Rainfall variability maintains grass‐forb species coexistence

Environmental variability can structure species coexistence by enhancing niche partitioning. Modern coexistence theory highlights two fluctuation‐dependent temporal coexistence mechanisms —the storage effect and relative nonlinearity – but empirical tests are rare. Here, we experimentally test if environmental fluctuations enhance coexistence in a California annual grassland. We manipulate rainfall timing and relative densities of the grass Avena barbata and forb Erodium botrys, parameterise a demographic model, and partition coexistence mechanisms. Rainfall variability was integral to grass–forb coexistence. Variability enhanced growth rates of both species, and early‐season drought was essential for Erodium persistence. While theoretical developments have focused on the storage effect, it was not critical for coexistence. In comparison, relative nonlinearity strongly stabilised coexistence, where Erodium experienced disproportionately high growth under early‐season drought due to competitive release from Avena. Our results underscore the importance of environmental variability and suggest that relative nonlinearity is a critical if underappreciated coexistence mechanism.     

Water‐use efficiency in a semi‐arid woodland with high rainfall variability

As the ratio of carbon uptake to water use by vegetation, water‐use efficiency (WUE) is a key ecosystem property linking global carbon and water cycles. It can be estimated in several ways, but it is currently unclear how different measures of WUE relate, and how well they each capture variation in WUE with soil moisture availability. We evaluated WUE in an Acacia‐dominated woodland ecosystem of central Australia at various spatial and temporal scales using stable carbon isotope analysis, leaf gas exchange and eddy covariance (EC) fluxes. Semi‐arid Australia has a highly variable rainfall pattern, making it an ideal system to study how WUE varies with water availability. We normalized our measures of WUE across a range of vapour pressure deficits using g₁, which is a parameter derived from an optimal stomatal conductance model and which is inversely related to WUE. Continuous measures of whole‐ecosystem g₁ obtained from EC data were elevated in the 3 days following rain, indicating a strong effect of soil evaporation. Once these values were removed, a close relationship of g₁ with soil moisture content was observed. Leaf‐scale values of g₁ derived from gas exchange were in close agreement with ecosystem‐scale values. In contrast, values of g₁ obtained from stable isotopes did not vary with soil moisture availability, potentially indicating remobilization of stored carbon during dry periods. Our comprehensive comparison of alternative measures of WUE shows the importance of stomatal control of fluxes in this highly variable rainfall climate and demonstrates the ability of these different measures to quantify this effect. Our study provides the empirical evidence required to better predict the dynamic carbon–water relations in semi‐arid Australian ecosystems.     

Photo‐inactivation of Bacillus endospores: inter‐specific variability of inactivation efficiency

The aims of this work were to (a) evaluate the susceptibility of endospores of Bacillus cereus, B. licheniformis, B. sphaericus and B. subtilis to photodynamic inactivation using a tricationic porphyrin as photosensitizer, (b) assess the efficiency of adsorption of the photosensitizer in endospore material as a determinant of the susceptibility of endospores of different Bacillus species to photo‐inactivation, (c) determine the value of B. cereus as a model organism for studies of antimicrobial photodynamic inactivation of bacterial endospores. The results of irradiation experiments with endospores of four species of Bacillus showed that B. cereus was the only species for which efficient endospore photo‐inactivation (> 3 log reduction) could be achieved. Endospores of B. licheniformis, B. sphaericus and B. subtilis were virtually resistant to photo‐inactivation with tricationic porphyrin. The amount of porphyrin bound to endospore material was not significantly different between species, regardless of the presence of an exosporium or exosporium‐like outer layer. The sensitivity of endospores to photodynamic inactivation with a tricationic porphyrin is highly variable among different species of the genus Bacillus. The presence of an exosporium in endospores of B. cereus and B. sphaericus, or an exosporium‐like glycoprotein layer in endospores of B. subtilis, did not affect the amount of bound photosensitizer and did not explain the inter‐species variability in susceptibility to photodynamic inactivation. The results imply that the use of B. cereus as a more amenable surrogate of the exosporium‐producing B. anthracis must be carefully considered when testing new photosensitizers for their antimicrobial photo‐inactivation properties.     

Single‐cell profiling screen identifies microtubule‐dependent reduction of variability in signaling

Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell‐to‐cell variability in signal strength and cellular response. Here, we screened 1,141 non‐essential genes to identify 50 “variability genes”. Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct “axes” of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4. We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane‐localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule‐dependent signal stabilization might also operate throughout metazoans.     

