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

2. Microbial Colonies

Diggle, Stephen, et al. Quorum Sensing. Current Biology. 17/21, 2007. University of Nottingham biologists provide a succinct tutorial on the discovery that microbes engage in constant chemical communication as they achieve viable biofilms and colonies.

If we examine more complex environments like the rhizosphere, where many different, quorum-sensing signal producing bacteria co-exist, it would be easy to imagine the existence of a highly complex intercellular quorum sensing-driven signaling network which enables these poly-microbial communities to maintain an ecological balance. (R909)

Dinet, Celine, et al. Linking Single-Cell Decisions to Collective Behaviors in Social Bacteria. Philosophical Transactions of the Royal Society B. Volume 1820, January, 2021. In this Basal Cognition issue, CNRS-Aix-Marseille University, Turing Center for Living Systems, find evidence even at this unitary phase of cognitive and communicative processes which serve reproduction and survival, akin to all other organismic domains.

Social bacteria display complex behaviours whereby thousands of cells collectively change their form and function in response to nutrient availability and environmental conditions. In this review, we focus on Myxococcus xanthus motility, which supports transitions based on access to prey across its life cycle. A large body of work suggests that these behaviours require sensory capacity at the single-cell level. Focusing on recent genetic work on a core cellular pathway required for single-cell directional decisions, we argue that signal integration, multi-modal sensing and memory are at the root of decision making leading to multicellular behaviours. (Abstract excerpt)

Myxococcus Xanthus is a gram-negative, rod-shaped species of myxobacteria that exhibits various forms of self-organizing behavior in response to environmental cues. Under normal conditions with abundant food, it exists as a predatory, saprophytic single-species biofilm called a swarm.

The Turing Centre for Living Systems (CENTURI) is an interdisciplinary project located in Marseille (France). CENTURI aims at developing an integrated interdisciplinary community, to decipher the complexity of biological systems through the understanding of how biological function emerges from the organization and dynamics of living systems.

Doolittle, W. Ford and Olga Zhaxybayeva. Metagenomics and the Units of Biological Organization. BioScience. 60/2, 2010. A notable contribution to the increasing attribution of organism-like qualities to communal groupings, in this case a true genetic component for bacterial colonies. Ford Doolittle is the renowned Dalhousie University biologist and Olga Zhaxybayeva a Senior Bioinformatics Scientist with Environmental Proteomics, New Brunswick. Such collective communities then ought to merit ontological status, so as to qualify as further ‘units of selection,’ because they indeed have their own systems genome. An important statement with extensive references.

Metagenomics is a complex of research methodologies aimed at characterizing microbial communities and cataloging microbial diversity and distribution without isolating or culturing organisms. This approach will unavoidably engender new ways of thinking about microbial ecology that supplant the concept of “species.” This concept—thanks to comparative genomics—has in any case become increasingly unsustainable, either as a way of binning diversity or as a biological reality. Communities will become the units of evolutionary and ecological study. Although metagenomic methods will increasingly find uses in protistology and mycology, the emphasis so far has been, and our focus here will be, on prokaryotes (bacteria and archaea). (Abstract, 102)

Dupre, John and Maureen O’Malley. Metagenomics and Biological Ontology. Studies in History and Philosophy of Biological and Biomedical Sciences. 38/4, 2007. The University of Exeter editors of a special section Towards a Philosophy of Microbiology contribute in their article to the welling adjustment across many fields from a 20th century, albeit necessary, emphasis on particulate entities to an appreciation of their interactive communication which sustains cooperative colonies and groups. In this regard genetic complements are not isolated in any one creature, but rather by lateral or horizontal gene transfer (LGT or HGT) can seamlessly move across species and ecosystems. Since this feature is especially prevalent in microbial realms such as biofilms, it might be extended to a planetary scale much as if a biospherical organism.

Metagenomics – also called environmental genomics, community genomics, ecogenomics or microbial population genomics – consists of the genome-based analysis of entire communities of complexly interacting organisms in diverse ecological contexts. (835) Ultimately, metagenomics is about ‘the community of all communities’ on this planet, and, uncomfortable as the notion may be for many philosophers, for some practitioners metagenomics is perceived to be moving us inexorably in the direction of a Gaia-like concept of the world. (841)

Fuqua, Clay, et al. Regulation of Gene Expression by Cell-to-Cell Communication. Annual Review of Genetics. 35/439, 2001. A ten year report by the group that articulated how bacteria colonies are in constant dialogue from bioluminescence to signal molecules to swarming motility so as to better their survival. For this notable community dimension, they initiated the name “quorum sensing.”

