Use of loop-mediated isothermal ampliflcation for detection of Ophiostoma clavatum, the primary blue stain fungus associated with Ips acuminatus

Applied and Environmental Microbiology

Volumn 79, Issue 8, 2013, Pages 2527-2533

  Villari, Caterina ^a   Tomlinson, Jennifer ^b   Battisti, Andrea ^a   Boonham, Neil ^b   Capretti, Paolo ^c   Faccoli, Massimo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b FOOD AND ENVIRONMENT RESEARCH AGENCY   (United Kingdom)

^c UNIVERSITY OF FLORENCE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BARK BEETLE; BLUE STAIN; LAMP TECHNOLOGY; MOLECULAR TOOLS; PINUS SYLVESTRIS; SAMPLING SITE; SCOTS PINE;

ASSAYS; FUNGI; ISOTHERMS; POPULATION STATISTICS;

FORESTRY;

AMPLIFICATION; BEETLE; BIOASSAY; COLONIZATION; DATA ACQUISITION; FUNGUS; INFECTIOUS DISEASE; PATHOGEN; POPULATION CHARACTERISTICS; SAMPLING; SPECIES DIVERSITY; SURVEYING; SYMBIOSIS;

ANIMAL; ARTICLE; BEETLE; CLASSIFICATION; GENETICS; METHODOLOGY; MICROBIOLOGY; NUCLEIC ACID AMPLIFICATION; OPHIOSTOMA; SCOTS PINE; SYMBIOSIS;

ANIMALS; BEETLES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OPHIOSTOMA; PINUS SYLVESTRIS; SYMBIOSIS;

BIOLOGICAL POPULATIONS; FORESTRY; FUNGI; ISOTHERMS; STATISTICS;

NEW ZEALAND; SOUTH ISLAND; SOUTHERN ALPS;

FUNGI; HEXAPODA; IPS ACUMINATUS; OPHIOSTOMA; OPHIOSTOMA BRUNNEO-CILIATUM; PINUS SYLVESTRIS; SCOLYTINAE;

EID: 84876197374     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03612-12     Document Type: Article

References (54)

