Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils.

A modified protocol for DNA amplification by polymerase chain reaction (PCR) coupled with laser densitometric determination of the amount of PCR products, which allowed quantitation of target sequence numbers in soil extracts, was developed. The method was applied to monitor target loss during incubation of purified plasmid DNA in natural nonsterile soils. It revealed soil-specific kinetics of target loss. After 60 days, 0.2, 0.05, and 0.01% of the initially added nahA genes on plasmids were detectable by PCR in a loamy sand soil, a clay soil, and a silty clay soil, respectively. Electroporation of Escherichia coli was used in parallel to quantitate plasmid molecules in soil extracts by their transforming activity. It was found that transformation by electroporation was about 20 times more efficient and much less inhibited by constituents of soil extracts than transformation of Ca(2+)-treated cells (G. Romanowski, M.G. Lorenz, G. Sayler, and W. Wackernagel, Appl. Environ. Microbiol. 58:3012-3019, 1992). By electroporation, greater than 10,000-fold plasmid loss was monitored in nonsterile soils. Transforming activity was found up to 60 days after inoculation of the soils. The studies indicate that PCR and electroporation are sensitive methods for monitoring the persistence of extracellular plasmid DNA in soil. It is proposed that plasmid transformation by electroporation can be used for the monitoring in soil and other environments of genetically engineered organisms with recombinant plasmids. The data suggest that genetic material may persist in soil for weeks and even for months after its release from cells.     

Evaluation of Biological and Physical Protection against Nuclease Degradation of Clay-Bound Plasmid DNA

In order to determine the mechanisms involved in the persistence of extracellular DNA in soils and to monitor whether bacterial transformation could occur in such an environment, we developed artificial models composed of plasmid DNA adsorbed on clay particles. We determined that clay-bound DNA submitted to an increasing range of nuclease concentrations was physically protected. The protection mechanism was mainly related to the adsorption of the nuclease on the clay mineral. The biological potential of the resulting DNA was monitored by transforming the naturally competent proteobacterium Acinetobacter sp. strain BD413, allowing us to demonstrate that adsorbed DNA was only partially available for transformation. This part of the clay-bound DNA which was available for bacteria, was also accessible to nucleases, while the remaining fraction escaped both transformation and degradation. Finally, transformation efficiency was related to the perpetuation mechanism, with homologous recombination being less sensitive to nucleases than autonomous replication, which requires intact molecules.     

Replication and amplification of recombinant plasmid molecules as extra chromosomal elements in transformed mammalian cells

Mouse thymidine kinase negative (TK^?) L cells, F4-12B2TK^? Friend erythroleukemic cells and hamster BHKTK^? cells were transformed in the absence of carrier DNA with closed circular molecules of herpes simplex virus 1 TK DNA cloned in plasmid pAT153 (pTK-1). The physical status of donor DNA in the transformed cells was studied by Southern blot hybridization and spot hybridization techniques. Up to 65 copies of pTK-1 DNA molecules/cell were present in transformed cells grown under selective conditions. Whereas a steady increase in the number of pTK-1 copies/cell was found during the first few weeks of growth in selective medium, 2–8 months later copy numbers varied within the same cell line and their numbers rarely exceeded fifty copies/cell. Donor DNA sequences were found both in the Hirt precipitate and in the supernatant showing that some of the pTK-1 molecules existed in circular form. Many of the cell lines gave a Southern blot hybridization pattern indicative of pTK-1 sequences integrated into high molecular weight DNA as well as present in a circular configuration.     

Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA

In order to determine the mechanisms involved in the persistence of extracellular DNA in soils and to monitor whether bacterial transformation could occur in such an environment, we developed artificial models composed of plasmid DNA adsorbed on clay particles. We determined that clay-bound DNA submitted to an increasing range of nuclease concentrations was physically protected. The protection mechanism was mainly related to the adsorption of the nuclease on the clay mineral. The biological potential of the resulting DNA was monitored by transforming the naturally competent proteobacterium Acinetobacter sp. strain BD413, allowing us to demonstrate that adsorbed DNA was only partially available for transformation. This part of the clay-bound DNA which was available for bacteria, was also accessible to nucleases, while the remaining fraction escaped both transformation and degradation. Finally, transformation efficiency was related to the perpetuation mechanism, with homologous recombination being less sensitive to nucleases than autonomous replication, which requires intact molecules.     

