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.
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!
Thursday, 30 April 2009
Wednesday, 1 April 2009
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.
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!")
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.)
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.
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.
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.
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.
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.
... 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!!!
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.
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!!!
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.
Friday, 6 March 2009
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.
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!!!
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