Microbiological assessment of ecological status in the Pearl River Estuary, China

•The PRE ecological status was “poor” on average (microgAMBI = 3.82).•The microgAMBI index could represent both eutrophication and fecal pollution levels.•57 genus level bio-indicators for the PRE eutrophication or hypoxia were identified. Microbial assemblages, as fundamental components of the ecosystem, are largely neglected in current ecological monitoring. In this study, we employed a microbial community-based index (microgAMBI) to assess the ecological status of the Pearl River estuary (PRE) in China. Microorganisms of different water layers and size fractions were collected. The assessment results showed that the PRE ecological status was “poor” on average (microgAMBI = 3.82). The index values decreased from the upper estuary to offshore areas and showed positive correlations with nutrients, and fecal indicator bacteria, suggesting that the index could represent both eutrophication and fecal pollution levels. In addition, using a machine learning analysis (LEfSe), we identified hgcI clade, Ottowia, Marinobacterium, and 54 more taxa at the genus level as eutrophication or hypoxia bio-indicators, which could supplement the database of the microgAMBI to improve assessment accuracy. Further monitoring programs should consider incorporating this microbial community-based index to achieve a higher level of integrative assessment.