Lubricating Bacteria Model for Branching growth of Bacterial Colonies

Various bacterial strains (e.g. strains belonging to the genera Bacillus, Paenibacillus, Serratia and Salmonella) exhibit colonial branching patterns during growth on poor semi-solid substrates. These patterns reflect the bacterial cooperative self-organization. Central part of the cooperation is the collective formation of lubricant on top of the agar which enables the bacteria to swim. Hence it provides the colony means to advance towards the food. One method of modeling the colonial development is via coupled reaction-diffusion equations which describe the time evolution of the bacterial density and the concentrations of the relevant chemical fields. This idea has been pursued by a number of groups. Here we present an additional model which specifically includes an evolution equation for the lubricant excreted by the bacteria. We show that when the diffusion of the fluid is governed by nonlinear diffusion coefficient branching patterns evolves. We study the effect of the rates of emission and decomposition of the lubricant fluid on the observed patterns. The results are compared with experimental observations. We also include fields of chemotactic agents and food chemotaxis and conclude that these features are needed in order to explain the observations.Comment: 1 latex file, 16 jpeg files, submitted to Phys. Rev.

Studies of Bacterial Branching Growth using Reaction-Diffusion Models for Colonial Development

Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of communication, regulation and control employed during colonial development. One method of modeling is the continuous, or coupled reaction-diffusion approach, in which continuous time evolution equations describe the bacterial density and the concentration of the relevant chemical fields. In the context of branching growth, this idea has been pursued by a number of groups. We present an additional model which includes a lubrication fluid excreted by the bacteria. We also add fields of chemotactic agents to the other models. We then present a critique of this whole enterprise with focus on the models' potential for revealing new biological features.Comment: 1 latex file, 40 gif/jpeg files (compressed into tar-gzip). Physica A, in pres

A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the Wrinkly Spreader

Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm—forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments

Examining c-di-GMP and possible quorum sensing regulation in Pseudomonas fluorescens SBW25:links between intra and inter-cellular regulation benefits community cooperative activities such as biofilm formation

Bacterial success in colonizing complex environments requires individual response to micro-scale conditions as well as community-level cooperation to produce large-scale structures such as biofilms. Connecting individual and community responses could be achieved by linking the intracellular sensory and regulatory systems mediated by bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) and other compounds of individuals with intercellular quorum sensing (QS) regulation controlling populations. There is growing evidence to suggest that biofilm formation by many pseudomonads is regulated by both intra and intercellular systems, though in the case of the model Pseudomonas fluorescens SBW25 Wrinkly Spreader in which mutations increasing c-di-GMP levels result in the production of a robust cellulose-based air-liquid interface biofilm, no evidence for the involvement of QS regulation has been reported. However, our recent review of the P. fluorescens SBW25 genome has identified a potential QS regulatory pathway and other QS–associated genes linked to c-di-GMP homeostasis, and QS signal molecules have also been identified in culture supernatants. These findings suggest a possible link between c-di-GMP and QS regulation in P. fluorescens SBW25 which might allow a more sophisticated and responsive control of cellulose production and biofilm formation when colonising the soil and plant-associated environments P. fluorescens SBW25 normally inhabits.Анализ ц-ди-ГМФ и возможного чувства кворума у Pseudomonas fluorescens SBW 25: связь между внутри и межклеточной регуляцией способствует кооперативному поведению в сообществе и формированию биоплёнкиУспешность бактериальной колонизации сложных экониш требует индивидуального ответа на изменения условий на микроуровне равно как и кооперации на уровне сообщества для продукции таких крупно масштабных структур как биоплёнки. Координация индивидуальных ответ ов и ответов сообщества может быть достигнута путем связывания внутриклеточных сенсорных и регуляторных систем, опосредуемых бис-(3',5')-циклическим димерным гуанозинмонофосфатом (ц-ди-ГМФ) и другими соединениями индивидуумов с межклеточной регуляцией - чувством кворума (ЧК), контролирующем популяци ю. Накапливается всё больше доказательств того, что формирование биопленки многими псевдомонадами регулируется как внутри клеточными, так и меж клеточными регуляторными системами, хотя в случае модельной Pseudomonas fluorescens SBW25 Wrinkly Spreader, у которой мутации, повышающ ие уровни ц-ди-ГМФ, приводят к созданию прочной целлюлозной биоплёнки на границе раздела фаз воздух-жидкость, не было обнаружено ни ка кого свидетельства вовлечения кворум-зависимой регуляции. Однако наш недавний обзор генома P. fluorescens SBW25 выявил потенциальный ЧК-зависимый регуляторный пу ть и другие ЧК-зависимые гены, связанные с гомеостазом ц-ди-ГМФ, а молекулы ЧК-сигналинга были идентифицированы в культуре. Эти данные свидетельствуют о возможной связи между ц-ди-ГМФ-регуляцией и ЧК у P. fluorescens SBW25, что позволяет более сложный и гибкий контроль над продукцией целлюлозы и образовани ем биопленки при колонизации почв и экониш, aссоциированных с растениям и, - естественными средами обитания P. fluorescens SBW25