Inter‐group variability in seed dispersal by white‐handed gibbons in mosaic forest

Seed dispersers, like white‐handed gibbons (Hylobates lar), can display wide inter‐group variability in response to distribution and abundance of resources in their habitat. In different home ranges, they can modify their movement patterns along with the shape and scale of seed shadow produced. However, the effect of inter‐group variability on the destination of dispersed seeds is still poorly explained. In this study, we evaluate how seed dispersal patterns of this arboreal territorial frugivore varies between two neighboring groups, one inhabiting high quality evergreen forest and one inhabiting low quality mosaic forest. We predicted a difference in seed dispersal distance between the two groups (longer in the poor quality forest). We hypothesized that this difference would be explained by differences in home range size, daily path length, and ranging tortuosity. After 6 months of data collection, the evergreen group had a smaller home range (12.4 ha) than the mosaic group (20.9 ha), significantly longer daily path lengths (1507 m vs. 1114 m respectively) and greater tortuosity (39.1 vs. 16.1 respectively). Using gut passage times and displacement rates, we estimated the median seed dispersal distance as 163 m for the evergreen group (high quality forest) and of 116 m for the mosaic group (low quality forest). This contradiction with our initial prediction can be explained in term of social context, resource distribution, and habitat quality. Our results indicate that gibbons are dispersers of seeds between habitats and that dispersal distances provided by gibbons are influenced by a range of factors, including habitat and social context.     

Natural sequence variants of yeast environmental sensors confer cell‐to‐cell expression variability

Living systems may have evolved probabilistic bet hedging strategies that generate cell‐to‐cell phenotypic diversity in anticipation of environmental catastrophes, as opposed to adaptation via a deterministic response to environmental changes. Evolution of bet hedging assumes that genotypes segregating in natural populations modulate the level of intraclonal diversity, which so far has largely remained hypothetical. Using a fluorescent P_met17‐GFP reporter, we mapped four genetic loci conferring to a wild yeast strain an elevated cell‐to‐cell variability in the expression of MET17, a gene regulated by the methionine pathway. A frameshift mutation in the Erc1p transmembrane transporter, probably resulting from a release of laboratory strains from negative selection, reduced P_met17‐GFP expression variability. At a second locus, cis‐regulatory polymorphisms increased mean expression of the Mup1p methionine permease, causing increased expression variability in trans. These results demonstrate that an expression quantitative trait locus (eQTL) can simultaneously have a deterministic effect in cis and a probabilistic effect in trans. Our observations indicate that the evolution of transmembrane transporter genes can tune intraclonal variation and may therefore be implicated in both reactive and anticipatory strategies of adaptation.     

Investigating trophic‐level variability in Celtic Sea fish predators

The trophic level (T_L) mean and variance, and the degree of omnivory for five Celtic Sea fish predators were estimated using a database of stomach content records characterized by a high level of taxonomic resolution. The predators occupied a high position in the food web, i.e. 4·75 for Atlantic cod Gadus morhua, 4·44 for haddock Melanogrammus aeglefinus, 4·88 for European hake Merluccius merluccius, 5·00 for megrim Lepidorhombus whiffiagonis and 5·27 for whiting Merlangius merlangus. The level of taxonomic resolution of the prey did not greatly affect mean T_L predator values; an effect on variance was evident, low resolution masking intra‐population variability in T_L. Generalized additive models (GAM) were used to explain the variability of predator T_L caused by environmental variables (International Council for the Exploration of the Sea, ICES, division and season) and predator characteristics (total length, L_T). Significant year, location season and interaction effects were found for some species and with L_T at the scale of ICES subdivision. The species‐specific variability of T_L could be due to spatio‐temporal variations in prey availability and in predator selectivity following ontogenetic changes. Omnivorous fish T_L was less affected by spatio‐temporal variations. In addition, results showed that the omnivory index and T_L variability provide dissimilar information on predator feeding strategy. Combining information on T_L variability and omnivory allowed between within‐individual and between‐individual components contributing to trophic niche width to be separated and the type of generalization of fish predators to be identified.     