Influence of soil variables on in situ plasmid transfer from Escherichia coli to Rhizobium fredii

A model system was established to determine whether intergeneric plasmid transfer occurs in soil and how various soil variables affect the rate of plasmid transfer. The donor bacterium, Escherichia coli HB101 carrying plasmid pBLK1-2 (pRK2073::Tn5), and the recipient bacterium, Rhizobium fredii USDA 201, were inoculated into a sterile Adelphia fine-sandy-loam soil. Transconjugants were enumerated by direct plating on antibiotic-amended HM [N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid; 2-(N-morpholino) ethanesulfonic acid] salts medium. Randomly chosen transconjugants were verified by serological typing and Southern hybridization with a Tn5 gene probe. The maximum transfer frequency was observed after 5 days of incubation (1.8 x 10(-4) per recipient). The influences of clay (0 to 50% addition), organic matter (0 to 15% addition), soil pH (4.3 to 7.25), soil moisture (2 to 40%), and soil incubation temperature (5 to 40 degrees C) on plasmid transfer were examined. Maximum transfer frequencies were noted at a clay addition of 15%, an organic matter addition of 5%, a soil pH of 7.25, a soil moisture content of 8%, and a soil incubation temperature of 28 degrees C. These results indicate that intergeneric plasmid transfer may occur in soil and that soil variables may significantly affect the rate of transfer.     

Influence of soil variables on in situ plasmid transfer from Escherichia coli to Rhizobium fredii.

A model system was established to determine whether intergeneric plasmid transfer occurs in soil and how various soil variables affect the rate of plasmid transfer. The donor bacterium, Escherichia coli HB101 carrying plasmid pBLK1-2 (pRK2073::Tn5), and the recipient bacterium, Rhizobium fredii USDA 201, were inoculated into a sterile Adelphia fine-sandy-loam soil. Transconjugants were enumerated by direct plating on antibiotic-amended HM [N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid; 2-(N-morpholino) ethanesulfonic acid] salts medium. Randomly chosen transconjugants were verified by serological typing and Southern hybridization with a Tn5 gene probe. The maximum transfer frequency was observed after 5 days of incubation (1.8 x 10(-4) per recipient). The influences of clay (0 to 50% addition), organic matter (0 to 15% addition), soil pH (4.3 to 7.25), soil moisture (2 to 40%), and soil incubation temperature (5 to 40 degrees C) on plasmid transfer were examined. Maximum transfer frequencies were noted at a clay addition of 15%, an organic matter addition of 5%, a soil pH of 7.25, a soil moisture content of 8%, and a soil incubation temperature of 28 degrees C. These results indicate that intergeneric plasmid transfer may occur in soil and that soil variables may significantly affect the rate of transfer.     

Transformation of Bacillus subtilis by DNA bound on clay in non-sterile soil

Abstract Chromosomal DNA from Bacillus subtilis and different forms of plasmid pHV14 (covalently closed circular (CCC), linear monomer (M), and linear multimer (LM)) were adsorbed and bound on the clay mineral montmorillonite. After extensive washing of the clay-DNA complexes with DNA buffer (pH 7.5), approx. 25% of the chromosomal DNA, and approx. 30, 90, and 5%, respectively, of the CCC, M and LM form remained bound. Chromosomal and plasmid DNA bound on clay were capable of transforming competent cells, with different specific activities. The clay-DNA complexes persisted in non-sterile soil and retained transforming ability up to 15 days after their addition to the soil. DNA bound on montmortillonite was protected from the activity of Eco RI, supporting the evidence that DNA adsorbed on soil components was resistant to degradation by nucleases.     

