Turning the Tide on Plastics

The human genome project, which was completed in 2003, was an international collaboration to read the entire genetic code - or sequence - of the human genome - the DNA recipe that makes you you. It ultimately took over 13 years, cost billions of Pounds and involved warehouse-scale buildings full of car-sized sequencing machines to do it. A third of the work was completed down the road from where we are at the Sanger Institute near Cambridge. Since those days, sequencing technology has come on leaps and bounds, and this week scientists announced that they’ve achieved the same feat - sequencing a whole human genome - but this time with a machine smaller than a chocolate bar. It took weeks, rather than years, and cost only about a thousand pounds. Lewis Thomson has been hearing how…

Lewis - Inside each of your cells a huge amount of DNA is tightly wrapped up. In fact, if all of the DNA from just one cell was stretched out, it would be about two metres long even though it fits inside a space just a hundreth of a millimetre across.

This DNA in its entirety is called your genome and it’s made up of lots of smaller subunits called bases - As, Ts, Cs, and Gs. The human genome is three billion bases long and the sequence of these bases is what determines the function of each gene - a bit like a computer code.

Being able to sequence a genome quickly and at low cost could affect how disease is diagnosed and treated, and this possibility is now one step closer. Matt Loose from the University of Nottingham told me more…

Matt - The goal of this project was to really try and push the boundaries of DNA sequencing on a new technology which is the Oxford Nanopore minION Sequencer. This sequencer was introduced about four years ago now, and it became clear around a year ago that it would be possible to sequence a human genome one a minION sequencer. The thing that’s remarkable about that is that the sequencer itself is about the size of a chocolate bar or a small mobile phone. It’s an extremely portable device and you just plug it into a laptop and you can sequence DNA anywhere that you want to.

Lewis - Most genome sequences used today by scientists are extremely large expensive machines which require specialist training. The minION sequencer is much smaller and cheaper. But how does it work?

Matt - Essentially, it’s a rectangular metal box. It has a cartridge that slips inside it and that cartridge or flow cell, as we call it, contains a membrane and in that membrane are lots of nanopores, and nanopores are essentially small holes. The way the sequencer works is it applies a voltage across the surface of the membrane, that allows a current to flow through those small holes. Also, DNA can pass through those holes and as the DNA passes through the hole it of course blocks, and changes, and alters the current flow. It turns out that the changes in current flow are proportional to the sequence that’s present in the nanopore at that moment in time. So, effectively what you get is a current trace, or we call it a squiggle, which reflects the underlying As, Ts, Gs, and Cs.

Lewis - For several years, the minION sequencer was much less accurate than the large sequencing machines used by most scientists. However, the technology has now improved to the point of being almost as accurate and, in addition to its size and cost, it has other benefits. Many current methods involve cutting the DNA sample up into tiny fragments of just a few hundred bases to be sequenced. A computer then has to the assemble these short sequences together to make the full genome sequence. This takes a great deal of time and can also lead to inaccuracies. The minION sequencer has a much higher read length - in other words it can sequence much longer fragments of DNA - fragments which are hundreds of thousands of bases long.

Matt - The advantage of this technology over other competing technologies essentially is the read length that you can generate, plus the real time nature that you can look at the sequence. So with respect to the read length, we can see parts of the genome that we haven’t been able to see before. Things like telomeres: the ends of chromosomes which can be absolutely critical in understanding particular tumour types.

I think the other issue is in nanopore sequencing, in principle, you can start looking at the sequences the moment they appear from the sequencer. So if you were looking for a particular bacteria or detecting a virus, you can see that the moment that it appears in the sequencer. There are lots of examples of people taking nanopore sequencers into the field; some of my co-authors were involved in sequencing Ebola during the outbreak. They went on to sequence Zika virus during the recent outbreak in Brazil and others are applying this technology in similar situations around the world to get real time, rapid information about the pathogens in the environment and about their sequences.

Lewis - So maybe in the future doctors could use this handheld sequencing technology to diagnose illnesses, whether that’s identifying the genome of a particular virus or bacterium or even sequencing a cancer tumour to work out which treatment would be the most effective. Thirty years ago, this would have been impossible. Now, it’s looking more and more likely.

In recent years Oklahoma City has been subjected to hundreds of earthquakes. A decade or so ago though it was recording only one or two. Why? The answer, a new study suggests, is that it’s down to the oil and gas industry. Contaminated water that’s been used to force out oil under pressure from below ground is being disposed of by injecting it back deep into the bedrock where it’s causing things to slip and slide about. Izzie Clarke...

