Beauty of Kitchen Sink Experiments

I strongly believe “kitchen sink” should be the heart of science activity in any house hold. Just think about it; 100’s of fluid mechanics problems when a jet hits a flat sheet. You add soap to it, and loads of foam problems to think about. And now, since you have a microscope, you can add tons of biological problems to it. So this post is about – what’s growing in my kitchen.

Just from last night kitchen cleaning, I discovered a beautiful single layer thick cell sheet (probably a bacilus bacterial interfacial biofilm – but j need to confirm it) that I imaged with my foldscope. It was beautiful!!

Some observations
1. The film truly was single cell later thick.
2. The patterns arise from buckling of a thin sheet. Imagine a sheet that is growing but only has a fixed area. What does it do – it wrinkles.
3. I saw a “black” substance in the films; which was only present in parts that were intact. I am really curious about that.. It could be a secreted compound that gives an irrescident feel to the film. I only found it in intact films.
4. At the edges, they easily break into single cells.

I head is spinning with so many questions. Can’t even begin to write them down. Are these films hydrophobic. Are they hydrophobic on one side, and Philic on the other. What about water underneath. Do they cut evaporation completely?

I am just mesmerized by the beauty of the microscopic world. Another reason to not clean my kitchen (or not clean it so frequently).

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5 Comments Add yours

  1. laksiyer says:

    Great pics. Loved the colony. Wish you could id it and then we can have a database of bacterial colony morphologies. Do you have any high mag picture? Was it motile? Any refractile bodies? Were they bunched or in chains? Sorry to ask, but did it have a distinctive odor?

    It is fascinating how it existed as a pure colony in an exposed place where any bacterium can grow, or where a mixed colony can grow. We now know it is a war out there with antibiotics, spears and guns (polymorphic toxins), siderophores ahd what not. Essentially all these are forms of kin selection that allow the self-type of bacterium to propagate. This is truly is one of the most fascinating aspects of bacterial biology that is in serious need of foldscoping. Great stuff.

  2. Manu Prakash says:

    Wonderful set of questions. Unfortunately (and I feel silly to have done that) I cleaned and washed that dish. I should I have kept the colony.. Maybe long enough wait and it will come back. I will try that right away. Now I might wait forever and never grow that same colony ever again. Isn’t that so fascinating!!!

    I did notice some very specific things that I was really surprised with as well. It was very late last night; and I had a “huge” pile of dishes to do as well. So I did not take any high mag pictures – but here are some observations that I did not have time to write in morning train.

    1. It truly was a single type of cells. They are non-motile; since I watched separated cells for long while.
    2. In the sheets that form, they are single cell thick. I actually played for a long time to get a perfect replica of the sheet transferred from the water to the glass surface, and did get them. I was astonished that such a thin sheet that sustain itself – with no holes.
    3. Tell me – what you mean by refractive bodies?? I made a strange observation, that a film is made of “black” things and “white things” – white things are cells clearly. But why do I not see anything black when I suspend the same in separated cells. I saw crack formation if I watched the sheet for a long time, as they might be drying as well. Clearly at the crack, lots of single cells start releasing. But never this black stuff. So could the black stuff be just an optical effect because of stacking in a particular way? Can you point me to what you mean by refractive bodies.
    4. It’s clear to me, that the patterns are buckling patterns that emerge as the sheet keeps growing with the fixed area on the surface of water. So it can grow with some pressure as well. In the edges, it started crawling in dry parts of the bowl; and also the spoons. So clearly some it survives semi-dry.
    5. But again, I thought – the buckling patterns naturally provide ultra-fine channels in this 2D sheet – which should give rise to capillary flow – so the film always has water (and nutrition) from the bath.
    6. Regarding a single colony – my sense is in one phase; lots of species are competing for the surface of water – it;s such a great place to be. Once one of them grows to a certain size; it really actually gets rid of anything else (I can not imagine in my kitchen – nothing else would land on this water surface). If you see the state of my kitchen; you would know what I mean 🙂
    7. Since I just seeded some new cultures, I will watch this war in action.
    8. I also just remembered; a faint purple colony was growing in one of the dishes either embedded or on top of this sheet. I paid no attention to it; but now your comments make me realize – that could have been a competing colony.

    Question: Do you have advice on how to sample and keep colonies that I grow in my kitchen – so that if I have money later on, I could try to sequence and ID them. Any specific fixation protocols compared to generic stuff. I will also collect high mag data.. if they grow again.

    cheers
    manu

    ps: I got so excited with your questions – I dug in the garbage bag and found slides I had thrown away. In one of them, I found a little bit of water and a live set of cells. So I “plated” in a new dish the same colony and will try to grow it. Now – this was in a dish that had udon noodles – so as a replacement I put ramen noodles and some pulses and some wheat. Let’s see what I get.

