Rhizodeposition: Its contribution to microbial growth and carbon and nitrogen turnover within the rhizosphere

A greenhouse rhizobox experiment was carried out to investigate the fate and turnover of ¹³C‐ and ¹⁵N‐labeled rhizodeposits within a rhizosphere gradient from 0–8 mm distance to the roots of wheat. Rhizosphere soil layers from 0–1, 1–2, 2–3, 3–4, 4–6, and 6–8 mm distance to separated roots were investigated in an incubation experiment (42 d, 15°C) for changes in total C and N and that derived from rhizodeposition in total soil, in soil microbial biomass, and in the 0.05 M K₂SO₄–extractable soil fraction. CO₂‐C respiration in total and that derived from rhizodeposition were measured from the incubated rhizosphere soil samples. Rhizodeposition C was detected in rhizosphere soil up to 4–6 mm distance from the separated roots. Rhizodeposition N was only detected in the rhizosphere soils up to 3–4 mm distance from the roots. Microbial biomass C and N was increased with increasing proximity to the separated roots. Beside ¹³C and ¹⁵N derived from rhizodeposits, unlabeled soil C and N (native SOM) were incorporated into the growing microbial biomass towards the roots, indicating a distinct acceleration of soil organic matter (SOM) decomposition and N immobilization into the growing microbial biomass, even under the competition of plant growth. During the soil incubation, microbial biomass C and N decreased in all samples. Any decrease in microbial biomass C and N in the incubated rhizosphere soil layers is attributed mainly to a decrease of unlabeled (native) C and N, whereas the main portion of previously incorporated rhizodeposition C and N during the plant growth period remained immobilized in the microbial biomass during the incubation. Mineralization of native SOM C and N was enhanced within the entire investigated rhizosphere gradient. The results indicate complex interactions between substrate input derived from rhizodeposition, microbial growth, and accelerated C and N turnover, including the decomposition of native SOM (i.e., rhizosphere priming effects) at a high spatial resolution from the roots.     

Rhizodeposition-induced decomposition increases N availability to wild and cultivated wheat genotypes under elevated CO2

Elevated CO₂ may increase nutrient availability in the rhizosphere by stimulating N release from recalcitrant soil organic matter (SOM) pools through enhanced rhizodeposition. We aimed to elucidate how CO₂-induced increases in rhizodeposition affect N release from recalcitrant SOM, and how wild versus cultivated genotypes of wheat mediated differential responses in soil N cycling under elevated CO₂. To quantify root-derived soil carbon (C) input and release of N from stable SOM pools, plants were grown for 1 month in microcosms, exposed to ¹³C labeling at ambient (392 μmol mol⁻¹) and elevated (792 μmol mol⁻¹) CO₂ concentrations, in soil containing ¹⁵N predominantly incorporated into recalcitrant SOM pools. Decomposition of stable soil C increased by 43%, root-derived soil C increased by 59%, and microbial-¹³C was enhanced by 50% under elevated compared to ambient CO₂. Concurrently, plant ¹⁵N uptake increased (+7%) under elevated CO₂ while ¹⁵N contents in the microbial biomass and mineral N pool decreased. Wild genotypes allocated more C to their roots, while cultivated genotypes allocated more C to their shoots under ambient and elevated CO₂. This led to increased stable C decomposition, but not to increased N acquisition for the wild genotypes. Data suggest that increased rhizodeposition under elevated CO₂ can stimulate mineralization of N from recalcitrant SOM pools and that contrasting C allocation patterns cannot fully explain plant mediated differential responses in soil N cycling to elevated CO₂.     

