Fate of low molecular weight organic substances in an arable soil: From microbial uptake to utilisation and stabilisation

Microbial uptake and utilisation are the main transformation pathways of low molecular weight organic substances (LMWOS) in soil, but details on transformations are strongly limited. As various LMWOS classes enter biochemical cycles at different steps, we hypothesize that the percentage of their carbon (C) incorporation into microbial biomass and consequently stabilisation in soil are different.Representatives of the three main groups of LMWOS: amino acids (alanine, glutamate), sugars (glucose, ribose) and carboxylic acids (acetate, palmitate) – were applied at naturally-occurring concentrations into a loamy arable Luvisol in a field experiment. Incorporation of ¹³C from these LMWOS into extractable microbial biomass (EMB) and into phospholipid fatty acids (PLFAs) was investigated 3 d and 10 d after application. The microbial utilisation of LMWOS for cell membrane construction was estimated by replacement of PLFA-C with ¹³C.35–80% of initially applied LMWOS-¹³C was still present in the composition of soil organic matter after 10 days of experiment, with 10–24% of ¹³C incorporation into EMB at day three and 1–15% at day 10. Maximal incorporation of ¹³C into EMB was observed from sugars and the least from amino acids. Strong differences in microbial utilisation between LMWOS were observed mainly at day 10. Thus, despite similar initial rapid uptake by microorganisms, further metabolism within microbial cells accounts for the specific fate of C from various LMWOS in soils.¹³C from each LMWOS was incorporated into each PLFA. This reflects the ubiquitous utilisation of all LMWOS by all functional microbial groups. The preferential incorporation of palmitate into PLFAs reflects its role as a direct precursor for fatty acids. Higher ¹³C incorporation from alanine and glucose into specific PLFAs compared to glutamate, ribose and acetate reflects the preferential use of glycolysis-derived substances in the fatty acids synthesis.Gram-negative bacteria (16:1ω7c and 18:1ω7c) were the most abundant and active in LMWOS utilisation. Their high activity corresponds to a high demand for anabolic products, e.g. to dominance of pentose-phosphate pathway, i.e. incorporation of ribose-C into PLFAs. The ¹³C incorporation from sugars and amino acids into filamentous microorganisms was lower than into all prokaryotic groups. However, for carboxylic acids, the incorporation was in the same range (0.1–0.2% of the applied carboxylic acid ¹³C) as that of gram-positive bacteria. This may reflect the dominance of fungi and other filamentous microorganisms for utilisation of acidic and complex organics.Thus, we showed that despite similar initial uptake, C from individual LMWOS follows deviating metabolic pathways which accounts for the individual fate of LMWOS-C over 10 days. Consequently, stabilisation of C in soil is mainly connected with its incorporation into microbial compounds of various stability and not with its initial microbial uptake.     

Using metabolic tracer techniques to assess the impact of tillage and straw management on microbial carbon use efficiency in soil

Tillage practices and straw management can affect soil microbial activities with consequences for soil organic carbon (C) dynamics. Microorganisms metabolize soil organic C and in doing so gain energy and building blocks for biosynthesis, and release CO₂ to the atmosphere. Insight into the response of microbial metabolic processes and C use efficiency (CUE; microbial C produced per substrate C utilized) to management practices may therefore help to predict long term changes in soil C stocks. In this study, we assessed the effects of reduced (RT) and conventional tillage (CT) on the microbial central C metabolic network, using soil samples from a 12-year-old field experiment in an Irish winter wheat cropping system. Straw was removed from half of the RT and CT plots after harvest or incorporated into the soil in the other half, resulting in four treatment combinations. We added 1-¹³C and 2,3-¹³C pyruvate and 1-¹³C and U-¹³C glucose as metabolic tracer isotopomers to composite soil samples taken at two depths (0–15 cm and 15–30 cm) from each of the treatments and used the rate of position-specific respired ¹³CO₂ to parameterize a metabolic model. Model outcomes were then used to calculate CUE of the microbial community. Whereas the composite samples differed in CUE, the changes were small, with values ranging between 0.757 and 0.783 across treatments and soil depth. Increases in CUE were associated with a reduced tricarboxylic acid cycle and reductive pentose phosphate pathway activity and increased consumption of metabolic intermediates for biosynthesis. Our results suggest that RT and straw incorporation do not substantially affect CUE.     

