Pool Turnover Research Articles

Chemically Induced Conditional Rescue of the Reduced Epidermal Fluorescence8 Mutant of Arabidopsis Reveals Rapid Restoration of Growth and Selective Turnover of Secondary Metabolite Pools

The phenylpropanoid pathway is responsible for the biosynthesis of diverse and important secondary metabolites including lignin and flavonoids. The reduced epidermal fluorescence8 (ref8) mutant of Arabidopsis (Arabidopsis thaliana), which is defective in a lignin biosynthetic enzyme p-coumaroyl shikimate 3'-hydroxylase (C3'H), exhibits severe dwarfism and sterility. To better understand the impact of perturbation of phenylpropanoid metabolism on plant growth, we generated a chemically inducible C3'H expression construct and transformed it into the ref8 mutant. Application of dexamethasone to these plants greatly alleviates the dwarfism and sterility and substantially reverses the biochemical phenotypes of ref8 plants, including the reduction of lignin content and hyperaccumulation of flavonoids and p-coumarate esters. Induction of C3'H expression at different developmental stages has distinct impacts on plant growth. Although early induction effectively restored the elongation of primary inflorescence stem, application to 7-week-old plants enabled them to produce new rosette inflorescence stems. Examination of hypocotyls of these plants revealed normal vasculature in the newly formed secondary xylem, presumably restoring water transport in the mutant. The ref8 mutant accumulates higher levels of salicylic acid than the wild type, but depletion of this compound in ref8 did not relieve the mutant's growth defects, suggesting that the hyperaccumulation of salicylic acid is unlikely to be responsible for dwarfism in this mutant.

Influence of redox conditions and rice straw incorporation on nitrogen availability in fertilized paddy soils

Temporal nitrogen (N) availability in fertilized rice paddies is the result of a balance of processes, mainly the gross rates of N mineralization, microbial and abiotic immobilization, and N losses. Water and crop residue management practices often confound these established relationships making N the most difficult nutrient to manage in rice cropping systems. To investigate and quantify the interactive effects of soil redox conditions and straw incorporation on temporal fertilizer-N availability, we treated a paddy soil with enriched ammonium-15N and incubated for 160 days under flooded or non-flooded conditions, with or without the addition of rice straw. Changes in total available N as well as available and immobilized fertilizer-derived N (FDN) during incubation were evaluated. Under both oxic and waterlogged soils, about 45–53 % of applied N was rapidly immobilized. Whereas in the former most of this FDN was released contributing to the available N pool, flooded soils experienced significant losses from the soil/water system (≈ 67 % of applied N). Addition of rice straw enhanced N immobilization, particularly under flooded conditions, that also contributed to limiting losses. Moreover, turnover of this labile organic matter pool supplied significant amounts of available N towards the later stages of the incubation, partly compensating for the immobilization of fertilizer-N.

Molecular transformation and degradation of refractory dissolved organic matter in the Atlantic and Southern Ocean

More than 90% of the global ocean dissolved organic carbon (DOC) is refractory, has an average age of 4000–6000years and a lifespan from months to millennia. The fraction of dissolved organic matter (DOM) that is resistant to degradation is a long-term buffer in the global carbon cycle but its chemical composition, structure, and biochemical formation and degradation mechanisms are still unresolved. We have compiled the most comprehensive molecular dataset of 197 Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analyses from solid-phase extracted marine DOM covering two major oceans, the Atlantic sector of the Southern Ocean and the East Atlantic Ocean (ranging from 50°N to 70°S). Molecular trends and radiocarbon dating of 34 DOM samples (comprising Δ14C values from −229‰ to −495‰) were combined to model an integrated degradation rate for bulk DOC resulting in a predicted age of >24ka for the most persistent DOM fraction. First order kinetic degradation rates for 1557 mass peaks indicate that numerous DOM molecules cycle on timescales much longer than the turnover of the bulk DOC pool (estimated residence times of up to ~100ka) and the range of validity of radiocarbon dating. Changes in elemental composition were determined by assigning molecular formulae to the detected mass peaks. The combination of residence times with molecular information enabled modelling of the average elemental composition of the slowest degrading fraction of the DOM pool. In our dataset, a group of 361 molecular formulae represented the most stable composition in the oceanic environment (“island of stability”). These most persistent compounds encompass only a narrow range of the molecular elemental ratios H/C (average of 1.17±0.13), and O/C (average of 0.52±0.10) and molecular masses (360±28 and 497±51Da). In the Weddell Sea DOC concentrations in the surface waters were low (46.3±3.3μM) while the organic radiocarbon was significantly more depleted than that of the East Atlantic, representing average surface water DOM ages of 4920±180a. These results are in accordance with a highly degraded DOM in the Weddell Sea surface water as also shown by the molecular degradation index IDEG obtained from FT-ICR MS data. Further, we identified 339 molecular formulae which probably contribute to an increased DOC concentration in the Southern Ocean and potentially reflect an accumulation or enhanced sequestration of refractory DOC in the Weddell Sea. These results will contribute to a better understanding of the persistent nature of marine DOM and its role as an oceanic carbon buffer in a changing climate.