Izzie - Oklahoma: a state that’s home to four million people, where the voicemail was invented and, in the 20th century, produced the most oil of any state or territory in the  United States. In fact, oil was first discovered there by accident in 1859 but now, they’ve got another accident on their hands that’s shaking things up…

Tom - My name is Tom Gernon and I’m an Associate Professor in Earth Sciences at the University of Southampton.

Oklahoma has experienced some pretty intense seismicity over the last decade. Seismicity is the frequency at which earthquakes repeat through time and, in the case of Oklahoma, if you think back to 2008, they had one earthquake which was over magnitude three - by definition, an earthquake that  you can feel. In 2015, the number of earthquakes was 903, so that just gives you some sense of the scale of the problem here. These earthquakes are linked to the injection of water underground into deep rock formations.

Izzie - The reason for this process is to extract oil from the ground. Across Oklahoma there are 10,000 or so wells where water is injected at high pressure deep underground to help release oil and gas which is locked up in the rocks. This contaminated water and oil combination then comes back out of the well, is separated and yes, the oil companies have their oil... but what about all that waste water?

Tom - If you think about it, you’ve got 2.3 billion barrels of  waste water and you’re in a sort of landlocked state in the centre of the US. Very expensive to ship it elsewhere to be processed and treated and disposed of, so it’s economically more efficient to inject this deep underground because it’s otherwise very expensive to get rid of.

Izzie - This constant cycle of injecting wastewater into the ground not only weakens the rocks but acts as a lubricant, which is part of the problem. The University of Bristol and Southampton University developed a statistical model that was able to analyse a combination of impacting factors…

Tom - What we looked at was data from these injection wells: the injection volumes, injection depths, and injection locations through time. We looked at all these different parameters and the correlation between those different parameters and the seismicity - the earthquakes that are happening - within a given radius of the injection wells. And, I should say, typically the injection depth is about one or two kilometres beneath the surface.

Izzie - The injection depth a few kilometres underground was a huge factor for the frequencies of these earthquakes due to the type of rock lying there…

Tom - The wastewater is normally injected into sedimentary rocks which are overlying much deeper crystalline, very old rocks - you can think of granite maybe, or metamorphic rocks which are heavily fractured and so on. Liquids can then find a way downwards basically into the boundary between these two different rock types, and we know that most of the earthquakes in Oklahoma are happening in these deep, what’s called crystalline basement rocks. These are, presumably, very heavily fractured; there’s lots of old ancient faults in there which allows the stress to build up and release.

We have most of the biggest earthquakes which have happened over the past decade have actually been in this rock. The closer you inject to that level, the more earthquakes you’re going to experience. This is incredibly important; it’s not been shown before; it carries a lot of implications for regulation in Oklahoma, and potentially elsewhere. The operators could use this information to change their practices and, potentially, raise well levels to reduce the earthquakes that are happening.

Izzie - Another key finding was that there’s even a time lag. Wastewater would injected into the ground and the resulting earthquake would then hit a few months or even years afterwards. With over two billion barrels of wastewater injected into the ground every year, for Oklahoma worse may be yet to come…

Tom - Another thing we need to consider is that the oil demand hasn’t really been very high over the last two years. The number of earthquakes has dropped slightly since 2015, although we have had some of the biggest earthquakes - I think magnitude 5.8 Pawnee earthquake which struck in September 2016. This is the largest magnitude earthquake that has ever happened in Oklahoma and this caused injury and damage to buildings. This happened at a time when injection had actually been reduced by the regulators. This shows that there are these potentially significant time lags between injection and seismicity.

We all know about problematic plastic filling the oceans and destroying marine life. But what is plastic, how is it made and why does it last for so long? Plus, could we get bacteria to biodegrade it for us? Georgia Mills got the low-down from Cambridge University chemist Steven Lee...

Steven - A plastic, when chemists think of plastics, what we’re thinking about is repeat monomer units, so the word polymer you may have heard is that’s how chemist’s don’t really think about plastics. That’s essentially, a bit long chain molecule that consists of much smaller molecules linked together typically via a carbon link.

Georgia - So a monomer is like a little unit, a little pod, and then a polymer is a load of these strung together?

Steven - Exactly. Poly meaning many, and mer meaning unit, comes from the Greek polymer.

Georgia - Ah, it all makes sense. So how do you make a plastic?

Steven - There’s lots of ways to make a plastic and they have very large meanings. But I think in the general terms when people think about a plastic spade or some wrapper, the way you do that is you take a small molecule that has a carbon/carbon double bonding and you apply by various heats or chemical reactions you can encourage that to form long long chains. That typically can be done by small molecules that come from the petrochemical industry for instance.