Modeling soil metabolic processes using isotopologue pairs of position-specific C-labeled glucose and pyruvate

Most organic carbon (C) in soils eventually turns into CO₂ after passing through microbial metabolic pathways, while providing cells with energy and biosynthetic precursors. Therefore, detailed insight into these metabolic processes may help elucidate mechanisms of soil C cycling processes. Here, we describe a modeling approach to quantify the C flux through metabolic pathways by adding 1-¹³C and 2,3-¹³C pyruvate and 1-¹³C and U-¹³C glucose as metabolic tracers to intact soil microbial communities. The model calculates, assuming steady-state conditions and glucose as the only substrate, the reaction rates through glycolysis, Krebs cycle, pentose phosphate pathway, anaplerotic activity through pyruvate carboxylase, and various biosynthesis reactions. The model assumes a known and constant microbial proportional precursor demand, estimated from literature data. The model is parameterized with experimentally determined ratios of ¹³CO₂ production from pyruvate and glucose isotopologue pairs. Model sensitivity analysis shows that metabolic flux patterns are especially responsive to changes in experimentally determined ¹³CO₂ ratios from pyruvate and glucose. Calculated fluxes are far less sensitive to assumptions concerning microbial chemical and community composition. The calculated metabolic flux pattern for a young volcanic soil indicates significant pentose phosphate pathway activity in excess of pentose precursor demand and significant anaplerotic activity. These C flux patterns can be used to calculate C use efficiency, energy production and consumption for growth and maintenance purposes, substrate consumption, nitrogen demand, oxygen consumption, and microbial C isotope composition. The metabolic labeling and modeling methods may improve our ability to study the biochemistry and ecophysiology of intact and undisturbed soil microbial communities.     

13C标记磷脂脂肪酸分析在土壤微生物生态 研究中的应用

磷脂脂肪酸(PLFA)是微生物细胞膜的重要组成成分,不同微生物群落可通过不同生化途径合成不同的PLFA,因此可选择某些PLFA作为微生物群落结构变化的生物标志物。PLFA与稳定性同位素~(13)C标记(~(13)C-PLFA)技术结合,不仅能够确定原位土壤环境中微生物群落组成,而且能够定向发掘土壤生态系统中参与碳源代谢过程的微生物群落,提供复杂群落中土壤微生物相互作用的信息,具有广阔的应用前景。其基本原理为:将富集~(13)C稳定同位素的基质加入土壤中,土壤中的某些微生物群落利用基质~(13)C合成PLFA,提取并纯化土壤微生物的PLFA,利用气相色谱-燃烧-同位素比例质谱(GC-C-IRMS)测定其~(13)C丰度,通过对比分析,从而获取微生物群落组成与其功能的直接信息。本文在介绍了~(13)C-PLFA原理的基础上,综述了该技术在光合同化碳的根际微生物利用、土壤有机质分解的激发效应、甲烷氧化、有机污染物降解、外源简单碳源和外源复杂碳源的微生物利用等方面的应用,对此项技术的优缺点进行了分析并展望了其未来应用。     

Glucose uptake by maize roots and its transformation in the rhizosphere

The flow of carbon from roots into the rhizosphere represents a significant C loss from plants. However, roots have the capacity to recapture low molecular weight C from soil although this is in direct competition with soil microorganisms. The aim of this study was to investigate the behaviour of glucose in rhizosphere and non-rhizosphere soil, the plant's potential to recapture sugars from soil and translocation and utilization of the recaptured sugars. In microcosms containing maize plants we injected ¹⁴C-glucose into the rhizosphere and followed its uptake into plants, upward and downward transport in the plant and soil, evolution as ¹⁴CO₂ and incorporation into the soil microbial biomass. These fluxes were compared with non-rhizosphere soil. Glucose was rapidly mineralized in soil and the rate of turnover was significantly greater in the rhizosphere in comparison to non-rhizosphere soil. The amount of glucose captured by the maize plants was low (<10% of the total ¹⁴C-glucose added) in comparison to that captured by the soil microbial biomass. Only small amounts of the ¹⁴C-glucose were transported to the shoot (0.6% of the total). The degree of glucose capture by maize roots whilst in competition with soil microorganisms was similar to similar experiments performed for amino acids. We conclude that while plant roots can recapture low molecular weight C from the rhizosphere, intense competition from soil microorganisms may reduce the efficiency of this process.     