Release of C and N from roots of peas and oats and their availability to soil microorganisms

Nutrient mobilisation in the rhizosphere is driven by soil microorganisms and controlled by the release of available C compounds from roots. It is not known how the quality of release influences this process in situ. Therefore, the present study was conducted to investigate the amount and turnover of rhizodeposition, in this study defined as root-derived C or N present in the soil after removal of roots and root fragments, released at different growth stages of peas (Pisum sativum L.) and oats (Avena sativa L.). Plants were grown in soil columns placed in a raised bed under outdoor conditions and simultaneously pulse labelled in situ with a ¹³C-glucose-¹⁵N-urea solution using a stem feeding method. After harvest, ¹³C and ¹⁵N was recovered in plant parts and soil pools, including the microbial biomass. Net rhizodeposition of C and N as a percentage of total plant C and N was higher in peas than in oats. Moreover, the C-to-N ratio of the rhizodeposits was lower in peas, and a higher proportion of the microbial biomass and inorganic N was derived from rhizodeposition. These results suggest a positive plant-soil feedback shaping nutrient mobilisation. This process is driven by the C and N supply of roots, which has a higher availability in peas than in oats.     

Incorporation of 13C-labelled rice rhizodeposition carbon into soil microbial communities under different water status

The overall processes by which carbon is fixed by plants in photosynthesis then released into the soil by rhizodeposition and subsequently utilized by soil micro-organisms, links the atmospheric and soil carbon pools. The objective of this study was to determine the plant derived ¹³C incorporated into the phospholipid fatty acid (PLFA) pattern in paddy soil, to test whether utilization of rice rhizodeposition carbon by soil micro-organisms is affected by soil water status. This is essential to understand the importance of flooded conditions in regulating soil microbial community structure and activity in wetland rice systems. Rice plants were grown in soil derived from a paddy system under controlled irrigation (CI), or with continuous waterlogging (CW). Most of the ¹³C-labelled rice rhizodeposition carbon was distributed into the PLFAs 16:0, 18:1ω7 and 18:1ω9 in both the CW and CI treatments. The bacterial PLFAs i15:0 and a15:0, both indicative of gram positive bacteria, were relatively more abundant in the treatments without rice plants. When rice plants were present rates of ¹³C-incorporation into i15:0 and a15:0 was slow; the microbes containing these PLFAs may derive most of their carbon from more recalcitrant C (soil organic matter). PLFAs, 18:1ω7 and 16:1ω7c, indicative of gram negative bacteria showed a greater amount incorporation of labelled plant derived carbon in the CW treatment. In contrast, 18:2ω6,9 indicative of fungi and 18:1ω9 indicative of aerobes but also potentially fungi and plant roots had greater incorporation in the CI treatment. The greater root mass concomitant with lower incorporation of ¹³C into the total PLFA pool in the CW treatment suggests that the microbial communities in wetland rice soil are limited by factors other than substrate availability in flooded conditions. In this study differing soil microbial communities were established through manipulating the water status of paddy soils. Steady state ¹³C labelling enabled us to determine that the microbial community utilizing plant derived carbon was also affected by water status.     

Estimating N rhizodeposition of grain legumes using a N in situ stem labelling method

Grain legumes in crop rotations cause significant increases in yield for succeeding non-legumes, which cannot be explained simply by the small effect that legumes have on the soil nitrogen balance, as found in the analysis of N in crop residues. Besides known positive non-N-effects, other effects, mainly rhizodeposition and its contribution to the N balance and nitrogen dynamics after harvesting the grain, are poorly understood. In this study, N rhizodeposition, defined as root-derived N in the soil after removal of visible roots, was measured in faba bean (Vicia faba L.), pea (Pisum sativum L.) and white lupin (Lupinus albus L.). In a pot experiment the legumes were pulse labelled in situ with ¹⁵N urea using a cotton wick method. About 84% of the applied ¹⁵N was recovered for the three legume species at maturity. The ¹⁵N was comparatively uniformly distributed among plant parts. The N rhizodeposition constituted 13% of total plant N for faba bean and pea and 16% for white lupin at maturity, about 80% of below ground plant N, respectively. Some 7% (lupin)-31% (pea) of the total N rhizodeposits were recovered as micro-roots by wet sieving (200 μm) the soil after all visible roots had been removed. Only 14-18% of the rhizodeposition N was found in the microbial biomass and a very small amount of 3-7% was found in the mineral N fraction. In pea, 48% and in lupin 72% of N rhizodeposits could not be recovered in the mentioned pools and a major part of the unrecovered N was probably immobilised in microbial residues. The results of this study clearly indicate that N rhizodeposition from grain legumes represent a significant pool for N balance and N dynamics in crop rotations.     

