Spatial Self-organization Research Articles

Membrane‐Mediated Self‐Organization of Rod‐Like DNA Origami on Supported Lipid Bilayers (Adv. Mater. Interfaces 24/2021)

Membrane-Mediated Self-Organization of DNA Origami In article number 2101094, Alena Khmelinskaia, Eugene Petrov, and co-workers find surprisingly strong surface-mediated interparticle attraction of otherwise repulsive DNA origami particles on locally deformable lipid membranes, resulting in spatial self-organization. On the cover, the authors contrast two different worlds (macro and nano) with very different laws, however resulting in a similar phenomenon: the bundling of “logs”.

Multi-camera joint spatial self-organization for intelligent interconnection surveillance

The construction of smart city makes information interconnection play an increasingly important role in intelligent surveillance systems. Especially the interconnection among massive cameras is the key to realizing the evolution from current fragmented monitoring to interconnection surveillance. However, it remains a challenging problem in practical systems due to large sensor quantity, various camera types, and complex spatial layout. Aimed at this problem, this paper proposes a novel multi-camera joint spatial self-organization approach, which realizes interconnection surveillance by unifying cameras into one imaging space. Differing from existing back-end data association strategy, our method takes front-end data calibration as a breakthrough to relate surveillance data. Specifically, this paper first initials camera spatial parameter by sequence complementary feature integration. Through integrating complementarity and redundancy among sequence features, our method has robustness under scene dynamic changes and noise. Then, we propose a multi-camera joint optimization method based on common monitoring coverage correlation analysis to estimate a more accurate relative relationship. By leveraging the two strategies, the spatial relationship and visual data association across monitoring cameras are returned finally. Our system organizes all cameras into a unified imaging space by itself. Extensive experimental evaluations on an actual campus environment demonstrate our method achieves remarkable performance.

THE STUDY OF THE YARD SPACE AS A CONFLICT TERRITORY

The aspects of the mutual influence of the environment and local communities at various levels of spatial development are considered. Using the example of the city of Samara, it is studied how the social and demographic composition of the inhabitants has a direct impact on territorial relations within the district. The main trends and prospects of self-development for characteristic socio-spatial units of the city, as well as planning and administrative methods of preventing territorial conflicts are presented. The necessary conditions for spatial self-organization and the formation of viable urban communities are described.

Linking spatial self-organization to community assembly and biodiversity.

Temporal shifts to drier climates impose environmental stresses on plant communities that may result in community reassembly and threatened ecosystem services, but also may trigger self-organization in spatial patterns of biota and resources, which act to relax these stresses. The complex relationships between these counteracting processes - community reassembly and spatial self-organization - have hardly been studied. Using a spatio-temporal model of dryland plant communities and a trait-based approach, we study the response of such communities to increasing water-deficit stress. We first show that spatial patterning acts to reverse shifts from fast-growing species to stress-tolerant species, as well as to reverse functional-diversity loss. We then show that spatial self-organization buffers the impact of further stress on community structure. Finally, we identify multistability ranges of uniform and patterned community states and use them to propose forms of non-uniform ecosystem management that integrate the need for provisioning ecosystem services with the need to preserve community structure.

Maize genotype-specific exudation strategies: An adaptive mechanism to increase microbial activity in the rhizosphere

Plants stimulate microbial enzyme production in the rhizosphere, regulating soil organic matter decomposition and nutrient cycling. The availability of labile organic compounds (i.e. exudates) and water is the main prerequisite for such microbial activity and enzyme production, thus shaping the rhizosphere. Root morphology (i.e., root hairs) and exudate composition define the spatial distribution of properties and functions in the rhizosphere. However, the role of root architecture and exudate composition in this spatial self-organization of the rhizosphere remains unknown.We coupled three in situ imaging approaches: 14C imaging to localize exudates, soil zymography to analyze enzyme activity distribution, and neutron radiography for water fluxes to trace the spatial structure of the rhizosphere of three maize genotypes (wild-type, mutant with defective root-hair prolongation rth3, and mutant with reduced benzoxazinoid content in root exudates bx1). The co-localization of these three soil images revealed the pivotal role of both optimal water content (neutron radiography) and root exudation (14C imaging) for β-glucosidase production by the rhizosphere microbiome and its hydrolytic activity (zymography). Root hairs increased the exudate release and enlarged the spatial extent of increased β-glucosidase activity around the root axis by 35%, leading to a two-fold faster decomposition of 14C exudates compared to the mutant with defective root hairs. In contrast, benzoxazinoids suppressed β-glucosidase activity by 30%, reflecting decreased microbial activity, whereas their absence broadened the rhizosphere. Overall, root hairs in wild-type maize increased microbial activity (i.e. β-glucosidase production), whereas the benzoxazinoids in root exudates suppressed microorganisms.

