Abstract
The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators) of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR) of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively), and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 μgN h−1 gdw−1 and 1.68 ± 0.11 μgN h−1 gdw−1, being higher in soils with higher clay content (1.09 ± 0.12 μgN h−1 gdw−1) and lower in soils with lower clay percentages (0.27 ± 0.04 μgN h−1 gdw−1). Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10%) the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%). Similar trends were observed for the sizes of these communities. The present work represents a first step toward defining a NOR for soil nitrification. The sensitivity of the process and organisms to impacts from the milieu support their use as proxies in the NOR of agricultural soils. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil type-specific manner.
Highlights
The diversity of microorganisms on Earth is astonishing. Torsvik et al (1990) estimated the number of bacterial genomes in a mixed sample using DNA:DNA hybridization
Soil pH, nitrate, ammonium and organic matter (OM) levels and water content were determined in triplicate across all soil samples
The relevance of soil type has been found in studies focusing on macroorganisms, in which gene expression of the soil-dwelling collembolan Folsomia candida was differentially regulated in clayey versus sandy soil. These results suggest that differences in chemical composition observed between sandy and clay soils are of great relevance when studying soil organisms in general, suggesting that a soil type-dependent normal operating range (NOR) should be envisaged
Summary
The diversity of microorganisms on Earth is astonishing. Torsvik et al (1990) estimated the number of bacterial genomes in a mixed sample using DNA:DNA hybridization. The number of bacterial species in a gram of boreal forest soil was estimated to approximate 10,000. Microorganisms dominate soil communities and have a profound impact on ecosystem functioning, being drivers of key processes in the cycling of energy and nutrients. The natural variation of soil processes over time, in response to fluctuations in ecological factors can be depicted as the highs and lows in soil process rates. These high and lows comprise the upper and lower borders of what has been coined the normal operating range (NOR). In order to capture the natural amplitude of variation in OM in forest soils, measurement should be taken over a large timespan, on the order of decades. Due to its sensitivity to external drivers, processes like nitrification are considered to represent good indicators of soil quality (Doran and Zeiss, 2000; Bruinsma et al, 2003)
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