Turnover of grain legume N rhizodeposits and effect of rhizodeposition on the turnover of crop residues

The turnover of N derived from rhizodeposition of faba bean (Vicia faba L.), pea (Pisum sativum L.) and white lupin (Lupinus albus L.) and the effects of the rhizodeposition on the subsequent C and N turnover of its crop residues were investigated in an incubation experiment (168 days, 15 °C). A sandy loam soil for the experiment was either stored at 6 °C or planted with the respective grain legume in pots. Legumes were in situ ¹⁵N stem labelled during growth and visible roots were removed at maturity. The remaining plant-derived N in soil was defined as N rhizodeposition. In the experiment the turnover of C and N was compared in soils with and without previous growth of three legumes and with and without incorporation of crop residues. After 168 days, 21% (lupin), 26% (faba bean) and 27% (pea) of rhizodeposition N was mineralised in the treatments without crop residues. A smaller amount of 15–17% was present as microbial biomass and between 30 and 55% of mineralised rhizodeposition N was present as microbial residue pool, which consists of microbial exoenzymes, mucous substances and dead microbial biomass. The effect of rhizodeposition on the C and N turnover of crop residues was inconsistent. Rhizodeposition increased the crop residue C mineralisation only in the lupin treatment; a similar pattern was found for microbial C, whereas the microbial N was increased by rhizodeposition in all treatments. The recovery of residual ¹⁵N in the microbial and mineral N pool was similar between the treatments containing only labelled crop residues and labelled crop residues + labelled rhizodeposits. This indicates a similar decomposability of both rhizodeposition N and crop residue N and may be attributable to an immobilisation of both N sources (rhizodeposits and crop residues) as microbial residues and a subsequent remineralisation mainly from this pool.Abbreviations C or N_dec C or N decomposed from residues - C or N_mic microbial C or N - C or N_micres microbial residue C or N - C or N_min mineralised C or N - C or N_input added C or N as crop residues and/or rhizodeposits - dfr derived from residues - dfR derived from rhizodeposition - Ndfr N derived from residues - NdfR N derived from rhizodeposition - N_loss losses of N derived from residues - SOM soil organic matter - WHC water holding capacity     

Fate of C- and N-labelled rhizodeposition of Lolium perenne as function of the distance to the root surface

A greenhouse rhizobox experiment was carried out to quantify the incorporation of ¹³C- and ¹⁵N-labelled rhizodeposits into different soil pools, especially into the rhizosphere microbial biomass, with increasing distances to the root surface of Lolium perenne. Five layers were analysed over 0-4.2 mm distance to an artificial root surface. C and N derived from rhizodeposition were 4.2% of total C and 2.8% of total N in soil at 0-1.0 mm distance and decreased rapidly with increasing distance. Microbial biomass C and N increased significantly towards the roots. At 0-1.0 mm distance microbial biomass C and N accounted for 66% and 29% of C and N derived from rhizodeposition, respectively. These percentages declined with increasing distance to the roots, but were still traceable up to 4.2 mm distance. Only small amounts of root released C and N were found in the 0.05 M K₂SO₄-extractable fraction. Extractable C and N derived from rhizodeposition varied around means of 4% of total C and N derived from rhizodeposition and increased only marginally with increasing distance to the roots. C derived from rhizodeposition in the non-extractable soil organic matter increased from 65 to 89% of total C derived from rhizodeposition at 0-3.4 mm distance. Conversely, microbial biomass C derived from rhizodeposition decreased from 33 to 4%. N derived from rhizodeposition in the non-extractable soil organic matter increased from 61 to 79% of total N derived from rhizodeposition at 0-2.6 mm distance, followed by a decline to roughly 55% in the two outer layers. Microbial biomass N decreased from 37 to 16% at 0-2.6 mm distance, followed by an increase to roughly 41% in the two outer layers. The C/N ratio of total C and N derived from rhizodeposition as well as that of extractable C and N derived from rhizodeposition increased with increasing distance to the roots to values above 30. In contrast, the C/N ratio of incorporated rhizodeposition C and N into the microbial biomass decreased to values less than 5 at 2.6-4.2 mm distance. The data indicate differential microbial response to C and N derived from rhizodeposition at a high spatial resolution from the root surface. The turnover of C and N derived from rhizodeposition in the rhizosphere as a function of the distance to the root surface is discussed.     