Microbial mechanisms coupling carbon and phosphorus cycles in phosphorus-limited northern Adriatic Sea

The coastal northern Adriatic Sea receives pulsed inputs of riverine nutrients, causing phytoplankton blooms and seasonally sustained dissolved organic carbon (DOC) accumulation—hypothesized to cause episodes of massive mucilage. The underlying mechanisms regulating P and C cycles and their coupling are unclear. Extensive biogeochemical parameters, processes and community composition were measured in a 64-day mesocosms deployed off Piran, Slovenia. We followed the temporal trends of C and P fluxes in P-enriched (P+) and unenriched (P−) mesocosms. An intense diatom bloom developed then crashed; however, substantial primary production was maintained throughout, supported by tightly coupled P regeneration by bacteria and phytoplankton. Results provide novel insights on post-bloom C and P dynamics and mechanisms. 1) Post-bloom DOC accumulation to 186μM remained elevated despite high bacterial carbon demand. Presumably, a large part of DOC accumulated due to the bacterial ectohydrolytic processing of primary productivity that adventitiously generated slow-to-degrade DOC; 2) bacteria heavily colonized post-bloom diatom aggregates, rendering them microscale hotspots of P regeneration due to locally intense bacterial ectohydrolase activities; 3) Pi turnover was rapid thus suggesting high P flux through the DOP pool (dissolved organic phosphorus) turnover; 4) Alpha- and Gamma-proteobacteria dominated the bacterial communities despite great differences of C and P pools and fluxes in both mesocosms. However, minor taxa showed dramatic changes in community compositions. Major OTUs were presumably generalists adapted to diverse productivity regimes.We suggest that variation in bacterial ectohydrolase activities on aggregates, regulating the rates of POM→DOM transition as well as dissolved polymer hydrolysis, could become a bottleneck in P regeneration. This could be another regulatory step, in addition to APase, in the microbial regulation of P cycle and the coupling between C and P cycles.

Effect of poly(γ-glutamic acid) on microbial community and nitrogen pools of soil

Given the numerous environmental problems caused by chemical fertilizer overuse, agricultural practices are shifting toward the development of environmentally friendly nitrogen (N) fertilizers. In this study, a pot experiment was conducted to investigate the effect of poly(γ-glutamic acid) (γ-PGA), an effective fertilizer synergist, on rapeseed (Brassica napus cv. Qinyou No. 9) productivity, soil N pools, and soil enzymes. Seven treatments were implemented: T1, a check without urea; T2, a check with urea only; T3, urea mixed with glutamic acid; T4, urea mixed with 3 mg of γ-PGA per kilogram of soil; T5, urea mixed with 10 mg of γ-PGA per kilogram of soil; T6, urea coated with γ-PGA (0.9%, m/m); and T7, urea coated with γ-PGA (3.1%, m/m). The results demonstrated that the application of γ-PGA increased the above-ground fresh weight of rapeseed by 7.57–9.26% and the grain yield per pot by 6.46–10.98% compared with T2. The rapeseed grain yield significantly increased from 15.94 ± 0.55 g pot−1 in T2 to 17.69 ± 0.78 g pot−1 in T7. With the increase in pod numbers and seed numbers per pod, the seed yield was significantly improved after γ-PGA application. Culturable soil microbial count and microbial diversity were increased by γ-PGA application. In addition, the effects of application method of γ-PGA have a more important role on the soil microflora than its amount. The reduced loss of N can be attributed to the capacity of γ-PGA to increase the “ turnover pool.” More mineral N in the soil was immobilized by clays, soil microbes, and γ-PGA at the early growth stage, and the immobilized N was then released at the later growth stage for plant growth. Moreover, urease activity also increased with γ-PGA application. These findings indicated that the urea coated with γ-PGA could be a better choice for agricultural applications.

