V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

2. Microbial Colonies

Wang, Weijia, et al. The Impact of Individual Perceptual and Cognitive Factors on Collective States in a Fish School Model.. PLOS Computational Biology. March, 2022. University of Toulouse and Beijing Normal University researchers including Guy Theraulaz quantify how interactive behaviors become altogether coordinated for both member and group benefit. See also Global Dynamics of Microbial Communities Emerge from Local Interactions Rules by Simon Van Vliet, et al (Canada, Switzerland) in the same issue. We can once again note that in these papers, cases, and across the site, a definitive pattern and process can be seen in independent, recurrent effect. Phenotype-like communal entities over many scales arise from and are guided by an independent, universal, genotypic source code. But into 2022, these diverse entries in an open Public Library of Science are by researchers aware of work in their field, but still sans any sense of a novel Earthuman faculty learning on her/his own, nor of any phenomenal ecosmic universe reality they manifestly arise from.

Waters, Christopher and Bonnie Bassler. Quorum Sensing: Cell-to-Cell Communication in Bacteria. Annual Review of Cell and Developmental Biology. 21/319, 2005. Prokaryotic microbes are seen to act as multi-cellular organisms as they communicate via chemical signal molecules. In so doing, hormone-like agents are constantly produced, released, and detected in response to changing environments, which then result in an overall favorable behavior. Compare with the same phenomena found in honey bee swarms as reported by Seeley, et al.

West, Stuart, at al. The Social Lives of Microbes. Annual Review of Ecology, Evolution, and Systematics. 38/53, 2007. From the Universities of Edinburgh, Nottingham, and Oxford, another report on the epochal shift from discrete amoeba long taught in schools to an appreciation of their true, viable communal essence.

Our understanding of the social lives of microbes has been revolutionized over the past 20 years. It used to be assumed that bacteria and other microorganisms lived relatively independent unicellular lives, without the cooperative behaviors that have provoked so much interest in mammals, birds, and insects. However, a rapidly expanding body of research has completely overturned this idea, showing that microbes indulge in a variety of social behaviors involving complex systems of cooperation, communication, and synchronization.

West, Stuart, et al. Social Evolution Theory for Microorganisms. Nature Reviews Microbiology. 4/8, 2007. A research program is described to see if propensities to advantageously cooperate which pervade groups of organisms can also be recognized in the microbial behaviors of dispersal, nutrient acquisition, biofilm formation, and quorum sensing. The tacit assumption is that they similarly do. In this regard see a follow up report: Diggle, S., et al. Cooperation and Conflict in Quorum-Sensing Bacterial Populations (Nature. 450/411, 2007), and also Frank, Steven. All of Life is Social (Current Biology. 17/16, 2007).

Witzany, Gunther, ed. Biocommunication in Soil Microorganisms. New York: Springer, 2011. After 2009 and 2010 overviews noted in Emergent Genetic Information, in this edited volume the Austrian biophilosopher and many colleagues consider how chemical semiotic sensing across intracellular, intercellular, and trans-kingdom stages between microbes aids their viable assemblies. By way of Springer’s advanced website, on the main book page one can click on a Read Online button to access the table of contents and abstracts for each chapter.

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context-dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular biocommunication between soil microorganisms. This includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (Synopsis)

Woese, Carl. A New Biology for a New Century. Microbiology and Molecular Biology Reviews. 68/2, 2004. The bacterial, archaeal and eukaryotic kingdoms began in a “pre-Darwinian,” RNA world of horizontal gene transfer within a continuum of modular, semiautonomous, “subcellular” groupings.

The community of primitive evolving biological entities as a whole as well as the surrounding field of cosmopolitan genes participates in a collective reticulate (network) evolution. (182)

Wong, Gerard, et al. Roadmap Concepts in the Physical Biology of Bacterial Biofilms. Physical Biology. 18/051501, 2021. Some 40 micorbiologists from every continent including Bonnie Bassler post considerations of 18 aspects from The Role of bacterial flagella in surface sensing and Gliding mobility of social bacterium to Membrane vesicles and bacterial signaling and Self-organized collective motion in bacterial communities. Each segment comes with its own expert and to do summary.

