from the undiscovered-waters-and-undreamed-shores dept.
Tapping the ocean as a source of natural products:
Despite this significant role, research into the diversity of microorganisms found in the ocean has thus far been only rudimentary. So, a group of researchers led by Shinichi Sunagawa, Professor of Microbiome Research, is working closely with Jörn Piel's group to investigate this diversity. Both groups are at the Institute of Microbiology at ETH Zurich.
To detect new natural products made by bacteria, Sunagawa and his team examined publicly available DNA data from 1,000 water samples collected at different depths from every ocean region in the world. The data came from such sources as ocean expeditions and observation platforms positioned out at sea.
Thanks to modern technologies like environmental DNA (eDNA) analysis, it has become easier to search for new species and discover which known organisms can be found where. But what is hardly known at all is what special effects the marine microorganisms offer -- in other words, what chemical compounds they make that are important for interactions between organisms. In the best-case scenario, such compounds would benefit humans as well. Underpinning the research is the assumption that the ocean microbiome harbours great potential for natural products that could prove beneficial, for instance for their antibiotic properties.
The extracted eDNA present in the samples was sequenced by the original researchers of the various expeditions. By reconstructing entire genomes on the computer, the scientists succeeded in decrypting the encoded information -- the blueprints for proteins. Finally, they consolidated this new data together with the existing 8,500 genome data sets for marine microorganisms in a single database.
This gave them 35,000 genomes to draw on when searching for new microbial species and, in particular, for promising biosynthetic gene clusters (BGCs). A BGC is a group of genes that provide the synthetic pathway for a natural product.
In this genome data, the researchers detected not only many potentially useful BGCs -- some 40,000 in all -- but also previously undiscovered species of bacteria belonging to the phylum Eremiobacterota. This group of bacteria had been known to exist only in terrestrial environments and didn't exhibit any special biosynthetic diversity.
Sunagawa and his team named a new family of these bacteria as Eudoremicrobiaceae, and also were able to demonstrate that these bacteria are common and widespread: one species belonging to this family, Eudoremicrobium malaspinii, accounts for up to 6 percent of all bacteria present in certain areas of the ocean.
"The relatives in the ocean possess what for bacteria is a giant genome. Fully decrypting it was technically challenging because the organisms had not been cultivated before," Sunagawa says. Moreover, the new bacteria turned out to belong to the group of microorganisms that boasts the highest BGC diversity of all the samples examined. "As things stand, they are the most biosynthetically diverse family in the oceanic water column," he says. The researchers looked at two Eudoremicrobiaceae BGCs in detail. One was a gene cluster containing the genetic code for enzymes that, according to Sunagawa, have never been found in this constellation in a bacterial BGC before. The other examined example was a bioactive natural product that inhibits a proteolytic enzyme.
Journal Reference:
Paoli, Lucas, Ruscheweyh, Hans-Joachim, Forneris, Clarissa C., et al. Biosynthetic potential of the global ocean microbiome [open], Nature (DOI: 10.1038/s41586-022-04862-3)
(Score: 3, Insightful) by JoeMerchant on Monday June 27 2022, @02:17PM (14 children)
70 years ago, the trope: "The solution to pollution is dilution" was repeated, and widely accepted, in scientific circles.
70 years ago, world human population was 1/3 what it is today, and World GDP per capita was 1/20th of today's level.
70 years ago, when the human population had less than 1/60th the economic power as it does today, the ocean was reasonably accurately modeled as an "infinite renewable resource."
The ocean is a resource, the atmosphere is a resource, even if population stabilizes at 8 or 10 or 5 billion people - those people are going to continue to grow their economic power, and responsibility to use the Earth's resources in a renewable fashion - including the biodiversity that created us.
If we keep developing 100% of available resources into monoculture crops optimized only for maximum yield of profits, the diverse genomes of the ocean's bacteria will capitalize on the resources (pollution) we are feeding them and bloom, like red tide on excess phosphate, with results that have nothing to do with extending the holocene.
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(Score: 1) by khallow on Tuesday June 28 2022, @12:11PM (13 children)
IF. But we're not actually doing that - such as with the growing amount of land and ocean being permanently set aside.
(Score: 2) by JoeMerchant on Tuesday June 28 2022, @02:13PM (12 children)
>But we're not actually doing that - such as with the growing amount of land and ocean being permanently set aside.
Wearing a fig leaf to lay in the sun all day doesn't prevent massive sunburn. We're setting aside small pieces of undesirable habitat for not long enough periods of time. https://www.half-earthproject.org/ [half-earthproject.org]
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(Score: 1) by khallow on Tuesday June 28 2022, @10:31PM (11 children)
Depends how big that fig leaf is. This one is large and growing.