Sugars in soil and sweets for microorganisms: Review of origin,content, composition and fate

Sugars are the most abundant organic compounds in the biosphere because they are monomers of all polysaccharides. We summarize the results of the last 40 years on the sources, content, composition and fate of sugars in soil and discuss their main functions. We especially focus on sugar uptake, utilization and recycling by microorganisms as this is by far the dominating process of sugar transformation in soil compared to sorption, leaching or plant uptake. Moreover, sugars are the most important carbon (C) and energy source for soil microorganisms.Two databases have been created. The 1st database focused on the contents of cellulose, non-cellulose, hot-water and cold-water extractable sugars in soils (348 data, 32 studies). This enabled determining the primary (plant-derived) and secondary (microbially and soil organic matter (SOM) derived) sources of carbohydrates in soil based on the galactose + mannose/arabinose + xylose (GM/AX) ratio. The 2nd database focused on the fate of sugar C in soils (734 data pairs, 32 studies using ¹³C or ¹⁴C labeled sugars). ¹³C and ¹⁴C dynamics enabled calculating the: 1) initial rate of sugar mineralization, 2) mean residence time (MRT) of C of the applied sugars, and 3) MRT of sugar C incorporated into 3a) microbial biomass and 3b) SOM.The content of hexoses was 3–4 times higher than pentoses, because hexoses originate from plants and microorganisms. The GM/AX ratio of non-cellulose sugars revealed a lower contribution of hexoses in cropland and grassland (ratio 0.7–1) compare to forest (ratio 1.5) soils.¹³C and ¹⁴C studies showed very high initial rate of glucose mineralization (1.1% min⁻¹) and much higher rate of sugars uptake by microorganisms from the soil solution. Considering this rate along with the glucose input from plants and its content in soil solution, we estimate that only about 20% of all sugars in soil originate from the primary source – decomposition of plant litter and rhizodeposits. The remaining 80% originates from the secondary source – microorganisms and their residues. The estimated MRT of sugar C in microbial biomass was about 230 days, showing intense and efficient internal recycling within microorganisms. The assessed MRT of sugar C in SOM was about 360 days, reflecting the considerable accumulation of sugar C in microbial residues and its comparatively slow external recycling.The very rapid uptake of sugars by microorganisms and intensive recycling clearly demonstrate the importance of sugars for microbes in soil. We speculate that the most important functions of sugars in soil are to maintain and stimulate microbial activities in the rhizosphere and detritusphere leading to mobilization of nutrients by accelerated SOM decomposition – priming effects. We conclude that the actual contribution of sugar C (not only whole sugar molecules, which are usually determined) to SOM is much higher than the 10 ± 5% commonly measured based on their content.     

Probing carbon flux patterns through soil microbial metabolic networks using parallel position-specific tracer labeling

In order to study controls on metabolic processes in soils, we determined the dynamics of ¹³CO₂ production from two position-specific ¹³C-labeled pyruvate isotopologues in the presence and absence of glucose, succinate, pine, and legume leaf litter, and under anaerobic conditions. We also compared ¹³CO₂ production in soils along a semiarid substrate age gradient in Arizona. We observed that the C from the carboxyl group (C₁) of pyruvate was lost as CO₂ much faster than its other C atoms (C_2,3). Addition of glucose, pine and legume leaf litter reduced the ratio between ¹³CO₂ production from 1-¹³C pyruvate and 2,3-¹³C pyruvate (C₁/C_2,3 ratio), whereas anaerobic conditions increased this ratio. Young volcanic soils exhibited a lower C₁/C_2,3 ratio than older volcanic soils. We interpret a low C₁/C_2,3 ratio as an indication of increased Krebs cycle activity in response to carbon inputs, while the higher ratio implies a reduced Krebs cycle activity in response to anaerobic conditions. Succinate, a gluconeogenic substrate, reduced ¹³CO₂ production from pyruvate to near zero, likely reflecting increased carbohydrate biosynthesis from Krebs cycle intermediates. The difference in ¹³CO₂ production rate from pyruvate isotopologues disappeared 4-5 days after pyruvate addition, indicating that C positions were scrambled by ongoing soil microbial transformations. This work demonstrates that metabolic tracers such as pyruvate can be used to determine qualitative aspects of C flux patterns through metabolic pathways of soil microbial communities. Understanding the controls over metabolic processes in soil may improve our understanding of soil C cycling processes.     

