The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km² to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere.     

High plasma level of long pentraxin 3 (PTX3) is associated with fatal disease in bacteremic patients: a prospective cohort study

Introduction

Long pentraxin 3 (PTX3) is an acute-phase protein secreted by various cells, including leukocytes and endothelial cells. Like C-reactive protein (CRP), it belongs to the pentraxin superfamily. Recent studies indicate that high levels of PTX3 may be associated with mortality in sepsis. The prognostic value of plasma PTX3 in bacteremic patients is unknown.

Methods

Plasma PTX3 levels were measured in 132 patients with bacteremia caused by Staphylococcus aureus, Streptococcus pneumoniae, β-hemolytic streptococcae and Escherichia coli, using a commercial solid-phase enzyme-linked immunosorbent assay (ELISA). Values were measured on days 1–4 after positive blood culture, on day 13–18 and on recovery.

Results

The maximum PTX3 values on days 1–4 were markedly higher in nonsurvivors compared to survivors (44.8 vs 6.4 ng/ml, p<0.001) and the AUC^ROC in the prediction of case fatality was 0.82 (95% CI 0.73–0.91). PTX3 at a cut-off level of 15 ng/ml showed 72% sensitivity and 81% specificity for fatal disease. High PTX3 (>15 ng/ml) was associated with hypotension (MAP <70 mmHg)(OR 7.9;95% CI 3.3–19.0) and high SOFA score (≥4)(OR 13.2; 95% CI 4.9–35.4). The CRP level (maximum value on days 1 to 4) did not predict case fatality at any cut-off level in the ROC curve (p = 0.132). High PTX3 (>15 ng/ml) remained an independent risk factor for case fatality in a logistic regression model adjusted for potential confounders.

Conclusions

PTX3 proved to be a specific independent prognostic biomarker in bacteremia. PTX3 during the first days after diagnosis showed better prognostic value as compared to CRP, a widely used biomarker in clinical settings. PTX3 measurement offers a novel opportunity for the prognostic stratification of bacteremia patients.     

Determination of Serotonin and Dopamine Metabolites in Human Brain Microdialysis and Cerebrospinal Fluid Samples by UPLC-MS/MS: Discovery of Intact Glucuronide and Sulfate Conjugates

An UPLC-MS/MS method was developed for the determination of serotonin (5-HT), dopamine (DA), their phase I metabolites 5-HIAA, DOPAC and HVA, and their sulfate and glucuronide conjugates in human brain microdialysis samples obtained from two patients with acute brain injuries, ventricular cerebrospinal fluid (CSF) samples obtained from four patients with obstructive hydrocephalus, and a lumbar CSF sample pooled mainly from patients undergoing spinal anesthesia in preparation for orthopedic surgery. The method was validated by determining the limits of detection and quantification, linearity, repeatability and specificity. The direct method enabled the analysis of the intact phase II metabolites of 5-HT and DA, without hydrolysis of the conjugates. The method also enabled the analysis of the regioisomers of the conjugates, and several intact glucuronide and sulfate conjugates were identified and quantified for the first time in the human brain microdialysis and CSF samples. We were able to show the presence of 5-HIAA sulfate, and that dopamine-3-O-sulfate predominates over dopamine-4-O-sulfate in the human brain. The quantitative results suggest that sulfonation is a more important phase II metabolism pathway than glucuronidation in the human brain.     

The impact of thermal seasonality on terrestrial endotherm food web dynamics: a revision of the Exploitation Ecosystem Hypothesis

Many terrestrial endotherm food webs constitute three trophic level cascades. Others have two trophic level dynamics (food limited herbivores; plants adapted to tackle intense herbivory) or one trophic level dynamic (herbivorous endotherms absent, thus plants compete for the few places where they can survive and grow). According to the Exploitation Ecosystems Hypothesis (EEH), these contrasting dynamics are consequences of differences in primary productivity. The productivity thresholds for changing food web dynamics were assumed to be global constants. We challenged this assumption and found that several model parameters are sensitive to the contrast between persistently warm and seasonally cold climates. In persistently warm environments, three trophic level dynamics can be expected to prevail almost everywhere, save the most extreme deserts. We revised EEH accordingly and tested it by compiling direct evidence of three and two trophic level dynamics and by studying the global distribution of felids. In seasonally cold environments, we found evidence for three trophic level dynamics only in productive ecosystems, while evidence for two trophic level dynamics appeared in ecosystems with low primary productivity. In persistently warm environments, we found evidence for three trophic level dynamics in all types of ecosystems. The distribution of felids corroborated these results. The empirical evidence thus indicates that two trophic level dynamics, as defined by EEH, are restricted to seasonally cold biomes with low primary productivity, such as the artic–alpine tundra and the temperate steppe.     

GluA4 Dependent Plasticity Mechanisms Contribute to Developmental Synchronization of the CA3–CA1 Circuitry in the Hippocampus

During the course of development, molecular mechanisms underlying activity-dependent synaptic plasticity change considerably. At immature CA3–CA1 synapses in the hippocampus, PKA-driven synaptic insertion of GluA4 AMPA receptors is the predominant mechanism for synaptic strengthening. However, the physiological significance of the developmentally restricted GluA4-dependent plasticity mechanisms is poorly understood. Here we have used microelectrode array (MEA) recordings in GluA4 deficient slice cultures to study the role of GluA4 in early development of the hippocampal circuit function. We find that during the first week in culture (DIV2–6) when GluA4 expression is restricted to pyramidal neurons, loss of GluA4 has no effect on the overall excitability of the immature network, but significantly impairs synchronization of the CA3 and CA1 neuronal populations. In the absence of GluA4, the temporal correlation of the population spiking activity between CA3–CA1 neurons was significantly lower as compared to wild-types at DIV6. Our data show that synapse-level defects in transmission and plasticity mechanisms are efficiently compensated for to normalize population firing rate at the immature hippocampal network. However, lack of the plasticity mechanisms typical for the immature synapses may perturb functional coupling between neuronal sub-populations, a defect frequently implicated in the context of developmentally originating neuropsychiatric disorders.

