Juan A. Bonachela

Termite mounds can increase the robustness of dryland ecosystems to climatic change

Termites can stabilize tropical grasslands Spotty vegetation patterns in tropical savannas and grasslands can be a warning sign of imminent desertification. However, Bonachela et al. find that termites can also produce spotty patterns. Their theoretical study, confirmed by field data from Kenya, shows that patterns produced by termite mounds are not harbingers of desertification. Indeed, the presence of termites buffers these ecosystems against climate change. Science, this issue p. 651 Termites shape vegetation patterns in arid landscapes and buffer ecosystems against desertification. Self-organized spatial vegetation patterning is widespread and has been described using models of scale-dependent feedback between plants and water on homogeneous substrates. As rainfall decreases, these models yield a characteristic sequence of patterns with increasingly sparse vegetation, followed by sudden collapse to desert. Thus, the final, spot-like pattern may provide early warning for such catastrophic shifts. In many arid ecosystems, however, termite nests impart substrate heterogeneity by altering soil properties, thereby enhancing plant growth. We show that termite-induced heterogeneity interacts with scale-dependent feedbacks to produce vegetation patterns at different spatial grains. Although the coarse-grained patterning resembles that created by scale-dependent feedback alone, it does not indicate imminent desertification. Rather, mound-field landscapes are more robust to aridity, suggesting that termites may help stabilize ecosystems under global change.

Dynamic model of flexible phytoplankton nutrient uptake

The metabolic machinery of marine microbes can be remarkably plastic, allowing organisms to persist under extreme nutrient limitation. With some exceptions, most theoretical approaches to nutrient uptake in phytoplankton are largely dominated by the classic Michaelis–Menten (MM) uptake functional form, whose constant parameters cannot account for the observed plasticity in the uptake apparatus. Following seminal ideas by earlier researchers, we propose a simple cell-level model based on a dynamic view of the uptake process whereby the cell can regulate the synthesis of uptake proteins in response to changes in both internal and external nutrient concentrations. In our flexible approach, the maximum uptake rate and nutrient affinity increase monotonically as the external nutrient concentration decreases. For low to medium nutrient availability, our model predicts uptake and growth rates larger than the classic MM counterparts, while matching the classic MM results for large nutrient concentrations. These results have important consequences for global coupled models of ocean circulation and biogeochemistry, which lack this regulatory mechanism and are thus likely to underestimate phytoplankton abundances and growth rates in oligotrophic regions of the ocean.

Impact of ocean phytoplankton diversity on phosphate uptake

Significance Nutrient uptake is a central property of ocean biogeochemistry, but our understanding of this process is based on laboratory cultures or bulk environmental studies. Thus, mathematical descriptions of nutrient uptake, at the heart of most biogeochemical models, must rely on this limited information. Hence, we have little knowledge of how natural phytoplankton populations vary in their abilities to take up key nutrients. Using advanced analytical techniques, this study provides the first comprehensive in situ quantification of nutrient uptake capabilities among dominant phytoplankton groups. Supported by a model that considers plastic ecological responses in an evolutionary context, this work further provides a fundamentally new framework for the integration of microbial diversity to describe and understand the controls of ocean nutrient assimilation. We have a limited understanding of the consequences of variations in microbial biodiversity on ocean ecosystem functioning and global biogeochemical cycles. A core process is macronutrient uptake by microorganisms, as the uptake of nutrients controls ocean CO2 fixation rates in many regions. Here, we ask whether variations in ocean phytoplankton biodiversity lead to novel functional relationships between environmental variability and phosphate (Pi) uptake. We analyzed Pi uptake capabilities and cellular allocations among phytoplankton groups and the whole community throughout the extremely Pi-depleted western North Atlantic Ocean. Pi uptake capabilities of individual populations were well described by a classic uptake function but displayed adaptive differences in uptake capabilities that depend on cell size and nutrient availability. Using an eco-evolutionary model as well as observations of in situ uptake across the region, we confirmed that differences among populations lead to previously uncharacterized relationships between ambient Pi concentrations and uptake. Supported by novel theory, this work provides a robust empirical basis for describing and understanding assimilation of limiting nutrients in the oceans. Thus, it demonstrates that microbial biodiversity, beyond cell size, is important for understanding the global cycling of nutrients.

