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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

2. Microbial Colonies

McFall-Nagl, Margaret, et al. Animals in a Bacterial World, a New Imperative for the Life Sciences. Proceedings of the National Academy of Sciences. 110/3229, 2013. Some 26 biological and medical scientists at major institutions in the USA and Europe from Hawaii to Croatia, including Andrew Knoll, Scott Gilbert, and Angela Douglas, propose a novel vista of life’s temporal and spatial evolution as if a singular phylogenesis, suffused and informed by a proactive microbial milieu. In regard, features such as Interdomain Communication via quorum sensing, Nested Ecosystems, and pervasive Symbiosis would gain more inclusion and import.

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world. (Abstract)

For much of her professional career, Lynn Margulis (1938-2011), a controversial visionary in biology, predicted that we would come to recognize the impact of the microbial world on the form and function of the entire biosphere, from its molecular structure to its ecosystems. The weight of evidence supporting this view has finally reached a tipping point. The examples come from animal-bacterial interactions, as described here, and also from relationships between and among viruses, Archaea, protists, plants, and fungi. These new data are demanding a reexamination of the very concepts of what constitutes a genome, a population, an environment, and an organism. Similarly, features once considered exceptional such as symbiosis, are now recognized as likely the rule, and novel models for research are emerging across biology. As a consequence, the New Synthesis of the 1930s and beyond must be reconsidered in terms of three areas in which it has proven weakest: symbiosis, development, and microbiology. (3234)

Menon, Shakti, et al. Information Integration and Collective Motility in Phototactic Cyanobacteria. PLoS Computational Biology. April, 2020. Institute of Mathematical Sciences, Tamil Nadu, India researchers describe how bacterial groupings can be seen to exhibit and be modeled by active matter phenomena. In regard, quorum sensing is interpreted to proceed by way of integrating relevant information. Altogether another manifestation of universal principles and formations.

Microbial colonies in the wild often consist of large groups of heterogeneous cells that coordinate and integrate information across multiple spatio-temporal scales. We describe a computational model for the collective behavior of phototaxis in the cyanobacterium Synechocystis that move in response to light. The results suggest that tracking individual cyanobacteria may provide a way to determine their mode of information integration. Our model allows us to address the emergent nature of this class of collective bacterial motion, linking individual cell response to the large scale dynamics of the colony. (Summary)

Molina, Nacho and Erik van Nimwegen. Scaling Laws in Functional Genome Content Across Prokaryotic Clades and Lifestyles. Trends in Genetics. 25/6, 2009. University of Basel information biologists report finding constant, nested patterns throughout all manner of microbial, and microcellular life forms, quite suggestive of a universal generative source. (See also Beslin, G., et al “Scaling Laws in Bacterial Genomes” in BioSystems (102/1, 2010).

For high-level functional categories that are represented in almost all prokaryotic genomes, the numbers of genes in these categories scale as power-laws in the total number of genes. We present a comprehensive analysis of the variation in these scaling laws across prokaryotic clades and lifestyles. For the large majority of functional categories, including transcription regulators, the inferred scaling laws are statistically indistinguishable across clades and lifestyles, supporting the simple hypothesis that these scaling laws are universally shared by all prokaryotes. (243)

These results support the idea that the origins of the scaling laws must lie in fundamental physical and/or evolutionary principles. At this point it is still unclear whether the scaling laws originate mainly from physico-chemical constraints that apply to all prokaryotes or whether they are an inherent feature of the evolutionary dynamics. (247)

Nayfach, Stephen, et al. A Genomic Catalog of Earth’s Microbiomes. Nature Biotechnology. 39/4, 2021. A 35 member international team with affiliations such as the Integrated Microbial Genomes Data Consortium and Genomes from Earth’s Microbiomes report current progress as our EarthWise sapience proceeds to retro-quantify all the living systems that brought our presence to be here.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering Earth’s continents and oceans, including human and animal hosts, and natural agricultural soils, so to capture microbial, metabolic and functional domains This comprehensive catalog includes 52,515 metagenomes for 12,556 species-level taxonomic units spanning 135 phyla. This resource highlights the value of genome-centric approaches for sequencing microorganisms that affect ecosystem processes. (Abstract excerpt)

Niu, Ben, et al. Bacterial Foraging Based Approaches to Portfolio Optimization with Liquidity Risk. Neurocomputing. 98/90, 2012. An apropos entry for this section as Chinese computer scientists draw upon microbial colonies seen as an archetypal example of successful self-organizing systems. In regard, they are availed to similarly guide such financial foraging. FYI, the February 2013 issue of this journal is about “Advances in Extreme Learning Machines.” This website indeed forages the vast Rosetta-like literature now readily online - what discoveries might we altogether glean?