Short-term effects of biological and physical forces on aggregate formation in soils with different clay mineralogy

The mechanisms resulting in the binding of primary soil particles into stable aggregates vary with soil parent material, climate, vegetation, and management practices. In this study, we investigated short-term effects of: (i) nutrient addition (Hoagland's solution), (ii) organic carbon (OC) input (wheat residue), (iii) drying and wetting action, and (iv) root growth, with or without dry–wet cycles, on aggregate formation and stabilization in three soils differing in weathering status and clay mineralogy. These soils included a young, slightly weathered temperate soil dominated by 2:1 (illite and chlorite) clay minerals; a moderately weathered soil with mixed [2:1 (vermiculite) and 1:1 (kaolinite)] clay mineralogy and oxides; and a highly weathered tropical soil dominated by 1:1 (kaolinite) clay minerals and oxides. Air-dried soil was dry sieved through a 250 m sieve to break up all macroaggregates and 100 g-subsamples were brought to field capacity and incubated for 42 days. After 14 and 42 days, aggregate stability was measured on field moist and air-dried soil, to determine unstable and stable aggregation respectively. In control treatments (i.e., without nutrient or organic matter addition, without roots and at constant moisture), the formation of unstable and stable macroaggregates (> 250 m) increased in the order: 2:1 clay soil < mixed clay soil < 1:1 clay soil. After 42 days of incubation, nutrient addition significantly increased both unstable and stable macroaggregates in the 2:1 and 1:1 clay soils. In all soils, additional OC input increased both unstable and stable macroaggregate formation. The increase in macroaggregation with OC input was highest for the mixed clay soil and lowest for the 1:1 clay soil. In general, drying and wetting cycles had a positive effect on the formation of macroaggregates. Root growth caused a decrease in unstable macroaggregates in all soils. Larger amounts of macroaggregates were found in the mixed clay and oxides soil when plants were grown under 50% compared to 100% field capacity conditions. We concluded that soils dominated by variable charge clay minerals (1:1 clays and oxides) have higher potential to form stable aggregates when OC concentrations are low. With additional OC inputs, the greatest response in stable macroaggregate formation occurred in soils with mixed mineralogy, which is probably a result of different binding mechanisms occurring: i.e., electrostatic bindings between 2:1 clays, 1:1 clays and oxides (i.e. mineral-mineral bindings), in addition to OM functioning as a binding agent between 2:1 and 1:1 clays.     

Natural Transformation of Acinetobacter calcoaceticus by Plasmid DNA Adsorbed on Sand and Groundwater Aquifer Material

It is known that plasmid DNA and linear duplex DNA molecules adsorb to chemically purified mineral grains of sand and to particles of several clay fractions. It seemed desirable to examine whether plasmid DNA would also adsorb to nonpurified mineral materials taken from the environment and, particularly, whether adsorbed plasmid DNA would be available for natural transformation of bacteria. Therefore, microcosms consisting of chemically pure sea sand plus buffered CaCl₂ solution were compared with microcosms consisting of material sampled directly from a groundwater aquifer (GWA) plus groundwater (GW) with respect to the natural transformation of Acinetobacter calcoaceticus by mineral-associated DNA. The GWA minerals were mostly sand with inorganic precipitates and organic material plus minor quantities of silt and clay (illite and kaolinite). The amount of plasmid DNA which adsorbed to GWA (in GW) was about 80% of the amount which adsorbed to purified sand (in buffered CaCl₂ solution). Plasmid DNA adsorbed on sand transformed A. calcoaceticus significantly less efficiently than did plasmid DNA in solution. In contrast, the transformation by sand-adsorbed chromosomal DNA was as high as that by DNA in solution. In GWA/GW microcosms, the efficiency of transformation by chromosomal DNA was similar to that in sand microcosms, whereas plasmid transformation was not detectable. However, plasmid transformants were found at a low frequency when GWA was loaded with both chromosomal and plasmid DNA. Reasons for the low transformation efficiency of plasmid DNA adsorbed to mineral surfaces are discussed. Control experiments showed that the amounts of plasmid and chromosomal DNA desorbing from sand during incubation with a cell-free filtrate of a competent cell suspension did not greatly contribute to transformation in sand microcosms, suggesting that transformation occurred by direct uptake of DNA from the mineral surfaces. Taken together, the observations suggest that plasmid DNA and chromosomal DNA fragments which are adsorbed on mineral surfaces in a sedimentary or soil habitat may be available (although with different efficiencies for the two DNA species) for transformation of a naturally competent gram-negative soil bacterium.     

