower rate of toluene degradation occurred when styrene was present. Both 4-chlorophenol and 4-ethylphenol had an antagonistic effect on the ability of M. vaccae to degrade other aromatic compounds. Studies with [14C]benzene indicated that M. vaccae can mineralize small amounts of this compound. These results suggest that components in mixtures may have a positive or a negative effect on the rates of biodegradation of other pollutants.
Elimination of Escherichia coli O157:H7 in meats by gamma irradiation
Authors: Thayer D W , Boyd G
Published: January 2020

Undercooked and raw meat has been linked to outbreaks of hemorrhagic diarrhea due to the presence of Escherichia coli O157:H7; therefore, treatment with ionizing radiation was investigated as a potential method for the elimination of this organism. Response-surface methods were used to study the effects of irradiation dose (0 to 2.0 kGy), temperature (-20 to +20 degrees C), and atmosphere (air and vacuum) on E. coli O157:H7 in mechanically deboned chicken meat. Differences in irradiation dose and temperature significantly affected the results. Ninety percent of the viable E. coli in chicken meat was eliminated by doses of 0.27 kGy at +5 degrees C and 0.42 kGy at -5 degrees C. Small, but significant, differences in radiation resistance by E. coli were found when finely ground lean beef rather than chicken was the substrate. Unlike nonirradiated samples, no measurable verotoxin was found in finely ground lean beef which had been inoculated with 10(4.8) CFU of E. coli O157:H7 per g, irradiated at a minimum dose of 1.5 kGy, and temperature abused at 35 degrees C for 20 h. Irradiation is an effective method to control this food-borne pathogen.
Conjugative Plasmid Transfer between Bacteria under Simulated Marine Oligotrophic Conditions
Authors: Goodman A. E. , Hild E. , Marshall K. C. , Hermansson M.
Published: January 2020

Marine
Vibrio
S14 strains and an
Escherichia coli
strain were starved in artificial seawater (NSS) with no added carbon, nitrogen, or phosphorus. The broad-host-range plasmid RP1 was transferred between the starving S14 strains and also from the
E. coli
donor to the S14 recipient under oligotrophic conditions, in which mixtures of donor and recipient cells were held on Nuclepore filters either floated on NSS or held such that NSS flowed through the filter. Transconjugants were obtained from S14 donors and recipients starved for at least 15 days before being mixed together for conjugation, whereas transconjugants were recovered from the
E. coli
donor and S14 recipient for up to 3 days of prestarvation, but not after 5 days. Transconjugants were obtained when there were as few as about 10
5
and 10
4
cells of starving S14 donors and recipients, respectively, per ml held on the filters. Starved donor and recipient mixtures incubated at 4 or 26°C, as well as those allowed to mate for 2, 5, or 24 h, all yielded numbers of transconjugants which were not significantly (
P
> 0.05) different.
Mode of Action of Lactococcin B, a Thiol-Activated Bacteriocin from
Lactococcus lactis
Authors: Venema K. , Abee T. , Haandrikman A. J. , Leenhouts K. J. , Kok J. , Konings W. N. , Venema G.
Published: January 2020

Lactococcin B (LcnB) is a small, hydrophobic, positively charged bacteriocin produced by
Lactococcus lactis
subsp.
cremoris
9B4. Purified LcnB has a bactericidal effect on sensitive
L. lactis
cells by dissipating the proton motive force and causing leakage of intracellular substrates. The activity of LcnB depends on the reduced state of the Cys-24 residue. Uptake and efflux studies of different solutes suggest that LcnB forms pores in the cytoplasmic membrane of sensitive
L. lactis
cells in the absence of a proton motive force. At low concentrations of LcnB, efflux of those ions and amino acids which are taken up by proton motive force-driven systems was observed. However, a 150-fold higher LcnB concentration was required for efflux of glutamate, previously taken up via a unidirectional ATP-driven transport system. Strains carrying the genetic information for the immunity protein against LcnB were not affected by LcnB. The proton motive force of immune cells was not dissipated, and no leakage of intracellular substrates could be detected.
Metabolic Pathways in
Methanococcus jannaschii
and Other Methanogenic Bacteria
Authors: Sprott G. Dennis , Ekiel Irena , Patel Girishchandra B.
Published: January 2020

