Preferential Substrate Utilization Research Articles

Priming effect depending on land use and soil types in a typical semi-arid landscape in Kenya

Addition of labile carbon (C) inputs to soil can accelerate or slow down the decomposition of soil organic matter (SOM), a phenomenon known as priming effect (PE). However, the magnitude and direction of PE is often difficult to predict, consequently making its relationship with labile C inputs and nutrient availability elusive. To assess this relationship, we added 13C labelled glucose (corresponding to 50% of initial soil microbial biomass C) to two soil types (Vertisol and Acrisol) with different concentrations of available N and from four land use systems (agricultural, pasture, grassland and shrubland). Parallel laboratory incubations i.e. short-term (6 days) and long-term (6 months), were set up to determine the effect of land use and soil type (N availability) on PE. Addition of labelled glucose in solution led to the retardation of SOM mineralization (negative PE) in both soil types and across all land use systems. This is attributed to preferential substrate utilization characterized by the higher mineralization of added glucose. Land use systems and soil types with higher N-availability displayed weaker negative PE, which is in line with the stoichiometric decomposition theory. In conclusion, our study demonstrate that N-availability plays a major role in determining mineralization of labile C inputs, magnitude and direction of PE in the studied dryland soils and land use systems. The fact that 15–27% of the added 13C remained in the soil at the end of the 6 months incubation and PE was negative, indicates that continuous labile C inputs could contribute to C immobilization and stabilization in these semiarid soils. Moreover, 13C glucose remaining in soils after 6 months in semi-natural pastures was comparable to those under natural grassland and shrubland systems especially in Acrisols. This demonstrates that incorporation and maintaining a perennial cover of native pastures has the potential to increase C sequestration in African semi-arid agricultural soils and landscapes.

Effects of nitrogen addition on carbonate-derived CO2 emission after biochar addition

We studied the effect of nitrogen and biochar on CO2 emission from SOC and SIC. Nitrogen increased SIC-derived CO2 by 41% but decreased SOC-derived CO2 by 20%. Biochar reduced total soil-derived CO2 by neutralizing nitrogen-induced acidity. We proposed a method for 3- or 4-source partitioning CO2 emission from calcareous soils. Biochar addition generally increases the alkalinity regeneration to resist soil acidification driven by nitrogen (N) fertilization. Calcareous soils contain soil organic carbon (SOC) and inorganic C (SIC). Owing to technical limitations in three-source partitioning CO2, how biochar addition affects SOC- and SIC-derived CO2 emission has not been clarified yet. Therefore, we conducted a 70-day incubation experiment of ammonium-N and maize-straw-derived biochar additions to investigate the N plus biochar impacts on SOC- and SIC-derived CO2 emission. Over the 70-day incubation, we found that the N-only addition increased the SIC-derived CO2 emission by approximately 41% compared with the control, but decreased the SOC-derived CO2 emission by approximately 20%. This suggests that the distinct responses of SIC- and SOC-derived CO2 emission to N-only addition come from N-induced acidification and preferential substrate (N) utilization of soil microorganisms, respectively. Compared with N-only addition, N plus biochar addition decreased the SIC-derived CO2 emission by 17%–20% during the first 20 days of incubation, but increased it by 54% during the next 50 days. This result suggested that biochar addition reduced the SIC-derived CO2 emission likely due to the alkalization capacity of biochar exceeding the acidification capacity of ammonium-N in the short term, but it may increase the SIC-derived CO2 emission induced by the weak acidity produced from biochar mineralization in the long term. This study is helpful to improve the quantification of CO2 emission from calcareous soils.

Divergent carbon stabilization pathways in aggregates in Ultisols with and without organic amendments: Implications from 13C natural abundance and NMR analysis

