The Tiny Biology of BACTERIA and VIRUSES

In this episode, we cover both the bacterial stuff and the viruses. Next week, I’ll try my best to convince you that plankton is cool, and then we’ll slowly move on to more and more complex life.

Types of Life: The Very Basics

On a very basic level, life can be split into three domains:

Eukaryotes is the domain that includes our own species, Homo sapiens, but also other animals, plants, fungi, and protists. Protists are simple eukaryotic organisms, many of which seem like the eukaryotic equivalent of the bacteria.

Then there are the prokaryotes, now divided into the two other domains: archaea and bacteria. Archaea are essentially the in-between of eukaryotes and bacteria. They are a lot like bacteria (and most people wouldn’t be able to tell the difference), but the way they transcribe and translate their genetic material is a lot more like that of eukaryotes. Together, bacteria and archaea make up the prokaryotes. So, prokaryotes might be taken as a synonym to bacteria for most people, but bacteria are actually just one of the two domains in that group.

Last time, we talked about the LUCA, that great-great-great-great-[…]-great-grandfather of every living organism on this planet.

From there, the first large split happened: bacteria and archaea went their separate ways. Or rather, the archaea developed away from the prokaryotes. This was about 3.5 billion years ago. And just a short while later—on a timescale so huge we can’t comprehend it—the eukaryotes broke off again. The organism at this fork in the road is very creatively called the LECA, the Last Eukaryotic Common Ancestor.

But what distinguishes the eukaryotes from the prokaryotes?

Prokaryotes are usually smaller than eukaryotes. I mean, prokaryotes are, for all intents and purposes, single-celled, while Eukaryotes can be multicellular, so that makes sense.

One of the most interesting differences is that while eukaryotes store their genetic material as chromosomes in the nucleus, so behind a protective shell, prokaryotes do not have a nucleus. Instead, their DNA is stored in a circular strand in the cytoplasm, so just floating around the cell’s liquid.

The cell walls of prokaryotes are typically complex and made from glycoproteins—probably a good thing, considering their DNA is floating around behind those walls. Animal cells (and thus humans) do not have cell walls at all, but other eukaryotes do: Plant cell walls are made from polysaccharides (sugars) and fungal cell walls are typically from chitin—yes, that stuff a bee’s exoskeleton is made from, too.

What I did find interesting was that bacteria are often toxic for the simple reason that they suck at waste management. If you are single-celled, and you don’t have any inner organization, there’s exactly one place for your waste to go: into the liquid of your cell. So, while eukaryotes usually create vesicles (kinda like storage balloons inside the cell) to store the waste products and then move them out of the cell by melting that balloon to the cell wall and dumping out the contents, prokaryotes just keep it around inside them. No wonder, eating them can be a little hazardous.

So, how did we get from here to multicellularity, so I can finally start talking about things I understand a bit better—and care about a lot more. Please, let’s get out of this realm of too small things and move on to, um, bigger and better things? Philosophical question: are we really better than bacteria? Nevermind.

As I said last time, multicellularity developed about 50 times independently, so it’s a pretty big deal. There is this theory called the endosymbiotic theory (Remember: A theory in science means a lot more than in everyday life. Scientists don’t call something a theory until it’s pretty likely. Before that, it’s a hypothesis. I’m simplifying, of course.) In essence, larger single-celled organisms engulfed smaller ones and instead of digesting them decided to live in symbiosis. There’s this really cool pioneer called an alpha-proteo bacterium that was first to figure out how to breathe. The breathing cycle is a pretty big deal, so when this alpha-proteo bacterium was ingested by larger anaerobic bacteria, they apparently decided to keep them and work together. Today, they are the mitochondria in our cells, so the powerhouses. More on organelles in a moment. For now, tadaa, we’ve got the beginnings of heterotroph eukaryotes. That’s us! Well, and animals.

You already know how cool I think cyanobacteria are, so it’s probably not a surprise that they get involved yet again. Even more impressively, they are the ancestors of all plants on earth. Cool, right? Some of the organisms who already had mitochondria ingested these cyanos and thus started the evolution of plants. The cyanos developed into chloroplasts, so the place where photosynthesis happens.

