Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment

Abstract

Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

Relationships between ammonia-oxidizing communities, soil methane uptake and nitrous oxide fluxes in a subtropical plantation soil with nitrogen enrichment

“…Soil AOB gene sequences were significantly amplified and detected from two of fifteen soil samples, despite using the FastDigest ® Mbo I enzyme, a procedure that was successfully applied to the typical steppe soils in northern China [34]. Other studies reported that AOB was not detected in the acidic forest soils, either [33,36]. This is partly attributed to the low soil pH in the subtropical region (Fig.…”

“…Theoretically, the decrease in soil pH caused by N additions reduces soil NH 3 availability because of the formation of ionized NH 4 þ [51,52]. The concentration of ammonia substrate in soils is considered below the growth threshold of cultured AOB in soil when pH is below 4.5, and this is in turn favorable to the growth of high-affinity AOA community [33,50]. Soil pH at all treatment plots was below 4.5 (Fig.…”

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

“…A majority of acidic soils selected higher AOA abundance over AOB (Leininger et al, 2006;He et al, 2007) implying a strong ability of AOA ecotypes adapting to low-pH soils. Moreover, high nitrification rates were presumably associated with growth of AOA in an acidic forest soil in the absence of AOB (Stopnisek et al, 2010), and a significant correlation between AOA community abundance and nitrification potential was observed in Chinese acidic tea orchard soils (Yao et al, 2011). In addition, physiological and genomic studies of the first isolate AOA, Nitrosopumilus maritimus, demonstrated a low-level ammonia substrate threshold that was significantly lower than the requirement by cultivated AOB (Martens-Habbena et al, 2009), and significantly divergent pathways of ammonia oxidation from AOB offering ecological advantage in ammonia-limited environments (Walker et al, 2010).…”

Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil

“…However, it is currently unclear whether their competitive strength and ammonia oxidation activity varies depending on the availability of ammonium. Field and microcosm studies show either enhanced abundance and activity of AOA or inhibition in response to nitrogen (N) fertilization (Di et al, 2009;Stopnisek et al, 2010;Pratscher et al, 2011;Verhamme et al, 2011;Levicnik-Hofferle et al, 2012;Ke et al, 2013).…”