Periplasmic flagellar export apparatus protein, FliH, is involved in post-transcriptional regulation of FlaB, motility and virulence of the relapsing fever spirochete Borrelia hermsii.

Spirochetes are bacteria characterized in part by rotating periplasmic flagella that impart their helical or flat-wave morphology and motility. While most other bacteria rely on a transcriptional cascade to regulate the expression of motility genes, spirochetes employ post-transcriptional mechanism(s) that are only partially known. In the present study, we characterize a spontaneous non-motile mutant of the relapsing fever spirochete Borrelia hermsii that was straight, non-motile and deficient in periplasmic flagella. We used next generation DNA sequencing of the mutant’s genome, which when compared to the wild-type genome identified a 142 bp deletion in the chromosomal gene encoding the flagellar export apparatus protein FliH. Immunoblot and transcription analyses showed that the mutant phenotype was linked to the posttranscriptional deficiency in the synthesis of the major periplasmic flagellar filament core protein FlaB. Despite the lack of FlaB, the amount of FlaA produced by the fliH mutant was similar to the wild-type level. The turnover of the residual pool of FlaB produced by the fliH mutant was comparable to the wild-type spirochete. The non-motile mutant was not infectious in mice and its inoculation did not induce an antibody response. Trans-complementation of the mutant with an intact fliH gene restored the synthesis of FlaB, a normal morphology, motility and infectivity in mice. Therefore, we propose that the flagellar export apparatus protein regulates motility of B. hermsii at the post-transcriptional level by influencing the synthesis of FlaB.

Nitrogen Stress Affects the Turnover and Size of Nitrogen Pools Supplying Leaf Growth in a Grass

The effect of nitrogen (N) stress on the pool system supplying currently assimilated and (re)mobilized N for leaf growth of a grass was explored by dynamic ¹⁵N labeling, assessment of total and labeled N import into leaf growth zones, and compartmental analysis of the label import data. Perennial ryegrass (Lolium perenne) plants, grown with low or high levels of N fertilization, were labeled with ¹⁵NO₃⁻/¹⁴NO₃⁻ from 2 h to more than 20 d. In both treatments, the tracer time course in N imported into the growth zones fitted a two-pool model (r² > 0.99). This consisted of a "substrate pool," which received N from current uptake and supplied the growth zone, and a recycling/mobilizing "store," which exchanged with the substrate pool. N deficiency halved the leaf elongation rate, decreased N import into the growth zone, lengthened the delay between tracer uptake and its arrival in the growth zone (2.2 h versus 0.9 h), slowed the turnover of the substrate pool (half-life of 3.2 h versus 0.6 h), and increased its size (12.4 μg versus 5.9 μg). The store contained the equivalent of approximately 10 times (low N) and approximately five times (high N) the total daily N import into the growth zone. Its turnover agreed with that of protein turnover. Remarkably, the relative contribution of mobilization to leaf growth was large and similar (approximately 45%) in both treatments. We conclude that turnover and size of the substrate pool are related to the sink strength of the growth zone, whereas the contribution of the store is influenced by partitioning between sinks.

Protein Sorting Motifs in the Cytoplasmic Tail of SorCS1 Control Generation of Alzheimer's Amyloid-β Peptide

Endosomal sorting of the Alzheimer amyloid precursor protein (APP) plays a key role in the biogenesis of the amyloid-β (Aβ) peptide. Genetic lesions underlying Alzheimer's disease (AD) can act by interfering with this physiological process. Specifically, proteins involved in trafficking between endosomal compartments and the trans-Golgi network (TGN) [including the retromer complex (Vps35, Vps26) and its putative receptors (sortilin, SorL1, SorCS1)] have been implicated in the molecular pathology of late-onset AD. Previously, we demonstrated a role for SorCS1 in APP metabolism and Aβ production and, while we implicated a role for the retromer in this regulation, the underlying mechanism remained poorly understood. Here, we provide evidence for a motif within the SorCS1c cytoplasmic tail that, when manipulated, results in perturbed sorting of APP and/or its fragments to endosomal compartments, decreased retrograde TGN trafficking, and increased Aβ production in H4 neuroglioma cells. These perturbations apparently do not involve turnover of the cell surface APP pool, but rather they involve intracellular APP and/or its fragments, downstream of APP endocytosis.

