bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in Bacterial Numbers and Leucine Assimilation during Estimations of Microbial Respiratory Rates in Seawater by the Precision Winkler Method
Authors: Pomeroy Lawrence R. , Sheldon Joan E. , Sheldon Wade M.
Published: January 2020

During incubation of seawater in bottles, the decrease in dissolved oxygen is often nonlinear over time scales frequently used to measure respiration. Numbers of bacteria always increase, and rates of assimilation of dissolved leucine often increase exponentially. This suggests that sample handling disrupts the previously existing food web, leading to shifts of trophic state and unbalanced growth. Potential errors in measuring respiratory rate can be minimized by documenting these variables.
Heterologous expression of endo-beta-1,4-D-glucanase from Clostridium cellulovorans in Clostridium acetobutylicum ATCC 824 following transformation of the engB gene
Authors: Kim A Y , Attwood G T , Holt S M , White B A , Blaschek H P
Published: January 2020

Heterologous expression of the Clostridium cellulovorans engB gene by Clostridium acetobutylicum BKW-1 was detected as zones of hydrolysis on carboxymethyl cellulose (CMC) Trypticase glucose yeast plates stained with Congo red. The extracellular cellulase preparation from C. acetobutylicum BKW-1 has a specific activity towards CMC which is more than fourfold that present in C. acetobutylicum ATCC 824. Western blot (immunoblot) analysis using the C. cellulovorans anti-EngB primary antibody demonstrated that an additional 44-kDa protein band was present in the supernatant derived from C. acetobutylicum BKW-1 but was not present in ATCC 824 or ATCC 824(pMTL500E).
Transcriptional enhancement of the Listeria monocytogenes PCR and simple immunoenzymatic assay of the product using anti-RNA:DNA antibodies
Authors: Blais B W
Published: January 2020

A method was developed to enhance the sensitivity of a Listeria monocytogenes PCR detection system by in vitro transcription of amplicons incorporating bacteriophage T7 RNA polymerase promoter sequences in one of the priming oligonucleotides. The resulting transcript can be detected by hybridization with a DNA probe immobilized in the wells of a microtiter plate, followed by immunoenzymatic assay of the RNA-DNA hybrids with an anti-RNA-DNA hybrid antibody. This highly sensitive method was reactive in the assay of various L. monocytogenes isolates but not with other Listeria or non-Listeria species.
Aerobic degradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by Alcaligenes eutrophus A5
Authors: Nadeau L J , Menn F M , Breen A , Sayler G S
Published: January 2020

Biotransformation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by Alcaligenes eutrophus A5 was demonstrated by analysis of ethyl acetate-extracted products from resting cell cultures. Gas chromatography-mass spectrometry characterization of the neutral extracts revealed two hydroxy-DDT intermediates (m/z = 370) with retention times at 19.55 and 19.80 min that shared identical mass spectra. This result suggested that the hydroxylations occurred at the ortho and meta positions on the aromatic ring. UV-visible spectrum spectrophotometric analysis of a yellow metabolite in the culture supernatant showed a maximum A402 with, under acidic and basic conditions, spectrophotometric characteristics similar to those of the aromatic ring meta-cleavage products. 4-Chlorobenzoic acid was detected by thin-layer chromatography radiochemical scanning in samples from mineralization experiments by comparison of Rf values of [14C]DDT intermediates with that of an authentic standard. These results were further confirmed by gas chromatography-mass spectrometry analysis. This study indicates that DDT appears to be oxidized by a dioxygenase in A. eutrophus A5 and that the products of this oxidation are subsequently subjected to ring fission to eventually yield 4-chlorobenzoic acid as a major stable intermediate.
Distribution of the catabolic transposon Tn5271 in a groundwater bioremediation system
Authors: Wyndham R C , Nakatsu C , Peel M , Cashore A , Ng J , Szilagyi F
Published: January 2020

The distribution of Tn5271-related DNA sequences in samples of groundwater and a groundwater bioremediation system at the Hyde Park (Niagara Falls, N.Y.) chemical landfill site was investigated. PCR amplification of target sequences within the cha genes of Tn5271 revealed similar sequences in the groundwater community and in samples from the sequencing batch reactors treating that groundwater. Cell dilution combined with PCR amplification indicated that cha sequences were carried in about 1 of 10 culturable bacteria from the treatment system. Characterization of isolates involved in chlorobenzoate and toluene biodegradation in the treatment system indicated that two phenotypic clusters, Alcaligenes faecalis type 2 and CDC group IVC-2, contained all of the Tn5271 probe-positive isolates from the community. These two groups differed phenotypically from recipient groups isolated following horizontal transfer of pBRC60 (Tn5271) in pristine freshwater microcosms. A genetic rearrangement in Tn5271 attributable to the intramolecular transposition of the flanking element IS1071R was detected in an isolate from the treatment system. Comparison of the structure of the intramolecular transposition derivative from groundwater isolate OCC13(pBRC13) with a laboratory-derived intramolecular transposition derivative of pBRC60 revealed similarities. The rearrangement was shown to increase the stability of the plasmid under starvation conditions.
Production and release of polyphosphate by a genetically engineered strain of Escherichia coli
Authors: Hardoyo  , Yamada K , Shinjo H , Kato J , Ohtake H
Published: January 2020