Belowground feedbacks as drivers of spatial self-organization and community assembly.

Vegetation patterning in water-limited and other resource-limited ecosystems highlights spatial self-organization processes as potentially key drivers of community assembly. These processes provide insight into predictable landscape-level relationships between organisms and their abiotic environment in the form of regular and irregular patterns of biota and resources. However, two aspects have largely been overlooked; the roles played by plant - soil-biota feedbacks and allelopathy in spatial self-organization, and their potential contribution, along with plant-resource feedbacks, to community assembly through spatial self-organization. Here, we expand the drivers of spatial self-organization from a focus on plant-resource feedbacks to include plant - soil-biota feedbacks and allelopathy, and integrate concepts of nonlinear physics and community ecology to generate a new hypothesis. According to this hypothesis, below-ground processes can affect community assemblages through two types of spatial self-organization, global and local. The former occurs simultaneously across whole ecosystems, leading to self-organized patterns of biota, allelochemicals and resources, and niche partitioning. The latter occurs locally in ecotones, and determines ecotone structure and motion, invasion dynamics, and species coexistence. Studies of the two forms of spatial self-organization are important for understanding the organization of plant communities in drier climates which are likely to involve spatial patterning or re-patterning. Such studies are also important for developing new practices of ecosystem management, based on local manipulations at ecotones, to slow invasion dynamics or induce transitions from transitive to intransitive networks of interspecific interactions which increase species diversity.

The Use of Fractal Formalism for the Description of Microstructures Engineering Materials

In this paper, the structures of spatial self-organization of steels after thermos-cyclic exposure were studied, using the fractal formalism method. It is shown that the structures, observed after cyclic heat exposure, can be characterized by the presence of the invariance property of their structure at different scale levels.

Density-Dependent and Species-Specific Effects on Self-Organization Modulate the Resistance of Mussel Bed Ecosystems to Hydrodynamic Stress.

AbstractSelf-organized, regular spatial patterns emerging from local interactions among individuals enhance the ability of ecosystems to respond to environmental disturbances. Mussels self-organize to form large, regularly patterned biogenic structures that modify the biotic and abiotic environment and provide numerous ecosystem functions and services. We used two mussel species that form monospecific and mixed beds to investigate how species-specific behavior affects self-organization and resistance to wave stress. Perna perna has strong attachment but low motility, while Mytilus galloprovincialis shows the reverse. At low density, the less motile P. perna has limited spatial self-organization compared with M. galloprovincialis, while when coexisting, the two species formed random spatial patterns. At high density, the two species self-organized in similar ways, while when coexisting, patterns were less strong. Spatial pattern formations significantly shaped resistance to hydrodynamic stress. At low density, P. perna beds with strong attachment and M. galloprovincialis beds with strong spatial organization showed higher retention rates than mixed beds. At high density, the presence of strongly attached P. perna significantly increased retention in mixed and P. perna beds compared with M. galloprovincialis beds. Our study emphasizes the importance of the interplay of species-specific behaviors to spatial self-organization and stress tolerance in natural communities.

