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View Full Version : Genetically Engineering a Bleach-Proof Coral Reef


taricha
07/22/2017, 06:37 AM
Oddball topic, it's not technically about what goes on in our tanks, but it's clearly stuff we all care about. Coral bleaching events are getting more attention as the amount of ongoing worldwide reef casualties are becoming even clearer.

These scientists are aiming to genetically engineer the zooxanthellae (symbiodinium dinoflagellate) (https://scienmag.com/a-super-algae-to-save-our-seas/) that lives in the corals to make the dinoflagellate-coral symbiosis more temperature resilient.
Different species of Symbiodinium have large genetic variation and diverse thermal tolerances which effect the bleaching tolerance of corals. In research published in Frontiers in Microbiology, the researchers use sequencing data from Symbiodinium to design genetic engineering strategies for enhancing stress tolerance of Symbiodinium, which may reduce coral bleaching due to rising ocean temperatures.

"Very little [genetic information] is known about Symbiodinium, thus very little information is available to improve coral reef conservation efforts....
The researchers have now highlighted key Symbiodinium genes that could be targeted to prevent coral bleaching.
"Symbiodinium that have been genetically enhanced to maintain their symbiosis with corals under rising ocean temperatures has great potential to reduce coral bleaching globally" they suggest.


Wanted to flag this because I'd been poking around to see if there was anyone out there doing this (genetically modifying symbiodinium) and I didn't find any reference to it before yesterday. It's a thought that's been bugging me for a few months since i ran across articles talking about the presence of symbiodinium living in coral in the gulf of Oman that handle 90+ degree ocean temps.
Papers like this one (http://www.pnas.org/content/113/16/4416.full.pdf) with an interesting thesis
Currently, it is unknown whether this symbiont originated elsewhere or emerged from unexpectedly fast evolution catalyzed by the extreme environment. Analyzing genetic diversity of symbiotic algae across >5,000 km of the PAG[Persian/Arabian Gulf], the Gulf of Oman, and the Red Sea coastline, we show that S. thermophilum is a member of a highly diverse, ancient group of symbionts cryptically distributed outside the PAG. We argue that the adjustment to temperature extremes by PAG corals was facilitated by the positive selection of preadapted symbionts. Our findings suggest that maintaining the largest possible pool of potentially stress-tolerant genotypes by protecting existing biodiversity is crucial to promote rapid adaptation to present-day climate change, not only for coral reefs, but for ecosystems in general.
In other words, these corals found a better zooxanthellae for their crazy hot environment.
So...
1) Extreme temperature tolerance already exists within the genetic variation of current symbiodinium species.
2) not crazy to think that Genetically Modified strains of symbiodinium could be created with different temperature tolerances than those currently present in reefs
3) the presence of temperature tolerant symbiodinium within the reef phytoplankton may allow corals a wider variety of viable symbionts and allow more coral colonies to survive stressful heating events.

Back to the current research. The full paper is here (http://journal.frontiersin.org/article/10.3389/fmicb.2017.01220/full)
and it seems like they aren't just shooting in the dark here on poking around in the person-sized genome of the symbiodinium dinoflagellate.
Recent transcriptomic studies have been fundamental in the discovery of Symbiodinium nuclear genes that underpin phenotypic traits, such as those related to cell adhesion... sexual reproduction... antiviral response..., and antioxidant activity/thermal tolerance. Symbiodinium antioxidant genes are of particular interests because of their potential role in defining bleaching susceptibility of the coral host

And later they talk about how CRISPR might be applied in this situation to alter genes of the dinoflagellate, and they suggest target locations.
Our analysis revealed 1792 conserved single copy orthologs, 261 of which have an optimal target site compatible with all genomes The 261 single copy orthologs for CRISPR/Cas9 genome editing were enriched for a wide array of functional gene groups of interest, including cellular components for photosynthesis and biological pathways for oxidation-reduction and for response to UV-B.