Ultisols with high physio-chemical protection and high acidity prevent soil organic carbon (SOC) from microbial decomposition and accumulate plant-derived recalcitrant C by forming organo-metal complexes. Therefore, the C stabilization pathways in Ultisols may challenge the current common understanding, which is that the major pathway is the stabilization of microbial-derived C to minerals. In addition, organic amendments are expected to affect C stabilization pathways by promoting SOC decomposition and changing SOC composition. However, limited evidence has been found for Ultisols, and the underlying mechanism remains under discussion. C stabilization processes lead to 13C fractionation and changes in SOC composition among aggregate fractions. Therefore, 13C natural abundance and 13C nuclear magnetic resonance spectrometry approaches were applied to investigate 13C fractionation and SOC composition, especially the relative content of recalcitrant C, such as lignin and lipids, and the humification degree represented by the O-alkyl/alkyl ratio, between aggregate size classes. Five fertilization regimes from an 8-year field experiment were selected: no fertilization (CK), inorganic fertilizer (NPK), NPK + straw (NS), NPK + straw and manure (NSM), and NPK + biochar (NC). The bulk soil was separated into three aggregate fractions: >2000 μm, 250–2000 μm, and < 250 μm. In all treatments, 13C presented greater depletion in microaggregates (<250 μm) than macroaggregates (>2000 μm and 250–2000 μm). Regarding the changes in SOC composition, in non-organic-amended treatments (CK and NPK) and NC, recalcitrant C fractions, such as lignin and lipids, were more abundant in < 250 μm aggregates. With the fresh organic material (OM) application (NS and NSM), the lowest O-alkyl/alkyl ratio was found in the > 2000 μm aggregates, suggesting a high humification degree. Summarizing the δ13C and SOC composition results, in the non-organic-amended treatments and NC, the depletion of δ13C in microaggregates coincided with the enrichment of recalcitrant C, which suggests that the depletion of δ13C was primarily controlled by the preferential substrate utilization mechanism. Thus, labile C with heavier δ13C is preferentially decomposed while partially oxidized recalcitrant C with lighter δ13C was adsorbed to the mineral surface and protected in microaggregates. Because the δ13C value decreases with the aggregate size, C flow (modeled in a scheme) primarily occurred from macroaggregates to microaggregates. With fresh OM input (NS and NSM), the C stabilization pathway was primarily governed by the kinetic fractionation mechanism; that is, heavier δ13C remained after microbial utilization, which was reflected by the association of heavier δ13C and a lower O-alkyl/alkyl ratio. With macroaggregates exhibiting 13C enrichment, the C flow was primarily from microaggregates to macroaggregates. These results highlight the importance of the accumulation and protection of plant-derived recalcitrant C in microaggregates in the C stabilization pathway of Ultisols and emphasize that the C stabilizing mechanisms largely depend on organic amendments.

Microbial metabolic efficiency functions as a mediator to regulate rhizosphere priming effects

Microbial metabolic efficiency (MME), a key physiological property that indicates the allocation of carbon (C) to microbial growth, is surely one potential pathway involved in the regulation of priming effect within soil systems. However, the function and mechanism concerning the regulation of the rhizosphere priming effects (RPE) by MME in plant-soil systems remain unclear. In this study, we performed a pot experiment that included two soil types (paddy soil and lou soil), two plant species (sorghum [Sorghum bicolor (L.) Moench] and maize [Zea mays L.]) and three stages of growth (big trumpet, blooming and mature stage) to investigate the MME mechanism of RPE. Both positive (up to 76% at the big trumpet stage) and negative (down to −11% at the mature stage) RPE were observed. A shift in related enzyme activities and microbial biomass indicated that the ‘microbial activation’ and ‘microbial nitrogen (N) mining’ hypotheses functioned together at first. The ‘preferential substrate utilization’ hypothesis then functioned at the latter two stages. After that, according to a correlation analysis method, the MME was introduced to regulate the RPE: the availability of soil C and N and the microbial biomass jointly shaped the microbial C: N imbalance (MIC:N), and the microbes then regulated their MME based on the MIC:N, thus, regulating the RPE. Specifically, the lower MME induced by a higher MIC:N was responsible for a greater RPE at the big trumpet stage across all the planted treatments, while a higher MME induced by a lower MIC:N was responsible for the lower or negative RPE at the blooming and mature stages. Overall, these findings demonstrate that the MME shaped by MIC:N functions as a mediator to regulate the RPE in planted soil.

Distribution, sources, and decomposition of soil organic matter along a salinity gradient in estuarine wetlands characterized by C:N ratio, δ13 C-δ15 N, and lignin biomarker.

Despite increasing recognition of the critical role of coastal wetlands in mitigating climate change, sea-level rise, and salinity increase, soil organic carbon (SOC) sequestration mechanisms in estuarine wetlands remain poorly understood. Here, we present new results on the source, decomposition, and storage of SOC in estuarine wetlands with four vegetation types, including single Phragmites australis (P, habitat I), a mixture of P. australis and Suaeda salsa (P+S, habitat II), single S. salsa (S, habitat III), and tidal flat (TF, habitat IV) across a salinity gradient. Values of δ13 C increased with depth in aerobic soil layers (0-40cm) but slightly decreased in anaerobic soil layers (40-100cm). The δ15 N was significantly enriched in soil organic matter at all depths than in the living plant tissues, indicating a preferential decomposition of 14 N-enriched organic components. Thus, the kinetic isotope fractionation during microbial degradation and the preferential substrate utilization are the dominant mechanisms in regulating isotopic compositions in aerobic and anaerobic conditions, respectively. Stable isotopic (δ13 C and δ15 N), elemental (C and N), and lignin composition (inherited (Ad/Al)s and C/V) were not completely consistent in reflecting the differences in SOC decomposition or accumulation among four vegetation types, possibly due to differences in litter inputs, root distributions, substrate quality, water-table level, salinity, and microbial community composition/activity. Organic C contents and storage decreased from upstream to downstream, likely due to primarily changes in autochthonous sources (e.g., decreased onsite plant biomass input) and allochthonous materials (e.g., decreased fluvially transported upland river inputs, and increased tidally induced marine algae and phytoplankton). Our results revealed that multiple indicators are essential to unravel the degree of SOC decomposition and accumulation, and a combination of C:N ratios, δ13 C, δ15 N, and lignin biomarker provides a robust approach to decipher the decomposition and source of sedimentary organic matter along the river-estuary-ocean continuum.