Fate in soil of a recombinant plasmid carrying aDrosophila gene

A recombinant plasmid (C357; 3.5 Mdal) containing heterologous DNA (pBR322 [2.6 Mdal] with cDNA for an egg yolk protein fromDrosophila grimshawi) inEscherichia coli strain HB101 survived in and was recovered on selective media from sterile and nonsterile soil during 27 days at frequencies similar to those of theE. coli(pBR322) system. In sterile saline, the numbers of all cells decreased during 34 days, but the numbers of the plasmidless host declined less. There was no selective loss of the heterologous DNA in either soil or saline, as determined by colony hybridization with a³²P-labeled DNA probe for the cDNA, but the HB101(C357) appeared to be less able than HB101(pBR322) to cope with conditions of starvation. These results suggested that nonessential eucaryotic DNA inserted into plasmid DNA has little effect on the survival in soil or saline of the bacterial host and the maintenance of the vector.     

Soil organic matter dynamics in density and particle-size fractions following destruction of tropical rainforest and the subsequent establishment of Imperata grassland in Indonesian Borneo using stable carbon isotopes

Background and aims

Large portions of the deforested areas in Southeast Asia have been ultimately replaced by the invasive grass Imperata cylindrica, but the dynamics of soil organic matter (SOM) during such land transitions are poorly understood. This study presents SOM dynamics in density and particle-size fractions following rainforest destruction and the subsequent establishment and persistence of Imperata grassland.

Methods

We examined soil C stock and natural ¹³C abundance in these fractions to depths of 100 cm. We predicted future soil C storage and evaluated C turnover rates in these fractions using a simple exponential model. Because soil texture strongly affects soil C storage, two chronosequences of soils differing in soil texture were compared (n?=?1 in each chronosequence).

Results

The clay-associated SOM increased in all soil layers (0–100 cm) along the forest-to-grassland chronosequence, whereas light-fraction SOM in the surface soil layer (0–5 cm) decreased.

Conclusions

In the surface layer, all SOM fractions exhibited rapid replacement of forest-derived C to grassland-derived C, indicating fast turnover. Meanwhile, δ¹³C values of the light fraction in the surface layer indicated that forest-derived charcoal and/or occluded low-density organic matter constituted unexpectedly large proportions of the light fraction. Mathematical modelling (0–50 cm) showed that grassland-derived C in the clay and silt fractions in all soil layers increased almost linearly for at least 50 years after grassland establishment. In the meantime, the forest-derived C stock in the clay fraction constituted 82 % of the total stable C pool at 0–50-cm depths even under steady-state conditions (t = ∞), indicating that residue of forest-derived SOM associated with clay largely contributed to preserving the soil C pool. Comparing soils with different soil textures, clay and silt particles in coarse-textured soil exhibited a substantially higher degree of organo-mineral interactions per unit volume of clay or silt compared to fine-textured soils.     

Mineralization Potential of Atrazine and Degradation Intermediates from Clustered Characteristics in Inoculated Soils

