Fungus creates a fast track for carbon

Stanford scientists find epidemics of fungal infections in algae alter carbon cycling


Research News


Tiny algae in Earth’s oceans and lakes take in sunlight and carbon dioxide and turn them into sugars that sustain the rest of the aquatic food web, gobbling up about as much carbon as all the world’s trees and plants combined.

New research shows a crucial piece has been missing from the conventional explanation for what happens between this first “fixing” of CO2 into phytoplankton and its eventual release to the atmosphere or descent to depths where it no longer contributes to global warming. The missing piece? Fungus.

“Basically, carbon moves up the food chain in aquatic environments differently than we commonly think it does,” said Anne Dekas, an assistant professor of Earth system science at Stanford University. Dekas is the senior author of a paper published June 1 in Proceedings of the National Academy of Sciences that quantifies how much carbon goes into parasitic fungi that attack microalgae.

Underwater merry-go-round

Researchers until now have predicted that most carbon fixed into colonies of hard-shelled, single-celled algae known as diatoms then funnels directly into bacteria – or dissolves like tea in the surrounding water, where it’s largely taken up by other bacteria. Conventional thinking assumes carbon escapes from this microbial loop mainly through larger organisms that graze on the bacteria or diatoms, or through the CO2 that returns to the atmosphere as the microbes breathe.

This journey is important in the context of climate change. “For carbon sequestration to occur, carbon from CO2 needs to go up the food chain into big enough pieces of biomass that it can sink down into the bottom of the ocean,” Dekas said. “That’s how it’s really removed from the atmosphere. If it just cycles for long periods in the surface of the ocean, it can be released back to the air as CO2.”

It turns out fungus creates an underappreciated express lane for carbon, “shunting” as much as 20 percent of the carbon fixed by diatoms out of the microbial loop and into the fungal parasite. “Instead of going through this merry-go-round, where the carbon could eventually go back to the atmosphere, you have a more direct route to the higher levels in the food web,” Dekas said.

The findings also have implications for industrial and recreational settings that deal with harmful algal blooms. “In aquaculture, in order to keep the primary crop, like fish, healthy, fungicides might be added to the water,” Dekas said. That will prevent fungal infection of the fish, but it may also eliminate a natural check on algal blooms that cost the industry some $8 billion per year. “Until we understand the dynamics between these organisms, we need to be pretty careful about the management policies we’re using.”

Microbial interactions

The authors based their estimates on experiments with populations of chytrid fungi called Rhizophydiales and their host, a type of freshwater algae or diatom named Asterionella formosa. Coauthors in Germany worked to isolate these microbes, as well as bacteria found in and around their cells, from water collected from Lake Stechlin, about 60 miles north of Berlin.

“Isolating one microorganism from nature and growing it in the laboratory is difficult, but isolating and maintaining two microorganisms as a pathosystem, in which one kills the other, is a true challenge,” said lead author Isabell Klawonn, who worked on the research as a postdoctoral scholar in Dekas’ lab at Stanford. “Only a few model systems are therefore available to research such parasitic interactions.”

Scientists surmised as early as the 1940s that parasites played an important role in controlling the abundance of phytoplankton, and they observed epidemics of chytrid fungus infecting Asterionella blooms in lake water. Technological advances have made it possible to pick apart these invisible worlds in fine and measurable detail – and begin to see their influence in a much bigger picture.

“We’re realizing as a community that it’s not just the capabilities of an individual microorganism that’s important for understanding what happens in the environment. It’s how these microorganisms interact,” Dekas said.

The authors measured and analyzed interactions within the Lake Stechlin pathosystem using genomic sequencing; a fluorescence microscopy technique that involves attaching fluorescent dye to RNA within microbial cells; and a highly specialized instrument at Stanford – one of only a few dozen in the world – called NanoSIMS, which creates nanoscale maps of the isotopes of elements that are present in materials in vanishingly small amounts. Dekas said, “To get these single-cell measurements to show how photosynthetic carbon is flowing between specific cells, from the diatom to the fungus to the associated bacteria, it’s the only way to do it.”

The exact amount of carbon diverted to fungus from the microbial merry-go-round may differ in other environments. But the discovery that it can be as high as 20 percent in even one setting is significant, Dekas said. “If you’re changing this system by more than a few percent in any direction, it can have dramatic implications for biogeochemical cycling. It makes a big difference for our climate.”


