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Applied and Environmental Microbiology, June 1999, p. 2307-2311, Vol. 65, No. 6
Entomology and Nematology Department,
University of Florida, Gainesville, Florida
32611,1 and Entomology and
Nematology Department and North Florida Research and Education
Center, University of Florida, Quincy, Florida
323512
Received 21 December 1998/Accepted 19 March 1999
Two methods, phenol-ether and magnetic capture-hybridization (MCH),
were developed and compared with regard to their sensitivities and
abilities to extract the DNA of the insect baculovirus Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) from soil
and to produce DNA amplifiable by PCR. Laboratory experiments were
performed with 0.25 g of autoclaved soil inoculated with different
viral concentrations to optimize both methods of baculovirus DNA
extraction and to determine their sensitivities. Both procedures
produced amplifiable DNA; however, the MCH method was 100-fold more
sensitive than the phenol-ether procedure. The removal of PCR
inhibitors from the soil appeared to be complete when MCH was used as
the viral DNA isolation method, because undiluted aliquots of the DNA
preparations could be amplified by PCR. The phenol-ether procedure probably did not completely remove PCR inhibitors from the soil, since
PCR products were observed only when the AgMNPV DNA
preparations were diluted 10- or 100-fold. AgMNPV DNA was
detected in field-collected soil samples from 15 to 180 days after
virus application when the MCH procedure to isolate DNA was coupled
with PCR amplification of the polyhedrin region.
Baculoviruses are large,
double-stranded, circular DNA viruses, which are infective to
invertebrates. These viruses are mostly found in insects and have been
reported to infect over 600 insect species (21).
Baculoviruses have been employed to control important agricultural
(10, 26) and forest (2, 20, 30) insect pests.
However, this use of baculoviruses has been limited by the long length
of time required for these viruses to kill their insect hosts. Genetic
engineering of baculoviruses has enhanced their speed of killing, and
it could potentially expand the use of these viruses as agents of
insect control.
Baculoviruses are classified in the family Baculoviridae,
presenting two genera, Nucleopolyhedrovirus and
Granulovirus (27). Virions of
nucleopolyhedroviruses (NPVs) and granuloviruses (GVs) are occluded in
large protein crystals, which are mostly formed by a single protein,
called polyhedrin in NPVs and granulin in GVs. The occlusion bodies
protect the virus particles, conferring resistance to solubilization,
except under strong alkaline conditions (31). These
properties enable baculoviruses to remain viable for many years outside
the insect host, with the soil being the major long-term reservoir for
these viruses in the environment (5, 6). Many studies have
reported the persistence of baculoviruses in soil for periods of up to
5 years (4, 16, 23). Therefore, the detection of
baculoviruses in the environment, especially in the soil, is extremely
important to the study of the ecology and environmental fate of both
wild-type and genetically engineered baculoviruses.
The detection of baculovirus polyhedra varies in sensitivity according
to soil type (7, 9) and pH (11). Polyhedra are
adsorbed by soil particles mainly by Coulomb forces; that is,
negatively charged polyhedra are retained on the positively charged
sites of the soil particles (11). Different reagents have
been used to extract baculovirus polyhedra from soil, with efficiencies
of polyhedra recovery ranging from 7% for cytoplasmic polyhedrosis
virus (12) to 24% for Autographa californica NPV (AcMNPV) (39). There are no reports of the direct
detection of baculovirus DNA from soil. Nonetheless, DNA from bacteria
(1, 13, 14, 29, 37) and viruses such as enteroviruses
(34) has been directly extracted from soil and sediments
before amplification by PCR. The main challenge regarding the
extraction of DNA from soil is the presence of humic acids and phenolic
compounds that are coextracted with the DNA and are inhibitory to
enzymes used in DNA manipulation, such as restriction endonucleases and
DNA polymerases (35, 36).
The objectives of this study were to develop a method for extracting
baculovirus DNA from soil for further PCR amplification and to use the
developed method to detect baculovirus DNA from field samples collected
over a 1-year period after virus application. The Anticarsia
gemmatalis NPV (AgMNPV) was chosen as a model because of its widespread use in Brazil and potential for use in southeastern United States to control the velvet bean caterpillar in soybeans. The
abilities to detect baculovirus polyhedra and DNA in the soil will be
useful tools in studies seeking to better understand baculovirus epizootics in general, to elucidate their environmental fate, and to
assess risks associated with the release of genetically improved baculoviruses.
Polyhedral extraction and viral DNA purification.
A series
of experiments were performed to optimize the extraction of baculovirus
DNA from soil samples for subsequent PCR amplification. The treatments
consisted of 0.25 g of an autoclaved Dothan loamy fine sand soil
collected from soybean fields being placed in 1.5-ml microcentrifuge
tubes and inoculated with 50 µl of different dilutions of
AgMNPV polyhedra. The soil samples were autoclaved to ensure
that the only baculovirus present in the samples was AgMNPV
at the viral concentration inoculated per treatment, in order to
compare the sensitivities of two DNA extraction methods. The viral
concentrations tested were 107, 105,
104, 103, 102, 101, and
1 polyhedron per 0.25 g of soil. The last concentration of virus
was tested only in the magnetic capture-hybridization (MCH)
experiments. Two different methods were tested, and their efficiencies
in extracting baculovirus DNA were compared.