A recombinant strain of Escherichia coli MV1184, which contains plasmid-borne genes encoding the phosphate-specific transport (Pst) system and polyphosphate (polyP) kinase, accumulated high levels of Pi and released polyP into the medium. PolyP could be separated from the culture supernatant by DEAE-Toyopearl 650M chromatography and identified by high-resolution 31P nuclear magnetic resonance spectroscopy. Once E. coli recombinants accumulated high levels of polyP, they released polyP concomitantly with Pi uptake. PolyP release did not accompany the decrease in the cell density, indicating that it is not simply a result of cell lysis. PolyP release ceased when Pi became depleted in the medium and resumed upon addition of Pi to the medium. When Pi uptake was inhibited by 0.1 mM carbonyl cyanide m-chlorophenylhydrazone (CCCP), no polyP release was observed. Furthermore, neither Pi uptake nor polyP release occurred when cells were incubated at 4 degrees C. These findings suggest that the occurrence of polyP release is a possible mechanism that limits a further increase in the cellular polyP concentration in E. coli recombinants. High-resolution 31P nuclear magnetic resonance spectroscopy also detected a surface pool of polyP in intact cells of the E. coli recombinant. The polyP resonance increased when cells were treated with EDTA and broadened upon the addition of a shift reagent, praseodymium. Although the mechanism of surface polyP accumulation is unclear, surface polyP seems to serve as the source for polyP release.
Mechanistic Analysis of Ammonium Inhibition of Atmospheric Methane Consumption in Forest Soils
Authors: Schnell Sylvia , King Gary M.
Published: January 2020

Methane consumption by forest soil was studied in situ and in vitro with respect to responses to nitrogen additions at atmospheric and elevated methane concentrations. Methane concentrations in intact soil decreased continuously from atmospheric levels at the surface to 0.5 ppm at a depth of 14 cm. The consumption rate of atmospheric methane in soils, however, was highest in the 4- to 8-cm depth interval (2.9 nmol per g of dry soil per day), with much lower activities below and above this zone. In contrast, extractable ammonium and nitrate concentrations were highest in the surface layer (0 to 2 cm; 22 and 1.6 μmol per g of dry soil, respectively), as was potential ammonium-oxidizing activity (19 nmol per g of dry soil per day). The difference in zonation between ammonium oxidation and methane consumption suggested that ammonia-oxidizing bacteria did not contribute significantly to atmospheric methane consumption. Exogenous ammonium inhibited methane consumption in situ and in vitro, but the pattern of inhibition did not conform to expectations based on simple competition between ammonia and methane for methane monooxygenase. The extent of ammonium inhibition increased with increasing methane concentration. Inhibition by a single ammonium addition remained constant over a period of 39 days. In addition, nitrite, the end product of methanotrophic ammonia oxidation, was a more effective inhibitor of methane consumption than ammonium. Factors that stimulated ammonium oxidation in soil, e.g., elevated methane concentrations and the availability of cosubstrates such as formate, methanol, or β-hydroxybutyrate, enhanced ammonium inhibition of methane oxidation, probably as a result of enhanced nitrite production.
Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol
Authors: Cole J R , Cascarelli A L , Mohn W W , Tiedje J M
Published: January 2020

A bacterium capable of anaerobic growth via reductive dehalogenation of 2-chlorophenol was isolated from a culture enriched from sediment taken from a small stream near Lansing, Mich. The organism, designated strain 2CP-1, is a gram-negative rod ca. 3 by 0.5 micron in size and is a catalase-negative, oxidase-negative, facultative anaerobe that forms small red colonies in anaerobic media. The organism grew in reduced anaerobic mineral medium supplemented with 2-chlorophenol, acetate, and vitamins, producing phenol as a product. It did not grow when either 2-chlorophenol or acetate was omitted. The growth yield was about 3 g of protein per mol of 2-chlorophenol dechlorinated, and the doubling time was 3.7 days. Only the ortho position was dehalogenated, and additional chlorines at other positions decreased or blocked ortho dechlorination. The organism also grew with fumarate as its electron acceptor. Dechlorination activity is inducible, since cultures grown in fumarate containing medium with 2-chlorophenol rapidly dechlorinated additional 2-chlorophenol, while cultures grown in the same medium without 2-chlorophenol did not. Analysis of the organism's 16S rRNA sequence revealed that it is a member of the delta proteobacteria, more closely related to the myxobacteria than to the sulfidogenic bacteria.
Stabilization and rational design of serine protease AprM under highly alkaline and high-temperature conditions
Authors: Masui A , Fujiwara N , Imanaka T
Published: January 2020

Rational shift of the optimum pH toward alkalinity and enhancement of thermostability were investigated by using a thermostable extremely alkaline protease (optimum pH, 12 to 13) from the alkaliphilic and thermophilic Bacillus sp. strain B18'. The protease gene (aprM) was cloned, and the sequence analysis revealed an open reading frame of 361 amino acids that was composed of a putative signal sequence (24 amino acids), a prosequence (69 amino acids), and a mature enzyme (268 amino acids) (molecular weight, 27,664). The amino acid sequence of this protease was compared with those of other serine proteases. A direct correlation of higher optimum pH with an increase in the number of arginine residues was observed. An even more thermostable mutant enzyme was created by introducing a point mutation. When the position of the beta-turn, Thr-203, was replaced by Pro, the residual activity of this mutant enzyme at 80 degrees C for 30 min was higher than that of the wild-type enzyme (50% versus 10%). The specific activity of this mutant enzyme at 70 degrees C was 105% of that of the wild-type enzyme under nondenaturation condition. These data suggest that the higher content of Arg residues favors the alkalinity of the serine protease and that introduction of a Pro residue into the beta-turn structure stabilizes the enzyme.
Methods for Assessment of Biodegradability of Plastic Films in Soil
Authors: Yabannavar Asha V. , Bartha Richard
Published: January 2020

