The Final Post

April 29 - I’m going to miss my Winogradsky columns. This is my last blog entry and as I was taking photos of my columns for this posting it suddenly hit me that I wouldn’t be able to see what happens next, what new colors (or smells) would emerge from the layering of water and mud/soil. I got a bit sad… One of these days, when I’m living somewhere with enough room to keep a couple of columns for a much more extended period of time, I’ll have to make some more columns and see what happens over the course of a couple of … maybe years. I mean, seeing the incredible changes in my columns after only a few months has been very exciting. I wonder if a column of a few years would constantly change, or would it reach a growth/development plateau at some point and then stop changing. Well, something to find out in the future!

On to my final observations and conclusions for these columns.

Over the course of the two+ months that my Winogradsky columns have been sitting, I’ve observed a lot of changes in all four columns (fig. 1). As a reminder, I had set up three experimental columns and one control, with my objective being to see what would grow in columns filled with Thames mud and/or water. Column A (Potting Soil + Tap Water) was my control. My experimental columns were Column B (Potting Soil + Thames Water), Column C (Thames Mud + Tap Water) and Column D (Thames Mud + Tap Water).

(a) (b)

Fig. 1 My four Winogradsky Columns: from left, Column A, B, C and D. (a) What all four columns looked like at the very beginning of the experiment (after a day of settling). (b) What all four columns looked like at the end of the experiment.

The columns that were the most productive were Columns C and D, though during the last couple of weeks I started to see changes in the columns with potting soil (more on that later!). There were many similarities in the microbial growth in Columns C and D (fig. 2). Both had extensive growth throughout the mud layer, with first orange and then green patches of microbes. The growth started in the sides of the column facing the sunlight, and then spread out from there, which suggests (especially with the green growth) that those were phototrophs. At the end of the experiment, there was a portion of the columns that still did not exhibit microbial growth in the mud section (fig. 3).

Fig. 2 Columns C and D at the end of the experiment. As you can see by just looking at them, the changes that took place are pretty similar between the two, though growth occurred at faster and greater rate in Column C.

Fig 3 A closer look at Column C, where you can really see where there is growth in the mud layer and where there is none. (Sorry about the glare, though if you enlarge the photo the difference is very striking). The area where there is no visible growth was facing away from the sunlight.

The water in both turned a light green color, and there was a lot of growth on the walls of the column in the aqueous part (fig. 4), both green and brown colored. As there was more green then brown, it looks like the brown was growth that came later.

Fig. 4 Closeup of the water layers in Columns C and D. You can see the separate brown splotches more clearly in Column D (on the right) as they have merged together more in Column C. Also, note the difference in the transition zones between the mud and the water in both columns. In Column C, the difference is less distinct than in Column D, likely due to the buildup of growth.

There was noticeable biofilm development in both columns (though Column D never reached the amount that was seen by the end of the first month in Column C), and when the cling film was removed from the columns, they had a similar earthy smell, though Column C’s might have been just a bit sharper.

While there were many similarities between Columns C and D, there were also several differences, mainly in the sheer amount of growth. Column C had much larger patches throughout the mud, and there were more green particles and brown patches on the sides of the bottle throughout the water column. Also, at the transition point between the mud and the water, there was considerable growth in Column C, where as in Column D the transition was very distinct. Though Column D ended the experiment with larger amounts of biofilm on the water’s surface (fig. 5), had Column C not experienced its tragic accident I am confident that the biofilm on the surface would have been quite thick indeed. It makes me wonder how porous the cling film I used to wrap the top of the columns was, and if the microorganisms that made up the biofilm were aerobes or not. If the cling film was thick enough, eventually the atmosphere in the columns would have become anaerobic as the oxygen was used up. Would the microbes on the surface have died then? Or would the (potential) photoautotrophs have produced enough oxygen to sustain the biofilm? I guess had I left the columns grow for longer, that is something I would have been able to better discover!

(a) (b)

Fig. 5 (a) The biofilm on the surface of Column C, post-accident. Note the bubbles indicating gas production. (b) The biofilm on the surface of Column D. Seems to be better established than what is seen in Column C.

One thing that really surprised me from what I observed in Columns C and D, was that the column with tap water was much more productive than the column with Thames water. I had expected that the river water would create an environment that mimicked natural conditions and would therefore be more productive. I wonder if the slightly brackish nature of the river water inhibited growth? Looking at Columns A and B there seemed to be greater productivity in Column A, (Tap Water), over Column B (Thames Water), which supports the observation that the tap water was more supportive of growth than the Thames water.