Application of 13C-labeled litter and root materials for in situ decomposition studies using phospholipid fatty acids

Microorganisms play a central role in litter decomposition and partitioning C between CO₂ evolution and sequestration of C into semi-permanent pools in soils. At the ecosystem level, forest stand age influences rates of litter accumulation and quality, and micro-climatology which could affect the microbial community structure and C sequestration processes. Although numerous laboratory experiments have studied the decomposition of model ¹³C-labeled compounds, few studies have verified these findings under field conditions. The objective of this study was to track decomposition of ¹³C-labeled Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) materials into the soil microbial community using ¹³C-phospholipids fatty acid (PLFA) analysis in three different aged forest stands. A field experiment was conducted that had three forest stand age treatments: old-growth (>500 yrs); 8-year-old clear-cut (CC8); and 25-year-old clear-cut (CC25) (landscape reps of n = 2). Each stand age had in situ microcosms that were amended with either ¹³C-labeled surface litter or root material. Microcosms were destructively sampled seven times over a 22-month period and the soil was analyzed for the relative amounts of ¹³C incorporated (¹³C%_INCORP) into PLFAs and the proportional distribution of ¹³C incorporated into PLFAs. The ¹³C%_INCORP was affected by stand age and ¹³C source with greater ¹³C%_INCORP in samples from CC8 than OG or CC25. Also, the level of ¹³C%_INCORP was greater for labeled litter than root material in five out of the seven sample dates. In general, 18:1ω9 and 18:2ω6,9 (common fungal biomarkers) had the greatest amount of ¹³C incorporation throughout the study period in both clear-cut and old-growth sites, especially in plots with ¹³C-labeled litter. Our data showed a low fungal ¹³C-PLFA: bacterial ¹³C-PLFA ratio (0.45) 1 month after incubation was initiated compared to 5, 7 and 9 months after incubation (two of these dates were >1.0). This suggests that initially bacteria played a greater role in the decomposition of the added needles with fungi playing a more important role in subsequent sample dates. Our results illustrate that the use of ¹³C-labeled materials in field studies coupled with¹³C-PLFA profiling is a powerful tool for determining microbial dynamics during decomposition – enabling statistically significant detection of land management treatment effects on C acquisition by microbial functional groups.     

Plant species influence microbial diversity and carbon allocation in the rhizosphere

Plant species effects on microbial communities are attributed to changes in microbial community composition and biomass, and may depend on plant species specific differences in the quality of resources (carbon) inputs. We examined the idea that plant-soil feedbacks can be explained by a chance effect, which is the probability of a highly productive or keystone plant species is present in the community and will influence the functions more than the number of species per se. A ¹³C pulse labelling technique was applied to three plant species and a species mixture in a greenhouse experiment to examine the carbon flow from plants to soil microbial communities. The ¹³C label was given as CO₂ to shoots of a legume (Lotus corniculatus), a forb (Plantago lanceolata), a grass (Holcus lanatus) and a mixture of the three species. Microbial phospholipid fatty acids (PLFA) was analysed in order to determine the biomass and composition of the soil microbial community. The incorporation of the stable isotope into soil microorganisms was determined through GC-IRMS analyses of the microbial PLFAs. Plant species identity did not influence the microbial biomass when determined as total carbon of microbial phospholipid fatty acids. However, the labelled carbon showed that the grass monoculture (H. lanatus) and the plant mixture allocated more ¹³C into bacteria and actinomycete biomass than the other plant species. H. lanatus monocultures had also the highest amounts of ¹³C allocated to AM-fungi and saprophytic fungi. The carbon allocation from plants to soil microorganisms in a plant species mixture can thus be explained by the presence of a highly productive species that influence soil functions.     

