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DNA Detectives Count Thousands of Fish Using a Glass of Water

samzenpus posted about 7 months ago | from the where's-walleye dept.

Biotech 61

vinces99 writes "A mere glass full of water from Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank is all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there. Researchers also discerned which of the species were most plentiful in the tank. Being able to determine the relative abundance of fish species in a body of water is the next step in possibly using modern DNA identification techniques to census fish in the open ocean, according to Ryan Kelly, University of Washington assistant professor of marine and environmental affairs, and lead author of a paper in the Jan. 15 issue of PLOS ONE. 'It might be unpleasant to think about when going for a swim in the ocean, but the water is a soup of cells shed by what lives there,' Kelly said. Fish shed cells from their skin, damaged tissues and as body wastes. 'Every one of those cells has DNA and if you have the right tools you can tell what species the cell came from. Now we're working to find the relative abundance of each species present,' he said."

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So, IOW (1)

Anonymous Coward | about 7 months ago | (#45971587)

Fish do piss in the water.

The next logical step ? (4, Interesting)

Taco Cowboy (5327) | about 7 months ago | (#45971715)

Fish do piss in the water.

As far as I can see, the next logical step for the technique as outlined in TFA is to take a glass of sewage from a city sewage treatment center and analyze for the % of the number of human beings with a particular type of disease (HIV, TB, Polio or whatever).

Re:The next logical step ? (-1)

Anonymous Coward | about 7 months ago | (#45971817)

Haiti: 100% HIV
India: 100% sewage - nothing else (it would've been 99% sewage and 1% Polio but they just got rid of that one)

Re:The next logical step ? (2)

Ol Biscuitbarrel (1859702) | about 7 months ago | (#45971979)

“I don't drink water. Fish fuck in it.”

  W.C. Fields

Also:

"I certainly do not drink all the time. I have to sleep you know."

"Don't worry about your heart, it will last you as long as you live."

Re:The next logical step ? (1)

Cryacin (657549) | about 7 months ago | (#45972057)

Discerning accurate population demographics, drug usage levels and nutritional trends. All from our ablution.

Re:The next logical step ? (0)

Anonymous Coward | about 7 months ago | (#45974559)

No, India would have an astoundingly high percentage of rape dna as well. Definitely not just sewage.

Re:The next logical step ? (0)

Anonymous Coward | about 7 months ago | (#45972495)

They already do this. At least where I live.

Re:The next logical step ? (1)

sjames (1099) | about 7 months ago | (#45974093)

I know that in Finland they do that now to detect polio.

Re:The next logical step ? (1)

Mr D from 63 (3395377) | about 7 months ago | (#45974815)

Or maybe the NSA could track us through swimming pool samples.

Re:So, IOW (0)

Anonymous Coward | about 7 months ago | (#45972257)

(And I very much doubt they get kicked out of the pool for it.)

Re:So, IOW (0)

Anonymous Coward | about 7 months ago | (#45972397)

Limnologists often describe lakes as nothing more than dilute fish pee. The same can be said for the ocean...

Re:So, IOW (2)

riverat1 (1048260) | about 7 months ago | (#45973073)

,quote>Fish do piss in the water.

Well, if you think about it practically every bit of water on the planet has been pissed by an animal at one time or another or at least is commingled with water that has.

blink (1)

Anonymous Coward | about 7 months ago | (#45971609)

Fish use glasses of water?

Quelle surprise! (1)

zurtle (785688) | about 7 months ago | (#45971619)

Also, for the squeamish, fish, whales, penguins, sharks, jellyfish and manta rays don't use condoms. Not sure about crocodiles or wombats.

Re:Quelle surprise! (1)

Anonymous Coward | about 7 months ago | (#45971675)

I can confirm that I didn't use a condom with my wombat.

yeah (4, Funny)

hamburger lady (218108) | about 7 months ago | (#45971629)

Being able to determine the relative abundance of fish species in a body of water is the next step in possibly using modern DNA identification techniques to census fish in the open ocean

"the machine says that by far the pacific is full of a fish called...poly vinyl chloride. hm, that's a funny name."

Re:yeah (1)

c0lo (1497653) | about 7 months ago | (#45971757)

"the machine says that by far the pacific is full of a fish called...poly vinyl chloride. hm, that's a funny name."

I guess it's more likely to identify the "Poly Yeti Lenne" species - rationale: PVC will sink to the bottom [wikipedia.org] (30-45% denser than the water).

