Chaotic turnover of rare and abundant species in a strongly interacting model community.

The composition of ecological communities varies not only between different locations but also in time. Understanding the fundamental processes that drive species toward rarity or abundance is crucial to assessing ecosystem resilience and adaptation to changing environmental conditions. In plankton communities in particular, large temporal fluctuations in species abundances have been associated with chaotic dynamics. On the other hand, microbial diversity is overwhelmingly sustained by a "rare biosphere" of species with very low abundances. We consider here the possibility that interactions within a species-rich community can relate both phenomena. We use a Lotka-Volterra model with weak immigration and strong, disordered, and mostly competitive interactions between hundreds of species to bridge single-species temporal fluctuations and abundance distribution patterns. We highlight a generic chaotic regime where a few species at a time achieve dominance but are continuously overturned by the invasion of formerly rare species. We derive a focal-species model that captures the intermittent boom-and-bust dynamics that every species undergoes. Although species cannot be treated as effectively uncorrelated in their abundances, the community's effect on a focal species can nonetheless be described by a time-correlated noise characterized by a few effective parameters that can be estimated from time series. The model predicts a nonunitary exponent of the power-law abundance decay, which varies weakly with ecological parameters, consistent with observation in marine protist communities. The chaotic turnover regime is thus poised to capture relevant ecological features of species-rich microbial communities.

Artificial selection of communities drives the emergence of structured interactions.

Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level functions of interest. These experiments typically involve selection acting on populations of communities, each of which is composed of multiple species. If numerical simulations started to explore the evolutionary dynamics of this complex, multi-scale system, a comprehensive theoretical understanding of the process of artificial selection of communities is still lacking. Here, we propose a general model for the evolutionary dynamics of communities composed of a large number of interacting species, described by disordered generalised Lotka-Volterra equations. Our analytical and numerical results reveal that selection for scalar community functions leads to the emergence, along an evolutionary trajectory, of a low-dimensional structure in an initially featureless interaction matrix. Such structure reflects the combination of the properties of the ancestral community and of the selective pressure. Our analysis determines how the speed of adaptation scales with the system parameters and the abundance distribution of the evolved communities. Artificial selection for larger total abundance is thus shown to drive increased levels of mutualism and interaction diversity. Inference of the interaction matrix is proposed as a method to assess the emergence of structured interactions from experimentally accessible measures.

Aggregative cycles evolve as a solution to conflicts in social investment.

Multicellular organization is particularly vulnerable to conflicts between different cell types when the body forms from initially isolated cells, as in aggregative multicellular microbes. Like other functions of the multicellular phase, coordinated collective movement can be undermined by conflicts between cells that spend energy in fuelling motion and 'cheaters' that get carried along. The evolutionary stability of collective behaviours against such conflicts is typically addressed in populations that undergo extrinsically imposed phases of aggregation and dispersal. Here, via a shift in perspective, we propose that aggregative multicellular cycles may have emerged as a way to temporally compartmentalize social conflicts. Through an eco-evolutionary mathematical model that accounts for individual and collective strategies of resource acquisition, we address regimes where different motility types coexist. Particularly interesting is the oscillatory regime that, similarly to life cycles of aggregative multicellular organisms, alternates on the timescale of several cell generations phases of prevalent solitary living and starvation-triggered aggregation. Crucially, such self-organized oscillations emerge as a result of evolution of cell traits associated to conflict escalation within multicellular aggregates.

The Crohn's disease-associated Escherichia coli strain LF82 relies on SOS and stringent responses to survive, multiply and tolerate antibiotics within macrophages.

Adherent Invasive Escherichia coli (AIEC) strains recovered from Crohn's disease lesions survive and multiply within macrophages. A reference strain for this pathovar, AIEC LF82, forms microcolonies within phagolysosomes, an environment that prevents commensal E. coli multiplication. Little is known about the LF82 intracellular growth status, and signals leading to macrophage intra-vacuolar multiplication. We used single-cell analysis, genetic dissection and mathematical models to monitor the growth status and cell cycle regulation of intracellular LF82. We found that within macrophages, bacteria may replicate or undergo non-growing phenotypic switches. This switch results from stringent response firing immediately after uptake by macrophages or at later stages, following genotoxic damage and SOS induction during intracellular replication. Importantly, non-growers resist treatment with various antibiotics. Thus, intracellular challenges induce AIEC LF82 phenotypic heterogeneity and non-growing bacteria that could provide a reservoir for antibiotic-tolerant bacteria responsible for relapsing infections.

Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase.