Microbial uptake of low‐molecular‐weight organic substances out‐competes sorption in soil

Low‐molecular‐weight organic substances (LMWOS) such as amino acids, sugars and carboxylates, are rapidly turned over in soil. Despite their importance, it remains unknown how the competition between microbial uptake and sorption to the soil matrix affects the LMWOS turnover in soil solution. This study describes the dynamics of LMWOS fluxes (10 µm ) in various pools (dissolved, sorbed, decomposed to CO₂ and incorporated into microbial biomass) and also assesses the LMWOS distribution in these pools over a very wide concentration range (0.01–1000 µm ). Representatives of each LMWOS group (glucose for sugars, alanine for amino acids, acetate for carboxylates), uniformly ¹⁴C‐labelled, were added to sterilized or non‐sterilized soil and analysed in different pools between 1 minute and 5.6 hours after addition. LMWOS were almost completely taken up by microorganisms within the first 30 minutes. Surprisingly, microbial uptake was much faster than the physicochemical sorption (estimated in sterilized soil), which needed 60 minutes to reach quasi‐equilibrium for alanine and about 400 minutes for glucose. Only acetate sorption was instantaneous. At a concentration of 100 µm , microbial decomposition after 4.5 hours was greater for alanine (76.7 ± 1.1%) than for acetate (55.2 ± 0.9%) or glucose (28.5 ± 1.5%). In contrast, incorporation into microbial biomass was greater for glucose (59.8 ± 1.2%) than for acetate (23.4 ± 5.9%) or alanine (5.2 ± 2.8%). Between 10 and 500 µm , the pathways of the three LMWOS changed: at 500 µm , alanine and acetate were less mineralized and more was incorporated into microbial biomass than at 10 µm , while glucose incorporation decreased. Despite the fact that the LMWOS concentrations in soil solution were important for competition between sorption and microbial uptake, their fate in soil is mainly determined by microbial uptake and further microbial transformations. For these substances, which represent the three main groups of LMWOS in soil, the microbial uptake out‐competes sorption.     

Rice rhizodeposition and its utilization by microbial groups depends on N fertilization

Rhizodeposits have received considerable attention, as they play an important role in the regulation of soil carbon (C) sequestration and global C cycling and represent an important C and energy source for soil microorganisms. However, the utilization of rhizodeposits by microbial groups, their role in the turnover of soil organic matter (SOM) pools in rice paddies, and the effects of nitrogen (N) fertilization on rhizodeposition are nearly unknown. Rice (Oryza sativa L.) plants were grown in soil at five N fertilization rates (0, 10, 20, 40, or 60 mg N kg^?1 soil) and continuously labeled in a ¹³CO₂ atmosphere for 18 days during tillering. The utilization of root-derived C by microbial groups was assessed by ¹³C incorporation into phospholipid fatty acids. Rice shoot and root biomass strongly increased with N fertilization. Rhizodeposition increased with N fertilization, whereas the total ¹³C incorporation into microorganisms, as indicated by the percentage of ¹³C recovered in microbial biomass, decreased. The contribution of root-derived ¹³C to SOM formation increased with root biomass. The ratio of ¹³C in soil pools (SOM and microbial biomass) to ¹³C in roots decreased with N fertilization showing less incorporation and faster turnover with N. The ¹³C incorporation into fungi (18:2ω6,9c and 18:1ω9c), arbuscular mycorrhizal fungi (16:1ω5c), and actinomycetes (10Me 16:0 and 10Me 18:0) increased with N fertilization, whereas the ¹³C incorporation into gram-positive (i14:0, i15:0, a15:0, i16:0, i17:0, and a17:0) and gram-negative (16:1ω7c, 18:1ω7c, cy17:0, and cy19:0) bacteria decreased with N fertilization. Thus, the uptake and microbial processing of root-derived C was affected by N availability in soil. Compared with the unfertilized soil, the contribution of rhizodeposits to SOM and microorganisms increased at low to intermediate N fertilization rates but decreased at the maximum N input. We conclude that belowground C allocation and rhizodeposition by rice, microbial utilization of rhizodeposited C, and its stabilization within SOM pools are strongly affected by N availability: N fertilization adequate to the plant demand increases C incorporation in all these polls, but excessive N fertilization has negative effects not only on environmental pollution but also on C sequestration in soil.     