Soil properties impact pesticide persistence. Because these characteristics operate together in situ, identification of their clustered associations can help explain pesticide fate. Factor analysis was used to reduce the dimensionality of soil characteristics by grouping them into clustered independent factors, which were then related to the mineralization of atrazine and selected degradation intermediates. A Sharpsburg silty clay loam, Ortello sandy loam, and Hord silt loam were inoculated with a Hord soil that had a high capacity for atrazine mineralization. The soils were spiked with ¹⁴C-radiolabeled atrazine, deethylatrazine, hydroxyatrazine, N-isopropylammeline, N-isopropylammelide or cyanuric acid and sampled during incubation for 80 d (atrazine) or 40 d (degradation intermediates) at 22°C. Low mineralization in uninoculated soils demonstrated that the absence of atrazine-mineralizing microorganisms was most limiting. In inoculated soils, regression analysis indicated mineralization of atrazine (R² = 0.88) and its degradation intermediates (R² ≥ 0.89) was related to factors associated with bioavailability and microbial activity. For atrazine, this relationship indicated mineralization may be positively influenced by higher pH and available phosphorus, lower NO₃-N, organic carbon and clay contents, and lower adsorption. Our results show how factor analysis can be used in conjunction with multiple regression to determine mineralization potential and thus help identify soils with limited degradation capacities and possible long-term persistence.     

DNA recovery from soils of diverse composition.

A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk of chimera formation from small template DNA during subsequent PCR. The method was based on lysis with a high-salt extraction buffer (1.5 M NaCl) and extended heating (2 to 3 h) of the soil suspension in the presence of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, and proteinase K. The extraction method required 6 h and was tested on eight soils differing in organic carbon, clay content, and pH, including ones from which DNA extraction is difficult. The DNA fragment size in crude extracts from all soils was > 23 kb. Preliminary trials indicated that DNA recovery from two soils seeded with gram-negative bacteria was 92 to 99%. When the method was tested on all eight unseeded soils, microscopic examination of indigenous bacteria in soil pellets before and after extraction showed variable cell lysis efficiency (26 to 92%). Crude DNA yields from the eight soils ranged from 2.5 to 26.9 micrograms of DNA g-1, and these were positively correlated with the organic carbon content in the soil (r = 0.73). DNA yields from gram-positive bacteria from pure cultures were two to six times higher when the high-salt-SDS-heat method was combined with mortar-and-pestle grinding and freeze-thawing, and most DNA recovered was of high molecular weight. Four methods for purifying crude DNA were also evaluated for percent recovery, fragment size, speed, enzyme restriction, PCR amplification, and DNA-DNA hybridization. In general, all methods produced DNA pure enough for PCR amplification. Since soil type and microbial community characteristics will influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods on the basis of experimental goals.     

Effects of Zeolite-Containing Material and Ammonium Nitrate on Biodegradation of n-Tridecane in Heavy Clay-Loam Leached Chernozem with High Organic Matter Content

Biostimulation based on usage of soil amendments is growing due to their efficiency in removing different petroleum hydrocarbons (PHC) from contaminated sand or loam-sand soils. However, the research on clay-rich soils with higher organic carbon content, in which PHC biodegradation may proceed differently and which are more difficult to clean up, has been less extensive. In a pot experiment, we studied and compared the effects of two soil amendments, natural zeolite-containing material (ZCM, 50 g kg^?1) as a bulking agent and ammonium nitrate (0.3 g N kg^?1) as a nitrogen fertilizer, on biodegradation of n-tridecane (1 wt.%) in a weakly acidic heavy clay loam leached chernozem with fairly high organic carbon content (3.71%). After 48 days, the nitrogen-amended contaminated soil showed enhancement of both respiratory activity (basal and substrate-induced respiration rates) and the number of n-tridecane- degraders. As a consequence, the extent of n-tridecane biodegradation (86.5%) was essentially higher in the presence of added nitrogen than that in the non-amended soil (73.7%). In contrast, due to the partial retention of n-tridecane molecules in its pores, ZCM retarded biodegradation to 56.0%, showed no significant effect on the number of n-tridecane-degraders and, moreover, enhanced the decomposition of the soil intrinsic organic matter. The obtained data indicate that more precautions should be considered when using porous sorbents such as ZCM for remedial arrangements in PHC-contaminated soils.     

