Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to the coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of the coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine teleost and elasmobranch fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly lower during the sampled dry season. With the influx of freshwater and agricultural run-off during the wet season, teleost and elasmobranch taxa richness significantly decreased in all three estuaries, along with pronounced changes in fish community composition which were largely associated with environmental variables (particularly salinity). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Within the wet season, differing compositions of fish communities were observed among the four sampled locations, with this variation being significantly correlated with environmental variables (salinity, chlorophyll, DOC) and contaminants from agricultural run-off, i.e., nutrients (nitrogen and phosphorus) and pesticides. Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects (e.g., changes in salinity) play a key role in shaping the community structure of estuarine fish in this region, agricultural contaminants (nutrients and pesticides) are also important contributors in some systems.

澳大利亚麦凯-惠森迪（Mackay-Whitsunday）地区的农业径流，是大堡礁沿海与近岸生态系统面临营养盐与农药污染的主要来源。尽管该区域珊瑚与海草生境受径流影响的相关研究已有充分记载，但作为径流直接接收体的河口生态系统所受的生态影响却鲜为人知，这一点在鱼类群落层面尤为显著——鱼类群落的组成深受热带沿岸水道理化性质的影响，而这类理化性质在热带区域差异显著。为填补这一研究空白，本研究采用环境DNA（eDNA）宏条形码（metabarcoding）技术，对湿季与旱季期间、受不同程度农业径流影响的4个采样点位（3个河口与1个港湾）的硬骨鱼类与板鳃鱼类群落展开调查。本次采样覆盖的旱季时段，农药与营养盐浓度均显著偏低。随着湿季淡水径流与农业径流的涌入，3个河口的硬骨鱼类与板鳃鱼类类群丰富度均显著下降，同时鱼类群落组成发生显著变化，这类变化主要与沿岸水环境的理化变量（尤以盐度为甚）密切相关。与之形成鲜明对比的是，邻近的麦凯港湾（Mackay Harbour）群落结构更为稳定，两次采样季之间未观测到鱼类群落出现明显变化。在湿季内部，4个采样点位的鱼类群落组成存在显著差异，且该差异与环境变量（盐度、叶绿素、溶解性有机碳（Dissolved Organic Carbon, DOC））以及农业径流带来的污染物（即氮、磷等营养盐与农药）显著相关。历史上受污染与相对未受影响的河口均各自形成了独特的鱼类群落，这反映了其所在集水区的土地利用特征。本研究结果表明，尽管季节效应（如盐度变化）在塑造该区域河口鱼类群落结构方面发挥着关键作用，但农业污染物（营养盐与农药）在部分生态系统中也是重要的影响因子。