Linking individual response to biotic interactions with community structure: a trait-based framework

1.  Due to species-specificity of the outcomes of biotic interactions, it is difficult to generalize from observed biotic interactions at the individual plant level to the effect of those interactions at the community level. To evaluate the importance of biotic interactions in shaping plant communities, it is necessary to understand how the outcomes of the complex interactions observed at the individual level can influence community structure.
2.  Here, we propose a trait-based framework that identifies and organises mechanisms affecting community structure (here described with relative abundances of plant functional traits – i.e. the distribution of trait values at the community level). We applied our approach to a single leaf trait, specific leaf area (SLA), to link individual responses to plant interactions with community structure (SLA distribution observed at the community level) and to test whether biotic interactions can predict the functional composition of subalpine grasslands. We evaluated the generality of our model through a cross-validation with a set of eight subalpine grasslands independent from the four fields used to build the model.
3.  We found that competition and facilitation were able to explain the functional composition of subalpine grasslands, and the relevant fitness components (survival or growth) explaining this link changed depending on the limiting resources. When soil water availability was limiting, positive plant-plant interactions acting on survival were able to explain community structure. In contrast, when no water limitation was observed competition acting on individual growth was the main driver of community structure.
4.  Our framework enables evaluation of the consequences of biotic interactions observed at individual level on community structure, thereby indicating when and where different types of plant-plant interactions are important.     

Tracking tumor evolution via prostate-specific antigen: an individual post-operative study

Background  

The progress of the prostate-specific antigen (PSA) level after radical prostatectomy is observed for a patient in order to extract information about the mode of tumor cell growth. Although PSA values are determined routinely to find the doubling time of the prostate marker, to our knowledge, this analysis is the first in the literature.     

Allocating nitrogen away from a herbivore: a novel compensatory response to root herbivory

Centaurea maculosa, an invasive North American plant species, shows a high degree of tolerance to the root-boring biocontrol herbivore, Agapeta zoegana. For example, infested individuals of C. maculosa often exhibit more rigorous growth and reproduction compared with their non-infested counterparts. Compensatory responses to aboveground herbivores often involve increases in leaf area and/or photosynthetic capacity, but considerably less is known about root system compensatory responses to belowground herbivory. We used a ¹⁵N labeling approach to evaluate whether compensatory adjustments in N acquisition via changes in root morphology and/or physiological uptake capacity could explain the ability of C. maculosa to tolerate root herbivory. Root herbivory reduced whole plant N uptake by more than 30% and root uptake capacity by about 50%. Despite a marked reduction in N procurement, herbivory did not affect total biomass or shoot N status. Infested plants maintained shoot N status by shifting more of the acquired N from the root to the shoot. To our knowledge, shifting N allocation away from a root herbivore has not been reported and provides a plausible mechanism for the host plant to overcome an otherwise devastating effect of a root herbivore-induced N deficit.     

The disposition index: from individual to population approach

To correctly evaluate the glucose control system, it is crucial to account for both insulin sensitivity and secretion. The disposition index (DI) is the most widely accepted method to do so. The original paradigm (hyperbolic law) consists of the multiplicative product of indices related to insulin sensitivity and secretion, but more recently, an alternative formula has been proposed with the exponent α (power function law). Traditionally, curve-fitting approaches have been used to evaluate the DI in a population: the algorithmic implementations often introduce some critical issues, such as the assumption that one of the two indices is error free or the effects of the log transformation on the measurement errors. In this work, we review the commonly used approaches and show that they provide biased estimates. Then we propose a novel nonlinear total least square (NLTLS) approach, which does not need to use the approximations built in the previously proposed alternatives, and show its superiority. All of the traditional fit procedures, including NLTLS, account only for uncertainty affecting insulin sensitivity and secretion indices when they are estimated from noisy data. Thus, they fail when part of the observed variability is due to inherent differences in DI values between individuals. To handle this inevitable source of variability, we propose a nonlinear mixed-effects approach that describes the DI using population hyperparameters such as the population typical values and covariance matrix. On simulated data, this novel technique is much more reliable than the curve-fitting approaches, and it proves robust even when no or small population variability is present in the DI values. Applying this new approach to the analysis of real IVGTT data suggests a value of α significantly smaller than 1, supporting the importance of testing the power function law as an alternative to the simpler hyperbolic law.     

Below-ground nitrogen transfer from oak seedlings facilitates Molinia growth: 15N pulse-chase labelling

Plant and Soil - Manganese (Mn) is toxic to plants at high concentrations with recent evidence indicating slowed tropical-tree growth by high soil Mn concentrations. However, little information...     

