Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter

Microbial carbon use efficiency (CUE) is a critical regulator of soil organic matter dynamics and terrestrial carbon fluxes, with strong implications for soil biogeochemistry models. While ecologists increasingly appreciate the importance of CUE, its core concepts remain ambiguous: terminology is inconsistent and confusing, methods capture variable temporal and spatial scales, and the significance of many fundamental drivers remains inconclusive. Here we outline the processes underlying microbial efficiency and propose a conceptual framework that structures the definition of CUE according to increasingly broad temporal and spatial drivers where (1) CUEP reflects population-scale carbon use efficiency of microbes governed by species-specific metabolic and thermodynamic constraints, (2) CUEC defines community-scale microbial efficiency as gross biomass production per unit substrate taken up over short time scales, largely excluding recycling of microbial necromass and exudates, and (3) CUEE reflects the ecosystem-scale efficiency of net microbial biomass production (growth) per unit substrate taken up as iterative breakdown and recycling of microbial products occurs. CUEE integrates all internal and extracellular constraints on CUE and hence embodies an ecosystem perspective that fully captures all drivers of microbial biomass synthesis and decay. These three definitions are distinct yet complementary, capturing the capacity for carbon storage in microbial biomass across different ecological scales. By unifying the existing concepts and terminology underlying microbial efficiency, our framework enhances data interpretation and theoretical advances

Effects of natural and NH4-charged zeolite amendments and their combination with 3,4-dimethylpyrazole phosphate (DMPP) on soil gross ammonification and nitrification rates

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Effects of Different Chabazite Zeolite Amendments to Sorption of Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate (DMPP) in Soil

Application of natural zeolitites (ZTs, rock with > 50% of zeolites) as a soil amendment is recognized as a suitable method for increasing substrate quality. ZT is used at natural state or pre-enriched with specific cations (e.g., NH4+) to slow-release nutrients. ZT at natural state has been shown to mitigate gaseous N losses and favor crop yield, while NH4-enriched ZT has been reported to show quick NO3 12 production and relatively high gaseous N losses. The use of nitrification inhibitors (NIs) could alleviate these losses. In this work, the sorption behavior of a synthetic NI 3,4-dimethylpyrazole phosphate (DMPP) on different soil-ZT mixtures as well as on pure ZTs (natural and NH4-enriched) was tested. High sorption of NI can reduce its inhibitory effects and consequently the nitrogen use efficiency (NUE). Results show that natural ZTs had a deficient capacity for DMPP sorption and thus decreased the possibility to retain DMPP once applied to the soil. The sorption capacity strongly positively correlated to soil organic C content, supporting that sorption was mainly driven by soil organic matter. Any types of ZT added to the soil, notably that at natural state, have decreased the potential sorption of DMPP principally because of a dilution of the total organic C which reduced substrate hydrophobicity. A lower DMPP sorption in the substrate can mean higher availability of DMPP to soil microbial biomass and thus a higher potential in inhibiting nitrification. These beneficial effects may result in an advantageous strategy for increasing NUE

Temporal changes in the efficiency of biochar- and compost-based amendments on copper immobilization in vineyard soils

