Microbial landscapes

How much time do you devote to thinking about the microbial organisms that share our environment with us. Perhaps you think of them before washing your hands or when someone sneezes next to you in the bus. Perhaps you think about them all the time. Perhaps you are not willing to confess here, just how much you think about bacteria, fungi and protozoans swimming in the water, covering all surfaces, floating in the air.

Honestly, I would love to be able to see them. I realize that scale is an issue and I would need to be around 10um tall to be able to appreciate the marvels of the microbial world. Thus, I fully prepared for the advent of technology that will make us tiny. Here is my top 5 of sights to see if I ever get to be around 10 um tall.

  1. Colony on agar:

Early microbiologists relied on colony morphology to identify, describe and study microorganisms. They would report the size, color (pigmentation), shape, margin, texture and abundance. Importantly, each colony is made out of thousands of cells arranged along a density gradient from a dense center of the colony to a sparse periphery. If you were walking on top of the agar towards the colony, you would first see few cells, arranged seemingly at random – not unlike walking towards a patch of forest and finding trees are sparse at the edge. Then, cells will become more densely packed, probably one on top of the other, to the point where the colony is elevated over the substrate and cells are packed in dense layers. Interestingly, cells arrangements would differ across bacterial species as they differ across types of forests. But bear in mind that each colony grows from a single cell and all of its constituents are clones of one another. You have just walked through a forest of clones. See some spectacular pictures of bacterial cell arrangements here and, less spectacular but more informative, see here for electron microscopy of different sections of colonies of B. subtilis and B. cereus.

  1. Bacterioplankton

Bacteria floating in lakes, rivers and oceans are critical for chemical transformations providing resources for phytoplankton and zooplankton alike. Bacteria are capable of fixing nitrogen, providing critical nutrients for photosynthetic processes, thus fueling primary productivity. But bacteria are also important in recycling organic matter and in providing resource for bacterivorous species of ciliates, flagellates, and other eukaryotic microorganisms. This is an incomplete list of the role bacteria play in aquatic systems (they can also transform sulfur, iron, manganese and mercury, among many more). I can imagine immersing myself in this environment, to see them clump around copepod fecal pellets, colonize the surface of diatoms or turning into a nanoflagellate’s lunch. It has to be a fantastic view, tiny bacterial cells moving across an aquatic landscape of colorful eukaryotic plankton. It sounds terrifying to be chased by a ciliate, unable to swim due to drag. Perhaps I’ll bring a little propeller with me.

  1. Marine biofilm

Submerged surfaces in aquatic environments are readily colonized by microorganisms. In particular, bacteria attach to the surface and begin the formation of a three dimensional structure composed of exopolysaccharide (EPS) and protein secretions. This newly formed habitat can then house other kinds of bacteria, in addition to algae and diatoms becoming a complex tiny jungle, a mature biofilm. I imagine climbing through the bridges of EPS as one climbs across the roots of a mangrove forest. I wonder if we can see slow migrations of cells across the different layers, sudden changes in the chemical environment driven by quorum sensing or the death of an old biofilm, when all inhabitants leave and the structures degrade like an old, abandoned city.

  1. Gut bacterial community

The entrails of our bodies remain a source of inquiry for scientists and non-scientists alike. I vividly remember cartoons and drawings of voyages (accidental or on purpose) across the gut. Now we know that a large portion of the function of our stomach and intestines is facilitated by millions of bacterial cells that reside right there, inside of us (see here for the Human Microbiome Project). I can imagine being able to walk down the small intestine, trying not to step on large colonies of bacteria lining the floor, walls and roof around me. It would be interesting to see whether they are clumped, well distributed or completely randomized in their distribution across the surface. I would not want to be there when the food bolus coming in – a mix between the scene from Indiana Jones running away from a big rock sphere and a laparoscopic video of your small intestine.

  1. Hydrothermal vents.

I would like to see this full ecosystem thriving away from the sunlight. As columns of thick smoke seep into the cold waters, bacteria chemosynthesis provides resources for worms, crustaceans and snails in an oasis of productivity amongst a desert of darkness and emptiness. I would like to see yeti crabs waving their hairy claws full of bacteria, or vestimentiferan tube worms waving in the current like weird bald palm trees. I would like to see the bacteria on their tissues and the mats of bacteria covering the seeps. I would even settle for visiting while fully human sized, the deep see seems as a crazy place as the microbial world.

What microbial habitats would you like to see if you were 10 um tall?

Note 1: I have to confess I am aquatic in my heart which is reflected in the lack of terrestrial habitats.

Note 2: Michael Crichton is way ahead of me, and if this is all sounding interesting to you, you should probably read Micro too.

Note 3: But I did write a song about it.

Notice: before you go wondering around as a 10um sized creature, remember that drag, gravity and viscosity will work differently on a tiny organism. Practice swimming in honey.

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