Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs

Abstract

Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86°C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) gene and transcript sequences, representing a total of 41 amoA operational taxonomic units (OTUs) at 2% identity. The amoA gene sequences were highly diverse, yet they clustered within two major clades of archaeal amoA sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few amoA OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A amoA genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammoniaoxidizing archaea (AOA). The amoA genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring amoA genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that amoA genes were transcribed in situ in one spring and the transcripts were closely related to the amoA genes amplified from the same spring. Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA.

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

“…High influence of airborne dust nutrients has also been reported Reche et al, 2009) that may fuel AOA nitrification activity. These results reflect the wide set of ecological and thermal conditions where AOA are distributed, ranging from hot springs (Zhang et al, 2008) to the ice layers reported here. Intriguingly, the presence of a potential nitrification zone at 20 m is more difficult to understand because both photoinhibition (Merbt et al, 2012) and preference for a dark environment (Church et al, 2010;Merbt et al, 2011) has been recently reported for some types of AOA.…”

GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

“…The presence of archaeal amoA genes was confirmed by positive PCR amplification using archaeal amoA-specific primers; however, PCR amplification of bacterial amoA genes failed. The nitrifying archaea may be derived from mixing of seawater with the vent fluid or from thermophilic nitrifying archaea in the chimney, because thermophilic and moderately thermophilic nitrifying archaea have been enriched from hot spring environments (29)(30)(31). Most of the nir sequences detected were from uncultured organisms from various environments (Fig.…”

Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera gargensis, a thermophilic Group I.1b Archaeon

“…Environmental analyses demonstrating the presence of abundant and diverse putative Group I Crenarchaeota-associated genes coding for 16S rRNA and the a subunit of ammonia monooxygenase (amoA) in the marine water column (Francis et al, 2005), estuarine sediments (Beman and Francis, 2006), sponges (Steger et al, 2008), soils (Leininger et al, 2006) and hot springs (Zhang et al, 2008), indicate that these prevalent Archaea are also predominantly ammonia oxidizers. Archaeal amoA copy numbers often exceed those of bacteria, thus suggesting that Archaea may even dominate bacteria in ammonia oxidation under certain conditions (for example, Leininger et al, 2006;Wuchter et al, 2006;Mincer et al, 2007;Martens-Habbena et al, 2009).…”