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

2. Microbial Colonies

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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