Roots increase microbial activities depending on exudate composition, especially on the ratios of sugars, carboxylic and amino acids, and thus structure enzyme activities in the rhizosphere. We introduce a new approach combining soil zymography and simulated exudates released from Rhizon® samplers to stimulate microbial activities but avoid the direct release of enzymes by living roots. This enabled visualizing, localizing and analyzing the effects of simulated root exudates on activity of five microbial enzymes involved in carbon (C) (β-glucosidase, cellobiohydrolase), nitrogen (N) (leucine aminopeptidase), phosphorus (P) (phosphatase) and sulfur (S) (sulfatase) cycles. We tested the hypotheses that 1) artificial exudates stimulate microorganisms for enzyme production and form spatial gradients around roots, and 2) the extent of microbial enzyme activities in the rhizosphere is component-specific. In line with these hypotheses, the activities of P-, N- and S-related enzymes were higher near the artificial root and gradually decreased as a function of distance from the root. The pattern for C-cycle enzymes was uniform and independent of the exudate composition. Among all components, alanine increased the rhizosphere extent much stronger than other substances, while methionine had no effect on the spatial distribution of enzyme activities. Vmax of all enzymes increased with alanine addition, but decreased after adding citrate. The ratios of enzyme activities demonstrated that rhizosphere microorganisms release more leucine aminopeptidase than other enzymes to meet their N demand. Glucose increased the Km of cellobiohydrolase and β-glucosidase, while alanine had the greatest effect on the Km of leucine aminopeptidase and sulfatase. Phosphatase is the enzyme most sensitive to the composition of root exudates; consequently, any factor influencing root exudate composition can strongly affect the P cycle. We conclude that the rhizosphere extent of microbial-derived enzyme activities is component- and enzyme-specific and that this extent depends on the substrate stoichiometry and microbial nutrient demand.
The applications of biochar (BC) and polyacrylamide (PAM) may have interactive effects on carbon (C) dynamics and sequestration for improving the soil qual
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. Despite the importance of carbon (C) pools and CO2 fluxes in terrestrial ecosystems and especially in soils, as well as many attempts to assign fluxes to specific pools, this challenge remains unsolved. Interestingly, scientists investigating pools are not closely linked with scientists studying fluxes. This mini-review therefore focused on experimental approaches enabling soil C pools to be linked with CO2 flux from the soil. The background, advantages and shortcomings of uncoupled approaches (measuring only pools or fluxes) and of coupled approaches (measuring both pools and fluxes) were evaluated and their prerequisites – steady state of pools and isotopic steady state – described. The uncoupled approaches include: (i) monitoring the decrease of C pools in long-term fallow bare soil lacking C input over decades, (ii) analyzing components of CO2 efflux dynamics by incubating soil without new C input over months or a few years, and (iii) analyzing turnover rates of C pools based on their 13C and 14C isotopic signature. The uncoupled approaches are applicable for non steady state conditions only and have limited explanatory power. The more advantageous coupled approaches partition simultaneously pools and fluxes and are based on one of three types of changes in the isotopic signature of input C compared to soil C: (i) abrupt permanent, (ii) gradual permanent, and (iii) abrupt temporary impacts. I show how the maximal sensitivity of the approaches depends on the differences in the isotopic signature of pools with fast and slow turnover rates. The promising coupled approaches include: (a) &delta13C of C pools and CO2 efflux from soil after C3/C4 vegetation changes or in FACE experiments (both corresponding to continuous labeling), (b) addition of 13C or 14C labeled organics (corresponding to pulse labeling), and (c) bomb-14C. I show that physical separation of soil C pools is not a~prerequisite to estimate pool size or to link pools with fluxes. The future challenges include combining two or more promising approaches to elucidate more than two C sources for CO2 fluxes, and linking scientific communities investigating the pools with those investigating the fluxes.