Traditional and novel techniques were tested and compared for their usefulness in evaluating biodegrad-ability claims made for newly formulated “degradable” plastic film products. Photosensitized polyethylene (PE), starch-PE, extensively plasticized polyvinyl chloride (PVC), and polypropylene (PP) films were incorporated into aerobic soil. Biodegradation was measured for 3 months under generally favorable conditions. Carbon dioxide evolution, residual weight recovery, and loss of tensile strength measurements were supplemented, for some films, by gas chromatographic measurements of plasticizer loss and gel permeation chromatographic (GPC) measurement of polymer molecular size distribution. Six- and 12-week sunlight exposures of photosensitized PE films resulted in extensive photochemical damage that failed to promote subsequent mineralization in soil. An 8% starch-PE film and the plasticized PVC film evolved significant amounts of CO
2
in biodegradation tests and lost residual weight and tensile strength, but GPC measurements demonstrated that all these changes were confined to the additives and the PE and PVC polymers were not degraded. Carbon dioxide evolution was found to be a useful screening tool for plastic film biodegradation, but for films with additives, polymer biodegradation needs to be confirmed by GPC. Photochemical cross-linking of polymer strands reduces solubility and may interfere with GPC measurements of polymer degradation.
Spatial Variability in Biodegradation Rates as Evidenced by Methane Production from an Aquifer
Authors: Adrian Neal R. , Robinson Joseph A. , Suflita Joseph M.
Published: January 2020

Accurate predictions of carbon and energy cycling rates in the environment depend on sampling frequencies and on the spatial variability associated with biological activities. We examined the variability associated with anaerobic biodegradation rates at two sites in an alluvial sand aquifer polluted by municipal landfill leachate. In situ rates of methane production were measured for almost a year, using anaerobic wells installed at two sites. Methane production ranged from 0 to 560 μmol · m
-2
· day
-1
at one site (A), while a range of 0 to 120,000 μmol · m
-2
· day
-1
was measured at site B. The mean and standard deviations associated with methane production at site A were 17 and 57 μmol · m
-2
· day
-1
, respectively. The comparable summary statistics for site B were 2,000 and 9,900 μmol · m
-2
· day
-1
. The coefficients of variation at sites A and B were 340 and 490%, respectively. Despite these differences, the two sites had similar seasonal trends, with the maximal rate of methane production occurring in summer. However, the relative variability associated with the seasonal rates changed very little. Our results suggest that (i) two spatially distinct sites exist in the aquifer, (ii) methanogenesis is a highly variable process, (iii) the coefficient of variation varied little with the rate of methane production, and (iv) in situ anaerobic biodegradation rates are lognormally distributed.
The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: development of probes for Ruminococcus species and evidence for bacteriocin production
Authors: Odenyo A A , Mackie R I , Stahl D A , White B A
Published: January 2020

A total of six oligonucleotide probes, complementary to the 16S rRNA, were evaluated for quantitative and determinative studies of Ruminococcus albus and Ruminococcus flavefaciens. On the basis of specificity studies, probes for R. albus (probe RAL196) and R. flavefaciens (probe RFL196) were selected to quantitate these species in mixed culture. In combination with a Fibrobacter succinogenes S85 subspecies probe (SUB1) and a domain Bacteria (formerly kingdom Eubacteria) probe (EUB338), they were used to quantitate these species competing in mixed cultures for cellobiose as the carbon source. In dicultures containing R. albus 8 and F. succinogenes S85, competition was not observed. However, R. flavefaciens FD-1 eventually outcompeted F. succinogenes S85 when cellobiose was the substrate. When R. albus 8 and R. flavefaciens FD-1 were grown together on cellobiose medium, R. albus 8 outcompeted R. flavefaciens FD-1, resulting in undetectable R. flavefaciens 16S rRNA only 1 to 3 h after inoculation, suggesting production of an antagonistic compound by R. albus 8 during rapid growth on soluble substrates. Further, when R. albus 8, R. flavefaciens FD-1, and F. succinogenes S85 were grown together in a triculture, R. flavefaciens FD-1 16S rRNA was detectable for only 2 h after inoculation, while R. albus 8 and F. succinogenes S85 showed a similar competition pattern to that of the dicultures. The results show that the Ruminococcus probes were effective in the measurement of relative populations of selected R. albus and R. flavefaciens strains during in vitro competition studies with F. succinogenes.(ABSTRACT TRUNCATED AT 250 WORDS)
Effects of ruminal protozoa on cellulose degradation and the growth of an anaerobic ruminal fungus, Piromyces sp. strain OTS1, in vitro
Authors: Morgavi D P , Sakurada M , Mizokami M , Tomita Y , Onodera R
Published: January 2020

An anaerobic rumen fungus, Piromyces sp. strain OTS1, was incubated in the presence or absence of a mixed, A-type, protozoal population obtained from a goat, in a medium containing filter paper cellulose as energy source and antibiotics to suppress bacterial growth. Fermentation end products, cellulose degradation, and chitin as an indicator of fungal biomass were examined. In the presence of protozoa, total volatile fatty acids, notably propionate and butyrate, increased, and lactate decreased. In fungus-protozoan coincubations, formate was not detected at the end of the experiment and the amount of reducing sugars remained low throughout the incubation period. The fungal growth in the coincubations was negatively affected. While protozoal predation on zoospores was one mechanism of inhibition, mature fungal cells were also affected. Total cellulose degradation was greater in fungal monocultures, but the amount of cellulose degraded per unit of fungal biomass was 25% larger in the coincubations. The negative effects that the protozoal predatory activity had on the fungal growth and subsequently on the amount of cellulose degraded by Piromyces sp. strain OTS1 were partially attenuated by the protozoal fibrolytic activity or by an enhanced fungal activity due to a more favorable environment.
Evaluation of counting error due to colony masking in bioaerosol sampling
Authors: Chang C W , Hwang Y H , Grinshpun S A , Macher J M , Willeke K
Published: January 2020