Hypothesis: Local dNTP depletion as the cause of microsatellite repeat instability during replication (Comment on DOI 10.1002/bies.201200128)

Nucleotide depletion in vivo is correlated with global genomic instability and tumorigenesis 1-3. In contrast, localized instability of low complexity microsatellite sequences causes multiple neurodegenerative diseases (e.g. Huntington's disease, myotonic dystrophy, spinocerebellar ataxias), depending on the host gene. CNG microsatellites are particularly prone to the formation of imperfectly base paired hairpin structures in vitro 4 and in vivo 5, and are sites of genome instability exacerbated by replication fork slowing. Current models of microsatellite instability invoke the formation of hairpin structures during replication, repair or transcription. In replication or repair models, the microsatellite sequence or structure directly inhibits DNA polymerase movement. Contractions arise via two mechanisms: (i) slowing of the polymerase and consequent increase in hairpin formation in extended leading or lagging strand template ssDNA at the replication fork; (ii) threading of the leading strand template through the MCM helicase without concurrent polymerization. Expansions are provoked by nascent strand hairpins, because the repeat sequence directly causes polymerase ‘stuttering’ and primer slippage. In contrast, the new model presented in the current issue of BioEssays proposes that polymerase slowing and nascent strand hairpins are not direct effects of the repeat on the polymerase; rather they are indirect consequences of local nucleotide depletion, which results from a local stoichiometric imbalance in nucleotide incorporation into the nascent DNA (repeat sequences manifest such imbalanced stoichiometries) 6. The hypothesis predicts that nucleotide diffusion through the cell should be slower than the rate of precursor consumption at an individual replication fork. Although nucleotide diffusion rates have not been determined experimentally, based on the turnover of nucleotide pools in vivo, it is argued that the rate of nucleotide incorporation may be equal to or greater than the rate of diffusion. Additionally, replication is thought to occur in congregated replication forks, or factories: this raises the concern that if several forks simultaneously draw nucleotides from a common pool, imbalanced incorporation by a single fork would not have significant impact. However, the author presents evidence from ultra-high resolution microscopy that individual replication factories may contain only two forks, hence isolating the effects of nucleotide depletion. Trinucleotide repeat expansion or contraction in bacteria or yeast have shown significantly greater instability for CNG repeats than GNC repeats, possibly due to differences in the structure, stability or downstream metabolism of the respective hairpins. Dr. Kuzminov suggests in vitro tests of the nucleotide depletion model by analysis of replication in the response to differing nucleotide doses. Since nucleotide depletion by replication of CTG or GTC repeats should be similar, an alternative in vivo test of whether nucleotide depletion is the immediate cause of fork slowing would be to compare the distribution of replication intermediates by 2D gel electrophoresis during replication of plasmids containing CTG and GTC isomeric repeat sequences. Verification of the hypothesis that local nucleotide depletion potentiates microsatellite instability could lead to novel approaches to prognosis, prevention or therapy of neurodegenerative disorders.

