A few common bacteria account for majority of carbon use in soil


Research News


Just a few bacterial taxa found in ecosystems across the planet are responsible for more than half of carbon cycling in soils. These new findings, made by researchers at Northern Arizona University and published in Nature Communications this week, suggest that despite the diversity of microbial taxa found in wild soils gathered from four different ecosystems, only three to six groups of bacteria common among these ecosystems were responsible for most of the carbon use that occurred.

Soil contains twice as much carbon as all vegetation on earth, and so predicting how carbon is stored in soil and released as CO2 is a critical calculation in understanding future climate dynamics. The research team, which included scientists from Pacific Northwest National Laboratory, Lawrence Livermore National Laboratory, University of Massachusetts-Amherst, and West Virginia University, is asking how such key bacterial processes should be accounted for in earth system and climate models.

“We found that carbon cycling is really controlled by a few groups of common bacteria,” said Bram Stone, a postdoctoral researcher at the Center for Ecosystem Science and Society at Northern Arizona University who led the study. “The sequencing era has delivered incredible insight into how diverse the microbial world is,” said Stone, who is now at Pacific Northwest National Laboratory. “But our data suggest that when it comes to important functions like soil respiration, there might be a lot of redundancy built into the soil community. It’s a few common, abundant actors who are making the most difference.”

Those bacteria–Bradyrhizobium, the Acidobacteria RB41, and Streptomyces–were better than their rarer counterparts at using both existing soil carbon and nutrients added to the soil. When carbon and nitrogen were added, these already dominant lineages of bacteria consolidated their control of nutrients, gobbling up more and growing faster relative to other taxa present. Though the researchers identified thousands of unique organisms, and hundreds of distinct genera, or collections of species (for example, the genus Canis includes wolves, coyotes, and dogs), only six were needed to account for more than 50 percent of carbon use, and only three were responsible for more than half the carbon use in the nutrient-boosted soil.

Using water labeled with special isotopes of oxygen, Stone and his team sequenced DNA found in soil samples, following the oxygen isotopes to see which taxa incorporated it into their DNA, a signal that indicates growth. This technique, called quantitative stable isotope probing (qSIP), allows scientists to track which bacteria are growing in wild soil at the level of individual taxa. Then the team accounted for the abundance of each taxon and modeled how efficiently bacteria consume soil carbon. The model that included taxonomic specificity, genome size, and growth predicted the measured CO2 release much more accurately than models that looked only at how abundant each bacterial group was. It also showed that just a few taxa produced most of the CO2 that the researchers observed.

“Better understanding how individual organisms contribute to carbon cycling has important implications for managing soil fertility and reducing uncertainty in climate change projections,” said Kirsten Hofmockel, Microbiome Science Team Lead at Pacific Northwest National Laboratory and a co-author of the study. “This research teases apart taxonomic and functional diversity of soil microorganisms and asks us to consider biodiversity in a new way.”

“The microbial demographic data that this technique reveals lets us ask more nuanced questions,” said Stone. “Where we used to characterize a microbial community by its dominant function, the way a whole state is often reported to have voted ‘for’ or ‘against’ a ballot proposition, now, with qSIP, we can see who is driving that larger pattern–the ‘election results,’ if you will–at the level of individual microbial neighborhoods, city blocks.

“In this way, we can start to identify which soil organisms are performing important functions, like carbon sequestration, and study those more closely.”


This research was supported by grants from the Department of Energy’s Biological Systems Science Division Program in Genomic Science (Nos. DE-SC0016207 and DE-SCSC0020172), and by the National Science Foundation (No. DEB-1645596). Research conducted at Lawrence Livermore National Laboratory was supported by the U.S. Department of Energy Office of Science, via awards SCW1679 and SCW1590, conducted under the auspices of DOE Contract DE-AC52- 07NA27344. Research conducted at Pacific Northwest National Laboratory was supported by the U.S. Department of Energy Office of Science, via awards FWP 68907 and FWP 74475, conducted under the auspices of DOE Contract DE-AC05-76RL01830.

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Geoff Sherrington
June 7, 2021 11:00 pm

This work is welcomed as the intensity increases from alarmists wanting to save the earth by adding carbon to the soil. One easy way is to crush coal and spread it into agricultural soils, but like many proposals, this misses the point that enhanced plant growth from more available soil carbon comes at the expense of consuming some of that available soil carbon. The big question is, how much is consumed to give better growth – and that question is better understood by knowlegde of relevant soil bacteria. Geoff S

Reply to  Geoff Sherrington
June 8, 2021 5:15 am

Do plants consune soil carbon? My impression was that the plants fix atmospheric carbon dioxide, and then fungi and bacteria break down the cellulose to reuse it again.
Where this happens slowly or poorly you get bands of carbon rich peat and coal forming

Reply to  Leo Smith
June 8, 2021 5:46 am

Correct. Plants convert CO2 in the atmosphere to plant mass – cellulose – via photosynthesis, and do not “suck it up” from the soil. Carbon is in the soil due to the biodegradation of dead plant matter, so that carbon sink is a second order response to photosynthesis, not a source of photosynthesis.

