Characterization and molecular identification of bacteria from mackerel bekasam in Sorong City, Southwest Papua Province, Indonesia




Abstract. Sukmawati S, Ratna R, Sipriyadi, Yunita M. 2023. Characterization and molecular identification of bacteria from mackerel bekasam in Sorong City, Southwest Papua Province, Indonesia. Biodiversitas 24: 4967-4977. Bekasam is traditional food type produced by traditional fermented fish. Microbes that grow through fermentation play an important role in forming the product’s aroma, texture, and overall quality. The study aimed to determine the biochemical characteristic of bacteria from mackerel (Scomberomorus sp.) bekasam in Sorong City and identify bacteria at the molecular level. This research was a descriptive study, which described the results of the characterization of bacteria from fermented mackerel fish and the results of molecular identification to the species level through the PCR (Polymerase Chain Reaction) technique. Then, the DNA sequences were further analyzed using the agarose gel electrophoretic separation method to visualize the bacterial DNA profile. The biochemical characterization of bacterial isolates from mackerel showed that all isolates were negative indole, and eight isolates were positive in reducing nitrate. In comparison, four isolates were negative in reducing nitrate, then all isolates had proteolytic activity except the FST 3.1 and FST 3.2 isolates. Eleven isolates were positive in hydrolyzing fat, and one isolate could not hydrolyze fat. According to the DNA patterns seen in electrophoresis and alignment of the 16 sRNA gene sequences, several types of bacteria had been identified as Bacillus paramycoides strain 2883 FST 1.1, Bacillus paramycoides strain 3665 FST 2.1, Bacillus mobilis strain ICA-144 FST 3.1, Bacillus cereus strain ATCC 14579 FNT 1.1, Bacillus mobilis strain ICA-144 FNT 2.1, and Bacillus cereus strain ATCC 14579 FNT 3.1.


Adawyah R. 2016. Pengantar teknologi hasil perikanan. Banjarmasin (ID): Lambung Mangkurat University Press.
Adetunji AI, Olaniran AO. 2021. Production strategies and biotechnological relevance of microbial lipases: a review. Brazilian Journal of Microbiology 52:1257-1269.
Ardilla YA, Anggreini KW, Puri T, Rahmani D. 2022. Peran bakteri asam laktat indigen genus Lactobacillus pada fermentasi buah durian (Durio zibethinus) sebagai bahan pembuatan tempoyak the role of indigenous lactic acid bacteria genus Lactobacillus in the fermentation process of durian (Durio zibethinu. Berkala Ilmiah Biologi 13(2):42-52. DOI: 10.22146/bib.v13i1.4619.
Arfianty BN, Farisi S, Ekowati CN. 2017. Dinamika populasi bakteri dan total asam pada fermentasi bekasam ikan patin (Pangasius hypopthalmus). Jurnal Ilmiah Biologi Eksperimen dan Keanekaragaman Hayati (J-BEKH) 4(2): 43-49.
Daroonpunt R, Tanaka N, Uchino M, Tanasupawat S. 2018. Characterization and screening of lipolytic bacteria from Thai fermented fish. Sains Malaysiana 47(1):91-97.
Ding A, Zhu M, Qian X, Shi L, Huang H, Xiong G, Wang L. 2020. Effect of fatty acids on the flavor formation of fish sauce. Lwt 134:110259.
Donkor ON, Henriksson A, Vasiljevic T, Shah NP. 2007. Proteolytic activity of dairy lactic acid bacteria and probiotics as determinant of growth and in vitro angiotensin-converting enzyme inhibitory activity in fermented milk. Le Lait 87(1): 21-38.
Dueramae S, Bovornreungroj P, Enomoto T, Kantachote D. 2017. Purification and characterization of an extracellular lipolytic enzyme from the fermented fish-originated halotolerant bacterium, Virgibacillus alimentarius LBU20907. Chemical Papers 71: 1975-1984. doi 10.1007/s11696-017-0191-y.
Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4): 783–791.
Gu Y, Chen X, Liu L, Wang S, Yu X, Jia Z, Zhou X. 2023. Cr (VI)-bioremediation mechanism of a novel strain Bacillus paramycoides Cr6 with the powerful ability to remove Cr (VI) from contaminated water. Journal of Hazardous Materials 455:131519.
Hossini H, Shafie B, Niri AD, Nazari M, Esfahlan AJ, Ahmadpour M, Hoseinzadeh E. 2022. A comprehensive review on human health effects of chromium: Insights on induced toxicity. Environmental Science and Pollution Research 29(47):70686-70705.
Jessberger N, Dietrich R, Granum PE, Märtlbauer E. 2020. The Bacillus cereus food infection as multifactorial process. Toxins 12(11):701. doi:10.3390/toxins12110701.