Georgia - Why does it stick around for so long?

Steven - The reason is there’s not the traditional method for things that degrade. When we think about something’s rusting or trees or organic waste being digested, there are biological organisms that have spent billions of years evolving lots of complex pathways to be able to break those bonds. In the case of cellulose that’s a polysaccharide, that’s a polymer as well but it’s made of lots of sugar molecules. But in the case of a polymer like a plastic bag at a shopping centre, that’s typically made of polythene or polyethylene and so that’s a very different kind of chemistry - one that’s got to break a carbon/carbon bond. That’s much harder for the natural world to break down and so, unfortunately, we haven’t had the bacteria and other environments and haven’t had to time to deal with that.

Georgia - Right. Something like cellulose which is actually kind of similar to a plastic can be broken down just because it’s been around for millions of years within plants?

Steven - That’s true, it’s called a biopolymer. There’s three kinds of biopolymers, but what we’re talking about here is this unusual class which we see every day but, on the timescale of evolution is a relative newcomer and we’ve only had the first completely synthetic plastic since 1907.

Georgia - Why can’t we just recycle it? Why can’t we put it like in the opposite way through the plastic machine?

Steven - Yeah. That’s a thermodynamic answer to that. It to do with all the technology to understand why plastics don’t mix is the same chemistry and the same physics that we worked out in the industrial revolution. In fact, what it’s to do with is that if you take two compounds and try and mix them together, sometimes they mix, sometimes the dont, but polymers don’t like to do that because they don’t gain as much entropy - this term about how disordered something is. So, what that really means is because polymers don’t mix, if I just take a mixture of my compounds and just try and heat them up to kind of regenerate a big slush of plastic, it means that they all phase separate. They’re much like oil and water don’t mix, you get the same thing with plastics, so what that really means is that it’s quite difficult to separate them out in order to recycle them in a way that, for instance, aluminium or metal isn’t quite as difficult.

Georgia - I guess, quite often within the same product you have a few different types of plastic all in one place?

Steven - Absolutely. If you look very carefully on the bottom of your plastic baby or on the bottom of your bottle of diet coke, you’ll see that there’s a little mark and that terms the type of plastic. What that means is that if you have polyethylene or polythene, that’s possibly recyclable with other clumps of polythene, but it’s not if you use polymethyl methacrylate or polystyrene or any other synthetic polymer we use traditionally today.

Georgia - Could we use nature to help us then. Is there anything out there that might be able to munch away at these carbon bonds?

Steven - There’s president in the literature for various bacteria and also fungus to degrade very specific types of plastic. In biology there’s lots of ways in which we can digest plastic, but the chemistry to be able to digest these specific compounds is unusual and, therefore, doesn’t exist at lot. There absolutely could be, but we haven’t found anything yet. There have been some studies where the way people actually look for them is they look in and around plastic plants because they think if the bacteria could start eating plastic it would be a limitless source of food. It’s an all you can eat buffet of energy to the bacterium, so there is a clear push for them to be able to use it. Unfortunately, normally what happens is we have to find one, because of all the chemistry that I was talking about is very specific, it means that bacteria have to evolve different ways to be able to digest specific plastics. So you don’t get one bacteria that will eat all plastics, but there are samples of bacteria that eat very specific kinds but just not very very well at the moment.

Georgia - Very briefly, do you think we could modify something in a lab - a super bacteria - to just go into the oceans and destroy all the plastic and solve all of our problems?

Steven - Yeah. “Catch a spider to kill a fly.” It’s possible and I think loads of people are working on really interesting ways to be able to modify bacteria. We have lots and lots of genetic tools in the laboratory to be able to change bacteria to do our bidding, as it were. The trouble is is that the specificicity to be able to break this carbon/carbon bond in my plastic bag and not break the carbon bond in me is very different, and that’s the challenge going forward.

Could we switch to an alternative that isn’t so long lasting? Bioplastics aim to do this, by using alternatives to oil in the production process. One team is aiming to cut waste even further by making bioplastics from waste itself! Georgia spoke to Damian Laird at Murdoch University in Perth.

Damian - We like to tell people that we’re making plastics from poo but, in reality, what we’re trying to do is utilise resources that are in waste streams and turn them into something profitable. Rather than just basically treat them and send them out into another stream, try and make a product out of them.

Georgia - What kind of product can you make from sewage?

Damian - To be frank, we don’t quite use the sewage. We use the bacterial cultures that are in the sewage and they can produce a bioplastic. That’s biodegradable and we can use it for packaging and some other types of things and replace oil based plastics.