Reply to  Duane
June 9, 2021 4:22 am

Right…The term “soil carbon” was originally used as synecdoche (a part for the whole, as in “a hired hand”) by agronomists in referring to fibrous organic matter added to soil to increase its water holding capacity and making nutrients more available to roots.The term has become perverted by the ignorant popular press corps.

Geoff Sherrington
Reply to  Leo Smith
June 8, 2021 4:36 pm

You missed the key word “available” which is far from total. Geoff S

Joao Martins
Reply to  Geoff Sherrington
June 8, 2021 6:52 am

“… enhanced plant growth from more available soil carbon comes at the expense of consuming some of that available soil carbon…”

WRONG! Plants do not feed on carbon from soil (or any organic substances): they feed on atmospheric CO2, ligth from the sun, and water!

This work is nothing new: just read any good textbook of microbiology published in the 1950s to 1970s: it is all there!

Nowadays a lot of “specialists” are “re-discovering” what they have not learned, and should have learned, in their university studies!

The last three paragraphs quoted in this post are ridiculous: they show that its authors have not the smallest knowledge about all that “biological diversity” encompasses! No reflection about the subject! Confusion between diversity in the taxonomic context and niche diversity in ecology, something discussed and elucidated during the 1960s! (and they show lack of understanding of many other fundamental biological concepts that would be boring to list here: they were basic when I made my studies more than 50 years ago).

Geoff Sherrington
Reply to  Joao Martins
June 8, 2021 4:42 pm

Key word was ‘available’ carbon that you took for total.
Are you trying to say that carbon in plant and soil chemistry in immune from all relevant reactions in the soil? What mechanism do you propose that excludes it from being a player?

June 7, 2021 11:10 pm

No clear hypothesis, no discussion of biochemical processes. Simply simple models and adding sugar and nitrogen to the soil in vitro! I did the same experiment in grade 6 sans PCR. The world’s most powerful tool to study soil biology is still looking for an interesting hypothesis.

Geoff Sherrington
Reply to  BCBill
June 7, 2021 11:12 pm

world’s most powerful tool”
I thought you folks in the USA had found him. Geoff S

Reply to  Geoff Sherrington
June 8, 2021 9:28 am

Not only found him, found a way to make him POTUS.

Reply to  BCBill
June 8, 2021 3:00 am

No wonder they hide the Methods and the end of Nature Communication papers – they interfere with the narrative:

Three replicates of soil samples were collected from the top 10 cm in of plant-free patches in four ecosystems along the C. Hart Merriam elevation gradient in Northern Arizona beginning at high desert grassland (1760 m), and followed at higher elevations by piñon-pine juniper woodland (2020 m), ponderosa pine forest (2344 m), and mixed conifer forest (2620 m).”

There is no ‘ecosystem’ replication at all and 3 samples from the top 10 cm of ‘plant-free’ soil allows generalising these results to what exactly?

How about all that carbon tied up in the layer of surface detritus? The three coniferous sites should have mor soils with a cover of needles. Coniferous soils are supposedly dominated by fungal decomposition anyway, but not a word about fungi.

I’m extremely skeptical of this paper meaning anything at all.

Reply to  DaveW
June 8, 2021 5:14 am

Excellent points.

Unfortunately, or fortunately depending on perspective, research funding has become a kind of welfare for the educated, and a tool really for story telling. Real science not needed.

Just in my backyard, I observed that there are more mushrooms than I ever recall. It’s been a cold and wet spring for us. These mushrooms tend to follow a root path from a neighbors cotton wood tree across my yard and the grass is noticeably greener and grows faster in the yard following the same pattern.

It seems there is some symbiosis going on in this “ecosystem.” Anyway, I wish I could easily get rid of the neighbor’s tree roots because they inevitably send out suckers. I don’t mind the mushrooms as they are temporary, but I wish I could replicate the health of the grass uniformly.

I don’t have the patience for such study, however.

Joao Martins
Reply to  DaveW
June 8, 2021 6:55 am

Those so-called “Methods”!… Complete nonsense for anyone deserving (by competence and knowledge) a professional title in Biology.

Last edited 12 days ago by Joao Martins
June 8, 2021 12:25 am

This is another WUWT post with a obtuse heading. The results are not for global soil, but any specific data is actually about Arizona desert grass lands and Arizona conifer/pine/pinon-juniper forests.

As for making those soil (aerobic) bacterial cells it takes 1 Kg of carbon (among other things) to make 0.82 Kg of cells. That carbon is used for synthesis of new cell material, synthesis of extra-cellular products bacteria exude (ex: polysaccharides for avoiding desiccation and binding metal ions), energy to complete reactions of synthesis, to maintain concentration gradients between interior and exterior of cell, and to accomplish turnover reactions within cells.