Stanford coauthors include Alma E. Parada and Nestor Arandia-Gorostidi, postdoctoral research fellows in the Department of Earth System Science at the School of Earth, Energy & Environmental Sciences (Stanford Earth). Additional coauthors are affiliated with Leibniz-Institute of Freshwater Ecology and Inland Fisheries, the Swedish Museum of Natural History and Potsdam University. Klawonn is now affiliated with Leibniz Institute for Baltic Sea Research.

The research was supported by the German Academic Exchange Service, the Simons Foundation and the German Research Foundation.

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Michael S. Kelly
June 4, 2021 10:54 pm

Huh. And I thought my athlete’s foot was a nuisance. Who knew it could save the planet?

Reply to  Michael S. Kelly
June 5, 2021 5:42 am

And jock itch can be enjoyed by everyone.

Reply to  Scissor
June 5, 2021 7:50 am

Thank you for that!

Curious George
Reply to  Michael S. Kelly
June 5, 2021 8:03 am

Does this research come from Professor Paul Ehrlich’s school?

Reply to  Michael S. Kelly
June 6, 2021 9:37 am

Now whales are the major predator of phytoplankton so maybe the Japanese have the right idea and we need to kill those eco-vandals 🙂

June 5, 2021 12:17 am

In different terrestrial plants the response to elevated CO2 shows variable experimental data results. When the relationship of different plants with their respective type of fungus was examined it was the type of fungus that naturally associates with a different plant that put the variable results to elevated CO2 into context.

M Courtney
June 5, 2021 12:42 am

Going a bit Beatrix Potter here, if phytoplankton and fungi are involved I’m willing to bet that the role of yeasts is not understood either.
Still, proper research. I’m ‘lichen’ it.

Although this simile annoyed me, “dissolves like tea”.

Clyde Spencer
Reply to  M Courtney
June 5, 2021 10:54 am

It teed me off, too.

Reply to  Clyde Spencer
June 5, 2021 9:44 pm

Yah, but… as M Courtney found, ‘dissolves’ da’ puzzle.

June 5, 2021 1:24 am

The compost earthworm is an animal that is excellent at fixing carbon in the soil. It needs cellulose to reproduce. It converts ordinary paper into excellent black soil.

Peta of Newark
Reply to  ren
June 5, 2021 2:36 am

Perfectly nailed it ren
And, if these algae blooms were ‘harvested’, brought ashore and mixed into farmland dirt, the worms would go crazy and multiply like a multiplying thing (i nearly said wildfire there but thought better)

Climate would be fixed. In more ways than one ##
And if we, following the natural instinct of our own children, ate a fresh raw earthworm now and again, we’d add to the bacteria in our guts that make Vitamin B = the vitamins that control our immune systems, our nervous systems and help prevent us going crazy from Alzheimer’s and other dementia.
But we poison the feedstock while it’s still out in the ocean IOW: we burn the Biomass because we think it’s bad and burning it will save us.
How wrong is it possible to be about anything – how do you break a positive feedback loop like that?

## The craziness that eating earthworms fixes, is also = the craziness that is Climate Change

In that vein….
Here’s a video for ya – a very good looking girl who knows her own mind- AND the minds of children; (Remember the climatologist’s constant cry = “Think Of The Children”)

The whole 48 mins is simultaneously heartbreaking and angrifying – you are not human if she she doesn’t get to you
If you’re rushed and who isn’t, start at about 18 minutes in and listen what the guy ‘Larry’ has to say.
If that doesn’t resonate with what’s powering Climate Change then:
Game Over and The Zombies have won.
Boys and Girls, I present Leila Centner

Reply to  Peta of Newark
June 5, 2021 3:47 am

Where do you think the black soil called black earth comes from? Grass is one of earthworms’ favorite foods. You can grow all demanding plants on such soil. Do you like tomatoes? I do.

Joseph Zorzin
Reply to  ren
June 5, 2021 4:17 am

When I mow the lawn- the worms come to the surface for lunch- then come the robins to have the worms for lunch. I never remove the cut grass and can’t understand why anyone does. Cut grass is great fertilizer for the grass and I like robins.

Reply to  Joseph Zorzin
June 5, 2021 5:48 am

You are a part of nature that you understand and love.

Reply to  Joseph Zorzin
June 5, 2021 9:36 am

On my lawn, if the clippings aren’t removed, they kill the green growth as they rot…

Clyde Spencer
Reply to  DMacKenzie,
June 5, 2021 10:56 am

Mow more frequently.

Reply to  DMacKenzie,
June 5, 2021 10:57 am

They must be scattered to dry. Then they will disappear on their own.

Reply to  DMacKenzie,
June 5, 2021 12:10 pm

Always mow during ascending moon; that’s when farmers make hay ; the grass dries more reliably.
Lawn grass mown wet feeds bacteria ; wilted grass feeds fungi.

