"Non-metabolizable" glucose analogue shines new light on primingmechanisms: Triggering of microbial metabolism

The rhizosphere and detritusphere are characterized by increased carbon availability, including low-molecular weight organic substances. Such easily biodegradable organic substances can change the mineralization rates of pre-existing soil organic matter, a phenomenon termed priming. Priming of soil organic matter decomposition has attracted much research interest, yet a conclusive mechanistic explanation remains elusive. One proposal is that low molecular weight organic substances might “trigger” an acceleration of microbial metabolism. For the first time, we applied a glucose analogue to soil to demonstrate triggering of microbial metabolism, and to estimate its relative contribution to priming. “Non-metabolizable” glucose analogues have been widely used in pure culture studies to mimic glucose, but never in soil biochemistry. We hypothesized that analogue molecules will elicit a metabolic response in microorganisms despite limited catabolism, and thereby confirm the proposed triggering. The effect of 14C-labeled 3-O-methyl-D-glucose (OMG) – a common “non-metabolizable” glucose analogue – on soil organic matter mineralization was compared to that of 14C-labeled D-glucose. OMG was mineralized, but its mineralization was initially impeded and substantially delayed, relative to glucose. OMG caused brief but strong priming in the first 24 h, increasing unlabeled CO2 efflux by 173%, 89% and 36% above control for additions of 0.49, 2.4 and 4.9 mmol OMG g-1 soil, respectively. In contrast, glucose caused low or negative priming on the first day. On the first day after OMG addition, a negative correlation between priming and OMG mineralization indicated that triggering is a valid mechanism of microbial activation during a famine-feast transition, but is short-lived. Glucose mineralization peaked on the second day for medium and high additions, coinciding with peaks in positive priming. Maximum substrate mineralization also coincided with peaks in priming for medium and high OMG levels, but these occurred 9 and 11 days after addition, respectively. This revealed non-triggering priming mechanisms, which contributed most to priming and were closely coupled to substrate mineralization. By separating energy- and substrate-dependent metabolic processes from triggering processes, the glucose analogue 3-O-methyl-D-glucose enabled triggering to be demonstrated, but triggering by glucose occurs without contributing greatly to priming

Peat decomposition indicators of two contrasting bogs in the Eastern Alps, Austria

Since carbon (C) in peatlands is labile and sensitive to disturbances, peatlands have the potential to release high C amounts by land use changes and to accelerate global warming. Therefore, adequate peat decomposition indicators (PDI) are necessary to assess the peatland degradation status and potential for CO2 release. In order to assess the peat degradation status of nine sites in Alpine bogs (Enns valley, Austria), we compared PDI of two peat bogs with contrasting land-use histories. The conventional PDI: loss on ignition, bulk density, C:N ratios, water table depths (WTD) were compared with the recently introduced PDI: stable carbon isotope signature (d13C) and nitrogen isotope signature (d15N). The most PDI were different between the two bogs and the study sites with contrasting WTD and degree of peat decomposition. We demonstrated strong relationships and similar depth profiles of variables: Loss of ignition of strongly degraded peat decreases from the acrotelm to the catotelm, but remains stable at less degraded peat. Bulk density generally increases with depth, and was lowest in the acrotelm of the central bog area and highest in the catotelm of the former peat cutting areas. C:N ratios increased slightly with the degree of peat decomposition. d13C and d15N increased from the top to the depths of -24 to -42 cm at all study sites. In the catotelm, dC13 were significantly lower in strongly decomposed peat compared to the less degraded sites. Higher d15N values in acrotelm and catotelm of strongly degraded peat may be evidence for more pronounced N fractionation during decomposition compared to less degraded sites. Decomposers tend to preferably use substances with 12C for respiration, resulting in a relative enrichment of 13C in the residual organic matter. Accordingly, the increase of d13C with depth in the acrotelm in strongly decayed peat may be assigned to 12C loss by respiration