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.     

Three-source-partitioning of microbial biomass and of CO2 efflux from soil to evaluate mechanisms of priming effects

We propose and successfully applied a new approach for 3-source-partitioning based on a combination of ¹⁴C labeling with ¹³C natural abundance. By adding ¹⁴C-labeled glucose to soil after C₃ - C₄ vegetation change, we partitioned three C sources in three compartments, namely CO₂, microbial biomass and dissolved organic C (DOC). This enabled us to estimate mechanisms and sources of priming effects (PE).Glucose application at low and high rate (GL: 100 and GH: 1000 μg C g⁻¹, respectively) caused positive PE both short-term (during 1-3 days) and long-term (3-55 days). Despite a 10-fold difference in the amount of substrate added, the PE observed was larger by a factor of only 1.6 at the high versus low rate of glucose. The real and apparent priming effects were distinguished by partitioning of microbial C for glucose-C and SOM-derived C. As the amount of primed CO₂ respired during short-term PE was 40% lower than microbial C, and the contribution of soil C in microbial biomass did not increase, we concluded that such short-term PE was apparent and was mainly caused by accelerated microbial turnover (at GL) and by pool substitution (at GH). Both the amount of primed CO₂-C, which was 1.3-2.1 times larger than microbial C, and the increased contribution of soil C in microbial biomass allowed us to consider the long-term PE as being real. The sole source of real PE (GL treatment) was the “recent” soil organic matter, which is younger than 12-year-old C. The real PE-induced by a glucose amount exceeding microbial biomass (GH) was due to the almost equal contribution of ‘recent’ (<12 years) and ‘old’ (>12 years) C. Thus, the decomposition of old recalcitrant SOM was induced only by an amount of primer exceeding microbial C. We conclude that combining ¹⁴C labeling with ¹³C natural abundance helped disentangle three C sources in CO₂, microbial biomass and DOC and evaluate mechanisms and sources of PE.     

Earthworms increase soil microbial biomass carrying capacity and nitrogen retention in northern hardwood forests

Earthworms have been shown to produce contrasting effects on soil carbon (C) and nitrogen (N) pools and dynamics. We measured soil C and N pools and processes and traced the flow of ¹³C and ¹⁵N from sugar maple (Acer saccharum Marsh.) litter into soil microbial biomass and respirable C and mineralizable and inorganic N pools in mature northern hardwood forest plots with variable earthworm communities. Previous studies have shown that plots dominated by either Lumbricus rubellus or Lumbricus terrestris have markedly lower total soil C than uncolonized plots. Here we show that total soil N pools in earthworm colonized plots were reduced much less than C, but significantly so in plots dominated by contain L. rubellus. Pools of microbial biomass C and N were higher in earthworm-colonized (especially those dominated by L. rubellus) plots and more ¹³C and ¹⁵N were recovered in microbial biomass and less was recovered in mineralizable and inorganic N pools in these plots. These plots also had lower rates of potential net N mineralization and nitrification than uncolonized reference plots. These results suggest that earthworm stimulation of microbial biomass and activity underlie depletion of soil C and retention and maintenance of soil N pools, at least in northern hardwood forests. Earthworms increase the carrying capacity of soil for microbial biomass and facilitate the flow of N from litter into stable soil organic matter. However, declines in soil C and C:N ratio may increase the potential for hydrologic and gaseous losses in earthworm-colonized sites under changing environmental conditions.     