Persistence and impact on microorganisms of Bacillus thuringiensis proteins in some Zimbabwean soils

The persistence of the Bacillus thuringiensis subsp. kurstaki (Btk) toxin (Cry1Ab protein) from Bt maize (MON810, Yieldgard®) residues incorporated in a vertisol (739 g clay kg^?1) was investigated. The maize residues were incubated in the soil for 4 weeks, and activity of the toxin in the residues was bioassayed using larvae of the diamondback moth, Plutella xylostella (Lepidoptera: Yponomeutidae). Corrected mortality of P. xylostella in the bioassays decreased from 76% to 30% in less than a week of incubation in the soil. In addition to the above observations, the effects of Btk, Bt subsp. israelensis (Bti), and Bt subsp. tenebrionis (Btt) proteins on the soil microbiota were examined using a vertisol, an alfisol, and an oxisol. The pre-incubated soils (7 days after moisture adjustment) were treated with crystal proteins of Btk, Bti, and Btt and incubated for further a 7-day period. Microbial biomass carbon (MBC) and counts of culturable bacteria and fungi were determined. The proteins did not show effects on MBC or bacterial and fungal counts, possibly as a result of adsorption of the proteins on soil particles, which could have rendered the proteins inaccessible for microbial utilization. Microbial biomass carbon and counts arranged in decreasing order were vertisol>oxisol>alfisol, similar to the amounts of organic C and clay in the soils. However, bacteria and fungi counts were higher in the vertisol than in the alfisol and the oxisol soils. Our observations suggest that larvicidal proteins produced by different subspecies of Bt and Bt maize could persist in tropical soils as a result of adsorption on soil clays but that there were no observable effect on the soil microbiota.     

Monitoring survival and gene transfer in soil microcosms of recombinant Escherichia coli designed to represent an industrial production strain

Summary A genetically engineered microorganism (GEM) was designed to exemplify bacterial strains used for the production of biological material in industry. The recombinant DNA was located on a safety plasmid (pUC19). Survival and persistence of the GEM and its recombinant DNA (rDNA) was determined in soil microcosms by using different monitoring methods, including the polymerase-chain reaction, to amplify and detect the specific rDNA. Depending on nutritional status, both the GEM and its rDNA had disappeared within 16 (amended soil) or 28 days (non-amended soil) with a limit of detection of 5 cells/g soil and 20 fg DNA/g soil.Offprint requests to: F.Schmidt     

A specific marker,pat, for studying the fate of introduced bacteria and their DNA in soil using a combination of detection techniques

A specific eucaryotic DNA marker from Solanum tuberosum cv Bintje (688 bp patatin cDNA fragment) was cloned into the unique HindIII-site of plasmid RP4. RP4:: pat was transferred from Escherichia coli to Pseudomonas fluorescens R2f by filter mating.Homology to pat was not detected in the microbial population of Ede loamy sand soil, nor in that of the rhizosphere of wheat growing in this soil, as evidenced by colony filter hybridization. More sensitive molecular detection techniques like most-probable-number recovery/hybridization analysis, and analysis of total community DNA from soil by polymerase chain reaction (PCR) amplification did not reveal the presence of the pat sequence either. P. fluorescens R2f (RP4:: pat), introduced into sterile soil extract microcosms, initially showed poor survival and plasmid loss, after which the introduced populations grew and stabilized at a level of about Log₁₀ 7 cfu per mL. Between 25 and 50% of the population maintained the plasmid, as evidenced by filter hybridization of colonies from non-selective agar plates using the pat fragment as probe.Introduced R2f (RP4:: pat) could be recovered from soil microcosms using selective plating followed by colony hybridization and MPN recovery/hybridization with the pat probe. The presence of the pat marker always coincided with the presence of the resistance genes on RP4:: pat, indicating pat was an adequate marker of the presence of this plasmid. In addition, it adequately described the population dynamics of the introduced strain in soil, since no loss of the plasmid occurred.Hybridization to pat was also useful to show transfer of plasmid RP4:: pat to a recipient strain in soil; transfer to indigenous bacteria was not detected.Analysis by slot-blot hybridization of total community DNA extracted from inoculated soils indicated about Log₁₀ 6 cfu per g of dry soil were still detectable. Application of the PCR on this DNA indicated pat was detectable at least at a level of Log₁₀ 4 immunofluorescence-detectable cells per g of dry soil. Thus extraction of total community DNA followed by PCR permitted the detection of genetically engineered microorganisms present in soil as non-culturable cells.     

