Application of Polymerase Chain Reaction (PCR) for the Detection of Environmental Pollution (Water, Air, and Soil): A Review

Maya Novenda; Noor Rizqi Nadzifa Hidayati; Hafidha Khairunnisa; Elza Putri Ariyani

doi:10.30598/rumphiusv6i1p006-023

Maya Novenda Universitas Negeri Semarang
Noor Rizqi Nadzifa Hidayati Universitas Negeri Semarang
Hafidha Khairunnisa Universitas Negeri Semarang
Elza Putri Ariyani Universitas Negeri Semarang

DOI: https://doi.org/10.30598/rumphiusv6i1p006-023

Abstract

The environment is an important unit in the life of living creatures. The environment provides resources that are beneficial for life such as water, soil, air, minerals, flora, and fauna. Environmental pollution is a problem that often occurs and will impact the survival of living things. The aim of writing this article is to provide information on PCR technology in the living environment. Data collection was carried out by searching literature in the form of international articles for the last 5 years from 2018-2023 and produced 36 research articles related to PCR applications in the environment. Data searches were carried out via search engines, namely Google, PubMed, NCBI, and Publish or Perish 8 software. Based on the article, the PCR method can be used to detect microorganisms that are markers of environmental pollution

Downloads

Download data is not yet available.

References

Baboli, Z., Neisi, N., Babaei, A. A., Ahmadi, M., Sorooshian, A., Birgani, Y. T., & Goudarzi, G. (2021). On the airborne transmission of SARS-CoV-2 and relationship with indoor conditions at a hospital. Atmospheric Environment, 261. https://doi.org/10.1016/j.atmosenv.2021.118563.

Barbieri, P., Zupin, L., Licen, S., Torboli, V., Semeraro, S., Cozzutto, S., Palmisani, J., Di Gilio, A., de Gennaro, G., Fontana, F., Omiciuolo, C., Pallavicini, A., Ruscio, M., & Crovella, S. (2021). Molecular detection of SARS-CoV-2 from indoor air samples in environmental monitoring needs adequate temporal coverage and infectivity assessment. Environmental Research, 198. https://doi.org/10.1016/j.envres.2021.111200.

Bozack, A., Pierre, S., DeFelice, N., Colicino, E., Jack, D., Chillrud, S. N., Rundle, A., Astua, A., Quinn, J. W., McGuinn, L., Yang, Q., Johnson, K., Masci, J., Lukban, L., Maru, D., & Lee, A. G. (2022). Long-Term Air Pollution Exposure and COVID-19 Mortality: A Patient-Level Analysis from New York City. American Journal of Respiratory and Critical Care Medicine, 205(6), 651–662. https://doi.org/10.1164/rccm.202104-0845OC.

Brumfield, K. D., Cotruvo, J. A., Shanks, O. C., Sivaganesan, M., Hey, J., Hasan, N. A., Huq, A., Colwell R. R., & Leddy, M. B. (2021). Metagenomic sequencing and quantitative real-time PCR for fecal pollution assessment in an urban watershed. Frontiers in Water, 3, 626849. https://doi.org/10.3389/frwa.2021.626849.

Cao, Y., Yu, M., Dong, G., Chen, B., & Zhang, B. (2020). Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 25(3), 706. https://doi.org/10.3390/MOLECULES25030706.

Chan, V. W. M., So, S. Y. C., Chen, J. H. K., Yip, C. C. Y., Chan, K. H., Chu, H., Chung, T. W. H., Sridhar, S., To, K. K. W., Chan, J. F. W., Hung, I. F. N., Ho, P. L., & Yuen, K. Y. (2020). Air and environmental sampling for SARS-CoV-2 around hospitalized patients with coronavirus disease 2019 (COVID-19). Infection Control and Hospital Epidemiology, 41(11), 1258–1265. https://doi.org/10.1017/ice.2020.282.

Cheng, Z., Shi, J., He, Y., Wu, L., & Xu, J. (2022). Assembly of root-associated bacterial community in cadmium contaminated soil following five-year consecutive application of soil amendments: Evidences for improved soil health. Journal of Hazardous Materials, 426. https://doi.org/10.1016/j.jhazmat.2021.128095.

Chia, P. Y., Coleman, K. K., Tan, Y. K., Ong, S. W. X., Gum, M., Lau, S. K., Lim, X. F., Lim, A. S., Sutjipto, S., Lee, P. H., Son, T. T., Young, B. E., Milton, D. K., Gray, G. C., Schuster, S., Barkham, T., De, P. P., Vasoo, S., Chan, M., … Moses, D. (2020). Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16670-2.

