McKnight Michelle M, Neufeld Josh D
Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
Appl Environ Microbiol. 2024 Jul 24;90(7):e0010424. doi: 10.1128/aem.00104-24. Epub 2024 Jun 20.
Nitrification by aquarium biofilters transforms ammonia waste (NH/NH) to less toxic nitrate (NO) via nitrite (NO). Prior to the discovery of complete ammonia-oxidizing ("comammox" or CMX) , previous research revealed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Here, we profiled aquarium biofilter microbial communities and quantified the abundance of all three known ammonia oxidizers using 16S rRNA gene sequencing and quantitative PCR (qPCR), respectively. Biofilter and water samples were each collected from representative residential and commercial freshwater and saltwater aquaria. Distinct biofilter microbial communities were associated with freshwater and saltwater biofilters. Comammox genes were detected in all 38 freshwater biofilter samples (average CMX genes: 2.2 × 10 ± 1.5 × 10 copies/ng) and dominant in 30, whereas AOA were present in 35 freshwater biofilter samples (average AOA genes: 1.1 × 10 ± 2.7 × 10 copies/ng) and only dominant in 7 of them. The AOB were at relatively low abundance within biofilters (average of 3.2 × 10 ± 1.1 × 10 copies of AOB genes/ng of DNA), except for the aquarium with the highest ammonia concentration. For saltwater biofilters, AOA or AOB were differentially abundant, with no comammox detected. Additional sequencing of genes revealed differential distributions, suggesting niche adaptation based on water chemistry (e.g., ammonia, carbonate hardness, and alkalinity). Network analysis of freshwater microbial communities demonstrated positive correlations between nitrifiers and heterotrophs, suggesting metabolic and ecological interactions within biofilters. These results demonstrate that comammox plays a previously overlooked, but important role in home aquarium biofilter nitrification.
Nitrification is a crucial process that converts toxic ammonia waste into less harmful nitrate that occurs in aquarium biofilters. Prior research found that ammonia-oxidizing archaea (AOA) were dominant over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Our study profiled microbial communities of aquarium biofilters and quantified the abundance of all currently known groups of aerobic ammonia oxidizers. The findings reveal that complete ammonia-oxidizing (comammox) were present in all freshwater aquarium biofilter samples in high abundance, challenging our previous understanding of aquarium nitrification. We also highlight niche adaptation of ammonia oxidizers based on salinity. The network analysis of freshwater biofilter microbial communities revealed significant positive correlations among nitrifiers and other community members, suggesting intricate interactions within biofilter communities. Overall, this study expands our understanding of nitrification in aquarium biofilters, emphasizes the role of comammox , and highlights the value of aquaria as microcosms for studying nitrifier ecology.
水族箱生物滤池的硝化作用通过亚硝酸盐（NO₂）将氨废物（NH₃/NH₄⁺）转化为毒性较小的硝酸盐（NO₃⁻）。在发现完全氨氧化菌（“全程氨氧化菌”或CMX）之前，先前的研究表明，在淡水水族箱生物滤池中，氨氧化古菌（AOA）比氨氧化细菌（AOB）占优势。在此，我们对水族箱生物滤池微生物群落进行了分析，并分别使用16S rRNA基因测序和定量PCR（qPCR）对所有三种已知氨氧化菌的丰度进行了定量。生物滤池和水样分别从具有代表性的住宅和商业淡水及海水水族箱中采集。不同的生物滤池微生物群落与淡水和海水生物滤池相关。在所有38个淡水生物滤池样本中均检测到全程氨氧化菌基因（平均CMX基因：2.2×10⁶±1.5×10⁶拷贝/纳克），其中30个样本中占主导地位，而35个淡水生物滤池样本中存在氨氧化古菌基因（平均AOA基因：1.1×10⁶±2.7×10⁶拷贝/纳克），其中只有7个样本中占主导地位。除氨浓度最高的水族箱外，生物滤池中氨氧化细菌的丰度相对较低（平均每纳克DNA中AOB基因拷贝数为3.2×10⁴±1.1×10⁴）。对于海水生物滤池，氨氧化古菌或氨氧化细菌的丰度存在差异，未检测到全程氨氧化菌。对amoA基因的进一步测序揭示了不同的分布，表明基于水化学性质（如氨、碳酸盐硬度和碱度）的生态位适应性。淡水微生物群落的网络分析表明，硝化菌与异养菌之间存在正相关，表明生物滤池内存在代谢和生态相互作用。这些结果表明，全程氨氧化菌在家庭水族箱生物滤池硝化作用中发挥了先前被忽视但重要的作用。
硝化作用是将有毒氨废物转化为危害较小的硝酸盐的关键过程，发生在水族箱生物滤池中。先前的研究发现，在淡水水族箱生物滤池中，氨氧化古菌（AOA）比氨氧化细菌（AOB）占优势。我们的研究分析了水族箱生物滤池的微生物群落，并对所有目前已知的好氧氨氧化菌群的丰度进行了定量。研究结果表明，完全氨氧化菌（全程氨氧化菌）在所有淡水水族箱生物滤池样本中大量存在，挑战了我们先前对水族箱硝化作用的理解。我们还强调了氨氧化菌基于盐度的生态位适应性。淡水生物滤池微生物群落的网络分析揭示了硝化菌与其他群落成员之间存在显著正相关，表明生物滤池群落内存在复杂的相互作用。总体而言，本研究扩展了我们对水族箱生物滤池硝化作用的理解，强调了全程氨氧化菌的作用，并突出了水族箱作为研究硝化菌生态学微观世界的价值。