1. Lieutier F, Day KR, Battisti A, Grégoire J-C, Evans HF (ed). 2004. Bark and wood boring insects in living trees in Europe, a synthesis. Springer, Dordrecht, Netherlands.
2. Raffa KF, Aukema BH, Bentz BJ, Carroll AL, Hicke JA, Turner MG, Romme WH. 2008. Cross-scale drivers of natural disturbances prone to anthropogenic ampliflcation: the dynamics of bark beetle eruptions. Bioscience 58:501-517.
3. Kirisits T. 2004. Fungal associates of European bark beetles with special emphasis on the ophiostomatoid fungi, p 181-236. In Lieutier F, Day KR, Battisti A, Gŕegoire J-C, Evans HF (ed), Bark and wood boring insects in living trees in Europe, a synthesis. Springer, Dordrecht, Netherlands.
4. Paine TD, Raffa KF, Harrington TC. 1997. Interactions among scolytid bark beetles, their associated fungi, and live host conifers. Annu. Rev. Entomol. 42:179-206.
5. Six D. 2012. Ecological and evolutionary determinants of bark beetle-fungus symbioses. Insects 3:339-366.
6. Lieutier F, Yart A, Salle A. 2009. Stimulation of tree defenses by Ophiostomatoid fungi can explain attack success of bark beetles on conifers. Ann. For. Sci. doi:10.1051/forest/2009066.
7. Coulson RN. 1979. Population dynamics of bark beetles. Annu. Rev. Entomol. 24:417-447.
8. Wallner WE. 1987. Factors affecting insect population dynamics: differences between outbreak and non-outbreak species. Annu. Rev. Entomol. 32:317-340.
9. Raffa KF, Berryman AA. 1983. The role of host plant resistance in the colonization behavior and ecology of bark beetles (Coleoptera: Scolytidae). Ecol. Monogr. 53:27-49.
10. Hofstetter RW, Cronin JT, Klepzig KD, Moser JC, Ayres MP. 2006. Antagonisms, mutualisms and commensalisms affect outbreak dynamics of the southern pine beetle. Oecologia 147:679-691.
11. Solheim H. 1993. Ecological aspects of fungi associated with Ips typographus in Norway, p 235-242. In Wingfleld MJ, Seifert KA, Webber JF (ed), Ceratocystis and Ophiostoma: taxonomy, ecology and pathogenicity. APS Press, St. Paul, MN.
12. Solheim H. 1993. Fungi associated with the spruce bark beetle Ips typographus in an endemic area in Norway. Scand. J. For. Res. 8:118-122.
13. Harding S. 1989. The influence of mutualistic blue-stain fungi on bark beetle population dynamics. Ph.D. thesis. Royal Veterinary and Agricultural University, Copenhagen, Denmark.
14. Kirisits T. 2001. Studies on the association of ophiostomatoid fungi with bark beetles in Austria with special emphasis on Ips typographus and Ips cembrae and their associated fungi Ceratocystis polonica and Ceratocystis laricicola. Ph.D. thesis. Universität für Bodenkultur, Vienna, Austria.
15. Colombari F, Schroeder L, Battisti A, Faccoli M. 2013. Spatio-temporal dynamics of an Ips acuminatus outbreak and implications for management. Agric. For. Entomol. 15:34-42.
16. Batra LR. 1967. Ambrosia fungi: a taxonomic revision, and nutritional studies of some species. Mycologia 59:976-1017.
17. Francke-Grosmann H. 1963. Die Übertragung der Pilzflora bei dem Borkenkäfer Ips acuminatus Gyll.: ein Eintrag zur Kenntnis der IpidenSymbiosen. J. Appl. Entomol. 52:355-361.
18. Harrington TC, Aghayeva DN, Fraedrich SW. 2010. New combinations in Raffaelea, Ambrosiella, and Hyalorhinocladiella, and four new species from the redbay ambrosia beetle, Xyleborus glabratus. Mycotaxon 111: 337-361.
19. Guérard N, Dreyer E, Lieutier F. 2000. Interactions between Scots pine, Ips acuminatus (Gyll.) and Ophiostoma brunneo-ciliatum (Math.): estimation of the critical thresholds of attack and inoculation densities and effects on hydraulic properties in the stem. Ann. For. Sci. 57:681-690.
20. Lieutier F, Garcia J, Yart A, Vouland G, Pettinetti M, Morelet M. 1991. Ophiostomatales (Ascomycetes) associated with Ips acuminatus Gyll (Coleoptera, Scolytidae) in Scots pine (Pinus sylvestris L) in South-Eastern France, and comparison with Ips sexdentatus Boern. Agronomie 11:807-817.
21. Villari C, Battisti A, Chakraborty S, Michelozzi M, Bonello P, Faccoli M. 2012. Nutritional and pathogenic fungi associated with the pine engraver beetle trigger comparable defenses in Scots pine. Tree Physiol. 37: 867-879.
22. Mathiesen-Käärik A. 1953. Eine Übersicht uber die gewöhnlichsten mit Borkenkäfern assoziierten Bläuepilze in Schweden und einige für Sweden neue Bläuepilze. Meddn. St. SkogsforskInst. 43:1-74.
23. Mathiesen A. 1950. Über einige mit Borkenkäfern assoziierte Bläuepilze in Schweden. Oikos 2:275-308.
24. Mathiesen A. 1951. Einige neue Ophiostoma-Arten in Schweden. Sven. Bot. Tids. 45:203-232.
25. Rennerfelt E. 1950. Über den Zusammenhang zwischen dem Verblauen des Holzes und den Insekten. Oikos 2:120-137.
26. Zipfel RD, de Beer ZW, Jacobs K, Wingfleld BD, Wingfleld MJ. 2006. Multi-gene phylogenies deflne Ceratocystiopsis and Grosmannia distinct from Ophiostoma. Stud. Mycol. 55:75-97.
27. Luchi N, Mancini V, Feducci M, Santini A, Capretti P. 2011. Leptoglossus occidentalis and Diplodia pinea: a new insect-fungus association in Mediterranean forests. For. Pathol. 42:246-251.
