Existential biotech hazard that was designed in the 90s?

post by EGI · 2015-03-08T01:08:54.154Z · score: 5 (8 votes) · LW · GW · Legacy · 19 comments

Does anyone know something about this alteration of Klebsiella planticola? Paywalled paper here. (If someone has got access please PM me, I would like to read the paper to write a more fleshed out article.)

While I am not convinced that it would really have spread to every terrestrial ecosystem, or even every wheat field and I am not even sure if it could compete successfully with the wild type, I certainly would not bet the world on that. Even if it might only have become a nasty crop bug instead of an ecosystem killer, I think this may be the closest encounter with a true existential risk we have had so far. This suggests, that even our current low end biotech may be the greatest existential risk we face at the moment. Or is this just hyped bullshit for some reason I do not see right now (without reading the paper)?

 

Edit: Upon reading the original paper I am quite sure Cracked.com greatly exagerated the potential threat. 10^8 cfu (colony formin units) K. planticolata per gram soil (dry weight) was added on day 0, but after 8 weeks only 10^2 cfu survived (this is true for both wild type and modified K. planticolata). This suggests, that K. planticolata in the wild has typical densities more like 10^2 cfu per g than 10^8 cfu per g. 10^2 cfu per g is nowhere near enough to produce lethal ethanol concentrations in the soil, even if the modified strain could compete in the wild. Furthermore the concentration of the modified K. planticolata decreased faster than the concentration of the wild type suggesting reduced fitness of the GMO. On the other hand after 8 weeks both K. planticolata strains arrived at the same density of 100 cfu per g indicating comparable medium term survivability in unsterilized soil (I am not sure if indigenous K. planticolata which could compete with the GMO was present in the soil sample used). Yes, they did avoid the obvious failure mode of not differentiating between wild type and modified K. planticolata during recovery of K. planticola strains from the samples.

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comment by [deleted] · 2015-03-08T01:42:43.690Z · score: 6 (6 votes) · LW · GW

I can't find any good resources (a quick google search shows that this incident doesn't really appear outside of Cracked and anti-GMO websites), but I don't believe this organism would be able to cause any harm in the way suggested. This bacteria produces alcohol at a cost, for no benefit to itself. It would quickly get out-competed in the wild by other similar, less wasteful bacteria, or it would quickly evolve to stop producing such pointless amounts of alcohol.

I had an idea a while ago that's quite similar to this; chlorophyll most strongly absorbs blue light, followed by red, and absorbs green least of all. But the most abundant wavelength that reaches Earth's surface is green! What if you engineered a plant with a completely new pigment that absorbed most strongly at green wavelengths? Would it outcompete all other plants on the planet?

Even in that case, I doubt it. It can't fill all the varieties of niches occupied by the world's plants, who have the advantage of already being highly specialized. The super-plant may outcompete the plants in the niche it most closely fills, but other plants would most likely be unaffected; the new plant can't do their jobs as well as they can.

EDIT: Here is a note from the Green Party of NZ, apologizing for incorrectly citing the original paper and making grandiose claims about the destruction of all plant life:

4) The Green Party also would like to make clear in regard to the same paragraph, that the published literature shows that when a genetically engineered Klebsiella planticola was added to one particular type of soil with plants, plants unexpectedly died. The correct reference for this paragraph is MT Holmes, ER Ingham, JD Doyle, CS Hendricks "Effects of Klebsiella planticola SDF20 on soil biota and wheat growth in sandy soil" Applied Soil Ecology 11 (1999) 67-78.

5) This is an example of an unanticipated effect from the introduction of a genetically engineered organism. It should be taken to say no more nor less that that. The Green Party does not believe the published research so far supports the further conclusion that the likely effect of allowing a field trial of the genetically engineered bacterium to go ahead would have been to destroy all terrestrial plants.

comment by passive_fist · 2015-03-08T02:01:00.920Z · score: 1 (1 votes) · LW · GW

What if you engineered a plant with a completely new pigment that absorbed most strongly at green wavelengths?