Plant soil interactions alter carbon cycling in an upland grassland soil

Soil carbon (C) storage is dependent upon the complex dynamics of fresh and native organic matter cycling, which are regulated by plant and soil-microbial activities. A fundamental challenge exists to link microbial biodiversity with plant-soil C cycling processes to elucidate the underlying mechanisms regulating soil carbon. To address this, we contrasted vegetated grassland soils with bare soils, which had been plant-free for 3 years, using stable isotope (13C) labeled substrate assays and molecular analyses of bacterial communities. Vegetated soils had higher C and N contents, biomass, and substrate-specific respiration rates. Conversely, following substrate addition unlabeled, native soil C cycling was accelerated in bare soil and retarded in vegetated soil; indicative of differential priming effects. Functional differences were reflected in bacterial biodiversity with Alphaproteobacteria and Acidobacteria dominating vegetated and bare soils, respectively. Significant isotopic enrichment of soil RNA was found after substrate addition and rates varied according to substrate type. However, assimilation was independent of plant presence which, in contrast to large differences in 13CO2 respiration rates, indicated greater substrate C use efficiency in bare, Acidobacteria-dominated soils. Stable isotope probing (SIP) revealed most community members had utilized substrates with little evidence for competitive outgrowth of sub-populations. Our findings support theories on how plant-mediated soil resource availability affects the turnover of different pools of soil carbon, and we further identify a potential role of soil microbial biodiversity. Specifically we conclude that emerging theories on the life histories of dominant soil taxa can be invoked to explain changes in soil carbon cycling linked to resource availability, and that there is a strong case for considering microbial biodiversity in future studies investigating the turnover of different pools of soil carbon.

Substrate cycles in Penicillium chrysogenum quantified by isotopic non-stationary flux analysis

BackgroundPenicillium chrysogenum, the main production strain for penicillin-G, has a high content of intracellular carbohydrates, especially reduced sugars such as mannitol, arabitol, erythritol, as well as trehalose and glycogen. In previous steady state 13C wash-in experiments a delay of labeling enrichments in glycolytic intermediates was observed, which suggests turnover of storage carbohydrates. The turnover of storage pools consumes ATP which is expected to reduce the product yield for energy demanding production pathways like penicillin-G.ResultsIn this study, a 13C labeling wash-in experiment of 1 hour was performed to systematically quantify the intracellular flux distribution including eight substrate cycles. The experiments were performed using a mixed carbon source of 85% CmolGlc/CmolGlc+EtOH labeled glucose (mixture of 90% [1-13C1] and 10% [U-13C6]) and 15% ethanol [U-13C2]. It was found, that (1) also several extracellular pools are enriched with 13C labeling rapidly (trehalose, mannitol, and others), (2) the intra- to extracellular metabolite concentration ratios were comparable for a large set of metabolites while for some carbohydrates (mannitol, trehalose, and glucose) the measured ratios were much higher.ConclusionsThe fast enrichment of several extracellular carbohydrates and a concentration ratio higher than the ratio expected from cell lysis (2%) indicate active (e.g. ATP consuming) transport cycles over the cellular membrane. The flux estimation indicates, that substrate cycles account for about 52% of the gap in the ATP balance based on metabolic flux analysis.

Erosion-induced CO2 flux of small watersheds

Soil erosion not only results in severe ecological damage, but also interferes with soil organic carbon formation and decomposition, influencing the global green-house effect. However, there is controversy as to whether a typical small watershed presumed as the basic unit of sediment yield acts as a CO2 sink or source. This paper proposes a discriminant equation for the direction of CO2 flux in small watersheds, basing on the concept of Sediment Delivery Ratio (SDR). Using this equation, watersheds can be classified as Sink Watersheds, Source Watersheds, or Transition Watersheds, noting that small watersheds can act either as a CO2 sink or as a CO2 source. A mathematical model for calculating the two discriminant coefficients in the equation is set up to analyze the conditions under which each type of watershed would occur. After assigning the model parameter values at three levels (low, medium, and high), and considering 486 scenarios in total, the influences are examined for turnover rate of the carbon pool, erosion rate, deposition rate, cultivation depth and period. The effect of adopting conservation measures like residue return, contour farming, terracing, and conservation tillage is also analyzed. The results show that Sink Watersheds are more likely to result in conditions of high erosion rate, long cultivation period, high deposition rate, fast carbon pool turnover rate, and small depth of cultivation; otherwise, Source Watersheds would possibly occur. The results also indicate that residue return and conservation tillage are beneficial for CO2 sequestration.

