Carbon and energy utilization in microbial cell extracts from soil

Microbial carbon use efficiency (CUE), the ratio of carbon retained in biomass vs. total C uptake, is central to our understanding of organic C turnover in soil. A precise quantification of CUE in soils can be challenging, given the considerable analytical uncertainties of organic and inorganic C backgrounds. At the same time, CUE measured for model pure cultures will be distinct from a diverse microbiota in soil. As a proxy between laboratory cultures and complex soil microbiomes, we tested soil-free microbial cell extracts (SFCE) to unravel patterns of C utilization in soil-derived microbiomes of reduced complexity. For this, we have revisited and optimized established protocols to extract microbial cells from agricultural soil via Nycodenz density centrifugation. The total extracted cells were quantified, accounting for up to ∼3.5 × 10⁷ cells g⁻¹ soil and representing ∼12.5 % of the original soil microbiome. The diversity of microbes in SFCE, while consistently reduced compared to soil, still retained a surprisingly high proportion of the original soil microbiome, with ASVs recovered from 21 phyla. We then inferred CUE from calorespirometric measurements (metabolic heat flow and CO₂ production) to compare values between SFCE and intact soil. Both were amended with substrates (glucose, glutamine, and glycerol) of different C and N content, and C oxidation state (NOSC). SFCE showed CUE values principally comparable to that of the intact soil, but with substrate-specific distinctions. Amplicon sequencing and qPCR-based quantification showed typical soil taxa like Pseudomonas, Pseudarthrobacter, and Bacteroidota to respond to substrate addition in soil and SFCE. Our results support the use of SFCE as a valuable and complementary approach toward elucidating microbial CUE and growth patterns for complex soil microbiota.