George, Ashish, et al. Functional Universality in Microbial Communities Arises from Thermodynamic Constraints. iv:2203.06128. University of Illinois biologists study slow-growing colonies and find that such energy gradients provide a common structuring occasion.

Our results make predictions for the metabolic structure and resource environment created by the communities in low-energy environments, based on the thermodynamics of microbial metabolism. This requires knowledge of the free energy differences and metabolomic data of the resource environment. Recent advances in computational methods make the outlook promising. (9)

Gewin, Virginia. The Sequencing Machine. Nature. 487/156, 2012. A news report on the Earth Microbiome Project, a collaboration to sequence and characterize the microbial communities of some 200,000 environments such as soil and water samples collected around the globe. Its subtitle notes this work as part of an endeavor to “sequence the Earth.” Might we humankind go on to imagine a “Cosmic Macrobiome Project” of digital text and analogue image unto the discovery of a human genesis uniVerse?

Gitai, Zemer. The New Bacterial Cell Biology: Moving Parts and Subcellular Architecture. Cell. 120/5, 2005. Microbes are in fact quite intricate and exhibit a dynamic homologous arrangement, alone and in colonies, that later manifests as nucleated cells.

Recent advances have demonstrated that bacterial cells have an exquisitely organized and dynamic subcellular architecture. Like there eukaryotic counterparts, bacteria employ a full complement of cytoskeletal proteins, localize proteins and DNA to specific subcellular addresses at specific times, and use intercellular signaling to coordinate multicellular events. (577)

Goldford, Joshua, et al. Emergent Simplicity in Microbial Community Assembly. Science. 361/469, 2018. A nine member team from Boston, Harvard, Stanford, and Yale University studied thousands of bacterial groupings under a wide variety of environmental conditions to see whether common topologies and processes appear across this large sample. Indeed it is found that a viable recurrent presence can indeed be identified. By extension, an independent, universally manifest source which communal life draws upon and exemplifies is equally implied and illuminated.

A major unresolved question in microbiome research is whether the complex taxonomic architectures observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media. Both the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability. By generalizing classical ecological models to include widespread nonspecific cross-feeding, we show that these features are all emergent properties of the assembly of large microbial communities, explaining their ubiquity in natural microbiomes. (Abstract)

Green, Jessica and Brendan Bohannan. Spatial Scaling of Microbial Biodiversity. Trends in Ecology and Evolution. 21/9, 2006. Although the distributions and variety of sizable organisms scale in the same way everywhere, it has long been thought that the bacterial realm, due to its vast numbers (~109 microbes in a gram of soil), spreads out evenly. This report argues for a revision whereby the larger patterns of similarly hold for and continue into this minute milieu, revealing a universality of spatial geometries.

We focus on three spatial patterns: the distance-decay relationship (how community composition changes with geographic distance), the taxa-area relationship, and the local:global taxa richness ratio. Recent empirical analyses of these patterns for microorganisms suggest that there are biodiversity scaling rules common to all forms of life. (501)

Gross, Michael. Shining New Light on Quorum Sensing. Current Biology. 27/24, 2017. In his biweekly column, the Oxford science writer here reports on further visual evidence that bacterial communities effectively avail a beneficial common consensus.

Single-cell organisms often are anything but single cells. They co-operate and communicate in multiple and complex ways that science is only beginning to understand. By communicating with each other and acting collectively, they can deliver many complex functions ranging from the bright light in luminescent fish through to the digestion of food in our intestines and also including pathogen invasions.

Hahn, Aria, et al. The Information Science of Microbial Ecology. Current Opinion in Microbiology. 31/209, 2016. University of British Columbia and MIT ecoinformatic theorists seek better understandings of bacterial realms by way of previously underappreciated communicative phenomena. By this vista, common parallels far afield are traced between research publications, genomic trajectories, and life’s nested emergence from cells to populations, communities, and the Earth system (210). Again an informative perspective is seen to vitalize a field, along with illuming nature’s universal repetitions in kind. The future thus lies in the “clouds,” whence “interconnected networks of multi-omic sequences” can have an affinity to “Internet connections on the Worldwide Web” (213).

A revolution is unfolding in microbial ecology where petabytes of ‘multi-omics’ data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. (Abstract)

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