Eksplorasi Gen Fungsional Bakteri Tanah pada Kebun Percobaan Kelapa Sawit Cikabayan IPB Dramaga secara Metagenomik

Abstract

Kebun Percobaan Kelapa Sawit Cikabayan adalah perkebunan monokultur tropis dengan kanopi terbuka, tanah asam, dan unsur hara esensial yang memengaruhi struktur dan fungsi komunitas bakteri tanah. Penelitian ini bertujuan mengeksplorasi keanekaragaman bakteri tanah dan gen fungsional melalui metagenomik. Metode: DNA tanah diekstraksi dengan FastDNA SPIN Kit for Soil, kualitas DNA dievaluasi melalui elektroforesis, fluorometri, dan spektrofotometri. Pustaka DNA disiapkan dengan Rapid Sequencing Kit DNA V14, disekuensing menggunakan PromethION 2 Solo (ONT), dan dianalisis dengan bioinformatika. Hasil menunjukkan data sekuensing berkualitas tinggi (Q19,3 dan Q16,5). Komunitas bakteri didominasi Streptomyces dan Bradyrhizobium. Tiga MAGs berkualitas sedang berpotensi sebagai spesies baru dengan gen fungsional terkait metabolisme asam amino, sistem transpor ABC, two-component system, resistensi beta-laktam, dan sintesis metabolit sekunder (terpen dan lantipeptida). Simpulan menunjukkan keragaman komunitas bakteri tanah dengan kapasitas metabolisme, adaptasi lingkungan dan aktivitas antropogenik, serta potensi biosintesis senyawa bioaktif sebagai bioinput untuk perkebunan berkelanjutan.

The Experimental Oil Palm Plantation Cikabayan is a tropical monoculture plantation characterized by an open canopy, acidic soils, and essential nutrients that influence the structure and function of soil bacterial communities. This study aimed to explore soil bacterial diversity and functional genes using metagenomics. Methods: Soil DNA was extracted using the FastDNA SPIN Kit for Soil, DNA quality was evaluated through electrophoresis, fluorometry, and spectrophotometry. DNA libraries were prepared using the Rapid Sequencing Kit DNA V14, sequenced on the PromethION 2 Solo (ONT), and analyzed using bioinformatics. The results showed high-quality sequencing data (Q19.3 and Q16.5). The bacterial community was dominated by Streptomyces and Bradyrhizobium. Three medium-quality MAGs were identified as potential novel species harboring functional genes associated with amino acid metabolism, ABC transport systems, two-component system, beta-lactam resistance, and secondary metabolite biosynthesis (terpenes and lanthipeptides). In conclusion, soil bacterial communities exhibit diversity with metabolic capacities, adaptability to environmental and anthropogenic activities, and biosynthetic potential for bioactive compounds as bioinputs for sustainable plantation systems.