Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
PLoS One. 2011;6(8):e23281. doi: 10.1371/journal.pone.0023281. Epub 2011 Aug 16.
Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.
氨氧化古菌（AOA）在许多陆地和水生环境中的数量多于氨氧化细菌（AOB）。尽管硝化作用是水族馆生物过滤器的主要功能，但很少有研究调查负责水族馆中这一过程的微生物。本研究使用定量实时 PCR（qPCR）来定量淡水水族馆生物过滤器中的细菌和泉古菌的氨单加氧酶（amoA）和 16S rRNA 基因，此外还通过变性梯度凝胶电泳（DGGE）和克隆文库评估 AOA amoA 基因的多样性。在 27 个淡水生物过滤器中，有 23 个 AOA 数量上占优势，在其中 12 个生物过滤器中，AOA 贡献了所有可检测的 amoA 基因。还包括 8 个海水水族馆和 2 个商业水族馆硝化剂补充剂进行比较。所有海水样本中均检测到 thaumarchaeotal 和细菌 amoA 基因，在 8 个生物过滤器中有 5 个中 AOA 基因数量多于 AOB 基因。两种补充剂中均含有丰富的细菌 amoA 基因，但无法检测到泉古菌 amoA 和 16S rRNA 基因。对于淡水水族馆，AOA amoA 基因相对于 AOB 的比例与铵浓度呈反比。AOA amoA 基因的 DGGE 显示出样本之间的多样性变化，非度量多维尺度分析（NMDS）表明淡水和海水指纹的分离。AOA amoA 基因的复合克隆文库显示出明显的淡水和海水聚类，以及包含淡水和海水 amoA 基因序列的混合聚类。这些结果揭示了常见住宅生物过滤器的内幕，并表明水族馆生物过滤器可能是未来研究 AOA 生态学的有价值的生物膜微宇宙。