Soil cation exchange capacity: main factor of shell carbonate diagenesis

Shell carbonate diagenesis occurs in interaction with soil solution, where the concentration of Ca2+ is in equilibrium with exchangeable Ca2+ and weathering of Ca-bearing minerals. While the exchange process takes place within seconds, the dissolution equilibrium with Ca-bearing minerals achieves after months. We hypothesized that shell carbonate diagenesis proceeds slower in soils with high cation exchange capacity (CEC) than those with low CEC. The goal of this study was to determine the effects of soil CEC and exchangeable cations on shell carbonate diagenesis. Shells of Protothaca staminea were mixed in glass bottles with 1) carbonate-free sand (CEC = 0.37 cmol+kg-1) (S), 2) a native loamy soil (CEC = 16 cmol+kg-1) (LS) and 3) the same loamy soil saturated with KCl (replacing exchangeable cations with K+) (LSK). Samples were incubated at room temperature for 5, 20, 60 and 120 days. Bottles air was labeled with 14CO2 at the beginning and day 55. 14C was measured at sampling dates in bottles air, soil solutions, bulk soils and shells. Dissolved and exchangeable cations were measured. Shell carbonate diagenesis in LS and LSK (0.016 and 0.024 mg CaCO3, respectively) was one order of magnitude lower than in S (0.13 mg CaCO3). Shell carbonate dissolution and consequently recrystallization decreased at high amounts of exchangeable Ca2+ because exchange is faster than dissolution. Therefore, soil CEC and composition of exchangeable cations is a determinant factor of shell carbonate diagenesis and it should be considered by radiocarbon dating. Because shells in soils with lower CEC undergo more intensive diagenesis, they need further pretreatments before dating. Soil CEC should be also included in shell carbonate diagenesis models. Furthermore, 14C labeling can be used to investigate the rates of minerals weathering - at least for Ca-bearing minerals - and soil acidification

Root development controls hotspots localization and temperature sensitivity of enzyme activity in the rhizosphere

The rhizosphere is a very important and dynamic hotspot of microbial activity in soil. Consequently, the enzyme activities in the rhizosphere are a footprint of complex plant-microbial interactions and may reflect functional response to climate changes.The temperature sensitivity of enzymes responsible for organic matter decomposition in soil is crucial for predicting the effects of global warming on the carbon cycle and sequestration. For the first time, we applied the in situ soil zymography for identification and localization of hotspots of phosphatase and chitinase activity in the rhizosphere of rice (Oryza sativa L.) under warming effect - (18 and 25 °C) after 14 and 30 days. Thus, we test the hypotheses that due to high inputs of easily degradable organic compounds from the roots canceling effect: strong reduction of temperature sensitvity (Q10~1) of catalytic reactions will not accoure in the rhizosphere. Correspondingly, the Q10 values for reaction rates were always >1, at root-soil interface, with the average range of 1.3 –1.4 Independent of enzymes, canceling was never observed at vicinity of root. Thus, canceling effect is a substrate concentration dependence phenomenon. To our knowledge, this is the first study explored the canceling effect in the rhizosphere. Absence of canceling at root-soil interface for phosphates and chitinase revealed that warming will accelerate P and N mobilization in the rhizosphere. Altogether, for the first time we showed that extent of enzyme activity’s rhizosphere is constant, temporally however, there is a temporal heterogeneity of enzymatic hotspots localization in soil. Thus, increasing in temperature had a positive impact on overall enzyme activities, Rice growth and root development, conducted an enzyme specific impact on hotspots percentage and localization patterns. We conclude that absence of canceling at root-soil interface for tested enzymes revealed that warming will accelerate nutrient mobilization in the rhizosphere more than root free soil

Soil carbon losses and estimation of erosion and decomposition by δ Carbon-13 in riparian soils under lowland rainforest transformation systems on Sumatra, Indonesia