The magic-bead concept: an integrated approach to nitrogen removal with co-immobilized micro-organisms

This paper describes both qualitative and quantitative aspects of simultaneous autotrophic nitrification and heterotrophic denitrification by, respectively, the nitrifierNitrisomonas europaea and either of the denitrifiersPseudomonas denitrificans orParacoccus denitrificans co-immobilized in double-layer gel beads. The system is based on the establishment of well-defined oxic and anoxic zones within the cell supports and on physical separation of the nitrifying and denitrifying populations. Nitrification and denitrification rates were obtained from measured bulk concentrations and head-space analysis. The latter analyses showed that ammonia was primarily converted into molecular nitrogen. Nitrous oxide was not detected. High nitrogen removal rates (up to 5.1 mmol N m^–3 gel s^–1) were achieved in continuous reactors under aerobic conditions. The overall rate of nitrogen removal was controlled by the nitrifying step. The approach followed is, in principle, also suitable to the coupling of other oxidative and reductive bioprocesses having complementary metabolic routes. Two-stage bioconversion processes can be thus conducted as if single-staged, which results in more compact reactor systems.     

Effects of nitrogen deposition and insect herbivory on patterns of ecosystem-level carbon and nitrogen dynamics: results from the CENTURY model

Atmospheric nitrogen deposition may indirectly affect ecosystems through deposition-induced changes in the rates of insect herbivory. Plant nitrogen (N) status can affect the consumption rates and population dynamics of herbivorous insects, but the extent to which N deposition-induced changes in herbivory might lead to changes in ecosystem-level carbon (C) and N dynamics is unknown. We created three insect herbivory functions based on empirical responses of insect consumption and population dynamics to changes in foliar N and implemented them into the CENTURY model. We modeled the responses of C and N storage patterns and flux rates to N deposition and insect herbivory in an herbaceous system. Results from the model indicate that N deposition caused a strong increase in plant production, decreased plant C : N ratios, increased soil organic C (SOC), and enhanced rates of N mineralization. In contrast, herbivory decreased both vegetative and SOC storage and depressed N mineralization rates. The results suggest that herbivory plays a particularly important role in affecting ecosystem processes by regulating the threshold value of N deposition at which ecosystem C storage saturates; C storage saturated at lower rates of N deposition with increasing intensity of herbivory. Differences in the results among the modeled insect herbivory functions suggests that distinct physiological and population response of insect herbivores can have a large impact on ecosystem processes. Including the effects of herbivory in ecosystem studies, particularly in systems where rates of herbivory are high and linked to plant C : N, will be important in generating accurate predictions of the effects of atmospheric N deposition on ecosystem C and N dynamics.     

Heterogeneous dissolved organic nitrogen supply over a coral reef: first evidence from nitrogen stable isotope ratios

Dissolved organic nitrogen (DON) potentially plays a major role in sustaining the high productivity and biological diversity of coral reefs. However, data are scarce regarding sources and sinks of DON. This study, for the first time, determined the ¹⁵N isotopic composition of total dissolved nitrogen (δ¹⁵N_TDN), reflecting the isotopic signature of DON, in the water column over a coral reef. The uniformity in δ¹⁵N_TDN during high tide (3.2 ± 0.3 ‰) indicated that the DON was mainly derived from offshore waters. In contrast, higher spatial heterogeneity of δ¹⁵N_TDN (3.1 ± 0.9 ‰) and DON concentrations during low tide indicated the existence of local DON sources patchily distributed over the reef. Low δ¹⁵N_TDN values located mid-reef were indicative of DON release from organisms that obtained their N via N₂ fixation, whereas high δ¹⁵N_TDN appeared to reflect localized release of DON by organisms exposed to dissolved inorganic nitrogen with elevated ¹⁵N, such as from terrestrial and offshore inputs. Collectively, the results highlight the importance of spatial patterns in DON release from reef communities in the N cycling of coral reefs.     

Factors influencing nitrogen processing in lakes: an experimental approach

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Epigenetic responses of hare barley (Hordeum murinum subsp. leporinum) to climate change: an experimental,trait-based approach

The impact of reduced rainfall and increased temperatures forecasted by climate change models on plant communities will depend on the capacity of plant species to acclimate and adapt to new environmental conditions. The acclimation process is mainly driven by epigenetic regulation, including structural and chemical modifications on the genome that do not affect the nucleotide sequence. In plants, one of the best-known epigenetic mechanisms is cytosine-methylation. We evaluated the impact of 30% reduced rainfall (hereafter “drought” treatment; D), 3 °C increased air temperature (“warming”; W), and the combination of D and W (WD) on the phenotypic and epigenetic variability of Hordeum murinum subsp. leporinum L., a grass species of high relevance in Mediterranean agroforestry systems. A full factorial experiment was set up in a savannah-like ecosystem located in southwestern Spain. H. murinum exhibited a large phenotypic plasticity in response to climatic conditions. Plants subjected to warmer conditions (i.e., W and WD treatments) flowered earlier, and those subjected to combined stress (WD) showed a higher investment in leaf area per unit of leaf mass (i.e., higher SLA) and produced heavier seeds. Our results also indicated that both the level and patterns of methylation varied substantially with the climatic treatments, with the combination of D and W inducing a clearly different epigenetic response compared to that promoted by D and W separately. The main conclusion achieved in this work suggests a potential role of epigenetic regulation of gene expression for the maintenance of homoeostasis and functional stability under future climate change scenarios.Subject terms: Climate-change ecology, Molecular ecology     