Speaking of Columns A and B, over the course of the experiment there was much less growth in these two than in Columns C and D, and I despaired of seeing development at all. (Well, for Column A that would have been a good thing, as it was my control column!) However, by the end of the trial I was happily surprised (please see entry "Action in Columns A and B!!!"). As well, what I observed was fairly different from what I saw in the other two columns, which made things even more interesting. First of all, the water in both columns was a foggy, light brown color (fig. 6) likely due to color leaching out from the potting soil. If there had been any photosynthetic bacteria, I was not able to identify it by color.

Fig. 6 Changes in Columns A and B! Note the foggy, light brown color of the water, as well as the indeterminate transition zones between the potting soil and the water. If you enlarge the photo, you'll be able to see the bubble layer on top pretty well.

Also, as the material from the surface had eventually (finally!) settled to the bottom, I was able to see activity on the surface, in the form of lots of bubbles in (fig. 7) and a little bit of green growth around the circumference of the water’s surface in Column A (fig. 8)!

(a) (b)

Fig. 7 The bubbles at the surface of (a) Column A and (b) Column B.

Fig. 8 Green growth around the circumference of the water's surface! (Also visible in fig. 7a)

Column B had a hazy funnel of material in the middle of the water column, (fig. 9) and both columns had a very indefinite transition between the potting soil and the water (see back to fig. 6 again). Also interesting to note, there seemed to have been a lot more evaporation in Columns A and B, than in Columns C and D. They did start out with lower water levels (please see entry “Get Ready, Get Set Up”), however at the end there was far less than at the beginning.

Fig. 9 I found this funnel of material in the center of Column B to be very interesting as none of the others had this.

The most impressive development I saw in those columns was in Column A (fig. 10). Along the part of the column that faced the sun, there was a large swath of grayish growth that led up from the soil layer all the way to the top of the water layer. It looked like there were little bits of green; perhaps it was the precursor to more photosynthetic organisms. I’m curious though as to why there was much evidence of it in the water portion, but no growth in the soil portion. Perhaps, when compared with the gray-colored Thames mud, the potting soil was too dark to be able to provide a good look at what may or may not have been growing there. Also, there was a difference in the smell between Columns A and B. Column B’s smell was very similar to that of Columns C and D, earthy. Column A, however not only had an earthy smell, but also smelled strikingly of rotten eggs. Sulfur production???

Fig. 10 Please excuse the camera angle, but it was the best way to show the swath of gray running from the top of the mud layer to the top of the bubbles on the surface of the water. This was the side that received the most sunlight.

One thing I do wish I had had access to throughout this experiment would have been a microscope and slides. I think it would have been very interesting to see what was growing close up, though I did have fun just watching colors and patterns appear on a macro scale. I found it very interesting the range of changes I saw, especially considering that I did not add anything to the columns to promote growth. I wonder if whatever was in the Thames river water served to inhibit growth? Also, I wonder if potting soil columns are normally that slow to develop and if they really do not have that much in the way of microbes living in it. I would have thought that even though it was a commercially packaged soil, there would still be ample nutrients to encourage growth, as it is supposed to be a good medium for plant life (hmmmm, maybe that’s why my plants aren’t doing so well…). Even though Column A was supposed to be my control, and perhaps I wasn’t supposed to see any growth in it, maybe it showed what baseline columns are supposed to be like. Maybe next time I’ll try this experiment with a variety of potting soils and see how they all compare.

As I said, I’ll miss my columns, but I had a lot of fun watching them grow! Thank you for the opportunity!

Action in Columns A and B!!!

April 20 - At long last, there's some action in Columns A (Potting Soil + Tap Water) and B (Potting Soil + Thames Water). Actually, I shouldn't really be excited about the action in Column A as it is supposed to be my control, however new growth/activity is exciting and I won't be suppressed!!!

Ok. Compared with Columns C (Thames Mud + Tap Water) and D (Thames Mud + Thames Water) the changes in Columns A and B aren't incredibly exciting, but it is something! The potting soil sediment that had been resting at the surface has finally started to sink, leaving the surface of the water open to observation (fig. 1).

Fig. 1 The material from the surface has started to sink! Soon I'll be able to see if there's anything growing on the surface, that is, if the bubbles in Column B clear away (maybe the bubbles are a sign of growth!) Column A doesn't have any bubbles at the surface.

In Column B, there is also a thick layer of bubbles on the surface (fig. 2). When I removed the cling film in order to take a better photo, I found that the smell was rather earthy, fairly similar to what I smelled in Column C.

Fig. 2 The bubbles on the surface of Column B. Even though the materials are mostly gone from the surface, it is still hard to see if there is anything growing on top of the water.