Eleven strains of methanogenic bacteria were divided into two groups on the basis of the directionality (oxidative or reductive) of their citric acid pathways. These pathways were readily identified for most methanogens from the patterns of carbon atom labeling in glutamate, following growth in the presence of [2-
13
C]acetate. All used noncyclic pathways, but members of the family
Methanosarcinaceae
were the only methanogens found to use the oxidative direction.
Methanococcus jannaschii
failed to incorporate carbon from acetate despite transmembrane equilibration comparable to other weak acids. This organism was devoid of detectable activities of the acetate-incorporating enzymes acetyl coenzyme A synthetase, acetate kinase, and phosphotransacetylase. However, incorporation of [1-
13
C]-, [2-
13
C]-, or [3-
13
C]pyruvate during the growth of
M. jannaschii
was possible and resulted in labeling patterns indicative of a noncyclic citric acid pathway operating in the reductive direction to synthesize amino acids. Carbohydrates were labeled consistent with glucogenesis from pyruvate. Leucine, isoleucine, phenylalanine, lysine, formate, glycerol, and mevalonate were incorporated when supplied to the growth medium. Lysine was preferentially incorporated into the lipid fraction, suggesting a role as a phytanyl chain precursor.
Effects of pH and Osmotic Stress on Cellular Polyamine Contents in the Soybean Rhizobia
Rhizobium fredii
P220 and
Bradyrhizobium japonicum
A1017
Authors: Fujihara Shinsuke , Yoneyama Tadakatsu
Published: January 2020

Homospermidine is a polyamine present in its highest concentrations in root nodule bacteria. By using the soybean rhizobia
Rhizobium fredii
P220 and
Bradyrhizobium japonicum
A1017, the effects of the pH and osmolarity of the medium on rhizobial growth and cellular polyamine contents were investigated. Elevation of medium pH repressed the growth of slowly growing
B. japonicum
A1017 and resulted in a slight increase in cellular putrescine, while homospermidine content was not significantly affected. In contrast, in fast-growing
R. fredii
P220, which showed good growth over a wide range of the medium pHs from 4.0 to 9.5, homospermidine content increased with the lowering of the medium pH. Under the acid-stressed conditions, cellular Mg
2+
content in strain P220 also increased. Strain P220 was able to grow in NaCl concentrations up to 0.4 M, while strain A1017 did not grow in media containing 0.15 M NaCl. Glutamic acid and K
+
contents of salt-tolerant P220 cells increased in response to NaCl concentrations, but homospermidine and Mg
2+
contents were inversely related to the NaCl concentrations. External salinity had no effect on the contents of other polyamines in P220 cells. On the basis of osmotic strength, NaCl, KCl, sucrose, or glycerol induced similar decreases in cellular homospermidine content. These results suggested that the cellular levels of homospermidine in strain P220 may be regulated by mechanisms related to their pH and osmotic tolerance.
Microbial production of D-malate from maleate
Authors: Asano Y , Ueda M , Yamada H
Published: January 2020

To produce D-malate from maleate by a microbial reaction, we screened a number of maleate-utilizing microorganisms for enzyme activity by an intact cell system. The strain which showed the best productivity among the 440 strains tested was identified taxonomically as Arthrobacter sp. strain MCI2612. The optical purity of the malate produced by this strain was 100% D type. The culture and reaction conditions for the production were studied for this strain. Addition of amino acids such as L-proline, L-histidine, and L-arginine to the culture medium promoted the formation of reaction activity as well as cell growth. Under optimum conditions, 87 g of D-malate per liter was produced in 20 h. The yield was 72 mol%.
Growth of Syntrophic Propionate-Oxidizing Bacteria with Fumarate in the Absence of Methanogenic Bacteria
Authors: Stams Alfons J. M. , Van Dijk Johan B. , Dijkema Cor , Plugge Caroline M.
Published: January 2020

Oxidation of succinate to fumarate is an energetically difficult step in the biochemical pathway of propionate oxidation by syntrophic methanogenic cultures. Therefore, the effect of fumarate on propionate oxidation by two different propionate-oxidizing cultures was investigated. When the methanogens in a newly enriched propionate-oxidizing methanogenic culture were inhibited by bromoethanesulfonate, fumarate could act as an apparent terminal electron acceptor in propionate oxidation.
13
C-nuclear magnetic resonance experiments showed that propionate was carboxylated to succinate while fumarate was partly oxidized to acetate and partly reduced to succinate. Fumarate alone was fermented to succinate and CO
2
. Bacteria growing on fumarate were enriched and obtained free of methanogens. Propionate was metabolized by these bacteria when either fumarate or
Methanospirillum hungatii
was added. In cocultures with
Syntrophobacter wolinii
, such effects were not observed upon addition of fumarate. Possible slow growth of
S. wolinii
on fumarate could not be demonstrated because of the presence of a
Desulfovibrio
strain which grew rapidly on fumarate in both the absence and presence of sulfate.
The assumed assimilation of cholesterol by Lactobacilli and Bifidobacterium bifidum is due to their bile salt-deconjugating activity
Authors: Klaver F A , van der Meer R
Published: January 2020