Relevance of substrate quality and nutrients for microbial C-turnover in top- and subsoil of a Dystric Cambisol

The generally high apparent 14C age of soil organic carbon (SOC) in subsoils suggests a high stability against microbial degradation. However, the SOC decomposition in subsoils may also be limited by easily available substrates and nutrients, such as N and P. In topsoils, priming effects in response to substrate additions are largely determined by substrate quality which also differently affects the microbial community, while the knowledge for deep soil layers is very scarce. In order to gain further insight into processes controlling SOC decomposition in subsoils, we conducted a laboratory incubation experiment for 105days to investigate the impact of different substrates and mineral N and P on SOC mineralization in a Dystric Cambisol sampled at 2–12, 35–65 and 135–165cm. We studied the impacts of 14C-labeled citric, vanillic and palmitic acid and of N or P alone and in combination with two of the substrates on changes in SOC mineralization. The choice of substrates was based on their nominal oxidation state of carbon, which reflects the energy yield and the biogeochemical reactivity of a compound. Further, the impact of the treatments on the activity of six extracellular enzymes involved in C-, N-, P- and S-acquisition, of peroxidase and phenoloxidase and of the intracellular dehydrogenase was investigated to clarify if substrate qualities and nutrients differently affect the decomposition potential and nutrient demand of the microbial community. Our results show that microbial metabolism is limited by N in both subsoil layers, although the upper subsoil (35–65cm) may have become P limited during the later stage of incubation. Even after 105days, C-cycling enzymes and dehydrogenase activity were highly elevated in the lower subsoil (135–165cm) in response to N additions which indicates a sustained higher decomposition potential and activity of the microbial community once the N-limitation is overcome. In the upper subsoil (35–65cm), we found high amounts of labile C, indicating a high proportion of fast cycling SOC. Furthermore, all added substrates induced negative priming effects, while positive priming effects were only induced with N addition which was related to N limiting metabolism. The suppressed SOC mineralization likely occurred because the present microbial community was adapted to more labile carbon compounds, resulting in preferential substrate utilization. In the lower subsoil (135–165cm), real positive priming was induced by vanillic acid and palmitic acid, while citric acid had no effect on SOC mineralization. This clearly reflects that substrate quality matters for inducing positive priming in this subsoil. Altogether, this study evidently shows that in consequence of altered substrate and N input deep SOC storage is destabilized in forest soils.

Cerebral Ketone Body Oxidation Is Facilitated by a High Fat Diet Enriched with Advanced Glycation End Products in Normal and Diabetic Rats

Diabetes mellitus (DM) causes important modifications in the availability and use of different energy substrates in various organs and tissues. Similarly, dietary manipulations such as high fat diets also affect systemic energy metabolism. However, how the brain adapts to these situations remains unclear. To investigate these issues, control and alloxan-induced type I diabetic rats were fed either a standard or a high fat diet enriched with advanced glycation end products (AGEs) (HAGE diet). The HAGE diet increased their levels of blood ketone bodies, and this effect was exacerbated by DM induction. To determine the effects of diet and/or DM induction on key cerebral bioenergetic parameters, both ketone bodies (β-hydroxybutyric acid) and lactate oxidation were measured. In parallel, the expression of Monocarboxylate Transporter 1 (MCT1) and 2 (MCT2) isoforms in hippocampal and cortical slices from rats submitted to these diets was assessed. Ketone body oxidation increased while lactate oxidation decreased in hippocampal and cortical slices in both control and diabetic rats fed a HAGE diet. In parallel, the expression of both MCT1 and MCT2 increased only in the cerebral cortex in diabetic rats fed a HAGE diet. These results suggest a shift in the preferential cerebral energy substrate utilization in favor of ketone bodies in animals fed a HAGE diet, an effect that, in DM animals, is accompanied by the enhanced expression of the related transporters.

Microbial control of soil organic matter mineralization responses to labile carbon in subarctic climate change treatments.

