Carbon allocation and carbon isotope fluxes in the plant-soil-atmosphere continuum: A review

The terrestrial carbon (C) cycle has received increasing interest over the past few decades, however, there is still a lack of understanding of the fate of newly assimilated C allocated within plants and to the soil, stored within ecosystems and lost to the atmosphere. Stable carbon isotope studies can give novel insights into these issues. In this review we provide an overview of an emerging picture of plant-soil-atmosphere C fluxes, as based on C isotope studies, and identify processes determining related C isotope signatures. The first part of the review focuses on isotopic fractionation processes within plants during and after photosynthesis. The second major part elaborates on plant-internal and plant-rhizosphere C allocation patterns at different time scales (diel, seasonal, interannual), including the speed of C transfer and time lags in the coupling of assimilation and respiration, as well as the magnitude and controls of plant-soil C allocation and respiratory fluxes. Plant responses to changing environmental conditions, the functional relationship between the physiological and phenological status of plants and C transfer, and interactions between C, water and nutrient dynamics are discussed. The role of the C counterflow from the rhizosphere to the aboveground parts of the plants, e.g. via CO2 dissolved in the xylem water or as xylem-transported sugars, is highlighted. The third part is centered around belowground C turnover, focusing especially on above- and belowground litter inputs, soil organic matter formation and turnover, production and loss of dissolved organic C, soil respiration and CO2 fixation by soil microbes. Furthermore, plant controls on microbial communities and activity via exudates and litter production as well as microbial community effects on C mineralization are reviewed. A further part of the paper is dedicated to physical interactions between soil CO2 and the soil matrix, such as CO2 diffusion and dissolution processes within the soil profile. Finally, we highlight state-of-the-art stable isotope methodologies and their latest developments. From the presented evidence we conclude that there exists a tight coupling of physical, chemical and biological processes involved in C cycling and C isotope fluxes in the plant-soil-atmosphere system. Generally, research using information from C isotopes allows an integrated view of the different processes involved. However, complex interactions among the range of processes complicate or currently impede the interpretation of isotopic signals in CO2 or organic compounds at the plant and ecosystem level. This review tries to identify present knowledge gaps in correctly interpreting carbon stable isotope signals in the plant-soil-atmosphere system and how future research approaches could contribute to closing these gaps

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007-2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted at the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. The result demonstrated that there was no consistent effect of either organic or conventional soil management across the three years on the diversity or quantity of either diazotrophic or total bacterial communities. However, ordination analyses carried out on data from each individual year showed that factors associated with the different fertility management measures including availability of nitrogen species, organic carbon and pH, did exert significant effects on the structure of both diazotrophic and total bacterial communities. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions. The diazotrophic community showed no significant change in diversity across the three years, however, the total bacterial community significantly increased in diversity year on year. Diversity was always greatest during March for both diazotrophic and total bacterial communities. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. Seasonal effects were less consistent in this quantitative study

Effect of plant litter addition on element leaching in young sandy soils.

The knowledge about element leaching and biogeochemical cycles during initial stages of soil development is very limited. Therefore, we studied the effects of parent material characteristics and plant litter addition on element leaching from young sandy soils in a microcosm experiment. Our objective was to evaluate the function of young soils as a source and/or sink for nutrients during initial pedogenesis and to identify main processes which are involved in the initial development of biogeochemical cycles. The main research questions were: (1) How do differences in parent material characteristics affect nutrient leaching?; and (2) How is nutrient leaching of young soils influenced by litter addition of different plant functional groups (e. g., legume and grass species)? Combined treatments of two minimally weathered parent materials (pure sand and loamy sand) with plant litter of two plant species (Lotus corniculatus L. and Calamagrostis epigejos L.) were investigated in a soil column experiment. In addition, control columns with parent material or plant litter only were included. Carbonate weathering as a main source for calcium leaching was induced by the moderately acidic irrigation solution used in the experiment. It was 7.5 fold greater for the loamy sand parent material compared to the pure sand despite lower carbonate contents in the loamy sand. Leaching of K was very low for both parent materials but greater for the loamy sand parent material, likely due to transfer processes from fixed to exchangeable potassium forms in the clay minerals of the loamy sand. Plant litter addition generally increased leaching losses. Carbonate dissolution was intensified by both plant litter types, especially by L. corniculatus, very likely due to H+ released during nitrification of N released from plant litter and an increase in partial pressure of CO2 from microbial respiration. In contrast, K was largely retained in the soils, probably due to fixation by clay minerals and microbial immobilization. Only the pure sand treated with L. corniculatus litter leached K, resulting in 4-6 fold greater leaching losses compared to all other treatments. Nitrogen released from L. corniculatus litter was almost completely nitrified and was nearly doubled as compared to that from C. epigejos, resulting in greater N leaching. The results of our study allow identifying the general function and processes of vegetation patches in young ecosystems formed as a result of initial parent material characteristics and invading vegetation with respect to litter decomposition, soil solution composition, nutrient retention and leaching, and effects on the soil mineral phase. These patterns are not mere additive effects of parent materials plus plant litter, but reflect differences in biogeochemical process intensities and could result in an increasing heterogeneity of soil properties, nutrient availability, and element leaching fluxes with time

