Sunday, October 21, 2012

Microbiome Part 6: Carbon Cycle

Note: This program first aired on Saturday October 20, 2012.

We are carbon based life forms, ask anyone at NASA*, Earth is covered with the stuff. Plants use carbon to hydrogen bonds to store the energy of the sun, that is the essence of photosynthesis. They also use the carbon they take out of the atmosphere (or fix) to build the structure of their bodies. We eat the plants (or the things that eat the plants, or even the things that eat the things that eat the plants), getting not only energy from those carbon to hydrogen bonds, but also the building blocks of our bodies as well. If that were the end of the story, life on Earth would have ended a long time ago, because we would have run out of our main source material, carbon.

Like all elements, carbon isn’t satisfied to simply stay put. It moves around the Earth and in and out of various forms over the course of time. The regularity of the journey of carbon is well documented, and referred to as the “carbon cycle”.  There are several sinks or reservoirs of  carbon; some are short term and others are long term. The long term sinks are thinks like the fossilized carbon that make up underground beds of fossil fuels we so love to burn, or limestone, a sedimentary rock formed at the bottom of the ocean from the chemical union of carbon dioxide gas and various minerals** present in sea water. Once carbon makes it to one of these reseviors, its stuck there for a while, baring some physical process that brings it to the surface of the earth for weathering. The parts of the carbon cycle we are more interested in today are the “fast” components; the movement of carbon dioxide out of the atmosphere, into plants (via photosynthesis), and then back out again (via respiration both by the plant and the things that eat the plant, but probably more importantly respiration by the microbes that decompose all that plant and animal matter, liberating and recycling the carbon and many other nutrients, making them available for use once more).

If you play out the thought experiment “what if all the bacteria disappeared tomorrow?”, the result might look something like this: piles and piles of dead plants and animals, just stacking up, and the amount of carbon available steadily dropping. What would essentially be happening is that carbon would be moving out of the atmosphere into biological material, via photosynthesis and the food chain. The carbon would be building up in a biological “carbon sink or resevior” in the form of organic biomass. If nothing ever decomposed, that carbon doesn’t get to move out of the sink its stuck in and the sink would get fuller and fuller as time went on.

The soil is the largest land based carbon sink in the carbon cycle (the oceans hold over an order of magnitude more, much of which gets locked eventually into abiotic limestone). Soil is comprised of both mineral elements and organic elements. Its those organic elements (dead plants and animals) that comprise the carbon sink part of the soil. One concern with the increase in average global temperature that is accompanying climate change is the idea that as temperature increases, bacterial decay of organic material in the soil will also increase, freeing up much of the carbon stored in the soil, liberating it back to the atmosphere. So would it make sense to try to get rid of all those soil bacteria and prevent them from doing their ecological job? Besides being impossible, I think this would be foolhardy. In the words of John Muir, the visionary nature man himself: “When we try to pick out anything by itself, we find it hitched to everything else in the Universe”.

The decomposition part of the carbon cycle isn’t something we like to think about, we think of decomposition as a bad think in the back of the refrigerator. Think too long about bacterial decay and you eventually come around to the question of what happens to your own body when you are done with it. So I can’t blame people from shying away from this aspect of the carbon cycle. I can only hope that by focusing on the grand cycles of the building blocks of life, we can learn to see death, and its accompanying decay, as liberation. Bacteria are literally the doulas and midwives of this cycle, ushering carbon, our most essential substance, from one phase of existence to the next. So the next time you dig in the garden, dump the compost or simply walk in the woods and smell that wonderful leaf decay smell, pause and reflect on, and revel in, the moment for what it is, a snap shot of grand loop that is much bigger than you.

Post Script:
*And just WHY are we strictly carbon based? Because carbon is unique among elements in that it has four spots each atom that can form bonds, and it can bond in a wide variety of shapes. Similar atoms (same column of the periodic table), like Silicon, also have four bonding spots, but tend to form crystal lattices, instead of the wide variety of that carbon can attain. It’s also apparently the fourth most abundant element around, meaning, there’s lots of it out there.

** Mostly calcium and magnesium.


Kenneth Todar “Online Text book of Bacteriology”

Totally worth looking at: from the American Society for Microbiology

From one of my favorite websites, NASA’s Earth Observatory

From the American Museum of Natural History

Ah the Union of Concerned Scientists…
Thanks for all your level headed thinking.

Microbiome Part 5: Decomposers

Note: This program first aired on Saturday October 13, 2012.

No one really knows how many bacteria are on the Earth. People have come up with models and sampling protocols to try to determine how many individual bacterial cells are on Earth (five million trillion trillion), how many species are in any given proverbial teaspoon of soil (five thousand or more), and how many different species exist globally (a few thousand to a billion). Many scientists believe that the bacterial biomass on the planet far exceeds the biomass of all other living things. Needless to say, there is little consensus and much research needs to be and is being done.