Half the global soil carbon (C) is held in high-latitude systems. Climate change will expose these to warming and a shift towards plant communities with more labile C input. Labile C can also increase the rate of loss of native soil organic matter (SOM); a phenomenon termed 'priming'. We investigated how warming (+1.1°C over ambient using open top chambers) and litter addition (90gm-2 yr-1 ) treatments in the subarctic influenced the susceptibility of SOM mineralization to priming, and its microbial underpinnings. Labile C appeared to inhibit the mineralization of C from SOM by up to 60% within hours. In contrast, the mineralization of N from SOM was stimulated by up to 300%. These responses occurred rapidly and were unrelated to microbial successional dynamics, suggesting catabolic responses. Considered separately, the labile C inhibited C mineralization is compatible with previously reported findings termed 'preferential substrate utilization' or 'negative apparent priming', while the stimulated N mineralization responses echo recent reports of 'real priming' of SOM mineralization. However, C and N mineralization responses derived from the same SOM source must be interpreted together: This suggested that the microbial SOM-use decreased in magnitude and shifted to components richer in N. This finding highlights that only considering SOM in terms of C may be simplistic, and will not capture all changes in SOM decomposition. The selective mining for N increased in climate change treatments with higher fungal dominance. In conclusion, labile C appeared to trigger catabolic responses of the resident microbial community that shifted the SOM mining to N-rich components; an effect that increased with higher fungal dominance. Extrapolating from these findings, the predicted shrub expansion in the subarctic could result in an altered microbial use of SOM, selectively mining it for N-rich components, and leading to a reduced total SOM-use.

Skeletal muscle conditioning may be an effective rehabilitation intervention preceding functional electrical stimulation cycling.

In our recent effort, we introduced a submaximal index that utilized ventilatory efficiency relative to CO2 production (VE/CO2) to evaluate the cardiovascular effectiveness to functional electrical stimulation lower-extremity cycling (FES-LEC) in persons with spinal cord injury (SCI) (Gorgey and Lawrence, 2016). When compared to the resting state, we found that an acute bout of FES-LEC resulted in increased ventilation during exercise and a significant decrease of approximately 22% in the VE/CO2 ratio, suggesting that this ratio could be utilized to monitor the cardiovascular response during submaximal FES-LEC in the SCI population. The study demonstrated that a potential limitation to the FES-LEC application is a heavy reliance on carbohydrate storage as a main source of substrate utilization. Reliance on carbohydrate utilization, transformation to fast-twitch fibers following SCI and random muscle recruitment are likely to introduce rapid muscle fatigue during FES-LEC applications. This may limit oxygen uptake and outcomes regarding cardiovascular profile. In this perspective, we propose that skeletal muscle conditioning via surface neuromuscular electrical stimulation (NMES) may be an essential rehabilitation intervention to improve the outcomes of FES-LEC applications.

Substrate selection for heterotrophic bacterial growth in the sea

Growth of heterotrophic microbes requires the extraction of energy, electrons, carbon, and nutrients from a complex and dynamic reservoir of potential substrates. We employed a matrix of selected organic substrates with varying characteristics, and experimentally followed the kinetics of assimilation and respiration to explore the basic principles that govern selection and preferential use based on carbon, nitrogen, and energy content. We further competed these substrates in a combinatorial fashion to evaluate preferential substrate utilization in natural microbial assemblages. Several substrates displayed biphasic kinetic responses and variable respiration: assimilation ratios. Amino acids had the shortest turnover times and were taken up preferentially at ambient concentrations. We also identified a linear relationship between substrate uptake rates and affinity, suggesting that the microbial community optimizes the relative abundances of membrane transporters according to substrate demand. When competed against one another at saturating concentrations, substrate assimilation and respiration rates were enhanced or inhibited by up to two orders of magnitude, compared to competitor-free controls. Further, we describe an unexpected trend between the substrate energy density and turnover times, with more energetic, reduced carbon substrates turning over more slowly than more oxidized substrates.

Interlinked population balance and cybernetic models for the simultaneous saccharification and fermentation of natural polymers.

