Wang Haitao, Bagnoud Alexandre, Ponce-Toledo Rafael I, Kerou Melina, Weil Micha, Schleper Christa, Urich Tim
Institute of Microbiology, University of Greifswald, Greifswald, Germany.
Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
mSystems. 2021 Aug 31;6(4):101128msystems0054621. doi: 10.1128/mSystems.00546-21.
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase () was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal and 16S rRNA genes to link 16S rRNA gene classification to the novel taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class to seven different AOA () clades, including two of the most frequently detected clades ( γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. The recently established phylogeny of provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
最近基于氨单加氧酶α亚基（）建立了一种高度解析的氨氧化古菌（AOA）分类法，该分类法揭示了AOA新的环境模式，对先前的普遍认知提出了挑战。然而，许多微生物组研究将16S rRNA基因作为标记；因此，这种新分类法目前的应用有限。在这里，我们利用古菌和16S rRNA基因的系统发育一致性，将16S rRNA基因分类与新的分类法联系起来。我们在公开可用的古菌基因组和重叠群中筛选同时存在的和16S rRNA基因，并构建了一个具有相应分类法分支分类的16S rRNA基因数据库。两个标记基因的系统发育树证实了一致性，从而能够识别分支。我们用来自泥炭地土壤的16S rRNA基因扩增子数据验证了这种方法。我们成功地将属于类的16S rRNA基因扩增子序列变体与七个不同的AOA（）分支联系起来，包括两个最常检测到的分支（γ和δ分支），目前尚无它们的纯培养物。水分状况显著影响AOA分支的分布以及整个AOA群落结构，这与pH、硝酸盐和铵相关，与先前的分支预测一致。我们的研究强调，有必要区分具有不同生态生理学和环境偏好的AOA分支，以便更好地理解全球丰富的AOA的生态学。最近建立的系统发育比以前的研究提供了更高的分辨率，允许在目水平之外对AOA进行聚类，从而揭示新的分支。虽然16S rRNA基因在微生物组研究中最受重视，但这种新的系统发育应用有限。在这里，我们提供了一条通过使用16S rRNA基因测序数据，用这种新的、高度解析的分类法鉴定AOA的替代途径。我们基于它们的系统发育一致性，构建了一个具有相关分类法分支分类的16S rRNA基因数据库。有了这个数据库，我们能够将来自泥炭地土壤的16S rRNA基因扩增子分配到不同的AOA分支，其分辨率水平以前仅由系统发育提供。由于16S rRNA基因扩增子测序仍广泛用于微生物组研究，我们的数据库可能在解释全球丰富的AOA的生态学方面有广泛应用。