More to come!

Wow! Green Stuff!

April 14 — Wow! What a trooper. Even after having to go through the trauma of the loss of the biofilm layer, Column C (Thames Mud + Tap Water) continues to impress with new development and new growth. I went to go take a look at it today and saw that on the sunny side, there was a lot of new, dark green growth that definitely had not been there the last time I looked! (fig. 1). As it is green, and on the sunny side of the column, I'm guessing it's a phototrophic type of microorganism, probably anaerobic as it is well in the mud. Otherwise, the orange growth continues to spread and has covered two thirds of the surface of the mud section, and there continues to be more green growth in the water column.

(a) (b)

Fig. 1 The new growth in Column C! (a) All the changes in Column C. The water has gotten more green, and you can see the green mixed in with the orange in the mud layer on the sunny side of the column. (b) A close-up of the mud layer - here you can really see how the green growth is found throughout the mud layer of the column.

More to come!

R.I.P. Biofilm

A sad, sad day for Column C (Thames Mud + Tap Water). The beautiful biofilm layer on the surface is no more.

Due to an emergency with my indoor compost bin (which is henceforth to be converted into an outdoor planter), I had to move all of the columns so I could open the door to my balcony. Knowing how precariously balanced the biofilm was a result of the last move (half resting on the surface of the water, half suspended perpendicular in the water (sort of like the Titanic, once it broke in half) see the entries "Oops" and "Phew!"), I tried to be very careful when moving Column C. However, my efforts were for naught. The small jostling was enough to displace the remaining portion at the surface and the entire biofilm sank to the bottom of the water layer (fig. 1). There is still lots of new formation on the surface (fig. 2), but now it looks more like Column D (Thames Mud + Thames Water), lightly dotted with film. I'm very upset with myself, I would have liked to see what would've eventually happened had the biofilm been given the entire time frame in which to grow. May you rest in peace in your watery grave.

Fig. 1 You can see the biofilm resting at the bottom of the water layer. In the photo it is on the left hand side, and is sort of circular. If you look at the black ring at the surface of the mud, it's right on top of the ring.

Fig. 2 In this photo you can clearly see the new growth, as well as new bubbles. Hopefully the survivors on the surface form a new layer to rival the old biofilm! (Also, while I had the cling film pulled back to get a good photo, I took a whiff of Column C. It smelled like decomposing, (actually, it smelled like the compost bin that had to be put outside), fairly earthy. I had been avoiding smelling them because I was afraid it would cause discomfort to the house guests we had staying over... I guess I was just being chicken.)

As a side note, this does show a disadvantage to the biofilm, increased mass/density makes it more susceptible to disturbances. I observed that the little pools of film at the surface rode the disturbances on the water's surface easily, however the larger structure was brought under. It was very impressive though how long the biofilm stayed at the surface, with half of it submerged (see "Oops!" and "Phew!")

Phew!!! (and more!)

March 28th — An update on Column C (Thames Mud + Tap Water). It is later in the day post-unfortunate accident, and things look promising. The biofilm that stayed on the surface is as it was (fig. 1), and I've been able to see new growth on the surface. Looks like the microbes are going to make a stand!

Fig. 1 Here you can see the portion that is still on the surface of the water. The blurry stuff around it is the microbial growth on the surface.

While I've been worrying over the biofilm, I took a closer look at what else was going on with the columns. As before (and could be seen in the post "Oops!") Columns A (Potting Soil + Tap Water) and B (Potting Soil +Thames Water) showed no change. I did notice some things with Columns C and D (Thames Mud + Thames Water). First, there's a green ring around the surface of the water in Column C (fig. 2). Perhaps this is residue from the collapsed biofilm. The water also seems to be a bit daker than before, possibly because of the stirring up of the water, or maybe microbes that are able are "jumping ship" from the drowned portion of the biofilm.

Fig. 2 A green ring around the surface of the water in Column C. Also notice the tan color of the water. The dark brown in the water below the green ring is the half of the biofilm that is suspended in the water.

Second, I took a closer look at the side of the column facing the window and there are lots of orange patches in the mud! (fig. 3). I guess I've been so preoccupied with the biofilm that I failed to examine the mud closely, however I don't remember seeing any orange patches when I checked the columns on March 14th. This is the side of the column that gets the most sun. I wonder if I rotated the columns if I'd see orange growth all around, or would the microbes on the side facing away from the window die out? Also, I find it interesting that the dark ring that was found where the mud met the water has now largely disapated. There are some black specks on the wall of the column above the mud, but nothing like what it was before.