Simultaneous Saccharification and Fermentation (SSF) is a process where microbes have to first excrete extracellular enzymes to break polymeric substrates such as starch or cellulose into edible nutrients, followed by in situ conversion of those nutrients into more valuable metabolites via fermentation. As such, SSF is very attractive as a one-pot synthesis method of biological products. However, due to the co-existence of multiple biochemical steps, modeling SSF faces two major challenges. The first is to capture the successive chain-end and/or random scission of the polymeric substrates over time, which determines the rate of generation of various fermentable substrates. The second is to incorporate the response of microbes, including their preferential substrate utilization, to such a complex broth. Each of the above-mentioned challenges has manifested itself in many related areas, and has been competently but separately attacked with two diametrically different tools, i.e., the Population Balance Modeling (PBM) and the Cybernetic Modeling (CM), respectively. To date, they have yet to be applied in unison on SSF resulting in a general inadequacy or haphazard approaches to examine the dynamics and interactions of depolymerization and fermentation. To overcome this unsatisfactory state of affairs, here, the general linkage between PBM and CM is established to model SSF. A notable feature is the flexible linkage, which allows the individual PBM and CM models to be independently modified to the desired levels of detail. A more general treatment of the secretion of extracellular enzyme is also proposed in the CM model. Through a case study on the growth of a recombinant Saccharomyces cerevisiae capable of excreting a chain-end scission enzyme (glucoamylase) on starch, the interlinked model calibrated using data from the literature (Nakamura et al., Biotechnol. Bioeng. 53:21-25, 1997), captured features not attainable by existing approaches. In particular, the effect of various enzymatic actions on the temporal evolution of the polymer distribution and how the microbes respond to the diverse polymeric environment can be studied through this framework.

Negative Priming Effect on Organic Matter Mineralisation in NE Atlantic Slope Sediments

The priming effect (PE) is a complex phenomenon which describes a modification (acceleration or retardation) in the mineralisation rate of refractory organic matter (OM) following inputs of labile material. PEs are well-studied in terrestrial ecosystems owing to their potential importance in the evolution of soil carbon stocks but have been largely ignored in aquatic systems despite the fact that the prerequisite for their occurrence, i.e. the co-existence of labile and refractory OM, is also true for sediments. We conducted stable isotope tracer experiments in continental margin sediments from the NE Atlantic (550–950 m) to study PE occurrence and intensity in relation to labile OM input. Sediment slurries were treated with increasing quantities of the 13C-labelled diatom Thalassiosira rotula and PE was quantified after 7, 14 and 21 days. There was a stepwise effect of diatom quantity on its mineralisation although mineralisation efficiency dropped with increasing substrate amounts. The addition of diatomaceous OM yielded a negative PE (i.e. retardation of existing sediment OM mineralisation) at the end of the experiment regardless of diatom quantity. Negative PE is often the result of preferential utilisation of the newly deposited labile material by the microbial community (“preferential substrate utilization”, PSU) which is usually observed at excessive substrate additions. The fact that PSU and the associated negative PE occurred even at low substrate levels in this study could be attributed to limited amounts of OM subject to priming in our study area (∼0.2% organic carbon [OC]) which seems to be an exception among continental slopes (typically >0.5%OC). We postulate that PEs will normally be positive in continental slope sediments and that their intensity will be a direct function of sediment OC content. More experiments with varying supply of substrate targeting C-poor vs. C-rich sediments are needed to confirm these hypotheses.

Identification of General Patterns of Nutrient and Labile Carbon Control on Soil Carbon Dynamics Across a Successional Gradient

Carbon (C) inputs and nutrient availability are known to affect soil organic carbon (SOC) stocks. However, general rules regarding the operation of these factors across a range of soil nutrient availabilities and substrate qualities are unidentified. “Priming” (stimulated decomposition by labile C inputs) and ‘preferential substrate utilization’ (retarded decomposition due to shifts in community composition towards microbes that do not mineralize SOC) are two hypotheses to explain effects of labile C additions on SOC dynamics. For effects of nutrient additions (nitrogen and phosphorus) on SOC dynamics, the stoichiometric (faster decomposition of materials of low carbon-to-nutrient ratios) and ‘microbial mining’ (that is, reduced breakdown of recalcitrant C forms for nutrients under fertile conditions) hypotheses have been proposed. Using the natural gradient of soil nutrient availability and substrate quality of a chronosequence, combined with labile C and nutrient amendments, we explored the support for these contrasting hypotheses. Additions of labile C, nitrogen (N), phosphorus (P), and combinations of C and N and C and P were applied to three sites: 2-year fallow grassland, mature grassland and forest, and the effects of site and nutrient additions on litter decomposition and soil C dynamics were assessed. The response to C addition supported the preferential substrate hypothesis for easily degradable litter C and the priming hypothesis for SOC, but only in nitrogen-enriched soils of the forest site. Responses to N addition supported the microbial mining hypothesis irrespective of C substrate (litter or SOC), but only in the forest site. Further, P addition effects on SOC support the stoichiometric hypothesis; P availability appeared key to soil C release (priming) in the forest site if labile C and N is available. These results clearly link previously contrasting hypotheses of the factors controlling SOC with the natural gradient in litter quality and nutrient availability that exists in ecosystems at different successional stages. A holistic theory that incorporates this variability of responses, due to different mechanisms, depending on nutrient availability and substrate quality is essential for devising management strategies to safeguard soil C stocks.