Eluding catastrophic shifts

Significance Catastrophic shifts such as desertification processes, massive extinctions, or stock market collapses are ubiquitous threats in nature and society. In these events, there is a shift from one steady state to a radically different one, from which recovery is exceedingly difficult. Thus, there is a huge interest in predicting and eventually preventing catastrophic shifts. Here we explore the influence of key mechanisms such as demographic fluctuations, heterogeneity, and diffusion, which appear generically in real circumstances. The mechanisms we study could ideally be exploited to smooth abrupt shifts and to make transitions progressive and easier to revert. Thus, our findings could be of potential importance for ecosystem management and biodiversity conservation. Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences.

Evolution of a modular software network

“Evolution behaves like a tinkerer” (François Jacob, Science, 1977). Software systems provide a singular opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to explore the evolution of a complex network in a unique way. The modular design detected during its growth is based on the reuse of existing code in order to minimize costs during programming. The increase of modularity experienced by the system over time has not counterbalanced the increase in incompatibilities between software packages within modules. This negative effect is far from being a failure of design. A random process of package installation shows that the higher the modularity, the larger the fraction of packages working properly in a local computer. The decrease in the relative number of conflicts between packages from different modules avoids a failure in the functionality of one package spreading throughout the entire system. Some potential analogies with the evolutionary and ecological processes determining the structure of ecological networks of interacting species are discussed.

A theoretical foundation for multi-scale regular vegetation patterns

Self-organized regular vegetation patterns are widespread and thought to mediate ecosystem functions such as productivity and robustness, but the mechanisms underlying their origin and maintenance remain disputed. Particularly controversial are landscapes of overdispersed (evenly spaced) elements, such as North American Mima mounds, Brazilian murundus, South African heuweltjies, and, famously, Namibian fairy circles. Two competing hypotheses are currently debated. On the one hand, models of scale-dependent feedbacks, whereby plants facilitate neighbours while competing with distant individuals, can reproduce various regular patterns identified in satellite imagery. Owing to deep theoretical roots and apparent generality, scale-dependent feedbacks are widely viewed as a unifying and near-universal principle of regular-pattern formation despite scant empirical evidence. On the other hand, many overdispersed vegetation patterns worldwide have been attributed to subterranean ecosystem engineers such as termites, ants, and rodents. Although potentially consistent with territorial competition, this interpretation has been challenged theoretically and empirically and (unlike scale-dependent feedbacks) lacks a unifying dynamical theory, fuelling scepticism about its plausibility and generality. Here we provide a general theoretical foundation for self-organization of social-insect colonies, validated using data from four continents, which demonstrates that intraspecific competition between territorial animals can generate the large-scale hexagonal regularity of these patterns. However, this mechanism is not mutually exclusive with scale-dependent feedbacks. Using Namib Desert fairy circles as a case study, we present field data showing that these landscapes exhibit multi-scale patterning—previously undocumented in this system—that cannot be explained by either mechanism in isolation. These multi-scale patterns and other emergent properties, such as enhanced resistance to and recovery from drought, instead arise from dynamic interactions in our theoretical framework, which couples both mechanisms. The potentially global extent of animal-induced regularity in vegetation—which can modulate other patterning processes in functionally important ways—emphasizes the need to integrate multiple mechanisms of ecological self-organization.