Indonesia´s forest is ranked among the Amazonian and the Kongo Basin as the largest tropical rainforest area worldwide. However, the country experiences a severe forest loss since the 1970s. Besides a growing population, the primary pressures are export-orientated timber production and a global commodity demand that lead to a permanent conversion from forest to agricultural areas. The roles of resulting transformation systems of tropical riparian rainforests for ecological functions have yet received little attention in scientific research. Especially C stocks in riparian zones are strongly affected by climate and land use changes that lead to changes in water regime and ground water level drops. We investigated the effects of land transformations in riparian ecosystems of Sumatra, on soil C content, stocks and decomposability. C losses in rubber and oil palm plantations and rainforests were compared and the contribution of soil erosion and organic matter mineralization was estimated. Based on δ Carbon-13 along soil depth, two processes decreasing C stocks were distinguished: erosion and mineralization of soil organic matter (SOM). Depending on the shift of the δ Carbon-13 value of SOC in the topsoil from the linear regression calculated by δ Carbon-13 value with log(SOC) in the topsoil, modification of C turnover rate in the top soil was evaluated. Erosion was estimated by the shift of the δCarbon-13 value of SOC in the subsoil under plantations. The Ah-horizons in non-riparian soils under oil palm and rubber plantations showed with 70% and 62 % a strong reduction in C content and a strong erosion: 35 ±8 cm in oil palm and 33 ±10 cm in rubber plantations. Within the riparian zones an inhomogenous spatial distribution of C content is expected, due to the trend of increasing C stocks from terrestrial through semi –terrestrial to wet conditions. By comparing decreasing δ Carbon-13 values of SOC in the topsoil to those in subsoil, a lower erosion in all transformation systems in riparian zones could be detected

Towards to physiological status of soil microorganisms determined by RNA:dsDNA ratio

Despite soil microorganisms spend most of their lifetime in a state of dormancy, they are quickly activated by substrate input and easily switch to growth. As both the dsDNA- and RNA- contents increase during microbial growth, the RNA:dsDNA ratio reflects a promising predictor, whether the response of a microbial community to environmental changes is due to an increase in population (by dsDNA) or due to an increase in activity (by RNA). This prediction of the RNA:dsDNA ratio can be accomplished by the comparison of microbial incubation approaches with and without addition of easily available substrates. We exhibited the RNA:dsDNA ratios for four contrasting soil types during substrate-induced growth. Overall, after glucose addition, a strong increase of dsDNA and RNA contents were determined in most of the soil types during 72 h of incubation. Furthermore, we identified distinct temporal soil-specific RNA:dsDNA patterns. The dsDNA- and RNA-contents yielded 26–174 and 0.3–30 µg g-1 soil, respectively. The soil texture was strongly associated with the reduction of RNA recovery, by means of an exponential decrease of RNA-content with increasing clay content. The lower RNA recovery in virgin and arable Chernozem (>30%) compared to soil types with lower clay contents (<17% for Retisol, Luvisol and Calcisol) suggests, that the undercount 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 with clay contents exceeding 30%

Microbial hotspots and hot moments in soil: Concept & review

© 2015 Elsevier Ltd. Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time - the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the average rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates.For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2-20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output - by decomposition rates of litter - and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. We estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil. By this review, we raised the importance of concepts and ecological theory of distribution and functioning of microorganisms in soil

The above-belowground coupling of the C cycle: fast and slow mechanisms of C transfer for root and rhizomicrobial respiration

© 2016 Springer International Publishing SwitzerlandBackground and aims: The coupling of photosynthesis with belowground processes appears to be much faster than the time needed for assimilate translocation with the phloem flow. Pressure/concentration waves have been hypothesized to release belowground C already present in the phloem, resulting in a very fast feedback of rhizosphere processes to photosynthesis changes. We evaluate the speed of aboveground-rhizosphere coupling under maize by two mechanisms: pressure/concentration waves and direct phloem transport. Methods: We combined two isotopic approaches: 1) the speed of direct phloem transport was evaluated by labeling shoots in 14CO2 and tracing 14C in the nutrient solution and in the CO2 flux, 2) pressure/concentration waves were evaluated by labeling the solution with [13C] glucose and tracing the isotope dilution during photoassimilation. Results: 14C shoot labeling of maize plants showed that 12 h were needed for 14C to peak in root-derived CO2. In contrast, in the solution labeling approach, CO2 flux increased within 2 h after switching on the light. Pressure/concentration waves contributed 5 % to diurnal respiration efflux and affected only root respiration. Root exudation was independent of the fast mechanism of above-belowground coupling. Conclusions: Photosynthesis affected root and rhizomicrobial respiration on variable time-scales: root respiration within the first 2 h by pressure/concentration waves, whereas rhizomicrobial respiration may depend on internal circadian cycles in regulating exudation rather than on light directly