Is there a linear relationship between priming effect intensity and the amount of organic matter input?

Inputs of fresh organic matter (FOM) are known to affect the rate of soil organic matter (SOM) mineralization. SOM mineralization can be accelerated or decelerated by FOM inputs. This phenomenon, known as the Priming effect (PE), may largely influence the carbon (C) storage capacity of soils. However, the link between PE intensity and FOM inputs is not clearly understood. Indeed, almost all the studies about PE used only one FOM amount which is generally largely below the amount of FOM observed in field conditions. In our study, we incubated soil amended with three levels of 13C-labeled straw as FOM and a control without FOM amendment for 80 days. The three levels used were in the same range as the natural FOM inputs observed on our sampling site. Various levels of mineral nitrogen were added within each level of straw supply so that the final input C:N ratios ranged among 44, 30 and 20. CO 2 and δ 13C-CO 2 were measured during the experiment allowing us to distinguish the FOM respired CO 2 from the SOM respired CO 2. We observed that PE intensity did not increase linearly with increasing FOM additions. Moreover, decreasing the input C:N ratios did not systematically affect PE intensity probably because of shifts in the microbial characteristics such as their C:N ratio or their assimilation yields. These results suggest that PE is a saturating function of FOM inputs that is only weakly influenced by initial N availability. Our results may be explained (i) by the existence of a limited SOM pool subject to PE (ii) or by the occurrence of two simultaneous and antagonistic mechanisms: an increase of the total active microbial biomass accelerating SOM mineralization (i.e. a positive PE) and a preferential substrate utilization of FOM over SOM decreasing SOM mineralization (i.e. a negative PE). Finally, irrespective of the mechanisms implied, our results suggest that the importance of positive PE relatively to the amount of FOM may decrease when FOM inputs increase, which is favorable to carbon sequestration in soils. Indeed, in the case of the lower amount of FOM, the PE corresponded to 6.25% of the total amount of CO 2 mineralized at the end of the experiment while, for the higher amount of FOM, the PE corresponded to 5% of the total amount of CO 2 mineralized at the end of the experiment.

Turnover of soil organic matter and of microbial biomass under C3–C4 vegetation change: Consideration of 13C fractionation and preferential substrate utilization

Two processes contribute to changes of the δ13C signature in soil pools: 13C fractionation per se and preferential microbial utilization of various substrates with different δ13C signature. These two processes were disentangled by simultaneously tracking δ13C in three pools – soil organic matter (SOM), microbial biomass, dissolved organic carbon (DOC) – and in CO2 efflux during incubation of 1) soil after C3–C4 vegetation change, and 2) the reference C3 soil. The study was done on the Ap horizon of a loamy Gleyic Cambisol developed under C3 vegetation. Miscanthus giganteus – a perennial C4 plant – was grown for 12 years, and the δ13C signature was used to distinguish between ‘old’ SOM (>12 years) and ‘recent’ Miscanthus-derived C (<12 years). The differences in δ13C signature of the three C pools and of CO2 in the reference C3 soil were less than 1‰, and only δ13C of microbial biomass was significantly different compared to other pools. Nontheless, the neglecting of isotopic fractionation can cause up to 10% of errors in calculations. In contrast to the reference soil, the δ13C of all pools in the soil after C3–C4 vegetation change was significantly different. Old C contributed only 20% to the microbial biomass but 60% to CO2. This indicates that most of the old C was decomposed by microorganisms catabolically, without being utilized for growth. Based on δ13C changes in DOC, CO2 and microbial biomass during 54 days of incubation in Miscanthus and reference soils, we concluded that the main process contributing to changes of the δ13C signature in soil pools was preferential utilization of recent versus old C (causing an up to 9.1‰ shift in δ13C values) and not 13C fractionation per se. Based on the δ13C changes in SOM, we showed that the estimated turnover time of old SOM increased by two years per year in 9 years after the vegetation change. The relative increase in the turnover rate of recent microbial C was 3 times faster than that of old C indicating preferential utilization of available recent C versus the old C. Combining long-term field observations with soil incubation reveals that the turnover time of C in microbial biomass was 200 times faster than in total SOM. Our study clearly showed that estimating the residence time of easily degradable microbial compounds and biomarkers should be done at time scales reflecting microbial turnover times (days) and not those of bulk SOM turnover (years and decades). This is necessary because the absence of C reutilization is a prerequisite for correct estimation of SOM turnover. We conclude that comparing the δ13C signature of linked pools helps calculate the relative turnover of old and recent pools.

