Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

Ricardo J Eloy Alves,Tim Urich,Arndt Von Haeseler,Christa Schleper,Bui Quang Minh

doi:10.1038/s41467-018-03861-1

Abstract

Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.

Highlights

Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling
Preliminary analyses indicated that the initial dataset included a large number of chimeras, which precluded reconstruction of stable phylogenetic trees
We detected a large number of chimeras among publicly available amoA sequences, which deteriorate tree topology and likely constituted

Summary

Introduction

Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. Associations between ecological, functional and phylogenetic patterns of AOA have been difficult to relate between studies, and their global phylogenetic breadth and coherence have remained largely ambiguous These patterns were mainly inferred on subjective phylogenetic levels in different phylogenies and often based on polyphyletic or unsupported clades[24,26,27,29,30,31,32], being prone to generate inconsistent categorical assumptions. To circumvent these bottlenecks, comprehensive phylogenetic/taxonomic frameworks that allow integration of sequence data and associated information in a global context are essential, as are those available for 16S rRNA genes[14,16,17].

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Conclusion