Digging deeper: microbial communities in subsoil are strongly promoted by trees in temperate agroforestry systems

Abstract

Aims Temperate alley-cropping agroforestry systems maintain agricultural production while offering several environmental benefits. Central benefits of agroforestry systems such as the ‘safety-net’-role of the trees for leached nutrients are mainly due to processes occurring below the soil surface: the subsoil. Microorganisms in the subsoil may play a key role in the ‘safety-net’-function as they can improve the capturing and uptake of nutrients by the trees. Systematic investigations of microbial communities in temperate agroforestry systems, however, are restricted to topsoil. Methods We quantified bacteria, fungi, and functional groups of microorganisms in the topsoil and subsoil of two alley-cropping systems using real-time PCR. Topsoil and subsoil samples were collected in the tree rows and at multiple distances from the trees within the crop rows of the agroforestry systems as well as at an adjacent monoculture cropland. Results Microbial population size decreased with soil depth likely due to limited resource availability in subsoil. Tree rows in agroforestry systems not only promote soil microbial populations in both the topsoil and subsoil but the promotion also extends gradually into the crop rows of the systems. The promotion of microorganisms through trees is stronger in subsoil than topsoil, pointing at more intense resource scarcity in the subsoil than topsoil. Conclusions We propose that tree root-derived resources and root litter, which are scarce in agricultural subsoils, triggered the strong positive response of the subsoil community to the trees. Finally, we provide initial evidence that subsoil microorganisms contribute to the ‘safety-net’-role of the trees in agroforestry systems.

Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers

“…Therefore, even though dispersal limitation is important in the assembly of deep soil microbial communities, the key role of deterministic processes driven by potential biological interactions (e.g., plant–fungi and bacteria‐fungi associations) in deep soil microbial assembly cannot be ignored. Deterministic processes dominated by fungi and constant presence of arbuscular mycorrhizal and dominant determinism for fungal assembly down to deep depth in the present study also confirmed this point (Figure 1b and Figures S7 and S10), as arbuscular mycorrhizal is a representative of the direct association between fungi and plant roots (Beule et al., 2022; Carteron et al., 2021; Lozano et al., 2021). By comparison, a susceptible environment between sampling locations in topsoil would create more diverse environmental heterogeneity that shapes the microbiome and enhances the influence of environmental factors.…”

“…of arbuscular mycorrhizal and dominant determinism for fungal assembly down to deep depth in the present study also confirmed this point (Figure 1b and Figures S7 and S10), as arbuscular mycorrhizal is a representative of the direct association between fungi and plant roots (Beule et al, 2022;Carteron et al, 2021;Lozano et al, 2021). By comparison, a susceptible environment between sampling locations in topsoil would create more diverse environmental heterogeneity that shapes the microbiome and enhances the influence of environmental factors.…”

Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach

“…The depth of soil sampling is significantly affected abundance and diversity of microbial community ( Böer et al, 2009 ; Mendes and Tsai, 2014 ; Fu et al, 2023 ). The selection of the 0–10 cm depth range for collecting sediment samples is often based on the findings of earlier researchers ( Zhao et al, 2021 ; Beule et al, 2022 ). Randomly collected samples were mixed to get one composite sample from each site, Site-1, and Site-2, and were designated as PPS-1 and PPS-2, respectively.…”

Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat

“…Deep subsoil microbiota close to the roots is crucial for agricultural soil system functioning (Ryan et al, 2023) and nutrient cycling (Beule et al, 2022;Naylor et al, 2022;Naylor et al, 2023), especially in agricultural production systems during drought, low nutrient supply, and extensive agriculture practices. Most root microbiome studies are conducted at the plow horizon (0-30 cm), where most roots are located (Maeght et al, 2013;Simonin et al, 2020;Jaiswal et al, 2022;Naylor et al, 2022).…”