Abstract In contrast to the macrophyte‐dominated regime (MDR), the phytoplankton‐dominated regime (PDR) in shallow lakes is characterized by relatively high nutrient concentrations, excessive phytoplankton growth and turbid water column. Some floating‐leaved plants can grow under both regimes and aid in reducing nutrient concentrations in water bodies. Their epiphytic bacterial assemblages play an essential role in the health and adaptation of these plants; however, there is limited understanding of this plant‐bacteria interaction. Here, we used 16S rRNA gene‐based high‐throughput sequencing to compare the diversity, composition and co‐occurrence patterns of planktonic and epiphytic bacterial assemblages associated with the submerged roots and floating leaves of Trapa natans, growing under the PDR and MDR in Lake Taihu, China. Alpha diversity of PDR epiphytic bacterial assemblages was lower than in MDR. The opposite trend was observed for planktonic bacterial assemblages. We detected a strong compositional difference between epiphytic and planktonic bacterial assemblages. Bacterial assemblages found on root and leaf surfaces showed only minimal compositional overlap with those in the water column. The composition of epiphytic bacterial assemblages differed more between the two regimes than did planktonic bacterial assemblages. The PDR co‐occurrence network of bacterial assemblages was more complex than that of the MDR, with the PDR epiphytic habitats enriched more network keystone taxa. The proportion of positive edges was also greater in the PDR networks of epiphytic bacterial assemblages than in the epiphytic MDR networks, whereas it was lower in the planktonic bacterial network from the PDR than from the MDR. The comprehensive view of the diversity, composition and co‐occurrence patterns of epiphytic and planktonic bacterial assemblages of MDR and PDR in large shallow lakes provided by our results showed that the structure of epiphytic bacterial assemblages was mediated by both host and water properties, and the observed core taxa and network keystone species may play an important role in maintaining plant growth and adaptation to environmental change.
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