Eksplorasi Gen Fungsional Bakteri Tanah Kebun Karet Cikabayan IPB Dramaga melalui Pendekatan Metagenomik

Abstract

Tanah kebun karet adalah ekosistem yang menyimpan keanekaragaman komunitas bakteri dengan peran biogeokimia krusial. Penelitian ini bertujuan menganalisis keanekaragaman taksonomi bakteri dan gen fungsional ekologisnya pada tanah Kebun Karet Cikabayan Kampus IPB Dramaga menggunakan metode pendekatan metagenomik berbasis sequencing nanopore. Hasil analisis sampel berasal dari tiga lokasi dimana dua sampel (KRT1 dan KRT2) berhasil disequencing dengan hasil 856.725 dan 1.099.921 reads, serta menghasilkan 9.319 contigs (KRT) dengan N50 sebesar 11.115 bp. Filum Proteobacteria dan Actinobacteria mendominasi kedua sampel, dengan genus Bradyrhizobium dominan di KRT1 dan Streptomyces dominan di KRT2. Kurva rarefaksi menunjukkan diversitas komunitas moderat (nilai OTU <150), khas ekosistem monokultur perkebunan. Gen fungsional pada hasil binning mengungkap kapasitas komunitas dalam siklus nitrogen, siklus karbon, dan mobilisasi fosfat. Ekosistem tanah tersebut dinilai relatif sehat secara biologis dengan tidak adanya dominasi patogen tanah, namun terlihat potensi munculnya kerentanan ekologis jangka panjang.

Rubber plantation soil is an ecosystem that harbours a diverse bacterial community with crucial biogeochemical roles. This study aims to analyse taxonomic diversity of bacteria and their ecologically functional genes in the soil of the Cikabayan Rubber Plantation at the IPB Dramaga Campus using a metagenomic approach based on nanopore sequencing. Samples were collected from three sites, with two samples (KRT1 and KRT2) successfully sequenced, yielding 856,725 and 1,099,921 reads which yielded 9,319 contigs (KRT) through assembly. The phyla Proteobacteria and Actinobacteria were dominant in both samples, with the Bradyrhizobium dominant in KRT1 and Streptomyces dominant in KRT2. The rarefaction curve indicated moderate community diversity (OTU count <150), characteristic of a monoculture plantation ecosystem. Functional genes identified in the binning results reveal the community’s capacity in nitrogen cycle, carbon cycle, and phosphate mobilisation. The soil ecosystem was assessed as being relatively biologically healthy with no dominance of soil pathogens, however, there is a potential for long-term ecological vulnerability due to moderate diversity.