Georgia - Would this look like an ordinary plastic? Would it smell?

Damian - No, no, they just look like ordinary plastics at this stage. They definitely don’t smell, the cultures themselves don’t even smell which is great because it makes the lab much more interesting. But, yeah, we’re hoping that we can reproduce the same characteristics of an oil based plastic but hopefully use a biological process to get it done, so whilst the biological process is cleaning the water we’re getting a product at the same time.

Georgia - How does this technology work?

Leonie - My names Leonie Hughes and I’m a lecturer in chemistry at Murdoch University in Perth, Western Australia.

Basically, it’s the equivalent of us eating too much food and getting fat. The bacteria are put under conditions where they are given far too much food, but not enough of an oxidant source, such as oxygen or ammonia, something like that. So they get too much of chips and not enough fruit and veggies and exercise. Under those conditions they effectively store the rich carbon source that they get given so that they can hide it from other bacteria. It’s an evolutionary thing that advantages them over other bacteria. And then, under conditions where they suddenly have no external source of carbon but a rich source of oxygen or ammonia, they can then use that to continue growing when no-one else can.

Georgia - I’m imagining the bacteria equivalent of a hamster stuffing seeds in its cheeks?

Leonie - Pretty much. It actually form vacuoles in the cells that you can visualise as big lumps of plastic basically.

Georgia - What do you have to put into the bacteria to get this plastic out?

Leonie - Many many many bacteria are shown to do this, obviously some are better than others. You just need to give them something like glucose or vinegar, something rich in carbon, and let them do it. Just try not to give them too much oxygen or too much nitrogen at the same time and they pretty much go for it themselves.

Georgia - Then they create these bags of plastic in their cells, how do you then get this out of them?

Leonie - At the moment this is the un-environmentally friendly bit, potentially. This is the bit where we have to use solvents and thing to kill the bacteria and extract out the plastic, so that part of it, at the moment, is not looking particularly nice. However, there are some people doing some research in similar areas with things like algae that can extrude thing like bio oils or potentially even the plastic so there are other ways of looking at it.

Georgia - How is this plastic different from ordinary plastic?

Leonie - It’s not. It’s what’s classed as a thermoplastic. It still has the same kind of properties that plastics that you see in shampoo bottles and things have. It does need some post-processing, so it doesn’t have the cross-linking things, the more complicated third degree structure that plastics have that get used commercially. But those are things you can add in a chemical sense after they’ve been extracted from the bacteria. We might be able to design the feed that we give the bacteria better to enhance the production of copolymers, so polymers made up of more than one monomer, more than one building block and, if we do that, plastics will come out closer to commercial plastics at that point already.

Georgia - How easy will this be to scale up? How are you going to get a usable amount of plastic from this process?

Leonie - Yeah, it’s not trivial. We would have to do things like high density cell cultures and they’re quite hard to manage. You would need to have membrane technologies and things like that to have maximum, maximum, number of bacteria in small footprints of space so that you’ve got minimal amount of water, maximum amount of bacteria and, therefore, ease of extraction of the bacteria. These are not trivial questions but, if we can get the technology working at the lab scale, then that’s where we would link up with an engineer who would solve, hopefully, those problems for us.

Georgia - Then, at the end of this process you hopefully have a plastic that is biodegradable. Why is it biodegradable?

Leonie - Just purely because of the nature of why the bacteria make it. They make it so they have carbon source later when they have abundance of oxygen, but they don’t have any carbon external to the cell. It has to be degradable by them otherwise they wouldn’t have made it for the advantage of getting the fat in their cells and stealing it from other bacteria, so that automatically means it’s biodegradable.

Georgia - Best case scenario: what are you hoping that this can do?

Damian - The big picture is that we could hopefully locate one of these plants next to an industrial site, take their waste water, clean up the nitrogen in particular that comes out of it that the bacteria can use, and then also produce a product. We can hopefully create a product that we can change that product at will for different uses.

One of the really big ideas we’d like is not just to take traditional waste streams like you would expect in a wastewater treatment plant, but industrial waste streams as well. There are lots of industries - wineries for example, breweries that use use bacterial cultures to clean their water before they release it, but that contains a lot of carbon. We hope that what we can do is create carbon, create these polymers from that waste carbon in a sense, and then may be able to produce the packaging for the beer along the way.

Georgia - Using a product that would have been created anyway by this other process that would have otherwise gone to waste?

Damian - Yeah. And so that whole process them becomes very microbiological because you use yeast to make the beer in the first place. Bacteria in yeast to clean the water and then produce the packaging potentially for the product, which is amazing.