     

Quantitative characterization of clumping in Scots pine crowns

Background and Aims

Proper characterization of the clumped structure of forests is needed for calculation of the absorbed radiation and photosynthetic production by a canopy. This study examined the dependency of crown-level clumping on tree size and growth conditions in Scots pine (Pinus sylvestris), and determined the ability of statistical canopy radiation models to quantify the degree of self-shading within crowns as a result of the clumping effect.

Methods

Twelve 3-D Scots pine trees were generated using an application of the LIGNUM model, and the crown-level clumping as quantified by the crown silhouette to total needle area ratio (STAR_crown) was calculated. The results were compared with those produced by the stochastic approach of modelling tree crowns as geometric shapes filled with a random medium.

Key Results

Crown clumping was independent of tree height, needle area and growth conditions. The results supported the capability of the stochastic approach in characterizing clumping in crowns given that the outer shell of the tree crown is well represented.

Conclusions

Variation in the whole-stand clumping index is induced by differences in the spatial pattern of trees as a function of, for example, stand age rather than by changes in the degree of self-shading within individual crowns as they grow bigger.     

Long-Term Experiments Reveal Strong Interactions Between Lemmings and Plants in the Fennoscandian Highland Tundra

Both the theory and the observations suggest that, there are strong links between herbivores and plants in terrestrial ecosystems; although, the effect of herbivores on plant community biomass is often attributed to variations in plant palatability. The existence of a strong link is commonly tested by constructing exclosures that exclude herbivores during a period of time. We here present data from two long-term (9 and 20 years, respectively) herbivore exclosure studies in lemming habitats on arctic tundra in northernmost Norway. The exclusion of all mammalian herbivores triggered strong increases in community level plant biomass and substantial changes in plant community composition. Palatable plants like graminoids and large bryophytes, as well as unpalatable plants like evergreen ericoids, deciduous shrubs, and lichens were all favored by excluding lemmings. These results reveal that a substantial increase in community biomass which occurs only when plant species capable of accumulating biomass are present, and palatability is a poor predictor of long-term responses of plants to excluding herbivores.     

Biocompatibility of mannan nanogel—safe interaction with plasma proteins

Background

Self-assembled mannan nanogels are designed to provide a therapeutic or vaccine delivery platform based on the bioactive properties of mannan to target mannose receptor expressed on the surface of antigen-presenting cells, combined with the performance of nanogels as carriers of biologically active agents.

Methods

Proteins in the corona around mannan nanogel formed in human plasma were identified by mass spectrometry after size exclusion chromatography or centrifugation followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Structural changes and time dependent binding of human apolipoprotein A-I (apoA-I) and human serum albumin (HSA) to mannan nanogel were studied using intrinsic tryptophan fluorescence and circular dichroism spectroscopy. The mannan nanogel effect on blood coagulation and fibrillation of Alzheimer's disease-associated amyloid β peptide and hemodialysis-associated amyloidosis β2 microglobulin was evaluated using thrombin generation assay or thioflavin T fluorescence assay, respectively.

Results

The protein corona around mannan nanogel is formed through a slow process, is quite specific comprising apolipoproteins B-100, A-I and E and HSA, evolves over time, and the equilibrium is reached after hours to days. Structural changes and time dependent binding of apoA-I and HSA to mannan nanogel are minor. The mannan nanogel does not affect blood coagulation and retards the fibril formation.

Conclusions

Mannan nanogel has a high biosafety and biocompatibility, which is mandatory for nanomaterials to be used in biomedical applications.

General Significance

Our research provides a molecular approach to evaluate the safety aspects of nanomaterials, which is of general concern in society and science.     

Contributions of leaf photosynthetic capacity, leaf angle and self-shading to the maximization of net photosynthesis in Acer saccharum: a modelling assessment

Background and Aims

Plants are expected to maximize their net photosynthetic gains and efficiently use available resources, but the fundamental principles governing trade-offs in suites of traits related to resource-use optimization remain uncertain. This study investigated whether Acer saccharum (sugar maple) saplings could maximize their net photosynthetic gains through a combination of crown structure and foliar characteristics that let all leaves maximize their photosynthetic light-use efficiency (ɛ).

Methods

A functional–structural model, LIGNUM, was used to simulate individuals of different leaf area index (LAI_ind) together with a genetic algorithm to find distributions of leaf angle (L_A) and leaf photosynthetic capacity (A_max) that maximized net carbon gain at the whole-plant level. Saplings grown in either the open or in a forest gap were simulated with A_max either unconstrained or constrained to an upper value consistent with reported values for A_max in A. saccharum.

Key Results

It was found that total net photosynthetic gain was highest when whole-plant PPFD absorption and leaf ɛ were simultaneously maximized. Maximization of ɛ required simultaneous adjustments in L_A and A_max along gradients of PPFD in the plants. When A_max was constrained to a maximum, plants growing in the open maximized their PPFD absorption but not ɛ because PPFD incident on leaves was higher than the PPFD at which ɛ_max was attainable. Average leaf ɛ in constrained plants nonetheless improved with increasing LAI_ind because of an increase in self-shading.

Conclusions

It is concluded that there are selective pressures for plants to simultaneously maximize both PPFD absorption at the scale of the whole individual and ɛ at the scale of leaves, which requires a highly integrated response between L_A, A_max and LAI_ind. The results also suggest that to maximize ɛ plants have evolved mechanisms that co-ordinate the L_A and A_max of individual leaves with PPFD availability.