Comammox Nitrospira amoA genes were detected across all 38 freshwater aquarium biofilter samples and were dominant ammonia oxidizers within 30 of the freshwater biofilters
Microbial profiles of freshwater biofilters revealed that community composition was correlated with temperature, aquarium size, and general hardness of the water. Other studies have demonstrated the importance of environmental, biological, and physical factors, such as temperature, filter support material, and fish species as being involved in differentiating biofilter microbial communities in systems like RAS, water treatment, and aquaponics
We observed that the majority of the aquarium biofilters were dominated by either AOA or comammox Nitrospira, although it is not clear what factors may be contributing to their distributions. Previously, pH and ammonia concentration were identified as two key factors governing the abundance of different ammonia oxidizing microorganisms in the environment (50). Our results do support the observations from previous studies that comammox Nitrospira and AOA are dominant in lower ammonia conditions. Previous work shows that both AOA and comammox Nitrospira compete favourably in low ammonia conditions, with several cultivated representatives having high affinities for ammonia including Nitrospira inopinata, Ca. N. kreftii, Nitrosopumilus maritimus, and Ca. Nitrosotenuis aquarius (38, 51, 52). However, at this time there are only have a few cultivated representatives of comammox Nitrospira where ammonia affinities have been measured. Additionally, there are several AOA species that are also known to have tolerance for higher ammonia concentrations, such as those from the genus Nitrosocosmicus (53). We noticed that there was a higher relative abundance of Nitrosotenuis spp. than Nitrosocosmicus spp. for freshwater samples.
Although most freshwater aquaria sampled were low in ammonia, there was one sampled aquarium (FW-F34) that had a high concentration of total ammonia and was dominated by AOB amoA genes. In all other freshwater samples, AOB fell below 14% RA, with most being < 1% of the total ammonia oxidizers detected with qPCR. The low abundance of both detected comammox Nitrospira and AOB is reflected in the overall microbial community of FW-F34 where associated genera of Nitrospira and Nitrosomonas are both present at a RA of > 0.5%. Although this sample suggests AOB might favour high ammonia concentrations over AOA and comammox, more data is needed to support this hypothesis. The effects of ammonia concentration on ammonia oxidizer abundance may be easier to test under experimental conditions with controlled ammonia concentrations as most aquaria naturally have low levels of ammonia with well-established nitrifying communities in their biofilms.
Overall, this work has further clarified our understanding of ammonia oxidation in aquarium biofilters revealing that comammox Nitrospira are ubiquitous in freshwater biofilters, and the dominant ammonia oxidizers are either comammox Nitrospira and AOA. Now that we hopefully have completed our picture of the autotrophic microbial members involved in aquarium ammonia oxidation, future research should work to further address the factors that may be involved in niche differentiation in these environments and explore the contributions from each group to ammonia oxidation in the biofilters. An improved understanding of this microbially mediated process in aquaria is important to improve and optimize current water treatment in the aquaculture industry and could potentially lead to the development of new and improved supplements for aquarium biofilters.
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