Modeling branching and chiral colonial patterning of lubricating bacteria

In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via extra-membrane polymers, collective production of extracellular "wetting" fluid for movement on hard surfaces, long range chemical signaling such as quorum sensing and chemotactic (bias of movement according to gradient of chemical agent) signaling, collective activation and deactivation of genes and even exchange of genetic material. Utilizing these capabilities, the colonies develop complex spatio-temporal patterns in response to adverse growth conditions. We present a wealth of branching and chiral patterns formed during colonial development of lubricating bacteria (bacteria which produce a wetting layer of fluid for their movement). Invoking ideas from pattern formation in non-living systems and using ``generic'' modeling we are able to reveal novel survival strategies which account for the salient features of the evolved patterns. Using the models, we demonstrate how communication leads to self-organization via cooperative behavior of the cells. In this regard, pattern formation in microorganisms can be viewed as the result of the exchange of information between the micro-level (the individual cells) and the macro-level (the colony). We mainly review known results, but include a new model of chiral growth, which enables us to study the effect of chemotactic signaling on the chiral growth. We also introduce a measure for weak chirality and use this measure to compare the results of model simulations with experimental observations.Comment: 50 pages, 24 images in 44 GIF/JPEG files, Proceedings of IMA workshop: Pattern Formation and Morphogenesis (1998

Functional plasticity in the type IV secretion system of Helicobacter pylori.

Helicobacter pylori causes clinical disease primarily in those individuals infected with a strain that carries the cytotoxin associated gene pathogenicity island (cagPAI). The cagPAI encodes a type IV secretion system (T4SS) that injects the CagA oncoprotein into epithelial cells and is required for induction of the pro-inflammatory cytokine, interleukin-8 (IL-8). CagY is an essential component of the H. pylori T4SS that has an unusual sequence structure, in which an extraordinary number of direct DNA repeats is predicted to cause rearrangements that invariably yield in-frame insertions or deletions. Here we demonstrate in murine and non-human primate models that immune-driven host selection of rearrangements in CagY is sufficient to cause gain or loss of function in the H. pylori T4SS. We propose that CagY functions as a sort of molecular switch or perhaps a rheostat that alters the function of the T4SS and "tunes" the host inflammatory response so as to maximize persistent infection

Causes and biophysical consequences of cellulose production by Pseudomonas fluorescens SBW25 at the air-liquid interface

Cellulose over-producing wrinkly spreader mutants of Pseudomonas fluorescens SBW25 have been the focus of much investigation, but conditions promoting the production of cellulose in ancestral SBW25, its effects and consequences have escaped in-depth investigation through lack of in vitro phenotype. Here, using a custom built device, we reveal that in static broth microcosms ancestral SBW25 encounters environmental signals at the air-liquid interface that activate, via three diguanylate cyclase-encoding pathways (Wsp, Aws and Mws), production of cellulose. Secretion of the polymer at the meniscus leads to modification of the environment and growth of numerous micro-colonies that extend from the surface. Accumulation of cellulose and associated microbial growth leads to Rayleigh-Taylor instability resulting in bioconvection and rapid transport of water-soluble products over tens of millimetres. Drawing upon data we build a mathematical model that recapitulates experimental results and captures the interactions between biological, chemical and physical processes.IMPORTANCE This work reveals a hitherto unrecognized behaviour that manifests at the air-liquid interface, which depends on production of cellulose, and hints to undiscovered dimensions to bacterial life at surfaces. Additionally, the study links activation of known diguanylate cyclase-encoding pathways to cellulose expression and to signals encountered at the meniscus. Further significance stems from recognition of the consequences of fluid instabilities arising from surface production of cellulose for transport of water-soluble products over large distances

Modeling Life as Cognitive Info-Computation

This article presents a naturalist approach to cognition understood as a network of info-computational, autopoietic processes in living systems. It provides a conceptual framework for the unified view of cognition as evolved from the simplest to the most complex organisms, based on new empirical and theoretical results. It addresses three fundamental questions: what cognition is, how cognition works and what cognition does at different levels of complexity of living organisms. By explicating the info-computational character of cognition, its evolution, agent-dependency and generative mechanisms we can better understand its life-sustaining and life-propagating role. The info-computational approach contributes to rethinking cognition as a process of natural computation in living beings that can be applied for cognitive computation in artificial systems.Comment: Manuscript submitted to Computability in Europe CiE 201

Continuous and discrete models of cooperation in complex bacterial colonies

We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the elements of the macroscopic pattern. We present two types of models. The first is the Communicating Walkers model, a hybrid model composed of both continuous fields and discrete entities - walkers, which are coarse-graining of the bacteria. Models of the second type are systems of reaction diffusion equations, where the branching of the pattern is due to non-constant diffusion coefficient of the bacterial field. The diffusion coefficient represents the effect of self-generated lubrication fluid on the bacterial movement. We implement the discreteness of the biological system by introducing a cutoff in the growth term at low bacterial densities. We demonstrate that the cutoff does not improve the models in any way. Its only effect is to decrease the effective surface tension of the front, making it more sensitive to anisotropy. We compare the models by introducing food chemotaxis and repulsive chemotactic signaling into the models. We find that the growth dynamics of the Communication Walkers model and the growth dynamics of the Non-Linear diffusion model are affected in the same manner. From such similarities and from the insensitivity of the Communication Walkers model to implicit anisotropy we conclude that the increased discreteness, introduced be the coarse-graining of the walkers, is small enough to be neglected.Comment: 16 pages, 10 figures in 13 gif files, to be published in proceeding of CMDS