Colony counting error due to indistinguishable colony overlap (i.e., masking) was evaluated theoretically and experimentally. A theoretical model to predict colony masking was used to determine colony counting efficiency by Monte Carlo computer simulation of microorganism collection and development into CFU. The computer simulation was verified experimentally by collecting aerosolized Bacillus subtilis spores and examining micro- and macroscopic colonies. Colony counting efficiency decreased (i) with increasing density of collected culturable microorganisms, (ii) with increasing colony size, and (iii) with decreasing ability of an observation system to distinguish adjacent colonies as separate units. Counting efficiency for 2-mm colonies, at optimal resolution, decreased from 98 to 85% when colony density increased from 1 to 10 microorganisms cm-2, in contrast to an efficiency decrease from 90 to 45% for 5-mm colonies. No statistically significant difference (alpha = 0.05) between experimental and theoretical results was found when colony shape was used to estimate the number of individual colonies in a CFU. Experimental colony counts were 1.2 times simulation estimates when colony shape was not considered, because of nonuniformity of actual colony size and the better discrimination ability of the human eye relative to the model. Colony surface densities associated with high counting accuracy were compared with recommended upper plate count limits and found to depend on colony size and an observation system's ability to identify overlapped colonies. Correction factors were developed to estimate the actual number of collected microorganisms from observed colony counts.(ABSTRACT TRUNCATED AT 250 WORDS)
A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA
Authors: Ahrenholtz I , Lorenz M G , Wackernagel W
Published: January 2020

The potential risks associated with the intentional or unintentional release of genetically engineered microorganisms led to the construction of biological containment systems by which bacteria are killed in a controlled suicide process. In previously published suicide systems, cell killing was caused by proteins destroying the cell membrane or cell wall. Here a conditional cell killing system based on the intracellular degradation of cellular DNA is presented. The nuclease gene used was that of the extracellular nuclease of Serratia marcescens. The nuclease gene was deleted for the leader-coding sequence, and the truncated gene was put under the control of the lambda pL promoter. Following thermoinduction of the nuclease gene cassette in Escherichia coli, cell survival dropped to 2 x 10(-5), and more than 80% of the radioactively labeled DNA was converted to acid-soluble material within 2.5 h in the absence of cell lysis. The majority (84%) of clones which survived thermoinduced killing turned out to be as sensitive to a second thermoinduction as the original strain. The other clones showed somewhat slower killing kinetics or slightly higher final levels of survivors. The suicide system described combines the regulated killing of cells with the destruction of intracellular DNA otherwise potentially available for horizontal gene transfer processes.
Cloning of the aapT gene and characterization of its product, alpha-amylase-pullulanase (AapT), from thermophilic and alkaliphilic Bacillus sp. strain XAL601
Authors: Lee S P , Morikawa M , Takagi M , Imanaka T
Published: January 2020

A thermophilic and alkaliphilic Bacillus sp. strain, XAL601, was isolated from soil. It produces a thermostable and alkaline-stable enzyme with both alpha-amylase and pullulanase activities. The alpha-amylase-pullulanase gene (aapT) from this Bacillus strain was cloned, and its nucleotide sequence was determined (GenBank accession number D28467). A very large open reading frame composed of 6,096 bases, which encodes 2,032 amino acid residues with an M(r) of 224,992, was found. The deduced amino acid sequence revealed that the four highly conserved regions that are common among amylolytic enzymes were well conserved. These include an active center and common substrate-binding sites of various amylases. In the C-terminal region, a six-amino-acid sequence (Gly-Ser-Gly-Thr-Thr-Pro) is repeated 12 times. The aapT gene was then subcloned in Escherichia coli and overexpressed under the control of the lac promoter. Purification of AapT from this recombinant E. coli was performed, and it was shown that the aapT gene product exhibits both alpha-amylase and pullulanase activities with one active site. The optimum temperature and pH for enzyme activity were found to be 70 degrees C and pH 9, respectively. Furthermore, AapT was found to strongly adsorb to crystalline cellulose (Avicel) and raw corn starch. Final hydrolyzed products from soluble starch range from maltose (G2) to maltotetraose (G4). Only maltotriose (G3) was produced from pullulan. The enzyme also hydrolyzes raw starch under a broad range of conditions (60 to 70 degrees C and pH 8 to 9).
Survival, Growth, and Localization of Epiphytic Fitness Mutants of
Pseudomonas syringae
on Leaves
Authors: Beattie Gwyn A. , Lindow Steven E.
Published: January 2020