Du, Y., Zhang, D., Zhou, D., Liu, L., Wu, J., Chen, H., Jin, D., & Yan, M. (2021). The growth of plants and indigenous bacterial community were significantly affected by cadmium contamination in soil–plant system. AMB Express, 11(1). https://doi.org/10.1186/s13568-021-01264-y.

Faridi, S., Niazi, S., Sadeghi, K., Naddafi, K., Yavarian, J., Shamsipour, M., Jandaghi, N. Z. S., Sadeghniiat, K., Nabizadeh, R., Yunesian, M., Momeniha, F., Mokamel, A., Hassanvand, M. S., & MokhtariAzad, T. (2020). A field indoor air measurement of SARS-CoV-2 in the patient rooms of the largest hospital in Iran. Science of the Total Environment, 725. https://doi.org/10.1016/j.scitotenv.2020.138401.

Gu, Y., Shen, S., Han, B., Tian, X., Yang, F., & Zhang, K. (2020). Family livestock waste: An ignored pollutant resource of antibiotic resistance genes. Ecotoxicology and Environmental Safety, 197. https://doi.org/10.1016/j.ecoenv.2020.110567.

Guo, T., Lou, C., Zhai, W., Tang, X., Hashmi, M. Z., Murtaza, R., Li, Y., Liu, X., & Xu, J. (2018). Increased occurrence of heavy metals, antibiotics and resistance genes in surface soil after long-term application of manure. Science of the Total Environment, 635, 995–1003. https://doi.org/10.1016/j.scitotenv.2018.04.194.

Hamza, I.A., & Leifels, M. (2024). Assessment of PCR Inhibitor Removal Methods to Monitor Viruses in Environmental Water Samples: DAX-8 Outperforms Competitors. Water Air Soil Pollut, 235, 20. https://doi.org/10.1007/s11270-023-06821-8.

Holcomb, D. A., Knee, J., Sumner, T., Adriano, Z., de Bruijn, E., Nalá, R., Cumming, O., Brown, J., & Stewart, J. R. (2020). Human fecal contamination of water, soil, and surfaces in households sharing poor-quality sanitation facilities in Maputo, Mozambique. International Journal of Hygiene and Environmental Health, 226. https://doi.org/10.1016/j.ijheh.2020.113496.

Karunakaran, E., Battarbee, R., Tait, S., Brentan, B. M., Berney, C., Grinham, J., ... & Douterelo, I. (2024). Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters. Science of the Total Environment, 912, 168565. https://doi.org/10.1016/j.scitotenv.2023.168565.

Kayalar, Ö., Arı, A., Babuççu, G., Konyalılar, N., Doğan, Ö., Can, F., Şahin, Ü. A., Gaga, E. O., Levent Kuzu, S., Arı, P. E., Odabaşı, M., Taşdemir, Y., Sıddık Cindoruk, S., Esen, F., Sakın, E., Çalışkan, B., Tecer, L. H., Fıçıcı, M., Altın, A., … Bayram, H. (2021). Existence of SARS-CoV-2 RNA on ambient particulate matter samples: A nationwide study in Turkey. Science of the Total Environment, 789. https://doi.org/10.1016/j.scitotenv.2021.147976.

Kenarkoohi, A., Noorimotlagh, Z., Falahi, S., Amarloei, A., Mirzaee, S. A., Pakzad, I., & Bastani, E. (2020). Hospital indoor air quality monitoring for the detection of SARS-CoV-2 (COVID-19) virus. Science of the Total Environment, 748. https://doi.org/10.1016/j.scitotenv.2020.141324.

Klepeis, N. E., Nelson, W. C., Ott, W. R., Robinson, J. P., Tsang, A. M., Switzer, P., Behar, J. V., Hern, S. C., & Engelmann, W. H. (2001). The National Human Activity Pattern Survey (NHAPS): a resource for assessing exposure to environmental pollutants. Journal of Exposure Analysis and Environmental Epidemiology, 11(3), 231–252. https://doi.org/10.1038/SJ.JEA.7500165.

Kogevinas, M., Castaño-Vinyals, G., Karachaliou, M., Espinosa, A., de Cid, R., Garcia-Aymerich, J., Carreras, A., Cortés, B., Pleguezuelos, V., Jiménez, A., Vidal, M., O’callaghan-Gordo, C., Cirach, M., Santano, R., Barrios, D., Puyol, L., Rubio, R., Izquierdo, L., Nieuwenhuijsen, M., … Tonne, C. (2021). Ambient air pollution in relation to SARS-CoV-2 infection, antibody response, and COVID-19 disease: A cohort study in Catalonia, Spain (COVICAT study). Environmental Health Perspectives, 129(11). https://doi.org/10.1289/EHP9726.