To study the mechanism of the propsed assimilation of cholesterol, we cultured various strains of Lactobacillus acidophilus and a Bifidobacterium sp. in the presence of cholesterol and oxgall. During culturing, both cholesterol and bile salts were precipitated. Because of bacterial bile salt deconjugation, no conjugated bile salts were observed in either the culture fluids or the pellets. During incubation, the cell count and optical density decreased. The degree of precipitation of bile salts and of cholesterol was dependent on the culture conditions. If L. acidophilus RP32 was cultured under acidifying conditions, the degree of precipitation of deconjugated bile salts was higher than if the pH was maintained at 6.0. Under acidifying conditions, cholesterol was coprecipitated with the bile salts, whereas in pH-controlled cultures, no coprecipitation of cholesterol was observed. From control experiments with different mixtures of bile salts, it appeared that coprecipitation of cholesterol during culturing was a result of formation of deconjugated bile salts, which have a decreased solubility at pH values lower than 6.0. It is concluded that the removal of cholesterol from the culture medium by L. acidophilus RP32 and other species is not due to bacterial uptake of cholesterol, but results from bacterial bile salt-deconjugating activity.
Cloning of a novel cryIC-type gene from a strain of Bacillus thuringiensis subsp. galleriae
Authors: Kalman S , Kiehne K L , Libs J L , Yamamoto T
Published: January 2020

A novel cryIC-type gene was isolated from a strain of Bacillus thuringiensis subsp. galleriae. A new polymerase chain reaction (PCR) technique with a set of several oligonucleotide primer pairs specific to the cryIC gene was used to screen a number of B. thuringiensis strains. PCR amplified several DNA fragments ranging from 100 bp to 1 kb for B. thuringiensis strains containing a cryIC gene. PCR fragments amplified from the Bacillus thuringiensis subsp. galleriae HD29 DNA differed from the fragments amplified from other cryIC-containing strains, indicating strain HD29 contained a novel cryIC-type gene. To isolate crystal genes homologous to cryIC, an HD29 gene library was probed with a 984-bp fragment of the amino-terminal coding region of the cryIC gene cloned from Bacillus thuringiensis subsp. aizawai HD229. A putative toxin gene was isolated from a phage that hybridized strongly to the cryIC probe. Translation of the putative toxin DNA sequence revealed an open reading frame of 1,176 amino acids whose predicted molecular mass was 132.8 kDa. Comparisons of the toxin gene sequence with sequences of other cry genes indicated that this gene is a subclass of cryIC. We propose to designate this gene cryIC(b). In Escherichia coli, the cryIC(b) gene produced a protein of approximately 130 kDa toxic to Spodoptera exigua and Trichoplusia ni.
Rapid isolation and sequencing of purified plasmid DNA from Bacillus subtilis
Authors: Voskuil M I , Chambliss G H
Published: January 2020

We report two methods for isolation of plasmid DNA from the gram-positive bacterium Bacillus subtilis. The protoplast alkaline lysis procedure was developed for general use, and the protoplast alkaline lysis magic procedure was developed for isolation of DNA for sequencing. Both procedures yielded large amounts of high-quality DNA in less than 1 h, while current protocols require 4 to 7 h to perform and give lower yields and quality. Plasmid DNA was obtained from strains containing either high- or low-copy-number plasmids. In addition, the procedures were easily adapted to yield large amounts of plasmid DNA suitable for sequencing from another gram-positive organism, Staphylococcus aureus. Further, we demonstrated that neither chloramphenicol, used for plasmid selection, nor the mutation recE4 reduced plasmid DNA yield from the strains we examined.
Influence of alternative electron acceptors on the anaerobic biodegradability of chlorinated phenols and benzoic acids
Authors: Häggblom M M , Rivera M D , Young L Y
Published: January 2020