Causes and consequences of pattern diversification in a spatially self-organizing microbial community

Surface-attached microbial communities constitute a vast amount of life on our planet. They contribute to all major biogeochemical cycles, provide essential services to our society and environment, and have important effects on human health and disease. They typically consist of different interacting genotypes that arrange themselves non-randomly across space (referred to hereafter as spatial self-organization). While spatial self-organization is important for the functioning, ecology, and evolution of these communities, the underlying determinants of spatial self-organization remain unclear. Here, we performed a combination of experiments, statistical modeling, and mathematical simulations with a synthetic cross-feeding microbial community consisting of two isogenic strains. We found that two different patterns of spatial self-organization emerged at the same length and time scales, thus demonstrating pattern diversification. This pattern diversification was not caused by initial environmental heterogeneity or by genetic heterogeneity within populations. Instead, it was caused by nongenetic heterogeneity within populations, and we provide evidence that the source of this nongenetic heterogeneity is local differences in the initial spatial positionings of individuals. We further demonstrate that the different patterns exhibit different community-level properties; namely, they have different expansion speeds. Together, our results demonstrate that pattern diversification can emerge in the absence of initial environmental heterogeneity or genetic heterogeneity within populations and can affect community-level properties, thus providing novel insights into the causes and consequences of microbial spatial self-organization.

Viscoelastic control of spatiotemporal order in bacterial active matter.

Active matter consists of units that generate mechanical work by consuming energy1. Examples include living systems (such as assemblies of bacteria2-5 and biological tissues6,7), biopolymers driven by molecular motors8-11 and suspensions of synthetic self-propelled particles12-14. A central goal is to understand and control the self-organization of active assemblies in space and time. Most active systems exhibit either spatial order mediated by interactions that coordinate the spatial structure and the motion of active agents12,14,15 or the temporal synchronization of individual oscillatory dynamics2. The simultaneous control of spatial and temporal organization is more challenging and generally requires complex interactions, such as reaction-diffusion hierarchies16 or genetically engineered cellular circuits2. Here we report a simple technique to simultaneously control the spatial and temporal self-organization of bacterial active matter. We confine dense active suspensions of Escherichia coli cells and manipulate a single macroscopic parameter-namely, the viscoelasticity of the suspending fluid- through the addition of purified genomic DNA. This reveals self-driven spatial and temporal organization in the form of a millimetre-scale rotating vortex with periodically oscillating global chirality of tunable frequency, reminiscent of a torsional pendulum. By combining experiments with an active-matter model, we explain this behaviour in terms of the interplay between active forcing and viscoelastic stress relaxation. Our findings provide insight into the influence of bacterial motile behaviour in complex fluids, which may be of interest in health- and ecology-related research, and demonstrate experimentally that rheological properties can be harnessed to control active-matter flows17,18. We envisage that our millimetre-scale, tunable, self-oscillating bacterial vortex may be coupled to actuation systems to act a 'clock generator' capable of providing timing signals for rhythmic locomotion of soft robots and for programmed microfluidic pumping19, for example, by triggering the action of a shift register in soft-robotic logic devices20.

Spatial Self-Organization of Laser-Induced Graphite Nanonetwork in Diamond

The interior of spontaneously growing graphitized microstructures formed in diamond bulk by picosecond laser pulses has been studied. Longitudinal and cross sections of microstructures, prepared using mechanical polishing and focused ion beam, have been studied by Raman spectroscopy and scanning electron–ion microscopy. The laser irradiation of diamond bulk is found to induce formation of a graphite nanonetwork in the processed region and its subsequent spontaneous growth towards the laser beam by a distance of ~60 µm. The graphite nanonetwork consists of many ~130-nm-thick graphite sheets clustered into segments. It is shown that the thickness of graphite sheets decreases with a decrease in the laser fluence at the modification front, whereas the segment length (~2.6 µm) is independent of the laser fluence at the modification front. A three-dimensional structural model of microsegment has been constructed based on the analysis of several longitudinal and cross sections of microstructures. The mechanism of graphite nanosheet clustering into microsegments is discussed.

Spatial Self-Organization as a New Perspective on Cold-Water Coral Mound Development

Cold-water corals build extensive reefs on the seafloor that are oases of biodiversity, biomass, and organic matter processing rates. The reefs baffle sediments, and when coral growth and sedimentation outweigh ambient sedimentation, carbonate mounds of tens to hundreds of meters high and several kilometres wide can form. Because coral mounds form over ten-thousands of years, their development process remains elusive. While several environmental factors influence mound development, the mounds also have a major impact on their environment. This feedback between environment and mounds, and how this drives mound development is the focus of this paper. Based on the similarity of spatial coral mound patterns and patterns in self-organized ecosystems, we provide a new perspective on coral mound development. In accordance with the theory of self-organization through scale-dependent feedbacks, we first elicit the processes that are known to affect mound development, and might cause scale-dependent feedbacks. Then we demonstrate this concept with model output from a study on the Logachev area, SW Rockall Trough margin. Spatial patterns in mound provinces are the result of a complex set of interacting processes. Spatial self-organisation provides a framework in which to place and compare these processes, so as to assess if and how they contribute to pattern formation in coral mounds.