Fig. 3 Orange growth! Orange growth!! (Also notice the absence of the black ring that had previously been seen where the mud met the water).

Also, I wonder why Column C is so much more productive than any of the other columns? My initial prediction was that Column D, with the Thames Mud AND Thames Water, would have been the most productive, but it has not produced anywhere near the amount of biofilm that Column C produced. Maybe having tap/distilled(ish) water promotes the growth of the microbes better than the slightly saline water found in the river. I'll look for more info about that. Speaking of Column D, here's a good picture of the black particles right above the mud line (fig. 4). It's interesting that the moving of the columns did not seem to affect Column D as it did Column C. The growth on the side of the bottle seems to be doing just fine. Also, there is some orange growth in the mud in Column D too (yay!), though not as much as see in Column C.

Fig. 4 The black colored growth on the sides of the walls of Column D , just above the mud line. Also notice the orange growth in the mud. (For this picture, to best show the black growth, I rotated the column, which is why the orange in the mud is facing away from the window. I later rotated it back to the way it was.)

Oops!!!

March 28th — Yikes! I had to move my columns a bit to get out onto my balcony. I thought I had been very careful, but apparently enough water in Column C (Thames Mud + Tap Water, middle right) sloshed on top of the biofilm on the surface, enough to sink part of it! (fig. 1). The biofilm, which had been covering the entire surface, has now bent in the middle, with half of the film hanging down into the water. I wonder what will happen to all those microorganisms... The other three columns appear unaltered.

(a) (b)

Fig. 1 (a) What the biofilm looks like post-accident. (b) A close up of the carnage.

... And A Couple Weeks Later!

March 14th — So a couple weeks later from the results described in my last post, some more changes can be seen in the columns (fig. 1). As before, Columns A (Potting Soil + Tap Water, far left) and B (Potting Soil + Thames Water, middle left), still appear as they did initially. I'd guess that the color from the soil has steeped into the water, giving it that tea-color, however no growth has been observed either in the soil layer, in the water column, or in the sediment at the surface.

Fig. 1 All four columns a month on. Columns A (far left) and B (middle left) show little change from before. The most change has been seen in Column C (middle right), with minimal change in Column D (far right).

The most obvious difference between the results seen in this post and last post is the change in the color of Column C (Thames Mud + Tap Water), which has gone from black and opaque to more like Column D (Thames Mud + Thames Water). There is a dusting of dark in the water above the mud line (fig. 2), as was observed in Column D last time, which makes me wonder if all the coloration (microbial growth?) has either settled to just above the mud, or has dispersed throughout the water column. Now that the water is transparent, filamentous growth can be seen at the base of the biofilm at the surface, which is just as robust as it was the last time. There seems to be little change in Column D, except for maybe a decline in the filamentous growth at the surface of the water. I'll keep my eyes on these guys and keep you updated!!!

(a) (b)

Fig. 2 - Here you can really clearly see the change in Column C. (a) The water in Column C (second from right) is fairly transparent. It's easy to see the filamentous growth extending into the water from the biofilm layer. (b) In this photo from last month you can see how dark the water in Column C is compared with Column D.

Almost a Month Later!

March 5th — A month into the project and the columns are taking on personalities of their own! Looking at all four of them side by side, it is clear that there are considerable differences, especially between Columns C and D from columns A and B (fig. 2). Fig. 1 All four columns side by side. From left, Columns A (Potting Soil + Tap Water), B (Potting Soil + Thames Water), C (Thames Mud + Tap Water) and D (Thames Mud + Thames Water).

By far, Column C (Thames Mud + Tap Water) has been the most productive, having developed a very thick biofilm on the surface of the water. There are two large "bubbles" of growth (fig. 2), and the entire film is a dark brown color with bits of light splotches, and dark patches where the growth is closer to the water. The biofilm is about 2-3 mm thick on the surface of the water, however the "bubbles" are almost a centimeter thick!
Fig. 2 - Column C's beautiful, thick biofilm layer on the surface. The large rise (seen at the bottom of the photo) is about a centimeter high from the surface of the water!

The rest of Column C has been pretty productive. As seen in Fig. 1 and in Fig. 3, the entire water column has gone very dark. There seems to be a darker ring right where the water meets the mud, but the entire water column is pretty opaque. It looks as though Column D is following suit, just more slowly. There is a strong, dark ring where the mud meets the water, and right above that the water is a gray color, but above that the water is still transparent. Whereas in Column C, the biofilm dominates the entire surface area of the water, in Column D growth is more subdued. There is biofilm formation occuring, (fig. 4), but it is not growing nearly as fast as Column C. There does seem to be some filamentous growth at the water's surface, where the water meets the bottle, which cannot be seen in Column C. However, Column C's coloration makes seeing filaments like that in Column D incredibly difficult.