Microbial immobilisation of C rhizodeposits in rhizosphere and root-free soil under continuous C labelling of oats

A greenhouse experiment was conducted by growing oats (Avenasativa L.) in a continuously ¹³CO₂ labeled atmosphere. The allocation of ¹³C-labeled photosynthates in plants, microbial biomass in rhizosphere and root-free soil, pools of soil organic C, and CO₂ emissions were examined over the plant's life cycle. To isolate rhizosphere from root-free soil, plant seedlings were placed into bags made of nylon monofilament screen tissue (16 μm mesh) filled with soil. Two peaks of ¹³C in rhizosphere pools of microbial biomass and dissolved organic carbon (DOC), as well as in CO₂ emissions at the earing and ripeness stages were revealed. These ¹³C maxima corresponded to: (i) the end of rapid root growth and (ii) beginning of root decomposition, respectively. The δ¹³C values of microbial biomass were higher than those of DOC and of soil organic matter (SOM). The microbial biomass C accounted for up to 56 and 39% of ¹³C recovered in the rhizosphere and root-free soil, respectively. Between 4 and 28% of ¹³C assimilated was recovered in the root-free soil. Depending on the phenological stage, the contribution of root-derived C to total CO₂ emission from soil varied from 61 to 92% of total CO₂ evolved, including 4-23% attributed to rhizomicrobial respiration. While 81-91% of C substrates used for microbial growth in the root-free soil and rhizosphere came from SOM, the remaining 9-19% of C substrates utilized by the microbial biomass was attributable to rhizodeposition. The use of continuous isotopic labelling and physical separation of root-free and rhizosphere soil, combined with natural ¹³C abundance were effective in gaining new insight on soil and rhizosphere C-cycling.     

Nitrogen fertilization increases rhizodeposit incorporation into microbial biomass and reduces soil organic matter losses

Agricultural soils receive large amounts of anthropogenic nitrogen (N), which directly and indirectly affect soil organic matter (SOM) stocks and CO₂ fluxes. However, our current understanding of mechanisms on how N fertilization affects SOM pools of various ages and turnover remains poor. The δ¹³C values of SOM after wheat (C₃)-maize (C₄) vegetation change were used to calculate the contribution of C₄-derived rhizodeposited C (rhizo-C) and C₃-derived SOM pools, i.e., rhizo-C and SOM. Soil (Ap from Haplic Luvisol) sampled from maize rhizosphere was incubated over 56 days with increasing N fertilization (four levels up to 300 kg N ha^?1), and CO₂ efflux and its δ¹³C were measured. Nitrogen fertilization decreased CO₂ efflux by 27–42% as compared to unfertilized soil. This CO₂ decrease was mainly caused by the retardation of SOM (C₃) mineralization. Microbial availability of rhizo-C (released by maize roots within 4 weeks) was about 10 times higher than that of SOM (older than 4 weeks). Microbial biomass and dissolved organic C remained at the same level with increasing N. However, N fertilization increased the relative contribution of rhizo-C to microbial biomass by two to five times and to CO₂ for about two times. This increased contribution of rhizo-C reflects strongly accelerated microbial biomass turnover by N addition. The decomposition rate of rhizo-C was 3.7 times faster than that of SOM, and it increased additionally by 6.5 times under 300 kg N ha^?1 N fertilization. This is the first report estimating the turnover and incorporation of very recent rhizo-C (4 weeks old) into soil C pools and shows that the turnover of rhizo-C was much faster than that of SOM. We conclude that the contribution of rhizo-C to CO₂ and to microbial biomass is highly dependent on N fertilization. Despite acceleration of rhizo-C turnover, the increased N fertilization facilitates C sequestration by decreasing SOM decomposition.     

Linking Microbial Community Dynamics Associated with Rhizosphere Carbon Flow in a Biofuel Crop (Jatropha curcas L.)

