Potential of Bacillus sp. as a Nitrifying Agent in Coastal Ecosystems: Isolation and Characterization from Awur Bay Beach, Jepara, Indonesia
DOI:
https://doi.org/10.61741/JMBI.2025.v3.p89-96Keywords:
ammonia-oxidizing bacteria, Bacillus sp, coastal waters, nitrification, Water Quality ParametersAbstract
Coastal waters often experience nitrogen pollution, which can be harmful to aquaculture. One potential approach to mitigate this issue involves the use of biological agents that can transform nitrogen compounds through nitrification and denitrification. This study aimed to identify local nitrifying bacteria capable of adapting to marine environments and reducing the ammonia concentrations. Seawater and sediment samples were collected from the Awur Bay Beach in Jepara, Central Java, Indonesia.. Isolation and purification processes employed specific autotrophic media to cultivate ammonia-oxidizing bacteria (AOB). The measured parameters included the concentrations of nitrogen species, such as ammonia, nitrite, and nitrate, in the media before and after inoculation with the bacterial isolate. The incubation period was seven days. Nine pure isolates (four from seawater and five from sediment) were obtained and screened to identify bacteria that thrive at high ammonia concentrations. The results indicated that one potential isolate, S20-7, was identified as Bacillus sp. using 16S rRNA sequencing. Bacillus sp. demonstrated the ability to thrive in media with a salinity of 20‰ and reduced ammonia concentration by 37.19% from an initial concentration of 500 mg/L. This study highlights the potential of Bacillus sp. as a nitrogen waste degradation agent in coastal waters, particularly in wastewater treatment and aquaculture. Its ability to efficiently degrade ammonia nitrogen and nitrite, coupled with its tolerance to high concentrations of these compounds, makes it a valuable tool for improving water quality and mitigating the effects of nitrogen pollution in coastal ecosystems.
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Anwar, K., Safitri, R., Fajriani, N., Gifari, Z. A., Wariata, I. W., Rosyidi, A., Amin, M., & Ali, M. 2021. In Vitro screening of ammonia and nitrite-degrading bacteria isolated from broiler chicken (Gallus gallus domesticus) intestines and pond sediment of Nile tilapia (Oreochromis niloticus): A preliminary study. IOP Conference Series: Earth and Environmental Science, 913(1). https://doi.org/10.1088/1755-1315/913/1/012072
American Public Health Association. 2017. Standard Methods. In R. Baird, A. D. Eaton., & E. W. Rice (Eds.), Standard Methods for the Examination of Water and Wastewater (23rd ed.). American Public Health Association, Washington. pp. 114-136.
Ardiansyah, A., Amrullah, A., Jaya, A. A., Dahlia, D., & Nurhayati. 2019. Isolation and identification of facultative mixotrophic ammonia-oxidizing bacteria from Bone Regency, Indonesia. AACL Bioflux, 12(1): 133–142.
Baskaran, V., Patil, P. K., Antony, M. L., Avunje, S., Nagaraju, V. T., Ghate, S. D., Nathamuni, S., Dineshkumar, N., Alavandi, S. V., & Vijayan, K. K. 2020. Microbial community profiling of ammonia and nitrite-oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species. Scientific Reports, 10(1): 1–11. https://doi.org/10.1038/ s41598-020-62183-9
Boyd, C. E., Mcnevin, A. A., & Davis, R. P. 2022. The contribution of fisheries and aquaculture to the global protein supply. Food Security, 14(3), 805–827. https://doi.org/7/s12571-021-01246-9
Carballeira Braña, C. B., Cerbule, K., Senff, P., & Stolz, I. K. (2021). Towards Environmental Sustainability in Marine Finfish Aquaculture. Frontiers in Marine Science, 8: 1–24.