Among 82 epiphytic fitness mutants of a
Pseudomonas syringae
pv. syringae strain that were characterized in a previous study, 4 mutants were particularly intolerant of the stresses associated with dry leaf surfaces. These four mutants each exhibited distinctive behaviors when inoculated onto and into plant leaves. For example, while none showed measurable growth on dry potato leaf surfaces, they grew to different population sizes in the intercellular spaces of bean leaves and on dry bean leaf surfaces, and one mutant appeared incapable of growth in both environments although it grew well on moist bean leaves. The presence of the parental strain did not influence the survival of the mutants immediately following exposure of leaves to dry, high-light incubation conditions, suggesting that the reduced survival of the mutants did not result from an inability to produce extracellular factors in planta. On moist bean leaves that were colonized by either a mutant or the wild type, the proportion of the total epiphytic population that was located in sites protected from a surface sterilant was smaller for the mutants than for the wild type, indicating that the mutants were reduced in their ability to locate, multiply in, and/or survive in such protected sites. This reduced ability was only one of possibly several factors contributing to the reduced epiphytic fitness of each mutant. Their reduced fitness was not specific to the host plant bean, since they also exhibited reduced fitness on the nonhost plant potato; the functions altered in these strains are thus of interest for their contribution to the general fitness of bacterial epiphytes.
Isolation and characterization of Linocin M18, a bacteriocin produced by Brevibacterium linens
Authors: Valdés-Stauber N , Scherer S
Published: January 2020

Brevibacterium linens M18, isolated from red smear cheese, produces a substance that inhibits the growth of Listeria spp. and several coryneform and other gram-positive bacteria. No gram-negative bacteria were inhibited. The substance is heat labile, sensitive to proteolytic enzymes, and stable between pH 3 and 12. High levels of this bacteriocin, named Linocin M18, were obtained in the stationary growth phase. Linocin M18 was purified by ultrafiltration, ultracentrifugation, and gel filtration chromatography. In its native form, it is a proteinaceous aggregate with a high molecular weight. Fractions with Linocin M18 activity contained particles of 20 to 30 nm in diameter. The bacteriocin consists of a single protein subunit with a molecular mass of 31 kDa and an isoelectric point of 4.5 N-terminal sequence analysis yielded Met-Asn-Asn-Leu-Tyr-Arg-Glu-Leu-Ala-Pro-Ile-Pro-Gly-Pro-Ala-Ala-Ala-Glu- Ile. Significant homology with published sequences was lacking.
Immobilization of Escherichia coli expressing the lux genes of Xenorhabdus luminescens
Authors: Marincs F , White D W
Published: January 2020

The luxCDABE operon of Xenorhabdus luminescens was cloned into pUC18 to make pLITE27. Expression of the lux genes from the lac promoter resulted in strong constitutive light emission by Escherichia coli DH5 carrying the recombinant lux plasmid, pLITE27. When strain DH5(pLITE27) was immobilized with sodium alginate-CaCl2, the embedded cells retained their luminescence up to 2 weeks under appropriate storage conditions.
Detection of Aeromonas salmonicida, causal agent of furunculosis in salmonid fish, from the tank effluent of hatchery-reared Atlantic salmon smolts
Authors: O'Brien D , Mooney J , Ryan D , Powell E , Hiney M , Smith P R , Powell R
Published: January 2020

The fish pathogen, Aeromonas salmonicida, could be detected only by bacteriological culture from the kidney of dead or moribund fish in one tank in a hatchery rearing Atlantic salmon (Salmo salar L.) smolts. However, by using a DNA probe specific for this species, allied to a PCR assay, the pathogen could be detected in water, feces and effluent samples taken from this fish tank. Also, the presence of the pathogen was found in effluent samples from two fish tanks containing apparently healthy fish. Subsequently, the presence of pathogen in these tanks was confirmed by an increase in the daily mortality rate and by a plate culture from moribund fish.
Cotransformation and Targeted Gene Inactivation in the Maize Anthracnose Fungus,
Glomerella graminicola
Authors: Vaillancourt Lisa J. , Hanau Robert M.
Published: January 2020

Cotransformation of
Glomerella graminicola
was achieved with the
G. graminicola
genes
TUB1
R1 (encoding a β-tubulin which confers resistance to the fungicide benomyl) and
PYR1
(encoding orotate phosphoribosyl transferase, which confers pyrimidine prototrophy). The cotransformation frequency was about 30% when selection was for pyrimidine prototrophy (Pyr
+
) and 87% when selection was for benomyl-resistant (Bml
r
) transformants. Southern blots confirmed that both transforming DNAs had integrated into the genomes of transformants which were expressing both Pyr
+
and Bml
r
phenotypes. A plasmid, p23, which contained a truncated 500-bp segment representing the central region of the
PYR1
gene was constructed. The plasmid was introduced with pCG7, containing
TUB1
R1, into
G. graminicola
M1.001 (Pyr
+
Bml
s
), and Bml
r
transformants were selected. The Bml
r
transformants were screened on medium which did not contain uridine in order to identify Pyr
-
mutants created by integration of p23 at the
PYR1
locus. None of the primary transformants were Pyr
-
, but 0.2% of uninucleate conidia collected from the pooled primary transformants gave rise to Pyr
-
auxotrophs. Southern blots representing two of these Pyr
-
mutants confirmed that they had the expected homologous integration of p23 at the
PYR1
locus. This suggested that integration resulted in production of two nonfunctional copies of the gene, one lacking the 5′ sequences and the other lacking the 3′ sequences. This study demonstrates the feasibility of using cotransformation to perform targeted gene disruptions in
G. graminicola
.
Production of beauvericin by a strain of Fusarium proliferatum isolated from corn fodder for swine
Authors: Plattner R D , Nelson P E
Published: January 2020