Photosynthetically derived rhizodeposits are an important source of carbon (C) for microbes in root vicinity and can influence the microbial community dynamics. Pulse labeling of carbon dioxide (¹³CO₂) coupled with stable isotope probing techniques have potential to track recently fixed photosynthate into rhizosphere microbial taxa. Therefore, the present investigation assessed the microbial community change associated with the rhizosphere and bulk soil in Jatropha curcas L. (a biofuel crop) by combining phospholipid fatty acid (¹³C-PLFA) profiling using a stable isotope ¹³CO₂ labeling approach. The labeling (¹³C) took place after 45 days of germination, PLFAs were extracted from both soils (rhizosphere and bulk) after 1 and 20 days pulse labeling and analyzed by gas chromatography-isotope ratio mass spectrometry. There was no significant temporal effect on the PLFA profiles in the bulk soil, but significantly increased abundance of Gram positive (i15:0) and Gram negative (16:1ω7c and 16:1ω5c) biomarkers was observed in the rhizosphere soil from day 1 to day 20 after labeling. The Gram negative (16:1ω7c) decreased and fungal (18:2ω6,9c) increased significantly in rhizospheric soil compared to bulk soil after day 1 of labeling. Whereas, after 20 days of labeling, the Gram negative biomarker (16:1ω7c and 18:1ω7c) decreased and Gram positive (a15:0) increased significantly in rhizospheric soil compared to bulk soil. One day following labeling, i15:0, a15:0, i16:0, 16:1ω5c, 16:0, i17:0, a17:0, 18:2ω6,9c, 18:1ω9c, and 18:0 PLFAs were significantly more enriched in δ¹³C in the rhizosphere than in the bulk soil. Twenty days after labeling, 16:1ω5c (Gram negative) and 18:2ω6,9c (fungal) were significantly more enriched in δ¹³C in the rhizosphere than in the bulk soil. These results shows the effectives of PLFA coupled using the pulse chase labeling technique to examine the microbial community changes in response to recently fixed photosynthetic C flow in rhizodeposits.     

Soil nitrogen availability alters rhizodeposition carbon flux into the soil microbial community

Purpose

Soil microorganisms are important in the cycling of plant nutrients. Soil microbial biomass, community structure, and activity are mainly affected by carbon substrate and nutrient availability. The objective was to test if both the overall soil microbial community structure and the community-utilizing plant-derived carbon entering the soil as rhizodeposition were affected by soil carbon (C) and nitrogen (N) availability.

Materials and methods

A ¹³C-CO₂ steady-state labeling experiment was conducted in a ryegrass system. Four soil treatments were established: control, amendment with carboxymethyl cellulose (CMC), amendment with ammonium nitrate (NF), combined CMC and NF. Soil phospholipid fatty acid (PLFA) and ¹³C labeling PLFA were extracted and detected by isotope ratio mass spectrometer.

Results and discussion

The combined CMC and NF treatment with appropriate C/N ratio (20) significantly enhanced soil microbial biomass C and N, but resulted in lower soil inorganic N concentrations. There was no significant difference in soil PLFA profile pattern between different treatments. In contrast, most of the ¹³C was distributed into PLFAs 18:2ω6,9c, 18:1ω7c, and 18:1ω9c, indicative of fungi and gram-negative bacteria. The inorganic-only treatment was distinct in ¹³C PLFA pattern from the other treatments in the first period of labeling. Factor loadings of individual PLFAs confirmed that gram-positive bacteria had relatively greater plant-derived C contents in the inorganic-only treatment, but fungi were more enriched in the other treatments.

Conclusions

Amendments with CMC can improve N transformation processes, and the ryegrass rhizodeposition carbon flux into the soil microbial community is strongly modified by soil N availability.

