Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae)

Amplifying microbial DNA by the polymerase chain reaction (PCR) from single phytoseiid mites has been difficult, perhaps due to the low titer of bacteria and to interference by the relatively larger amounts of mite genomic DNA. In this paper we evaluate the efficiency of standard and high-fidelity PCR protocols subsequent to amplification of the whole genome by a multiple displacement amplification (MDA) procedure developed by Dean et al. DNA from the phytoseiid Phytoseiulus persimilis (Athias-Henriot) was tested because it lacks a Cytophaga-like organism (CLO) and we could add known amounts of a plasmid containing a cloned 16S rRNA gene fragment from a CLO from Metaseiulus occidentalis (Nesbitt). P. persimilis genomic DNA was mixed with the serially diluted plasmid and amplified using MDA followed by either standard or high-fidelity PCR. MDA followed by high-fidelity PCR was most efficient and successfully amplified an expected 1.5-kb band from as little as 0.01fg of the plasmid, which is equivalent to about 1 copy. MDA followed by high-fidelity PCR also consistently amplified Wolbachia- or CLO-specific products from naturally infected single females or eggs of M. occidentalis, which will allow detailed studies of infection frequency and transmission of several microorganisms associated with this predatory mite.     

First divergence time estimate of spiders,scorpions, mites and ticks (subphylum: Chelicerata) inferred from mitochondrial phylogeny

Spiders, scorpions, mites and ticks (chelicerates) form one of the most diverse groups of arthropods on land, but their origin and times of diversification are not yet established. We estimated, for the first time, the molecular divergence times for these chelicerates using complete mitochondrial sequences from 25 taxa. All mitochondrial genes were evaluated individually or after concatenation. Sequences belonging to three missing genes (ND3, 6, and tRNA-Asp) from three taxa, as well as the faster-evolving ribosomal RNAs (12S and 16S), tRNAs, and the third base of each codon from 11 protein-coding genes (PCGs) (COI-III, CYTB, ATP8, 6, ND1-2, 4L, and 4-5), were identified and removed. The remaining concatenated sequences from 11 PCGs produced a completely resolved phylogenetic tree and confirmed that all chelicerates are monophyletic. Removing the third base from each codon was essential to resolve the phylogeny, which allowed deep divergence times to be calculated using three nodes calibrated with upper and lower priors. Our estimates indicate that the orders and classes of spiders, scorpions, mites, and ticks diversified in the late Paleozoic, much earlier than previously reported from fossil date estimates. The divergence time estimated for ticks suggests that their first land hosts could have been amphibians rather than reptiles. Using molecular data, we separated the spider-scorpion clades and estimated their divergence times at 397 ± 23 million years ago. Algae, fungi, plants, and animals, including insects, were well established on land when these chelicerates diversified. Future analyses, involving mitochondrial sequences from additional chelicerate taxa and the inclusion of nuclear genes (or entire genomes) will provide a more complete picture of the evolution of the Chelicerata, the second most abundant group of animals on earth. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A new approach for enhanced multiplication of arbuscular mycorrhizal fungi and isolation of ITS regions from Glomus deserticola and Laccaria fraterna

Rootlets induced from the petiole base of L. purpureus, using IAA and kinetin was used for enhanced multiplication of arbuscular mycorrhizal (AM) fungus, G. deserticula. Using conserved short arbitrary oligonucleotides, as specific primers, we amplified the ITS-region, a molecular marker for fungal identification, from the genomic DNA extracted from cultured spores of G. deserticola, and genomic DNA extracted from the mycelium of L. fraterna. The capacity of fungal colonization and subsequent spore formation of G. deserticola, compared with the natural root system was evaluated. This technology would provide a simple way to multiply AM fungi and to produce spores without microbial contamination useful for further molecular characterization.     

Long PCR Is a Sensitive Method for Detecting Liberobacter asiaticum in Parasitoids Undergoing Risk Assessment in Quarantine

The accidental importation of plant pathogens in or on the bodies of parasitoids imported as natural enemies has been raised as a potential risk of classical biological control projects involving insects that serve as vectors of plant diseases. During quarantine evaluation of two parasitoids, Tamarixia radiata Waterston and Diaphorencyrtus aligarhensis (Shafee, Alam and Agarwal), imported for classical biological control of Asian citrus psylla Diaphorina citri (Kuwayama) in Florida, we were asked to determine whether these parasitoids were free of the causal agent of Asian greening disease, the bacterium Liberobacter asiaticum. Preliminary tests with allele-specific polymerase chain reaction (Standard PCR) suggested that the assays were prone to false negatives. Another PCR protocol, Long PCR, previously was shown to be more reliable than Standard PCR for screening of insects for another bacterium (Wolbachia). The sensitivity of Long and Standard PCR protocols was compared by use of plasmid DNA containing two DNA fragments from the greening disease agent or plasmid mixed with DNA extracted from host plants, psyllids, or parasitoids. Results indicated that inhibitors of the PCR were present in both plant and insect DNA, making the Standard PCR relatively insensitive and allowing high levels of false negatives. Long PCR, which incorporates a second DNA polymerase with proof-reading activity, yielded consistent results and was orders of magnitude more sensitive than the Standard PCR. As few as 100 copies of plasmid mixed with either plant or insect DNA consistently could be detected. Long PCR assays conducted on pooled and individual T. radiata and D. aligarhensis, their psyllid hosts, or their host plants over a period of 6 months failed to produce any positives, indicating that release of these two parasitoids should elicit little concern that greening bacteria would be introduced accidentally into Florida through this classical biological control program.     