13C fractionation at the root–microorganisms–soil interface: A review and outlook for partitioning studies

Abstract Natural variations of the 13 C/ 12 C ratio have been frequently used over the last three decades to trace C sources and fluxes between plants, microorganisms, and soil. Many of these studies have used the natural- 13 C-labelling approach, i.e. natural δ 13 C variation after C 3 –C 4 vegetation changes. In this review, we focus on 13 C fractionation in main processes at the interface between roots, microorganisms, and soil: root respiration, microbial respiration, formation of dissolved organic carbon, as well as microbial uptake and utilization of soil organic matter (SOM). Based on literature data and our own studies, we estimated that, on average, the roots of C 3 and C 4 plants are 13 C enriched compared to shoots by +1.2 ± 0.6‰ and +0.3 ± 0.4‰, respectively. The CO 2 released by root respiration was 13 C depleted by about −2.1 ± 2.2‰ for C 3 plants and −1.3 ± 2.4‰ for C 4 plants compared to root tissue. However, only a very few studies investigated 13 C fractionation by root respiration. This urgently calls for further research. In soils developed under C 3 vegetation, the microbial biomass was 13 C enriched by +1.2 ± 2.6‰ and microbial CO 2 was also 13 C enriched by +0.7 ± 2.8‰ compared to SOM. This discrimination pattern suggests preferential utilization of 13 C-enriched substances by microorganisms, but a respiration of lighter compounds from this fraction. The δ 13 C signature of the microbial pool is composed of metabolically active and dormant microorganisms; the respired CO 2 , however, derives mainly from active organisms. This discrepancy and the preferential substrate utilization explain the δ 13 C differences between microorganisms and CO 2 by an ‘apparent’ 13 C discrimination. Preferential consumption of easily decomposable substrates and less negative δ 13 C values were common for substances with low C/N ratios. Preferential substrate utilization was more important for C 3 soils because, in C 4 soils, microbial respiration strictly followed kinetics, i.e. microorganisms incorporated heavier C (∆ = +1.1‰) and respired lighter C (∆ = −1.1‰) than SOM. Temperature and precipitation had no significant effect on the 13 C fractionation in these processes in C 3 soils. Increasing temperature and decreasing precipitation led, however, to increasing δ 13 C of soil C pools. Based on these 13 C fractionations we developed a number of consequences for C partitioning studies using 13 C natural abundance. In the framework of standard isotope mixing models, we calculated CO 2 partitioning using the natural- 13 C-labelling approach at a vegetation change from C 3 to C 4 plants assuming a root-derived fraction between 0% and 100% to total soil CO 2 . Disregarding any 13 C fractionation processes, the calculated results deviated by up to 10% from the assumed fractions. Accounting for 13 C fractionation in the standard deviations of the C 4 source and the mixing pool did not improve the exactness of the partitioning results; rather, it doubled the standard errors of the CO 2 pools. Including 13 C fractionations directly into the mass balance equations reproduced the assumed CO 2 partitioning exactly. At the end, we therefore give recommendations on how to consider 13 C fractionations in research on carbon flows between plants, microorganisms, and soil.

Grass invasion of a hardwood forest is associated with declines in belowground carbon pools

AbstractInvasive plant species affect a range of ecosystem processes but their impact on belowground carbon (C) pools is relatively unexplored. This is particularly true for grass invasions of forested ecosystems. Such invasions may alter both the quantity and quality of forest floor inputs. Dependent on both, two theories, ‘priming’ and ‘preferential substrate utilization’, suggest these changes may decrease, increase, or leave unchanged native plant‐derived soil C. Decreases are expected under ‘priming’ theory due to increased soil microbial activity. Under ‘preferential substrate utilization’, either an increase or no change is expected because the invasive plant's inputs are used by the microbial community instead of soil C. Here, we examine how Microstegium vimineum affects belowground C‐cycling in a southeastern US forest. Following predictions of priming theory, M. vimineum's presence is associated with decreases in native‐derived, C pools. For example, in September 2006 M. vimineum is associated with 24%, 34%, 36%, and 72% declines in total organic, particulate organic matter, mineralizable (a measure of microbially‐available C), and microbial biomass C, respectively. Soil C derived from M. vimineum does not compensate for these decreases, meaning that the sum of native‐ plus invasive‐derived C pools is smaller than native‐derived pools in uninvaded plots. Supporting our inferences that C‐cycling accelerates under invasion, the microbial community is more active per unit biomass: added 13C‐glucose is respired more rapidly in invaded plots. Our work suggests that this invader may accelerate C‐cycling in forest soils and deplete C stocks. The paucity of studies investigating impacts of grass invasion on C‐cycling in forests highlights the need to study further M. vimineum and other invasive grasses to assess their impacts on C sink strength and forest fertility.