     

Rhizosphere priming effect: Its functional relationships with microbial turnover, evapotranspiration, and C–N budgets

Understanding soil organic matter (SOM) decomposition and its interaction with rhizosphere processes is a crucial topic in soil biology and ecology. Using a natural ¹³C tracer method to separately measure SOM-derived CO₂ from root-derived CO₂, this study aims to connect the level of rhizosphere-dependent SOM decomposition with the C and N balance of the whole plant–soil system, and to mechanistically link the rhizosphere priming effect to soil microbial turnover and evapotranspiration. Results indicated that the magnitude of the rhizosphere priming effect on SOM decomposition varied widely, from zero to more than 380% of the unplanted control, and was largely influenced by plant species and phenology. Balancing the extra soil C loss from the strong rhizosphere priming effect in the planted treatments with C inputs from rhizodeposits and root biomass, the whole plant–soil system remained with a net carbon gain at the end of the experiment. The increased soil microbial biomass turnover rate and the enhanced evapotranspiration rate in the planted treatments had clear positive relationships with the level of the rhizosphere priming effect. The rhizosphere enhancement of soil carbon mineralization in the planted treatments did not result in a proportional increase in net N mineralization, suggesting a possible de-coupling of C cycling with N cycling in the rhizosphere.     

Microbial response to rhizodeposition depending on water regimes in paddy soils

Rhizodeposit-carbon (rhizo-C) serves as a primary energy and C source for microorganisms in the rhizosphere. Despite important progress in understanding the fate of rhizo-C in upland soils, little is known about microbial community dynamics associated with rhizo-C in flooded soils, especially depending on water regimes in rice systems. In this study, rice grown under non-flooded, continuously flooded and alternating water regimes was pulse labeled with ¹³CO₂ and the incorporation of rhizo-C into specific microbial groups was determined by ¹³C in phospholipid fatty acids (PLFAs) at day 2 and 14 after the labeling.A decreased C released from roots under continuously flooded condition was accompanied with lower total ¹³C incorporation into microorganisms compared to the non-flooded and alternating water regimes treatments. Continuous flooding caused a relative increase of ¹³C incorporation in Gram positive bacteria (i14:0, i15:0, a15:0, i16:0, i17:0, a17:0). In contrast, Gram negative bacteria (16:1ω7c, 18:1ω7c, cy17:0, cy 19:0) and fungi (18:2ω6, 9c, 18:1ω9c) showed greater rhizo-C incorporation coupled with a higher turnover under non-flooded and alternating water regimes treatments. These observations suggest that microbial groups processing rhizo-C differed among rice systems with varying water regimes. In contrast to non-flooded and alternating water regimes, there was little to no temporal ¹³C change in most microbial groups under continuous flooding condition between day 2 and 14 after the labeling, which may demonstrate slower microbial processing turnover. In summary, our findings indicate that belowground C input by rhizodeposition and its biological cycling was significantly influenced by water regimes in rice systems.     

Root-derived carbon in soil respiration and microbial biomass determined by 14C and 13C

Two approaches to quantitatively estimating root-derived carbon in soil CO₂ efflux and in microbial biomass were compared under controlled conditions. In the ¹⁴C labelling approach, maize (Zea mays) was pulse labelled and the tracer was chased in plant and soil compartments. Root-derived carbon in CO₂ efflux and in microbial biomass was estimated based on a linear relationship between the plant shoots and the below-ground compartment. Since the maize plants were grown on C₃ soil, in a second approach the differences in ¹³C natural abundance between C₃ and C₄ plants were used to calculate root-derived carbon in the CO₂ efflux and in the microbial biomass. The root-derived carbon in the total CO₂ efflux was between 69% and 94% using the ¹⁴C labelling approach and between 86% and 94% in the natural ¹³C labelling approach. At a ¹³C fractionation measured to be 5.2‰ between soil organic matter (SOM) and CO₂, the root-derived contribution to CO₂ ranged from 70% to 88% and was much closer to the results of the ¹⁴C labelling approach. Root-derived contributions to the microbial biomass carbon ranged from 2% to 9% using ¹⁴C labelling and from 16% to 36% using natural ¹³C labelling. At a 3.2‰ ¹³C fractionation between SOM and microbial biomass, both labelling approaches yielded an equal contribution of root-derived C in the microbial biomass. Both approaches may therefore be used to partition CO₂ efflux and to quantify the C sources of microbial biomass. However, the assumed ¹³C fractionation strongly affects the contributions of individual C sources.     

