The CocoDish: a natural, sustainable, and reusable vessel for culturing bacteria

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When I began to study microbiology some 30 years ago we used to use a lot of reusable glassware. For example, Glass Petri Dishes, Universal Bottles, Bijous, McCartney Bottles, Pasteur Pipettes, Glass pipettes and Glass Spreaders. We also used to use metal loops for sub-culturing and again these could be sterilised and then reused by passing then through the flame of a Bunsen Burner. Today, much of the above has been replaced by plastic consumables, which are used just once before disposal, and thus microbiology has become a very wasteful scientific practice. Moreover, microbiology is not alone here, and many other biological sciences use vast amounts of disposable plastic laboratory ware.

 

As a challenge to this wasteful practice and to bring it to light as a problem in terms of sustainability, I’ve developed the CocoDish, a sustainable, reusable and entirely natural vessel for culturing bacteria based on the Coconut. As proof of utility here is a CocoDish containing Kitchen Bioluminescent Agar (KBA) and a culture of the bioluminescent bacterium Photobacterium phosphoreum HB (in light and in the dark). No need for plastic! Could also be used in locations where plastic Petri dishes are difficult to source.

Empty CocoDishes below

 

 

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A CocoDish filled with bacteriological agar. It fits beautifully into the hand, and unlike its plastic counterpart, has a wonderful warm, rustic, and organic feel.

 

Below, a CocoDish with a culture of the bioluminescent bacterium Photobacterium phosphoreum HB. imaged in the dark (left) and in light (right).

 

 

Satellites of Summer

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At this time of year, every evening, House Martins gather in the sky above our house. For over 25 years they have provided the soundtrack of our Summers. As the sun sets, and as they pitch and turn, they occasionally catch its light so that their white markings flare like ephemeral satellites against the darkening sky.

These are the tracks that they make above our house. We also have a young House Martin family that live in a muddy home attached to ours.

 

Taken with NightCap Pro. Light Trails mode, 14.99 second exposure.

14.99 second exposure.

Taken with NightCap Pro. Light Trails mode, 23.17 second exposure.

23.17 second exposure.

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Domestications

Microvideos of various infusoria that I found in my garden and recorded using a field microscope in my kitchen and with the sounds of this domesticated environment. Dishwashers, washing machines etc. The machines of domestication and complex biological machines together. Magnification 100x

Natural Frequencies III

I’ve developed a novel process that rather than recording micro-videos in real-time, records instead the paths taken by microscopic creatures under the microscope. The images generated, result from the accumulation of the activity tracks of these usually invisible life forms and reveal the hugely complicated dynamic of their manifold activities and interactions. The process generates images that are in some sense similar to those of radioactive decay, or atomic particle collisions, as they are seen using cloud chambers.

The process reveals another level of reality that is usually withheld from us and so it seems that each body of natural water vibrates to.

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Taken with NightCap Pro. Light Trails mode, 86.56 second exposure.

86.56 second exposure.

Taken with NightCap Pro. Light Trails mode, 86.56 second exposure.

86.56 second exposure.

Taken with NightCap Pro. Light Trails mode, 75.08 second exposure.

75.08 second exposure.

Taken with NightCap Pro. Light Trails mode, 40.72 second exposure.

40.72 second exposure.

Taken with NightCap Pro. Light Trails mode, 75.08 second exposure.

75.08 second exposure.

Taken with NightCap Pro. Light Trails mode, 40.72 second exposure.

40.72 second exposure.

Natural Frequencies II

I’ve developed a novel process that rather than recording micro-videos in real-time, records instead the paths taken by microscopic creatures under the microscope. The images generated, result from the accumulation of the activity tracks of these usually invisible life forms and reveal the hugely complicated dynamic of their manifold activities and interactions. The process generates images that are in some sense similar to those of radioactive decay, or atomic particle collisions, as they are seen using cloud chambers.

The process reveals another level of reality that is usually withheld from us and so it seems that each body of natural water vibrates to.

 

Taken with NightCap Pro. Light Trails mode, 24.75 second exposure.

24.75 second exposure.

Taken with NightCap Pro. Light Trails mode, 57.28 second exposure.

57.28 second exposure.

Taken with NightCap Pro. Light Trails mode, 33.72 second exposure.

33.72 second exposure.

Taken with NightCap Pro. Light Trails mode, 26.44 second exposure.

26.44 second exposure.

Taken with NightCap Pro. Light Trails mode, 21.68 second exposure.

