The diversity of indigenous and potential bacteria as bioremediator of palm oil mill secondary effluent (POMSE) by metagenomics assessment
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Karno R, Arisoesilaningsih E, Mustafa I, Siswanto D. 2024. The diversity of indigenous and potential bacteria as bioremediator of palm oil mill secondary effluent (POMSE) by metagenomics assessment. Biodiversitas 25: 1194-1200. This study aimed to identify the indigenous bacteria for potential bioremediation agents of palm oil mill secondary effluent (POMSE). Samples were obtained from the secondary pond of palm oil mill treatment. The bacterial diversity on the POMSE water samples was revealed by Next Generation Sequencing (NGS) of 16S rRNA gene amplicons. The results showed that the high abundance of bacteria phylum was Pseudomonadota or Proteobacteria (50%), Bacillota (31%), Bacteroidota (5%), and Thermotogae (3%). A photosynthetic sulfur bacterium, Allochromatium humboldtianum, was the most abundant species detected in the POMSE, with more than 8% of the total Operational Taxonomic Unit (OTU) detected. It was followed by Allochromatium phaeobacterium (6%), Allochromatium sp. (6%), and Macromonas bipunctata (6%). Meanwhile, the level of physicochemical parameters in POMSE were relatively high for several main parameters of the quality standard of palm oil industry waste, such as Chemical Oxygen Demand (COD) and Biological Oxygen Demand (BOD). In contrast, oil and fat are low and meet the quality standards. The value of POMSE physicochemical parameters, including COD, BOD, and oil and fat, were 2,492.46, 852.96, and 6.20 mg/L, respectively. Metagenomic analysis showed that the bacterial community at POMSE was highly diverse. Nine dominant and codominant species found are Allochromatium humboldtianum, Allochromatium phaeobacterium, Allochromatium sp., Allochromatium vinosum, Macromonas bipunctata, Tepidibaculum saccharolyticum, Rhodocyclus purpureus, Comamonas nitrativorans, and Fervidobacterium riparium. Several indigenous bacterial species found in this research were bacteria that have potential as bioremediation agents for palm oil wastewater.
##plugins.themes.bootstrap3.article.details##
References
Ahmad, A., Ghufran, R., & Wahid, Z. A. (2011). Bioenergy from anaerobic degradation of lipids in palm oil mill effluent. Reviews in Environmental Science and Biotechnology, 10(4), 353–376. https://doi.org/10.1007/s11157-011-9253-8
Ahmad, A. L., Ismail, S., & Bhatia, S. (2003). Water recycling from palm oil mill effluent (POME) using membrane technology. Desalination, 157(1–3), 87–95. https://doi.org/10.1016/S0011-9164(03)00387-4
Al-Hawash, A. B., Zhang, X., & Ma, F. (2019). Removal and biodegradation of different petroleum hydrocarbons using the filamentous fungus Aspergillus sp. RFC-1. MicrobiologyOpen, 8(1), 1–14. https://doi.org/10.1002/mbo3.619
Andalib, M., Nakhla, G., & Zhu, J. (2012). High rate biological nutrient removal from high strength wastewater using anaerobic-circulating fluidized bed bioreactor (A-CFBBR). Bioresource Technology, 118, 526–535. https://doi.org/10.1016/j.biortech.2012.05.068
Bala, J. D., Lalung, J., Al-gheethi, A. A. S., & Hossain, K. (2018). Microbiota of Palm Oil Mill Wastewater in Malaysia Industrial wastewaters are essential habitat for diverse microbes . Generally , some of the microorganisms have been used for biotreatment of wastewaters ( Abdel- Raouf et al . 2012?; Bala et al . 2014a ,. 29(2), 131–163.