The role of spatial self-organization in the design of agroforestry systems.

The development of sustainable agricultural systems in drylands is currently a crucial issue in the context of mitigating the outcomes of population growth under the conditions of climatic changes. The need to meet the growing demand for food, fodder, and fuel, together with the hazards due to climate change, requires cross-disciplinary studies of ways to increase livelihood while minimizing the impact on the environment. Practices of agroforestry systems, in which herbaceous species are intercropped between rows of woody species plantations, have been shown to mitigate several of the predicaments of climatic changes. Focusing on agroforestry in drylands, we address the question of how we can improve the performance of agroforestry systems in those areas. As vegetation in drylands tends to self-organize in various patterns, it seems essential to explore the various patterns that agroforestry systems tend to form and their impact on the performance of these systems in terms of biomass production, resilience to droughts, and water use efficiency. We use a two-soil-layers vegetation model to study the relationship between deep-rooted woody vegetation and shallow herbaceous vegetation, and explore how self-organization in different spatial patterns influences the performance of agroforestry systems. We focus on three generic classes of patterns, spots, gaps, and stripes, assess these patterns using common metrics for agroforestry systems, and examine their resilience to droughts. We show that in contrast to the widespread practice of planting the woody and herbaceous species in alternating rows, that is, in a stripe pattern, planting the woody species in hexagonal spot patterns may increase the system’s resilience to droughts. Furthermore, hexagonal spot patterns reduce the suppression of herbs growth by the woody vegetation, therefore maintaining higher crop yields. We conclude by discussing some limitations of this study and their significance.

Self-organization of river vegetation leads to emergent buffering of river flows and water levels.

Global climate change is expected to impact hydrodynamic conditions in stream ecosystems. There is limited understanding of how stream ecosystems interact and possibly adapt to novel hydrodynamic conditions. Combining mathematical modelling with field data, we demonstrate that bio-physical feedback between plant growth and flow redistribution triggers spatial self-organization of in-channel vegetation that buffers for changed hydrological conditions. The interplay of vegetation growth and hydrodynamics results in a spatial separation of the stream into densely vegetated, low-flow zones divided by unvegetated channels of higher flow velocities. This self-organization process decouples both local flow velocities and water levels from the forcing effect of changing stream discharge. Field data from two lowland, baseflow-dominated streams support model predictions and highlight two important stream-level emergent properties: vegetation controls flow conveyance in fast-flowing channels throughout the annual growth cycle, and this buffering of discharge variations maintains water depths and wetted habitat for the stream community. Our results provide important evidence of how plant-driven self-organization allows stream ecosystems to adapt to changing hydrological conditions, maintaining suitable hydrodynamic conditions to support high biodiversity.

General model for vegetation patterns including rhizome growth

Vegetation patterns, a natural phenomenon observed worldwide, are typically driven by spatially distributed feedback. However, the spatial colonization mechanisms of clonal plants, driven by the growth of a rhizome, are usually not considered in prototypical models. Here we propose a general equation for the vegetation density that includes all main clonal-growth features as well as the essential ingredients leading to spatial self-organization. This generic model reproduces the phase diagram of a fully detailed model of clonal growth. The relation of each term of the model with the mechanisms of clonal growth is discussed.

