Abstract
Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.
Highlights
China is the world’s largest producer, consumer, processor, and exporter of fish
The oxidation of ammonium mainly occurs in the pond sediments, probably because of photoinhibition, and we previously found a low abundance of ammonia-oxidizing microorganisms in freshwater aquaculture water throughout the year (Lu et al, 2015)
Are able to assimilate organic substrates and thereby be able to grow mixotrophically or even heterotrophically. This view is supported by studies of archaeal isolates from soil and marine sediments (Tourna et al, 2011; Qin et al, 2014), our results are quite different from those that showed a negative correlation between ammonia-oxidizing archaea (AOA) abundance and total organic carbon (TOC) concentrations in the sediments of a eutrophic lake and river (Wu et al, 2010; Wang et al, 2014b)
Summary
China is the world’s largest producer, consumer, processor, and exporter of fish. To obtain more benefits from aquaculture, higher stocking densities are becoming prevalent. Large residual feed and feces are deposited into aquaculture sediments (Cao et al, 2015). A large amount of ammonia will be produced and released into the aquaculture water during the mineralization of organic matter. Ammonia significantly contributes to the eutrophication of aquaculture pond ecosystems, but is one of the most toxic substances in intensive fish farming (Ackefors and Enell, 1994; Randall and Tsui, 2002).
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
