Estuarine habitats contribute disproportionately as nursery habitats for marine fish, yet are amongst the most anthropogenically degraded ecosystems on Earth. Juvenile fish growing in urbanised estuarine habitats are subject to a mosaic of stressors, thus development of higher resolution methods to gain a more complete assessment of fish responses is vital. Accordingly, this study provides the first assessment of metabolomic profiling as a new bioindicator of habitat quality for juvenile fish. We matched traditional bioindicator methods (fish growth rates) with metabolomic profiles in juvenile snapper (Chrysophrys auratus), a culturally and commercially important species across Australia and New Zealand. Juvenile snapper were collected from, and within, harbour sites occupying a gradient in turbidity, a significant stressor for this species that is known to result in reduced weight, mortality and deleterious physiological responses.

We found that fish growth assessed using otolith increments was not reflective of the turbidity gradient with little discrimination among sites. However, metabolomic profiling was highly sensitive and reproducible, with 100% accuracy in discriminating fish from harbours with differing turbidity. These differences in metabolic profiles were largely driven by metabolites and pathways involved in energy production, processes of growth, or the immune response. In particular, the amino acids Cysteine and 4-aminobutyric acid (GABA), linked to growth and development in snapper, were elevated in juveniles from more pristine harbours, and offer promising candidates for use as a biomarker of habitat quality in this species.

Thus, we show that metabolomic approaches can uncover site differences that traditional and more coarse methods were unable to detect. This work provides a novel baseline for the use of metabolomic profiling on wild-caught snapper to inform management and conservation decisions, with the potential to identify biomarkers reflective of habitat quality.

河口栖息地作为海水鱼类苗圃栖息地的贡献不成比例，但仍是地球上人为退化最严重的生态系统之一。在城市化的河口栖息地中生长的幼鱼容易受应激因素的影响，因此开发更高分辨率的方法以获得对鱼反应的更完整评估至关重要。因此，本研究首次对代谢组学谱进行了评估，将其作为幼鱼栖息地质量的新生物指标。我们将传统的生物指示剂方法（鱼类生长速率）与少年鲷鱼（Chrysophrys auratus）的代谢组学特征进行了匹配），是澳大利亚和新西兰的重要文化和商业物种。幼鲷鱼是从浑浊度呈梯度变化的海港地点及其内部收集的，这是该物种的重要压力源，已知会导致体重减轻，死亡率降低和有害的生理反应。

我们发现，使用耳石增量评估的鱼类生长不能反映浊度梯度，并且在站点之间几乎没有区别。但是，代谢组学分析具有很高的灵敏度和可重复性，能够以100％的准确度将鱼与具有不同浊度的港口区分开。代谢谱的这些差异主要是由参与能量产生，生长过程或免疫反应的代谢物和途径驱动的。尤其是，与鲷鱼的生长和发育有关的半胱氨酸和4-氨基丁酸（GABA）氨基酸在更多来自原始港口的幼鱼中被升高，并有望用作该物种栖息地质量的生物标记。

因此，我们表明，代谢组学方法可以发现传统和更粗糙的方法无法检测到的位点差异。这项工作为在野生鲷鱼上进行代谢组学分析提供了新的基线，以指导管理和保护决策，并有可能识别出反映栖息地质量的生物标志物。