Journal of Soils and Sediments

, Volume 19, Issue 4, pp 2126–2142 | Cite as

Ammonia-oxidizing bacterial and archaeal communities in tropical bioaugmented zero water exchange shrimp production systems

  • Ramya R. Nair
  • R. Boobal
  • S. Vrinda
  • I. S. Bright Singh
  • Joseph ValsammaEmail author
Sediments, Sec 4 • Sediment-Ecology Interactions • Research Article



Ammonia oxidation is an important process in the removal of ammonia generated from feed and metabolic wastes in aquaculture systems. Considering the biogeochemical importance of ammonia oxidation in bioaugmented zero water exchange aquaculture systems, the diversity and abundance of bacterial and archaeal ammonia-oxidizing communities were analyzed in three selected ponds at different time intervals during the culture period, to unravel the key environmental factors influencing their distribution in the system.

Materials and methods

The diversity and abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in three tropical bioaugmented zero water exchange (ZWE) shrimp culture systems were analyzed using ammonia monooxygenase A (amoA) gene from the sediment metagenome during different phases of culture. The environmental factors associated with the variability in bacterial and archaeal amoA gene abundance and diversity were elucidated using RDA and Pearson correlation analysis.

Results and discussion

Ammonia-oxidizing archaea (AOA), Nitrosopumilus sp., Nitrosospharea sp., and ammonia-oxidizing bacteria (AOB), Nitrosomonas sp., were the dominant ammonia-oxidizing communities in the ZWE ponds studied. AOA shared 41 OTUs, and the maximum distribution was influenced by dissolved oxygen in the system, whereas AOB shared 4 OTUs. The copy numbers amoA gene determined using qPCR showed that the AOA amoA gene was 10- to 100-fold abundant than AOB amoA gene. Gene abundance of AOA was positively related to total organic carbon (TOC) and salinity of sediments, and the temperature had a negative impact on bacterial amoA gene abundance. The dissolved oxygen and TOC had a negative and redox potential a positive impact on the diversity of AOA, whereas pH had a negative impact on the diversity of AOB.


The ammonia-oxidizing archaeal communities dominated the bioaugmented zero water exchange aquaculture systems compared to bacteria based on the abundance and diversity analysis using amoA gene sequence-based OTU analysis and gene copy numbers. Dissolved oxygen, total organic carbon, and Eh of the sediments contributed to the distribution and abundance of AOA group in the ZWE ponds. This study points to the importance of environmental management in these culture systems for maintaining ammonia-oxidizing populations for optimal ammonia removal. The relative contribution of the archaea and bacteria to ammonia oxidation in these systems is to be further resolved along with that of anammox and comammox bacteria, which would help to develop appropriate biostimulation or bioaugmentation strategies for the management of these sustainable aquaculture production systems.


Ammonia monooxygenase gene Ammonia-oxidizing archaea Ammonia-oxidizing bacteria Bioaugmentation Zero water exchange aquaculture production system (ZWEAPS) 



The authors acknowledge the National Centre for Aquatic Animal Health, Cochin University of Science and Technology, India, for the financial support. The first author acknowledges the University Grants Commission, India, for the financial support in the form Junior and Senior Research Fellowships (Ref. No: 20-12/2009(ii)E-IV).

Compliance with ethical standards

Conflict of interest

No conflict of interest exists in the submission of this manuscript, and the manuscript is approved by all authors for publication.

Supplementary material

11368_2018_2185_MOESM1_ESM.docx (1.5 mb)
ESM 1 (DOCX 1578 kb)


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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.National Centre for Aquatic Animal HealthCochin University of Science and TechnologyKochiIndia

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