Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

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.

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

“…Sandy loam soil (soil-water pH 5.04) was collected from the top 15 cm of a well-characterized agricultural field in Buinen, The Netherlands (52°55′N, 6°49′E) from four (2 × 2 m) plots in April 20133839. Following collection, soils were homogenized by sieving through a 4 mm sieve, moisture was adjusted to 65% water holding capacity (~58% in the field) with sterile water, and soils were allowed to stabilize for one month at 4 °C before filling the microcosms.…”

Functional Redundancy and Ecosystem Function — The Soil Microbiota as a Case Study

“…Here, stability arises because the dynamics of the diverse systems are less dependent on individual species. This is particularly important in soils, which exhibit a very high species turnover rate: in one case, the bacterial and archaeal ammonia oxidizing communities in a range of Dutch agricultural soils showed above 50% change in community structure between seasons [61,62]. In another, it was shown that when colonizing a novel environment, the microbial community undergoes drastic rearrangement, and draws heavily from members of the 'rare biosphere' [9,63], a strategy which may be crucial for stressresponse [51].…”

Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

“…Microbial gene abundance did not differ between sorghum crop and grassland soils, but was generally lower in switchgrass soils as compared to nearby grassland soils. The differences we observed in soil chemistry and microbial communities are likely linked to differences in land use, agronomic practices, and soil type [37][38][39][40][41][42]. Higher macronutrient levels in the sorghum sites than nearby grassland sites are likely the result of fertilizer additions during cultivation.…”

“…Using the GeoChip FGA approach, which is based on DNA probes for functional microbial genes rather than for specific taxa, we observed some significant differences among the N cycling genes for nitrogen fixation, nitrification, and denitrification. In addition to the known effects of N fertilization on soil microbial communities [46][47][48][49], other factors reported to influence microbial composition and activities in soils include plant species and genotype, soil type, soil structure and pH, and the interactions and feedback between plants and soils [37][38][39][40][41][42]. Use of the GeoChip 4.0 allowed us to look for microbial gene diversity and abundance differences among diverse geographic samples across multiple gene categories that related to important ecosystem processes such as C, N, P, and S cycling.…”