Bedoya, K., Coltell-Simon, O., Cabarcas, F., & Alzate, J. F. (2019). Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia. Science of the Total Environment, 648(52), 572–581. https://doi.org/10.1016/j.scitotenv.2018.08.119
Begmatov, S., Dorofeev, A. G., Kadnikov, V. V., Beletsky, A. V., Pimenov, N. V., Ravin, N. V., & Mardanov, A. V. (2022). The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow. Scientific Reports, 12(1), 1–14. https://doi.org/10.1038/s41598-022-07132-4
Bhattacharya, J., Dev, S., & Das, B. (2018). Design of Wastewater Bioremediation Plant and Systems. In Low Cost Wastewater Bioremediation Technology. https://doi.org/10.1016/b978-0-12-812510-6.00011-5
Broszat, M., Nacke, H., Blasi, R., Siebe, C., Huebner, J., Daniel, R., & Grohmanna, E. (2014). Wastewater irrigation increases the abundance of potentially harmful Gammaproteobacteria in soils in Mezquital Valley, Mexico. Applied and Environmental Microbiology, 80(17), 5282–5291. https://doi.org/10.1128/AEM.01295-14
Cai, W., Li, Y., Wang, P., Niu, L., Zhang, W., & Wang, C. (2016). Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river. Environmental Science and Pollution Research, 23(15), 15727–15738. https://doi.org/10.1007/s11356-016-6757-3
Chen, X. H., Huang, Y. H., Lü, H., Mo, C. H., Xiang, L., Feng, N. X., Zhao, H. M., Li, H., Li, Y. W., & Cai, Q. Y. (2022). Plant-scale hyperthermophilic composting of sewage sludge shifts bacterial community and promotes the removal of organic pollutants. Bioresource Technology, 347(December 2021), 126702. https://doi.org/10.1016/j.biortech.2022.126702
Darajeh, N., Idris, A., Aziz, A. A., & Truong, P. (2014). Vetiver System Technology for Phytoremediation of Palm Oil Mill Effluent. Advances in Materials Science and Engineering, 2014, 1–13.
Darajeh, N., Idris, A., Fard Masoumi, H. R., Nourani, A., Truong, P., & Sairi, N. A. (2016). Modeling BOD and COD removal from Palm Oil Mill Secondary Effluent in floating wetland by Chrysopogon zizanioides (L.) using response surface methodology. Journal of Environmental Management, 181, 343–352. https://doi.org/10.1016/j.jenvman.2016.06.060
Darajeh, N., Idris, A., Reza, H., Masoumi, F., Nourani, A., Rezania, S., & Teknologi, U. (n.d.). Accepted manuscript. 1–42.
De La Cruz-Noriega, M., Benites, S. M., Rojas-Flores, S., Otiniano, N. M., Sabogal Vargas, A. M., Alfaro, R., Cabanillas-Chirinos, L., Rojas-Villacorta, W., Nazario-Naveda, R., & Delfín-Narciso, D. (2023). Use of Wastewater and Electrogenic Bacteria to Generate Eco-Friendly Electricity through Microbial Fuel Cells. Sustainability (Switzerland), 15(13). https://doi.org/10.3390/su151310640
Ganapathy, B., Yahya, A., & Ibrahim, N. (2019). Bioremediation of palm oil mill effluent (POME) using indigenous Meyerozyma guilliermondii. Environmental Science and Pollution Research, 26(11), 11113–11125. https://doi.org/10.1007/s11356-019-04334-8
Garner, E., Davis, B. C., Milligan, E., Blair, M. F., Keenum, I., Maile-Moskowitz, A., Pan, J., Gnegy, M., Liguori, K., Gupta, S., Prussin, A. J., Marr, L. C., Heath, L. S., Vikesland, P. J., Zhang, L., & Pruden, A. (2021). Next generation sequencing approaches to evaluate water and wastewater quality. Water Research, 194, 116907. https://doi.org/10.1016/j.watres.2021.116907
Gu, Y., Li, B., Zhong, X., Liu, C., & Ma, B. (2022). Bacterial Community Composition and Function in a Tropical Municipal Wastewater Treatment Plant. Water (Switzerland), 14(10). https://doi.org/10.3390/w14101537
Helwig, N. E., Hong, S., & Hsiao-wecksler, E. T. (n.d.). No ????????????????????? ?????????????????Title.