Effect of RH-2485 on development, metamorphosis and synthesis of major proteins in female silkworm Bombyx mori

Toxicological data on silkworm Bombyx mori are quite comparable to those of other lepidopteran pest insects, therefore, it is considered as a suitable model for exploring effects of any new synthetic formulations. In this study, female V instar larvae of silk moth B. mori were chosen to evaluate the lethal and sublethal toxicity effects of RH-2485 (methoxyfenozide), a non-steroidal ecdysteroid agonist and to substantiate the ecdysteroid mimicking action of RH-2485 on ovary development, vitellogenin incorporation and egg production in isolated pupal abdomen (IPA). Probit analysis was carried out to find the median lethal dose (LD₅₀) from 96 h cumulative mortality percent. Protein profile of haemolymph, fat body, ovary and eggs were separated in SDS-PAGE. Western blot analysis was carried out to confirm vitellogenin in the ovary. Sublethal effects on feeding, cocoon spinning, pupation, adult emergence and egg production were studied at doses of 1/5^th, 1/10^th and 1/20^th of LD₅₀. Significant changes were observed in all these parameters at all three sublethal doses. The morphological effects were related to underlying biochemical changes by finding the changes in haemolymph, fat body, ovary and egg protein profile. Marked changes were observed in storage proteins (80 kDa) and 30 kDa proteins in the haemolymph at all three sublethal doses. The larvae that escaped the sublethal effects at a dose of 1/20 of LD₅₀ and emerged as adults with malformed wings produced significantly lower number of eggs. The isolated pupal abdomen (IPA) treated with RH-2485 did not metamorphose into adult but the oocyte development and vitellogenesis were normal but the egg precursor processing was incomplete leading to failure in choriogenesis.     

Effect of Ash Pond Soil and Amendments on the Growth and Arbuscular Mycorrhizal Colonization of Allium cepa and Germination of Arachis hypogaea,Lycopersicon esculentum,and Vigna mungo Seeds

The effect of fly ash pond soil on the growth and yield of onion (Allium cepa var. microaggregatum) plants grown in pots was investigated. The fly ash pond soil was amended with combinations of red soil and press mud, a waste product from sugar mills. Water-holding capacity of ash pond soil amended with press mud increased; however, addition of press mud delayed onion bulb development. Onion bulb germination took place rapidly in ash pond soil; however, subsequent bulb development declined. The addition of red soil and press mud increased the growth and yield of onion plants. In all the soils and amendments, onion plant roots were colonized by native arbuscular mycorrhizal species. Both vesicles and arbuscules were present in the roots. Colonization was low in ash pond soil but increased with the addition of red soil. Effect of fly ash pond soil on germination of groundnut (Arachis hypogaea), tomato (Lycopersicon esculentum), and black gram (Vigna mungo) seeds was evaluated and compared with red soil in the laboratory. Ash pond soil increased the germination of tomato seeds but did not affect the germination of groundnut and black gram seeds.     

The mitochondrial genome of the predatory mite Metaseiulus occidentalis (Arthropoda: Chelicerata: Acari: Phytoseiidae) is unexpectedly large and contains several novel features

The complete mitochondrial genome of the phytoseiid Metaseiulus occidentalis (Arthropoda: Chelicerata: Acari: Phytoseiidae) has been sequenced. It is 24,961 bp in length and contains a 14,695-bp unique region, a 345-bp triplicated region, and a 9921-bp duplicated region, in that order. The A+T content of the unique region is 76.9% and contains 11 protein coding (COI-III; ATP6-8; CytB; ND1, 2, 4, 5 and 4L), two ribosomal RNA (srRNA and lrRNA), 22 transfer RNA (tRNA) genes, and two copies of D-loop control sequence. Two genes (ND3 and 6) appear to be missing, but there is a large intergenic spacer (390 bp) present, which could contain ND3 if a different codon usage is employed. The gene order is completely different from the pattern in all other known chelicerates, including the horseshoe crab Limulus polyphemus [Lavrov et al., Mol. Biol. Evol., 2000; 17:813-824]. All the inferred tRNA genes are missing the TPsiC arm, but this arm has fused with the variable arm to generate a TV replacement loop. The duplicated region (9921 bp) contains 18 genes in the same order as in the unique region from CytB to tRNA-His, plus one copy of D-loop control sequence (311 bp) and a partial tRNA-Leu2 sequence (34 bp). The small triplicated region (345 bp) contains a D-loop control sequence (311 bp) and a partial tRNA-Leu2 sequence (34 bp). Because of these anomalies, amplifying sequences posed technical difficulties, but were accomplished by using a primer-walking strategy and increasing the AT content to 75% in the high-fidelity PCR dNTP mix. This is the first phytoseiid mitochondrial genome to be completely sequenced and the largest (25 kb) detected from the Chelicerata.     

A DNA extraction procedure that allows mite specimens to be slide mounted: phytoseiid species evaluated as a model

Four protocols for extracting DNA from mites, using phytoseiid species as exemplars, were evaluated to determine whether the DNA obtained could be used to amplify nuclear, mitochondrial or Random Amplified Polymorphic DNA (RAPD) markers from males, females and eggs. Protocol 3 was identified as the best and this allowed High-fidelity PCR (Hf-PCR) and Hf-RAPD PCR to be used successfully; it left behind the intact body of adult mites so they could be slide mounted for morphological analyses, although the eggs had to be pricked in order to yield sufficient DNA for amplifications. Protocol 3 involved soaking intact specimens in a GuSCN buffer and using a silica matrix, which binds nucleic acids, to yield DNA for amplification. The DNA isolated could be stored up to a month, indicating that the quality was good. This DNA extraction protocol will allow researchers to collect mites, store them in 95% ethanol, and subsequently extract sufficient DNA from single adults or eggs to provide diagnostic PCR products from both nuclear and mitochondrial DNA, yet leave the bodies intact for morphological analyses.