Kerur SS, Bandekar S, Hanagadakar MS, Nandi SS, Ratnamala GM, Hegde PG. 2021. Removal of hexavalent chromium-industry treated water and wastewater: a review. Materials Today: Proceedings 42:1112-1121.
Khan AA, Mondal M. 2021. Low-cost adsorbents, removal techniques, and heavy metal removal efficiency. In New Trends in Removal of Heavy Metals from Industrial Wastewater, Elsevier 83-103.
Korobov VV, Zhurenko EI, Zharikova NV, Iasakov TR, Markusheva TV. 2019). Application of the new degrader strain Bacillus mobilis 34T for soil treatment from 2, 4, 5-trichlorophenoxyacetic acid. Moscow University Biological Sciences Bulletin 74:154-157. doi.10.3103/S0096392519030064.
Kraft B, Strous M, Tegetmeyer HE. 2011. Microbial nitrate respiration–genes, enzymes and environmental distribution. Journal of biotechnology 155(1):104-117.
Lee LP, Karbul HM, Citartan M, Gopinath SCB, Lakshmipriya T, Tang TH. 2015. Lipase secreting Bacillus species in an oil-contaminated habitat: promising strains to alleviate oil pollution. BioMed Research International.
Lestari S, Rinto R, Huriyah SB. 2018. Peningkatan sifat fungsional bekasam menggunakan starter Lactobacillus acidophilus. Jurnal Pengolahan Hasil Perikanan Indonesia 21(1): 179-187.
Liu Y, Huang Y, Wang Z, Cai S, Zhu B, Dong X. 2021. Recent advances in fishy odour in aquatic fish products, from formation to control. International Journal of Food Science & Technology 56(10): 4959-4969.
?ubkowska B, Je?ewska-Fr?ckowiak J, Sroczy?ski M, Dzitkowska-Zabielska M, Bojarczuk A, Skowron PM, Ci?szczyk P. 2023. Analysis of industrial Bacillus species as potential probiotics for dietary supplements. Microorganisms 11(2):488.
Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG. 1998. Design and evaluation of useful bacterium-spesific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol. 64:795-799.
Melizah A, Husin S, Alkaf S. 2018. Identification of lactic acid bacteria isolate from fermentation food bekasam. Bioscientia Medicina: Journal of Biomedicine and Translational Research 2(1):16-23.
Moslehishad M, Mirdamadi S, Ehsani MR, Ezzatpanah H, Moosavi?Movahedi AA. 2013. The proteolytic activity of selected lactic acid bacteria in fermenting cow's and camel's milk and the resultant sensory characteristics of the products. International Journal of Dairy Technology 66(2):279-285.
Moussa Z, Darwish DB, Alrdahe SS, Saber WI. 2021. Innovative artificial-intelligence-based approach for the biodegradation of feather keratin by Bacillus paramycoides, and cytotoxicity of the resulting amino acids. Frontiers in Microbiology 12:731262.
Müller V. 2001. Bacterial fermentation. Ludwig-Maximilians-Universitat Munchen, Munich, Germany. eLS.
Murtini JT. 2017. Pengaruh penambahan starter bakteri asam laktat pada pembuatan bekasam ikan sepat (Trichogaster trichopterus) terhadap mutu dan daya awetnya. Jurnal Penelitian Perikanan Indonesia 3(2): 71-82.
Oliphant K, Allen-Vercoe E. 2019. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome 7(1):1-15.
Patnala HS, Kabilan U, Gopalakrishnan L, Rao RMD, Kumar DS. 2016. Marine fungal and bacterial isolates for lipase production: a comparative study. In Advances in food and nutrition research. Academic Press 78:71-94.
Rashid A, Mirza SA, Keating C, Ali S, Campos LC. 2021. Hospital wastewater treated with a novel bacterial consortium (Alcaligenes faecalis and Bacillus paramycoides spp.) for phytotoxicity reduction in Berseem clover and tomato crops. Water Science and Technology 83(7):1764-1780.
Saha SK, Pathak NN, Saha SK, Pathak NN. 2021. Digestion, absorption and metabolism of nutrients. fundamentals of animal nutrition 219-246.
Sambrook J, Russell DW. 2001. Molecular cloning a laboratory manual. 3rd ed. New York. Cold Spring Harbor Laboratory Pr.
Shabeer MS, Nagar S, uppal H. 2016. Isolation and characterization bacteria related to aquaponics for testing its bio potential. B. Tech Biotechnology thesis, National Institute of Technology, Calicut, 60 p.