Finally they ask aloud if this is a reachable goal "Can We Reduce Coral Bleaching with Genetically Enhanced Symbiodinium?"
Exceptional genetic variability naturally exists within the genus Symbiodinium, suggesting that seeding vulnerable corals with more climate-change tolerant Symbiodinium variants could provide a means to reduce bleaching susceptibility of corals ... Although, uptake of non-native Symbiodinium variants by corals may not be widely achievable since many coral species only associate with specific Symbiodinium types
...most corals are pretty picky about precisely which symbiont they adopt, but if you tweak the symbiont species that a coral already uses...
Genetic engineering to increase stress tolerance of the Symbiodinium variants that are naturally harbored by at-risk corals holds potential to reduce bleaching susceptibility without negatively impacting the fitness of the coral host since existing Symbiodinium-coral partnerships would be preserved.
They then list the genes they think are most likely to confer the temperature tolerance.
Fe-sod, Mn-sod Prxd, and Hsp70 genes from Symbiodinium are standout candidates whose engineered up-regulation may enhance thermal and bleaching tolerance by reducing heat-induced oxidative damage, but thorough evaluation of how this artificial up-regulation contributes to long term fitness and the Symbiodinium-coral symbiosis would be mandatory.

I've heard of other projects, but none that sound to me like they have much of a chance to be effective, happen fast, and be scalable to a full reef. A group in Hawaii (http://coralhealth.uhh.hawaii.edu/node/190) is trying to identify the most tolerant coral colonies of individual species and through gradual pressures essentially domesticate them like dogs to effectively breed super-coral.
My hunch is, this'll be too slow and trying to breed a better Coral animal host is not going to be as effective. But perhaps it'll take both a better symbiont and a better host to survive the new "normal" in our oceans.

Thought I'd post this here - open up a discussion of the science - maybe even someone who understands the CRISPR & gene modification stuff will chime in and give their take, I'd be curious how to assess odds of success and the time frame for a project like this based on what's known now.

It makes me more optimistic than anything I've seen before on the topic. (Maybe Next: someone will work on genetically modifying coccolithophores to crank up the capacity of oceanic carbon sequestration :reading:)

ichthyogeek
07/24/2017, 04:50 PM
This sounds interesting and looks promising! For people who are kinda confused: corals bleach (eject their symbiotic zooxanthellae, mostly symbioodinium clades) when their symbionts (the symbioodinium) produce too much, and end up making too many free radicals which damage the polyp. Corals usually protect against this by developing their brilliant colors which limit the amount of light that reaches the zooxanthellae, but heat can also speed up the zooxanthellae production.

As for the article...I haven't read it yet, but are they considering using CRISPR to grab the relevant genes from the PAG variants, and use it again to create heat resistant zooxanthellae by injecting those genes into the relevant symbioodinium clades? That might work, but it would have to be over a very long time period with massive amounts of CRISPR used going on even with the "override" factor, the gene drive, to keep the reefs that are currently known today thriving.

As for CRISPR: In related news, Verily (related to Google) just released CRISPR modified mosquitoes into the wild to help reduce some form of parasite. If that experiment goes well, then maybe it might be considered for this same project. However, bioengineering ethics are hard and it's difficult to find the best path.

It kind of reminds me of proposals to mass fertilize iron into the ocean to boost microalgae growth in order to cause a mass algal bloom that would sink and lock away more carbon to be honest...sounds good, but also hard to predict consequences.

taricha
07/27/2017, 10:22 AM
are they considering using CRISPR to grab the relevant genes from the PAG variants, and use it again to create heat resistant zooxanthellae by injecting those genes into the relevant symbioodinium clades? That might work, but it would have to be over a very long time period with massive amounts of CRISPR used going on even with the "override" factor, the gene drive, to keep the reefs that are currently known today thriving.
confession: aside from the fact it's a powerful genetic tool for a bunch of problems, I dunno how CRISPR works.

Some reefs have only one or two species of symbiodinium floating around. some have like 9 (I think I remember reading somewhere). Idea is to take an existing coral symbiont, modify it, culture it up and release into the wild. Hopefully it would become one of the symbiodinium species floating wild on the reef, and its increased fitness during bleaching events would allow it to gradually become preferred by the coral hosts.

As for CRISPR: In related news, Verily (related to Google) just released CRISPR modified mosquitoes into the wild to help reduce some form of parasite. If that experiment goes well, then maybe it might be considered for this same project. However, bioengineering ethics are hard and it's difficult to find the best path.
yeah, the mosquito bit was a wake up to everyone that we can genetically engineer crazy stuff. Like Dr. Frankenstein level "should we be doing this?" kind of power. (And yesterday's headline "CRISPR edited human embryo in Portland, OR. It worked great.")