Distribution and fate of 13C-labeled root and straw residues from ryegrass and crimson clover in soil under western Oregon field conditions

Annual ryegrass (Lolium multiflorum Lam.) and crimson clover (Trifolium incarnatum L.) were pulse-labeled with ¹³C-CO₂ in the field between the initiation of late winter growth (mid-February) and through flowering and seed formation (late May). Straw was harvested after seed maturation (July), and soil containing ¹³C-labeled roots and root-derived C was left in the field until September. ¹³C-enriched and ¹³C-unenriched straw residues of each species were mixed in factorial combinations with soil containing either ¹³C-enriched or ¹³C-unenriched root-derived C and incubated in the field for 10 months. The contributions of C derived from straw, roots, and soil were measured in soil microbial biomass C, respired C, and soil C on five occasions after residue incorporation (September, October, November, April, and June). At straw incorporation (September), 25–30% of soil microbial biomass C was derived from root C in both ryegrass and clover treatments, and this value was sustained in the ryegrass treatment from September to April but declined in the clover treatment. By October, between 20 and 30% of soil microbial biomass C was derived from straw, with the percentage contribution from clover straw generally exceeding that from ryegrass straw throughout the incubation. By June, ryegrass root-derived C contributed 5.5% of the soil C pool, which was significantly greater than the contributions from any of the three other residue types (about 1.5%). This work has provided a framework for more studies of finer scale that should focus on the interactions between residue quality, soil organic matter C, and specific members of the soil microbial community.     

Free amino sugar reactions in soil in relation to soil carbon and nitrogen cycling

Amino sugars represent a major constituent of microbial cell walls and hydrolyzed soil organic matter. Despite their potential importance in soil nitrogen cycling, comparatively little is known about their dynamics in soil. The aim of this study was therefore to quantify the behaviour of glucosamine in two contrasting grassland soil profiles. Our results show that both free amino sugars and amino acids represented only a small proportion of dissolved organic N and C pool in soil. Based upon our findings we hypothesize that the low concentrations of free amino sugars found in soils is due to rapid removal from the soil solution rather than slow rates of production. Further, we showed that glucosamine removal from solution was a predominantly biotic process and that its half-life in soil solution ranged from 1 to 3 h. The rates of turnover were similar to those of glucose at low substrate concentrations, however, at higher glucosamine concentrations its microbial use was much less than for glucose. We hypothesized that this was due to the lack of expression of a low affinity transport systems in the microbial community. Glucosamine was only weakly sorbed to the soil's solid phase (K_d=6.4±1.0) and our results suggest that this did not limit its bioavailability in soil. Here we showed that glucosamine addition to soil resulted in rapid N mineralization and subsequent NO₃⁻ production. In contrast to some previous reports, our results suggest that free amino sugars turn over rapidly in soil and provide a suitable substrate for both microbial respiration and new biomass formation.     

Linking microbial community structure and allocation of plant-derived carbon in an organic agricultural soil using 13CO2 pulse-chase labelling combined with 13C-PLFA profiling

We conducted a ¹³CO₂ pulse-chase labelling experiment in a drained boreal organic (peat) soil cultivated with perennial crop, reed canary grass (RCG; Phalaris arundinacea) to study the flow of carbon from plants to soil microbes. Both limed and unlimed soils were studied, since liming is a common agricultural practice for acidic organic soils. Soil samples taken within three months after the labelling and three times in the following year were used for the δ¹³C analysis of microbial phospholipid fatty acids (PLFAs), root sugars and root lipids. We estimated the contribution of carbon from root exudates to microbial PLFA synthesis. The flow of carbon from plants to microbes was fast as the label allocation in PLFAs had a peak 1–3 days after labelling. The results showed that fungi were important in the incorporation of fresh, plant-derived carbon, including root sugars. None of the main microbial PLFA biomarker groups (fungi, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi) was completely lacking label over the measurement period. One year after the labelling, when the labelled carbon was widely distributed into plant biomass and soil, bacterial biomarkers increased their share of the label allocation. Liming had a minor effect on the label allocation rate into PLFAs. The mixing model approach used to calculate the root exudate contribution to microbial biomass resulted in a highly conservative estimate of utilization of this important C-source (0–6.5%, with highest incorporation into fungi). In summary, the results of this study provide new information about the role of various microbial groups in the turnover of plant-derived, fresh carbon in boreal organic soil.     

