Abstract Ammonia oxidation is crucial in removing ammonia produced from feed and waste products in aquaculture systems. The present study investigated the diversity and abundance of ammonia-oxidizing microorganisms in the grow beds of three different aquaponics systems. The diversity and abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were studied in these systems using ammonia monooxygenase A (amoA) gene as a marker. In two different aquaponics systems, a significant reduction in ammonia was noticed in water after passing through grow beds. The most abundant ammonia-oxidizing populations identified were AOA, including Nitrosopumilus sp. and Nitrososphaera sp., and AOB, including Nitrosomonas sp. On analyzing the amoA gene abundance using qPCR, AOA was found at a more significant level in two different systems (7.2×103 and 8.7×103 copies/µg of DNA) as compared to the respective AOB abundances (7.3×103 and 5.6×103 copies/µg of DNA). However, in the third system, the abundance of AOB was higher (4.6×103 copies/µg of DNA) rather than AOA (1.45×103 copies/µg of DNA). Gene abundance of AOA was positively related to nitrite (NO2), whereas DO, pH, and nitrate had a negative impact on bacterial and archaeal amoA gene abundances. This study demonstrates the important role of environmental management in these systems to maintain ammonia-oxidizing populations and ensure efficient ammonia removal. Further research will be necessary to understand the relative contributions of archaea and bacteria to ammonia oxidation, as well as the roles of comammox and nitrite-oxidizing bacteria, to devise effective bioaugmentation strategies for these sustainable aquaculture systems. Research highlights <OrderedList> <ListItem> <ItemNumber>1.</ItemNumber> <ItemContent> This study unveiled the significance of ammonia oxidizing populations in aquaponics grow beds, where AOA (e.g., Nitrosopumilus, Nitrososphaera) often more abundant than AOB (Nitrosomonas). </ItemContent> </ListItem> <ListItem> <ItemNumber>2.</ItemNumber> <ItemContent> Two aquaponics systems demonstrated a significant ammonia oxidation after pond water passed through grow beds, shows a higher AOA abundance. </ItemContent> </ListItem> <ListItem> <ItemNumber>3.</ItemNumber> <ItemContent> Real-time PCR analysis of amoA genes showed AOA outnumbering AOB in two systems; however, the third system exhibited a reverse trend, indicating AOB amoA gene abundance over AOA. </ItemContent> </ListItem> <ListItem> <ItemNumber>4.</ItemNumber> <ItemContent> Copy numbers of AOA were positively correlated with nitrite levels, but dissolved oxygen, pH, and nitrate had a negative impact on both AOA and AOB gene abundances, indicating the purpose of environmental management. </ItemContent> </ListItem> </OrderedList>

Diversity and abundance of ammonia-oxidizing bacterial and archaeal communities in tropical aquaponics systems

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发表日期：

2026年3月12日

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Jifiriya M J,
Boobal R,
Preena P G,
Bini C Das,
Rejishkumar V J

摘要

Abstract

Ammonia oxidation is crucial in removing ammonia produced from feed and waste products in aquaculture systems. The present study investigated the diversity and abundance of ammonia-oxidizing microorganisms in the grow beds of three different aquaponics systems. The diversity and abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were studied in these systems using ammonia monooxygenase A (amoA) gene as a marker. In two different aquaponics systems, a significant reduction in ammonia was noticed in water after passing through grow beds. The most abundant ammonia-oxidizing populations identified were AOA, including Nitrosopumilus sp. and Nitrososphaera sp., and AOB, including Nitrosomonas sp. On analyzing the amoA gene abundance using qPCR, AOA was found at a more significant level in two different systems (7.2×10³ and 8.7×10³ copies/µg of DNA) as compared to the respective AOB abundances (7.3×10³ and 5.6×10³ copies/µg of DNA). However, in the third system, the abundance of AOB was higher (4.6×10³ copies/µg of DNA) rather than AOA (1.45×10³ copies/µg of DNA). Gene abundance of AOA was positively related to nitrite (NO₂), whereas DO, pH, and nitrate had a negative impact on bacterial and archaeal amoA gene abundances. This study demonstrates the important role of environmental management in these systems to maintain ammonia-oxidizing populations and ensure efficient ammonia removal. Further research will be necessary to understand the relative contributions of archaea and bacteria to ammonia oxidation, as well as the roles of comammox and nitrite-oxidizing bacteria, to devise effective bioaugmentation strategies for these sustainable aquaculture systems.

Research highlights

This study unveiled the significance of ammonia oxidizing populations in aquaponics grow beds, where AOA (e.g., Nitrosopumilus, Nitrososphaera) often more abundant than AOB (Nitrosomonas).

Two aquaponics systems demonstrated a significant ammonia oxidation after pond water passed through grow beds, shows a higher AOA abundance.

Real-time PCR analysis of amoA genes showed AOA outnumbering AOB in two systems; however, the third system exhibited a reverse trend, indicating AOB amoA gene abundance over AOA.

Copy numbers of AOA were positively correlated with nitrite levels, but dissolved oxygen, pH, and nitrate had a negative impact on both AOA and AOB gene abundances, indicating the purpose of environmental management.