Metagenomics: Accessing the Aliens Inside Us

Microorganisms are the oldest, most plentiful, and most adaptable life forms on earth and consist of every kingdom of life including animal, plant, archaea, virus, etc. Our fossil record of them extends back at least 3 billion years (though studies show microbes may have changed little in that time), dwarfing the duration of macroscopic organisms. They are estimated to constitute at least 50% of the earth's total biomass (number may be much larger depending on concentrations in or around earth’s core) and in the human body there are 10 times as many microbial cells as human cells.

Though we have had proof of their existence since the invention of the microscope, until recently this silent majority of life on earth was relatively unstudied as 99% of all microbes may only survive in complex communities and are specialized for very specific ecological niches. Trillions of species pervading our earth and our own bodies and guts remained unknown due to their unwillingness to be grown and cultured in a laboratory Petri dish. Now a revolution in microbiology and genetic mapping (which may be to biology what the development of quantum mechanics was to physics) will allow the sampling of entire microbial communities simultaneously to create a Metagenome of microbial DNA in humans – a representation of far more genetic material than the Human Genome itself due to the multiplicity of species therein. This only goes to show that, apart from the infamous junk DNA, there is still a mountain of genetic data yet undiscovered in the human monolith.

How does it work? According to a National Academies news release: “Metagenomics studies begin by extracting DNA from all the microbes living in a particular environmental sample. The extracted genetic material consists of millions of random fragments of DNA that can be cloned into a form capable of being maintained in laboratory bacteria. These bacteria are used to create a 'library' that includes the genomes of all the microbes found in a habitat, the natural environment of the organisms. Although the genomes are fragmented, new DNA sequencing technology and more powerful computers are allowing scientists to begin making sense of these metagenomic jigsaw puzzles.”

This project is to be coordinated in a Global Metagenomics Initiative that includes a few large-scale, internationally coordinated projects and numerous medium- and small-sized studies. The results of these initiatives may contain the key to some of the most groundbreaking discoveries of the coming centuries in energy, environmental remediation, health, medicine, bio-technology, and space exploration. These breakthroughs could give rise to new paradigms in symbiotic social organization, the definition of self and being, as well as spirituality and religion.

The history of human technology can be viewed realistically (albeit humorously) as the severe copyright infringement of the techniques and designs of nature and other life forms. This retrograde progression is due to make another giant leap backwards by discovering the technology of the smallest among us. Microbes are alchemical masters, transmuting a multitude of compounds multi-directionally while producing hundreds of the drugs in our pharmacopeia, and presumably many thousands more yet to be discovered. Microbes equal the plant kingdom in photosynthetic energy production, and excel in creating potential fuel byproducts including hydrogen, methane, butanol, and even electric current. They are already crucial to maintaining environmental homeostasis, but with some scientific pleading, microbes may be coaxed into reversing our devastating pollution through their propensity for turning nuclear waste, oil spills, and other toxins unpleasant to most life forms into harmless byproducts.

They're also a vital part of our health, breaking down otherwise indigestible foods, making essential vitamins, and even shaping our immune system. Recent research suggests that our symbiotic relationship with microbes plays a role in fighting diseases such as ulcers, heart disease, and obesity. By studying the link between which microbial communities we are hosting and which diseases we contract, major illnesses can be cured by adding or subtracting specific microbe communities. In the future, a combination of emergent nanotechnology and advanced microbial understanding could produce a heretofore unimaginable integration of Life and Machines, placing the forces of Life itself so completely under our control that purely metallic and synthetic machines become clumsy and primitive artifacts compared to these new living technologies.

As a species we humans congratulate ourselves, however perversely, on being the single most transformative force on the surface of the earth, boasting that we have changed the world more in our short era than all other life on earth combined. The only problem with this theory is that the world as we know it was created by microbes. Billions of years ago, microbes which may have spontaneously emerged here (abiogenesis) or were seeded from elsewhere (panspermia) terraformed the early earth and converted nitrogen-rich atmosphere to oxygen, creating a viable planet for multi-cellular life to emerge.

In the present day, scientists are considering using the same technique on nearby planets, most notably Mars. Some scientists even propose that this process could take as little as a century, with the possibility that we could have trees growing there within another few centuries. Although skeptics estimate this process could take up to a million years, all are agreed that it is possible. Ethical considerations, such as the chance of disrupting pre-existent Martian life forms, gives us cause for deliberation, however. In addition to their already proven use in terraforming planets microbes may in the future be used to germinate other already habitable planets, as theorized by Francis Crick (the discoverer of DNA). This could in fact explain our own origin, as scattered grains of "living pollen" that drifted through space to land on a distant star.

We already know of a species of microbial extremophile called the tardigrade or "water-bear" who can survive in powerfully harsh conditions: temperatures close to absolute zero[4]; temperatures as high as 151°C (303°F); areas with 1,000 times more radiation than any other animal can withstand. In addition, the water-bear can live for nearly a decade without water and can survive in a vacuum like that found in space (it already looks suspiciously like a cosmonaut). Amazingly, these millimeter-sized animals are one of the few species untouched by human ecosystem disruption and can be found in abundance everywhere on earth. Furthermore, tardigrades carry the nickname "slow walker" for their admirable ability to suspend themselves in Cryptobiosis, or "living death," in response to any unpleasant environmental extreme, resuming metabolic functions upon return a more favorable environment (a good trick to remember next time you’re on line at the DMV).

As we shift from a conception of concretely distinct species to a gene swarm of laterally swapping DNA wherein the human super-organism is but a host, we can clearly see the analogy to the move toward an Internet society, where laterally traded information propagates memes that affect the Gaian super-host. Further study of the complex coordination of microbial communities may help model future human cooperative societies as they function through use of a “bucket brigade” system, in which each microbe performs its own individual task, with its end product becoming the starting fuel for its neighbor. For example, when some types of bacteria cause a depletion of oxygen in the groundwater near a gasoline spill, other types of bacteria that can use nitrate for energy begin biodegrading the gasoline. Bacteria that use iron, manganese, and sulfate follow. All community members work together in a pattern triggered by the movement of the leaking gasoline until the contaminants have been transformed into harmless carbon dioxide and water.

Thus, a task impossible for any one microbe is quite readily accomplished en masse, all orchestrated in anarchic order and without hierarchic oversight. What better model for understanding mystical unity could there be than microbes – the connective tissue of the earth, and perhaps the living pollen dispersal system of the stars.

Links:

Earth and Life Studies At The National Academies

Metagenomics: A Call for Bringing a New Science into the Classroom

The Next Human Genome Project