Nitrate, sulfate, and carbonate were used as electron acceptors to examine the anaerobic biodegradability of chlorinated aromatic compounds in estuarine and freshwater sediments. The respective denitrifying, sulfidogenic, and methanogenic enrichment cultures were established on each of the monochlorinated phenol and monochlorinated benzoic acid isomers, using sediment from the upper (freshwater) and lower (estuarine) Hudson River and the East River (estuarine) as source materials. Utilization of each chlorophenol and chlorobenzoate isomer was observed under at least one reducing condition; however, no single reducing condition permitted the metabolism of all six compounds tested. The anaerobic biodegradation of the chlorophenols and chlorobenzoates depended on the electron acceptor available and on the position of the chlorine substituent. In general, similar activities were observed under the different reducing conditions in both the freshwater and estuarine sediments. Under denitrifying conditions, degradation of 3- and 4-chlorobenzoate was accompanied by nitrate loss corresponding reasonably to the stoichiometric values expected for complete oxidation of the chlorobenzoate to CO2. Under sulfidogenic conditions, 3- and 4-chlorobenzoate, but not 2-chlorobenzoate, and all three monochlorophenol isomers were utilized, while under methanogenic conditions all compounds except 4-chlorobenzoate were metabolized. Given that the pattern of activity appears different for these chlorinated compounds under each reducing condition, their biodegradability appears to be more a function of the presence of competent microbial populations than one of inherent molecular structure.
Quantitative and Qualitative Analysis of Bacteria in Er(III) Solution by Thin-Film Magnetopheresis
Authors: Zborowski Maciej , Tada Yoko , Malchesky Paul S. , Hall Geraldine S.
Published: January 2020

Magnetic deposition, quantitation, and identification of bacteria reacting with the paramagnetic trivalent lanthanide ion, Er
3+
, was evaluated. The magnetic deposition method was dubbed thin-film magnetopheresis. The optimization of the magnetic deposition protocol was accomplished with
Escherichia coli
as a model organism in 150 mM NaCl and 5 mM ErCl
3
solution. Three gram-positive bacteria,
Staphylococcus epidermidis, Staphylococcus saprophyticus,
and
Enterococcus faecalis,
and four gram-negative bacteria,
E. coli, Pseudomonas aeruginosa, Proteus mirabilis,
and
Klebsiella pneumoniae,
were subsequently investigated. Quantitative analysis consisted of the microscopic cell count and a scattered-light scanning of the magnetically deposited material aided by the computer data acquisition system. Qualitative analysis consisted of Gram stain differentiation and fluorescein isothiocyanate staining in combination with selected antisera against specific types of bacteria on the solid substrate. The magnetic deposition protocol allowed quantitative detection of
E. coli
down to the concentration of 10
5
CFU ml
-1
, significant in clinical diagnosis applications such as urinary tract infections. Er
3+
did not interfere with the typical appearance of the Gram-stained bacteria nor with the antigen recognition by the antibody in the immunohistological evaluations. Indirect antiserum-fluorescein isothiocyanate labelling correctly revealed the presence of
E. faecalis
and
P. aeruginosa
in the magnetically deposited material obtained from the mixture of these two bacterial species. On average, the reaction of gram-positive organisms was significantly stronger to the magnetic field in the presence of Er
3+
than the reaction of gram-negative organisms. The thin-film magnetophoresis offers promise as a rapid method for quantitative and qualitative analysis of bacteria in solutions such as urine or environmental water.
Testing of some assumptions about biodegradability in soil as measured by carbon dioxide evolution
Authors: el-Din Sharabi N , Bartha R
Published: January 2020

Conversion to CO2 upon incubation in aerobic soil is one of the standard test procedures to assess biodegradability. It may be measured with unlabeled test compounds in biometer flasks. In this case, the background CO2 evolution by unamended soil is subtracted from the CO2 evolution by the amended soil and the resulting net CO2 evolution becomes the measure of biodegradation. Alternately, 14CO2 release from radiocarbon substrates is measured to assess biodegradability. Both approaches measure ultimate (complete) biodegradation and bypass the theoretical and technical limitations of residue analysis. This report examines the underlying assumptions that, except for carbon content, conversion percentage to CO2 is relatively independent of chemical composition, that CO2 production is proportional to the amount of added test compound, and that the background CO2 evolution of the soil is not influenced by the test substance. Work with unlabeled and radiolabeled substrates proved the first two assumptions to be essentially correct. However, more than half of net CO2 production may represent the mineralization of biomass and soil organic matter, some of it unrelated to the test compound. The soil microbial community in its nongrowing steady state appears to convert a much lower percentage of a radiocarbon substrate to 14CO2 than a growing soil community that responds to a substantial substrate addition. These findings may help to improve test methods and may aid in the interpretation of test results.
Degradation of poly(3-hydroxyoctanoic acid) [P(3HO)] by bacteria: purification and properties of a P(3HO) depolymerase from Pseudomonas fluorescens GK13
Authors: Schirmer A , Jendrossek D , Schlegel H G
Published: January 2020

