Did viruses make living rocks?


Breaking down the microbiology world one bite at a time

Did viruses make living rocks?

What is life? Where did it come from? Why does it exist? These questions have been with us, well for as long as anyone can remember. The answer to many of these questions and more may lie within the microbial world. 

Microbes (viruses, bacteria, fungi, protists) have been roaming this earth long before we have and have formed intimate relationships with each other, shaping their world until it became our world. Many of these ancient structures microbes have shaped are still around today and hold keys to earth’s history and the history of life. 

One of these structures you may have heard of, it’s called a stromatolite. Stromatolites look like rocks, but in actuality, they represent some of the earliest and most complex ecosystems ever known. Because of this, they are sometimes called “living rocks.” A stromatolite is a lithified sedimentary biofilm. They are thought to be one of the first visible to the nake eye life forms. Although 3.5 billion years ago when stromatolite dominated the earth there weren’t any eyes to look at them.

A biofilm is a sticky and sometimes slimy bacterial structure the microbes create to help protect themselves, think like the plaque on your teeth. It is made up of many microbes and their products including extracellular polymeric substances, substances found on the outside of their cells. When these multi-layer microbial cafeterias are built on solid surfaces we call them biofilm but when they are found on sediments we call them microbial mats. 

Microbial mats Yellowstone : Wikicommons

These ancient microbial mats can be found throughout history. Over time they can be converted into the solid rock-like structure of stromatolites. Microbial mats can contain nearly every kind of microorganism including protists, archaea, and viruses. However, not all microbial mats that existed throughout time still persist. The chemical and biological makeup of the microbial community plays a role in whether or not the microbial mat vanishes to time or becomes solid rock, preserving a little piece of the past. So at the intersection of biology, physics, chemistry, geology, and microbiology are these ‘living rocks’. They may just hold the secrets to the origin of life, or at the very least hold evolutionary secrets we are missing. 

In a recent article in Trends In Microbiology, the authors pondered the question of how a soft microbial mat can change to a hard rock-like structure. They hypothesize this transition is likely due to a microbial group that generally receives little attention outside of human health, viruses! 

It is estimated that there are 15 million different species on our planet, of which we only know of 2 million or so. It’s also estimated that a single gram of soil can hold up to 50,000 different species but currently most are not identified. These numbers are staggering but are nothing compared to the estimated global viral abundance of 10^31. This is 10x more than the stars in the sky! Whether it’s you or a microbe, viruses can not survive without a host, and as such, they are constantly changing the host and its environment. In the oceans alone it is thought that viral infections are causing a 20-50% turnover in microbial biomass.

The viral lifestyle is quite unique, they require a host to survive but their own survival often leads to the death of the host, forcing them to find a new host in a relatively short amount of time. To combat this challenge viruses have adapted a few different ways to survive. 

  1. At the very basic level, a virus will infect a cell, hi-jack the cell system to replicate its own viral genome, and then burst the cell open, ejecting many more copies of the virus to infect new cells. This is known as a lytic virus. This is obviously a very destructive process leaving the host dead in the end. 
  2. Another method of viral survival is to not lyse the cell but to simply leave the cell through budding off the cell membrane. 
  3. Then there are some viruses that are lysogenic instead of lytic. These viral particles will insert their genetic material into the host genome. 
Lytic and lysogenic cycles: Wikicommons

Either way, the uninvited viral guest will change the behavior of the host. Similar to the host seeing an unwanted guest at their party, they might become hostile, they might change their eating habits or overall behavior.

But what does all this viral biology have to do with the origin of life and stromatolites? White, Visscher, and Burns hypothesize that viruses may have manipulated other microbial behaviors leading to the transformation of microbial mats to hardened stromatolite structures. These may be in direct forms such as changing the host metabolism or in more indirect forms such as resistance against viruses or lysis events.

First let’s talk about indirect mechanisms, lysis, and resistance. In Lysis, the cells are broken open, spilling their genetic guts into the environment. These elements can serve as nutrients to other microbes within the microbial mat increasing metabolism like photosynthesis or strengthening the overall biofilm structure. As we can acquire resistance against certain bacteria, bacteria can acquire resistance against certain viruses. This resistance can change the overall microbial composition of the microbial mat and change the extracellular polymeric substances which change the architecture of the overall biofilm structure that may lead to lithification.

The direct mechanism of viral impacted stromatolite structure can come from a few different pathways. Viruses have the ability to insert their genes into the host and subsequently can also acquire genes from the host. For example, vAMGs are genes that the virus picks up from the host that enhances the bacterial host metabolism and alters the overall bacterial biogeochemical cycles. This in turn can alter the biofilm structure. Additionally, viruses can insert or remove other genes that might increase the fitness of the virus and the host which can change the behavior of the overall biofilm.

Indirect and direct mechanisms of viral impact on stromatolites structure

So far this has all been very theoretical. Is there any scientific evidence of this theory of viruses impacted microbial mats to transition into stromatolites? Well sort of, there is a recent report, by Zhongwu Lan and colleagues, that claims viruses were present in Neoproterozoic stromatolites in Northern China Platform.

We are only at the early stages of understanding our interactions with the microbes in our guts and are far from understanding how viruses impact microbes. However, I hope you can see just how dynamic microbial life can be. It is filled with ‘dark energy’ that has alluded us for centuries perhaps leading us to conclude erroneous ‘facts’ of our world. As technologies continue to improve researchers will get one step closer to understanding these tiny interactions which may hold the secrets to our universe.

History of earth and microbiology with Microbigals

Link to the original post: White, Richard Allen et al., Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats Trends in Microbiology, 2020

Featured image: Wikicommons https://commons.wikimedia.org/wiki/File:Stromatolites_in_Sharkbay.jpg