21.68 second exposure.

Taken with NightCap Pro. Light Trails mode, 37.77 second exposure.

37.77 second exposure.

Natural Frequencies I

 

I’ve developed a novel process that rather than recording micro-videos in real-time, records instead the paths taken by microscopic creatures under the microscope. The images generated, result from the accumulation of the activity tracks of these usually invisible life forms and reveal the hugely complicated dynamic of their manifold activities and interactions. The process generates images that are in some sense similar to those of radioactive decay, or atomic particle collisions, as they are seen using cloud chambers.

The process reveals another level of reality that is usually withheld from us and so it seems that each body of natural water vibrates to these invisible biological wavelengths and frequencies.

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Macroscopic. The pond

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The pond and portable field microscope

Taken with NightCap Pro. Light Trails mode, 56.00 second exposure.

56.00 second exposure.

Taken with NightCap Pro. Light Trails mode, 40.60 second exposure.

40.60 second exposure.

Taken with NightCap Pro. Light Trails mode, 43.34 second exposure.

43.34 second exposure.

 

Exploring The Invisible: microbiology and art workshop, University of Surrey

 

 

I ran the first microbiology and art workshop at the University of Surrey for over 30 participants last week. Here are the activities and outcomes.

Ehrlich Staining:  DIY histology and revealing the oral microbiome 

Paul Ehrlich made countless contributions to science  in fields as diverse as histology, haematology, immunology, oncology, microbiology and pharmacology. In the course of his investigations Ehrlich came across methylene blue, which he regarded as particularly suitable dye  for staining bacteria.

Here I have drawn upon Ehrlich’s early studies on staining bacteria and developed a simple off-the shelf/ DIYBio-staining procedure for bacteria and  human cells. It is based on methylene blue which is readily available as a “fish medicine”. The brand I used here is King British Methylene Blue. It works very well as it comes in the bottle, and without the need for any messy preparation. Here participants were asked to spit onto a microscope slide so that saliva could be examined for cheek cells, their nuclei, and the normal oral bacterial flora.

For comparison, below is an unstained saliva sample.

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Visualisation of saliva at 200x magnification using Differential Interference Contract Microscopy.

 

The stained saliva samples were initially observed at 200x magnification (below)

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Ehrlich staining of saliva, 200x magnification. If you look closely you can see cheek cells and the dark stained oval body inside is the nucleus of the cell.

 

When the stained saliva samples are observed at 1000x magnification far more detail is revealed (below).

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A saliva sample stained with methylene blue. Buccal epithelial cells are visible as large pale blue cells with a dark staining nucleus contained the genome/DNA. Numerous bacteria are visible either attached to the cells or in other parts of the stained sample. 1000x magnification

 

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A saliva sample stained with methylene blue. Buccal epithelial cells are visible as large pale blue cells with a dark staining nucleus contained the genome/DNA. Numerous bacteria are visible either attached to the cells or in other parts of the stained sample. 1000x magnification

 

Bacterial war-games: visualising bacterial motility, chemotaxis, quorum sensing, swarming and antibiotic production and resistance. 

“the microscope discovers, what motions, what tumult, what wars, what pursuits, what stratagems”  Samuel Taylor Coleridge

This process was inspired by  the boardgames of my childhood, Risk, Campaign and Diplomacy and the like,  and also by the inherent properties of bacteria.

Instead of coloured plastic counters, pigmented bacteria constitute the different armies  as billions of microscopic soldiers (bacteria) enter into battle.  Each colour is a different inoculum of living and pigmented bacteria, with each possessing a different characteristic/ability. The images here are of the initial inoculation (each differently coloured patch represents a seperate bacterial species), and the map after incubation, and after its nature has been changed dramatically as the bacteria became active, grew,  and interacted with each other. The red and purple pigmented bacteria are aggressive and swarm to infiltrate certain other species. Blue and yellow adopt a defensive strategies and produce powerful, and yet uncharacterized antibiotics, that kill red to protect their own territory. I can’t help but feel that this map is a metaphor for our own species and wonder, as bacteria predated us in evolutionary terms, whether the traits that we see here are hardwired into our own biology. The battles  take place on a layer of the fabric polycotton as  this facilitates the movement of the bacteria through its fibres.

The designs made by the participants before incubation.