Okie, Jordan, et al. Major Evolutionary Transitions of Life, Metabolic Scaling and the Number and Size of Mitochondria and Chloroplasts. Proceedings of the Royal Society B. 283/20160611, 2016. Biologists Okie, Arizona State University, with Val Smith, University of Kansas, and Merccedes Martin-Cereceda, Complutense University of Madrid, suggest that endosymbiosis effects (as the late Lynn Margulis professed for decades) play a leading role in the evolutionary advances of free-living and communal bacteria.

Penny, David. An Interpretive Review of the Origin of Life Research. Biology and Philosophy. 20/4, 2005. An extensive survey based on life as a natural property of matter. Four approaches are considered: the RNA-world hypothesis, intermediates between an RNA-world and organisms today via the evolution of protein synthesis, alternatives to an RNA-world, and the earliest stages from prebiotic systems to RNA. Penny concludes: My favored analysis at present is ‘metabolism, energy and organization first, metabolism makes RNA, RNA makes protein, and protein makes DNA.’

Pichards, Thomas, et al. Single Cell Ecology. Philosophical Transactions of the Royal Society B. 374/2019.0076, 2019. An introduction to a special issue of papers from a December 2018 two day meeting as multicellular, mammalian human beings collectively proceed to confer, quantify and reconstruct about how early life came to arise from prokaryote bacteria and eukaryote nucleates. We note Multicellular Behavior Enables Cooperation in Microbial Cell Aggregates by Ali Ebrahimi, et al, A Single-Cell Genome Perspective on Intracellular Associations in Eukaryotes by Tomas Tyml, et al, and Combining Morphology, Behavior and Genomics to Understand the Evolution and Ecology of Microbes.

This Single Cell Ecology interdisciplinary meeting will explore the use of single cell technologies to understand the function, diversity and interactions of microbes. By bringing together physicists who manipulate cells, microbiologists who seek to understand the nature of microbial communities and genomicists who are developing new approaches to study individual cells we will achieve a greater understanding of the potential of this new field. (Original 2018 abstract)

Rainey, Paul and Katrina Rainey. Evolution of Cooperation and Conflict in Experimental Bacterial Populations. Nature. 425/72, 2003. Laboratory studies find a deep tendency to form higher levels of multi-cellular complexity and individuality.

Roy, Anjan, et al.. A Unifying Autocatalytic Network-based Framework for Bacterial Growth Laws. Proceedings of the National Academy of Sciences. 118/33, 2021. Ben-Gurion University of the Negev and Abdus Salam International Center for Theoretical Physics, Trieste identify how such self-assembly processes are in common metabolic effect across the prokaryotic domains. See also Growth-laws and Invariants from Ribosome Biogenesis in Lower Eukarya by Sarah Kostinski and Shlomi Reuveni at arXiv:2008.11697.

In the clash between the physics-inspired strive for simple underlying laws of bacterial physiology and the biological hard-won understanding of the intricacies of life, we end in a middle ground. On one hand, we have found valid and simple growth laws. On the other hand, we demonstrated that the validity of a given growth law does not fully reveal the physiological state of the cell. Understanding how the cellular state is determined in response to internal and external cues, and how evolutionary stresses shaped different schemes for determining it, remains a formidable challenge. (10)

Sapp, Jan. The New Foundations of Evolution. Oxford: Oxford University Press, 2009. The York University biologist and historian, in collaboration with Carl Woese who writes a Foreword, achieves a novel extension and rooting of life's evolutionary "tree" and taxonomy in the vast prokaryotic microbial realms as revealed by the latest science of "molecular phylogenetics."

Schleper, Christa and Filipa Sousa. Meet the Relatives of Our Cellular Ancestor. Nature. 577/519, 2020. University of Vienna, Archaea Biology and Ecogenomics Group bioscientists cite a paper, Isolation of an Archaeon at the Prokaryote-Eukaryote Interface by Hiroyuki Imachi, et al in the same issue, as a significant quantification of how rudimentary microbal cells seem to have internal propensity (drive) to become nucleated cells on their long course to multicellularity.

Microorganisms related to lineages of the Asgard archaea group are thought to have evolved into complex eukaryotic cells. Now the first Asgard archaeal species to be grown in the laboratory reveals its metabolism and cell biology.

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