Reply to  Joseph Zorzin
June 5, 2021 4:20 pm

Yes! Here in Southern VT, I have had a 2 acre “lawn” for the last 40 years, never fertilized, just cut it every spring a few times. Over the decades the maturing trees have produced shade and mulch from their leaves (never raked) so there is now a 6 inch spongy mossy humus which I never mow. I do clip the young tree seedlings which sprout, but am careful not to walk over the the wild flowers (like Jack in the Pulpits and Lady Slippers) which abound in the spring. It is essentially a well kept forest with deep clear undergrowth. The Fall season produces an abundance of Chanterelle mushrooms, they vary by year. Last year we froze several pounds of Honey mushrooms. I try to manage the balance between wild growth and succession. The less I do, the better it gets.

Reply to  Joseph Zorzin
June 5, 2021 5:35 pm

Cutting grass releases volatile compounds related to hexanol. For earth worms hexanol fractions are an olfactory signal that there are more edible micro-organisms for them; and so the worms follow the volatile organic molecular gradient into the cut grass.

Reply to  Peta of Newark
June 5, 2021 4:02 am

Do you know what well-processed compost smells like? It is the smell of earth. No other fertilizer compares to it.

Reply to  Peta of Newark
June 5, 2021 9:51 pm

Not exactly what you had in mind, Peta, but nightcrawlers make excellent bait. I can’t think of a freshwater fish that will pass up a nightcrawler.

I eat 2nd-hand nightcrawlers after they’ve been processed by the fish I catch.

Reply to  ren
June 5, 2021 11:33 am

Just a distinction: earthworms consume the micro-organisms that themselves (microbes) form a sequential consortia of material degrading microbes. And the cellulose carbon is also relevant, not as something earthworms directly ingest but rather, as pertains to suitability of the earthworms immediate environment’s carbon to nitrogen ratio.

Reply to  gringojay
June 6, 2021 12:27 am

Influence of Carbon Sources on Natural Transformation of V. Eiseniae EF05-2r
The influence of nutrient status on the transformation of V. eiseniae EF05-2r was evaluated using a plasmid construct (pENTR/D-Topo-MCS:kanpilBC ) containing 1kb of t
his organism’s pilB and pilC region and a neomycin phosphotransferase gene (npt2) inserted between pilB and pilC. Integration of pilB:npt2:pilC into the V. eiseniae TFP gene cluster via a double crossover was confirmed in a subset of transformants by PCR amplification of the pUC origin (origin of replication for the plasmid used). The absence of amplifiable vector in the tested transformants was consistent with double crossover integration.

After testing several DNA concentrations (1, 25, 50, 100 ng/uL) and two incubation times (6 and 24 h) for transformation frequency of V. eiseniae EF05-2r in ACM (Table 2), a single DNA concentration (0.66 ng/uL, ∼100 copies per cell) and incubation period (24 h) were selected to evaluate the influence of carbon source on transformation. Under these conditions, transformation by pENTR/D-Topo-MCS:kanpilBC in MSM resulted in a two-fold increase in frequency compared to ACM (Table 3). Transformation frequency in MSM supplemented with 20 mM NH4Cl was not significantly different than ACM (Table 3). All carbon sources tested (Table 3) were previously shown to support growth of V. eiseniae [9]. After 24 h incubation with any one of the carbon sources except galactose, transformation frequencies decreased by at least two-fold (Table 3). The inclusion of 20 mM pyruvate in MSM resulted in a 24-fold decrease in frequency.

Reply to  ren
June 6, 2021 2:38 am

“Almost all Lumbricid earthworms (Oligochaeta: Lumbricidae) harbor extracellular species-specific bacterial symbionts of the genus Verminephrobacter (Betaproteobacteria) in their nephridia. The symbionts have a beneficial effect on host reproduction and likely live on their host’s waste products. They are vertically transmitted and presumably associated with earthworms already at the origin of Lumbricidae 62–136 million years ago.” 

June 5, 2021 2:41 am

We need more CO2, not less. The CO2 feeds the world population, cutting CO2 will increase price of food, increase poverty, diseases and pestilence.
Morons have taken over the planet.

Joseph Zorzin
Reply to  Vuk
June 5, 2021 4:19 am

“Morons have taken over the planet.” I think they’ve always run the show. It’s just different breeds of morons.

Peter W
Reply to  Vuk
June 5, 2021 9:38 am

Read the book “The Population Bomb” for an example of where we would be without the recent increase in CO2.