ETBE (ethyl tert butyl ether) and TAME (tert amyl methyl ether) affect microbial community structure and function in soils.

Ethyl tert butyl ether (ETBE) and tert amyl methyl ether (TAME) are oxygenates used in gasoline in order to reduce emissions from vehicles. The present study investigated their impact on a soil microflora that never was exposed to any contamination before. Therefore, soil was artificially contaminated and incubated over 6 weeks. Substrate induced respiration (SIR) measurements and phospholipid fatty acid (PLFA) analysis indicated shifts in both, microbial function and structure during incubation. The results showed an activation of microbial respiration in the presence of ETBE and TAME, suggesting biodegradation by the microflora. Furthermore, PLFA concentrations decreased in the presence of ETBE and TAME and Gram-positive bacteria became more dominant in the microbial community

<em>Acidovorax radicis</em> sp. nov., a wheat-root-colonizing bacterium.

Strain N35(T) was isolated from surface-sterilized wheat roots and is a Gram-negative, aerobic, motile straight rod. Strain N35(T) tested oxidase-positive and catalase-negative and grew optimally at pH 7.0, 30 &deg;C and in the absence of NaCl. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species Acidovorax delafieldii, A. facilis, A. defluvii, A. temperans, A. caeni and A. soli, as well as Acidovorax valerianellae, A. anthurii and Simplicispira metamorpha. DNA-DNA hybridization between strain N35(T) and phylogenetically closely related type strains was 25.3-55.7 %, which clearly separates the strain from these closely related species. Additionally, phenotypic properties, such as substrate metabolism profiles as determined by a Biolog GN2 assay and cell-wall fatty acid profiles, particularly contents of the fatty acids C(16 : 0), C(16 : 1)&omega;7c/t, C(17 : 0), C(17 : 0) cyclo, C(18 : 0) cyclo and C(19 : 0) cyclo, facilitated the differentiation of the newly isolated strain N35(T) from its closest relatives. The isolate underwent phenotypic variation at high frequency in laboratory media. The DNA G+C content was 64.9 mol%. We propose that strain N35(T) is classified as a representative of a novel species within the genus Acidovorax, and suggest the name Acidovorax radicis sp. nov. The type strain is strain N35(T) ( = DSM 23535(T)  = LMG 25767(T))

Mineralisation and leaching of C from ¹³C labelled plant litter along an initial soil chronosequence of a glacier forefield.

Soils are accumulating C during their initial development but little is known on the evolution of soil C fluxes and their components. In this study, we investigated soil CO2 effluxes and leaching of dissolved organic carbon (DOC) during initial stages of soil formation along the granitic Damma glacier forefield in the Swiss Alps. We added isotopic labelled litter (Leucanthemopsis alpina, &delta;13C&nbsp;=&nbsp;+88&permil;) to soil columns in three successional stages (10&nbsp;yr, 70&nbsp;yr, 120&nbsp;yr) and traced the &lsquo;new&rsquo; litter-derived C in soil CO2 effluxes, DOC leaching, and in phospholipid fatty acids (PLFA), biomarkers for soil microbial communities. The results showed increasing total soil C fluxes with progressing soil development due to increasing C stocks in plants and soils. Throughout three summer months, 15&ndash;63% of the added litter C were lost via mineralisation and leaching. Along the initial soil chronosequence, litter-derived CO2 C effluxes did not change systematically with soil age. The distribution of &delta;13C signatures in PLFAs was very similar at all site ages, suggesting that decomposer communities did almost not change with succession. Instead, moisture conditions of surface soils varying at the local scale seemed to primarily control litter mineralisation with the driest topsoils and lowest mineralisation at the oldest site. Only a small fraction of the added litter, less than 1% was leached as DOC at 10&nbsp;cm depth. This indicates a strong removal of litter-derived DOC with passage through the mineral soils. The highest litter-derived DOC leaching occurred in the initial soils with the smallest contents of secondary Fe and Al oxides as potential sorbents for DOC. Litter addition had a negligible priming effect on soil respiration and DOC leaching in all three successional stages