Mitochondria and chloroplasts are not the only organelles now commonly found in eukaryotic cells. Eukaryotes are pretty damn good at creating specialized cells and cell organelles, so it’s no surprise, we’ve got quite a few of them.

Here’s an overly simplified summary: The nucleus stores DNA and transcription takes place there. Attached to the nucleus, we find the endoplasmatic reticulum, the ER, for short. The rough ER, closer to the nucleus, is involved in protein folding and quality assurance, as well as tagging them for their final destinations. The smooth ER is involved in lipid (fat) manufacture and the metabolism, as well as steroid hormone production and detoxification. Quite an impressive list of responsibilities.

The Golgi body takes the proteins produced at the ER and modifies them in its vesicle (again, kinda like skin balloons) sacs for transport to the final destination. It also produces lysosomes, enzyme-filled organelles that help break down molecules.

Then there’s the vacuole, essentially a liquid-filled sac that plants use to keep the pressure in their cells up. This pressure is called the turgor. The vacuole(s) can make up 90 percent of the cell volume, depending on the turgor.

Some animals have vacuoles as well, but they are much smaller than in plants and don’t get involved in the pressure stuff. Instead, they store food, water, and other materials. In animal cells, we’ll also find lysosomes, small liquid-filled sacs that contain chemicals involved in breaking down food particles and worn-out cell parts.

The cytoplasm, the cell’s own liquid, contains the cytosol and the organelles. The cytosol is a gel-like, watery liquid with enzymes and cytoskeleton filaments, but mostly water.

We already discussed chloroplasts which take light and carbon dioxide to make energy and oxygen and mitochondria which are very involved in the metabolism and supply energy to the cells.

All of these are surrounded by a plasma membrane, a lipid bilayer, so two layers of these lipids facing their “heads” away from each other. And in organisms with cell walls, the membrane is attached to the cell wall, the outermost layer of the cell.

And then, there are fungi. Fungi are kinda like the weirdos of the eukaryotes, as they are neither like plants nor like animals, but rather somewhere in between. They have cell walls and a nucleus like plants but no chloroplasts, and a life cycle very different from both animals and plants. They definitely deserve a closer look at some point. I like weirdos, as you know.

Viruses: The Good, the Bad, and the Ugly

We’ve all had enough of viruses to last us a lifetime, and it’s easy to surmise that all viruses are bad. But not unlike everything else in life, it’s not that black and white.

Without viruses, mammals would exist. That alone is probably enough of a reason to look into them. It’s also about the only thing that stuck from a 24-page National Geographic article about viruses we had to read for a class. It’s a very good article, though, so I recommend reading it if you have the time.

In general, viruses are pretty involved in evolution and population control. In the ocean, this leads to another special role, but before we dive into all of that, let’s cover the basics.

What is a virus?

Viruses are not alive in the traditional sense, though the fact that smaller viruses can infect larger viruses (like the giant mama virus) turns this into a fun philosophical question: can something get sick without being alive? I recommend this Khan Academy post, which outlines what criteria for life viruses fulfill or don’t fulfill.

But, as it doesn’t strictly matter if they are alive or not, let’s focus on what we do know:

Viruses are essentially genetic material (RNA or DNA) covered by a capsid layer, sometimes an envelope “shell” and outer proteins which can detect and attach to hosts.

Viruses are categorized by their protective shell (All viruses have at least a primitive shell, but some are enveloped while others are non-enveloped.) and the type of genetic material inside (single-stranded or double-stranded DNA or RNA). Depending on the type of genetic material, the virus needs the host for different parts of the creation of new genetic material.

Remember our first episode of this series where we talked about evolution and how RNA played a major role? I keep wondering how all of this connects. There’s RNA everywhere, including RNA-type viruses. If everything started with RNA, did RNA essentially just build itself different “houses” to live in? Are humans just very elaborate RNA homes?

