It’s Bacteria All The Way Down

Most of us consider microorganisms to be invisible yet pervasive buggers that cause gum disease if we don’t brush our teeth, food poisoning in under-cooked or out-of-date food, and unanimously agree that they need to be destroyed. We buy products claiming to kill 99.9% of them from our homes and surfaces and try to push the worry about that 0.1% out of our minds. Maybe we even have a notion of “good” vs. “bad” bacteria. We are afraid of these organisms and are constantly at war. But should we fear them or praise them? Given the global pandemonium over the current COVID-19 outbreak, which is viral and not caused by a bacterium, the invisible world of microorganisms has grabbed our full attention .

By nonchalantly consuming and administering antibiotics we have grossly underestimated the efficiency and intelligence of these molecular sacs of lipid. Given the age of bacteria as a species, being the oldest kingdom of organisms existing on Earth, it is not surprising that our ancestors surpassing us by billions of years of evolution and adaptation to Earth’s conditions may eventually be the ones to wipe us out. As Homo Sapiens we like to consider ourselves a cut above the rest with our emergent properties of consciousness when in fact bacteria are the most evolved species on Earth having survived in an unbroken line from what we can presume was the beginning of life.

Our survival on this planet is utterly dependent on them. Bacteria are not only responsible for generating the building blocks of life, they colonize and are an indispensable part of every living structure on Earth.

I know they say it’s turtles all the way down, but in actual fact it’s bacteria. 

Let me throw down some points that should get you up to speed with the resistant and indestructible nature of these impressive micrometre beings. 

Thriving in adverse conditions

Bacteria love adverse conditions. They evolved during volatile conditions on Earth 4 billion years ago when the atmosphere consisted of nitrogen, argon, neon, carbon dioxide and water vapour. The Earth’s average temperature rising or fluctuations in the carbon dioxide composition of the atmosphere is disturbing for many species and ecosystems, see coral reef bleaching. Given the steep ancestral lineage of bacteria and the billion year old timeline they operate on, I imagine they won’t be too deeply perturbed considering their experience of adaptation to unpredictable climates.

Scientists stationed at a base on an East Antarctic ice sheet responsible for recording atmospheric and seismic readings discovered an ancient lake beneath the surface of a glacier that had been locked away in the ice for at least 420,000 years. They drilled down to reach the ice in Lake Vostok, located in this Antarctic region where the lowest temperature of minus 89.2°C has ever been recorded. After isolating DNA from the harvested ice samples and comparing the sequences to thousands of listed sequences in a database, sequence analysis showed they were closely related to existing bacteria alive today in extreme environments on Earth such as those living in the Mariana trench. Microbial life in Lake Vostok, Geomicrobiology of Subglacial Ice Above Lake Vostok, Antarctica.

We also know bacteria exist in volcanoes, at the boiling edges of sulfur lakes, and in trenches thousands of meters beneath the ocean. These organisms pushing the limits of existence have been rightly dubbed extremophiles. 

Bacteria inhabit every improbable corner of the planet. If anything happens to the life forms on earth, for example something on par with the dinosaur mass extinction event, we can rest assured that bacteria will survive and evolve into future life forms unimaginable to us.

Thrifty bacteria

The earliest forms of bacteria invented fermentation as a source of energy. They used sugar-breakdown processes to convert sugar to ATP. These are the bacteria we rely on today for their fermentation byproducts in brewing our beer and wine, as well as to ripen some cheeses.

Fermentation isn’t entirely efficient as the byproducts – alcohol and acids – are excreted and go to waste. Thrifty bacteria capitalized on this and evolved to eat the wastes of fermenting bacteria. Fermentation food chains where bacteria thrive on the waste of other bacteria still exist today in places where the quantity of oxygen and light are low, in our guts for example! We could learn a thing or two from these champion waste recyclers. 

Bacteria are such masters of adapting to their environments, mutant strains of bacteria capable of degrading plastics have been found! Bacterial enzyme which breaks down plastic.

Nitrogen fixation

One of the earliest bacterial lineages, Clostridia, a fermenter, acquired the remarkable ability to extract nitrogen gas from the atmosphere and string it onto the end of amino acids, nucleotides and other organic compounds as an ammonia-like side chain. Nitrogen manufacture for plant fertilizer is an intense industrial process requiring demanding conditions. An atmospheric pressure 300 times the norm and a temperature of 500°C. No plant or animal is capable of fixing nitrogen from the air, along with most microbes. 

Well what’s the big deal? Nitrogen is a critical component of protein. Proteins are the molecular scaffolds or structures that form the constituents of every component in our cells. They are the universal building blocks of life.

Every organism depends on this niche bacterial population capable of nitrogen-fixation. Without nitrogen-fixing bacteria capturing nitrogen from the air, life on Earth would have died due to nitrogen starvation. Thankfully, the clostridia, azotobacters, rhizobia and friends continue to supply the biosphere with vital nitrogen compounds. 

This process of extracting nitrogen from air and returning it to living organisms is just one maneuver in the balancing act that bacteria perform in sustaining life.