Microbial response to exudates in the rhizosphere of young beech trees (Fagus sylvatica L.) after dormancy.

Plants act as an important link between atmosphere and soil: CO2 is transformed into carbohydrates by photosynthesis. These assimilates are distributed within the plant and translocated via roots into the rhizosphere and soil microorganisms. In this study, 3 year old European beech trees (Fagus sylvatica L.) were exposed after the chilling period to an enriched 13C-CO2 atmosphere (&delta;13C&nbsp;=&nbsp;660 parts per thousand - 80 parts per thousand) at the time point when leaves development started. Temporal dynamics of assimilated carbon distribution in different plant parts, as well as into dissolved organic carbon and microbial communities in the rhizosphere and bulk soil have been investigated for a 20 days period. Photosynthetically fixed carbon could be traced into plant tissue, dissolved organic carbon and total microbial biomass, where it was utilized by different microbial communities. Due to carbon allocation into the rhizosphere, nutrient stress decreased; exudates were preferentially used by Gram-negative bacteria and (mycorrhizal) fungi, resulting in an enhanced growth. Other microorganisms, like Gram-positive bacteria and mainly micro eucaryotes benefited from the exudates via food web development. Overall our results indicate a fast turnover of exudates and the development of initial food web structures. Additionally a transport of assimilated carbon into bulk soil by (mycrorhizal) fungi was observed

Incorporation of carbon from decomposing litter of two pioneer plant species into microbial communities of the detritusphere.

Initial ecosystems are characterized by a low availability of nutrients and a low soil organic matter content. Interactions of plants and microorganisms in such environments, particularly in relation to litter decomposition, are very important for further ecosystem development. In a litter decomposition study using an initial substrate from a former mining area, we applied the litter of two contrasting pioneer plant species (legume vs. pasture plants), Lotus corniculatus and Calamagrostis epigejos, which are commonly observed in the study area. Litter decomposition was investigated and carbon (C) translocation from litter into soil microorganisms was described by following (13) C from labelled plant litter materials into the fraction of phospholipid fatty acids. Labile C compounds of both plant litter types were easily degraded during the first 4 weeks of litter decomposition. In contrast to climax ecosystems, where the importance of fungi for litter degradation has been shown in many studies, in our experiment, data clearly indicate an outcompetition of fungi by Gram-positive bacteria as soon as available nitrogen is limited in the detritusphere

Structure and activities of ectomycorrhizal and microbial communities in the rhizosphere of Fagus sylvatica under ozone and pathogen stress in a lysimeter study.

The aim was to study the influence of abiotic (elevated ozone) or biotic stress (Phytophthora citricola) or their combination on soil biological components and processes in the rhizosphere of young beech trees. Ectomycorrhizal and overall microbial community composition was studied at two soil depths in a lysimeter experiment with 7 year old trees of Fagus sylvatica. As a functional parameter, potential enzyme activities were measured in mycorrhizosphere soil and on excised mycorrhizal tips. The degree of mycorrhization, structure and potential enzymatic activities of mycorrhizal communities were only slightly influenced by treatments. Soil enzyme activities were depressed under elevated ozone and stimulated by P. citricola under ambient but not under elevated ozone. Overall microbial community composition (PLFA) and ectomycorrhizal diversity changed with depth. PLFA analyses not only suggested a reaction of the microbial community to elevated ozone but also indicated an increase in plant stress related components. No influence of the biotic stress on ectomycorrhizal or overall microbial community structure was detected. Changes in the mycorrhizosphere community structure and function due to ozone may be explained by the quality of plant derived carbon