Francis-Floyd, R., Watson, C., Petty, D., & Pouder, D. 2022. Ammonia in Aquatic Systems. Edis, 2022(4): 1–5. https://doi.org/10.32473/edis-fa031-2022
Franklin, D. A., & Edward, L. L. 2019. Ammonia toxicity and adaptive response in marine fishes - A review. Indian Journal of Geo-Marine Sciences, 48(3): 273–279.
Gao, H., Zhou, J., Dong, S., & Kitazawa, D. 2022. Sustainability Assessment of Marine Aquaculture Considering Nutrients Inflow from the Land in Kyushu Area. Water, 14(6). https://doi.org/10.3390/ w14060943
Hlordzi, V., Kuebutornye, F. K. A., Afriyie, G., Abarike, E. D., Lu, Y., Chi, S., & Anokyewaa, M. A. 2020. The use of Bacillus species in maintenance of water quality in aquaculture: A review. Aquaculture Reports, 18: 100503. https://doi.org/10.1016/j.aqrep.2020.100503
Hoang, P. H., Nguyễn, T. M., Le, N. C. T., Phan, K. S., Mai, T. T. T., & Ha, P. T. 2022. Characterization of isolated aerobic denitrifying bacteria and their potential use in the treatment of nitrogen-polluted aquaculture water. Current Microbiology, 79(7): 209 https://doi.org/10.1007/s00284-022-02898-2
James, G., Jose, S., Das, B. C., & V.J, R. K. 2021. Bacillus as an aquaculture friendly microbe. Aquaculture International, 29(1): 323–353. https://doi.org/10.1007/s10499-020-00630-0
Janka, E., Pathak, S., Rasti, A., Gyawali, S., & Wang, S. 2022. Simultaneous Heterotrophic Nitrification and Aerobic Denitrification of Water after Sludge Dewatering in Two Sequential Moving Bed Biofilm Reactors (MBBR). International Journal of Environmental Research and Public Health, 19(3). https://doi.org/10.3390/ ijerph19031841
Kasmuri, N & Lovitt, R.W. 2018. Inhibition of High Substrate Concentration of Ammonia-Nitrogen in Bio-Filter. International Journal of Engineering & Technology, 7: 292-296
Li, X., Luo, L., Wang, Y., Chen, J., & Zhang, X. 2020. Molecular characterization of heterotrophic nitrification and aerobic denitrification bacterium Bacillus sp. LY: Insight into the nitrogen removal pathway. Science of the Total Environment, 703: 134958. https://doi.org/10.1016/j.scitotenv.2019.134958
Liu, J., Guo, Y., Xu, J., Xu, J., & Li, J. 2023. Heterotrophic nitrification–aerobic denitrification by Bacillus strains: Mechanisms and application for wastewater treatment. Frontiers in Microbiology, 14:1187654. https://doi.org/10.3389/fmicb.2023.1187654
Marzan, L. W., Hossain, M., Mina, S. A., Akter, Y., & Chowdhury, A. M. M. A. 2017. Isolation and biochemical characterization of heavy-metal resistant bacteria from tannery effluent in Chittagong city, Bangladesh: Bioremediation viewpoint. Egyptian Journal of Aquatic Research, 43(1): 65–74. https://doi.org/10.1016/j.ejar.2016.11.002
Mendoza, L. F. D., Quimi Mujica, J. G., Risco Cunayque, J. M., Aroni Lucana, G. W., Intriago Angulo, J. J., Sernaquía De la Cruz, V. I., Cedeño Escobar, V. A., & Matonnier, E. M. 2019. Assessment of heterotrophic nitrification capacity in Bacillus spp. and its potential application in the removal of nitrogen from aquaculture water. Journal of Pure and Applied Microbiology, 13(4), 1893–1908. https://doi.org/10.22207/JPAM.13.4.02
Mir, D. H., & Rather, M. A. 2024. Kinetic and biosorption analysis of ammonia nitrogen (NH3−N) by Bacillus subtilis strain ON358108, isolated from eutrophicated Dal Lake waters in Srinagar, India. Bioresource Technology Reports, 26: 101857. https://doi.org/10.1016/j.biteb.2024.101857