Determination of the fate of C labelled maize and wheat rhizodeposit-C in two agricultural soils in a greenhouse experiment under C-CO2-enriched atmosphere

A deeper understanding of the contribution of carbon (C) released by plant roots (rhizodeposition) to soil organic matter (SOM) can help to increase our knowledge of global C-cycling. These insights can eventually lead to sustainable management of SOM especially in agricultural systems. This study was conducted to determine the fate of ¹³C labelled rhizodeposit-C of maize and wheat plants. They were grown in a greenhouse in permeable nylon bags filled with upper soil material from two agricultural soils of the same location, but with different crop yields. The bags were placed into pots, which were also filled with soil surrounding the bags. Soil inside the bags was considered as rhizosphere soil, wheras the one outside the bags represented bulk soil. The contributions of rhizodeposits to water extractable organic carbon (WEOC), microbial biomass-C (MB-C), CO₂-C evolution, and total organic carbon (C_org) were investigated during a 7-week growing period. The WEOC, MB-C, CO₂-C, C_org contents and the respective δ¹³C values were determined regularly, and a newly developed method for determining δ¹³C values in soil extracts was applied.In both soils, regardless of crop yield potential, significant incorporation of rhizodeposition-derived C was observed in the MB-C, CO₂-C, and C_org pool, but not in the WEOC. The pattern of C incorporation into the different pools was the same for both soils with both plants, and rhizodeposit-derived C was recovered in the order MB-C<C_org<CO₂-C. This showed that rhizodeposits were mainly respired, but since C_org was the second largest pool of the overall balances, they were also stabilized in the soils at least in the short term. It is suggested that the increased SOM mineralization observed in this study (positive priming effects) was probably induced by C exchange processes between the soil matrix and soluble rhizodeposits. Moreover, soluble rhizodeposit-C was detected in MB-C and CO₂-C evolved outside the direct root zone, showing the availability of these C-components in the bulk soil.     

Microbial community composition and rhizodeposit-carbon assimilation in differently managed temperate grassland soils

Rhizodeposit-carbon provides a major energy source for microbial growth in the rhizosphere of grassland soils. However, little is known about the microbial communities that mediate the rhizosphere carbon dynamics, especially how their activity is influenced by changes in soil management. We combined a ¹³CO₂ pulse-labeling experiment with phospholipid fatty acid (PLFA) analysis in differently managed Belgian grasslands to identify the active rhizodeposit-C assimilating microbial communities in these grasslands and to evaluate their response to management practices. Experimental treatments consisted of three mineral N fertilization levels (0, 225 and 450 kg N ha⁻¹ y⁻¹) and two mowing frequencies (3 and 5 times y⁻¹). Phospholipid fatty acids were extracted from surface (0-5 cm) bulk (BU) and root-adhering (RA) soil samples prior to and 24 h after pulse-labeling and were analyzed by gas chromatography-combustion-isotope ratio mass spectrometry (GC-c-IRMS). Soil habitats significantly differed in microbial community structure (as revealed by multivariate analysis of mol% biomarker PLFAs) as well as in gram-positive bacterial rhizodeposit-C uptake (as revealed by greater ¹³C-PLFA enrichment following pulse-labeling in RA compared to BU soil in the 450N/5M treatment). Mowing frequency did not significantly alter the relative abundance (mol%) or activity (¹³C enrichment) of microbial communities. In the non-fertilized treatment, the greatest ¹³C enrichment was seen in all fungal biomarker PLFAs (C16:1ω5, C18:1ω9, C18:2ω6,9 and C18:3ω3,6,9), which demonstrates a prominent contribution of fungi in the processing of new photosynthate-C in non-fertilized grassland soils. In all treatments, the lowest ¹³C enrichment was found in gram-positive bacterial and actinomycetes biomarker PLFAs. Fungal biomarker PLFAs had significantly lower ¹³C enrichment in the fertilized compared to non-fertilized treatments in BU soil (C16:1ω5, C18:1ω9) as well as RA soil (all fungal biomarkers). While these observations clearly indicated a negative effect of N fertilization on fungal assimilation of plant-derived C, the effect of N fertilization on fungal abundance could only be detected for the arbuscular mycorrhizal fungal (AMF) PLFA (C16:1ω5). On the other hand, increases in the relative abundance of gram-positive bacterial PLFAs with N fertilization were found without concomitant increases in ¹³C enrichment following pulse-labeling. We conclude that in situ¹³C pulse-labeling of PLFAs is an effective tool to detect functional changes of those microbial communities that are dominantly involved in the immediate processing of new rhizosphere-C.     

