Abstract
Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.
Highlights
The ecology of organisms belonging to the phylum Thaumarchaeota has been studied extensively for over 20 years since sequences associated with this lineage were first discovered in marine waters, followed by terrestrial and other aquatic habitats (DeLong, 1998)
Thaumarchaeotal ammonia monooxygenase subunit A (amoA) sequences deposited in GenBank are approximately fourfold more abundant than thaumarchaeotal 16S ribosomal RNA (rRNA)
Analysis of archaeal 16S rRNA genes indicated that C:N ratio is associated with thaumarchaeotal distribution (Bates et al, 2011) and correlations between thaumarchaeotal community composition and other factors have been found, including water content (Stres et al, 2008; Angel et al, 2010; Richter et al, 2014), total nitrogen content (Pester et al, 2012), organic carbon content (Pester et al, 2012; Bates et al, 2011), temperature (Bates et al, 2011; Stres et al, 2008; Tourna et al, 2008), oxygen concentration (Szukics et al, 2010) and concentra
Summary
Eduard Vico Oton, Christopher Quince, Graeme W Nicol, James I Prosser and Cécile Gubry-Rangin. The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. The ISME Journal (2016) 10, 85–96; doi:10.1038/ismej.2015.101; published online 3 July 2015
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