Niche specialization of terrestrial archaeal ammonia oxidizers

Abstract

Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA , a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5≤ pH <7), or alkalinophilic (pH ≥7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5–8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5–7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.

Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India

“…Irrespective of soil pollution, thaumarchaeal "group 1.1b (Nitrososphaera clusters)" is found to be widely distributed in these soils. The dominance of group 1.1b in a range of soils as well as wastewater treatment plants has been noticed in earlier studies (Gubry-Rangin et al 2011;Pester et al 2012;Limpiyakorn et al 2013). Thaumarchaeal "group 1.1b" is shown to participate in ammonia oxidation of strongly acidic soils as well as in heavy metal-contaminated thermal spring (Hatzenpichler et al 2008).…”

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

“…In fact, the SSU rRNA gene-sequencing analyses and quantitative PCR analyses of nitrifiers suggested the possible niche separation along with the transition of the entire microbial community structure and NH 4 + flux. Sunlight, pH, and salinity are additional significant factors that affect the niche separation of ammonia oxidizers besides the NH 4 + concentration (31)(32)(33). The salinity change is less than 1 in the water column on the Challenger Deep and is negligible in this case.…”

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

“…These shifts are likely related to Archaea being active drivers of the soil N cycle. For example, Nitrososphaeraceae can oxidize ammonia (29,37), a metabolism that is expected to be advantageous with elevated ammonium supply, which should have been elevated in the N addition plots, because urea is readily hydrolyzed to ammonium. Abundances of soil Crenarchaeota also are positively correlated with soil N content (36).…”