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Abstract Delineation of microbial habitats within the soil matrix and characterization of their environments are crucial to understand soil functioning and carbon (C) cycling. Yet, experimental identification of microbial communities populating specific micro-habitats and assessments of their biochemical properties have been persistently limited. Here we demonstrate how long-term disparities in vegetation history modify spatial distribution patterns and properties of soil pores and particulate organic matter (POM), and show striking differences in bacterial communities populating pores of contrasting sizes in soils from three vegetation systems on the same soil type: an intensive corn (Zea mays L.) rotation, monoculture switchgrass (Panicum virgatum L.), and restored North American prairie. We combined single- and triple-energy X-ray computed microtomography (µCT) with pore specific allocation of 13 C labeled glucose and subsequent stable isotope probing (13C-DNA/RNA-SIP) to show that large (30-150 µm Ø) and small (4-10 µm Ø) soil pores differed in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. Results demonstrate that soil pores created by different plant communities differ in ways that strongly influence microbial composition and activity, and thus impact ecosystem processes such as decomposition, nitrogen processing, and carbon sequestration. A proposed classification scheme may improve biogeochemical models of soil processes and as well suggest interventions to mitigate the environmental consequences of agricultural management.
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The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content
Microbial communities are known as the primary decomposers of all the carbon accumulated in the soil. However, how important soil structure and its conventional or organic management, moisture content, and how different plant species impact this process are less understood. To answer these questions, we generated a soil microcosm with decomposing corn and soy leaves, as well as soil adjacent to the leaves, and compared it to control samples. We then used high-throughput amplicon sequencing of the ITS and 16S rDNA regions to characterize these microbiomes. Leaf microbiomes were the least diverse and the most even in terms of OTU richness and abundance compared to near soil and far soil, especially in their bacterial component. Microbial composition was significantly and primarily affected by niche (leaves vs. soil) but also by soil management type and plant species in the fungal microbiome, while moisture content and pore sizes were more important drivers for the bacterial communities. The pore size effect was significantly dependent on moisture content, but only in the organic management type. Overall, our results refine our understanding of the decomposition of carbon residues in the soil and the factors that influence it, which are key for environmental sustainability and for evaluating changes in ecosystem functions.
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- PAR ID:
- 10464268
- Date Published:
- Journal Name:
- Frontiers in Microbiology
- Volume:
- 14
- ISSN:
- 1664-302X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fmicb.2023.1172862