It kind of reminds me of proposals to mass fertilize iron into the ocean to boost microalgae growth in order to cause a mass algal bloom that would sink and lock away more carbon to be honest...sounds good, but also hard to predict consequences.
yeah, they got permission to fertilize huge swathes of open ocean in multiple runs over several years. My impression is the overall result was an increase in ocean production, but not as big as anyone hoped or expected and a bunch of confused scientists.

karimwassef
07/27/2017, 10:38 AM
I think it's great if used to accelerate nature's own processes.

I grew up snorkeling the Arabian gulf and Red Sea and I was amazed that those smaller shallower seas could grow such impressive & super colorful coral in blistering temperatures.

The ocean fringe reefs have had such a gentle experience in contrast - temperature wise. But they've had to put up with massive weather incursions that rip them up. And so they worked through that.

Maybe transplant each species to the others' zone and have them mix it up would work. But that would take decades and the impact of human influence is much faster. So giving nature a helping hand would be a way to accelerate the normal switching of genes and dinos.

My concern is if we make a non-coral bound dino that is so temperature tolerant that it takes over and kills everything else. Hope someone is checking the symbiotic gene is not effected by the temperature tolerance gene splicing.

Oh- can we get more blue too? I'd love more blue coral with golden yellow polyps... j/k pun on parents wanting more blue eyed blonde genetically perfect babies. :D

sh4rkbyt3
08/18/2017, 10:52 AM
I think it's a good idea given the non-changing dilemma we're already facing but I would be highly cautious in that there are so many times science has gotten involved in these well intentioned endeavors and it hasn't always worked out for the best.

When a link in a chain is altered you also need to look at what it effects down the road in the long run. Given the fact some of the political climate has not taken the best turn eco-wise it may be an ugly or great alternative. I don't want this to be about a political rant either but fact is fact.

The other part is what else is going to change climatewise? So many variables to consider in what is in essence the first link of the chain of life here. I would absolutely hope for the best but be speculatively cautious.

DivingTheWorld
08/18/2017, 01:00 PM
Though I am an avid diver and hate to see the destruction of coral reefs, I prefer more of a conservation solution than a genetic one. I am not a fan of genetically altering nature and I'd prefer nature do it on it's own. IMO pollution is far more harmful to coral reefs than changes in temperature and these genetic changes would not help in that regard.

karimwassef
08/18/2017, 03:16 PM
Im an advocate for natural solutions too but when human behavior alters the environment faster than it can naturally respond, we should study opportunities to help.

Pollution + heat + CO2 = algae seas. In time, algae will fix things again, but the beautiful diversity we have may not make it...

taricha
08/26/2017, 03:42 PM
Here's a good explanation of CRISPR - CAS9 system.

https://youtu.be/MnYppmstxIs

Basically it allows you to use a sequence of RNA you dial up as a guide to hunt for a segment of DNA, then CAS9 protein cuts the DNA there. That will typically break the gene and make it ineffective, or you can couple it with your own DNA edit that you'd like to go in the cut.

Friggin amazing, biological cut and paste in a living cell genome.

Sent from my SAMSUNG-SGH-I337 using Tapatalk

karimwassef
08/26/2017, 03:47 PM
Custom corals, here we come!

MonsterRehab
09/05/2017, 03:31 PM
These scientists are aiming to genetically engineer the zooxanthellae (symbiodinium dinoflagellate) (https://scienmag.com/a-super-algae-to-save-our-seas/) that lives in the corals to make the dinoflagellate-coral symbiosis more temperature resilient.



Do we know for a fact that it's temperature causing bleaching? The average temperatures of great barrier reefs don't show significant elevation. Here's a random reef I picked going back to 1980. http://data.aims.gov.au/aimsrtds/datatool.xhtml?site=4
Never been above 29C. What am I missing?

I wonder about other factors. Fertilizer run off? I'm not a reef biologist, nor do I play one on TV. Just trying to understand here.

karimwassef
09/05/2017, 04:17 PM
It's not the average over time that counts. It's the spikes during the day.

If you experience 160F for one hour a day but 70F the other 23 hours, your average temp won't go up by much, but you'll still die of heat exhaustion.

Sustained peak temps over multiple days is painful on reefs.