Twenty-five gram-negative bacteria and one gram-positive bacterium capable of growing on poly(3-hydroxyoctanoic acid) [P(3HO)] as the sole source of carbon and energy were isolated from various soils, lake water, and activated sludge. Most of the isolates degraded only P(3HO) and copolymers of medium-chain-length (MCL) hydroxyalkanoic acids (HA). Except for the gram-positive strain, which was able to hydrolyze P(3HO) and poly(3-hydroxybutyric acid) [P(3HB)], no isolate was able to degrade polymers of short-chain-length HA, such as P(3HB) or poly(3-hydroxyvalerate) [P(3HV)]. All strains utilized a large variety of monomeric substrates for growth. All gram-negative strains, but not the gram-positive strain, accumulated poly(hydroxyalkanoic acids) (PHA), consisting of MCL HA, if they were cultivated under accumulation conditions. One strain, which was identified as Pseudomonas fluorescens GK13 (biovar V), was selected and the extracellular P(3HO) depolymerase of this strain was purified from the culture medium of P(3HO)-grown cells by chromatography with Octyl-Sepharose CL4B and by gel filtration with Superose 12. The relative molecular weights of the native and sodium dodecyl sulfate-treated enzymes were 48,000 and 25,000, respectively. The purified enzyme hydrolyzed P(3HO), copolymers of MCL HA, and para-nitrophenyl esters of fatty acids. P(3HB), P(3HV), and characteristic substrates for lipases, such as Tween 80 or triolein, were not hydrolyzed. The P(3HO) depolymerase of P. fluorescens GK13 was insensitive to phenylmethylsulfonyl fluoride and dithioerythritol, unlike other PHA depolymerases. The dimeric ester of 3-hydroxyoctanoic acid was identified as the main product of enzymatic hydrolysis of P(3HO).(ABSTRACT TRUNCATED AT 250 WORDS)
Use of autoradiography to assess viability of Helicobacter pylori in water
Authors: Shahamat M , Mai U , Paszko-Kolva C , Kessel M , Colwell R R
Published: January 2020

Autoradiographic methods have been developed to detect metabolic activity of viable but nonculturable cells of Helicobacter pylori in water. Four strains of H. pylori were studied by using microcosms containing suspensions of 72-h cultures in water. The suspensions of aged, nonculturable cells of H. pylori were incubated with [3H]thymidine for 24 to 72 h, after which the cell suspensions were exposed to Kodak NTB2 emulsion for 3 to 28 days. Each sample was processed with three separate controls to rule out false-positive reactions. The organism remains viable and culturable under these conditions for up to 48 h and, in some cases, 20 to 30 days, depending on physical conditions of the environment. We found that temperature was a significant (P < or equal to 0.01) environmental factor associated with the viability of H. pylori cells in water. Autoradiographs of tritium-labeled cells of H. pylori revealed aggregations of silver grains associated with uptake by H. pylori of radiolabelled substrate. Findings based on the autoradiographic approach give strong evidence supporting the hypothesis that there is a waterborne route of infection for H. pylori. The possibility that H. pylori may persist in water in a metabolically active stage but not actively growing and dividing is intriguing and relevant to public health concerns.
Secondary metabolites resulting from degradation of PR toxin by Penicillium roqueforti
Authors: Chang S C , Lu K L , Yeh S F
Published: January 2020

PR toxin is a secondary metabolite of the fungus Penicillium roqueforti. It is lethal to rats, mice, and cats. Usually, the amount of PR toxin in the culture medium decreases from its maximum on day 15 to zero within 3 to 4 days. We found that two were secondary metabolites produced in the culture medium of this fungus while the production of PR toxin was decreasing. We isolated and purified the two compounds in pure and colorless crystalline form. On the basis of elemental analysis and mass, 1H and 13C nuclear magnetic resonance, infrared, and UV spectroscopies, the two compounds were identified as PR-imine (C17H21O5N) and PR-amide (C17H21O6N). The structures of both compounds and of PR toxin (C17H20O6) were closely related, and the peak production of PR toxin appeared earlier than those of PR-imine and PR-amide. Moreover, PR toxin was transformed to PR-imine when PR toxin was incubated with the culture medium on a given culture day. Thus, we propose that PR toxin is degraded into PR-imine and PR-amide in the culture medium of P. roqueforti.