Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation

Abstract

Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.

Keywords: land-use change; oil palm soil; pH perturbation; stability; tropical forest soil.

FIG 1

Temporal changes in nitrite plus nitrate (NO_x⁻) concentration following incubation of microcosms for 15 (a) and 30 (b) days and putative contributions of ammonia oxidizers after 30 days (b). Microcosms were constructed using a gradient of land usage: two forest soils (LF and E), a riparian soil (RR), and 2- and 7-year-old oil palm soils (OP2 and OP7). NO_x⁻ production was calculated as the difference in NO_x⁻ concentration between day 0 and day 15 or 30 at native or modified pH, with the number above each column referring to soil pH (green and red numbers represent the high-pH and low-pH values, respectively, while the solid and dotted line boxes represent native-pH and modified-pH values, respectively). The contributions of AOA, AOB, and comammox to NO_x⁻ production after 30 days were estimated as the number of cells assimilating CO₂ (estimated by the number of cells in the heavy fractions of the ¹³CO₂-labeled microcosms) multiplied by their recorded highest maximum specific cell activity (2.6 fmol NH₃ cell⁻¹ h⁻¹ for AOA, 23 fmol NH₃ cell⁻¹ h⁻¹ for AOB and 2.6 fmol NH₃ cell⁻¹ h⁻¹ for comammox, respectively). The sum of these three absolute NO_x⁻ production estimates resulted in some cases in a lower theoretical value than the NO_x⁻ production value measured: hence the assignment of “unaccounted” contribution. Triplicate day 0 and six day 15 and six day 30 microcosms (triplicate ¹²CO₂-amended and triplicate ¹³CO₂-amended microcosms) were sampled to calculate mean values, and the error bars represent standard errors. Different letters above the bars in each panel indicate significant differences in the levels of NO_x⁻ production.

FIG 2

Temporal changes in archaeal (AOA), bacterial (AOB), and complete (comammox) ammonia oxidizer abundances in microcosms containing soils from the land-use gradient, consisting of two forest soils (LF and E), a riparian soil (RR), and 2- and 7-year-old oil palm soils (OP2 and OP7), at native pH and after changes in pH. Triplicate day 0, six day 15, and six day 30 microcosms (triplicate ¹²CO₂-amended and triplicate ¹³CO₂-amended microcosms) were sampled to calculate mean values, and the error bars represent standard errors. The number sign (#) indicates a significant temporal change (increase or decrease) in the measured abundance for each set of soil/pH incubation conditions (P < 0.05).

FIG 3

The stability of AOA, AOB, and comammox abundance following pH modification (acidification or liming) and incubation for 30 days of the five soils from the land-use gradient: two forest soils (LF and E), a riparian soil (RR), and 2- and 7-year-old oil palm soils (OP2 and OP7). Stability was estimated as the proportional change in archaeal, bacterial, or comammox amoA gene abundances in modified-pH (M) soils compared to native-pH (N) soils at day 30, using the following equation: stability = [(M − N)/N] × 100. For each community, the highest stability is achieved at the neutral point (stability = 0), while deviation from the neutral point indicates overcompensation (positive value) or undercompensation (negative value) mechanisms, representing a relative increase or decrease in the pH-perturbed environment compared to the native environment, respectively. An asterisk above or below a pair of bars indicates a significant difference between AOA, AOB, and comammox stability in the corresponding soil (P < 0.05).

FIG 4

Buoyant density distributions of archaeal (AOA), bacterial (AOB), and complete (comammox) ammonia oxidizer abundance after incubation of microcosms for 30 days with [¹²C]CO₂ or [¹³C]CO₂. Microcosms were constructed using a gradient of land usage: two forest soils (LF and E), a riparian soil (RR), and 2- and 7-year-old oil palm soils (OP2 and OP7). The plotted values are the relative abundances of AOA, AOB, or comammox amoA genes in each fraction as a proportion of the total abundance across the whole CsCl gradient. Vertical error bars represent standard errors of relative abundances from triplicate microcosms, and the horizontal error bars represent standard errors of buoyant density of the same order fraction from six microcosms (triplicate [¹²C]CO₂ and triplicate [¹³C]CO₂ treatments).