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Path: TopS1-Final ProjectBiology2017

KUANTIFIKASI KELIMPAHAN NITRITE OXIDIZING BACTERIA Nitrospira DI TANAH PERKEBUNAN KELAPA SAWIT

Undergraduate Theses from JBPTITBPP / 2017-09-14 15:53:25
Oleh : Tirta Widi Gilang Citradi (NIM : 10613030), School of Life Sciences and Technology
Dibuat : 2017-09-12, dengan 1 file

Keyword : Nitrospira, Tanah Perkebunan Kelapa Sawit, qPCR, nxrB

Nitrospira merupakan mikroba pengoksidasi nitrit yang beragam secara







filogenetik dan memiliki kelimpahan tinggi di tanah. Kelimpahan Nitrospira di







tanah perkebunan kelapa sawit belum banyak diteliti. Kelimpahan Nitrospira di







tanah perkebunan kelapa sawit dapat memberikan informasi penting terkait







ketersediaan nutrien untuk tanaman sawit maupun siklus N di tanah perkebunan.







Penelitian ini bertujuan untuk melakukan kuantifikasi Nitrospira di tanah







perkebunan kelapa sawit serta mengetahui korelasi faktor edafik terhadap







kelimpahan Nitrospira. Penelitian ini dibagi menjadi empat tahap yaitu persiapan,







deteksi, konfirmasi dan kuantifikasi. Pada tahap persiapan dilakukan isolasi DNA







tanah dan koleksi data edafik tanah perkebunan kelapa sawit. Deteksi keberadaan







Nitrospira di tanah dilakukan dengan PCR dengan gen target nxrB (Nitrite







Oxidoreductase Subunit β). Selanjutnya dilakukan kloning dan sekuensing pada







plasmid dan dianalisis menggunakan pendekatan bioinformatika untuk tahap







konfirmasi. Kuantifikasi kelimpahan Nitrospira di tanah PT Astra Agro Lestari







Tbk. dilakukan dengan qPCR. Hasil yang diperoleh terdeteksi dua pita DNA







berukuran ~200 bp dan ~500 bp. Hasil BLAST kloning menunjukkan kedua pita







tersebut positif merupakan gen nxrB Nitrospira. Analisis filogenetik menunjukkan







gen nxrB yang berhasil dikloning membentuk satu klad monofiletik dengan







Nitrospira moscoviensis, Candidatus Nitrospira defluvii dan Nitrospira japonica.







Sebanyak 10 sampel tanah dari 24 sampel berhasil teramplifikasi untuk gen nxrB







dengan qPCR. Kelimpahan Nitrospira hasil qPCR dari 10 sampel tanah yang







dapat teramplifikasi berada pada rentang 104-106 copies/ μl. Kelimpahan tertinggi







dijumpai di tanah PT PSKY OB22 sebanyak 6,74x106 copies/μl dan kelimpahan







terendah dijumpai di PT AAL sebanyak 1,56 x104 copies/μl. Sebanyak 14 sampel







tanah tidak dapat diamplifikasi berkorelasi dengan pH yang terlalu asam, clay







content pada tanah yang relatif lebih rendah atau tingginya Al3+ di tanah.







Kesimpulan penelitian ini adalah kelimpahan Nitrospira dipengaruhi oleh faktor







edafik terutama pH, Clay dan Al3+.

Deskripsi Alternatif :

Nitrospira is one of nitrite oxidizing bacteria that phylogenetically diverse and







highly abundant in soil. The abundance of Nitrospira indicates nitrate availability







and loss in palm oil plantation soil. The abundace of Nitrospira in soil is affected







by environmental factors such as edaphic factors. A little is known about edaphic







factors that relate to Nitrospira abundace espescially in palm oil plantation soil.







The objective of this research was to quantify the abundance of Nitrospira in







palm oil plantation soil and to study the key edaphic factors relating to Nitrospira







abundance. Research was conducted to four steps of preparation, detection,







confirmation and quantification. Preparation step included soil DNA isolation and







collection of soil physico-chemical characteristics data of palm oil plantation.







Detection of Nitrospira in palm oil plantation soil was carried out using nxrB







targeted PCR. Cloning, sequencing and bioinformatics analysis were carried out







in order to confirm the amplifed gene was Nitrospira nxrB. The last step was







absolute quantification of Nitrospira nxrB targeted qPCR. Two bands were







detected with approximate size ~200 bp and ~500 bp and were confirmed both are







Nitrospira nxrB. Phylogenetics analysis showed that Nitrospira in this research is







closely related to Nitrospira moscoviensis, Candidatus Nitrospira defluvii and







Nitrospira japonica which falls into Nitrospira sublineage I or II. qPCR could







only detect the presence of Nitrospira in 10 soil samples from 24 soil samples.







The abundance range that could be detected was 104-106 copies/ μl. The highest







abundance of Nitrospira was found in PT PSKY OB22 soil with DNA quantity







6,74x106 copies/μl whereas PT AAL abundance was the narrowest with DNA







quantity 1,56 x104 copies/μl. Soil samples that could not be detected for Nitrospira







abundance were due to highly acidic soil, less clayey soil and high concentration







of Al3+. This indicate that several edaphic factors contributing to Nitrospira







abundance in palm oil plantation soil yet the key factors are pH, clay content and







soil Aluminium ion concentration.

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