This is the absorbance spectrum of the various types of chlorophyll used in plants and bacteria: https://www.assignmentexpert.com/blog/wp-content/uploads/2014/08/absorption-of-light-by-chloroplast-pigments.jpg

We don't yet know the reason why light-harvesting molecules evolved for this spectrum. Without knowing the reason, it's hard to say if a black plant would have any evolutionary advantages at all. It's possible that this is the most efficient way of producing sugar from CO2 and water. It's also possible that it isn't.

comment by [deleted] · 2015-03-08T18:35:09.669Z · score: 0 (0 votes) · LW · GW

Maybe you don't want a whole plant, just a kind of artificial chloroplasts fixed on a membrane through which air is pumped? (I don't mean it as a solution, just that we might be thinking in a wrong direction.)

comment by Houshalter · 2015-03-08T11:13:30.302Z · score: 0 (0 votes) · LW · GW

Is it possible that the atmosphere absorbed more green light early on? Perhaps it was optimal at the time, but now they are stuck in a suboptimal configuration.

comment by [deleted] · 2015-03-08T14:19:09.701Z · score: 0 (0 votes) · LW · GW

I think it's more likely that chlorophyll and its related molecules were just the first photosynthetic pigments that came about, and new pigments couldn't compete with it because they'd have to start from square one, whereas existing life is already built around the specifics of chlorophyll. And as Romashka said, perhaps chlorophyll is already as efficient as possible so a new pigment wouldn't be beneficial anyway.

comment by CellBioGuy · 2015-03-08T16:04:41.424Z · score: 4 (4 votes) · LW · GW

I've seen interesting work noting that the absorption spectrum of chlorophyll is very approximately the inverse of that of purple sulfur bacteria, which were most likely much more common in the early earth due to differences in geochemistry and atmospheric composition. Something taking the scraps that were left behind?

Photosynthesis has evolved many many times, but what has only evolved once in the cyanobacteria (and then been appropriated by blue green algae and countless other endosymbiosis events) is oxygen-producing photysynthesis. This allows the fixation of carbon at much higher efficiency since it can use water as the required electron donor instead of sulfur or metal salts or organic molecules and thus had a big advantage.

The choice of electron source is ultimately independent of the pigments used, but they are linked by evolutionary history.

comment by [deleted] · 2015-03-08T11:40:01.483Z · score: 0 (0 votes) · LW · GW

What we see now might be as optimal as it gets, constrained by the electron transport systems that cannot deal with too much energy coming in. It could mean free radicals destroying the cell from inside. ETA and even if this particular problem is dealt with, accelerated sugar synthesis requires more efficient water transport (= changes in whole body development -> tradeoffs with reproduction and ability to withstand cold seasons) and CO2 intake (= thinner cuticle, larger stomata etc. -> increased susceptibility to disease).

And when you optimize for those things, a life form threatening existing ecosystems is entirely possible.

comment by CellBioGuy · 2015-03-08T17:18:20.959Z · score: 7 (7 votes) · LW · GW

One of the big constraints on photosynthetic land plants today is the sheer difficulty of fixing CO2 into organic molecules in the presence of oxygen, plus the resultant water stress.

Each of the double bonds of CO2 has an electron configuration remarkably similar to the electron configuration of the O2 double bond. Even though the RuBisCo enzyme that cracks CO2 and sticks it on an organic molecule to enlarge it is optimized to grab CO2, the ambient oxygen level is >400 times the ambient CO2 level. At that concentration difference, even a very selective enzyme is going to misincorporate oxygen a reasonable fraction of the time, producing a toxic peroxide that requires energy to square away and deal with. The faster the enzyme runs the less selective it can be. End result is that the RuBisCo of land plants today fixes perhaps one CO2 per enzyme per second, fantastically slow, so as to only misincorporate O2 something like 1/4 of the time. Slower and it would be a drag on growth, faster and it would poison the plant.

