CD Skripsi

Deteksi Kandidat Bacterial Key Species Pada Hutan Sekunder, Perkebunan Kelapa Sawit Dan Lahan Bekas Terbakar Di Cagar Biosfer Giam Siak Kecil - Bukit Batu, Riau

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ABSTRACT
Peatlands are the result of the decomposition of organic matter under anaerobic conditions that accumulate over hundreds of years naturally. A massive conversion of land function can lead degradation of the peatland quality. The purpose of this study was to determine candidate bacterial key species (BKS) and specific primer design to detect the 16S rRNA gene from BKS that was detected as an initial step for monitoring the quality of peatlands molecular.This research was conducted on secondary forest, oil palm plantations, and burnt land in the Giam Siak Kecil Biosphere Reserve, Bukit Batu (GSK-BR). The selected BKS candidates are BKS which only exist in secondary forest and are not found in locations that have been converted. This study used data on the 16S rRNA gene sequences as a result of the next generation sequencing (NGS) method. The research methods include: processing FASTQ into fasta format using the Galaxy program, constructing a phylogenetic tree using the MEGA version 6.06, determining BKS candidates based on phylogenetic tree construction, selecting BKS candidates using BLASTn: Align Two or More Sequence analysis, alignment and editing to determine sequences BKS candidates, primer design and in silico PCR analysis using FastPCR application. Based on the results of the selection of BKS candidates through phylogenetic tree construction, 92 BKS candidates were found only in secondary forest but not in oil palm plantations (BKS_SKS) and 19 BKS candidates who only existed in secondary forest but not in burnt land (BKS_SLT). The results of the BLASTn analysis showed 7 groups in BKS_SKS and 3 groups in BKS_SLT. Alignment and editing results showed 7 candidate sequences BKS_SKS with base length 435-459 bp and 3 candidate sequences BKS_SLT with base length 453-473 bp. The final result shows that there are 3 BKS candidate sequences, namely BKS_SKS4, BKS_SLT2, and BKS_SLT3. This BKS candidate was obtained based on the results of the primary sensitivity test. There are 4 sensitive primer candidates for BKS_SKS4 (455 bp). In BKS_SLT2 (455 bp) obtained 6 primer candidates and in BKS_SLT3 (473 bp) obtained 8 primer candidates which are sensitive only attached to the target sequence. The detected BKS candidates can be used as a first step for molecular monitoring of peatland quality.
Keywords: Bacterial key species, in silico PCR, Next generation sequencing, Peatland monitoring, Primer design

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Ketersediaan

Informasi Detail

Judul Seri

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No. Panggil

03 04. 121 (0021)

Penerbit

Pekanbaru : Universitas Riau - Fakultas Matematika Dan Ilmu Pengetahuan Alam - Biologi., 2021

Deskripsi Fisik

v, 107 hlm.: ill.: 29 cm

Bahasa

Indonesia

ISBN/ISSN

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Klasifikasi

03 04. 121 (0021)

Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

ELFITRA

Versi lain/terkait

Lampiran Berkas

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