Post-traumatic spatial self-organization of mobile populations

Since 2012, and particularly since 2014, instability and wars in North African countries and the Middle East have brought a wave of refugees, trying to flee from violence in their countries, to Europe. They usually go north, crossing the Mediterranean towards Italy, or the Aegean, going west to the Greek islands. In their quest for a safe refuge, a significant number drown or disappear. The rest reach in Europe carrying their traumatic experiences with them, and face immediate humanitarian needs. A major task for host cities is to provide shelter for the refugees, taking into consideration the influence of their psychological trauma on local societies. This complex task, which combines technical, economic, social, psychological, and political dimensions – simultaneously targeted on two social groups – constitutes the ‘post-traumatic urbanism’ which intervenes in the recreating of the refugees’ spatial and social networks in the host city. This paper discusses how the complex issue of post-traumatic housing triggers spatial self-organization by the refugees, in contrast to the ‘official’ provisions from host states, through the lens of complex adaptive theory (resilience). This article examines the features of refugee housing in Athens and Thessaloniki through qualitative research, quantitative methods and participatory observation. Through this study, it is highlighted that the post-trauma self-organization of mobile populations is a process of gaining dignity and self-respect in a new and often hostile environment, and a tool for spatial and social resilience.

Interaction-dependent effects of surface structure on microbial spatial self-organization.

Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Specialized cytonemes induce self-organization of stem cells

Spatial cellular organization is fundamental for embryogenesis. Remarkably, coculturing embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) recapitulates this process, forming embryo-like structures. However, mechanisms driving ESC-TSC interaction remain elusive. We describe specialized ESC-generated cytonemes that react to TSC-secreted Wnts. Cytoneme formation and length are controlled by actin, intracellular calcium stores, and components of the Wnt pathway. ESC cytonemes select self-renewal-promoting Wnts via crosstalk between Wnt receptors, activation of ionotropic glutamate receptors (iGluRs), and localized calcium transients. This crosstalk orchestrates Wnt signaling, ESC polarization, ESC-TSC pairing, and consequently synthetic embryogenesis. Our results uncover ESC-TSC contact-mediated signaling, reminiscent of the glutamatergic neuronal synapse, inducing spatial self-organization and embryonic cell specification.

Intraspecific competition in models for vegetation patterns: Decrease in resilience to aridity and facilitation of species coexistence

Patterned vegetation is a characteristic feature of many dryland ecosystems. While plant densities on the ecosystem-wide scale are typically low, a spatial self-organisation principle leads to the occurrence of alternating patches of high biomass and patches of bare soil. Nevertheless, intraspecific competition dynamics other than competition for water over long spatial scales are commonly ignored in mathematical models for vegetation patterns. In this paper, I address the impact of local intraspecific competition on a modelling framework for banded vegetation patterns. Firstly, I show that in the context of a single-species model, neglecting local intraspecific competition leads to an overestimation of a patterned ecosystem’s resilience to increases in aridity. Secondly, in the context of a multispecies model, I argue that local intraspecific competition is a key element in the successful capture of species coexistence in model solutions representing a vegetation pattern. For both models, a detailed bifurcation analysis is presented to analyse the onset, existence and stability of patterns. Besides the strengths of local intraspecific competition, also the difference between two species has a significant impact on the bifurcation structure, providing crucial insights into the complex ecosystem dynamics. Predictions on future ecosystem dynamics presented in this paper, especially on pattern onset and pattern stability, can aid the development of conservation programs.

Patterning in Mussel Beds Explained by the Interplay of Multi-Level Selection and Spatial Self-Organization

Cooperation, ubiquitous in nature, is difficult to explain from an evolutionary perspective. Many modelling studies strive to resolve this challenge, but their simplifying assumptions on population and interaction structure are rarely met in ecological settings. Here we use a modelling approach that includes more ecological detail to investigate evolution of cooperation in spatially self-organized mussel beds. Mussels cooperate with each other through aggregative movement and attachment using byssal threads. These cooperative behaviours shape the spatial structure of the mussel bed, which can range from scattered distributions to labyrinth-like patterns and dense mussel clumps. The spatial pattern in turn impacts an individual’s fitness at two levels: (i) proper attachment to neighbouring individuals decreases predation risk, and (ii) attachment to a sufficiently large group prevents dislodgement by wave stress. Without this second level of selection, our simulations do typically not result in evolutionary attractors that lead to the labyrinth-like spatial patterns that are characteristic for natural mussel beds. Yet, when group-level selection is included, labyrinth-like patterns emerge under a wide range of conditions. Our model demonstrates that multiple selection factors working at different spatial scales – predation of individuals and dislodgement of entire mussel clumps – combinedly determine evolution of cooperative traits in mussels and thereby result in emergence of the labyrinth-like spatial patterns that we observe in natural mussel beds.