Evert seen those CSI lights? (1)

rmdingler (1955220) | about 7 months ago | (#45971673)

You can scan a hotel room and the biologicals will light up like a 70's blacklight poster.

Why would you do that to yourself, for Odin's sake, if you planned to ever sleep in a hotel bed again?

Re:Evert seen those CSI lights? (0)

Anonymous Coward | about 7 months ago | (#45972273)

("... how did it get on the ceiling?")

What about... (4, Interesting)

c0lo (1497653) | about 7 months ago | (#45971711)

all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there

What about species no-one knows about?

Re:What about... speciation (2)

Cattrance (1537577) | about 7 months ago | (#45971933)

What about species no-one knows about?

As with other "soup" DNA techniques those species that they do not have DNA information for (I'm using this term loosely) would simply be separated by their genetic differentiation between each other. This is one of the primary problems with identifying species with "Soup" because organisms can be the same distance apart genetically but some may be different species morphologically and others may be the same.

In a simplified example say you have organisms A, B and C. A and B are closest genetically, A and C are furthest away while B and C are the same distance away from each other. One would look at this and assume A, B and C are separate species. However you then observe in the wild that B and C are able to breed, perhaps B and C are one species while A is separate? This is one of many examples of how genetic information can mislead species information

Unfortunately speciation is complicated and often not linear which leaves a confusing genetic trail. Fortunately, data telling us the genetic variation of an area can still be very useful for many scientific questions. Not to mention the usefulness of being able to identify the presence/ absence of well known species.

Re:What about... speciation (1)

c0lo (1497653) | about 7 months ago | (#45972087)

In a simplified example say you have organisms A, B and C. A and B are closest genetically, A and C are furthest away while B and C are the same distance away from each other. One would look at this and assume A, B and C are separate species. However you then observe in the wild that B and C are able to breed, perhaps B and C are one species while A is separate? This is one of many examples of how genetic information can mislead species information

Fine and dandy.
Now, let's take another case: you know species A, you know nothing about B and C. Thus you can tell "A was here" but... can you tell there are other (exactly) two that "were here" as well? Maybe they were only one, maybe more than two. How can you tell?

Re:What about... speciation (2)

Cattrance (1537577) | about 7 months ago | (#45972197)

Fine and dandy.
Now, let's take another case: you know species A, you know nothing about B and C. Thus you can tell "A was here" but... can you tell there are other (exactly) two that "were here" as well? Maybe they were only one, maybe more than two. How can you tell?

Welp, that's exactly the problem, that isn't to say there aren't other methods though. For example you could see how much genetic differentiation there is between known species in the area and make assumptions based on that. You could also use other types of DNA, mitochondrial DNA for example which may tell a different story.

Fact is, taxonomists are always fighting about which species is which, sometimes with fruition. DNA, while it is very useful in determining one species from another has added to the questions about what really defines a species and what differentiates one from the other. Even morphologically there has been debate as to whether the two specimens you are holding are one species or two. Take the Eclectus Parrot for an early example, the male is bright green whereas the female is red/purple, scientists thought them to be separate species until they actually saw them mating. Things can get even more confusing when species don't physically mate with each other (think pollen and plants) or when they mate between species. Hopefully this type of science will take us closer to the answer.

On the other hand, personally I like these kind of studies for other uses like saying "Hey! This spot has way more genetically different organisms, maybe it's more important to not pollute it"

Re:What about... (1)

wbr1 (2538558) | about 7 months ago | (#45972039)

Since not every thing is fully sequenced, I would wager a guess that they search the 'soup' for specific sequences that are known thought to be unique to a species. The rest would just be noise to the data they are seeking. However, if say bluefin tuna had a lesser or unknown related species that also had the same thought to be unique sequence, it could make their estimates high. However if it was an unknown species the fact that it is unknown means that there are probably very few and the difference would be negligible and within the margin of error.

Re:What about... (0)

Anonymous Coward | about 7 months ago | (#45972115)

all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there

What about species no-one knows about?

You think there were fish species no one knows about swimming in "Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank" (from the part of TFS you omitted)? How would they have gotten in there?

Re:What about... (0)

Anonymous Coward | about 7 months ago | (#45972259)

There is a difference between "Oh look I have a name for this species" (based on its physical trails) and "I have just sequenced a tank full of fish and other microscopic organisms".

Re:What about... (1)

c0lo (1497653) | about 7 months ago | (#45972499)

all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there

What about species no-one knows about?

You think there were fish species no one knows about swimming in "Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank" (from the part of TFS you omitted)? How would they have gotten in there?