Taxonomically, bacteria make up the roots of the tree of life. They had the planet to themselves for nearly 2 billion years, and then single celled eukaryotes and multicellular eukaryotes (us included) came along and stole the spotlight. We’ve talked before about the photosynthetic role of bacteria, but they have another equally or even more important ecological role on the planet. Bacteria, along with fungi are the great decomposers of our world.

Decomposition doesn’t sound like a very fun job, and to our sensibilities, it often doesn’t smell very good. It is incredibly important however, to the cycling of nutrients and raw materials of life. There are two major biochemical reactions that drive life as we know it (with of course, a few exceptions). The first is photosynthesis; plants use the energy of the sun to take simple molecules and turn them into more complex molecules. In doing so, they store some of the sun’s energy in the bonds that hold those complex molecules together. Simple to complex. The second major biochemical reaction is respiration. All organisms respire, meaning, they take large complex molecules and break them down into smaller simpler molecules, in the process gaining the energy that was stored in the bonds of those large molecules. This is what we do when we eat. This is why plants photosynthesize—they don’t do it for us, they do it to make food for themselves (we just happen to get it before they do in some instances).

Organisms that eat are also know as heterotrophic, hetero meaning different, trophic meaning eating, so heterotrophs eat food that is different from themselves (by comparison, photosynthesizers are autotrophic—they self feed). Heterotrophs have essentially two options for eating; they can ingest food and digest the complex molecules internally, or they can keep the food outside of them selves and digest it externally, absorbing the molecules only once they have been at least partially broken down. We are of the former type, we ingest our food, secrete acid and enzymes, and with the help of some bacteria, liberate nutrients and energy from that food. We don’t however, get all of the nutrients or energy from our food, not close. The classical ecological number is 10 percent, as in only 10% of the energy from one trophic level gets passed on to the next one, the other 90% is lost as waste (in the form of heat and feces). The reality is that this number varies quite a bit with different feeding levels, but the take home message here is that most of what we eat doesn’t actually get into us. My personal theory about why this is has to do with the difficulty of digestion. Our body has to work quite hard to chemically break down those big food molecules. If we work too at it, we might just start to digest our own bodily tissue—that is one of the roles of mucus in the digestive track, to protect ourselves from our own digestive enzymes.

Bacteria are of the latter type. They are external digesters, excreting digestive enzymes to break down food molecules (both large and those that are partially digested and excreted as feces) and then absorbing the smaller molecules that result. Again, I am not a microbiologist, but my personal theory on this is that bacteria, being prokaryotic, lack a nuclear membrane and have their DNA loose inside their cells. I expect that it is to their advantage to not in any way jeopardize their genetic material by having digestive enzymes also floating around inside their cells, hence, external digestion. Fungi, the other group of great decomposers also digest externally and this pattern leads me to believe that breaking down these larger molecules into smaller inorganic nutrients may be a rather harsh process, which is why both decomposers do it this way.

We’ll continue this discussion about the ecological role of bacteria next week as we look in more detail at the specific nutrients that bacteria are so vital in keeping in play in the biosphere.


From the master himself: Stephen Jay Gould, "Planet of the Bacteria," Washington Post Horizon, 1996, 119 (344): H1

The factoid about the microbial biomass making up the largest single carbon sink came from this author, but to be honest, I read it on Wikipedia…I’m not proud. Fenchel, Tom (1998). Bacterial biogeochemistry : the ecophysiology of mineral cycling (2nd ed. ed.). San Diego: Academic Press.

Just for fun:

“First-Ever Scientific Estimate Of Total Bacteria On Earth Shows Far Greater Numbers Than Ever Known Before” Science Daily, 1998

Microbiome Part 4: Photosynthesis

Note: This program first aired on Saturday October 6, 2012.

If all the bacteria on Earth were suddenly to vanish, would you care? They are too small to be seen (unless of course, you’ve left something alone in the back of the refrigerator for way way too long), so would you even know it? In fact, some of you, without thinking it through fully, might think it would be a good thing if all the bacteria on earth were to vanish. But, I can say unequivocably that that would be an unmitigated disaster. They have an important job to do here on Earth, many jobs in fact. If all the bacteria on Earth were suddenly to vanish there are many ways we would miss them.