  3. laksiyer says:

    Hi Manu: At the risk of foot-in-the-mouth disease, where all my intuitions could be wrong or misleading, here are a few thoughts

    1. If this is low power, then these cells are quite enormous in size (A good size comparison is to see the bacteria in commerical yogurt). Are they oval or is it my eyes? If oval then one might have to also consider the possibility that this is a Yeast colony. One quick test is to see if they stain with methylene blue. Live yeast cells never stain with MB, whereas bacteria easily do. Of course if you can see a nucleus like structure at high mag, it is a give away.

    2. Some bacteria have refractile bodies in each cell that do not get stained called endospores and Bacillus species often make them. You can see them as outlines within the cells when you change focus at high-mag and this is even more pronounced when you stain the cells with a simple stain (MB, Gentian Violet/Crystal violet etc). There is a spore staining procedure that I can send you if you think you seen something like this.

    3. The Black thing: There are two possibilities that my mind can conceive: 1 ) Iron sulfide. Bacteria often reduce sulfates to give H2S and if some iron sulfate is present in the medium it reacts with H2S to give Iron sulfide. One quick test is the smell test for H2S (rotten eggs).Also Iron sulfides easily react with even mild acid solutions to give H2S and you will see the color change immediately. 2) The second possibility is a pigment which may or may not be hyperchromic (i.e. high concentrations often change the color; the stacking effect that you were writing about).

    4. If you confirm that it is a bacterium, the first staining procedure I would recommend is the Gram staining process. I have done this at home and it works quite well.
    a) Suspend the colony in water and take a little on a slide and spread it.
    b) Let it dry and then heat fix it. If yo have a spirit lamp at home, pass the slide over the lamp, say 3-4 times but dont overheat it (One marker is to touch the back of the slide after heat-fixing, it shouldnt burn your skin). The bacteria will now also be stuck on the slide.
    c) Add Gentian Violet/Crystal Violet for 1-5 minutes and then wash it off.
    d) Add Lugol’s Iodine for 1-5 minutes and then wash it off. Fresh Lugol’s iodine is very important for this to work.
    e) Now rinse the slide with 70% ethanol.
    f) Stain it with a counterstain such as basic fuchsin/safranin for 1-5 minutes, wash off the stain, let the slide dry and observe. Gram positive bacteria will be purple and gram negative pink. It is quite amazing how you can narrow down your bacterial groups with this simple staining procedure (There is also a Gram staining kit available for home science).

    5. Another staining procedure is the capsule stain to see if your bacteria have a capsule. Put a drop of your culture on a slide and mix it with India ink and spread it like a blood smear and air dry. Add gentian violet/safranin or any such stain. Gently wash off.air dry . Capsules will form outlines around the colored cells.

    5. Colonies can be kept away in 10% skim milk 0r 15% glycerol in the deep freezer in eppendorfs tubes. Professional labs use glycerol, but skim milk seems to work well. If possible get the UHF skim milk, if not, at least boil your milk once before using it http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2551311/

    6. Now that you have re-inoculated the microbe, a couple of things to keep in mind are:
    – Rate of growth. How long does it take for the colony, i.e. 24-48 hours vs weeks. You can then guess if they are R-type or K-type (ref. Logistic growth equation), each of which have great meaning in bacteriology.
    – Smells.. H2S, alcohol, rancid, smell of rain (all give aways for different types of bacteria). Refer book below for a range of smell tests.

    7. Finally, as this stuff is growing on food, just exhibit the usual cautions as some of these can make you sick. When in doubt, bleach it out.

    8. We really need to understand the physics of the colony as you are investigating. The composition of the biofilms with protein, polysaccharides and DNA might provide new and interesting materials.

    A good reference book is “A field guide to Bacteria” by Betsey Dyer for macroscopic markers.

    — Laks

  4. Niramay Gogate says:

    Can you give detailed explanation of every photo that is posted in this article? I am unable to correlate them with what you have described.

  5. Manu says:

    Thanks. I will both update the post with details on all the pictures. Since I was able to revive the strain; I am really hoping I see again in my bowl. I will get the book you suggested as well.

    I am very certain the pattern arises from buckling with growth in a constrained surface area. I am away for two days – the moment I get home; this is what I will get to.

    Cheers
    Manu

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