(Score: 2) by JoeMerchant on Wednesday June 29 2022, @02:11AM (10 children)
So you choose to believe.
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(Score: 1) by khallow on Wednesday June 29 2022, @02:29AM (9 children)
(Score: 1) by khallow on Wednesday June 29 2022, @03:33AM (8 children)
(Score: 2) by JoeMerchant on Wednesday June 29 2022, @11:56AM (7 children)
11 & 15 % under some degree of protection. Woo fucking hoo.
Some degree of protection waffles as far as permitting commercial net fishing with bottom dragging weights. In many areas "protected" forests are clear-cut harvested and replanted with monoculture crops every 25-30 years, that's not protection, that's straight up exploitation - but counts in your rose tinted statistics.
The precious few actual wildlife sanctuaries, for instance: absolute no-take marine sanctuaries, work amazingly well - the net productivity of the sanctuary plus surrounding waters is manyfold more productive than when the entire area was under exploitation, and yet there is still tremendous resistance to establishing additional real sanctuaries.
As for the land under protection, take a look at what land makes up your 15% and tell me how you would like living most of it, say: including Antarctica, the Everglades swamps, deserts, regions so mountainous they haven't yet been fully explored... Yes, we need to protect those areas too, good job, great start - if this were the early 1900s and we continued apace to also preserve the biomes which gave rise to our species.
Too late really does matter when it comes to extinction.
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(Score: 1) by khallow on Wednesday June 29 2022, @11:10PM (6 children)
It's still vastly better than zero and getting better all the time.
How much extinction is there again? Need we recall that it was worse 10k years ago when there were vastly fewer humans on Earth?
(Score: 2) by JoeMerchant on Thursday June 30 2022, @02:25AM (5 children)
>Need we recall that it was worse 10k years ago when there were vastly fewer humans on Earth?
Was it, then? The holocene started roughly 12k years ago - and if there's much we can do to not bring it to a premature end, that would be the intelligent choice.
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(Score: 1) by khallow on Thursday June 30 2022, @03:38AM (4 children)
(Score: 2) by JoeMerchant on Thursday June 30 2022, @01:03PM (3 children)
>we're starting to do that.
Bring the holocene to an end? I certainly agree. Thing is, we're not just shooting for another ice age, we're headed more into a condition not seen for a million years or more. An ice age would be bad, hothouse Earth will be worse. One or the other are inevitably coming someday, but with all our intelligence and power we _should_ be able to forestall both for at least another 10,000 years, if we can act as a cooperative swarm instead of a self-competitive bunch of cannibals.
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(Score: 1) by khallow on Thursday June 30 2022, @10:14PM (2 children)
Prove it. A huge problem in this area is the incredible inability of advocates of various sorts of climate mitigation to show that doing their version of something is better than sticking your head in the sand and hoping it goes away.
What would be the value of that? My take is that the next 100 years is more important to the human race than the next 10k years. We can solve the really important problems like poverty, short lifespan, all eggs in the Earth basket, habitat destruction, corruption, etc in a century. If we don't do that, then it's possible we could end up in a pathological state where we can't solve them in 10k years.
(Score: 2) by JoeMerchant on Friday July 01 2022, @02:12AM (1 child)
My take is that the last 25 years were incredibly important, and while a small number of people knew we were going down a bad road they lacked the economic/political power to do anything useful with that information while those with the power used it to throw themselves a party that lasted longer than most of them did.
>We can solve the really important problems like poverty
Can we? Since the concept of money, or even proxy control of resources, has been around the collective _we_ have had the knowledge and ability to end poverty. What _we_ lack is the collective will to make it happen.
>short lifespan
Careful what you wish for there. My stepfather is currently leaking lymph from the skin of his lower legs, which tears the skin in many places. His quality of life has been, to all outward appearances, highly negative for the last 5 to 10 years. His primary impact on the world at this point is to make work for others, and he rarely gives them any good feelings while they help him. I am a strong advocate for extension of high quality of life lifespan, but FFS know when to say when.
>all eggs in the Earth basket
And poverty at the same time, right? Not saying the two are mutually exclusive, but we're already starting to get backlash against Musk, Bezos et. al. very reminiscent of what hit Apollo after 11 succeeded. "Fix our problems here, why are we _wasting_ all that money for a few white guys to get a thrill ride?" Maybe 50 years of political science has made enough progress to sell it to the masses this time, but so far it doesn't seem like it, and while Musk is bright enough to know he needs control of media like Twitter, I don't think he's got the personal wit to make it work effectively for him - hopefully he is sharp enough to hire a team to do that for him.
