{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T20:17:23Z","timestamp":1790885843374,"version":"4.1.0"},"reference-count":171,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T00:00:00Z","timestamp":1776729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research and Development Program of China","award":["2023YFD2403000"],"award-info":[{"award-number":["2023YFD2403000"]}]},{"name":"the Ministry of Science and Technology of the People\u2018s Republic of China, Shandong Provincial University Youth Innovation Team Project","award":["2024KJN029"],"award-info":[{"award-number":["2024KJN029"]}]},{"award":["2024KJN029"],"award-info":[{"award-number":["2024KJN029"]}],"id":[{"id":"https:\/\/ror.org\/027s68j25","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Microbial contamination in aquatic environments poses severe threats to aquaculture sustainability, ecological balance and public health. Traditional culture-based detection methods, while standardized, are time-consuming and labor-intensive, often failing to meet the urgent need for rapid on-site monitoring required to prevent disease outbreaks and manage water quality effectively. By integrating latest research advances (2020\u20132025), this study reviews advances in rapid detection technologies for aquatic microorganisms, including the evolution of nucleic acid amplification strategies, with a focused comparison of the analytical sensitivity and field deployability of quantitative polymerase chain reaction (qPCR) and mainstream isothermal amplification techniques (loop-mediated isothermal amplification, LAMP; recombinase polymerase amplification, RPA). Furthermore, this study reports on the emergence of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated protein (Cas) systems as next-generation diagnostic tools, highlighting their integration with microfluidic Lab-on-a-Chip (LOC) platforms to achieve attomolar sensitivity. We also consider the application of portable nanopore sequencing for real-time pathogen identification and the growing role of Artificial Intelligence (AI) in analyzing complex diagnostic datasets. Advanced molecular methods have achieved significant reductions in time consumption\u2014from days to less than one hour\u2014while challenges regarding sample preparation and environmental matrix inhibition remain. The future of aquatic monitoring lies in integrated, automated systems that combine the specificity of CRISPR-Cas diagnostics with the connectivity of IoT-enabled biosensors. Comparative analysis indicates that isothermal amplification methods (LAMP, RPA) coupled with CRISPR-Cas systems offer the optimal balance of sensitivity, speed, and field deployability for point-of-care aquaculture diagnostics, while qPCR\/dPCR remain indispensable for quantitative regulatory applications. We propose a structured technology selection framework to guide researchers and practitioners in choosing appropriate detection modalities based on specific sensitivity, cost, throughput, and deployment requirements.<\/jats:p>","DOI":"10.3390\/microorganisms14040939","type":"journal-article","created":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T12:00:32Z","timestamp":1776859232000},"page":"939","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Progress of Rapid Detection Technology for Aquatic Microorganisms: A Comprehensive Review"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2549-3425","authenticated-orcid":false,"given":"Qin","family":"Liu","sequence":"first","affiliation":[{"name":"College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuangzhuang","family":"Qiu","sequence":"additional","affiliation":[{"name":"School of Public Health, Jining Medical University, Jining 272002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengli","family":"Yao","sequence":"additional","affiliation":[{"name":"School of Public Health, Jining Medical University, Jining 272002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boyan","family":"Jiao","sequence":"additional","affiliation":[{"name":"Department of Laboratory, Jining Center for Disease Control and Prevention, Jining 272000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Public Health, Jining Medical University, Jining 272002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2978-8762","authenticated-orcid":false,"given":"Chenghua","family":"Li","sequence":"additional","affiliation":[{"name":"College of Marine Science, Ningbo University, Ningbo 315832, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haipeng","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0131-7697","authenticated-orcid":false,"given":"Lusheng","family":"Xin","sequence":"additional","affiliation":[{"name":"School of Public Health, Jining Medical University, Jining 272002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Xu, G., Cai, G., Liang, L., Cheng, J., Song, L., Sun, R., Shen, F., Liu, B., Feng, S., and Zhang, J. 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