Integrating empirical–modeling approaches to improve understanding of terrestrial ecology processes

Recent decades have seen tremendous increases in the quantity of empirical ecological data collected by individual investigators, as well as through research networks such as FLUXNET (Baldocchi et al., 2001). At the same time, advances in computer technology have facilitated the development and implementation of large and complex land surface and ecological process models. Separately, each of these information streams provides useful, but imperfect information about ecosystems. To develop the best scientific understanding of ecological processes, and most accurately predict how ecosystems may cope with global change, integration of empirical and modeling approaches is necessary. However, true integration - in which models inform empirical research, which in turn informs models (Fig. 1) - is not yet common in ecological research (Luo et al., 2011). The goal of this workshop, sponsored by the Department of Energy, Office of Science, Biological and Environmental Research (BER) program, was to bring together members of the empirical and modeling communities to exchange ideas and discuss scientific practices for increasing empirical - model integration, and to explore infrastructure and/or virtual network needs for institutionalizing empirical - model integration (Yiqi Luo, University of Oklahoma, Norman, OK, USA). The workshop included presentations and small group discussions that coveredmore » topics ranging from model-assisted experimental design to data driven modeling (e.g. benchmarking and data assimilation) to infrastructure needs for empirical - model integration. Ultimately, three central questions emerged. How can models be used to inform experiments and observations? How can experimental and observational results be used to inform models? What are effective strategies to promote empirical - model integration?« less

Carbon cycling in eroding landscapes: geomorphic controls on soil organic C pool composition and C stabilization

AbstractRecent studies have highlighted the tight coupling between geomorphic processes and soil carbon (C) turnover and suggested that eroding landscapes can stabilize more C than their non‐eroding counterparts. However, large uncertainties remain and a mechanistic understanding of geomorphic effects on C storage in soils is still lacking. Here, we quantified the soil organic carbon (SOC) stock and pool distribution along geomorphic gradients and combined data derived from soil organic matter fractionation and incubation experiments. The size and composition of the SOC pools were strongly related to geomorphic position: 1.6 to 6.2 times more C was stabilized in the subsoils (25–100cm) of depositional profiles than in those of eroding profiles. Subsoil C of depositional profiles is predominantly associated with microaggregates and silt‐sized particles which are associated with pools of intermediate stability. We observed a significantly higher mean residence time for the fast and intermediate turnover pools of buried C at depositional positions, relative to non‐eroding and eroding positions, resulting from the physical protection of C associated with microaggregates and silt particles. Conversely, significant amounts of C were replaced at eroding positions but the lower degree of decomposition and the lack of physically protected C, resulted in higher respiration rates. By considering C cycling at non‐eroding, eroding and depositional positions, we found that the eroding landscapes studied store up to 10% more C due to soil redistribution processes than non‐eroding landscapes. This is the result of the stabilization of C in former subsoil at eroding positions and partial preservation of buried C in pools of intermediate turnover at depositional positions. However, the sink strength was limited by significant losses of buried C as only a small fraction of the C was associated with stable pools.

Discrete functional pools of soil organic matter in a UK grassland soil are differentially affected by temperature and priming

We show that both temperature and priming act differently on distinct C pools in a temperate grassland soil. We used SOM which was 14C-labelled in four different ways: by labelling soil with 14C-glucose, by adding leaf litter from plants pre-labelled with 14CO2, and by labelling in situ with 14CO2 applied to the ryegrass canopy either 6 or 18 months earlier. Samples of each type of 14C labelled soil were incubated at either 4, 10, 15, or 20°C and the exponential loss of 14CO2 used to characterise treatment effects. 14C allocation to microbial fractions was greater, and so overall mineralization by microbes was greater, as temperature rose, but turnover of the microbial labile pool was temperature-insensitive, and the turnover of microbial structural material was reduced as temperature rose. The ability of the microbial population to degrade just one fraction of plant litter was increased greatly by temperature. A pool of SOM with a half-life of about 70d was degraded faster at higher temperatures. Less tractable but abundant pools of SOM were not accessed more readily at higher temperatures by the microbial population. Priming with glucose or amino-acids only speeded the mineralization of recent SOM (probably from the living microbial biomass), and was not altered by temperature. These results have implications for the impacts of climate change on soil C cycling.

