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

Recycling nitrogen from liquid digestate via novel reactive struvite and zeolite minerals to mitigate agricultural pollution

Recycling nutrients is of paramount importance. For this reason, struvite and nitrogen enriched zeolite fertilizers produced from wastewater treatments are receiving growing attention in European markets. However, their effects on agricultural soils are far from certain, especially struvite, which only recently was implemented in EU Fertilizing Product Regulations. In this paper, we investigate the effects of these materials in acid sandy arable soil, particularly focusing on N dynamics, evaluating potential losses, transformation pathways, and the effects of struvite and zeolitic tuffs on main soil biogeochemical parameters, in comparison to traditional fertilization with digestate. Liming effect (pH alkalinization) was observed in all treatments with varying intensities, affecting most of the soil processes. The struvite was quickly solubilized due to soil acidity, and the release of nutrients stimulated nitrifying and denitrifying microorganisms. Zeolitic tuff amendments decreased the NOx gas emissions, which are precursors to the powerful climate altering N2O gas, and the N enriched chabazite tuff also recorded smaller NH3 emissions compared to the digestate. However, a high dosage of zeolites in soil increased NH3 emissions after fertilization, due to pronounced pH shifts. Contrasting effects were observed between the two zeolitic tuffs when applied as soil amendments; while the chabazite tuff had a strong positive effect - increasing up to ∼90% the soil microbial N immobilization - the employed clinoptilolite tuff had immediate negative effects on the microbial biomass, likely due to the large quantities of sulphur released. However, when applied at lower dosages, the N enriched clinoptilolite also contributed to the increase of microbial N. From these outcomes, we confirm the potential of struvite and zeolites to mitigate the outfluxes of nutrients from agricultural systems. To gain the best results and significantly lower environmental impacts, extension practitioners could give recommendations based on the soils that are planned for zeolite application

Short-Term response of soil microbial biomass and gaseous emissions to different chabazite zeolitite amendments

Zeolitites (ZTs) are rocks containing more than 50 % of zeolites and are worldwide recognized as a suitable and valuable soil amendment. Once homogenized in the soil or in the cultivation substrate, ZTs enhance soil physicochemical properties and nitrogen (N) use efficiency. However, little is known about their effects on soil microbial biomass and on how they influence soil gaseous emissions, which may represent an important contribution of greenhouse effect. This study aims at i) evaluating short-term effects of different chabazite-rich ZT (CHAZT) amendments on soil microbial biomass and activity and ii) evaluating the effects of different CHAZT amendments on soil gaseous emissions (CO2, N2O, NOx and NH3) soon after the application. To reach these goals a silty-clay agricultural soil was amended with different percentages of natural CHAZT (NZ, at 5 and 15 wt%) and NH4-enriched CHAZT (CZ, at 10 wt%) in two separate incubation experiments. In the first incubation experiment, soil dissolved organic carbon (C), total dissolved N, NH4, NO3, NO2, microbial biomass C and N, and ergosterol were measured periodically over a 16 day period. To verify the microbial immobilization of the N derived from CZ, a naturally high 15N source (pig slurry) was used for enriching the mineral and microbial biomass 15N signature was monitored over the incubation. In the second incubation experiment, an investigation of soil CO2, N2O, NOx and NH3 fluxes was carried out for a total of 24 h both immediately after the application of urea and without a further N input. Concerning the effect on soil microbial biomass (first experiment), ergosterol content increased in the soil amended with 5 % NZ while no clear trends were observed in the soil amended with 15 % NZ, suggesting that fungal biomass was favored at lower application rate. CZ amended soil showed evidence of nitrification, since microbial biomass N was directly related to NO3 production and inversely related to NH4. Isotopic measurements confirmed immediate assimilation of N derived from CZ. In the second experiment, immediate CO2, N2O, NOx and especially NH3 emissions after fertilizer application were generally reduced (up to 60 %) in soils amended with NZ, indicating it as a valuable material for reducing soil C-N gaseous losses. CZ application lowered CO2 and N2O emissions, but very high NOx fluxes occurred even without applying any further N input. NH3 emissions were higher in NH4-enriched zeolites amended soil, but if the amendment is performed without further N inputs, the emissions can be significantly lowered with respect to a conventional urea fertilization. These results suggested that the CZ used in this study supplied an immediately available N pool to the microbial biomass and that NZ can be a suitable material for mitigating gaseous N and C losses from soil or substrates

Effects of stoichiometry and temperature perturbations on beech leaf litter decomposition, enzyme activities and protein expression

Microbes are major players in leaf litter decomposition and therefore advances in the understanding of their control on element cycling are of paramount importance. Our aim was to investigate the influence of leaf litter stoichiometry in terms of carbon (C) : nitrogen (N) : phosphorus (P) ratios on the decomposition processes and to track changes in microbial community structures and functions in response to temperature stress treatments. To elucidate how the stoichiometry of beech leaf litter (Fagus sylvatica L.) and stress treatments interactively affect the microbial decomposition processes, a terrestrial microcosm experiment was conducted. Beech litter from different Austrian sites covering C:N ratios from 39 to 61 and C:P ratios from 666 to 1729 were incubated at 15 °C and 60% moisture for six months. Part of the microcosms were then subjected to severe changes in temperature (+30 °C and −15 °C) to monitor the influence of temperature stress. Extracellular enzyme activities were assayed and respiratory activities measured. A semi-quantitative metaproteomics approach (1D-SDS PAGE combined with liquid chromatography and tandem mass spectrometry; unique spectral counting) was employed to investigate the impact of the applied stress treatments in dependency of litter stoichiometry on structure and function of the decomposing community. In litter with narrow C:nutrient (C:N, C:P) ratios, microbial decomposers were most abundant. Cellulase, chitinase, phosphatase and protease activity decreased after heat and freezing treatments. Decomposer communities and specific functions varied with site, i.e. stoichiometry. The applied stress combined with the respective time of sampling evoked changes of enzyme activities and litter pH. Freezing treatments resulted in a decline in residual plant litter material and increased fungal abundance, indicating slightly accelerated decomposition. Overall, a strong effect of litter stoichiometry on microbial community structures and functions was detected, but decomposition was mainly driven by a combination of the investigated factors. Temperature perturbations resulted in short- to medium-term alterations of microbial functions; especially high temperature treatments blocked decomposing enzymes