Mpongwana, N., Ntwampe, S. K. O., Omodanisi, E. I., Chidi, B. S., & Razanamahandry, L. C. 2019. Sustainable approach to eradicate the inhibitory effect of free-cyanide on simultaneous nitrification and aerobic denitrification during wastewater treatment. Sustainability, 11(21). https://doi.org/10.3390/su11216180
Pan, R., Zou, S., Zheng, G., Li, S., Guo, Z., & Xu, W. 2023. Cooperative adaptation strategies of different tissues in blunt snout bream (Megalobrama amblycephala) juvenile to acute ammonia nitrogen stress. Environmental Science and Pollution Research, 30(40): 92042–92052. https://doi.org/10.1007/s11356-023-28283-5
Peng, C., Gao, Y., Tan, Y., Sheng, G., Yang, Y., Huang, J., Sun, D., Zhang, D., Tao, H., & Li, F. 2022. Pollution and Release Characteristics of Nitrogen, Phosphorus and Organic Carbon in Pond Sediments in a Typical Polder Area of the Lake Taihu Basin. Water, 14(5). https://doi.org/10.3390/w14050820
Rahimi, S., Modin, O., & Mijakovic, I. 2020. Technologies for biological removal and recovery of nitrogen from wastewater. Biotechnology Advances, 43: 107570. https://doi.org/10.1016 /j.biotechadv.2020.107570
Ren, W., Wu, H., Guo, C., Xue, B., Long, H., Zhang, X., Cai, X., Huang, A., & Xie, Z. 2021. Multi-Strain Tropical Bacillus spp. as a Potential Probiotic Biocontrol Agent for Large-Scale Enhancement of Mariculture Water Quality. Frontiers in Microbiology, 12: 1–14. https://doi.org/10.3389/fmicb.2021.699378
Shalaby, M. E., El-Khateeb, N. M. M., El-Gremi, S. M., & El-Sayed, I. E. 2020. Biological remediation of ammonia in the river Nile by using efficient bacillus isolates under static culture conditions. Applied Ecology and Environmental Research, 18(1): 1183–1196. https://doi.org/10.15666/aeer/1801_11831196
Shimaya, C., & Hashimoto, T. 2008. Improvement of media for thermophilic ammonia-oxidizing bacteria in compost. Soil Science and Plant Nutrition, 54(4): 529–533. https://doi.org/10.1111/j.1747-0765.2008.00272.x
Wang, Z., Liu, H., & Cui, T. 2023. Identification of a strain degrading ammonia nitrogen, optimization of ammonia nitrogen degradation conditions, and gene expression of key degrading enzyme nitrite reductase. Fermentation, 9(4): 397. https://doi.org/10.3390/fermentation9040397
Wani, S. M., Chesti, A., Rehman, S., Chandra Nautiyal, V., Bhat, I. A., & Ahmad, I. 2025. Repurposing and reusing aquaculture wastes through a biosecure microfloc technology. Environmental Research, 121214. https://doi.org/10.1016/j.envres.2025.121214
Wardhani, S., Ridho, M. R., Arinafril, Arita, S., & Ngudiantoro. 2017. Consortium of heterotrophic nitrification bacteria Bacillus sp. and its application on urea fertilizer industrial wastewater treatment. Malaysian Journal of Microbiology, 13(3): 156–163. https://doi.org/10.21161/mjm.89316
Yan, W., Wang, N., Wang, Z., Shi, J., Tang, T., & Liu, L. 2025. Nitrogen removal characteristics and mechanism of the aerobic denitrifying bacterium Stutzerimonas stutzeri os3 isolated from shrimp aquaculture sediment. Marine Pollution Bulletin, 214: 117711. https://doi.org/10.1016/j.marpolbul.2025.117711
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The data that support the findings of this study are available from the corresponding author upon reasonable request.
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