Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows

Assessing biodiversity in marine nearshore ecosystems is crucial for
effective management, especially in the context of climate change and
overexploitation of marine resources. Conventional methods often fall
short in providing comprehensive information for managing seagrass
ecosystems. However, the emergence of environmental DNA (eDNA) techniques
has transformed the field by enabling non-invasive surveys that are
cost-effective and provide detailed information with high resolution. In
this study, we utilized eDNA to assess fish diversity and compared its
effectiveness to conventional techniques such as catch assessment surveys
and underwater surveys. We sampled three habitats (A: mangrove-seagrass,
B: seagrass only, and C: coral-seagrass) with 4 replicates. Site A
recorded 8 fish species, site B had 16 species, and site C, characterized
by coral and seagrass habitats, exhibited the highest fish diversity with
45 species (mean H' index = 2.455), underscoring its ecological
importance. To ensure accurate taxonomic identification, we utilized an
updated MiFish reference database containing a larger number of fish
species compared to the initial library. This expanded reference database
with 9,569 fish species, facilitated more precise identification and
enhanced the reliability of our findings. Notably, the eDNA technique
outperformed conventional methods by detecting 23 additional fish species
that went undetected using traditional surveys. Moreover, our study
documented five fish species previously unknown to occur within the study
region, further emphasizing the value of eDNA analysis in uncovering
hidden biodiversity. These findings strongly advocate for integrating eDNA
techniques into the monitoring and assessment of biodiversity in shallow
tropical habitats of the Western Indian Ocean. By leveraging eDNA surveys,
we can gain valuable insights into fish diversity, discover hidden
species, and make informed decisions for the conservation and management
of these ecologically significant areas.

近岸海洋生态系统的生物多样性评估对于高效管理具有重要意义，尤其在气候变化与海洋资源过度开发的背景下。传统调查方法往往难以满足海草床生态系统管理所需的全面信息需求。然而，环境DNA（environmental DNA, eDNA）技术的出现彻底改变了这一研究领域：该技术可实现非侵入式调查，兼具成本效益优势，且能提供高分辨率的详细数据。本研究利用环境DNA（eDNA）技术评估鱼类多样性，并将其与捕捞评估调查、水下调查等传统方法的应用效果进行对比。我们对3类生境（A：红树林-海草交错生境；B：纯海草生境；C：珊瑚-海草生境）开展了4次重复采样。其中，A位点共记录鱼类8种，B位点记录16种；C位点兼具珊瑚与海草生境，鱼类多样性最高，共记录45种鱼类（平均H'多样性指数=2.455），凸显了其极高的生态价值。为确保分类学鉴定的准确性，本研究使用了更新后的MiFish参考数据库，该数据库相较初始文库收录了更多鱼类物种。这个包含9569种鱼类的扩展参考数据库，有效提升了物种鉴定的精准度，增强了研究结果的可靠性。值得注意的是，eDNA技术的表现优于传统方法：其额外检测到23种传统调查未发现的鱼类。此外，本研究还记录到5种此前未在该研究区域分布的鱼类，进一步彰显了eDNA分析在挖掘隐藏生物多样性方面的重要价值。本研究结果有力支持将eDNA技术纳入西印度洋热带浅海生境的生物多样性监测与评估工作中。通过应用eDNA调查，我们能够深入解析鱼类多样性、发现隐存物种，并为这些具有重要生态意义区域的保护与管理提供科学决策依据。