Bacteria are the Earth’s undertakers

The consortium of bacterial teams on Earth are responsible for no less than maintaining the condition of the planet. Their functions are intricately woven into the maintenance of Earth’s atmospheric equilibrium. Bacteria recycle once-living matter by turning it into food and energy for others.

In the words of Lynn Margulis:

Bacteria purify the Earth’s water and make soil fertile. They perpetuate the chemical anomaly that is our atmosphere, constantly producing fresh supplies of reactive gases

James Lovelock, an atmospheric chemist, reckons that microbially produced gases play an intrinsic role in stabilizing the earth’s atmosphere:

• Methane may act as an oxygen regulator and anaerobic ventilator
• Ammonia (which must be continually resupplied by bacteria) may set the alkalinity of lakes and oceans, as well as controlling the ancient climate
• Carbon dioxide modulates the temperature of the planet
• Methyl chloride, present in trace amounts may regulate ozone concentration

Bacterial reproduction and gene transfer

Bacterial reproduction is very strange. They reproduce asexually by simple division and they reproduce fast. A daughter cell can bud off its parent cell every 20 minutes. In 2 days this asexual budding could in theory generate 2^144 individuals, a ghastly number far larger than the number of humans who’ve ever lived. After 4 days of reproduction, the number of new bacteria formed are more than the estimated number of protons (2^266) or quarks in the universe. Imagine having all the components inside of you to just grow a new human. You could grow a new you off the side of you. Forgive me for that image.

Bacteria also have “sex”. Not in the conventional “sperm-and-egg” way we associate with animal sex. Sex is different to reproduction here, it is independent and not related to reproduction. Bacteria can fluidly exchange genes at any time just by coming into contact with another bacterial cell through conjugation. The cell doesn’t even have to be alive for “sex” to occur and an opportunistic bacteria to acquire new genes from it. A bacterium can carry 90% new genes without even reproducing.

If conditions are challenging for bacterial sex for whatever reason, immobile bacteria have a genetic back-up plan. Minuscule packets of DNA or RNA called replicons, which usually comprise a whole chromosome, can travel from cell to cell and become integrated into a new bacterium’s genophore. This process is called transduction. When it comes to sharing genetic information, promiscuous is almost too kind of an adjective to describe bacteria.

Lynn Margulis’s analogy is that:

People and other eukaryotes are like solids frozen in a specific genetic mold, whereas the mobile, interchanging suite of bacterial genes is akin to a liquid or gas.

If the genetic properties of the microcosm were applied to larger creatures, we would have a science-fiction world in which green plants could share genes for photosynthesis with nearby mushrooms, or where people could exude perfumes or grow ivory by picking up genes from a rose or a walrus.

Bacteria work in teams

A bacterium never functions in isolation. In any given ecological niche, bacteria operate in teams, responding to and altering their environment. Each producing their own metabolites, their life cycles interlock. One bacteria feeds on the waste of another, another releases its biochemical enzymes when it senses a certain stage in another’s life cycle.

Given their rapid rate of reproduction, there are always new bacteria nearby to occupy resources, contribute byproducts or useful genes. Over time, this microbial microclimate stabilizes and becomes efficient in maintaining a complex group metabolism. Check out biofilms.

Bacteria not only coordinate processes within their bacterial teams, they also interact with other organisms in the eukaryotic world such as fungi, plants and animals. 

In the case of lichens, cyanobacteria form a coalition with fungi to operate harmoniously as a single organism.

Bacteria vs. Virus

When our cells are hijacked by a new virus and it injects its RNA self-reproducing instructions, it causes chaos within our bodies, recruiting and priming immune cells for a civil war, after it’s finally been detected that is. For bacteria though, a chance encounter with a new virus is an opportunity. Bacteria can try out some of the new viral genetic material and either adapt it or discard it as it pleases. 

Bacteria are so adapted for a viral RNA invasion they deploy a Cas9 enzyme to cut and neutralize viral RNA at certain sequences termed short palindromic repeats. The bacteria then acquires this new viral RNA by incorporating it into its own genome or genophore. 

The discovery of this billion year old bacterial defense mechanism has formed the basis of the technology underpinning CRISPR genetic editing in any type of cell today.

Drug resistance

Transduction and conjugation are the bacterial world’s chief methods of sharing immunity to drugs. We’ve seen how rapidly bacteria can multiply and how freely they can transfer genetic information to each other.

For every one in a million divisions, a daughter bacterium is genetically different from the parent. An error has occurred in replicating the genetic information from parent to child bud. The child is a mutant.

Most mutations are deleterious but what if their new genetic composition happens to confer resistance to a certain drug. It’s easy to see how quickly a successful mutant’s genes can be transferred to others and perpetuate the cycle of incremental leveling up against our best efforts.

Bacteria are the default OS

If I can try to cheekily distill bacteria down to a computer metaphor, it would be that they are Earth’s default operating system. If Earth is the hardware, bacteria are the OS that comes out of the box.

Bacteria maintain and spawn processes such as maintaining the Earth’s atmosphere, recycling of nutrients and fixing nitrogen into our cells which are crucial for overall system functioning.

If anything happens on Earth, it can reboot with a clean drive and the microbes can operate at maximum efficiency unhindered by garbage files and applications.

Sources

Microcosmos – Four billion years of microbial evolution