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Before

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Before

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Before

 

The designs after incubation (below). During incubation the bacteria move and interact with each other,  and dramatically change the participants designs. The outcome reflects our modern understanding of bacteria how they interact and communicate with each other, collaboration, antagonism,   swarming, chemotaxis, modes of motility and much much more. I feel that the bacteria contribute to these designs, just as much as the human participants, and that the bacteria are very much coauthors in the works.

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After

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After

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After

 

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A smiley face. The yellow pigmented bacterium is producing an antibiotic which is preventing the red pigmented one from claiming its territory.

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The dried war-games. The cotton swatches with the bacterial designs ready for sewing together.

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The dried war-games. The cotton swatches with the bacterial designs ready for sewing together.

 

Toxic change: bioluminescent bacteria as bioreporters for toxic metals.

When we make physical cash transactions we exchange far more than just metal tokens with monetary value.  Carried invisibly at ever  transfer, are hundreds of invisible bacteria (see image below) , or the toxic residues of what the coins are made from.

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The bacteria on a coin revealed by imprinting onto bacteriological growth medium and after incubation.

 

Bioluminescent bacteria naturally produce an ethereal blue light. Healthy cells of these bacteria produce light, those that are damaged are dimmer, and those that are dead are completely  dark. Because of this, bioluminescent bacteria are commonly used in laboratories as sensitive and effective monitors of pollution, for testing environmental samples and drinking water for example. In the workshop participants placed coins onto a confluent layer of bioluminescent bacteria. After overnight incubation,  obvious zones of darkness are apparent  around the coins which means that chemical toxins have diffused from them into the media and killed the bacteria. Most likely this toxic effect is due to the presence of metals like copper and sliver in the coins (see below)

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Coins on a confluent layer of bioluminescent bacteria. Dark zones of inhibition, where toxic compounds from the coins have killed the bacteria, are clearly visible.

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Coins on a confluent layer of bioluminescent bacteria. Dark zones of inhibition, where toxic compounds from the coins have killed the bacteria, are clearly visible.

 

Memories of Failure Externalised: visualising slime mould memories and intelligence 

One of the microbes we explored in the workshop was and old favourite, the yellow coloured slime mould Physarum polycephalum. This is a remarkable microorganism that can solve the shortest root through a maze and that also possesses a spatial memory. In essence, as it moves it lays down a layer of slime in a complex 2-dimensional network. When it has explored a region of its environment where there is no food or opportunity, it retracts from this area, but leaves its traces of slime behind. If it encounters these abandoned threads of slime again, it will not re-explore this region, as it knows that it has visited this area before and that there is no reward here. Here participants, like Hansel laid a trail of white pebble, set out a trail of slime mould food (porridge oats) for the organisms to seek out and follow.

I explored a number of  ways to represent the participants work and am most pleased with this process that uses  a discarded Overhead Projector (OHP) for this. The role of the yellow pigment,  that is characteristic of Physarum, is probably to absorb light and to protect the organism from its damaging impact. The images here (below) are of the slime mould as projected via the OHP, and thus after the microorganism has modified and interacted with the light passing through it. I have a strong sense that this process inverts usual microscopic practice, so that instead of a single observer peering down at microscopic worlds through complex series of lenses, the worlds themselves are projected directly into our own macroscopic reality where we can touch and interact with them.

 

Above the OHP projecting the trail made by the slime mould.

 

Below are projections of the slime mould, each over a metre in diameter

 

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Park’s Kitchen Agar (PKA): DIY bacteriological growth media

Plate Count Agar (PCA) is a widely used general media for isolated bacteria from many different environments. Park’s Kitchen Agar (PKA) is a novel modification of Plate Count Agar. It can be used for obtaining microbial counts from any environment, and is specifically designed for use in facilities where the availability of chemicals may be restricted by Health and Safety issues or by problems with supply. Unlike any other microbiological agar, it is edible, but consumption is not recommended once it has been inoculated.

The principles of the medium are as follows.  The casein present in dried skimmed milk powder provides amino acids and other complex nitrogenous substances that are necessary to support bacterial growth. Marmite, is a form of yeast extract, and primarily supplies the B-complex vitamins need as co-factors. Honey is a natural source of carbohydrates (fructose and glucose) and provides the energy source for growth. The medium can be supplemented with various natural chromogenic compounds that will change colour depending on microbial activity (extract of red cabbage and turmeric are recommended).

This medium wasn’t used for the current workshop but has been widely  and successfully used used in many microbiology workshops.

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Park’s Kitchen Agar. Uninoculated.