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Let restore our soils : using the soil food web to engineer the soil structure and functionning

Periodic Reporting for period 1 - AGG-REST-WEB (Let restore our soils : using the soil food web to engineer the soil structure and functionning)

Reporting period: 2017-06-01 to 2019-05-31

Soil structure is crucial for soil functioning, as it provides pathways for the transport of water, nutrients and gases, and forms the habitat of soil biota. On the other hand, soil organisms largely influence soil structure. However, the interactions between soil biota and soil structure is not well studied and there are important gaps of knowledge. For example, studies on the effects of soil organisms on soil structure mainly focused on ecosystem engineers, such as earthworms and ants among soil animals and microbes, namely bacteria and fungi. However, soil contains a densely packed soil biodiversity and interactions between individuals are commonplace. Since few years, trophic interactions emerged as being central to explain soil functioning, notably biochemical cycles, but their effect on the soil structure remains largely ignored. Feedbacks of soil physical structure on soil organisms are mainly considered at the microbial level, with a growing interdisciplinary community of soil physicists partnering with soil microbial ecologists. By contrast, effects of soil physical structure as main aspect of soil microhabitats on complex trophic interactions have not yet been addressed as focal research topic in soil sciences. The objectives of this project were to (i) experimentally test how trophic interactions influence soil physical structure and (ii) to set the conceptual basis to unravel feedback effects of soil physical structure on trophic interactions.
The work performed was divided in two main parts: (A) experimental works testing the effect of trophic interactions on soil structure and (B) a literature review establishing the main concepts and future research directions needed to investigate how trophic interactions are driven by soil physical structure.
(A1) The main objective was to investigate how trophic interactions impact soil aggregation, a main aspect of soil structure. We set up a microcosm experiment where I re-built two simplified soil consumer - prey systems: a bacterial-based system comprising amoebae (Acanthamoeba castellanii) feeding on a microbial community dominated by the free-living bacteria Pseudomonas fluorescens, and a fungal-based system comprising collembolans (Heteromurus nitidus) grazing on a microbial community dominated by the saprotrophic fungus Chaetomium globosum. After 6 weeks of incubation we measured soil aggregate stability as well as microbial community composition using phospholipids fatty acids markers (PLFA markers); further, C dynamics (microbial C use, SOC concentrations) and CO2 emission were measured twice over the incubation period. I found that (i) the amoeba A. castellanii enhanced the formation of soil aggregates, and tended to reduce their stability but did not affect microbial biomass and composition, and (ii) collembolans significantly modified microbial community composition and reduced fungal biomass, which resulted in lower soil aggregation. Overall, our work demonstrated that trophic interactions are important for achieving a mechanistic understanding of biological contributions to soil aggregation. Notably, they showed that changes in soil aggregation may occur without major changes in C dynamics, and with or without changes in the composition of the microbial community.
(A2) The main objective was to test how the effect of trophic interactions (collembolans – microbes) on soil aggregation vary with collembolan species. Using a similar experimental set-up as the one described in part A1, we re-built simplified consumer - prey interactions with the collembolan species Sinella curviseta, Falsomia candida, Ceratophysella denticulata and Protaphorura fimata feeding on a microbial community dominated by the saprotrophic fungus Chaetomium globosum. After 2.5 months of incubation, we observed a positive effect of collembolans on soil aggregate formation compared to microbes only and this occurred regardless of collembolan species. Soil aggregate stability showed no significant variations. Collembolans significantly modified the microbial community composition in macro- (250 µm – 2 mm) and microaggregates (50 – 250 µm) in a species-dependent manner. Overall, we showed here that long-term effects (2.5 months) of collembolans on soil aggregation vary from short term effects (6 weeks). In addition, we demonstrated important top-down regulation of the soil microbiome by collembolans at the aggregate scale.
(B) The main objective was to set the main concepts and methods available to address the role of soil structure as determinant of trophic interactions (and vice-versa). This literature review highlighted that the soil physical structure limits the sensing and modulate the accessibility to food resources/prey because of (i) reduced transport of sensing molecules, notably volatiles, (ii) pore size segregation of consumer/predators and food resources/prey in pores of contrasting size, and (iii) varying connectivity of soil pores and water films which essentially drive encounter probability between consumers/predator and food resources/prey.

Actions of dissemination, communication and outreach
Dissemination to foster sciences
- 1 peer-review article in Soil Biology and Biochemistry (Gold Open Access) & 1 pre-print in Biogeosciences (Open Access journal with open review)
- International conferences: 3 oral communications (Building Bridges conference, Goettingen, 2019; EGU2019; EGU2020), 1 poster (Wageningen Soil Conference, 2019) & organization of 2 sessions (EGU2019, EGU2020) and 1 workshop (Wageningen Soil Conference, 2019) on soil biota and soil structure.
- Lecture (3h/year) on “Soil Structure and soil biodiversity” at the University of Goettingen (Bachelor students).
- Lab seminars: 2 oral presentations in the weekly lab seminar of Prof. Dr. Scheu (University of Goettingen)
Awake awareness about soils
- Article in the city journal (Goettinger Tageblatt) informing about the launch of the MSC fellowship
- 1 popularized article about “soil food webs and feeding strategies in the soil” in Frontiers for Young Minds (accepted) – in English
- Lab open doors: Visits of kindergarten children (2 groups of 12 children) in the soil ecology lab
Our work is pioneer to integrate soil physics into soil food web ecology. Overall, our work provides experimental evidence as well as novel concepts and a review of the existing methods to unravel the role of physical structure on trophic interactions, and vice-versa. We expect that it will stimulate a new interdisciplinary research pathway, moving research on the role of soil microhabitats as drivers of trophic interactions into a more quantitative and mechanistic area. The effect of trophic interactions on soil structure may as well open up new directions in soil restoration.