This also produces water stress on plants because of their need to keep their stomata pores open while photosynthesizing because they can't deal with internal depletion of CO2, they need lots of airflow into their tissues to bring in the very thin gas. This airflow carries away lots of water from their tissue into the air via transpiration in all but the most humid of climates, increasing their water requirements. This is why C4 and CAM photosynthesis plants have evolved. These plants via various mechanisms concentrate CO2 from the air into their photosynthetic tissues. CAM plants like pineapples leave their stomata open only at night, sucking up CO2 in the cool air and sequestering it as organic acids using very little energy, then close up their pores during the day decompose the acids back to a high local CO2 concentration and then run their RuBisCo faster. C4 plants use various mechanisms to do something similar in surface tissues during the day and then transport the acids to specialized photosynthesizing cells where the CO2 is released at high concentration and a faster RuBisCo can run. These plants appear to have originated over 100 million years ago in marginal dry environments, saving water, and become much more common something like 30-40 million years ago as atmospheric carbon levels dropped precipitously. Modern C4 plants we all know and love include corn.

Both of those described systems involve very complicated anatomical structures and regulatory mechanisms. There are people who have tried to put faster RuBisCo into crop plants by itself and it's totally pointless. Marine RuBisCo runs something like 8 times as fast because there's oodles of carbonate and bicarbonate ions in the water which marine algae can enzymatically convert to CO2 in the cell for basically no cost. Someone in a tour de force of genetic engineering recently managed to get a marine RuBisCo working in tobacco plants as a demonstration with the justification that increasing carbon fixation rates in plants was good. And their tobacco plants did indeed fix carbon much faster per unit of RuBisCo protein. But it was pointless since they died horribly if exposed to light in air due to all the peroxide damage. They had to be kept in 10x enriched CO2 growth chambers and they still grew slower than normal.

The RuBisCo of land plants is pretty much at the optimum. C4 and CAM plants have a faster one since their anatomical structures and regulatory mechanisms allow it. Anything you do to mess with carbon fixation in open air runs into hard physical limits and requires much more complicated changes than messing with a few enzymes and stomata.

Now messing with NITROGEN fixation on the other hand... just look at Kudzu for an example of what good nitrogen fixation can do for a species.

(EDIT: just a note, plants can get a lot more energy from light than they can ultimately fix into a long-lasting form, so the further above mentioned idea of increasing light capture via new pigments is not hitting the process at the bottleneck)

comment by CronoDAS · 2015-03-08T22:41:02.355Z · score: 2 (2 votes) · LW · GW

Marine RuBisCo runs something like 8 times as fast because there's oodles of carbonate and bicarbonate ions in the water which marine algae can enzymatically convert to CO2 in the cell for basically no cost

So if we could grow crops underwater we could get a lot more energy?

comment by CellBioGuy · 2015-03-08T22:47:55.342Z · score: 5 (5 votes) · LW · GW

In a manner of speaking yes. That's part of how kelp and seaweed (and to a lesser extent coral) manage to grow so fricking fast and part of how free-floating phytoplankton replicates fast enough to feed a biomass of zooplankton larger than itself at any given moment.

Only a fraction of the wattage of the biological energy available to plants that is converted from light can actually be captured by the carbon-fixation system as carbs and biomass-production, a lot more just can't get stored long-term. In marine algae with all the extra carbon floating around, it's rather a larger fraction that can be stored.

There's other issues with marine agriculture, having to do with nutrient concentration and hervibory and the fact that the light only goes down through the water so far...

EDIT:
http://en.wikipedia.org/wiki/Aquaculture_of_giant_kelp

'M.pyrifera is one of the fastest-growing organisms on Earth. They can grow at a rate of 0.6 meters a day to reach over 45 metres (148 ft) long in one growing season.'

http://en.wikipedia.org/wiki/Seaweed_farming

Honestly not sure how these stack up in terms of energy capture per square meter.

