Effective Use of Microorganisms in Agriculture; Microbial Whole Genome Based Approaches

Abstract

The increasing population, urbanization, climate change, and the pressure on crop production threaten the long-term sustainability and functioning of ecosystems. In this context, the conservation of biodiversity and genetic resources forms the foundation of green sustainable agriculture strategies. Genomic-based research on plant-associated microorganisms has significantly expanded our knowledge of both plant pathogens and Plant Growth-Promoting Bacteria (PGPB). The expression of certain genes in microorganisms in natural environments can be suppressed when cultured under standard laboratory conditions due to the absence of natural triggers or stress signals. This study explores the opportunities provided by genomic approaches in understanding the diversity and functional significance of plant-associated microbiomes in sustainable agriculture. The full biosynthetic capacity of bacterial strains for primary and secondary metabolites, which are key indicators for both direct and indirect PGPB mechanisms, can be revealed through whole-genome sequencing analysis. The bacterial whole-genome approach can uncover determinants of various PGPB traits, including gene clusters involved in symbiotic nitrogen fixation, siderophore diversity, and genes associated with antimicrobial/heavy metal resistance. The use of genomic technologies will enable the modulation of beneficial plant-microorganism interactions, paving the way for the development of promising and environmentally friendly new applications for sustainable agriculture.

Keywords

• biodiversity
• microbial Genomes
• PGPB
• sustainable agriculture.

Tarımda Mikroorganizmaların Etkin Kullanımı; Mikrobiyal Tüm Genom Temelli Yaklaşımlar

Öz

Artan nüfus, şehirleşme, iklim değişikliği ve mahsul üretimi üzerindeki baskı, ekosistemin uzun vadeli sürdürülebilirliğini ve işleyişini tehdit etmektedir. Bu bağlamda, biyoçeşitliliğin ve genetik kaynakların korunması, yeşil sürdürülebilir tarım stratejilerinin önemli bir iş planını oluşturmaktadır. Bitki ile ilişkili mikroorganizmalar üzerine yapılan genom tabanlı araştırmalar hem bitki patojenleri hem de bitki gelişimini destekleyici bakterilerin (PGPB) tarımda kullanımı konusundaki bilgi birikimimizi büyük ölçüde geliştirmiştir. Mikroorganizmaların doğal ortamlardaki bazı gen ifadeleri standart laboratuvar koşullarında kültüre edildiklerinde, doğal tetikleyicilerin veya stres sinyallerinin yokluğundan dolayı baskılanabilmektedir. Bu çalışmada, sürdürülebilir tarımda bitki ile ilişkili mikrobiyom çeşitliliğinin ve işlevsel öneminin anlaşılmasında genomik yaklaşımların sunduğu fırsatlar ele alınmıştır. Bakteriyel suşların primer ve sekonder metabolitler için tam biyosentetik kapasitesi, yani doğrudan ve dolaylı PGPB mekanizmaları için anahtar belirteçler, tüm genom dizisinin analizi ile ortaya çıkarılabilmektedir. Bakteriyel tüm genom yaklaşımı simbiyotik azot fiksasyonunda rol oynayan gen kümeleri, siderofor çeşitliliği, antimikrobiyal/ağır metal direnci ile ilişkili genler başta olmak üzere birçok PGPB özelliklerinin determinantlarını açığa çıkarabilmektedir. Genomik teknolojilerin kullanımı, faydalı bitki-mikroorganizma etkileşimlerinin modülasyonunu sağlayarak sürdürülebilir tarım için umut verici ve çevre dostu yeni uygulamaların geliştirilmesine olanak tanıyacaktır.

Anahtar Kelimeler

• biyoçeşitlilik
• mikrobiyal genomlar
• PGPB
• sürdürülebilir tarım

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