It is often said that bacteria are responsible for much of the oxygen we breathe. This may come as a surprise but many bacteria are indeed photosynthetic. The only source of the free oxygen gas we breathe is photosynthesis, it always has been. Before there was photosynthesis, there was essentially no free oxygen in the atmosphere, and all life (entirely prokaryotic) was anaerobic. The photosynthetic bacteria are the cyanobacteria (popularly known as blue green algae), the green and purple sulfur bacteria, and the purple non-sulfur bacteria.  In terms of oxygen production, the cyanobacteria are the heavy hitters here. The sulfur bacteria by the way, photosynthesize using  the energy of light from the sun to change CO2 into sugar the same way plants do, except that they use hydrogen sulfide instead of water in the chemical reaction. This sounds crazy until you look at the periodic table and see that oxygen and sulfur are in the same column (and thus behave the same way, so the difference between H2O and H2S actually isn’t that great).

We can attribute essentially all of the oxygen we breathe to bacteria if we recognize that the chloroplasts in plant cells—the grass on your lawn, the leaves on the trees around your house, the algae in the ocean—were originally bacteria. This is the theory of endosymbiosis. The original plant was probably a hungry single celled protist that engulfed a cyanobacteria, but then failed to digest it. The bacteria realized it had a good gig there inside the protist, surrounded by a soup of half digested food and all. The protist had a good deal going as well, now housing its own sugar making factory, which is all that chloroplasts do inside a any cell, they absorb light and use that energy to rearrange some commonly found chemicals and store the energy of the sun in the chemical bonds in the sugar they make. The oxygen we breathe is a byproduct, really a waste product, of that process (note, those sulfur bacteria that don’t use water?  They don’t make oxygen either, their waste product is, unsurprisingly, sulfur).

So, directly (through photosynthesizing mats of cyanobacteria), and indirectly (by being responsible for the existence of chloroplasts in plant cells), bacteria save the day and make life  as we know it possible.  And the best part is, that isn’t even half of all the good stuff they do here on Earth, but we’ll have to save that for next time.

The University of California Museum of Paleontology has a huge and amazing website devoted to education about evolution and the tree of life, as well as the geologic past:

See for yourself, Oxygen and Sulfur ARE in the same column!

“From Endotymbiosis to Synthetic Photosynthetic Life”, Andreas Weber and Katherine Osteryoung (full text available)

Thursday, October 4, 2012

Microbiome Part 3: Antibiotic Resistance

 Note: This program first aired September 22, 2012.

The germ theory of disease, that certain diseases are caused by microscopic organisms, is well established in traditional western medicine today. Thinkers and healers flirted with the idea for centuries, but it took until the 1800’s in Europe for the idea to gain any traction, and after much controversy and resistance,  and to actually change behavior in many hospitals. Behavior like washing your hands after you finish an autopsy, before you go on to examine your next patient (who might be a woman about to give birth). We’ve come so far with the idea that now seconds after a doctor touches you, they rush to the sink to wash their hands, not wanting to risk their own safety with any of the germs (ie bacteria) that might be on your skin.

By the start of the early 20th century, many scientists and researchers had noticed that certain molds inhibited bacterial growth. This observation and the subsequent experimentation it spurred on led to the development of penicillin and the vast array of modern antibiotics we now have available, ushering in the age of modern medicine and the end of many now easily cured diseases. If you have been paying attention in the last decade or so, you will have heard about the growing problem of some of these wonderfully useful drugs not working anymore. Many of the harmful bacteria that are targeted by these drugs are becoming increasingly resistant to their effects.

Antibiotic resistance is a multifaceted problem. The first is a problem of evolution. Quite simply, there is genetic variation for any given trait in any given population. The variation arises from random mutation, and the ones that end up being helpful to an individual’s survival and reproduction get passed on. Ones that have a negative effect don’t get passed on as much, or at all. That’s evolution in a nutshell: differential reproduction. So in a population of bacteria, there may be a version of a gene that gives that particular bacterium resistance to an antibiotic (more on this in a moment). When we douse the bacteria with something that will kill them, the only ones that live and survive and reproduce are the ones who have that have the resistance gene. So, on an evolutionary level, antibiotics select for resistance genes.

Now let me tell you a story about a cave in New Mexico. It is one of the deepest and most isolated caves in the world. Virtually no one has been down there. Yet, when researchers took samples of bacteria, they found that nearly every strain of bacteria was resistant to at least one type of antibiotic currently in use. As a whole, the cave bacteria were resistant to nearly every antibiotic currently in use. The reason for this is fascinating. Essentially, antibiotics are weapons, and though we discovered them, we didn’t invent them, bacteria did. Bacteria evolved antibiotics to kill other bacteria, and gain competitive advantage in their environments. If humans were to use a chemical weapon, they have to protect themselves with a gas mask. The antibiotic resistance genes are the “gas mask” of a bacteria—the genes protect the bacteria from its own chemical weapon, so it can use it on other types of bacteria. The bacteria in the New Mexican cave demonstrate this—they don’t have antibiotic resistance genes because of us, they have them because of each other.