EDIT 2: It should also be noted that despite the fact that the ocean coveres 70+% of earth's surface and is full of carbon, it only represents something between 50 and 85% of the total photosynthesis that occurs on Earth depending on whose figures you listen to. Between low levels of many mineral nutrients, lack of a solid substrate near most of its surface, temperature variations, and dimming of sunlight with depth, it's not as naturally productive compared to land as its carbon levels would indicate. The aforementioned superkelp grows in shallow water near nutrient-rich upwelling cold water.

EDIT 3: A little more research on my part shows that given the pigments and the chemical processes involved, the maximum theoretical energy yield of photosynthesis in sunlight is ~25% and maximum theoretical carb yield of a plant is ~10-11 % which will go down with light as bright a sunlight because the machinery has a maximum rate per square centimeter at which it can work which is actually partially why most plants arent simple planes but have lots of leaves pointing every whichaway, so the light intensity on any given leaf is less and it can be more efficient. Typical wild land plants are doing a lot of non-carbon-fixing energy-using activities and are hamstrung by low CO2 and manage less than 1% carb production, a bunch of crop plants that have been optimized for energy storage rather than other energy-using processes manage something like 2%, and sugarcane (a domesticated C4 plant) in tropical high light high humidity conditions can manage 7 or 8%. Typical wild algae apparently easily manages ~4-5% and in artificial conditions can be boosted much higher.

comment by [deleted] · 2015-03-08T18:07:15.845Z · score: 0 (0 votes) · LW · GW

I was thinking more like, you need to re-evolve the whole lamina to re-juggle water conductivities in mesophyll, cuticle, vascular bundles and what else is there, to maintain water flow throughout the leaf. And all that newly made sugar which would have to be dealt with (don't remember how it influences osmosis.) Which means different auxin fluxes, which would rebuild the rest of the body.

But yes, of course it is at least that difficult.

comment by [deleted] · 2015-03-08T10:02:39.299Z · score: 0 (0 votes) · LW · GW

It would depend on other things, too, like where it would live by design. A floating life form, tolerant of salinity fluctuations (as happen in freshwater ecosystems), producing clonal offspring and with developed rhizoids (to take up inorganic nutrients) might be very handy from engineering point of view, but a disaster if it breaks free.

As to Green parties, well, they earn money.

comment by Douglas_Knight · 2015-03-08T02:09:07.263Z · score: 5 (5 votes) · LW · GW

Here is the paper, via google scholar.

comment by EGI · 2015-03-08T07:36:51.132Z · score: 1 (1 votes) · LW · GW

The Google Scholar link has got the same paywall for me but the ask-force.org link fortunately works. Thanks!

comment by Douglas_Knight · 2015-03-08T15:09:50.937Z · score: 2 (2 votes) · LW · GW

Google scholar has the paywalled link on the left but the open link on the right.

comment by EGI · 2015-03-08T18:17:16.543Z · score: 1 (1 votes) · LW · GW

Oh, never noticed! Thanks!

comment by CellBioGuy · 2015-03-08T16:08:17.517Z · score: 4 (4 votes) · LW · GW

Got the actual paper being discussed. Will go back and look at its references from the eighties as well on the university network later after working on some figures in the lab, to see exactly what sort of things were being done and how the experiment proceeded. Context is everything. I very much doubt a bacterium engineered to make excess ethanol via fermentation would not be outcompeted by wild bacteria in nature.

comment by CellBioGuy · 2015-03-10T02:53:13.600Z · score: 2 (2 votes) · LW · GW

Read the paper as well as the referenced chain of papers in which a soil bacterium was engineered to be an efficient producer of ethanol from Xylose. I love these old-school genetic engineering without-a-known-genome methods!

