Diversity and community composition of nirS-type denitrifying bacteria and ammonia-oxidizing archaea in biofilm samples attached to bio-substrate and abio-substrates in integrated ecological floating bed systems

In the present study, integrated ecological floating bed systems (IEFBs) were designed using a bio-substrate, Ipomoea aquatica (substrate-type referred to as G), in conjunction with three abio-substrates, namely nylon net (substrate-type W), artificial bionic macrophytes (substrate-type F) and pellets (substrate-type Q). IEFBs were operated in triplicate in a natural lake for approximately 72 days. Attached biofilms from the substrate surfaces were sampled separately. Next, nirS and amoA genes were chosen as molecular markers to investigate the diversities and community structures of nirS-type denitrifying bacteria and ammonia-oxidizing archaea (AOA), respectively, in the IEFBs. Results show that the elemental content in the attached biofilm were altered by the bio-substrate/abio-substrates differences. Such micro-niches and nutrients on the bio-substrate and abio-substrate surfaces potentially influenced the diversities and community compositions of nirS-type denitrifying bacteria and AOA in the IEFBs. For nirS-type denitrifying bacteria, the highest richness indices (Chao and ACE) were observed in the G3, whereas the highest Shannon indices were respectively obtained in the G2, indicating that biofilms from the bio-substrate had the higher alpha diversity. For the amoA gene, W substrates could increase the archaeal community richness in the IEFBs. Proteobacteria and Thaumarchaeota were the most shared microbial phylum in all collected samples. Total 19 and 4 genera were detected from collected samples with unclassified_p__Proteobacteria (7.21–60.97%), unclassified_c__Alphaproteobacteria (2.82–36.92%), unclassified_o__Burkholderiales (0–2.36%) for nirS-type denitrifying bacteria and Nitrososphaera (8.11–10.81%) for amoA gene. Unclassified sequences with relative abundance of 9.56–65.16% and 2.70–70.27% were also found in collected biofilm samples for nirS-type denitrifying bacteria and AOA. Nitrososphaera, Acidovorax, Rhodanobacter, Magnetospirillum, Paracoccus, Azospirillum genera were obtained with a smaller proportion. PERMANOVA and ANOSIM tests (Bray-Curtis) (P < 0.05) confirmed the significant differences in the beta diversity of the denitrifying bacterial and AOA among four substrates groups. Further, attached biofilms-associated physicochemical characteristics significantly driven bacterial and archaeal community composition. The above-mentioned taxa in the bio-substrate and three abio-substrate surfaces were essential for enriching the community structure of bacterial and archaeal in the IEFBs.