Interactions between growth-dependent changes in cell size, nutrient supply and cellular elemental stoichiometry of marine Synechococcus

The factors that control elemental ratios within phytoplankton, like carbon:nitrogen:phosphorus (C:N:P), are key to biogeochemical cycles. Previous studies have identified relationships between nutrient-limited growth and elemental ratios in large eukaryotes, but little is known about these interactions in small marine phytoplankton like the globally important Cyanobacteria. To improve our understanding of these interactions in picophytoplankton, we asked how cellular elemental stoichiometry varies as a function of steady-state, N- and P-limited growth in laboratory chemostat cultures of Synechococcus WH8102. By combining empirical data and theoretical modeling, we identified a previously unrecognized factor (growth-dependent variability in cell size) that controls the relationship between nutrient-limited growth and cellular elemental stoichiometry. To predict the cellular elemental stoichiometry of phytoplankton, previous theoretical models rely on the traditional Droop model, which purports that the acquisition of a single limiting nutrient suffices to explain the relationship between a cellular nutrient quota and growth rate. Our study, however, indicates that growth-dependent changes in cell size have an important role in regulating cell nutrient quotas. This key ingredient, along with nutrient-uptake protein regulation, enables our model to predict the cellular elemental stoichiometry of Synechococcus across a range of nutrient-limited conditions. Our analysis also adds to the growth rate hypothesis, suggesting that P-rich biomolecules other than nucleic acids are important drivers of stoichiometric variability in Synechococcus. Lastly, by comparing our data with field observations, our study has important ecological relevance as it provides a framework for understanding and predicting elemental ratios in ocean regions where small phytoplankton like Synechococcus dominates.

Temporal Griffiths Phases

Disorder is an unavoidable ingredient of real systems. Spatial disorder generates Griffiths phases (GPs) which, in analogy to critical points, are characterized by a slow relaxation of the order parameter and divergences of quantities such as the susceptibility. However, these singularities appear in an extended region of the parameter space and not just at a (critical) point, i.e., there is generic scale invariance. Here, we study the effects of temporal disorder, focusing on systems with absorbing states. We show that for dimensions d≥2 there are Temporal Griffiths phases (TGPs) characterized by generic power-law scaling of some magnitudes and generic divergences of the susceptibility. TGPs turn out to be a counterpart of GPs, but with space and time playing reversed roles. TGPs constitute a unifying concept, shedding light on the nontrivial effects of temporal disorder.

Universality in Bacterial Colonies

The emergent spatial patterns generated by growing bacterial colonies have been the focus of intense study in physics during the last twenty years. Both experimental and theoretical investigations have made possible a clear qualitative picture of the different structures that such colonies can exhibit, depending on the medium on which they are growing. However, there are relatively few quantitative descriptions of these patterns. In this paper, we use a mechanistically detailed simulation framework to measure the scaling exponents associated with the advancing fronts of bacterial colonies on hard agar substrata, aiming to discern the universality class to which the system belongs. We show that the universal behavior exhibited by the colonies can be much richer than previously reported, and we propose the possibility of up to four different sub-phases within the medium-to-high nutrient concentration regime. We hypothesize that the quenched disorder that characterizes one of these sub-phases is an emergent property of the growth and division of bacteria competing for limited space and nutrients.

Quenched disorder forbids discontinuous transitions in nonequilibrium low-dimensional systems

Quenched disorder affects significantly the behavior of phase transitions. The Imry-Ma-Aizenman-Wehr-Berker argument prohibits first-order or discontinuous transitions and their concomitant phase coexistence in low-dimensional equilibrium systems in the presence of random fields. Instead, discontinuous transitions become rounded or even continuous once disorder is introduced. Here we show that phase coexistence and first-order phase transitions are also precluded in nonequilibrium low-dimensional systems with quenched disorder: discontinuous transitions in two-dimensional systems with absorbing states become continuous in the presence of quenched disorder. We also study the universal features of this disorder-induced criticality and find them to be compatible with the universality class of the directed percolation with quenched disorder. Thus, we conclude that first-order transitions do not exist in low-dimensional disordered systems, not even in genuinely nonequilibrium systems with absorbing states.