The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/ respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.

Analysing the consequences of the decrease in biodiversity for ecosystem functioning and stability has been a major concern in ecology. However, the impact of decline in soil microbial diversity on ecosystem sustainability remains largely unknown. This has been assessed for decomposition, which is insured by a large proportion of the soil microbial community, but not for more specialized and less diverse microbial groups. We determined the impact of a decrease in soil microbial diversity on the stability (i.e. resistance and resilience following disturbance) of two more specialized bacterial functional groups: denitrifiers and nitrite oxidizers. Soil microbial diversity was reduced using serial dilutions of a suspension obtained from a non-sterile soil that led to loss of species with low cell abundance, inoculation of microcosms of the same sterile soil with these serial dilutions, and subsequent incubation to enable establishment of similar cell abundances between treatments. The structure, cell abundance and activity of denitrifying and nitrite-oxidizing communities were characterized after incubation. Increasing dilution led to a progressive decrease in community diversity as assessed by the number of denaturating gradient gel electrophoresis (DGGE) bands, while community functioning was not impaired when cell abundance recovered after incubation. The microcosms were then subjected to a model disturbance: heating to 42 degrees C for 24 h. Abundance, structure and activity of each community were measured 3 h after completion of the disturbance to assess resistance, and after incubation of microcosms for 1 month to assess resilience. Resistance and resilience to the disturbance differed between the two communities, nitrite oxidizers being more affected. However, reducing the diversity of the two microbial functional groups did not impair either their resistance or their resilience following the disturbance. These results demonstrate the low sensitivity of the resistance and resilience of both microbial groups to diversity decline provided that cell abundance is similar between treatments.

Forest fertilization in British Columbia is increasing, to alleviate timber shortfalls resulting from the mountain pine beetle epidemic. However, fertilization effects on soil microbial communities, and consequently ecosystem processes, are poorly understood. Fertilization has contrasting effects on ammonia-oxidizing bacteria and archaea (AOB and AOA) in grassland and agricultural ecosystems, but there are no studies on AOB and AOA in forests. We assessed the effect of periodic (6-yearly application 200 kg N ha⁻¹) and annual (c. 75 kg N ha⁻¹) fertilization of lodgepole pine and spruce stands at five long-term maximum productivity sites on potential nitrification (PN), and the abundance and diversity of AOB, AOA and Nitrobacter and Nitrospira-like nitrite-oxidizing bacteria (NOB). Fertilization increased AOB and Nitrobacter-like NOB abundances at some sites, but did not influence AOA and Nitrospira-like NOB abundances. AOB and Nitrobacter-like NOB abundances were correlated with PN and soil nitrate concentration; no such correlations were observed for AOA and Nitrospira-like NOB. Autotrophic nitrification dominated (55–97%) in these forests and PN rates were enhanced for up to 2 years following periodic fertilization. More changes in community composition between control and fertilized plots were observed for AOB and Nitrobacter-like NOB than AOA. We conclude that fertilization causes rapid shifts in the structure of AOB and Nitrobacter-like NOB communities that dominate nitrification in these forests.