Observations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases, and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacterium Pseudomonas fluorescens SBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation in carB that decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a preexisting but hitherto unrecognized phenotypic switch. Genetic components surrounding bifurcation of UTP flux toward DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses-and based on a combination of genetics, transcriptomics, biochemistry, and mathematical modeling-we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a positively autoregulated activator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a program that determines stochastic entry into a semiquiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.

Differential adhesion between moving particles as a mechanism for the evolution of social groups.

The evolutionary stability of cooperative traits, that are beneficial to other individuals but costly to their carrier, is considered possible only through the establishment of a sufficient degree of assortment between cooperators. Chimeric microbial populations, characterized by simple interactions between unrelated individuals, restrain the applicability of standard mechanisms generating such assortment, in particular when cells disperse between successive reproductive events such as happens in Dicyostelids and Myxobacteria. In this paper, we address the evolutionary dynamics of a costly trait that enhances attachment to others as well as group cohesion. By modeling cells as self-propelled particles moving on a plane according to local interaction forces and undergoing cycles of aggregation, reproduction and dispersal, we show that blind differential adhesion provides a basis for assortment in the process of group formation. When reproductive performance depends on the social context of players, evolution by natural selection can lead to the success of the social trait, and to the concomitant emergence of sizeable groups. We point out the conditions on the microscopic properties of motion and interaction that make such evolutionary outcome possible, stressing that the advent of sociality by differential adhesion is restricted to specific ecological contexts. Moreover, we show that the aggregation process naturally implies the existence of non-aggregated particles, and highlight their crucial evolutionary role despite being largely neglected in theoretical models for the evolution of sociality.

Fluid dynamical niches of phytoplankton types.

The biogeochemical role of phytoplanktonic organisms strongly varies from one plankton type to another, and their relative abundance and distribution have fundamental consequences at the global and climatological scales. In situ observations find dominant types often associated to specific physical and chemical water properties. However, the mechanisms and spatiotemporal scales by which marine ecosystems are organized are largely not known. Here we investigate the spatiotemporal organization of phytoplankton communities by combining multisatellite data, notably high-resolution ocean-color maps of dominant types and altimetry-derived Lagrangian diagnostics of the surface transport. We find that the phytoplanktonic landscape is organized in (sub-)mesoscale patches (10-100 km) of dominant types separated by physical fronts induced by horizontal stirring. These physical fronts delimit niches supported by water masses of similar history and whose lifetimes are comparable with the timescale of the bloom onset (few weeks). The resonance between biological activity and physical processes suggest that the spatiotemporal (sub-)mesoscales associated to stirring are determinant in the observation and modeling of marine ecosystems.

Single-cell phenotypic plasticity modulates social behavior in Dictyostelium discoideum.

In Dictyostelium chimeras, "cheaters" are strains that positively bias their contribution to the pool of spores, i.e., the reproductive cells resulting from development. On evolutionary time scales, the selective advantage; thus, gained by cheaters is predicted to undermine collective functions whenever social behaviors are genetically determined. Genotypes; however, are not the sole determinant of spore bias, but the relative role of genetic and plastic differences in evolutionary success is unclear. Here, we study chimeras composed of cells harvested in different phases of population growth. We show that such heterogeneity induces frequency-dependent, plastic variation in spore bias. In genetic chimeras, the magnitude of such variation is not negligible and can even reverse the classification of a strain's social behavior. Our results suggest that differential cell mechanical properties can underpin, through biases emerging during aggregation, a "lottery" in strains' reproductive success that may counter the evolution of cheating.

Evolving social behavior through selection of single-cell adhesion in Dictyostelium discoideum.

The social amoeba Dictyostelium discoideum commonly forms chimeric fruiting bodies. Genetic variants that produce a higher proportion of spores are predicted to undercut multicellular organization unless cooperators assort positively. Cell adhesion is considered a primary factor driving such assortment, but evolution of adhesion has not been experimentally connected to changes in social performance. We modified by experimental evolution the efficiency of individual cells in attaching to a surface. Surprisingly, evolution appears to have produced social cooperators irrespective of whether stronger or weaker adhesion was selected. Quantification of reproductive success, cell-cell adhesion, and developmental patterns, however, revealed two distinct social behaviors, as captured when the classical metric for social success is generalized by considering clonal spore production. Our work shows that cell mechanical interactions can constrain the evolution of development and sociality in chimeras and that elucidation of proximate mechanisms is necessary to understand the ultimate emergence of multicellular organization.

Dynamical quorum sensing: Population density encoded in cellular dynamics.

Mutual synchronization by exchange of chemicals is a mechanism for the emergence of collective dynamics in cellular populations. General theories exist on the transition to coherence, but no quantitative, experimental demonstration has been given. Here, we present a modeling and experimental analysis of cell-density-dependent glycolytic oscillations in yeast. We study the disappearance of oscillations at low cell density and show that this phenomenon occurs synchronously in all cells and not by desynchronization, as previously expected. This study identifies a general scenario for the emergence of collective cellular oscillations and suggests a quorum-sensing mechanism by which the cell density information is encoded in the intracellular dynamical state.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity.

Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.

Ubiquitous abundance distribution of non-dominant plankton across the global ocean.

Marine plankton populate 70% of Earth's surface, providing the energy that fuels ocean food webs and contributing to global biogeochemical cycles. Plankton communities are extremely diverse and geographically variable, and are overwhelmingly composed of low-abundance species. The role of this rare biosphere and its ecological underpinnings are however still unclear. Here, we analyse the extensive dataset generated by the Tara Oceans expedition for marine microbial eukaryotes (protists) and use an adaptive algorithm to explore how metabarcoding-based abundance distributions vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant operational taxonomic units, which comprise over 99% of local richness, is commonly governed by a power-law. Despite the high spatial turnover in species composition, the power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Such striking regularity suggests that the assembly of plankton communities in the dynamic and highly variable ocean environment is governed by large-scale ubiquitous processes. Understanding their origin and impact on plankton ecology will be important for evaluating the resilience of marine biodiversity in a changing ocean.

Estimating planktonic diversity through spatial dominance patterns in a model ocean.

In the open ocean, the observation and quantification of biodiversity patterns is challenging. Marine ecosystems are indeed largely composed by microbial planktonic communities whose niches are affected by highly dynamical physico-chemical conditions, and whose observation requires advanced methods for morphological and molecular classification. Optical remote sensing offers an appealing complement to these in-situ techniques. Global-scale coverage at high spatiotemporal resolution is however achieved at the cost of restrained information on the local assemblage. Here, we use a coupled physical and ecological model ocean simulation to explore one possible metrics for comparing measures performed on such different scales. We show that a large part of the local diversity of the virtual plankton ecosystem - corresponding to what accessible by genomic methods - can be inferred from crude, but spatially extended, information - as conveyed by remote sensing. Shannon diversity of the local community is indeed highly correlated to a 'seascape' index, which quantifies the surrounding spatial heterogeneity of the most abundant functional group. The error implied in drastically reducing the resolution of the plankton community is shown to be smaller in frontal regions as well as in regions of intermediate turbulent energy. On the spatial scale of hundreds of kms, patterns of virtual plankton diversity are thus largely sustained by mixing communities that occupy adjacent niches. We provide a proof of principle that in the open ocean information on spatial variability of communities can compensate for limited local knowledge, suggesting the possibility of integrating in-situ and satellite observations to monitor biodiversity distribution at the global scale.

The evolution of adhesiveness as a social adaptation.

Cellular adhesion is a key ingredient to sustain collective functions of microbial aggregates. Here, we investigate the evolutionary origins of adhesion and the emergence of groups of genealogically unrelated cells with a game-theoretical model. The considered adhesiveness trait is costly, continuous and affects both group formation and group-derived benefits. The formalism of adaptive dynamics reveals two evolutionary stable strategies, at each extreme on the axis of adhesiveness. We show that cohesive groups can evolve by small mutational steps, provided the population is already endowed with a minimum adhesiveness level. Assortment between more adhesive types, and in particular differential propensities to leave a fraction of individuals ungrouped at the end of the aggregation process, can compensate for the cost of increased adhesiveness. We also discuss the change in the social nature of more adhesive mutations along evolutionary trajectories, and find that altruism arises before directly beneficial behavior, despite being the most challenging form of cooperation.

Quasi-planktonic behavior of foraging top marine predators.

Monitoring marine top predators is fundamental for assessing the health and functioning of open ocean ecosystems. Although recently tracking observations have substantially increased, factors determining the horizontal exploration of the ocean by marine predators are still largely unknown, especially at the scale of behavioral switches (1-100 km, days-weeks). It is commonly assumed that the influence of water movement can be neglected for animals capable of swimming faster than the current. Here, we challenge this assumption by combining the use of biologging (GPS and accelerometry), satellite altimetry and in-situ oceanographic data (ADCP and drifting buoys) to investigate the effect of the mesoscale ocean dynamics on a marine predator, the southern elephant seal. A Lagrangian approach reveals that trajectories of elephant seals are characterized by quasi-planktonic bouts where the animals are horizontally drifting. These bouts correspond to periods of increased foraging effort, indicating that in the quasi-planktonic conditions energy is allocated to diving and chasing, rather than in horizontal search of favourable grounds. These results suggest that mesoscale features like eddies and fronts may act as a focal points for trophic interactions not only by bottom-up modulation of nutrient injection, but also by directly entraining horizontal displacements of the upper trophic levels.

