Soil-living archaea: Influence of pH, carbon and nitrogen on their abundance and activity

University dissertation from Department of Biology, Lund University

Abstract: During the last decade it has been discovered that around 2% of the soil-living prokaryotes belong to the domain Archaea. In many soils the most abundant archaeal group is the ammonia-oxidizing archaea (AOA) that, in addition to ammonia-oxidizing bacteria (AOB), preform the first and rate-limiting step in the nitrification process. The knowledge of factors that regulates the archaeal abundance and activity, and their importance in the carbon and nitrogen turnover in soil, is very limited. The aim of this thesis was to investigate how archaeal abundance and activity is influenced by carbon, pH and nitrogen amendments, and in the long run increase the knowledge of the role of soil-living archaea in carbon and nitrogen turnover. Soil pH was shown to be an important factor determining the archaeal 16S rRNA gene abundance. The lowest abundance was found at pH 5.1 and increased 150-fold with increasing pH (up to 8.3). In the low pH range (4.0-4.7), no correlation with pH was found. Furthermore, the archaeal 16S rRNA gene abundance was found to decrease in proximity to tree roots and mycorrhizal hyphae. Roots and mycorrhizal hyphae provide the soil with a constant supply of low-molecular weight (LMW) carbon in the form of sugars, amino acids and other organic acids. This creates an environment with a high microbial activity that seemed to disfavor archaea, which support previous suggestions that archaea have evolved to be more tolerant to energy stress than bacteria. Archaea might therefore have a poor competitive ability vs. bacteria in the proximity of the roots and hyphae. The abundance and activity of the specific archaeal group AOA (estimated by amoA gene abundance) was also negatively influenced by the presence of tree roots. When tree roots were excluded from the soil for 6 years, both the archaeal amoA gene abundance and gross ammonia oxidation rate increased. A plausible explanation for the decrease in abundance and activity of AOA when roots were excluded is the lower level of competition for ammonia when there is no uptake by roots. Previous reports show that activity of AOA often dominates over AOB in acidic soils, which was also found in this acidic forest soil where no AOB were detected. In contrast, in soil with higher pH (6.5) AOB was detected, but again in much lower numbers than AOA. When this soil was amended with nitrogen (amino acids or ammonium) AOB abundance and gross nitrification increased dramatically, while AOA numbers were unchanged. It thus seems as if the activity of AOB was favored at high ammonium concentrations, while AOA seems to prefer low substrate concentrations. Accordingly, we found a strong negative relationship between AOA:AOB and gross nitrification when nitrogen was added, and a strong positive relationship between AOA:AOB and gross nitrification in treatments that did not receive nitrogen. In summary, the abundance and activity of soil-living archaea, including AOA, is influenced by pH and the availability carbon and nitrogen compounds, such as root exudates. The results suggest that archaea does not play an important role in the turnover of LMW carbon, but that they are major players in the soil nitrification process, especially under nitrogen-poor and/or acidic conditions.

  This dissertation MIGHT be available in PDF-format. Check this page to see if it is available for download.