First, a brief geekout. The species modified in the work in the late 80s and early 90s is a facultative anaerobe, meaning it can get by fine without oxygen but prefers to have it. Without oxygen, like everything else it rearranges the sugar atoms into a lower energy state getting a bit less than 1/15 as much energy and much less biomass. They were interested in it because it can consume xylose, a sugar found in plant debris that is difficult for many things to digest. Without oxygen the natural bacterium squirts out a bunch of CO2, a little alcohol, some acetic acid, some lactate, some formic acid, and some weird complicated bigger alcohols when it ferments. The modified strain had a normal enzyme involved in both the production of some of those byproducts and other intermediates and the sucking of some of the carbon into biomass production deleted off the chromosome, plus a non-chromosomal plasmid containing a bacterial gene not normally found in that species that can take the substance piling up in the blocked-up pathway and release it into making ethanol. Has a side effect of making sure they don't acidify their growth media to all hell with acetic acid and formic acid, which makes them grow much faster in controlled pure culture where nothing else is eating the acetate aerobically. In the process of making energy they have to just throw the carbon through their metabolisms and make ethanol at fully 80% maximum theoretical efficiency.

Both this modified bacterium and the parent bacterium, with the deletion, caused a major disruption in the soil ecology of the soil samples they were added (at 10 million cells per gram) to and temporarily arrested plant shoot growth without arresting root growth, possibly having to do with screwing up the nematode and fungal populations in a chain reaction of effects of things feeding on each other. Both dropped down to something like 100 cells per gram within a few weeks which is probably closer to their natural concentration. The extra modified one also killed more plants, possibly from the transient ethanol production by the initial high population density affecting the ecology or the plants directly. I'd be interested in a double-inoculation experiment with the wild bacterium to see if one could outcompete the other. It's hard to say because the growth experiments were done in pure culture where the fact that the modded one doesn't acidify its environment made it grow much faster than the parent strain, but i suspect in the wild the original one would do better because it can make more biomass.

I was frankly surprised and flabbergasted the modified bacteria held onto their plasmids for 8 weeks such that they could even be detected via their plasmid-borne antibiotic resistance. When I have E. coli carrying plasmids for me (full of yeast genes, only bacterial gene is the antibiotic resistance), if I take them out of antibiotic selective pressure for a few hours almost all of them lose their plasmids due to it being easy to lose but hard to gain and due to those with the plasmids making more protein and thus growing slower. Course my lab E coli on rich broth have a generation time of 20 minutes while these guys in soil could've had a generation time of days. And the ability to unblock the clogged metabolic pathway caused by the chromosomal deletion could've been a selective advantage to holding onto the plasmid - a deleted gene is not something you evolve a workaround for in the timeframe of any experiment short of Lenski's.

Reasons I would not be terribly worried about this sort of thing:

The inserted gene (pyruvate decarboxylase) is not a rare gene in the eubacterial lineage, and bacteria are throwing genes back and forth horizontally over evolutionary time all the time. The bacteria fall in population quite rapidly to fairly normal levels. The faster growth of the modded bacteria is only observed in pure culture where their lack of acifification more than makes up for their lesser ability to make biomass.

My conclusion: they were right to test it and the dregs from this biofuel production process, full of this bacteria, would make a terrible soil amendment that would screw up your garden/farm's soil ecology for weeks at least. I'm not terribly surprised; I helped run the university community garden for years and its incredible how long it can take to get the bacterial balance back in the compost bin after someone thoughtlessly throws meat into the pile. Makes a good point about actually testing your genetically modified organisms in their ecological reactions with microbes, plants, and animals they are likely to interact with in the field. These systems are hella complicated and effects can compound up and down the food chain in ways you don't expect.

comment by CronoDAS · 2015-03-08T07:16:54.595Z · score: 0 (0 votes) · LW · GW

You could probably splice in the genes for producing botulinium toxin or some other nasty poison into E. coli or other types of bacteria that often get inside people, but I don't know how dangerous that would actually be...