Beauvericin, a cyclodepsipeptide, was produced by cultures of three strains of Fusarium proliferatum, M-5991, M-6992, and M-6993, grown on cracked corn. M-5991 produced approximately 1,000-mg/kg levels of fumonisins, moniliformin, and beauvericin.
Pertinence of indicator organisms and sampling variables to Vibrio concentrations
Authors: Koh E G , Huyn J H , LaRock P A
Published: January 2020

Vibrio-indicator relationships and effects of day, depth, and tidal levels on the density of vibrios enumerated by the most probable number technique were investigated. Counts of vibrios taken monthly from Apalachicola Bay, Fla., were either negatively correlated or showed no correlation with counts of indicator bacteria (Escherichia coli, enterococci, fecal coliforms, and total coliforms). Water samples collected on two days from the surface and bottom over a complete tidal cycle on each day were analyzed for differences in vibrio concentrations. Concentrations of vibrios in samples taken on different days, in those taken at different depths, and in those taken at different tidal levels were significantly different, indicating that these factors need to be taken into account in health-related studies.
Carbon Source Requirements for Exopolysaccharide Production by
Lactobacillus casei
CG11 and Partial Structure Analysis of the Polymer
Authors: Cerning J. , Renard C. M. G. C. , Thibault J. F. , Bouillanne C. , Landon M. , Desmazeaud M. , Topisirovic L.
Published: January 2020

Exopolysaccharide production by
Lactobacillus casei
CG11 was studied in basal minimum medium containing various carbon sources (galactose, glucose, lactose, sucrose, maltose, melibiose) at concentrations of 2, 5, 10, and 20 g/liter.
L. casei
CG11 produced exopolysaccharides in basal minimum medium containing each of the sugars tested; lactose and galactose were the poorest carbon sources, and glucose was by far the most efficient carbon source. Sugar concentrations had a marked effect on polymer yield. Plasmid-cured Muc
-
derivatives grew better in the presence of glucose and attained slightly higher populations than the wild-type strain. The values obtained with lactose were considerably lower for both growth and exopolysaccharide yield. The level of specific polymer production per cell obtained with glucose was distinctively lower for Muc
-
derivatives than for the Muc
+
strain. The polymer produced by
L. casei
CG11 in the presence of glucose was different from that formed in the presence of lactose. The polysaccharide produced by
L. casei
CG11 in basal minimum medium containing 20 g of glucose per liter had an intrinsic viscosity of 1.13 dl/g. It was rich in glucose (76%), which was present mostly as 2- or 3-linked residues along with some 2,3 doubly substituted glucose units, and in rhamnose (21%), which was present as 2-linked or terminal rhamnose; traces of mannose and galactose were also present.
Metabolism of benz[a]anthracene by the filamentous fungus Cunninghamella elegans
Authors: Cerniglia C E , Gibson D T , Dodge R H
Published: January 2020

The metabolism of the carcinogen benz[a]anthracene (BA), a tetracyclic aromatic hydrocarbon, by Cunninghamella elegans was investigated. C. elegans grown on Sabouraud dextrose broth transformed [14C]BA to labeled BA trans-8,9-dihydrodiol (90%), BA trans-10,11-dihydrodiol (6%), and BA trans-3,4-dihydrodiol (4%), but not to BA trans-5,6-dihydrodiol. These metabolites were separated by thin-layer chromatography and reversed-phase high-performance liquid chromatography and were identified by UV and mass spectral techniques. A BA tetraol, 8 beta,9 alpha,10 alpha,11 beta-tetrahydroxy-8 alpha, 9 beta,10 beta,11 alpha-tetrahydro-BA, was also identified as a metabolite and may have arisen as an additional oxidation product of either BA 8,9- or 10,11-dihydrodiol. This is the first study in which a biologically produced BA tetraol has been identified. Our results suggest that the transformation of BA to trans-dihydrodiols by C. elegans is similar to the transformation of BA found in mammals, except that BA 5,6-dihydrodiol is not produced.
Acetate metabolism by Escherichia coli in high-cell-density fermentation
Authors: Kleman G L , Strohl W R
Published: January 2020

Little is known about the cellular physiology of Escherichia coli at high cell densities (e.g., greater than 50 g [dry cell weight] per liter), particularly in relation to the cellular response to different growth conditions. E. coli W3100 cultures were grown under identical physical and nutritional conditions, by using a computer-controlled fermentation system which maintains the glucose concentration at 0.5 g/liter, to high cell densities at pH values of 6.0, 6.5, 7.0, and 7.5. The data suggest a relationship between the pH of the environment and the amount of acetate excreted by the organism during growth. At pH values of 6.0 and 6.5, the acetate reached a concentration of 6 g/liter, whereas at pH 7.5, the acetate reached a concentration of 12 g/liter. Furthermore, at pH values of 6.0 to 7.0, the E. coli culture undergoes a dramatic metabolic switch in which oxygen and glucose consumption and CO2 evolution all temporarily decreased by 50 to 80%, with a concomitant initiation of acetate utilization. After a 30-min pause in which approximately 50% of the available acetate is consumed, the culture recovers and resumes consuming glucose and oxygen and producing acetate and CO2 at preswitch levels. During the switch period, the specific activity of isocitrate lyase typically increases approximately fourfold.
Cloning and sequencing of a serine proteinase gene from a thermophilic Bacillus species and its expression in Escherichia coli
Authors: Maciver B , McHale R H , Saul D J , Bergquist P L
Published: January 2020