Soil and residue carbon mineralization as affected by soil aggregate size

The nature of the contact between fresh organic matter and soil depends mainly on the characteristics of the plant residues and on the physical properties of the soil. In a cultivated cropping system, changes in soil organic C cannot be entirely attributed to changes in organic matter input. Breakdown of aggregates caused by cultivation not only affects soil organic matter but also influences the rate of mineralization of added organic matter. Many models simulating organic matter decomposition in the field are calibrated with laboratory data from experiments where crop residues are ground and mixed homogeneously with soil aggregates. In the present study, soil aggregate size was used as a means of varying the contact between crop residue and the soil. The results demonstrated that cumulative soil carbon mineralization from different aggregates had a significant (r=0.60, p=0.05) and positive relationship with their oxidizable soil carbon content. Residue carbon mineralization in different aggregate size classes was inversely related to aggregate oxidizable soil carbon content (r=−0.95, p=0.01), cumulative soil carbon mineralization (r=−0.89, p=0.01) and resistant soil carbon pool (r=−0.80, p=0.01). Residue carbon mineralization in different aggregate size classes was also inversely (r=−0.61, p=0.05) related to the active carbon content (KMnO4 oxidizable carbon) of the aggregates. There was no significant difference in soil active carbon pool in different aggregate size classes. Determination of size and turnover of a slow pool showed significant difference in different aggregate size classes. The slow carbon pool in different aggregate size classes ranged from 13.7 to 25.5% with mean residence time of 1.8 to 5.4 years. Water soluble carbon and active carbon (alkaline KMnO4 oxidizable C) were significantly higher in macro-aggregates than in micro-aggregates.

Multi-objective optimisation of a model of the decomposition of animal slurry in soil: Tradeoffs between simulated C and N dynamics

To formulate best management practices for animal slurry, it is important to understand and predict its decomposition in the soil. Slurry decomposition dynamics can be studied by measuring CO2 fluxes and soil mineral nitrogen concentration during laboratory incubations and subsequently calibrating a simulation model. Carbon and nitrogen dynamics are linked and both should be properly simulated. In this work we wanted to identify the tradeoffs between errors in the simulation of C respiration and of soil inorganic N concentration.We optimised six parameters of CN-SIM (a mechanistic dynamic simulation model), using data of respired C and soil inorganic N measured during a 180-day laboratory incubation of five dairy slurries on three soils. Optimisation was carried out with a multi-objective genetic algorithm (NSGA-II), by minimising the Relative Root Mean Squared Error (RRMSE) between observations and simulations.The simulation of C respiration was frequently conflicting with the simulation of inorganic N, i.e. low RRMSE–CO2 corresponded with high RRMSE–N and vice versa. When minimising RRMSE–CO2 a set of parameters was obtained that enhanced microbial N immobilisation and reduced the turnover of the organic pools, to match the observed decrease of inorganic N in the 28 days after slurry addition to soil. Remineralisation occurring in the following 150 days caused a marked overestimation of inorganic N. When minimising RRMSE–N, the optimisation provided parameters that strongly reduced remineralisation of immobilised N by markedly diminishing C respiration, with a consequent underestimation of CO2 emission. A modified version of the model, containing a simple implementation of denitrification and of clay fixation/release of ammonium, performed better than the original model for most treatments.We conclude that the mineralisation/immobilisation turnover in the model is not fully adequate to represent C and N dynamics. We also discuss the implementation of changes (time-varying microbial efficiency and C to N ratio; simulation of ammonium clay fixation and emissions of N2/N2O) to improve model performance.

Microbial Group Specific Uptake Kinetics of Inorganic Phosphate and Adenosine-5′-Triphosphate (ATP) in the North Pacific Subtropical Gyre