So the genes for resistance to pretty much all antibiotics occur naturally in normal populations of bacteria.  We know how mechanisms of evolution then select for these resistant genes when we apply antibiotics to a population of bacteria. And we know from our discussion of lateral gene transfer, how readily bacteria will swap genes between species.  Putting these three things together leads to the perfect storm of rampant antibiotic resistance we see in our hospitals today.

The hard part is that we can’t do anything about the first factor (the naturally occurring resistance genes) or the last factor (lateral gene transfer is a process that is 3.5 billion years old and going strong).The only one we have any control over is the evolutionary one, and the only way we have influence there is to refrain from participating, in other words, not using the antibiotics, or at least, not using them unless we really really need them.

So bacteria may be at times our foes. In coming weeks, we will look at the other side of the coin, and examine how they are our friends as well. In fact they are such good friends to us,  that we couldn’t live without them.


From “Contagion” The Harvard University Open Collection on Diseases and Epidemics:

Dr. Hani (2010). History of Antibiotics. Retrieved 19 Sep. 2012 from Experiment Resources:

Science Daily “Key to New Antibiotics Could Be Deep Within Isolated Cave”

Genereux, Diane P. and Carl T. Bergstrom “Evolution in Action: Understanding Antibiotic Resistance” Chapter 13 Evolutionary Science and Society

Microbiome Part 2: Lateral Gene Transfer (aka Bump and Grind)

Note this program first aired September 15, 2012.

Bacteria are thought to be the original gangsters, the form in which life sprung forth from the primordial soup. And that was nearly 3.5 billion years ago. One line of questioning in the current fervor of microbial research is then “what is the evolutionary history of the prokaryotic clades?”—those groups of microorganisms with no membrane to keep their DNA nice and tidy, who may or may not be closely related to each other. And when we say evolutionary history, we mean how did the prokaryotic diversity we see today arise, who evolved from whom and which groups are more closely related, meaning, which groups evolved from a common ancestor relatively recently.

It turns out, this question is much easier to ask than it is to answer. And the reason for this is that we have to compare the genes of these various organisms in order to determine how related they are. The more genes they share, the more closely related we can assume them to be. It actually is quite complicated trying to decide which genes to compare. Some have said, why not compare them all? Well in some cases that is exactly what is going on. Researchers are comparing entire geneomes  from various prokaryotes. The trick is to get them all lined up correctly, so you are comparing the similar areas of each genome. And this only really works for organisms that have relatively few genes. Even the super computers get overwhelmed relatively quickly with large amounts of genetic data. Other researcher pick out specific types of genes, and compare just those. These minutia lead to terrific and heated debates about the relationships of various groups of organisms we can’t even see!

The real reason though, that reconstructing the evolutionary history of bacteria is so difficult is that they don’t behave the same way we do with respect to our genetic legacy. Pretty much all of us Eukaryotes reproduce sexually. We find a mate, combine our genetic material, and produce offspring that carries a mix of our DNA, some from one parent, and some from the other. That is the only way our genes move from individual to individual, through direct heredity. Tracing and comparing genes gives us a picture of lineage.

The problem is that prokaryotes don’t behave that way, when it comes to their DNA. Instead of finding that special someone to settle down with and start a family, they are all about one night stands. And infact, not only one night stands, but trans specific hook ups. Prokaryotes are willing and able to swap chunks of DNA with any other prokaryotic cell they encounter, regardless of whether or not it is the same species as them. This promiscuity is quite frankly, a little shocking.  This bump and grind life style is known as lateral gene transfer, and is the reason it is so hard to reconstruct the evolution of bacteria and archea. They don’t follow the lineage based model of our own genetic methodology. They swap genes all over the place, all the time, so the presence of a gene in a particular bacteria may not be telling you anything about that cell’s parent, it may just indicate that that cell happened to bump into some other prokaryotic species and they did a quick genetic switcheroo when no one was looking. Theoretically this MO, and not sexual recombination, accounts for diversification in early prokaryote evolution.

So what this means is that our models for piecing together the puzzle of the early evolution of prokaryotes doesn’t work. The chaos that is lateral gene transfer makes this virtually impossible at least for now. It also has some incredibly important implications for human health, all of which we will be talking about on future episodes of the World Around Us.

Timeline of early life on Earth from the New Scientist:

More than you ever wanted to know about comparing bacterial DNA:
“Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution” Se-Ran Juna, Gregory E. Simsa, Guohong A. Wua, and Sung-Hou Kim,

The pros and cons: “The advantages and disadvantages of horizontal gene transfer and the emergence of the first species” Aaron A Vogan and Paul G Higgs*