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Journals / Artvin Çoruh Üniversitesi Orman Fakültesi Dergisi / 2026 / Cilt: 27 Sayı: 4

Integration of Metagenomic and Classical Diagnostic Approaches for Phytopathogen Detection

Fitopatojenlerin Tespitinde Metagenomik ve Klasik Tanı Yöntemlerinin Entegrasyonu

Erşan Selvi(Ege Ormancılık Araştırma Enstitüsü Müdürlüğü)0000-0002-4278-4611
Tuğba Doğmuş Lehtijarvi(ISPARTA UYGULAMALI BİLİMLER ÜNİVERSİTESİ, ORMAN FAKÜLTESİ, ORMAN MÜHENDİSLİĞİ BÖLÜMÜ, ORMAN MÜHENDİSLİĞİ PR.)0000-0002-4971-0922
Pages
1–25
Publication Date
2026-10-08
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

In addition, a user-oriented decision framework is presented to guide the selection of the most appropriate method according to study objectives, budget, time requirements, and the need for validation.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Fungi and oomycetes that cause disease in forest ecosystems have become a greater threat to biosecurity with increasing global trade, the movement of plant material, and climate change.
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Key Findings & Data:In response to this threat, early detection and accurate species identification are critical not only for disease management, but also for quarantine, surveillance, and the protection of forest health.
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Conclusion & Impact:In addition, a user-oriented decision framework is presented to guide the selection of the most appropriate method according to study objectives, budget, time requirements, and the need for validation.
🔬Design:Review & Systematic Survey
📍Scope:Comprehensive Sample
⚙️Variables:Orman patolojisi · Mantar patojenleri · Oomisetler

Abstract

Fungi and oomycetes that cause disease in forest ecosystems have become a greater threat to biosecurity with increasing global trade, the movement of plant material, and climate change. In response to this threat, early detection and accurate species identification are critical not only for disease management, but also for quarantine, surveillance, and the protection of forest health. In this regard, this review provides not only a laboratory-based diagnostic assessment from a forest engineering perspective, but also practical decision support to ensure that decisions regarding nursery inspections, field surveillance, quarantine measures, risk prioritization, and disease control are based on more scientific data. Diagnostic methods used in forest pathology have historically progressed from classical approaches such as field observation, isolation, culturing, and morphological identification to serological tests, PCR-based molecular methods, quantitative PCR (qPCR), droplet digital PCR (ddPCR), isothermal amplification systems, and ultimately metagenomic approaches based on high-throughput sequencing. This developmental trajectory is not accidental; each new method emerged from the need to overcome the limitations of preceding approaches in terms of speed, sensitivity, specificity, scope, or field applicability. In this review, the historical progression from classical diagnostic methods to metagenomic approaches is discussed, with particular emphasis on the limitations that led to the development of each method and the reasons why they should now be used in an integrated manner. In addition, a user-oriented decision framework is presented to guide the selection of the most appropriate method according to study objectives, budget, time requirements, and the need for validation.

Özet

Orman ekosistemlerinde hastalık oluşturan mantar ve oomisetler, artan küresel ticaret, bitki materyali taşınımı ve iklim değişikliğiyle birlikte biyogüvenlik açısından daha büyük bir tehdit haline gelmiştir. Bu tehdit karşısında erken teşhis ve doğru tür tayini, yalnızca hastalık yönetimi için değil, aynı zamanda karantina, sürveyans ve orman sağlığının korunması için de kritik önemdedir. Bu yönüyle bu derleme, orman mühendisliği açısından yalnızca laboratuvar temelli bir tanı değerlendirmesi değil, aynı zamanda fidanlık denetimi, saha sürveyansı, karantina uygulamaları, risk önceliklendirmesi ve hastalıkla mücadele kararlarının daha bilimsel verilere dayandırılması için pratik bir karar desteği sunmaktadır. Orman patolojisinde kullanılan tanı yöntemleri tarihsel olarak saha gözlemi, izolasyon, kültür ve morfolojik tanımlama gibi klasik yaklaşımlardan başlamış; daha sonra serolojik testler, PCR temelli moleküler yöntemler, gerçek zamanlı PCR (qPCR), damlacık dijital PCR (ddPCR), izotermal amplifikasyon sistemleri ve nihayet yüksek başarımlı dizileme tabanlı metagenomik yaklaşımlara doğru evrilmiştir. Bu gelişim çizgisi rastlantısal değildir; her yeni yöntem, kendisinden önceki yaklaşımın hız, duyarlılık, özgüllük, kapsam ya da sahaya uygulanabilirlik bakımından bıraktığı boşlukları doldurma ihtiyacından doğmuştur. Bu derlemede, klasik tanı yöntemlerinden metagenomik yaklaşımlara uzanan tarihsel gelişim çizgisi üzerinden, her yöntemin hangi sınırlılıklar nedeniyle geliştirildiği ve günümüzde neden entegre biçimde kullanılmaları gerektiği tartışılmaktadır. Ayrıca amaca, bütçeye, hız gereksinimine ve doğrulama ihtiyacına göre hangi yöntemin ne zaman tercih edilmesi gerektiğine ilişkin kullanıcı odaklı bir karar çerçevesi de sunulmaktadır.

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Cite This Article

Selvi, E., Lehtijarvi, T. D. (2026). Integration of Metagenomic and Classical Diagnostic Approaches for Phytopathogen Detection. Artvin Çoruh Üniversitesi Orman Fakültesi Dergisi, Cilt: 27 Sayı: 4, 1–25. https://doi.org/10.17474/artvinofd.1953874

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