Bacterial biofilms are communities that exist as aggregates which can adhere to surfaces or be free-standing. This complex, social organization pervades the physiology and behaviors of microbes. Such biofilms are more than the sum of their parts: single-cells have a complex relation to collective community behavior, in a manner perhaps cognate to atomic physics and condensed matter physics. In this roadmap, we highlight the work of scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions exemplify how well physics and biology can be combined to achieve a new synthesis. (Abstract excerpt)

Xavier, Joao and Kevin Foster. Cooperation and Conflict in Microbial Biofilms. Proceedings of the National Academy of Sciences. 104/876, 2006. From the Center for Systems Biology at Harvard University, that bacterial colonies are not benignly communal but are found to occur and succeed by competitions such as between the quality of polymer production. By this view, microbes are similar to animal groupings.

Yusufaly, Tahir and James Boedicker. Mapping Quorum Sensing onto Neural Networks to Understand Collective Decision Making in Heterogeneous Microbial Communities. arXiv:1703.01353. University of Southern California biophysicists achieve further quantifications of how bacteria flourish by way of chemical communications. Of note is a use of neural net dynamics to gain better insights, which is another avail of this generic natural system. See also Spatial Dispersal of Bacterial Colonies induces a dynamical transition for Local to Global Quorum Sensing by the authors in Physical Review E (94/062410, 2016).

Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. Understanding these interactions is a prerequisite for deciphering the consequences of crosstalk in real ecosystems, where multiple AIs are regularly present in the same environment. As a step towards this goal, we map crosstalk in a heterogeneous community of variant QS strains onto an artificial neural network model. This formulation allows us to systematically analyze how crosstalk regulates the community's capacity for flexible decision making. (Abstract excerpt)

In summary, we have demonstrated a novel approach to compressing chemical details into simplified, generalizable neural network models, in order to study communication in complex real-world microbial ecosystems. The unexpected relationship between intercellular signaling dynamics and neural networks promises to be a valuable new theoretical tool for future studies of communication in heterogeneous microbial communities, with implications for both the basic science of microbial ecology and evolution, and also for synthetic biology efforts to engineer novel emergent behaviors in artificial multicellular consortia. (7)

Zarraonaindia, Iratxe, et al. Beyond the Genome: Community-Level Analysis of the Microbial World. Biology & Philosophy. 28/2, 2013. We cite this article by Basque Foundation for Science, Argonne National Laboratory, and University of Chicago, systems biologists to illustrate the growing trend to perceive life’s ecological domains from molecules and microbes to the viable biosphere by way of “meta-omics,” its broadly conceived pervasive genetic basis. Are we invited to proceed on to an incarnate “meta-cosmomics?”

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called ‘‘omic’’ techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment. (Abstract)

Zhang, H. P., et al. Collective Motion and Density Fluctuations in Bacterial Colonies. Proceedings of the National Academy of Sciences. 107/13626, 2010. University of Texas at Austin, Center for Nonlinear Dynamics, physicists make an important extension by finding that self-organized animal groupings across every taxa similarly occur amongst microbial assemblies. Circa 2010, a rush of reports such as this, e.g., Ahn, et al, are discovering a repetitive universality across all creatural communities. Is the great realization that an independent mathematical agency from which this phenomena must apparently arise and manifest be the creative presence of a natural genetic code?

Flocking birds, fish schools, and insect swarms are familiar examples of collective motion that plays a role in a range of problems, such as spreading of diseases. Models have provided a qualitative understanding of the collective motion, but progress has been hindered by the lack of detailed experimental data. Here we report simultaneous measurements of the positions, velocities, and orientations as a function of time for up to a thousand wild-type Bacillus subtilis bacteria in a colony. The bacteria spontaneously form closely packed dynamic clusters within which they move cooperatively. The number of bacteria in a cluster exhibits a power-law distribution truncated by an exponential tail. Our results demonstrate that bacteria are an excellent system to study the general phenomenon of collective motion. (13626)

Zhou, Yizhaung, et al. Omics-based Interpretation of Synergism in a Soil-derived Cellulose-degrading Microbial Community. Nature Scientific Reports. 4/5288, 2014. We note this paper in a British journal by 23 authors, mostly Chinese but with affiliations in Norway, Denmark, and Saudi Arabia, as a global collaboration, for its avail of genomic explanations, and, as the Abstract conveys, its sense of a greater phenomenal vitality on its own. To wit, archetypal, self-organized, reciprocal groupings are evident everywhere, as living Nature knows best.

Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes. Support for cellulolytic inter-species cooperation came from the discovery of F1RT microbes that encode and express complimentary enzymatic inventories that include both extracellular cellulosomes and secreted free-enzyme systems. Metabolic reconstruction of the seven F1RT phylotypes predicted a wider genomic rationale as to how this particular community functions as well as possible reasons as to why biomass conversion in nature relies on a structured and cooperative microbial community. (Abstract)

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