Living roots and their rhizodeposits can stimulate microbial activity and soil organic matter (SOM) decomposition up to several folds. This so-called rhizosphere priming effect (RPE) varies widely among plant species possibly due to species-specific differences in the quality and quantity of rhizodeposits and other root functions. However, whether the RPE is influenced by plant inter-species interactions remains largely unexplored, even though these interactions can fundamentally shape plant functions such as carbon allocation and nutrient uptake. In a 60-day greenhouse experiment, we continuously labeled monocultures and mixtures of sunflower, soybean and wheat with 13C-depleted CO2 and partitioned total CO2 efflux released from soil at two stages of plant development for SOM- and root-derived CO2. The RPE was calculated as the difference in SOM-derived CO2 between the planted and the unplanted soil, and was compared among the monocultures and mixtures. We found that the RPE was positive under all plants, ranging from 43% to 136% increase above the unplanted control. There were no significant differences in RPE at the vegetative stage. At the flowering stage however, the RPE in the soybean–wheat mixture was significantly higher than those in the sunflower monoculture, the sunflower–wheat mixture, and the sunflower–soybean mixture. These results indicated that the influence of plant inter-specific interactions on the RPE is case-specific and phenology-dependent. To evaluate the intensity of inter-specific effects on priming, we calculated an expected RPE for the mixtures based on the RPE of the monocultures weighted by their root biomass and compared it to the measured RPE under mixtures. At flowering, the measured RPE was significantly lower for the sunflower–wheat mixture than what can be expected from their monocultures, suggesting that RPE was significantly reduced by the inter-species effects of sunflower and wheat. In summary, our results clearly demonstrated that inter-species interactions can significantly modify rhizosphere priming on SOM decomposition.
Peatlands are C-rich but N-poor ecosystems that function as an important C sink but also as significant CH4 sources and thus contribute to global warming. To confirm that N fertilization strongly reduces peatland CH4 emissions by stimulating nitrite-dependent anaerobic methane oxidation (n-damo), we investigated CH4 efflux and concentration in the soil profiles of a peatland subjected to long-term N fertilization. Contrary to previously reported increase of CH4 emissions from paddy, forest and grassland soils, N fertilization of peatland reduced CH4 efflux by 87%, especially during the hottest summer months (from 3.8 mg m−2 h−1 in the unfertilized control to 0.5 mg m−2 h−1 in the N-fertilized site). The CH4 efflux was strongly reduced because the high organic matter content of the peat indirectly stimulated n-damo by providing CH4 (methanogens use organic matter to produce methane) and nitrite (denitrifiers use organic matter as an energy source). N fertilization reduced the CH4 concentration by 50–95% (from 7800–9500 ppm in the unfertilized control to 370–4800 ppm in the N-fertilized site) in the top 30-cm soil, whereas the abundance of Methylomirabilis bacteria increased for 170% and its activity raised for 220% compared to the unfertilized control soil. Consequently, the topsoil is a hotspot of Methylomirabilis activity that use NO2 − to oxidize CH4 and play an important role in reducing CH4 emissions in N-fertilized peatlands.
In this re-evaluation of our 10-year old paper on priming effects, I have considered the latest studies and tried to identify the most important needs for future research. Recent publications have shown that the increase or decrease in soil organic matter mineralization (measured as changes of CO 2 efflux and N mineralization) actually results from interactions between living (microbial biomass) and dead organic matter. The priming effect (PE) is not an artifact of incubation studies, as sometimes supposed, but is a natural process sequence in the rhizosphere and detritusphere that is induced by pulses or continuous inputs of fresh organics. The intensity of turnover processes in such hotspots is at least one order of magnitude higher than in the bulk soil. Various prerequisites for high-quality, informative PE studies are outlined: calculating the budget of labeled and total C; investigating the dynamics of released CO 2 and its sources; linking C and N dynamics with microbial biomass changes and enzyme activities; evaluating apparent and real PEs; and assessing PE sources as related to soil organic matter stabilization mechanisms. Different approaches for identifying priming, based on the assessment of more than two C sources in CO 2 and microbial biomass, are proposed and methodological and statistical uncertainties in PE estimation and approaches to eliminating them are discussed. Future studies should evaluate directions and magnitude of PEs according to expected climate and land-use changes and the increased rhizodeposition under elevated CO 2 as well as clarifying the ecological significance of PEs in natural and agricultural ecosystems. The conclusion is that PEs – the interactions between living and dead organic matter – should be incorporated in models of C and N dynamics, and that microbial biomass should regarded not only as a C pool but also as an active driver of C and N turnover.