Nascent multicellular life and the emergence of individuality.

The evolution of multicellular organisms from unicellular ancestors involves a shift in the level at which selection operates. It is usual to think about this shift in terms of the emergence of traits that cause heritable differences in reproductive output at the level of nascent collectives. Defining these traits and the causes of their origin lies at the heart of understanding the evolution of multicellular life. In working toward a mechanistic, take-nothing-for-granted account, we begin by recognizing that the standard Lewontin formulation of properties necessary and sufficient for evolution by natural selection does not necessarily encompass Darwinian evolution in primitive collectives where parent-offspring relationships may have been poorly defined. This, we suggest, limits the ability to conceptualize and capture the earliest manifestations of Darwinian properties. By way of solution we propose a relaxed interpretation of Lewontin's conditions and present these in the form of a set of necessary requirements for evolution by natural selection based upon the establishment of genealogical connections between recurrences of collectives. With emphasis on genealogy - as opposed to reproduction - it is possible to conceive selection acting on collectives prior to any manifestation of heritable variance in fitness. Such possibility draws attention to the evolutionary emergence of traits that strengthen causal relationships between recurrences - traits likely to underpin the emergence of forms of multiplication that establish parent-offspring relationships. Application of this framework to collectives of marginal status, particularly those whose recurrence is not defined by genealogy, makes clear that change at the level of collectives need not arise from selection acting at the higher level. We conclude by outlining applicability of our framework to loosely defined collectives of cells, such as those comprising the slugs of social amoeba and microbes that constitute the human microbiome.

Group formation and the evolution of sociality.

In spite of its intrinsic evolutionary instability, altruistic behavior in social groups is widespread in nature, spanning from organisms endowed with complex cognitive abilities to microbial populations. In this study, we show that if social individuals have an enhanced tendency to form groups and fitness increases with group cohesion, sociality can evolve and be maintained in the absence of actively assortative mechanisms such as kin recognition or nepotism toward other carriers of the social gene. When explicitly taken into account in a game-theoretical framework, the process of group formation qualitatively changes the evolutionary dynamics with respect to games played in groups of constant size and equal grouping tendencies. The evolutionary consequences of the rules underpinning the group size distribution are discussed for a simple model of microbial aggregation by differential attachment, indicating a way to the evolution of sociality bereft of peer recognition.

Can we detect oceanic biodiversity hotspots from space?

Understanding the variability of marine biodiversity is a central issue in microbiology. Current observational programs are based on in situ studies, but their implementation at the global scale is particularly challenging, owing to the ocean extent, its temporal variability and the heterogeneity of the data sources on which compilations are built. Here, we explore the possibility of identifying phytoplanktonic biodiversity hotspots from satellite. We define a Shannon entropy index based on patchiness in ocean color bio-optical anomalies. This index provides a high resolution (1 degree) global coverage. It shows a relation to temperature and mid-latitude maxima in accordance with those previously evidenced in microbiological biodiversity model and observational studies. Regional maxima are in remarkable agreement with several known biodiversity hotspots for plankton organisms and even for higher levels of the marine trophic chain, as well as with some in situ planktonic biodiversity estimates (from Atlantic Meridional Transect cruise). These results encourage to explore marine biodiversity with a coordinated effort of the molecular, ecological and remote sensing communities.

Frigatebird behaviour at the ocean-atmosphere interface: integrating animal behaviour with multi-satellite data.

Marine top predators such as seabirds are useful indicators of the integrated response of the marine ecosystem to environmental variability at different scales. Large-scale physical gradients constrain seabird habitat. Birds however respond behaviourally to physical heterogeneity at much smaller scales. Here, we use, for the first time, three-dimensional GPS tracking of a seabird, the great frigatebird (Fregata minor), in the Mozambique Channel. These data, which provide at the same time high-resolution vertical and horizontal positions, allow us to relate the behaviour of frigatebirds to the physical environment at the (sub-)mesoscale (10-100 km, days-weeks). Behavioural patterns are classified based on the birds' vertical displacement (e.g. fast/slow ascents and descents), and are overlaid on maps of physical properties of the ocean-atmosphere interface, obtained by a nonlinear analysis of multi-satellite data. We find that frigatebirds modify their behaviours concurrently to transport and thermal fronts. Our results suggest that the birds' co-occurrence with these structures is a consequence of their search not only for food (preferentially searched over thermal fronts) but also for upward vertical wind. This is also supported by their relationship with mesoscale patterns of wind divergence. Our multi-disciplinary method can be applied to forthcoming high-resolution animal tracking data, and aims to provide a mechanistic understanding of animals' habitat choice and of marine ecosystem responses to environmental change.