The gene for a serine proteinase from a thermophilic Bacillus species was identified by PCR amplification, and the complete gene was cloned after identification and isolation of suitably sized restriction fragments from Southern blots by using the PCR product as a probe. Two additional, distinct PCR products, which were shown to have been derived from other serine proteinase genes present in the thermophilic Bacillus species, were also obtained. Sequence analysis showed an open reading frame of 1,206 bp, coding for a polypeptide of 401 amino acids. The polypeptide was determined to be an extracellular serine proteinase with a signal sequence and prosequence. The mature proteinase possessed homology to the subtilisin-like serine proteinases from a number of Bacillus species and had 61% homology to thermitase, a serine proteinase from Thermoactinomyces vulgaris. The gene was expressed in Escherichia coli in the expression vector pJLA602 and as a fusion with the alpha-peptide of the lacZ gene in the cloning vector pGEM5. A recombinant proteinase from the lacZ fusion plasmid was used to determine some characteristics of the enzyme, which showed a pH optimum of 8.5, a temperature optimum of 75 degrees C, and thermostabilities ranging from a half-life of 12.2 min at 90 degrees C to a half-life of 40.3 h at 75 degrees C. The enzyme was bound to a bacitracin column, and this method provided a simple, one-step method for producing the proteinase, purified to near homogeneity.
Amino Acid Cycling in Colonies of the Planktonic Marine Cyanobacterium
Trichodesmium thiebautii
Authors: Capone Douglas G. , Ferrier M. Drew , Carpenter Edward J.
Published: January 2020

We examined diel trends in internal pools and net efflux of free amino acids in colonies of the nonheterocystous, diazotrophic cyanobacterium
Trichodesmium thiebautii
, freshly collected from waters of the Caribbean and the Bahamas. The kinetics of glutamate uptake by whole colonies were also examined. While intracolonial pools of most free amino acids were relatively constant through the day, pools of glutamate and glutamine varied over the diel cycle, with maxima during the early afternoon. This paralleled the daily cycle of nitrogenase activity. We also observed a large net release of these two amino acids from intact colonies. Glutamate release was typically 100 pmol of N colony
-1
h
-1
. This is about one-fourth the concurrent rate of N
2
fixation during the day. However, while nitrogenase activity only occurs during the day, net release of glutamate and glutamine persisted into the night and may therefore account for a greater loss of recently fixed N on a daily basis. This release may be an important route of new N input into tropical, oligotrophic waters. Whole colonies also displayed saturation kinetics with respect to glutamate uptake. The
K

s

for whole colonies varied from 1.6 to 3.2 μM, or about 100-fold greater than typical ambient concentrations. Thus, uptake systems appear to be adapted to the higher concentrations of glutamate found within the intracellular spaces of the colonies. This suggests that glutamate may be a vehicle for N exchange among trichomes in the colony.
Initial reactions in the anaerobic oxidation of toluene and m-xylene by denitrifying bacteria
Authors: Seyfried B , Glod G , Schocher R , Tschech A , Zeyer J
Published: January 2020

Pseudomonas sp. strain T and Pseudomonas sp. strain K172 grow with toluene under denitrifying conditions. We demonstrated that anaerobic degradation of toluene was initiated by direct oxidation of the methyl group. Benzaldehyde and benzoate accumulated sequentially after toluene was added when cell suspensions were incubated at 5 degrees C. Strain T also grows anaerobically with m-xylene, and we demonstrated that degradation was initiated by oxidation of one methyl group. In cell suspensions incubated at 5 degrees C 3-methylbenzaldehyde and 3-methylbenzoate accumulated after m-xylene was added. Toluene- or m-xylene-grown strain T cells were induced to the same extent for oxidation of both hydrocarbons. In addition, the methyl group-oxidizing enzyme system of strain T also catalyzed the oxidation of each isomer of the chloro- and fluorotoluenes to the corresponding halogenated benzoate derivatives. In contrast, strain K172 only oxidized 4-fluorotoluene to 4-fluorobenzoate, probably because of the narrow substrate specificity of the methyl group-oxidizing enzymatic system. During anaerobic growth with toluene strains T and K172 produced two transformation products, benzylsuccinate and benzylfumarate. About 0.5% of the toluene carbon was converted to these products.
Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil
Authors: Neilson J W , Josephson K L , Pepper I L , Arnold R B , Di Giovanni G D , Sinclair N A
Published: January 2020

Limited work has been done to assess the bioremediation potential of transfer of plasmid-borne degradative genes from introduced to indigenous organisms in the environment. Here we demonstrate the transfer by conjugation of the catabolic plasmid pJP4, using a model system with donor and recipient organisms. The donor organism was Alcaligenes eutrophus JMP134 and the recipient organism was Variovorax paradoxus isolated from a toxic waste site. Plasmid pJP4 contains genes for mercury resistance and 2,4-dichlorophenoxyacetic (2,4-D) acid degradation. A transfer frequency of approximately 1/10(3) donor and recipient cells (parent cells) was observed on solid agar media, decreasing to 1/10(5) parent cells in sterile soil and finally 1/10(6) parent cells in 2,4-D-amended, nonsterile soil. Presumptive transconjugants were confirmed to be resistant to Hg, to be capable of degrading 2,4-D, and to contain a plasmid of size comparable to that of pJP4. In addition, we confirmed the transfer through PCR amplifications of the tfdB gene. Although transfer of pJP4 did occur at a high frequency in pure culture, the rate was significantly decreased by the introduction of abiotic (sterile soil) and biotic (nonsterile soil) stresses. An evaluation of the data from this model system implies that the reliance on plasmid transfer from a donor organism as a remediative strategy has limited potential.
Structural and functional analysis of the nor-1 gene involved in the biosynthesis of aflatoxins by Aspergillus parasiticus
Authors: Trail F , Chang P K , Cary J , Linz J E
Published: January 2020