Fig. 3 Column C (on left) and D (on right). In this photo you can clearly see the color difference in the water layer. Column D has a bit of shading right above the mud layer, whereas Column C is dark throughout the entire water column. You can also see the difference in the size of the biofilm layer - well, you can see Column C's considerable biofilm layer. For Column D's you have to get up closer (fig. 4). But do note the filamentous growth where the water meets the bottle in Column D (you may have to zoom in to see it better).

Fig. 4 Column D's gas production. You can clearly see bubbles that have risen from the bottom. As well, you can see biofilm starting to form, but it is nowhere close to the amount of growth seen in Column C.

As for Columns A and B, there does not seem to have been much change since the initial set up (fig. 5). The water level has gone down slightly, which I'm guessing is due to evaporation. In both columns there is a layer of sediment (bark pieces, etc.) on the surface, which limits my ability to see if there's microbial growth. I plan on leaving the sediment at the surface for now, to see if any growth appears at the top. As well, I have not been able to tell if there's growth at the layer between the water and the soil. Occasionally bubbles rise to the surface, however these are minimal compared with Columns C and D.

Fig. 5 Columns A (left) and B (right). Little observable change since the initial set up.

The Next Day...

Thought you'd enjoy this photo of my Winogradsky Columns after a day of sitting. I found it really cool how all four have settled differently. Here you can also see the difference in the water levels.

PS - I know I'm posting this a month after I had taken the photo, sorry!!!

Get Ready, Get Set Up...

(Look at me, I'm a blogger!)

Day 1:

Introduction:

I live pretty much right on the south bank of the Thames here in London, pass by it every day, and I thought that this experiment would give me a good opportunity to learn more about this river that is so important to the the city of London (please see "The Thames: an Overview," to be posted shortly). I've had experience working with a Winogradsky Column before, but always with fresh water and with other additives so I am excited to see how the slightly brackish Thames water will work. To give myself the greatest opportunity for observation, I created four columns: a control column with tap water and organic potting soil, a column with potting soil and Thames river water, a column with Thames mud and tap water, and finally a column with both Thames mud and river water. I did not supplement my columns with any additional carbon or sulfur source, as I wanted to simply observe what happened with the basic ingredients.

Materials:

- 5 2L bottles, 4 with tops cut off
- Rubber bands
- Cling film (that's plastic/saran wrap to you Americans!)
- Bucket
- Thames river mud
- Thames river water
- Organic potting soil
- Tap water c/o the city of London
- Exacto knife
- Scoop
- 125g cup

Procedure:

Thames river mud and water was collected just after low tide from the tidal flats by the Vauxhall Bridge (fig. 1), accessed by the London Duck Tours boat ramp. Using the bucket and scoop, an ample quantity of mud - enough to half fill two 2L bottles - was collected, with care being taken to not collect any river rocks or twigs. A 2L bottle was filled with water from the river. Back at my flat, the tops of four of the 2L bottles was cut off using the exacto knife, so that the four bottles were the same height. To standardize the amount of potting soil and mud that was put into the four columns, a 125g container was used to scoop.



Fig. 1 - A view of the tidal flats by the Vauxhall Bridge just after low tide. The shallow pool in the center left of the image is where the mud was collected from.







Columns A and B each received three scoops of potting soil, Columns C and D each received three scoops of Thames mud. Then, using the same container (rinsed out), liquid was added to each column. Column A received four scoops of London tap water and Column B received four scoops of Thames river water. Column C received three scoops* of London tap water and Column D received three scoops* of Thames river water. I then covered each column with cling film, securing it with two rubber bands each, (fig. 2). I then lined the columns up by my balcony-side window so they would get equal amounts of the scant London sunlight while being in a temperature-controlled environment. My protocol was based on the one found at http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/winogradsky.html.








Fig. 2 - the set-up columns, pre-cling film. From left, A, B, C and D. Note the difference in the water level between A and B, and C and D, though C and D had one less scoop of water added.




(*When I went to add water to Columns C and D I found that after adding three scoops, the water level was already higher than the levels in Columns A and B (fig. 2) and so decided to stop rather than risk having the water level overflow. I hypothesize that the mud was already heavily saturated with water and so the added water rested on top rather than mixing as it did with Columns A and B).

PS - as stated, currently my columns are being kept inside, in a controlled environment. However, if they start to smell they're going to migrate to the other side of the balcony door...