Priming effects in Chernozem induced by glucose and N in relation to microbial growth strategies

Input of easily available C and N sources increases microbial activity in soil and may induce priming effects (PE)—short-term changes in SOM decomposition after substrate addition. The relationship between the origin of priming and growth characteristics of the microbial community is still unclear. We related real and apparent PEs induced by glucose and N addition with growth strategies of soil microorganisms. Two concentrations of uniformly labeled 14C glucose with and without N were added to Chernozem, and the released 14CO 2 and CO 2 efflux were monitored over a 300 h period. The shift in strategies after glucose addition was monitored by microbial growth kinetics based on the estimation of maximal specific growth rate. The production of unlabelled extra CO 2 induced by glucose was completed after 3 days and amounted to about 15–19% of the microbial biomass-C. The presence of real or apparent PE depended on the level of added C and N. An apparent positive PE was observed when the amount of applied glucose-C was 13 times lower than the amount of microbial biomass-C, i.e. under C-limiting conditions. Apparent PE was accompanied by a higher maximal microbial specific growth rate, i.e. by a shift towards r-strategy features. The absence of a priming effect was observed under N-limiting conditions at an eightfold excess of glucose-C versus microbial biomass-C. A large excess of glucose and N lowered maximal specific growth rates of soil microorganisms and had a negative priming effect. Accordingly, slow-growing microorganisms (K-strategists) switched from SOM mineralization to glucose uptake, probably due to preferential substrate utilization. Analysis of microbial growth kinetics was an efficient approach for evaluating short-term changes in the response of microorganisms to substrate addition; this approach is therefore suitable for assessing transitions between K and r strategies.

Sources and mechanisms of priming effect induced in two grassland soils amended with slurry and sugar

The mechanisms and specific sources of priming effects, i.e. short term changes of soil organic matter (SOM) decomposition after substance addition, are still not fully understood. These uncertainties are partly method related, i.e. until now only two C sources in released CO 2 could be identified. We used a novel approach separating three carbon (C) sources in CO 2 efflux from soil. The approach is based on combination of different substances originated from C 3 or C 4 plants in different treatments and identical transformation of substances like C 3 sugar (from sugar beet) and C 4 sugar (from sugar cane). We investigated the influence of the addition of two substances having different microbial utilizability, i.e. slurry and sugar on the SOM or/and slurry decomposition in two grassland soils with different levels of C org (2.3 vs. 5.1% C). Application of slurry to the soil slightly accelerated the SOM decomposition. Addition of sugar lead to changes of SOM and slurry decomposition clearly characterized by two phases: immediately after sugar addition, the microorganisms switched from the decomposition of hardly utilizable SOM to the decomposition of easily utilizable sugar. This first phase was very short (2–3 days), hence was frequently missed in other experiments. The second phase showed a slightly increased slurry and SOM decomposition (compared to the soil without sugar). The separation of three sources in CO 2 efflux from grassland soils allowed us to conclude that the C will be utilized according to its utilizability: sugar>slurry>SOM. Additionally, decomposition of more inert C (here SOM) during the period of intensive sugar decomposition was strongly reduced (negative priming effect). We conclude that, priming effects involve a chain of mechanisms: (i) preferential substrate utilization, (ii) activation of microbial biomass by easily utilizable substrate (iii) subsequent increased utilization of following substrates according to their utilizability, and (iv) decline to initial state.

Review: Factors affecting rhizosphere priming effects

Living plants change the local environment in the rhizosphere and consequently affect the rate of soil organic matter (SOM) decomposition. The rate may increase for 3- to 5-folds, or decrease by 10 % to 30 % by plant cultivation. Such short-term changes of rate (intensity) of SOM decomposition are due to the priming effect. In the presence of plants, a priming effect occurs in the direct vicinity of the living roots, and it is called rhizosphere priming effect (RPE). Plant-mediated and environmental factors, such as, plant species, development stage, soil organic matter content, photosynthesis intensity, and N fertilization which affect RPE are reviewed and discussed in this paper. It was concluded that root growth dynamics and photosynthesis intensity are the most important plant-mediated factors affecting RPE. Environmental factors such as amount of decomposable C in soil and N min content are responsible for the switch between following mechanisms of RPE: concurrence for N min between roots and microorganisms, microbial activation or preferential substrate utilization. Succession of mechanisms of RPE along the growing root in accordance with the rhizodeposition types is suggested. Different hypotheses for mechanisms of filling up the C amount loss by RPE are suggested. The ecosystematic relevance of priming effects by rhizodeposition relates to the connection between exudation of organic substances by roots, the increase of microbial activity in the rbizosphere through utilization of additional easily available C sources, and the subsequent intensive microbial mobilization of nutrients from the soil organic matter.