Diversity of β-Proteobacterial ammonia-oxidizing bacteria and ammonia-oxidizing archaea in shrimp farm sediment

Abstract:

Abstract：[Objective] In order to study the diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in shrimp farm sediment. [Methods] Total microbial DNA was directly extracted from the shrimp farm sediment. The clone library of amoA genes were constructed with β-Proteobacterial-AOB and AOA specific primers. The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced. [Results] Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from shrimp farm sediment were affiliated with Nitrosomonas (61.54%) or Nitrosomonas-like (38.46%) species and grouped into Nitrosomonas communis cluster、Nitrosomonas sp.Nm148 cluster、Nitrosomonas oligotropha cluster. All AOA sequences belonged to the kingdom Crenarchaeote except that one Operational Taxa Unit（OTU）sequence was Unclassified-Archaea and fell within cluster S (soil origin). AOB and AOA species composition included 13 OTUs and 9 OTUs. The clone coverage of bacterial and archaeal amoA genes was 73.47% and 90.43%. The Shannon-Wiener index, Evenness index，Simpson index and Richness index of AOB were higher than those of AOA. [Conclusion] These findings represent the first detailed examination of archaeal amoA diversity in shrimp farm sediment and demonstrate that diverse communities of Crenarchaeote capable of ammonia oxidation are present within shrimp farm sediment, where they may be actively involved in nitrification.