Hii, K. L., Yeap, S. P., & Mashitah, M. D. (2012). Cellulase production from palm oil mill effluent in Malaysia: Economical and technical perspectives. Engineering in Life Sciences, 12(1), 7–28. https://doi.org/10.1002/elsc.201000228
Jong, B. C., Liew, P. W. Y., Juri, M. L., Kim, B. H., Mohd. Dzomir, A. Z., Leo, K. W., & Awang, M. R. (2011). Performance and microbial diversity of palm oil mill effluent microbial fuel cell. Letters in Applied Microbiology, 53(6), 660–667. https://doi.org/10.1111/j.1472-765X.2011.03159.x
Karim, A., Islam, M. A., Khalid, Z. Bin, Yousuf, A., Khan, M. M. R., & Mohammad Faizal, C. K. (2021). Microbial lipid accumulation through bioremediation of palm oil mill effluent using a yeast-bacteria co-culture. Renewable Energy, 176, 106–114. https://doi.org/10.1016/j.renene.2021.05.055
Khalid, N. A., Rajandas, H., Parimannan, S., Croft, L. J., Loke, S., Chong, C. S., Bruce, N. C., & Yahya, A. (2019). Insights into microbial community structure and diversity in oil palm waste compost. 3 Biotech, 9(10), 1–11. https://doi.org/10.1007/s13205-019-1892-4
Khemkhao, M., Techkarnjanaruk, S., & Phalakornkule, C. (2015). Simultaneous treatment of raw palm oil mill effluent and biodegradation of palm fiber in a high-rate CSTR. Bioresource Technology, 177, 17–27. https://doi.org/10.1016/j.biortech.2014.11.052
Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge?: rapid and sensitive classification of metagenomic sequences. 1–9. https://doi.org/10.1101/gr.210641.116.Freely
Ma, K. li, Li, X. kun, & Bao, L. lin. (2019). Influence of organic loading rate on purified terephthalic acid wastewater treatment in a temperature staged anaerobic treatment (TSAT) system: Performance and metagenomic characteristics. Chemosphere, 220, 1091–1099. https://doi.org/10.1016/j.chemosphere.2019.01.028
Mamimin, C., Thongdumyu, P., Hniman, A., Prasertsan, P., Imai, T., & O-Thong, S. (2012). Simultaneous thermophilic hydrogen production and phenol removal from palm oil mill effluent by Thermoanaerobacterium-rich sludge. International Journal of Hydrogen Energy, 37(20), 15598–15606. https://doi.org/10.1016/j.ijhydene.2012.04.062
Medina-Bellver, J. I., Marín, P., Delgado, A., Rodríguez-Sánchez, A., Reyes, E., Ramos, J. L., & Marqués, S. (2005). Evidence for in situ crude oil biodegradation after the Prestige oil spill. Environmental Microbiology, 7(6), 773–779. https://doi.org/10.1111/j.1462-2920.2005.00742.x
Mesbah, N. M., Hedrick, D. B., Peacock, A. D., Rohde, M., & Wiegel, J. (2007). Natranaerobius thermophilus gen. nov., sp. nov., a holophilic, alkalithermophilic bacterium from soda lakes of the Wadi An Natrun, Egypt, and proposal of Natranaerobiaceae fam. nov. and Natranaerobiales ord. nov. International Journal of Systematic and Evolutionary Microbiology, 57(11), 2507–2512. https://doi.org/10.1099/ijs.0.65068-0
Mohd-Nor, D., Ramli, N., Sharuddin, S. S., Hassan, M. A., Mustapha, N. A., Amran, A., Sakai, K., Shirai, Y., & Maeda, T. (2018). Alcaligenaceae and Chromatiaceae as reliable bioindicators present in palm oil mill effluent final discharge treated by different biotreatment processes. Ecological Indicators, 95(August), 468–473. https://doi.org/10.1016/j.ecolind.2018.08.007
Nitipan, S., Mamimin, C., Intrasungkha, N., Birkeland, N. K., & O-Thong, S. (2014). Microbial community analysis of thermophilic mixed culture sludge for biohydrogen production from palm oil mill effluent. International Journal of Hydrogen Energy, 39(33), 19285–19293. https://doi.org/10.1016/j.ijhydene.2014.05.139
Nwuche, C. O., Aoyagi, H., & Ogbonna, J. C. (2014). Treatment of Palm Oil Mill Effluent by a Microbial Consortium Developed from Compost Soils. International Scholarly Research Notices, 2014, 1–8. https://doi.org/10.1155/2014/762070
Nygaard, A. B., Tunsjø, H. S., Meisal, R., & Charnock, C. (2020). OPEN A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. 1–10. https://doi.org/10.1038/s41598-020-59771-0
Ojonoma & Udeme, 2014. (2014). The International Journal of Biotechnology 2014. 3(3), 32–46.
Poh, P. E., Yong, W. J., & Chong, M. F. (2010). Palm oil mill effluent (POME) characteristic in high crop season and the applicability of high-rate anaerobic bioreactors for the treatment of pome. Industrial and Engineering Chemistry Research, 49(22), 11732–11740. https://doi.org/10.1021/ie101486w
Prasad, M. P., & Manjunath, K. (2011). Comparative study on biodegradation of lipid-rich wastewater using lipase producing bacterial species. Indian Journal of Biotechnology, 10(1), 121–124.
