DETEKSI BACTERIAL KEY SPECIES PADA HUTAN SEKUNDER DAN LAHAN BEKAS TERBAKAR: SEBAGAI UPAYA PENENTUAN BARKODE DNA
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Date
2021-05
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Abstract
Peatlands are the result of the decomposition of organic matter under anaerobic
conditions that naturally accumulated over hundreds of years. A massive
conversion of land function can lead to peatland degradation which has an impact
on the degradation of the peatland quality. Currently, more sensitive indicators are
needed to detect the initial disturbance of peatland degradation. This study aimed
to determine the bacterial key species (BKS) in secondary forest areas and burnt
areas which can then be used as DNA barcodes to monitor the quality of
peatlands. DNA barcodes were obtained by determining BKS with the criteria of
finding BKS that were only found in secondary forest and not found in locations
that had been converted. This study used 16S rRNA gene sequence data generated
from sequencing with the next generation sequencing (NGS) method. This
research method included processing FastQ into fasta format using the Galaxy
program, construction of phylogenetic trees using the MEGA program version
6.06, determining BKS candidates based on phylogenetic tree construction,
selection of BKS candidates using BLASTn analysis: Align Two or More
Sequence, alignment and editing of candidate DNAbarcode determination, primer
design and in silico PCR analysis using the FastPCR application. The results of
this study showed that 3 BKS were successfully detected which were only found
in secondary forest locations but not found on burnt land (BKS_SLT). There are 2
candidates for the DNA barcode on BKS_SLT, namely the BKS_SLT2 barcode
with 6 primers and the BKS_SLT3 barcode with 8 primers. The primers chosen
were primers that had been tested for their sensitivity through in silico PCR.
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Keywords
Bacterial key species, DNA barcodes, in silico PCR, Next generation sequencing, Peatland monitoring