>habitat destruction
Amen.
>corruption
Oh, yeah, like that's ever gonna happen. TIATA - Transparency Is Always The Answer, but we're nearly 25 years post broadscale adoption of the "virtually free data transfer" internet and precious little progress has been made on the transparency fronts where it matters, unless you're talking about police video surveillance through your bedroom windows.
>in a century
Take a look back at 1922. Tremendous progress has been made, mostly in areas that weren't even part of the public consciousness in 1922. I suspect the next 100 years will be much the same. Many of the same old problems will be persisting. Some will be dramatically solved, most of the rest will be mitigated into some kind of survivable state - often by solutions we haven't even begun to conceive of yet. If the recent past is anything to go by, the 1922 to 2022 "overall progress" increment should be matched by 2052 at the latest, but we'll still have throwback issues that make little or no progress. My prediction: poverty, in the form of wealth disparity (because the poor today have many things the kings of the 1700s couldn't obtain at any price), will perniciously persist in perpetuity, with corruption being a strong aide to maintenance of that disparity.
>If we don't do that, then it's possible we could end up in a pathological state where we can't solve them in 10k years.
The doomsday clock doesn't just apply to Global Thermonuclear War - though that's still an option on the table. There are a litany of things that can put the human race into a 10Kyr+ recovery pathological state in the next ten years, or less, and "progress" will be making that list longer, not shorter, as it progresses. Chief among them: your end of poverty. Already, while the earth's population tripled in the last 70 years, our command of the earth's resources has increased 20x per capita during the same time. If you put the power of $100 USD per day in the hands of every human on the planet, the potential for the masses to abuse that power in ways that crash society grow dramatically, chief among those is destruction of the environment by proxy, as compared to a world where the bulk of the population are subsistence farmers without even a metal ploughshare to work the land.
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(Score: 1) by khallow on Friday July 01 2022, @12:13PM
What small number of people? Neither your or my opinions are in any way rare. And I suppose we're just going to gloss over such things as a decades long pattern of dishonesty in the climate change argument or the considerable economic and political power that has managed to outspend Big Oil for the entire 25 year period.
My take is that we're already well on our way - a big part of the reason human fertility is declining is because people globally are becoming more wealthy and prosperous.
Irrelevant. An unproductive fight for life is not life extension.
You just don't get it. It doesn't matter what a bunch of envious, clueless idiots complain about. They'll be envious and clueless about something different tomorrow. And those demands for "fix our problems here" are merely signaling just how clueless and impotent they really are.
And yet, Russia logistics had severe tire problems when it mattered. Corruption blows back. The more of it your country has, the more obvious its effects become.
You won't find the present massive improvement in the human condition anywhere in human history. And we still have no reason to care about wealth disparity. It's a phantom menace.
The potential for "masses to abuse" hasn't been exercised in the real world. After all, every developed world country is moving towards greater environmental awareness and preparation - such as that growing amount of protected land you downplayed earlier. Keep in mind that no serious environmental problem aside from habitat destruction (sorry, hot house Earth needs some evidence) has been mentioned in this thread - and the developed world is addressing that.
(Score: 0) by Anonymous Coward on Monday June 27 2022, @04:02PM (2 children)
Now bacteria make to work and give us polution free fuel for ICE cars, so we can forget this E-car idiocy.
Yea, no , i didn't read through the whole thing, but that's my wish.
(Score: 3, Interesting) by JoeMerchant on Monday June 27 2022, @04:22PM
Fuel may be more difficult, but the "hard" problem of CO2 emissions when making concrete can be solved (unsurprisingly) with the bacterial processes that make coral reefs:
https://www.frontiersin.org/articles/10.3389/fmats.2019.00126/full#:~:text=Bioconcrete%20can%20be%20defined%20as,property%20(Jonkers%2C%202011). [frontiersin.org]
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(Score: -1, Flamebait) by Anonymous Coward on Monday June 27 2022, @05:03PM
It is called hydrogen, do you know how ICE and pollution work? Electric motors are idiocy? Guess you're a bug il idiot for using one to post online!
(Score: 0) by Anonymous Coward on Monday June 27 2022, @09:03PM (1 child)
But the Greens whine when the Japanese carve them up for sushi.
(Score: 2) by JoeMerchant on Tuesday June 28 2022, @12:44AM
Harvest some whales, sure... But first let's restore whale populations to pre- whaling levels and then take no more than can be sustained without reducing those levels.
Incidentally, whale poop sustains algal blooms which absorb globally significant amounts of CO2.
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