Inter‐individual variability in dispersal behaviours impacts connectivity estimates

The importance of landscape connectivity in determining biodiversity outcomes under environmental change has led to indices of connectivity becoming amongst the most widely used measures in conservation. Thus, it is vital that our understanding of connectivity and our use of indices describing it are reliable. Dispersal is the key ecological process involved in determining connectivity, and there is increasing evidence of substantial within‐population variability in dispersal behaviours. Here, we incorporate this inter‐individual variability into two approaches for estimating connectivity, least cost path analysis and stochastic movement simulation. Illustrative results demonstrate that including dispersal variability can yield substantially different estimates of connectivity. While connectivity is typically similar between nearby patches, the frequency of movements between patches further apart is often substantially increased when inter‐individual variability is included. Given the disproportionate role that unusual long‐distance dispersal events play in spatial dynamics, connectivity indices should seek to incorporate variability in dispersal behaviour.     

Analysis of individual cells identifies cell‐to‐cell variability following induction of cellular senescence

Senescent cells play important roles in both physiological and pathological processes, including cancer and aging. In all cases, however, senescent cells comprise only a small fraction of tissues. Senescent phenotypes have been studied largely in relatively homogeneous populations of cultured cells. In vivo, senescent cells are generally identified by a small number of markers, but whether and how these markers vary among individual cells is unknown. We therefore utilized a combination of single‐cell isolation and a nanofluidic PCR platform to determine the contributions of individual cells to the overall gene expression profile of senescent human fibroblast populations. Individual senescent cells were surprisingly heterogeneous in their gene expression signatures. This cell‐to‐cell variability resulted in a loss of correlation among the expression of several senescence‐associated genes. Many genes encoding senescence‐associated secretory phenotype (SASP) factors, a major contributor to the effects of senescent cells in vivo, showed marked variability with a subset of highly induced genes accounting for the increases observed at the population level. Inflammatory genes in clustered genomic loci showed a greater correlation with senescence compared to nonclustered loci, suggesting that these genes are coregulated by genomic location. Together, these data offer new insights into how genes are regulated in senescent cells and suggest that single markers are inadequate to identify senescent cells in vivo.     

Fractional killing arises from cell‐to‐cell variability in overcoming a caspase activity threshold

When cells are exposed to death ligands such as TRAIL, a fraction undergoes apoptosis and a fraction survives; if surviving cells are re‐exposed to TRAIL, fractional killing is once again observed. Therapeutic antibodies directed against TRAIL receptors also cause fractional killing, even at saturating concentrations, limiting their effectiveness. Fractional killing arises from cell‐to‐cell fluctuations in protein levels (extrinsic noise), but how this results in a clean bifurcation between life and death remains unclear. In this paper, we identify a threshold in the rate and timing of initiator caspase activation that distinguishes cells that live from those that die; by mapping this threshold, we can predict fractional killing of cells exposed to natural and synthetic agonists alone or in combination with sensitizing drugs such as bortezomib. A phenomenological model of the threshold also quantifies the contributions of two resistance genes (c‐FLIP and Bcl‐2), providing new insight into the control of cell fate by opposing pro‐death and pro‐survival proteins and suggesting new criteria for evaluating the efficacy of therapeutic TRAIL receptor agonists.     

Terrestrial biosphere model performance for inter‐annual variability of land‐atmosphere CO2 exchange

Interannual variability in biosphere‐atmosphere exchange of CO₂ is driven by a diverse range of biotic and abiotic factors. Replicating this variability thus represents the ‘acid test’ for terrestrial biosphere models. Although such models are commonly used to project responses to both normal and anomalous variability in climate, they are rarely tested explicitly against inter‐annual variability in observations. Herein, using standardized data from the North American Carbon Program, we assess the performance of 16 terrestrial biosphere models and 3 remote sensing products against long‐term measurements of biosphere‐atmosphere CO₂ exchange made with eddy‐covariance flux towers at 11 forested sites in North America. Instead of focusing on model‐data agreement we take a systematic, variability‐oriented approach and show that although the models tend to reproduce the mean magnitude of the observed annual flux variability, they fail to reproduce the timing. Large biases in modeled annual means are evident for all models. Observed interannual variability is found to commonly be on the order of magnitude of the mean fluxes. None of the models consistently reproduce observed interannual variability within measurement uncertainty. Underrepresentation of variability in spring phenology, soil thaw and snowpack melting, and difficulties in reproducing the lagged response to extreme climatic events are identified as systematic errors, common to all models included in this study.