Shan Y, Lai Y, Yan A. 2012. Metabolic reprogramming under microaerobic and anaerobic conditions in bacteria. Reprogramming microbial metabolic pathways 159-179.
Shekhawat K, Chatterjee S, Joshi B. 2015. Chromium toxicity and its health hazards. Int. J. Adv. Res 3(7):167-172.
Sornchuer P, Saninjuk K, Prathaphan P, Tiengtip R, Wattanaphansak S. 2022. Antimicrobial susceptibility profile and whole-genome analysis of a strong biofilm-forming Bacillus Sp. B87 strain isolated from food. Microorganisms 10(2): 252.
Srinath T, Verma T, Ramteke PW, Garg SK. 2002. Chromium (VI) biosorption and bioaccumulation by chromate resistant bacteria. Chemosphere 48(4):427-435.
Susanto E, Fahmi AS. 2012. Senyawa fungsional dari ikan: aplikasinya dalam pangan. Jurnal Aplikasi Teknologi Pangan 1(4):95-102.
Tatiyaborworntham N, Oz F, Richards MP, Wu H. 2022. Paradoxical effects of lipolysis on the lipid oxidation in meat and meat products. Food Chemistry 10(14): 100317.
Todorov SD, Dicks LM. 2009. Bacteriocin production by Pediococcus pentosaceus isolated from marula (Scerocarya birrea). International Journal of Food Microbiology 132(2-3):117-126.
Todorov SD, Ivanova IV, Popov I, Weeks R, Chikindas ML. 2022. Bacillus spore-forming probiotics: benefits with concerns. Critical Reviews in Microbiology 48(4):513-530.
Tourova TP, Sokolova DS, Semenova EM, Ershov AP, Grouzdev DS, Nazina TN. 2022. Genomic and physiological characterization of halophilic bacteria of the genera Halomonas and Marinobacter from petroleum reservoirs. Microbiology 91(3):235-248.
Verma P, Tripathi S, Yadav S, Chandra R. 2022. Degradation and decolourization potential of ligninolytic enzyme producing Bacillus paramycoides BL2 and Micrococcus luteus BL3 for pulp paper industrial effluent and its toxicity evaluation. Archives of Microbiology 204(10):642.
Wang H, Zhang X, Chen Z, Hao G, Li G. 2021. Two potential probiotic Bacillus with proteolytic activity to dietary protein from adult feces. Biocontrol Science 26(4):221-224.
Wang TY, Liu M, Portincasa P, Wang DQH. 2013. New insights into the molecular mechanism of intestinal fatty acid absorption. European journal of clinical investigation 43(11): 1203-1223.
Wikandari PR, Suparmo S, Marsono Y, Rahayu ES. 2012. Karakterisasi bakteri asam laktat proteolitik pada bekasam. Jurnal Natur Indonesia,14(1):120-125.
Yani AV, Savitri D, Sebayang NS. 2022. Analysis of protein levels of fermented sarden fish pempek. Indonesian Journal of Agricultural Research 5(03):170-176.
Yousuf S, Jamal MT, Al-Farawati RK, Al-Mur BA, Singh R. 2023. Evaluation of Bacillus paramycoides strains isolated from channa fish sp. on growth performance of labeo rohita fingerlings challenged by fish pathogen Aeromonas hydrophila MTCC 12301. Microorganisms 11(4):842.
Zang J, Xu Y, Xia W, Regenstein JM. 2020. Quality, functionality, and microbiology of fermented fish: a review. Critical Reviews in Food Science and Nutrition 60(7):1228-1242.
Zhang M, Wang X, Yang J, Wang D, Liang J, Zhou L. 2022. Nitrogen removal performance of high ammonium and high salt wastewater by adding carbon source from food waste fermentation with different acidogenic metabolic pathways. Chemosphere 292:133512.
Zhang Z, Guo H, Sun J, Wang H. 2020. Investigation of anaerobic phenanthrene biodegradation by a highly enriched co-culture, PheN9, with nitrate as an electron acceptor. Journal of hazardous materials 383:121191.
Zhang Z, Wang C, He J, Wang H. 2019. Anaerobic phenanthrene biodegradation with four kinds of electron acceptors enriched from the same mixed inoculum and exploration of metabolic pathways. Frontiers of Environmental Science & Engineering 13:1-12.
Zhong Z, Hu R, Zhao J, Liu W, Kwok LY, Sun Z, Chen Y. 2021. Acetate kinase and peptidases are associated with the proteolytic activity of Lactobacillus helveticus isolated from fermented food. Food Microbiology 94:103651.
Zhu W, Luan H, Bu Y, Li J, Li X, Zhang Y. 2021. Changes in taste substances during fermentation of fish sauce and the correlation with protease activity. Food Research International 144:110349.

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