Determining trophic niche width: an experimental test of the stable isotope approach

Determining the trophic niche width of an animal population and the relative degree to which a generalist population consists of dietary specialists are long‐standing problems of ecology. It has been proposed that the variance of stable isotope values in consumer tissues could be used to quantify trophic niche width of consumer populations. However, this promising idea has not yet been rigorously tested. By conducting controlled laboratory experiments using model consumer populations (Daphnia sp., Crustacea) with controlled diets, we investigated the effect of individual‐ and population‐level specialisation and generalism on consumer δ¹³C mean and variance values. While our experimental data follow general expectations, we extend current qualitative models to quantitative predictions of the dependence of isotopic variance on dietary correlation time, a measure for the typical time over which a consumer changes its diet. This quantitative approach allows us to pinpoint possible procedural pitfalls and critical sources of measurement uncertainty. Our results show that the stable isotope approach represents a powerful method for estimating trophic niche widths, especially when taking the quantitative concept of dietary correlation time into account.     

Variation in fluxes estimated from nitrogen isotope discrimination corresponds with independent measures of nitrogen flux in Populus balsamifera L.

Acquisition of mineral nitrogen by roots from the surrounding environment is often not completely efficient, in which a variable amount of leakage (efflux) relative to gross uptake (influx) occurs. The efflux/influx ratio (E/I) is, therefore, inversely related to the efficiency of nutrient uptake at the root level. Time‐integrated estimates of E/I and other nitrogen‐use traits may be obtainable from variation in stable isotope ratios or through compartmental analysis of tracer efflux (CATE) using radioactive or stable isotopes. To compare these two methods, Populus balsamifera L. genotypes were selected, a priori, for high or low nitrogen isotope discrimination. Vegetative cuttings were grown hydroponically, and E/I was calculated using an isotope mass balance model (IMB) and compared to E/I calculated using ¹⁵N CATE. Both methods indicated that plants grown with ammonium had greater E/I than nitrate‐grown plants. Genotypes with high or low E/I using CATE also had similarly high or low estimates of E/I using IMB, respectively. Genotype‐specific means were linearly correlated (r = 0.77; P = 0.0065). Discrepancies in E/I between methods may reflect uncertainties in discrimination factors for the assimilatory enzymes, or temporal differences in uptake patterns. By utilizing genotypes with known variation in nitrogen isotope discrimination, a relationship between nitrogen isotope discrimination and bidirectional nitrogen fluxes at the root level was observed.     

Protein turnover: measurement of proteome dynamics by whole animal metabolic labelling with stable isotope labelled amino acids

The measurement of protein turnover in tissues of intact animals is obtained by whole animal dynamic labelling studies, requiring dietary administration of precursor label. It is difficult to obtain full labelling of precursor amino acids in the diet and if partial labelling is used, calculation of the rate of turnover of each protein requires knowledge of the precursor relative isotope abundance (RIA). We describe an approach to dynamic labelling of proteins in the mouse with a commercial diet supplemented with a pure, deuterated essential amino acid. The pattern of isotopomer labelling can be used to recover the precursor RIA, and sampling of urinary secreted proteins can monitor the development of liver precursor RIA non-invasively. Time-series analysis of the labelling trajectories for individual proteins allows accurate determination of the first order rate constant for degradation. The acquisition of this parameter over multiple proteins permits turnover profiling of cellular proteins and comparisons of different tissues. The median rate of degradation of muscle protein is considerably lower than liver or kidney, with heart occupying an intermediate position.     

Factors characterizing phosphate oxygen isotope ratios in river water: an inter-watershed comparison approach

Limnology - We compared the oxygen isotope ratio of dissolved phosphate $$left( {delta^{{{18}}} {text{O}}_{{{text{PO}}_{{4}} }} } right)$$ in two rivers with different land-cover and...     

Lessons from the eradication of smallpox: an interview with D. A. Henderson

It has been more than 35 years since the last naturally occurring case of smallpox. Sufficient time has passed to allow an objective overview of what were the key factors in the success of the eradication effort and what lessons smallpox can offer to other campaigns. Professor D. A. Henderson headed the international effort to eradicate smallpox. Here, we present a summary of D. A. Henderson''s perspectives on the eradication of smallpox. This text is based upon the Unither Baruch Blumberg Lecture, delivered by D. A. Henderson at the University of Oxford in November 2012 and upon conversations and correspondence with Professor Henderson.