The nor-1 gene was cloned previously by complementation of a mutation (nor-1) in Aspergillus parasiticus SU-1 which blocked aflatoxin B1 biosynthesis, resulting in the accumulation of norsolorinic acid (NA). In this study, the nucleotide sequences of the cDNA and genomic DNA clones encompassing the coding region of the nor-1 gene were determined. The transcription initiation and polyadenylation sites of nor-1 were located by primer extension and RNase protection analyses and by comparison of the nucleotide sequences of the nor-1 genomic and cDNA clones. A plasmid, pNA51-82, was created for one-step disruption of the nor-1 gene by inserting a functional copy of the nitrate reductase (niaD) gene from A. parasiticus into the coding region of the nor-1 gene. Transformation of A. parasiticus NR-3 (niaD Afl+) with pNA51-82 resulted in niaD+ transformants that accumulated NA and produced reduced levels of aflatoxin as determined by thin-layer chromatography and enzyme-linked immunosorbent assay analyses of extracts from mycelia and the growth medium. Southern analysis of genomic DNA isolated from the NA-accumulating transformants indicated that the wild-type nor-1 gene in the chromosome had been replaced by the nonfunctional allele carried on pNA51-82. This recombinational inactivation event provides direct evidence that the nor-1 gene is functionally involved in aflatoxin biosynthesis. Comparison of the predicted nor-1 amino acid sequence with sequences in the GenBank and EMBL databases suggested that the protein is a member of the family of short-chain alcohol dehydrogenases, consistent with its proposed function as a keto reductase.
Efficient Transformation of the Cephamycin C Producer
Nocardia lactamdurans
and Development of Shuttle and Promoter-Probe Cloning Vectors
Authors: Kumar C. Vasant , Coque Juan-Jose R. , Martín Juan F.
Published: January 2020

A high transformation efficiency (1 × 10
5
to 7 × 10
5
transformants per μg of DNA) of
Nocardia lactamdurans
LC411 was obtained by direct treatment of mycelium with polyethylene glycol 1000 and cesium chloride. A variety of vectors from
Streptomyces lividans, Brevibacterium lactofermentum, Rhodococcus fascians
, and a
Nocardia (Amycolatopsis)
sp. were tested; transformants could be obtained only with vectors derived from an endogenous plasmid of the
Amycolatopsis
sp. strain DSM 43387. Vectors carrying the kanamycin resistance gene (
kan
) as a selective marker were constructed. The transformation procedure has been optimized by using one of these vectors (pULVK1) and studying the influence of the age of the culture, concentrations of cesium chloride and polyethylene glycol, amount of plasmid DNA, and nutrient supplementations of the growth medium. Versatile shuttle cloning vectors (pULVK2 and pULVK3) have been developed by subcloning the pBluescript KS(+) multiple cloning site or a synthetic polylinker containing several unique restriction sites (
Eco
RV,
Dra
I,
Bam
HI,
Sst
I,
Eco
RI, and
Hind
III). A second marker, the apramycin resistance gene (
amr
) has been added to the vectors (pULVK2A), allowing insertional inactivation of one of the markers while using the second one for selection. An alternative marker, the
amy
gene of
Streptomyces griseus
(pULAM2), which is easily detected by the release of extracellular amylase in transformants of
N. lactamdurans
carrying this vector, has been added. Two promoter-probe plasmids, pULVK4 and pULVK5, have been constructed, with the promoterless
xylE
gene as a reporter, for utilization in
N. lactamdurans
.
Nucleotide sequence and functional analysis of the genes encoding 2,4,5-trichlorophenoxyacetic acid oxygenase in Pseudomonas cepacia AC1100
Authors: Danganan C E , Ye R W , Daubaras D L , Xun L , Chakrabarty A M
Published: January 2020

Pseudomonas cepacia AC1100 is able to use the chlorinated aromatic compound 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as the sole source of carbon and energy. One of the early steps in this pathway is the conversion of 2,4,5-T to 2,4,5-trichlorophenol (2,4,5-TCP). 2,4,5-TCP accumulates in the culture medium when AC1100 is grown in the presence of 2,4,5-T. A DNA region from the AC1100 genome has been subcloned as a 2.7-kb SstI-XbaI DNA fragment, which on transfer to Pseudomonas aeruginosa PAO1 allows the conversion of 2,4,5-T to 2,4,5-TCP. We have determined the directions of transcription of these genes as well as the complete nucleotide sequences of the genes and the number and sizes of the polypeptides synthesized by pulse-labeling experiments. This 2.7-kb DNA fragment encodes two polypeptides with calculated molecular masses of 51 and 18 kDa. Proteins of similar sizes were seen in the T7 pulse-labeling experiment in Escherichia coli. We have designated the genes for these proteins tftA1 (which encodes the 51-kDa protein) and tftA2 (which encodes the 18-kDa protein). TftA1 and TftA2 have strong amino acid sequence homology to BenA and BenB from the benzoate 1,2-dioxygenase system of Acinetobacter calcoaceticus, as well as to XylX and XylY from the toluate 1,2-dioxygenase system of Pseudomonas putida. The Pseudomonas aeruginosa PAO1 strain containing the 2.7-kb SstI-XbaI fragment was able to convert not only 2,4,5-T to 2,4,5-TCP but also 2,4-dichlorophenoxyacetic acid to 2,4-dichlorophenol and phenoxyacetate to phenol.