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Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)

Soil bacteria from tropical environments play a significant role in resolving various environmental issues, including biodegradation. Exploratory research on biodiversity is crucial to develop and harness the potential of different types of soil bacteria that are highly abundant. The bacterial diver...

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Main Authors: Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah, Eli Hendrik Sanjaya, Eli Hendrik Sanjaya, Abdul Wahab, Roswanira, Susanti, Evi
Format: Article
Language:English
Published: Department of Chemistry, Faculty of Science and Technology, Syarif Hidayatullah Jakarta State Islamic University 2023
Subjects:
QD Chemistry
Online Access:http://eprints.utm.my/104997/1/RoswaniraAbdulWahab2023_ExplorationTheCandidatesofXenobioticDegrading.pdf
http://eprints.utm.my/104997/
http://dx.doi.org/10.15408/jkv.v9i2.34316
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spelling my.utm.1049972024-04-01T06:59:37Z http://eprints.utm.my/104997/ Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS) Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah Eli Hendrik Sanjaya, Eli Hendrik Sanjaya Abdul Wahab, Roswanira Susanti, Evi QD Chemistry Soil bacteria from tropical environments play a significant role in resolving various environmental issues, including biodegradation. Exploratory research on biodiversity is crucial to develop and harness the potential of different types of soil bacteria that are highly abundant. The bacterial diversity in landfills is typically high due to the decomposition of organic and inorganic waste, creating a favorable medium for the growth and development of soil bacteria. This study aims to assess the candidates of xenobiotic degrading indigenous bacteria from the Probolinggo City landfill using Next Generation Sequencing (NGS) method. The research stages include: 1) sampling, 2) isolation of genomic DNA from samples using the ZymoBIOMICS DNA MiniPrep Kit from Zymo Research, 3) amplification of isolated DNA with primers 16S 27F – 1429R, 4) sequencing the results of DNA amplification with NGS, 5) downstream analysis of the results using software Pavian Krona Tools, and 6) narrative analysis review to identify the candidates of xenobiotic degrading indigenous bacteria. The results show that soil samples from the Probolinggo City landfill exhibited a high diversity of bacterial communities. Based on NGS analysis, 2400 bacterial species were identified, comprising 56 genera, 17 orders, 4 classes, and 4 phyla, with respective abundances of Proteobacteria (70%), Firmicutes (15%), Planctomycetes (2%), and Cyanobacteria (0,3%). Based on the narrative analysis review, several bacteria in the Probolinggo City landfill exhibited potential as: 1) polypropylene-degrading bacteria, including Bacillus cereus, B. licheniformis and B. thuringiensis. 2) styrofoam degrading bacteria, namely Bacillus amyloliquefaciens, Bacillus cereus, Bacillus firmus and Pseudomonas aeruginosa. 3) total ammonia nitrogen (TAN) reducing bacteria, including Bacillus megaterium. 4) pesticide degrading bacteria Profenofos and Chlorantraniliprole, including Bacillus stearothermophilus. and 5) tannic acid degrading bacteria, including Pantoea dispersa. These results indicate that the Probolinggo City landfill is a good habitat for various xenobiotic-degrading bacteria, then the isolation of specific bacteria can be designed using an appropriate selective medium. Department of Chemistry, Faculty of Science and Technology, Syarif Hidayatullah Jakarta State Islamic University 2023-11 Article PeerReviewed application/pdf en http://eprints.utm.my/104997/1/RoswaniraAbdulWahab2023_ExplorationTheCandidatesofXenobioticDegrading.pdf Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah and Eli Hendrik Sanjaya, Eli Hendrik Sanjaya and Abdul Wahab, Roswanira and Susanti, Evi (2023) Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS). Jurnal Kimia Valensi, 9 (2). pp. 280-287. ISSN 2460-6065 http://dx.doi.org/10.15408/jkv.v9i2.34316 DOI:10.15408/jkv.v9i2.34316
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic QD Chemistry
spellingShingle QD Chemistry
Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah
Eli Hendrik Sanjaya, Eli Hendrik Sanjaya
Abdul Wahab, Roswanira
Susanti, Evi
Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)
description Soil bacteria from tropical environments play a significant role in resolving various environmental issues, including biodegradation. Exploratory research on biodiversity is crucial to develop and harness the potential of different types of soil bacteria that are highly abundant. The bacterial diversity in landfills is typically high due to the decomposition of organic and inorganic waste, creating a favorable medium for the growth and development of soil bacteria. This study aims to assess the candidates of xenobiotic degrading indigenous bacteria from the Probolinggo City landfill using Next Generation Sequencing (NGS) method. The research stages include: 1) sampling, 2) isolation of genomic DNA from samples using the ZymoBIOMICS DNA MiniPrep Kit from Zymo Research, 3) amplification of isolated DNA with primers 16S 27F – 1429R, 4) sequencing the results of DNA amplification with NGS, 5) downstream analysis of the results using software Pavian Krona Tools, and 6) narrative analysis review to identify the candidates of xenobiotic degrading indigenous bacteria. The results show that soil samples from the Probolinggo City landfill exhibited a high diversity of bacterial communities. Based on NGS analysis, 2400 bacterial species were identified, comprising 56 genera, 17 orders, 4 classes, and 4 phyla, with respective abundances of Proteobacteria (70%), Firmicutes (15%), Planctomycetes (2%), and Cyanobacteria (0,3%). Based on the narrative analysis review, several bacteria in the Probolinggo City landfill exhibited potential as: 1) polypropylene-degrading bacteria, including Bacillus cereus, B. licheniformis and B. thuringiensis. 2) styrofoam degrading bacteria, namely Bacillus amyloliquefaciens, Bacillus cereus, Bacillus firmus and Pseudomonas aeruginosa. 3) total ammonia nitrogen (TAN) reducing bacteria, including Bacillus megaterium. 4) pesticide degrading bacteria Profenofos and Chlorantraniliprole, including Bacillus stearothermophilus. and 5) tannic acid degrading bacteria, including Pantoea dispersa. These results indicate that the Probolinggo City landfill is a good habitat for various xenobiotic-degrading bacteria, then the isolation of specific bacteria can be designed using an appropriate selective medium.
format Article
author Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah
Eli Hendrik Sanjaya, Eli Hendrik Sanjaya
Abdul Wahab, Roswanira
Susanti, Evi
author_facet Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah
Eli Hendrik Sanjaya, Eli Hendrik Sanjaya
Abdul Wahab, Roswanira
Susanti, Evi
author_sort Nur Romadhona Lailatul Qodriyah, Nur Romadhona Lailatul Qodriyah
title Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)
title_short Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)
title_full Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)
title_fullStr Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)
title_full_unstemmed Exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (NGS)
title_sort exploration the candidates of xenobiotic degrading indigenous bacteria from probolinggo city landfill by using next generation sequencing (ngs)
publisher Department of Chemistry, Faculty of Science and Technology, Syarif Hidayatullah Jakarta State Islamic University
publishDate 2023
url http://eprints.utm.my/104997/1/RoswaniraAbdulWahab2023_ExplorationTheCandidatesofXenobioticDegrading.pdf
http://eprints.utm.my/104997/
http://dx.doi.org/10.15408/jkv.v9i2.34316
_version_ 1797905692330295296
score 13.211869

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