Dry-rewetting cycles regulate wheat carbon rhizodeposition,stabilization and nitrogen cycling

Drying and rewetting of soil can have large effects on carbon (C) and nitrogen (N) dynamics. Drying-rewetting effects have mostly been studied in the absence of plants, although it is well known that plant–microbe interactions can substantially alter soil C and N dynamics. We investigated for the first time how drying and rewetting affected rhizodeposition, its utilization by microbes, and its stabilization into soil (C associated with soil mineral phase). We also investigated how drying and rewetting influenced N mineralization and loss. We grew wheat (Triticum aestivum) in a controlled environment under constant moisture and under dry-rewetting cycles, and used a continuous ¹³C-labeling method to partition plant and soil organic matter (SOM) contribution to different soil pools. We applied a ¹⁵N label to the soil to determine N loss. We found that dry-rewetting decreased total input of plant C in microbial biomass (MB) and in the soil mineral phase, mainly due to a reduction of plant biomass. Plant derived C in MB and in the soil mineral phase were positively correlated (R² = 0.54; P = 0.0012). N loss was reduced with dry rewetting cycles, and mineralization increased after each rewetting event. Overall drying and rewetting reduced rhizodeposition and stabilization of new C, primary through biomass reduction. However, frequency of rewetting and intensity of drought may determine the fate of C in MB and consequently into the soil mineral phase. Frequency and intensity may also be crucial in stimulating N mineralization and reducing N loss in agricultural soils.     

Carbon flow from C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions

To better understand how residue quality and seasonal conditions influence the flow of C from both root and straw residues into the soil microbial community, we followed the incorporation of ¹³C-labeled crimson clover (Trifolium incarnatum) and ryegrass (Lolium multiflorum) root and straw residues into the phospholipid fatty acids (PLFA) of soil microbial biomass. After residue incorporation under field conditions in late summer (September), the ¹³C content of soil PLFA was measured in September, October, and November, 2002, and April and June, 2003. Multivariate non-metric multidimensional scaling techniques showed that the distribution of ¹³C among microbial PLFA differed among the four primary treatments (ryegrass straw and roots, clover straw and roots). Regardless of treatment, some PLFA remained poorly labeled with ¹³C throughout much of the study (16:1ω5, 10Me17:0; 0-5%), whereas other PLFA consistently contained a larger percentage of residue-derived C (16:0; 18:1ω9, 18:2ω6,9; 10-25%). The distribution of residue ¹³C among individual PLFA differed from the relative contributions of individual PLFA (mol%) to total PLFA-C, suggesting that a subset of the soil biomass was primarily responsible for assimilating residue-derived C. The distribution of ¹³C among soil PLFA differed between the sampling times, indicating that residue properties and soil conditions influenced which members of the community were assimilating residue-derived C. Our findings will provide the foundation for further studies to identify the nature of the community members responsible for residue decomposition at different times of the year, and what factors account for the dynamics of the community involved.     

Turnover of soil organic matter and of microbial biomass under C3-C4 vegetation change: Consideration of C 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.     

Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs

We combined microbial community phospholipid fatty acid (PLFA) analyses with an in situ stable isotope ¹³CO₂ labelling approach to identify microbial groups actively involved in assimilation of root-derived C in limed grassland soils. We hypothesized that the application of lime would stimulate more rapid ¹³C assimilation and turnover in microbial PLFAs. Four and 8 d after label application, 18:1ω9, 18:2ω6,9 (fungal biomarkers) and 16:1ω7, 18:1ω7, 19:0cy (Gram-negative bacterial biomarkers) showed the most ¹³C enrichment and rapid turnover rates. This suggests that these microorganisms were assimilating recently-photosynthesized root C inputs to soils. Contrary to our hypothesis, liming did not affect assimilation or turnover rates of ¹³C-labelled C. ¹³C stable isotope pulse-labelling technique paired with analyses of PLFA microbial biomarkers shows promise for in situ investigations of microbial function in soils.