Phenol-ether extraction.
The phenol-ether extraction method
consisted of the extraction of humic acids by incubating soil samples
in 1.0 ml of 1 M Na4P2O7 at pH 7.0 for 4 h in a rotary shaker at room temperature. The solution was
centrifuged at 12,000 × g for 10 min in a
microcentrifuge, and the pellet was resuspended in 1.0 ml of TE buffer
(10 mM Tris, 1 mM EDTA [pH 8.0]). The solution was centrifuged again
at 12,000 × g for 10 min. The pellet was subsequently
resuspended and incubated for 2 h in a solution containing 500 µl of TE buffer, 200 µl of a 3× dilute alkaline solution (0.3 M
Na2CO3, 0.03 M EDTA, 0.51 M NaCl) plus 500 µl
of 0.2 M NaOH to disrupt AgMNPV polyhedra. Sodium hydroxide
is also known to extract humic acids from soil (33). The
alkali-released virus was centrifuged at 1,800 × g for
5 min, to remove unsolubilized polyhedra and soil particles, and the
supernatant was centrifuged again at 12,000 × g for 20 min at 4°C. The pellet was resuspended in 500 µl of TE buffer and
incubated with 20 µl of proteinase K (5 mg/ml) overnight at 37°C or
for 2 h at 65°C in order to degrade the viral envelopes and
capsids. The virus DNA was then purified with successive phenol-ether extractions (three times each) and was subsequently used for PCR amplification of the polyhedrin gene (polh).
MCH.
The MCH method was modified from that described by
Jacobsen (14, 15). The method uses streptavidin-coated
magnetic beads (M-280; Dynal, Inc., Lake Success, N.Y.) conjugated to a
biotinylated probe specific for the AgMNPV polh
region to capture AgMNPV DNA by hybridization from soil
samples. The biotinylated probe contained a biotin molecule on a
five-carbon atom spacer arm incorporated at the 5' end of the
oligonucleotide. The oligonucleotide was 103 bp long (positions +240 to
+343 of polh) (40), and it was purified by
high-pressure liquid chromatography (DuPont, Inc., Wilmington, Del.).
Before conjugation, 200 µl of a 10-mg/ml suspension of streptavidin
magnetic beads was washed three times with a solution containing 400 µl of phosphate-buffered saline (PBS) (2.65 mM KCl, 1.46 mM
KH2HPO4, 136.9 mM NaCl, 8.0 mM
Na2HPO4) and 0.1% sodium dodecyl sulfate at pH
7.1 to remove sodium azide (part of the storage buffer). This amount of
beads is enough for 10 hybridization reactions. The magnetic beads were
resuspended in a solution containing 200 µl of TE buffer and 1 M NaCl
and conjugated to the biotinylated probe (approximately 100 ng) by
1 h of rotatory incubation at room temperature in a hybridization
oven (OV3; Biometra, Inc., Tampa, Fla.). Following conjugation, the
beads were washed three times with 400 µl of TE and 1 M NaCl and
incubated for 15 min in the hybridization oven at room temperature in a
solution containing 400 µl of 0.125 M NaOH and 0.1 M NaCl. After this
incubation, the conjugated beads were washed three times with the
solution containing 400 µl of TE and 1 M NaCl to remove any NaOH
and residual cDNA. The beads were then resuspended in 200 µl of
sterile distilled (SD) H2O and used for hybridization.
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Methods for Detection of Anticarsia
gemmatalis Nucleopolyhedrovirus DNA in Soil

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ABSTRACT
Top
Abstract
Introduction
Materials and Methods
References
![]()
INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
References
![]()
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials and Methods
References
PCR conditions. PCR amplification of the AgMNPV polh was performed as described elsewhere (24). The temperature program was run for 40 cycles. The DNA template was diluted 10- or 100-fold after the target DNA was obtained by the phenol-ether procedure. When the template DNA was obtained through the MCH procedure, PCR was performed in a total volume of 50 µl, containing 25 µl of resuspended beads and 25 µl of PCR master mix. The PCRs were carried out at a 200 µM final concentration of each deoxynucleoside triphosphate, 10 pmol of each primer, 2.5 mM MgCl2, and 0.5 U of Primezyme and corresponding buffer (Biometra, Inc.). Each reaction tube was covered with 50 µl of mineral oil to prevent reagent evaporation. The PCR primers utilized in this study were 100% homologous to AgMNPV. They were derived from conserved sequences within the coding region of polh (40) and their DNA sequences are 5' TA(CT)GTGTA(CT)GA(CT)AACAA(GA)T 3' (forward) and 5' TTGTA(GA)AAGTT(CT)TCCCA(AG)AT 3' (reverse) (24). The amplification products were analyzed by 0.7% Seakem LE agarose (FMC, Inc.) gel electrophoresis in Tris-acetate-EDTA buffer stained with ethidium bromide.
