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Aim: Low‐molecular‐weight organic substances (LMWOSs) are at the nexus between micro‐organisms, plant roots, detritus, and the soil mineral matrix. The nominal oxidation state of carbon (NOSC) has been suggested as a potential parameter for modelling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. Methods and Results: In this study, 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 micro‐organisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046–0.316 h−1) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co‐utilization of LMWOSs occurred for all three organisms. 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 relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16 to 0.99 and there was no observed relationship between NOSC and SUE. Conclusion: Our results do not provide compelling population‐level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. Significance and Impact of the Study: Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community‐level observations may be biased towards fast‐responding bacterial community members. [ABSTRACT FROM AUTHOR]

Biochar-manure co-compost (BM) has garnered considerable attention as a promising soil amendment for improving nutrient retention and mitigating the emission of greenhouse gases (GHGs). However, its efficacy often varies largely from one soil to another. By comparing soil CO 2 and N 2 O effluxes, solution chemistry, enzyme activities, and the abundances of N-cycle genes between BM and manure compost (M) across three soils of different texture classes through microcosm incubations, we aimed to develop biophysical mechanics to untangle the soil-dependent efficacy of BM in mediating soil carbon and nitrogen transformation processes. Compared to M addition, BM addition significantly reduced soil CO 2 and N 2 O emissions, but its effectiveness was soil texture-dependent, being strongest for CO 2 and N 2 O in fine-textured clay loam and coarse-textured sand, respectively. Such soil texture-dependent effects of BM versus M were also observed in soil enzyme activities and gene copy numbers of ammonia-oxidizing bacteria and denitrifiers. Our datasets suggest that BM interacted strongly with soil texture to modulate the pore scale-based diffusion of oxygen, thereby creating divergence in the aeration status among soils. Sequentially, soil phenol oxidase activity was greater in BM than in M under more aerobic conditions but no difference between BM and M in oxygen-limited soils. The balance between oxygen depletion due to microbial respiration of organic amendments and oxygen diffusion through soil/biochar pores also shaped the activities of nitrifying and denitrifying prokaryotes differently between coarse- and fine-textured soils. This logic model well-explained the magnitude of change in soil-dependent CO 2 and N 2 O emissions from organic amendments. The knowledge gained in this work will likely have profound practical ramifications for optimizing BM efficacy in mitigating the GHGs emission. Graphic abstract [Display omitted] • Impact of biochar-manure compost (BM) on CO 2 and N 2 O emissions is soil dependent. • BM interacted with soil texture to modulate pore scale-based oxygen diffusion. • Oxygen level regulated by BM addition affected abundance of N-cycling prokaryotes. • A biophysical mechanism is developed to explain the soil dependence of BM efficacy. [ABSTRACT FROM AUTHOR]

We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, Paraburkholderia sp. strain 1N. The growth of Paraburkholderia sp. 1N was monitored under aerobic conditions in a soilextracted solubilized organic matter medium, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the medium and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the medium, and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as Paraburkholderia sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of Paraburkholderia sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression. [ABSTRACT FROM AUTHOR]

Iron (Fe) minerals play an important role in carbon (C) and nutrient dynamics in redox fluctuating soils. We explored how the frequency of redox oscillations influence Fe reduction rates and C content in Puerto Rican soils. We hypothesized that iron reduction rates would be faster during short oscillation periods than in longer oscillation periods. Surface soils from an upland valley in a humid tropical forest were exposed to systematic redox oscillations over 49 days. The oxidation events were triggered by the introduction of air (21% O2), maintaining the time ratio under oxic or anoxic conditions at 1:6 (τox/τanox). After pre-conditioning the soil to fluctuating redox conditions for 1 month, we imposed 280- and 70-h (or 11.67- and 2.5-day) redox oscillations, measuring FeII every few days. We found that by the end of the experiment, Fe reduction rates were higher in the short oscillation period (τox = 10 h, τanox = 60 h) than in the long oscillation period (τox = 40 h, τanox = 240 h). Carbon and nitrogen loss however was similar for both treatments. These results suggest the characteristics of redox fluctuations can alter rates of Fe reduction and potentially influence ecosystem processes that depend on iron behavior. [ABSTRACT FROM AUTHOR]