But, viruses reproduce and evolve. They even go into evolutionary arms races with certain plankton types so cool that they get labels inspired by Alice in Wonderland. Emiliania huxleyi virus 86, Ehux-86, has been co-evolving with Ehux, Emiliania huxleyi, a coccolithophore, for quite some time. Each time one evolves, the other adapts, so they are pushing each other further and further. This is sometimes called the Red Queen effect, inspired by something the Red Queen says in Alice in Wonderland (Correction: Through the Looking Glass) about how staying still is falling behind and having to run to stay still. Ehux, as a coccolithophore, can switch between two life stages: haploid and diploid. The diploid phase is asexual division and very fast. This is how coccolithophore blooms happen. But Ehux are also vulnerable to their virus in this state. When the virus infects an Ehux, surrounding Ehux transform into the sexual (haploid) form undetectable by the virus—the Cheshire Cat effect because they vanish like that Cheshire grin in Alice’s Adventures.

But, even though coccolithophores are marginally more interesting to me than viruses, let’s return to viruses for a final round of knowledge before we get to talk about the ocean: the life cycle of viruses. To evolve, they need to reproduce. And viruses have two different ways to do so. And no, there is no virus sex. They aren’t even alive in the traditional sense, remember?

Viruses can follow the lytic (/ˈlɪtɪk/ LIT-ik) cycle or the lysogenic cycle. Most viruses can do both, depending on their needs. In addition, there’s a third way that is not often mentioned but especially cool as it doesn’t damage the host cell.

Viruses are pretty sneaky bastards (can you be a bastard if you don’t have parents?). They find and attach to their host and penetrate the cell to inject their genetic information. I know this sounds a lot like sex, but there’s nothing sexy about this, I promise. The unfair thing is that there is usually a latency phase next where nothing at all happens, so even if you suspected that you were getting sick, you’ll let your guard down because you don’t actually feel sick. You might even go outside and meet people. Sounds familiar? Oh yeah, there’s that pandemic that taught some of us how viruses work. Don’t worry, I won’t talk about R-values and measures here.

After the break of the latency phase, biosynthesis starts. The genetic material gets replicated and new virus proteins created. During maturation, the newly created viruses are assembled, before they finally rupture out of the cell, releasing the newly made viruses in a process called lysis.

The lysogenic cycle of a virus is pretty similar to the lytic cycle but introduces a few extra steps along the way. After injection, it does not destroy the host DNA but instead attaches its genetic material to it, so the viral material gets replicated alongside the host material. Pretty clever!

When the host enters certain environmental conditions (e.g. higher temperatures), the bacterial DNA gets excised from the host DNA and enters the lytic cycle, as before.

As mentioned before, there is a way viruses can reproduce without damaging the host. Budding is much slower than the other two cycles. A few viral particles are released in each bud. What’s budding? It means covering something in a vesicle (that balloon-like skin sack we talked about before) that merges with the cell wall and dumps out the contents without damaging the cell wall one bit. While not a symbiosis (the virus takes without giving), it must be preferable for the host to be infected by a minimally invasive virus.

And with that, I finally get to tell you what viruses have to do with the climate. The ocean is a pretty big carbon sink, as probably everyone knows by now. Trees are nothing against the ocean.

Small stuff gets eaten by bigger things. The bigger things poop, and their poop has the proper shape and density to sink quickly to the deeper parts of the ocean. More carbon gets stored in the actual organisms and when the bigger things die, they, too, sink to the bottom of the ocean. And, I probably don’t need to tell you that the bottom of the ocean is pretty far away from the atmosphere, and any carbon stored there doesn’t heat up the planet. So, where do viruses come into this?

Marine viruses play a pretty big role in the carbon sinking capabilities of the ocean. Viruses infect phytoplankton, which dies. Dead phytoplankton isn’t delicious, so the higher trophic levels leave it alone. Instead of getting ingested by the next rung of the food web, and moving up the trophic levels from there, the plankton’s remains dissolve into the water column and get taken up by microorganisms instead of moving up the ranks. Thus, a higher viral load actually means a decreased carbon export to the deep sea.

So, from an evolutionary standpoint and thanks to the whole placenta thing, I can appreciate that viruses play a vital role in our world. But much like fruit flies and ticks, I’d rather prefer if they could play their role somewhere away from me, please.



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