Martinez, C. E. | Search bioRxiv

bioRxiv2023

Improved characterization of soil organic matter by integrating FTICR-MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions

Knowledge of the type of carbon contained in soils is important for predicting carbon fluxes in a warming climate, yet most soil organic matter (SOM) components are unknown. We used an integrated three-part approach to characterize SOM from decaying root-detritus microcosms subject to either drought or normal conditions. To observe broad differences in SOM compositions we employed direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR-MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectra cosine similarity scores to relate unknowns and library matches through molecular networks. This approach allowed us to corroborate DI-FTICR-MS molecular formulas using library matches and infer structures of unknowns from molecular networks to improve SOM annotation. We found matches to fungal metabolites, and under drought conditions, greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas, and lower average nominal oxidation state of SOM carbon, suggesting reduced decomposition of carbon and/or microbes under stress. We propose this integrated approach as more comprehensive than individual analyses in parallel, with the potential to improve knowledge of the chemical composition and persistence of SOM. SynopsisStructural characterization and identifications are lacking for soil organic matter components. This study integrates molecular formula assignments and structural information from fragment ion spectra into molecular networks to better characterize unknown soil organic matter components. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/545455v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@140a98org.highwire.dtl.DTLVardef@1c3b26forg.highwire.dtl.DTLVardef@f7b82aorg.highwire.dtl.DTLVardef@15c012f_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2021

Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient

Constantly in flux, low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been put forward as one way to parameterize microbial uptake rates of LMWOSs and efficiency of carbon incorporation into new biomass. In this study, we employed an ecophysiological approach to test these proposed relationships using targeted exometabolomics (1H-NMR, HR-LCMS) coupled with stable isotope (13C) probing. We assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms (Penicillium spinulosum, Paraburkholderia solitsugae, and Ralstonia pickettii) in media containing 34 common LMWOSs. Microbial isolates were chosen to span a gradient in growth rate (0.046-0.316 hr-1) and differ phylogenetically (a fungal isolate and two bacterial isolates). Clustered, co-utilization of LMWOSs occured for all three organisms, but temporal cluster separation was most apparent for P. solitsugae. Potential trends (p <0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 > 0.15) and a small effect of NOSC indicate these are not useful relationships for prediction. The SUEs ranged from 0.16-0.99 and the hypothesized inverse relationship between NOSC and SUE was not observed. Thus, our results do not provide compelling support for NOSC as a predictive tool, implying that metabolic strategies of organisms may be more important than chemical identity in determining LMWOS cycling in soils. ImportanceCommunity-level observations from soils indicate that low-molecular-weight compounds of higher oxidation state tend to be depleted from soil solution faster and incorporated less efficiently into microbial biomass under oxic conditions. Here, we tested hypothetical relationships between substrate chemical characteristics and the order of substrate utilization by aerobic heterotrophs at the population-level in culture, using two bacterial isolates (Ralstonia pickettii and Paraburkholderia solitsugae) and one fungal isolate from soil (Penicillium spinulosum). We found weak relationships indicating earlier uptake of more oxidized substrates by the two bacterial isolates but no relationship for the fungal isolate. We found no relationship between substrate identity and substrate use efficiency. Our findings indicate that substrate chemical characteristics have limited utility for modeling the depletion of low-molecular-weight organics from soil solution and incorporation into biomass over broader phylogenetic gradients.

microbiology↗