Coastal eutrophication transforms shallow micro-benthic reef communities

Coral reefs are impacted worldwide by coastal eutrophication, which is often translated by a decrease in coral cover and an increase in potentially harmful invertebrates and algal blooms. Additionally to corals and other macro-benthos, micro-benthic communities are affected tremendously, however few studies reported the specific effect of eutrophication on those communities. This study addresses how micro-benthic communities are impacted by turbidity and associated eutrophication. To answer this question, we compared three groups that have been previously suggested as bioindicators of reef environmental conditions: foraminifera, diatoms and bacteria, from 12 islands (and 600 samples) in the Spermonde Archipelago (Indonesia) along a near- to offshore turbidity gradient. Insights from environmental DNA metabarcoding and satellite images highlighted differences between the reef slope (deep) and the reef flat (shallow) communities, a distinction that has been omitted in most previous studies. The reef flat communities were 1.5- to 2-fold more affected by turbidity parameters compared to the reef slope, which we argue is related to eutrophication. Based on previous work, we expected that prokaryotes would be the most impacted group by water quality. However, we found that large benthic foraminifera and diatom communities were highly impacted by turbidity, whereas the reef flat prokaryotic communities were primarily shaped by the substrate type. Additionally, a total of 112 exact sequence variants (ESVs) were identified as indicators of different turbidity levels, of which 87 foraminifera and diatom ESVs were associated with high-moderate turbid waters. Our study revealed fundamental knowledge and provides key information of the specific effect of turbidity and associated eutrophication and habitat variables (substrate type and reef area) on foraminifera, diatoms and prokaryotic communities. We argue that local and regional eutrophication participates in shaping reef flat micro-benthic communities, which may therefore play an important role as early warning signals for local degradation in coral reefs.