Qaderi, F., Sayahzadeh, A. H., & Azizi, M. (2018). Efficiency optimization of petroleum wastewater treatment by using of serial moving bed biofilm reactors. Journal of Cleaner Production, 192, 665–677. https://doi.org/10.1016/j.jclepro.2018.04.257
Rawat, S. R., Männistö, M. K., Starovoytov, V., Goodwin, L., Nolan, M., Hauser, L., Land, M., Davenport, K. W., Woyke, T., & Häggblom, M. M. (2013). Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil. Standards in Genomic Sciences, 9(3), 449–461. https://doi.org/10.4056/sigs.4648353
Rosdi, A., Dahalan, F. A., Zhan, L. Z., Babakhani, P., Shams, S., Engineering, C., & Area, P. (2022). Collection of samples. 2, 1–5.
Saisa-Ard, K., Saimmai, A., & Maneerat, S. (2014). Characterization and phylogenetic analysis of biosurfactant-producing bacteria isolated from palm oil contaminated soils. Songklanakarin Journal of Science and Technology, 36(2), 163–175.
Sawadogo, A., Harmonie, O. C., Sawadogo, J. B., Kaboré, A., Traoré, A. S., & Dianou, D. (2014). Isolation and Characterization of Hydrocarbon-Degrading Bacteria from Wastewaters in Ouagadougou, Burkina Faso. Journal of Environmental Protection, 05(12), 1183–1196. https://doi.org/10.4236/jep.2014.512115
Shairah, N., Shahrifun, A., Nazilah, N., Aris, A., Omar, Q., & Ahmad, N. (2015). Characterization of Palm Oil Mill Secondary Effluent (Pomse). Malaysian Journal of Civil Engineering, 27(1), 144–151.
Sharuddin, S. S., Ramli, N., Hassan, M. A., Mustapha, N. A., Amran, A., Mohd-Nor, D., Sakai, K., Tashiro, Y., Shirai, Y., & Maeda, T. (2017). Bacterial community shift revealed Chromatiaceae and Alcaligenaceae as potential bioindicators in the receiving river due to palm oil mill effluent final discharge. Ecological Indicators, 82(July), 526–529. https://doi.org/10.1016/j.ecolind.2017.07.038
Shen, Z., Shang, Z., Wang, F., Liang, Y., Zou, Y., & Liu, F. (2022). Bacterial diversity in surface sediments of collapsed lakes in Huaibei, China. Scientific Reports, 12(1), 1–12. https://doi.org/10.1038/s41598-022-20148-0
Soleimaninanadegani, M., & Manshad, S. (2014). Enhancement of Biodegradation of Palm Oil Mill Effluents by Local Isolated Microorganisms. International Scholarly Research Notices, 2014, 1–8. https://doi.org/10.1155/2014/727049
Tabatabaei, M., Sulaiman, A., M., A., Yusof, N., & Najafpour, G. (2011). Influential Parameters on Biomethane Generation in Anaerobic Wastewater Treatment Plants. Alternative Fuel, October 2016. https://doi.org/10.5772/24681
Tan Ai Wei, I. (2019). Phytoremediation of Palm Oil Mill Effluent (POME) Using Eichhornia crassipes. Journal of Applied Science & Process Engineering, 6(1), 340–354. https://doi.org/10.33736/jaspe.1349.2019
Verla, A. W., Adowei, P., & Verla, E. N. (2014). Physicochemical And Microbiological Characteristic Of Palm Oil Mill Effluent (Pome) In Nguru?: Aboh Mbaise, Eastern Nigeria. Acta Chim. Pharm. Indica, 4(3), 119–125. www.sadgurupublications.com
Walter, A., Franke-Whittle, I. H., Wagner, A. O., & Insam, H. (2015). Methane yields and methanogenic community changes during co-fermentation of cattle slurry with empty fruit bunches of oil palm. Bioresource Technology, 175, 619–623. https://doi.org/10.1016/j.biortech.2014.10.085
Wick, R. R., Judd, L. M., & Holt, K. E. (2019). Performance of neural network basecalling tools for Oxford Nanopore sequencing. 1–10.