Molecular genetic analysis of the response of three soil microbial communities to the application of 2, 4-D

The responses of three different soil microbial communities to the experimental application of 2, 4-dichlorophenoxyacetic acid (2, 4-D) were evaluated with a variety of molecular genetic techniques. Two of the three soil communities had histories of prior direct exposure to 2, 4-D, and one had no prior direct application of any herbicide. Dominant 2, 4-D degrading strains isolated from these soils the previous year were screened for hybridization with three catabolic genes (tfdA, tfdAII, and tfdB) cloned from the well-studied 2, 4-D degradative plasmid, pJP4, revealing varying degrees of similarity with the three genes. Hybridization of total community DNA from the three soils with the tfd gene probes also indicated that pJP4-like tfd genes were not harboured by a significant percentage of the community. Community level response was evaluated by the comparison of different treatments by Random Amplified Polymorphic DNA (RAPD) fingerprints and by community DNA cross-hybridization. No differences between treatments within the same soil were detected in any of the RAPD fingerprints generated with 17 primers. Community DNA cross-hybridization also indicated that the application of 2, 4-D at the applied rates did not quantitatively affect the structure of the soil microbial communities present in the three soils during the time-frame studied.     

Evidence for supercoiled hepatitis B virus DNA in chimpanzee liver and serum Dane particles: possible implications in persistent HBV infection

In chimpanzee hepatitis B virus (HBV) carriers, the mechanism of viral persistence has been examined by analyzing viral DNA molecules in liver and serum. Chimpanzee liver DNA contained two extrachromosomal HBV DNA molecules migrating on hybridization blots at 4.0 kb and 2.3 kb. There was no evidence for integration of HBV DNA into the host genome. The extrachromosomal molecules were distinct from Dane particle DNA and were converted to linear 3.25 kb full-length double-stranded HBV DNA on digestion with Eco RI. Nucleases S1 and Bal 31 converted "2.3 kb" HBV DNA to 3.25 kb via an intermediate of "4.0 kb" apparent length. The HBV DNA molecule that migrated at 2.3 kb represents a supercoiled form I of the HBV genome, and the molecule that migrated at 4.0 kb represents a full-length "nicked," relaxed circular form II. Evidence for supercoiled HBV DNA in serum Dane particles was obtained by production of form II molecules upon digestion with nuclease S1 or Bal 31. It is proposed that most Dane particles represent interfering noninfectious virus containing partially double-stranded DNA circles and that particles containing supercoiled HBV DNA may represent infectious hepatitis B virus.     

BamHI restriction endonuclease analysis of Yersinia ruckeri plasmids and their relatedness to the genus Yersinia 42- to 47-megadalton plasmid

The plasmid profile and BamHI restriction pattern of 17 sorbitol-negative and 1 sorbitol-positive French Yersinia ruckeri strain of the American type strain were studied. The 17 sorbitol-negative strains and the American strain harbored a 62-megadalton (MDa) plasmid with an identical BamHI restriction pattern. Southern hybridization indicated that this 62-MDa plasmid is common among these various strains. The sorbitol-positive strain had four plasmid bands (70, 62, 32, and 25 MDa), and there was no comigration of the DNA fragments of these cleaved plasmids with the fragments of the 62-MDa plasmid. Hybridization of these restricted plasmids with the common 62-MDa plasmid showed a weak DNA homology. The Y. ruckeri plasmid (62 MDa) had a different molecular weight than the virulence plasmid (42 to 47 MDa) of the genus Yersinia, and they had different BamHI restriction patterns. Furthermore, no sequence of the Y. ruckeri plasmid DNA was recognized after Southern hybridization when the 47-MDa plasmid of Y. enterocolitica was used as a probe.