Development of a microbial community-based index of biotic integrity (MC-IBI) for the assessment of ecological status of rivers in the Taihu Basin, China

The development of microbial community-based biological indicators for assessing aquatic ecological status is urgently needed in heavily impaired regions, due to the local extinction of traditional indicator macroorganisms. The aim of this study was to develop and validate a microbial community-based index of biotic integrity (MC-IBI) for the assessment of rivers in the Taihu Basin, China. MC-IBI was developed based on sediment samples collected from 55 sites of 42 rivers, with least disturbed sites as reference sites. High-throughput sequencing and real-time PCR methods were employed to measure the microbial diversity and abundance of the samples. A total of 341 candidate metrics related to microbial diversity, composition, pollution tolerance and function categories were established based on microbial data. Five core metrics, including% FCA (percentage of Firmicutes, Chloroflexi and Acidobacteria), log 16S rRNA/ARG (log the ratio of 16S rRNA gene to antibiotic resistance gene), log AOB/AOA (log the ratio of ammonium oxidizing bacteria to ammonium oxidizing archaea), nirK/nirS (ratio of nirK gene to nirS gene) and BFG/A (ratio of Bacteroidetes, Firmicutes and Gammaproteobacteria to Alphaproteobacteria), were identified to develop a MC-IBI. The developed MC-IBI was demonstrated to be robust using a validation dataset. Further, the MC-IBI showed a significantly negative association with the index of water quality. The river ecological conditions of the 55 sampled sites in the Taihu Basin were defined as excellent (9.1%), good (14.5%), moderate (25.5%), poor (23.6%) and bad (27.3%) separately based on the MC-IBI scores. Overall, the MC-IBI provides a novel assessment tool for the ecological health status of freshwater rivers.