We investigated the concentration dependent uptake of inorganic phosphate (Pi) and adenosine-5′-triphosphate (ATP) in microbial populations in the North Pacific Subtropical Gyre (NPSG). We used radiotracers to measure substrate uptake into whole water communities, differentiated microbial size classes, and two flow sorted groups; Prochlorococcus (PRO) and non-pigmented bacteria (NPB). The Pi concentrations, uptake rates, and Pi pool turnover times (Tt) were (mean, ±SD); 54.9 ± 35.0 nmol L−1 (n = 22), 4.8 ± 1.9 nmol L−1 day−1 (n = 19), and 14.7 ± 10.2 days (n = 19), respectively. Pi uptake into >2 μm cells was on average 12 ± 7% (n = 15) of the total uptake. The kinetic response to Pi (10–500 nmol L−1) was small, indicating that the microorganisms were close to their maximum uptake velocity (Vmax). Vmax averaged 8.0 ± 3.6 nmol L−1 day−1 (n = 19) in the >0.2 μm group, with half saturation constants (Km) of 40 ± 28 nmol L−1 (n = 19). PRO had three times the cell specific Pi uptake rate of NPB, at ambient concentrations, but when adjusted to cells L−1 the rates were similar, and these two groups were equally competitive for Pi. The Tt of γ-P-ATP in the >0.2 μm group were shorter than for the Pi pool (4.4 ± 1.0 days; n = 6), but this difference diminished in the larger size classes. The kinetic response to ATP was large in the >0.2 μm class with Vmax exceeding the rates at ambient concentrations (mean 62 ± 27 times; n = 6) with a mean Vmax for γ-P-ATP of 2.8 ± 1.0 nmol L−1 day−1, and Km at 11.5 ± 5.4 nmol L−1 (n = 6). The NPB contribution to γ-P-ATP uptake was high (95 ± 3%, n = 4) at ambient concentrations but decreased to ∼50% at the highest ATP amendment. PRO had Km values 5–10 times greater than NPB. The above indicates that PRO and NPB were in close competition in terms of Pi acquisition, whereas P uptake from ATP could be attributed to NPB. This apparent resource partitioning may be a niche separating strategy and an important factor in the successful co-existence within the oligotrophic upper ocean of the NPSG.

The Arabidopsis transcription factor PHR1 is essential for adaptation to high light and retaining functional photosynthesis during phosphate starvation

The transcription factor PHR1 (PHOSPHATE STARVATION RESPONSE 1; encoded by gene At4g28610) is central for adaptation to phosphate deficiency in Arabidopsis (Arabidopsis thaliana). A rapid turnover of phosphate pools in the leaves is essential for energy transfer and metabolism within photosynthesis, and consequently, we hypothesized that PHR1 is needed for adaptation to high-light stress during P deficiency. We analyzed three Arabidopsis plant lines: wild-type, a transgenic PHR1 overexpressor line and a knockout mutant, phr1. The plants were grown under phosphate-limiting and sufficient conditions and exposed to different light conditions. Photosynthetic activity and light stress of the leaves were characterized by analyzing accumulation of carbohydrates, chlorophyll fluorescence, immunoblot detection of photosystem subunits and anthocyanin accumulation. Compared to the wild-type and the overexpressor line, the phr1 mutant has decreased levels of phosphate, anthocyanins and carbohydrates during combined P deficiency and light stress. The stressed mutant also has strongly decreased photosystem II (PSII) quantum efficiency, and shows degradation of the core units of PSII demonstrating extensive irreversible photodamage. We conclude that PHR1 is needed for the metabolic balance, for retaining P(i) levels and for inducing anthocyanin production, and during P deficiency PHR1 is vital for adaptations to avoid permanent damage to photosystems during high-light conditions.

Immobilized Pool of NCAM180 in the Postsynaptic Membrane Is Homeostatically Replenished by the Flux of NCAM180 from Extrasynaptic Regions

Homeostatic mechanisms maintaining high levels of adhesion molecules in synapses over prolonged periods of time remain incompletely understood. We used fluorescence recovery after photobleaching experiments to analyze the steady state turnover of the immobile pool of green fluorescent protein-labeled NCAM180, the largest postsynaptically accumulating isoform of the neural cell adhesion molecule (NCAM). We show that there is a continuous flux of NCAM180 to the postsynaptic membrane from nonsynaptic regions of dendrites by diffusion. In the postsynaptic membrane, the newly delivered NCAM180 slowly intermixes with the immobilized pool of NCAM180. Preferential immobilization and accumulation of NCAM180 in the postsynaptic membrane is reduced after disruption of the association of NCAM180 with the spectrin cytoskeleton and in the absence of the homophilic interactions of NCAM180 in synapses. Our observations indicate that the homophilic interactions and binding to the cytoskeleton promote immobilization of NCAM180 and its accumulation in the postsynaptic membrane. Flux of NCAM180 from extrasynaptic regions and its slow intermixture with the immobile pool of NCAM180 in the postsynaptic membrane may be important for the continuous homeostatic replenishment of NCAM180 protein at synaptic contacts without compromising the long term synaptic contact stability.