Roots from beech (Fagus sylvatica L.) and ash (Fraxinus excelsior L.) differentially affect soil microorganisms and carbon dynamics

Knowledge about the influence of living roots on decomposition processes in soil is scarce but is needed to understand carbon dynamics in soil. We investigated the effect of dominant deciduous tree species of the Central European forest vegetation, European beech (Fagus sylvatica L.) and European ash (Fraxinus excelsior L.), on soil biota and carbon dynamics differentiating between root- and leaf litter-mediated effects. The influence of beech and ash seedlings on carbon and nitrogen flow was investigated using leaf litter enriched in ¹³C and ¹⁵N in double split-root rhizotrons planted with beech and ash seedlings as well as a mixture of both tree species and a control without plants. Stable isotope and compound-specific fatty acid analysis (¹³C-PLFA) were used to follow the incorporation of stable isotopes into microorganisms, soil animals and plants. Further, the bacterial community composition was analyzed using pyrosequencing of 16S rRNA gene amplicons. Although beech root biomass was significantly lower than that of ash only beech significantly decreased soil carbon and nitrogen concentrations after 475 days of incubation. In addition, beech significantly decreased microbial carbon use efficiency as indicated by higher specific respiration. Low soil pH probably increased specific respiration of bacteria suggesting that rhizodeposits of beech roots induced increased microbial respiration and therefore carbon loss from soil. Compared to beech δ¹³C and δ¹⁵N signatures of gamasid mites in ash rhizotrons were significantly higher indicating higher amounts of litter-derived carbon and nitrogen to reach higher trophic levels. Similar δ¹³C signatures of bacteria and fine roots indicate that mainly bacteria incorporated root-derived carbon in beech rhizotrons. The results suggest that beech and ash differentially impact soil processes with beech more strongly affecting the belowground system via root exudates and associated changes in rhizosphere microorganisms and carbon dynamics than ash.     

THE ORIGIN OF THE PENTOSE FRACTION OF SOIL POLYSACCHARIDE

Incubation of soil with monosaccharide for 224 days resulted in the evolution of about 80 per cent of the substrate carbon as CO₂ and the transformation of 3 per cent to soil sugars whether the substrate was ¹⁴C-glucose or xylose and whether the soil was pH 7.4 or pH 5.0. There was no detectable change in the total amounts of individual sugars in the soil during incubation. ¹⁴C-glucose and xylose gave the same distribution of radioactivity among the soil sugars : hexoses and 6-deoxy-hexoses were initially well labelled, with glucose having twice the specific activity of the other sugars. As the incubation progressed some activity appeared in the pentoses (the activity in xylose became very low within the first 14 days of the ¹⁴C-xylose incubation) and that in the hexoses slowly declined, with glucose no longer predominant. Nevertheless after 448 days the hexoses were still 3–4 times more radioactive than the pentoses. The activity in rhamnose did not decline with time so that eventually it became the most strongly labelled sugar. Incubation of soil with glucose and ¹⁴C-acetate showed very little transformation of the acetate to sugars indicating that glucose is not metabolized to C₂ compounds before it is transformed to other sugars. Ammo-acids in soil incubated for 7 days with ¹⁴C-glucose had much lower levels of radioactivity than hexoses or 6-deoxy-hexoses. It is concluded that if soil pentose originates by microbial synthesis it must accumulate slowly by a long process of selective decomposition of a mixture of polysaccharides.     

C and N natural abundance of the soil microbial biomass

Stable isotope analysis is a powerful tool in the study of soil organic matter formation. It is often observed that more decomposed soil organic matter is ¹³C, and especially ¹⁵N-enriched relative to fresh litter and recent organic matter. We investigated whether this shift in isotope composition relates to the isotope composition of the microbial biomass, an important source for soil organic matter. We developed a new approach to determine the natural abundance C and N isotope composition of the microbial biomass across a broad range of soil types, vegetation, and climates. We found consistently that the soil microbial biomass was ¹⁵N-enriched relative to the total (3.2 ‰) and extractable N pools (3.7 ‰), and ¹³C-enriched relative to the extractable C pool (2.5 ‰). The microbial biomass was also ¹³C-enriched relative to total C for soils that exhibited a C3-plant signature (1.6 ‰), but ¹³C-depleted for soils with a C4 signature (−1.1 ‰). The latter was probably associated with an increase of annual C3 forbs in C4 grasslands after an extreme drought. These findings are in agreement with the proposed contribution of microbial products to the stabilized soil organic matter and may help explain the shift in isotope composition during soil organic matter formation.