Abstract Although soil microorganisms spend most of their lifetime at dormant or resting states, they are quickly activated by substrate input and easily switch to growth. Under steady-state, the double-stranded DNA (dsDNA) content is considered as a measure of total microbial biomass while the RNA content mainly indicates the active microbial fraction. In growing population, however, an increase in DNA is solely related to replication of microbial cells, while the RNA, besides growth, is also involved in non-growth processes. Therefore, the dsDNA and RNA content increase differently during microbial growth, applying the RNA:dsDNA ratio as promising indicator of growth-related and non-growth microbial activity. To what extend the ratio can be used to comparatively infer investment in microbial biomass production versus maintenance-related synthesis following substrate induction remains to be studied. We measured the RNA:dsDNA ratios of representative soil types of four different ecozones before and after glucose addition to prove the prediction capacity of physiological status of soil microorganisms. The RNA:dsDNA ratio remained stable after activation of microorganisms in Retisol and Luvisol indicating balanced growth. In contrast, very moderate increase in DNA in sandy Calcisol was accompanied by disproportionally high increase in RNA. As a result, the RNA:dsDNA ratio in Calcisol with low nutrient status increased by 36-fold after glucose amendment, indicating strong non-growth related processes. The RNA recovery decreased exponentially with increasing clay content, indicating the strong association to the textures of the soil types. This suggests, that the underestimation of RNA yields in clayey soils biased the RNA:dsDNA ratio, and subsequently the physiological state of the microbial community is not adequately represented in soils clay contents exceeding 30%. Monitoring the relative changes in dynamics are required to overcome the restricted applicability of RNA:dsDNA ratio in soils with high clay content.
Greater plant diversity is known to facilitate soil C gains, yet the exact mechanisms of this effect are still under intensive discussion. Whether a plant grows in monoculture or in a multi-species mixture can affect allocation of plant assimilates, belowground exudation, and microbial stimulation. The goal of this study was to examine the effects of inter-cropping on a previously overlooked aspect of plant-soil interactions, namely, on locations where plant assimilated C is allocated within the soil pore system and its subsequent fate in relation to soil pore size distributions. The soil for the study originated from a greenhouse experiment with switchgrass (Panicum virgatum L.) (var. Cave'n'Rock) (SW), big bluestem (Andropogon gerardii Vitman) (BB), and wild bergamot (Monarda fistulosa L.) (WB) grown in monocultures and in inter-cropped pairs and subjected to species specific 13C pulse labeling (Kravchenko et al., 2021). Intact soil cores (8 mm Ø) were collected from the experimental pots, subjected to a short-term (10 day) incubation, X-ray computed micro-tomography (µCT) scanning, and soil 13C micro-sampling “geo-referenced” to µCT images. Results indicated that in the plant systems with demonstrated interplant C transfer soil 13C was positively correlated with < 10 µm Ø pores immediately after plant termination and with 20–80 µm Ø pores after the incubation. In the systems without marked interplant C transfer soil, 13C was positively correlated with 20–30 µm Ø pores, however, the correlations disappeared after the incubation. Soils from the systems with demonstrated belowground C transfer displayed lower losses of root-derived C during incubation than the systems where interplant C transfer was negligible. Factors facilitating interplant C transfer appear to also lead to placement of root-derived C into smaller pores and to its greater protection there.