AgMNPV detection from field soil samples.
Viral
inocula of the AgMNPV-2D genomic variant were obtained by
injecting 5 µl of extracellular virus (50% tissue culture infective
dose = 106 viruses/ml) into the hemocoel of
fourth-instar A. gemmatalis. Moribund larvae were frozen,
and their polyhedra were purified by standard procedures
(22). The amount of polyhedra was estimated by counting in a
hemacytometer chamber. AgMNPV-2D was applied to
300-m2 soybean plots at the North Florida Research and
Education Center, University of Florida, Quincy. The virus was applied
on 30 August 1995 with a dose of 1.0 × 1011
polyhedra/ha, as recommended for AgMNPV (26). The
experiment consisted of two replicates of AgMNPV-2D-treated
soybean plots and two replicates of control plots (i.e., plots in which
no virus was applied). The soybean plots were separated by a buffer
zone of 30 m, and the four outer soybean rows of each plot served
as borders. The soil was classified as a Dothan loamy fine sand and contained 70 to 85% sand, 10 to 20% clay, and 0 to 30% silt. Soil samples from the top 15 cm of five sampling sites in each plot were
collected with a core sampler. Soil samples weighed 69 g on
average. Control and AgMNPV-2D treatments were sampled at 1, 15, 45, 75, 180, and 330 days after virus application. The soil samples
were collected in individual plastic bags, put on ice, and taken to the
laboratory to be frozen at
20°C. In the laboratory, each soil
sample was homogenized manually, and a 0.5-g subsample was used for
baculovirus DNA extraction by the MCH procedure. A total of 10 0.5-g
soil subsamples were analyzed by PCR for each treatment and each
sampling date. Aliquots of the extracted DNA were used in PCR
amplification experiments for the detection of AgMNPV,
targeting the coding region of the polh (24).
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RESULTS AND DISCUSSION |
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Optimization of DNA extraction methods. The phenol-ether procedure extracted humic acids from soil by sequential incubation in sodium pyrophosphate and sodium hydroxide and then purified the viral DNA by successive phenol-ether extractions. Baculovirus DNA extractions by this method removed large amounts of humic acids from the soil samples, but there was still some inhibition during PCR amplification. Therefore, DNA samples had to be diluted 10- or 100-fold to be used in PCR experiments. A detection limit experiment repeated on three separate occasions showed that the limits of detection for this procedure ranged from 1.1 × 104 (in two experiments) to 1.1 × 105 (in one experiment) AgMNPV genome copies per g of soil, which corresponds to 4 × 102 to 4 × 103 polyhedra per g of soil (data not shown).
The MCH procedure used to isolate AgMNPV DNA from soil was efficient in removing humic acids and other inhibitors. Therefore, DNA aliquots were added directly in PCRs without dilution. Four replications of the same experiment determined that the detection limit for this procedure was 1.1 × 102 to 1.1 × 103 genome copies per g of soil, which is equivalent to 4 to 40 polyhedra per g of soil. The lowest limit of detection was obtained in three of the four experiments performed, and the results for one of these experiments are shown in Fig. 1 (lane 9). The size of the polyhedrin PCR product, which was 575 bp, and the decrease in intensity of the PCR products, resulting from smaller amounts of AgMNPV polyhedra being inoculated in the soil samples, are also shown in Fig. 1.
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AgMNPV detection from field soil samples. MCH followed by PCR amplification of the polh region did not detect AgMNPV DNA in soil samples collected from control plots and AgMNPV-2D treatments 1 day after virus application. In contrast, AgMNPV DNA was detected in 70, 100, 80, and 80% of soil samples collected from the AgMNPV-2D treatments at 15, 45, 75, and 180 days postapplication, respectively. AgMNPV DNA was not detected in soil from control plots 15 days postapplication, but it was detected in 40, 20, and 10% of the soil samples from control plots collected at 45, 75, and 180 days postapplication, respectively. No viral DNA was detected from soil samples collected 330 days postapplication (Fig. 2).
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ACKNOWLEDGMENTS |
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We thank A. Ogram for helpful criticism of earlier drafts and Alejandra Garcia-Maruniak for technical support and for help in revising the manuscript.
We thank DuPont Agricultural Enterprise, especially L. Flexner and J. Presnail, for providing financial support to develop the MCH method. R. R. de Moraes was supported by a Ph.D. fellowship from CNPq-Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazilian Ministry of Science and Technology.
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FOOTNOTES |
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* Corresponding author. Mailing address: Entomology and Nematology Department, University of Florida, P.O. Box 110620, Gainesville, FL 32611. Phone: (352) 392-1901. Fax: (352) 392-0190. E-mail: marun{at}nervm.nerdc.ufl.edu.
Publication no. R-06242 of the Florida Agricultural Experiment Station.
Present address: DuPont Ag Enterprises, Stine-Haskell Research
Center, Newark, DE 19714.
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