28. Roets F, Wingfleld MJ, Dreyer LL, Crous PW, Bellstedt DU. 2006. A PCR-based method to detect species of Gondwanamyces and Ophiostoma on surfaces of insects colonizing Protea flowers. Can. J. Bot. 84:989-994.
29. Schweigkofler W, Otrosina WJ, Smith SL, Cluck DR, Maeda K, Peay KG, Garbelotto M. 2005. Detection and quantiflcation of Leptographium wageneri, the cause of black-stain root disease, from bark beetles (Coleoptera: Scolytidae) in Northern California using regular and real-time PCR. Can. J. For. Res. 35:1798-1808.
30. Haugland RA, Brinkman N, Vesper SJ. 2002. Evaluation of rapid DNA extraction methods for the quantitative detection of fungi using real-time PCR analysis. J. Microbiol. Methods 50:319-323.
31. Ma Z, Michailides TJ. 2007. Approaches for eliminating PCR inhibitors and designing PCR primers for the detection of phytopathogenic fungi. Crop Prot. 26:145-161.
32. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. 2000. Loop-mediated isothermal ampliflcation of DNA. Nucleic Acids Res. 28:E63. doi:10.1093/nar/28.12.e63.
33. Parida M, Sannarangaiah S, Dash PK, Rao PVL, Morita K. 2008. Loop mediated isothermal ampliflcation (LAMP): a new generation of innovative gene ampliflcation technique; perspectives in clinical diagnosis of infectious diseases. Rev. Med. Virol. 18:407-421.
34. Nagamine K, Hase T, Notomi T. 2002. Accelerated reaction by loop-mediated isothermal ampliflcation using loop primers. Mol. Cell. Probes 16:223-229.
35. Tomlinson JA, Ostoja-Starzewska S, Adams IP, Miano DW, Abidrabo P, Kinyua Z, Alicai T, Dickinson MJ, Peters D, Boonham N, Smith J. 2012. Loop-mediated isothermal ampliflcation for rapid detection of the causal agents of cassava brown streak disease. J. Virol. Methods doi:10.1016/j.jviromet.2012.07.015.
36. Tomlinson JA, Dickinson MJ, Boonham N. 2010. Rapid detection of Phytophthora ramorum and P. kernoviae by two-minute DNA extraction followed by isothermal ampliflcation and amplicon detection by generic lateral flow device. Phytopathology 100:143-149.
37. Lozzia GC, Rigamonti IE. 2002. Notes on Ips acuminatus Gyll. damaging Pinus sylvestris in Valtellina (Northern Italy) {left open bracket}Lombardy{right open bracket}. Monti Boschi 53:20-22.
38. Faccoli M. 2004. A morphological illustrated key to European species of the genus Ips DeGeer (Coleoptera: Scolytidae). Coleopterist 13:103-119.
39. Luchi N, Capretti P, Surico G, Orlando C, Pazzagli M, Pinzani P. 2005. A real-time quantitative PCR assay for the detection of Sphaeropsis sapinea from inoculated Pinus nigra shoots. J. Phytopathol. 153:37-42.
40. Sabbatini Peverieri G, Capretti P, Tiberi R. 2006. Associations between Tomicus destruens and Leptographium spp. in Pinus pinea and P. pinaster stands in Tuscany, central Italy. For. Pathol. 36:14-20.
41. Gilbert MTP, Moore W, Melchior L, Worobey M. 2007. DNA extraction from dry museum beetles without conferring external morphological damage. PLoS One 2:e272. doi:10.1371/journal.pone.0000272.
42. Patwary MU, Kenchington EL, Bird CJ, Zouros E. 1994. The use of random amplifled polymorphic DNA markers in genetic studies of the sea scallop Placopecten magellanicus (Gmelin, 1791). J. Shellflsh Res. 13:547-553.
43. Linnakoski R, de Beer ZW, Ahtiainen J, Sidorov E, Niemela P, Pappinen A, Wingfleld MJ. 2010. Ophiostoma spp. associated with pine-and spruce-infesting bark beetles in Finland and Russia. Persoonia 25:72-93.
44. Cognato AI, Sperling FAH. 2000. Phylogeny of Ips DeGeer species (Coleoptera: Scolytidae) inferred from mitochondrial cytochrome oxidase I DNA sequence. Mol. Phylogenet. Evol. 14:445-460.
45. Cognato AI, Sun JH. 2007. DNA based cladograms augment the discovery of a new Ips species from China (Coleoptera: Curculionidae: Scolytinae). Cladistics 23:539-551.
46. Stauffer C, Lakatos F, Hewitt GM. 1997. The phylogenetic relationships of seven European Ips (Scolytidae, Ipinae) species. Insect Mol. Biol. 6:233-240.
47. Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7:203-214.
48. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
49. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-speciflc gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
50. Owczarzy R, Tataurov AV, Wu Y, Manthey JA, McQuisten KA, Almabrazi HG, Pedersen KF, Lin Y, Garretson J, McEntaggart NO, Sailor CA, Dawson RB, Peek AS. 2008. IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Res. 36:W163-W169. doi:10.1093/nar/gkn198.
51. Zuur AF, Ieno EN, Walker NJ, Saveliev AA, Smith GM. 2009. Mixed effects models and extensions in ecology with R. Springer, New York, NY.
52. R Development Core Team. 2011, posting date. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org.
53. Bates D, Maechler M, Bolker B. October 2011, posting date. lme4: linear mixed-effects models using S4 classes. R package version 0.999375-42. http://CRAN.R-project.org/package lme4.
54. Klepzig KD, Six DL. 2004. Bark beetle-fungal symbiosis: context dependency in complex associations. Symbiosis 37:189-205.