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Path: TopS1-Final ProjectBiology-SITH2017

KUANTIFIKASI KELIMPAHAN NITRITE OXIDIZING BACTERIA Nitrospira DI TANAH PERKEBUNAN KELAPA SAWIT

Undergraduate Theses from JBPTITBPP / 2017-09-27 10:13:35
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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