Joao Martins
June 5, 2021 4:37 am

Another generalization from a very particular case, trying to convince us that the whole universe is just its amplification…

Biology got lost long ago in the tangle of superstitious thought. (Try and check how it happened: follow the redefinition of “ecosystem” that lead to the concept losing all connection with the real world; try and see how it was done, check how the United Nations introduced the “concept” of “biodiversity” and try to understand what it realy means and what are its scientific grounds, if any).

H. D. Hoese
Reply to  Joao Martins
June 5, 2021 6:07 am

What are called fungi are more complicated nowadays, but been around as a concern for a long time, often resistant to antibiotics. About a century ago one nearly wiped out the Florida sponge industry. As to the ecosystem concept, a theoretical one coming from the German concept of a biocoenosis in European oysters (1877). Some ecologists don’t like the term ecosystem much, has some utility, got out of hand like many. Used now with oysters as “ecosystem services,” one of which is sequestering carbon, they hope, mass balance a problem.

A couple of examples.

   Andrews, J. D. 1955. Notes on fungus parasites of bivalve mollusks in Chesapeake Bay. Proceedings of the National Shellfisheries Association.. 45:157-167. 

   Couch, J. N. 1942, A new fungus on crab eggs. Journal of the Elisha Mitchell Scientific Society. 58:158-162.

“Isolating one microorganism from nature and growing it in the laboratory is difficult,…”Only a few model systems are therefore available to research such parasitic interactions.” Yep, we knew about the first sentence, may suffer from the second.

H. D. Hoese
Reply to  H. D. Hoese
June 5, 2021 8:23 am

I was going to give them some credit, and maybe they deserve it, but this is their first citation.Homage to Linnaeus: How many parasites? How many hosts?   From that abstract.
“We estimate that there are between 75,000 and 300,000 helminth species parasitizing the vertebrates. We have no credible way of estimating how many parasitic protozoa, fungi, bacteria, and viruses exist. We estimate that between 3% and 5% of parasitic helminths are threatened with extinction in the next 50 to 100 years.” Is the current parasitology emphasis now on saving them?

Reply to  H. D. Hoese
June 5, 2021 11:05 pm

Yes, believe it or not, parasitology is transitioning into a victim science. It started out not so non-sensical, simply noting that when a larger organism goes extinct, then so do its parasites. True and like most reasonable conservation – concentrate on saving habitat and you can keep hosts and their parasites going. But ‘save the parasites’, like ‘eat insects’, has become a bit of a mantra among the woke.

Chytrids are interesting organisms, but not fungi per se. I’m not sure that even the most extremely woke mycologist (for who else would study chytrids?) would be in favour of conserving the amphibian chytrid Batrachochytrium dendrobatidis that is credited for the great frog decline, but one never knows nowadays.

Andy Pattullo
June 5, 2021 7:58 am

Adding understanding to the carbon cycle is valuable. Assuming any CO2 added to the atmosphere is bad is just plain stupid. CO2 is the fundamental building block of all life on Earth. No one has published reliable objective evidence that rising atmospheric CO2 is doing harm (that all comes from climate models that fail virtually every test of validation), but there is ample evidence the world is becoming a better place for life as CO2 increases.

June 5, 2021 9:15 am

“need to be careful” as in a biohazard lab in Wuhan protected by the CCP news blackout or maybe a large graphite nuclear reactor in Chernobyl protected by another news blackout political Party?

June 5, 2021 9:21 am

Let’s see now we had a global pandemic before this one and we also had a snowball earth before. Let’s study it at lab in Wuhan with some federal funding and grants. Everything will be totally transparent.

June 5, 2021 9:24 am

When does the movie come out? There’s something strange happening in the waters near Wuhan, it’s in the rivers too.

Clyde Spencer
June 5, 2021 10:51 am

“If you’re changing this system by more than a few percent in any direction, it can have dramatic implications for biogeochemical cycling. It makes a big difference for our climate.”

The unstated assumption is that carbon dioxide is the ‘control knob’ of climate.

Reply to  Clyde Spencer
June 5, 2021 3:56 pm

Good Clyde! I think another unfounded assumption is that fungi biomass is not also representative of carbon capture. Another might be that carbon capture is defined.

Yet another implication that they might have missed: if, as they say, fungi contribute to CO2 in the atmopshere, then all atmospheric carbon is not anthropogenic.

Reply to  dk_
June 5, 2021 9:55 pm

I have zero hope of them coming to that realization, dk_.

June 6, 2021 9:40 pm

Channeling Andy Rooney: Did ya ever wonder how much of the ocean’s microplastics might be fungi spores?

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