Carbon input and partitioning in subsoil by chicory and alfalfa

© 2016, Springer International Publishing Switzerland.Background and Aims: Input of organic matter into soil creates microbial hotspots. Due to the low organic matter content in subsoil, microbial hotspots can improve nutrient availability to plants. Therefore, carbon (C) input of root biomass and rhizodeposition and the microbial utilization of root C by alfalfa and chicory, both deep-rooting taprooted preceding crops, was determined. Methods: Three replicate plots of alfalfa and chicory grown on a Haplic Luvisol were 13CO2 pulse labeled after 110 days of growth. 13C was traced in plant biomass, rhizosphere, bulk soil and in microbial biomass after 1 and 40 days. C stocks and δ13C signature were quantified in 15 cm intervals down to 105 cm depth. Results: Alfalfa plant biomass was higher and root biomass was more homogeneously distributed between top- (0–30 cm) and subsoil (30–105 cm) compared to chicory. C input into subsoil by alfalfa, including roots and rhizodeposited C, was 8 times higher (3820 kg C ha−1) into subsoil compared to chicory after 150 days of growth. Microbial biomass in subsoil increased with alfalfa but decreased with chicory. Conclusions: Despite their general ability to build biopores, taprooted preceding crops differ in creating microbial hotspots in subsoil. Higher C input and microbial growth in subsoil under alfalfa cultivation can improve physico-chemical and biological properties, and so enhance root growth and consequently the water and nutrient uptake from subsoil compared to chicory

Carbon and nitrogen availability in paddy soil affects rice photosynthate allocation, microbial community composition, and priming: combining continuous ¹³C labeling with PLFA analysis

© 2018, Springer Nature Switzerland AG. Background and aims: Carbon (C) and nitrogen (N) availability in soil change microbial community composition and activity and so, might affect soil organic matter (SOM) decomposition as well as allocation of plant assimilates. The study was focused on interactions between C and N availability and consequences for rhizodeposition and microbial community structure in paddy soil. Methods: Rice continuously labeled in a 13CO2 atmosphere was fertilized with either carboxymethyl cellulose (CMC) (+C), ammonium sulfate (+N), or their combination (+CN), and unfertilized soil was used as a control. 13C was traced in aboveground and belowground plant biomass, soil organic matter, and microbial biomass. Microbial community composition was analyzed by phospholipid fatty acids (PLFAs). Results: +CN application led to a higher yield and lower root C and N content: 13C assimilated in shoots increased by 1.39-fold and that in roots decreased by 0.75-fold. Correspondingly, after +CN addition, 13C from rhizodeposits incorporated into SOM and microorganisms decreased by 0.68-fold and 0.53-fold, respectively, as compared with that in the unfertilized soil. The application of +C or + N alone resulted in smaller changes. CMC led to a 3% of total N mobilized from SOM and resulted in a positive priming effect. Both fertilizations (+C, +N, or + CN) and plant growth stages affected soil microbial community composition. With decreasing microbial biomass C and N, and PLFA content under +CN amendment, +CN fertilization decreased Gram-positive (G+)/ Gram-negative (G-) ratios, and resulted in lower G+ bacteria and fungi abundance, whereas G- and actinomycetes were stimulated by N fertilization. Conclusions: Organic C fertilization led to a positive N priming effect. Organic C and mineral N application decreased C input by rhizodeposition associated with lower 13C recovery in SOM and microbial incorporation. C and N addition also altered microbial community composition, as +CN decreased content of microbial groups, such as G+ bacteria and fungi, but +N stimulated G- bacteria and actinomycetes