Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia.
Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
Sci Rep. 2022 Sep 29;12(1):16346. doi: 10.1038/s41598-022-19954-3.
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010-2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species-stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
生物多样性调查对于监测受威胁的水生生态系统（如热带河口和红树林）的状况至关重要。传统的监测方法具有侵入性、耗时、昂贵，并且在复杂生境中通常只能提供粗略估计。一种先进的监测方法，环境 DNA（eDNA）宏条形码技术，具有很大的潜力，尽管在热带红树林河口仅报道了少数应用。在这项研究中，我们探讨了 eDNA 宏条形码调查在马来西亚 Merbok 河口鱼类群落中的优势和局限性。COI 和 12S eDNA 宏条形码分析共检测到 178 种鱼类，分属于 127 属、68 科和 25 目。使用这种方法，过去十年（2010-2019 年）在 Merbok 河口检测到的物种数量显著多于传统调查，包括一些具有保护意义的物种。然而，我们强调了三个局限性：（1）在缺乏全面参考数据库的情况下，一些物种的身份尚未确定；（2）一些以前基于标本的多样性没有被当前方法捕获，这可能是由于 PCR 引物的特异性造成的；（3）检测到非本地物种-狭盐性淡水类群（如鲤科鱼类、海鳝科鱼类、攀鲈科鱼类）和海洋珊瑚礁类群（如 Holocentridae 科鱼类、部分合鳃鱼科鱼类和鲨鱼），这些物种不常出现在河口，推测它们的 DNA 通过水运动漂移到河口。群落分析表明，Merbok 河口鱼类多样性并不均匀，上游比下游更具多样性。这可能是由于河口不同的景观或人为影响程度不同所致。总之，我们证明了 eDNA 宏条形码在评估复杂而丰富的热带环境中的鱼类群落和结构方面的实用性，且在短时间内完成采样。然而，需要考虑并解决一些局限性，以充分发挥这种方法的效果。