Copper (Cu)-based fungicides have been an important tool against disease in viticulture since the 19th century. However, their prolonged use can lead to Cu accumulation in the soil and negatively affect soil microbiology and plant growth. The application of biochar (BC)-based amendments is a promising mitigation strategy, due to BC’s longevity in the soil and its potential to complex Cu. This study investigated temporal changes in the efficiency of various compost- and BC-based amendments to immobilize Cu in a calcareous and a slightly acidic Austrian vineyard soil. The immobilization of both historically accumulated Cu and freshly spiked Cu (250 mg kg⁻¹) was studied. The soils were treated with six combinations of amendments containing compost and BC, with and without surface modification, as well as an additional lime treatment for the acidic soil. After treatment, the soils were incubated for 6 weeks and 3 years, after which the 0.01 M CaCl₂-extractable Cu was measured. The amendments were not effective in reducing the mobility of the historically accumulated Cu in the calcareous soil, with pure compost doubling the soluble Cu. Pure wood-chip BC was the only organic amendment that led to a reduction (by 20%) of soluble Cu after 6 weeks in the acidic soil; however, after 3 years, the same amendment reduced soluble Cu by 40% and all other tested amendments were also effective in reducing the mobility of the historically accumulated Cu. The lime treatment achieved the greatest reduction in Cu mobility (56%). Freshly spiked Cu was strongly immobilized in both unamended soils, with 0.06% and 0.39% extractable after 6 weeks in the calcareous and slightly acidic soil, respectively. The amendments did not effectuate additional Cu immobilization in the calcareous soil, but in the acidic soil, the soluble Cu was further reduced to between 25% and 50% of the unamended control by the tested organic amendments and to 6% by the lime treatment after 6 weeks of incubation. Overall, the acidic soil exhibited a stronger response to the amendments than did the calcareous soil, suggesting the amendments’ effect on the soil pH was an important factor for Cu immobilization in this study. These results show the importance of developing site-specific remediation strategies for Cu accumulation in agricultural soils

Amplitude and frequency of wetting and drying cycles drive N2 and N2O emissions from a subtropical pasture

This study investigated the effects of irrigation frequency on N2 and N2O emissions from an intensively managed pasture in the subtropics. Irrigation volumes were estimated to replace evapotranspiration and were applied either once (low frequency) or split into four applications (high frequency). To test for legacy effects, a large rainfall event was simulated at the end of the experiment. Over 15 days, 7.9 ± 2.7 kg N2 + N2O-N ha−1 was emitted on average regardless of irrigation frequency, with N2O accounting for 25% of overall N2 + N2O. Repeated, small amounts of irrigation produced an equal amount of N2 + N2O losses as a single, large irrigation event. The increase in N2O emissions after the large rainfall event was smaller in the high-frequency treatment, shifting the N2O/(N2O + N2) ratio towards N2, indicating a treatment legacy effect. Cumulative losses of N2O and N2 did not differ between treatments, but higher CO2 emissions were observed in the high-frequency treatment. Our results suggest that the increase in microbial activity and related O2 consumption in response to small and repeated wetting events can offset the effects of increased soil gas diffusivity on denitrification, explaining the lack of treatment effect on cumulative N2O and N2 emissions and the abundance of N cycling marker genes. The observed legacy effect may be linked to increased mineralisation and subsequent increased dissolved organic carbon availability, suggesting that increased irrigation frequency can reduce the environmental impact (N2O), but not overall magnitude of N2O and N2 emissions from intensively managed pastures

Effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N-turnover, the N2O reductase-gene nosZ and N2O:N2 partitioning from agricultural soils

Nitrification inhibitors (NIs) have been shown to reduce emissions of the greenhouse gas nitrous oxide (N2O) from agricultural soils. However, their N2O reduction efficacy varies widely across different agro-ecosystems, and underlying mechanisms remain poorly understood. To investigate effects of the NI 3,4-dimethylpyrazole-phosphate (DMPP) on N-turnover from a pasture and a horticultural soil, we combined the quantification of N2 and N2O emissions with 15N tracing analysis and the quantification of the N2O-reductase gene (nosZ) in a soil microcosm study. Nitrogen fertilization suppressed nosZ abundance in both soils, showing that high nitrate availability and the preferential reduction of nitrate over N2O is responsible for large pulses of N2O after the fertilization of agricultural soils. DMPP attenuated this effect only in the horticultural soil, reducing nitrification while increasing nosZ abundance. DMPP reduced N2O emissions from the horticultural soil by >50% but did not affect overall N2 + N2O losses, demonstrating the shift in the N2O:N2 ratio towards N2 as a key mechanism of N2O mitigation by NIs. Under non-limiting NO3− availability, the efficacy of NIs to mitigate N2O emissions therefore depends on their ability to reduce the suppression of the N2O reductase by high NO3− concentrations in the soil, enabling complete denitrification to N2