Resistance and resilience of the soil microbiome to mechanical compaction under different agricultural management systems

The growing demand for food production over the past decades has led to an increase in agricultural land intensity that requires intensive management and use of highly mechanized equipment. The increasing weight of such equipment and the continuation of mechanized operations for tillage, seeding, fertilizing, spraying, and harvesting even at low frequency can lead to soil compaction. In Europe for example, soil compaction is estimated to affect about 32-36% of the agricultural areas and this percentage is constantly rising.

Soil compaction affects soil physical properties by increasing soil bulk density, changing aggregate size distribution and altering pore connectivity. As a result, macropore functions such as facilitating water infiltration, hydraulic conductivity, air permeability and diffusion are reduced. The decreased pore size and connectivity lead to a decrease in oxygen availability that further increases the number of anaerobic niches within soil. The impact of all these changes in soil physics and chemistry does ultimately affect the soil microbial community and shifts bacterial, archaeal and fungal diversity and function.

Although researchers, farmers and stakeholders have a relatively good understanding of the impact of soil compaction on physical and chemical soil properties, much less is known about what soil compaction does to microbes. However, microbes are the ultimate operators of all enzymatic transformations in every soil’s biogeochemical cycle, making their understanding crucial under soil compaction. Moreover, there is a lack of standard measurements to investigate compaction effects on soil microorganisms and their associated ecosystem functions. This often leads to inaccurate assessments of soil compaction effects on the entire ecosystem and, as a consequence, poor regulations and managerial decisions.

This thesis aims to improve the scientific understanding of the effects of soil compaction on microbial community diversity and function, as well as their resistance (impact) and resilience (recovery) under different agricultural management systems. The objectives of this study were (i) to assess the resistance and the resilience of the soil microbial community structure to compaction under different agricultural management systems, (ii) to assess if the previously observed shifts in microbial diversity under compaction translated into shifts in function potential and (iii) to provide more mechanistic insights into the nitrogen cycle in agricultural systems under different levels of soil compaction.

In the first chapter of this thesis, we assessed for the first time the resistance and the resilience of the soil microbial diversity to compaction under different agricultural management systems. For the purpose of this chapter, permanent ley and two crop rotations with and without tillage were used after a single compaction event in a long-term field experiment with a microbial DNA metabarcoding approach. The DNA metabarcoding approach highlighted a shift in microbial diversity under compaction, specific for each agricultural management system. A relative increase in potential anaerobically metabolizing prokaryotes and saprotrophic fungi and bacteria under soil compaction was found. Additionally, microorganisms with aerobic or plant-host-associated lifestyles were generally negatively affected. Those observations appear to be a unifying concept that agrees with previous studies carried out in forest soils. Whereas crop yield recovered after two growing seasons, for the microbial community four growing seasons were not sufficient to recover although soil properties were similar between compaction treatments and control at the end of the experiment.

Building on the first chapter, we assessed in the second chapter, if shifts in microbial diversity under compaction translated as well into shifts in its function potential because of functional redundancy among microbial species. For the purpose, shotgun metagenomics approach was used. For instance, shotgun metagenomics results confirmed the increase in metabolic potential of anaerobic functions and the decrease in the aerobic ones. This observation supported our previous findings on the microbial diversity and our inference on their potential lifestyle. However, in contrary to the microbial diversity, the shift in microbial metabolic potential under compaction was independent of agricultural management systems.

In the third and last chapter of this thesis, we tested the effect of different moisture contents on compaction severity and used a more closed system to better understand nitrogen partitioning in soil. For this purpose, we have set up pea and wheat cropping systems in microcosms and used the qPCR method to target key nitrogen function groups and further measured concentrations of different nitrogen forms (ammonium, nitrate and nitrous oxide). Our findings confirmed that the severity and effects of soil compaction are linked to the initial soil water content. This chapter highlighted that soil compaction favored denitrifying bacteria. As a result, soil nitrate concentration decreased and soil nitrous oxide concentration increased. Less clear observations were made regarding the nitrification process; whereas there was an accumulation of soil ammonium concentration, the abundance of nitrifying bacteria and archaea showed no notable change. Additionally, like for the previous chapters, those changes in functions involved in the nitrogen cycle were independent of the cropping system and not necessarily aligned with plant growth.

Overall, the results based on the hypotheses tested and methods used within this PhD thesis, either taken individually or combined, help to better understand the resistance and resilience of soil microbial community under different agricultural management systems affected by compaction. The combined use of molecular tools, such as metabarcoding and metagenomic approaches, was considered as a suitable approach to have an overview of the microbial diversity and metabolic potential. Those first observations can be the basis to formulate more precise hypothesis to be tested with qPCR as it has been done for this PhD thesis. Nevertheless, in order to make tangible inference on the potential lifestyle of each microbe and their potential metabolic function, these molecular tools -metabarcoding, metagenomics and qPCR - need to be upheld by physico-chemical soil analysis and metabolic process measurements. Only by using this combined approach, studies can finally interpret the increase or decrease in relative abundance of taxa or function under compaction. Finally, the interdisciplinary, long-term and mechanistic approaches involved in this thesis demonstrated that the studied biological actors (e.g., plant and microbes) as well as the soil physical properties were not necessarily aligned in their resistance and recovery. All those findings bring new and unique knowledges on the compaction impact on microbial diversity and function and highlight the need of assessing many components of the agricultural system in order to make policy recommendations towards a more sustainable agriculture.