From the same TFS that you referred:

Fish shed cells from their skin, damaged tissues and as body wastes. 'Every one of those cells has DNA and if you have the right tools you can tell what species the cell came from. Now we're working to find the relative abundance of each species present,' he said."

Do you think they are working to determine the abundance of each species in the "Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank"? 'Cause... you know?... that would be a question which can find an answer by more practical means.

Re:What about... (0)

Anonymous Coward | about 7 months ago | (#45973237)

Do you think they are working to determine the abundance of each species in the "Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank"? 'Cause... you know?... that would be a question which can find an answer by more practical means.

Yeah, I do. Usually when you are developing a new way to do something it helps to test it against an already-proven method.

Re:What about... (1)

KingOfBLASH (620432) | about 7 months ago | (#45973081)

Stick it in some fish embryos and see what grows.

(Ok maybe it's not possible NOW but give technology a couple decades.)

BEST case scenario, you get "frog eggs" (0)

Anonymous Coward | about 7 months ago | (#45975479)

we've all seen that movie, NO THANKS.

Re:What about... (1)

riverat1 (1048260) | about 7 months ago | (#45973119)

Well, in the Monterey Bay Aquarium there probably aren't any species that no-one knows about. But there certainly would also be DNA from the various microorganisms in the water as well. That brings to mind that the water in the tank comes from the ocean anyway and I doubt the filtering is good enough to remove all traces of "wild" DNA before it goes in the tank. So maybe they would find DNA from and unknown species.

Re:What about... (1)

interkin3tic (1469267) | about 7 months ago | (#45976737)

This technique will be used to identify them. It's already being used to that end. I went to a seminar talk years ago which was taking samples of sea water and sequencing every bit of DNA they could amplify from them, much like this. There's a problem in microbiology where what you can see under a microscope doesn't match what you can grow on an agar dish (which is necessary to really study something: you can't very well study a single bacterium cell.)

The take home message was we don't know anything about the vast majority of microbes in the ocean. Given that oceans cover most of the world, and most life on the planet in terms of variety and biomass IS microbes, that's a mind blowing amount about biology we don't know.

Next step (5, Funny)

easyTree (1042254) | about 7 months ago | (#45971727)

Being able to determine the relative abundance of fish species in a body of water is the next step in possibly using modern DNA identification techniques to census fish in the open ocean

Followed swiftly by fish taxation.

Oh man ... (1)

gstoddart (321705) | about 7 months ago | (#45971961)

Now you've ruined my winter vacation, and while I'm sitting on the beach sipping rum I'll know if I go in the ocean I'll be covered in fish goo.

*sigh* I'll just have to have another rum. Purely to fight infections you understand.

Re:Oh man ... (1)

pcwhalen (230935) | about 7 months ago | (#45972047)

Put lime in it. Wards off scurvy.

You're welcome. And wear 50.

Re:Oh man ... (1)

gstoddart (321705) | about 7 months ago | (#45972439)

Put lime in it. Wards off scurvy.

With some bitters, sugar and mint leaves, we call that a mojito. ;-)

And wear 50.

LOL, already on it.

Re:Oh man ... (1)

ruir (2709173) | about 7 months ago | (#45972627)

Actually it have been proved by consumer bodies factors above 35 dont work any better and they are just a scam to rip you off.

Re:Oh man ... (1)

gstoddart (321705) | about 7 months ago | (#45976447)

Actually it have been proved by consumer bodies factors above 35 dont work any better and they are just a scam to rip you off.

Given my pasty white complexion, I'll err on the side of caution.

Since 50 doesn't cost any more than 35 in my experience, what's the 'scam' part here?

Re:Oh man ... (0)

Anonymous Coward | about 7 months ago | (#45973729)

Rub the lime on the side of the beer and salt it to kill bacteria.

Re:Oh man ... (1)

riverat1 (1048260) | about 7 months ago | (#45973135)

Don't worry about it, the alcohol in your rum is the piss/shit of yeast cells.

Re:Oh man ... (1)

TangoMargarine (1617195) | about 7 months ago | (#45977907)

No, that's beer.

Re:Oh man ... (2)

TangoMargarine (1617195) | about 7 months ago | (#45977959)

Hmm...I stand corrected. It appears rum as well is flavored by the products of yeast.

WC Fields was right! (-1)

Anonymous Coward | about 7 months ago | (#45971983)

"I never drink water, fish fuck in it."

