Response of the microbial community to bioturbation by benthic macrofauna on intertidal flats

•Nutrient content were decreased significantly by bioturbation.•Pore-water profiles in sediments were significantly influenced by bioturbation.•The microbial community in sediments was not significantly changed by bioturbation.•The relative abundance of Nitrospirae and the number of AOB amoA copies were increased significantly by bioturbation.

Benthic macrofauna are considered to have important effects on the microbial-driven cycling of nutrients in sediments. The response of the microbial community to bioturbation by macrofauna is not fully understood. This study investigated variations in the microbial communities and nutrient profiles after bioturbation by the clam Meretrix meretrix and polychaete Perinereis aibuhitensis. The total nitrogen, total phosphorus, total organic carbon and dissolved inorganic nitrogen contents of sediments decreased dramatically in the presence of Meretrix meretrix and Perinereis aibuhitensis. In total, 64 bacterial phyla and three archaeal phyla were identified, where Proteobacteria were dominant and they accounted for > 30% in all reads with a stable percentage among all samples. Eleven bacterial phyla, i.e. unclassified, AC1, Acidobacteria, Actinobacteria, Cyanobacteria, Gemmatimonadetes, KSB3, Lentisphaerae, Nitrospirae, Spirochaetes, Verrucomicrobia and WS3, were influenced significantly by bioturbation using Meretrix meretrix or Perinereis aibuhitensis. Analysis of similarities and non-metric multidimensional scaling analysis demonstrated that the bacterial communities did not differ significantly in the control and macrofauna-inhabited sediments. The number of bacterial amoA copies increased significantly in the presence of macrofauna, but not the number of archaeal amoA copies. The results of this study demonstrate that bioturbation by Meretrix meretrix or Perinereis aibuhitensis can cause structural and compositional changes in sediment microbial communities by increasing the abundance of nitrogen-cycling bacteria and decreasing the nutrient levels in sediments.