Soil Microorganisms Involved in Glucose Assimilation in Small and Large Pore Micro-habitats of Different Plant Systems

Background. High plant diversity is known to increase carbon inputs to soils, impact soil microbial community composition and promote soil microbial activity. Large pores are likely to hold more roots residues, provide more efficient oxygen supply, and have more dissolved nutrients and carbon carried by water fluxes. Soil pore structure also impacts the activities of soil microbial communities. The aim of this study was to investigate the effects of 1) plant systems, representing a 9-year gradient of plant diversity (no plants, monoculture switchgrass (Panicum virgatum L.), and high diversity prairie), 2) soil pore size (small (4-10 µm Ø) and large (30-150 µm Ø)), and 3) incubation time (24 hr (short-term) and 30 days (long-term)) on the microbial communities involved in the utilization of a newly added carbon (glucose). This is the first work to explore the influence of soil micro-habitat, as presented by pores of different sizes ranges, on the microbial communities’ responses to new carbon inputs.

Methods. The intact soil cores (5 cm Ø) from the three systems were supplied with either 50 μM C g^-1 soil of ¹³C labeled glucose, unlabeled glucose, or no glucose. Glucose was added to small or large pores based on matrix potential approach. After 24 hr or 30 day incubations stable isotope probing (SIP) was used to identify the phylotypes actively responsible for glucose assimilation in the small and large pore micro-habitats. Both extracted DNA and the fractions separated by SIP were subject to 16S rRNA gene sequencing. PICRUST2 was used to predict the microbial functions of the sequencing data from KEGG orthologs.

Results. The overall microbial communities were affected by multiple years of contrasting vegetation, but not by pore sizes or incubation times. Pseudomonas (Proteobacteria) played an important role in carbon uptake from glucose in all short-term incubations and in the long-term incubations within large pores. In the long-term incubations of both switchgrass and prairie systems’ soils, the community compositions of carbon consumers acting within the small and large pore micro-habitats differed and could be linked to disparate carbon assimilation strategies (r- vs. K-strategists) and to disparate carbon acquisition ecological strategies (plant polymer decomposers, microbial necromass decomposers, predators, and passive consumers). The predicted enriched functional genes indicated the dominance of glucokinase in the soil of the prairie, but not switchgrass system, suggesting a competitive advantage for consuming glucose.