Lucky (0)

Anonymous Coward | about 7 months ago | (#45972221)

It't a good thing all fish are the same size and shed cells at the same rate so we can directly compare between species...

Sewage (0)

Anonymous Coward | about 7 months ago | (#45972235)

Imagine what you could do with a sample from the local sewage treatment facility!

Which ones could they not identify? (1)

DroneWhatever (3482785) | about 7 months ago | (#45972739)

This is really cool, great use of modern tech! I am curious as to which species they could not detect, and why they think that is? Too small of a population? Too small in size? Sampling size possibly not big enough? It seems like they would want to answer these questions as well.

Re:Which ones could they not identify? (1)

DroneWhatever (3482785) | about 7 months ago | (#45972789)

I know this is bad form to reply to your own post. Answering some of my own questions, after catching something I missed reading the article the first pass. "The primers were unable to detect DNA from two groups of vertebrates in the tank: the turtles and the fish with cartilage in place of bones, such as rays and sharks." Sharks and turtles are pretty big ones to miss, I hope they get this worked out, it sounds really promising in coming up with real numbers about the health of our oceans species versus the current estimation methods.

Interesting (0)

Anonymous Coward | about 7 months ago | (#45972845)

I would also imagine that the distance of a fish from the sample taken will also have an effect on the amount of cells from each fish collected in the sample (for instance, as the distance increases more of the cells will either deteriorate or settle down or wind up being absorbed by another organism?). Since different fish may hang out in different parts of the ocean depending on climate, depth of water, and other factors taking a sample only from one specific location may skew the results. Scarce fish in the region where the sample was taken may appear more abundant than more abundant fish slightly further away. Care must be taken to account for this.

% Human DNA in sample (0)

Anonymous Coward | about 7 months ago | (#45972847)

I just want to know what the % of human DNA was found in the sample, that will tell us how polluted the bay is.

Extrapolate. (1)

Z00L00K (682162) | about 7 months ago | (#45973171)

And you can use the same method at the sewage stations to be able to count the number of individuals in a town or city, then separate out the DNA of everyone that's there illegally and track them down.

Nobody will be safe from our civil masters.

So how many salt water fish (1)

iplayfast (166447) | about 7 months ago | (#45973691)

So how many salt water fish would they find in the sewers of every city. I think that just because the dna is present doesn't imply or cause the critter to be present. At least not alive.

So, not counting then (1)

wonkey_monkey (2592601) | about 7 months ago | (#45973913)

DNA Detectives Count Thousands of Fish Using a Glass of Water
Researchers also discerned which of the species were most plentiful in the tank.

Someone doesn't know what counting is (the article had the good grace to put it in scare quotes).

Re:So, not counting then (3, Funny)

worf_mo (193770) | about 7 months ago | (#45974775)

Two decades ago I worked in a small team of “fish counters” to earn something during my time at university. This team was from the local government’s department of environmental protection and headed by a biologist. We’d drive up to a river, pull out our portable generator, drop one pole in the water, and walk in the river with the other pole, stunning the fish between the poles (they don’t die electrocuted, they are just stunned for a little while). We’d fish them out with nets, place them in large buckets and bring them on land, where the biologist counted and classified them before returning them to the river. His reports were then mainly used to assess the damages after an environmental disaster.

Once we were called to a spot where an oil truck had ended up in a mountain river. While we approached the place we wondered how that could have happened - the road was straight, no obstacles, excellent road conditions. But when we arrived we understood: right before the spot where the truck had left the road was a huge billboard with an underwear ad, featuring a nice young lady in a thong and nothing else. The driver must have craned his neck until the truck touched down in the river.

Inaccurate (0)

Anonymous Coward | about 7 months ago | (#45974433)

You'll vastly overestimate the presence of any fish with ichthyosis.

As W.C. Fields said.... (0)

Anonymous Coward | about 7 months ago | (#45974645)

"I never drink water. Fish fuck in it."

Done Already (1)

the monolith (1174927) | about 7 months ago | (#45975035)

Almost every day I dive past one of the Smithsonian biomass accretion modules in Aqaba Marine Park, Jordan. You can see one of the collection modules here. [google.com]

If only academic departments/institutions collaborated or communicated a little bit more, maybe the research dollar would go a little further?

Cheers.

G

PADI instructor 636522

Re:Done Already (0)

Anonymous Coward | about 7 months ago | (#45978307)

If you check if someone has done something and find out they have a monopoly on it and you try to do a similar (doesn't even have to be exactly the same) thing you get sued/punished for more than if you try to do something without knowing others have done similar stuff.

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