Molaee, N., Abtahi, H., Ghannadzadeh, M.J. et al. (2015). Application of Reverse Transcriptase –PCR (RT-PCR) for rapid detection of viable Escherichia coli in drinking water samples. J Environ Health Sci Engineer, 13, 24. https://doi.org/10.1186/s40201-015-0177.

Neneng, L., Nugroho, R. A., Komai, Y., Takayama, N., & Kawamura, K. (2020). Water quality measurements with a simple molecular analysis (PCR-RFLP) of the microbiome in a metropolitan river system in Japan. Walailak Journal of Science and Technology (WJST), 17(3), 257-268. https://doi.org/10.48048/wjst.2020.5869

Noorimotlagh, Z., Jaafarzadeh, N., Silva Martínez, S., & Mirzaee, A. (2020). A systematic review of possible airborne transmission of the COVID-19 virus (SARS-CoV-2) in the indoor air environment. Environmental Research, 193, 110612. https://doi.org/10.1016/j.envres.2020.110612.

Paruch L. (2022). Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. Int J Environ Res Public Health, 19(9):5128. https://doi.org/10.3390/ijerph19095128

Pu, Q., Wang, H. T., Pan, T., Li, H., & Su, J. Q. (2020). Enhanced removal of ciprofloxacin and reduction of antibiotic resistance genes by earthworm Metaphire vulgaris in soil. Science of the Total Environment, 742. https://doi.org/10.1016/j.scitotenv.2020.140409.

Pu, Q., Zhao, L. X., Li, Y. T., & Su, J. Q. (2020). Manure fertilization increase antibiotic resistance in soils from typical greenhouse vegetable production bases, China. Journal of Hazardous Materials, 391. https://doi.org/10.1016/j.jhazmat.2020.122267.

Shanks, O. C., & Korajkic, A. (2020). Microbial source tracking: characterization of human fecal pollution in environmental waters with HF183 quantitative real-time PCR. Microbial Forensics (pp. 71-87). Academic Press. https://doi.org/10.1016/B978-0-12-815379-6.00006-4.

Some, S., Mondal, R., Mitra, D., Jain, D., Verma, D., & Das, S. (2021). Microbial pollution of water with special reference to coliform bacteria and their nexus with environment. Energy Nexus, 1, 100008. https://doi.org/10.1016/j.nexus.2021.100008

Sompotan, D. D., & Sinaga, J. (2022). Pencegahan Pencemaran Lingkungan. SAINTEKES: Jurnal Sains, Teknologi Dan Kesehatan, 1(1), 6–13. https://doi.org/10.55681/saintekes.v1i1.2.

Subashchandrabose, S. R., Venkateswarlu, K., Venkidusamy, K., Palanisami, T., Naidu, R., & Megharaj, M. (2019). Bioremediation of soil long-term contaminated with PAHs by algal–bacterial synergy of Chlorella sp. MM3 and Rhodococcus wratislaviensis strain 9 in slurry phase. Science of the Total Environment, 659, 724–731. https://doi.org/10.1016/j.scitotenv.2018.12.453.

Teixeira, P., Costa, S., Brown, B., Silva, S., Rodrigues, R., & Valerio, E. (2020). Quantitative PCR detection of enteric viruses in wastewater and environmental water sources by the Lisbon municipality: A case study. Water, 12(2), 544. https://doi.org/10.3390/w12020544.

Ukaogo, P. O., Ewuzie, U., & Onwuka, C. V. (2020). Environmental pollution: causes, effects, and the remedies. Microorganisms for Sustainable Environment and Health, 2020, 419-429. https://doi.org/10.1016/B978-0-12-819001-2.00021-8

Wang, X., Lu, X., Yi, X., Li, Z., Zhou, Y., Duan, G., & Lei, M. (2021). Changes in soil available cadmium and bacterial communities after fallowing depend on contamination levels. Soil and Landscape Ecology, 21, 1408–1419. https://doi.org/10.1007/s11368-021-02877-3.

Zhang, F., Zhao, X., Li, Q., Liu, J., Ding, J., Wu, H., Zhao, Z., Ba, Y., Cheng, X., Cui, L., Li, H., & Zhu, J. (2018). Bacterial community structure and abundances of antibiotic resistance genes in heavy metals contaminated agricultural soil. Environmental Science and Pollution Research, 25(10), 9547–9555. https://doi.org/10.1007/s11356-018-1251-8.