Wong, Y. S., Teng, T. T., Ong, S. A., Morad, N., & Rafatullah, M. (2014). Suspended growth kinetic analysis on biogas generation from newly isolated anaerobic bacterial communities for palm oil mill effluent at mesophilic temperature. RSC Advances, 4(110), 64659–64667. https://doi.org/10.1039/c4ra08483g
Yarlina, V. P., Andoyo, R., Djali, M., & Lani, M. N. (2022). Metagenomic Analysis for Indigenous Microbial Diversity in Soaking Process of Making Tempeh Jack Beans (Canavalia Ensiformis). Current Research in Nutrition and Food Science, 10(2), 620–632. https://doi.org/10.12944/CRNFSJ.10.2.18
Ye, L., & Zhang, T. (2013). Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Applied Microbiology and Biotechnology, 97(6), 2681–2690. https://doi.org/10.1007/s00253-012-4082-4
Yossan, S., O-Thong, S., & Prasertsan, P. (2012). Effect of initial pH, nutrients and temperature on hydrogen production from palm oil mill effluent using thermotolerant consortia and corresponding microbial communities. International Journal of Hydrogen Energy, 37(18), 13806–13814. https://doi.org/10.1016/j.ijhydene.2012.03.151
Zainudin, M. H. M., Hassan, M. A., Tokura, M., & Shirai, Y. (2013). Indigenous cellulolytic and hemicellulolytic bacteria enhanced rapid co-composting of lignocellulose oil palm empty fruit bunch with palm oil mill effluent anaerobic sludge. Bioresource Technology, 147, 632–635. https://doi.org/10.1016/j.biortech.2013.08.061
Zeng, T., Wang, L., Zhang, X., Song, X., Li, J., Yang, J., Chen, S., & Zhang, J. (2022). Characterization of Microbial Communities in Wastewater Treatment Plants Containing Heavy Metals Located in Chemical Industrial Zones. International Journal of Environmental Research and Public Health, 19(11). https://doi.org/10.3390/ijerph19116529
Zolkefli, N., Ramli, N., Mohamad-Zainal, N. S. L., Mustapha, N. A., Yusoff, M. Z. M., Hassan, M. A., & Maeda, T. (2020). Alcaligenaceae and Chromatiaceae as pollution bacterial bioindicators in palm oil mill effluent (POME) final discharge polluted rivers. Ecological Indicators, 111(December 2019). https://doi.org/10.1016/j.ecolind.2019.106048
Most read articles by the same author(s)
- SERAFINAH INDRIYANI, ENDANG ARISOESILANINGSIH, TATIK WARDIYATI, HERY PURNOBASUKI, A model of relationship between climate and soil factors related to oxalate content in porang (Amorphophallus muelleri Blume) corm , Biodiversitas Journal of Biological Diversity: Vol. 12 No. 1 (2011)
- YOSEPH NAHAK SERAN, SUDARTO SUDARTO, LUCHMAN HAKIM, ENDANG ARISOESILANINGSIH, Sandalwood (Santalum album) growth and farming success strengthen its natural conservation in the Timor Island, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 19 No. 4 (2018)
- SOEJONO SOEJONO, SUGENG BUDIHARTA, ENDANG ARISOESILANINGSIH, Proposing local trees diversity for rehabilitation of degraded lowland areas surrounding springs , Biodiversitas Journal of Biological Diversity: Vol. 14 No. 1 (2013)
- SISKA NURFITRIANI, ENDANG ARISOESILANINGSIH, YULIA NURAINI, EKO HANDAYANTO, Biofilm formation by mercury resistant bacteria from polluted soil small-scale gold mining waste , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 2 (2022)
- BUDIMAN BUDIMAN, ENDANG ARISOESILANINGSIH, Predictive model of Amorphophallus muelleri growth in some agroforestry in East Java by multiple regression analysis , Biodiversitas Journal of Biological Diversity: Vol. 13 No. 1 (2012)
- ZULFIKAR, ENDANG ARISOESILANINGSIH, SERAFINAH INDRIYANI, ADJI ACHMAD RINALDO FERNANDES4, Profile of geographical variation in marginal land and its relationship with the fruit tree species richness in Jombang District, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 6 (2021)
- CATUR RETNANINGDYAH, ENDANG ARISOESILANINGSIH, VIKY VIDAYANTI, PURNOMO, SATRIA CAHYA FEBRIANSYAH, Community structure and diversity of benthic macroinvertebrates as bioindicators of water quality in some waterfall ecosystems, Bawean Island, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 1 (2023)
- LAILA NUR HABIBAH, LUCHMAN HAKIM, EDRIANA PANGESTUTI, DIAN SISWANTO, BRIAN RAHARDI, Vegetation diversity, structure and composition in nature-based recreation sites as a potential tourist attraction in Banyuwangi, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 9 (2024)
- EVY ARYANTI, ESTRI LARAS ARUMINGTYAS, RODLIYATI AZRIANINGSIH, ENDANG ARISOESILANINGSIH, Phenotypic diversity of bamboo Schizostachyum lima (Blanco) Merr. population grown in several critical habitats on Lombok Island, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 5 (2023)
- MUHAMMAD ABDULLAH, LUCHMAN HAKIM, DIAN SISWANTO, DEWI LIESNOOR SETYOWATI, Mountain tourism impact on bird diversity along hiking trails of Mount Prau, Central Java, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 12 (2024)