Peta of Newark
June 8, 2021 1:05 am

Quote:”In this way, we can start to identify which soil organisms are performing important functions, like carbon sequestration

Perfectly completely vacant and Brain Dead.

The ‘soil organisms’ are living critters – they take in carbon and craete Carbon Dioxide.
They eat sugar & organic acids from the soil and their expired cousins directly or, they consume the ‘waste’ created by fungi as they take apart cellulose and lignin.

The very last thing they do is ‘Sequestrate’

Charcoal and soot left over from fires might be considered sequestration – ultimately the creation of oil, coal and gas

Yes some sequestration of organic carbon does occur but only when plants die and fall to the ground.
If decomposition is slowed by a (bacterial) nutrient deficiency, the layer of expired organics will get deeper & deeper, thicker thicker.
(Just how thick are some coal seams around this world/)

That nutrient is typically either/both water-soluble Nitrogen or Oxygen

But ‘sequestration’ of soil organics is a very slow process – the layer of highly organic soil never grows faster than one inch per century even in the best conditions.
The very best anyone has yet found is actually under the (Grouse hunting/shooting) moors of Scotland, reckoned to be laying down organic material at one inch per 160 years.
Beyond maybe 3 metres, Oxygen calls a halt and the process starts making Peat > Lignite > Coal and maybe oil. Lots of gas also,
Same gas as what happens in anaerobic decomposition = why you fart.
(Farts being result of anaerobic decomposition of organic material in your guts and the very last thing it is, is ‘funny’. Unless you do find Crohn’s, Irritable Bowels and Cancer = funny)

Are we any closer yet, to joining the dots of my constant ravings?
Because, what do farmers do if not encourage the soil bacteria?

  • They keep ploughing them up, introducing Oxygen
  • They give them water via irrigation
  • They give them, what appears to them, vast amounts of Ammonium Nitrate or Urea

Thus, under farmland everywhere, the sequestration of organic material has been thrown hard into reverse and the pedal has hit the metal.
Is it any wonder the level of CO2 in the air has gone up?

Pretty soon, those soil bacteria are going to come up against bedrock – to say there will be a ‘sickening thud’ and ‘complete stop’ will be *THE* Biggest Understatement of All Human Time

When you see brown, red or orange-coloured farmland soils, you see that bedrock getting very close to the surface.
Those orange soils are the amber warning light if you prefer, make no mistake – at present rate the red one is coming on soon.
Do try to bear that in mind next time you rave about ‘ever increasing yields’.
Of nothing more than the mind, body and soul-destroying shyte that is: sugar.

Even before you’re pointing to a ‘trend line on a graph‘, while trend-lines created by warmists represent ‘junk’.
Only sugar-eaters can justify that

## It’s a rat-trap baby, and you’ve been caught ##

Last edited 12 days ago by Peta of Newark
Reply to  Peta of Newark
June 8, 2021 5:18 am

Bacteria lives matter.

Reply to  Peta of Newark
June 8, 2021 10:15 pm

I beg to differ with you Peta .Our grasslands in New Zealand grazed by sheep and cattle build up top soil rapidly .From my own observations I have bulldozed farm access tracks and exposed red raw clay and in 5 years their is a sward of grass and 2 0r 3 inches of black soil from what the animals deposit .We aerial topdress mainly phosphate and some sulpher and we spread carbonate of lime with spreader trucks .
On our easy country we have grown many crops and one paddock was planted in maize (corn ) for grain for 18 years .
Yes plowing does release carbon from the soil .
I gotta go now .Graham.

Geoff Sherrington
Reply to  Peta of Newark
June 9, 2021 4:00 am


You might enjoy the images of laterite soil profiles in Weat Australia, which has had no soil-stripping glaciation for a very long time, and low rainfall for most of its development time.
Geoff S


Zig Zag Wanderer
June 8, 2021 1:06 am

CO2 molecules matter! Stop trying to get rid of them!

Reply to  Zig Zag Wanderer
June 8, 2021 5:23 am

There was a time when utilization of CO2 in industrial processes was considered “green chemistry.” This was before CO2 was demonized, but I remember it well.

I’ve just started a project where I use a special reagent to covalently bond CO2 into an aromatic class of compounds. I hope that some green can come from it.

M Courtney
June 8, 2021 1:58 am

Those bacteria–Bradyrhizobium, the Acidobacteria RB41, and Streptomyces–were better than their rarer counterparts at using both existing soil carbon and nutrients added to the soil.

Have we established cause and effect here?
If these bacteria are better at using their food they will be more abundant than those that are less able to utilise the available resources.

However, if one of the current winners went away there are lots of other bacteria that could fill their space. With no reason to expect any difference to the soil quality or the carbon cycle.

June 8, 2021 2:31 am

Most soil bacteria accumulate around the roots of plants with which they are in symbiosis.

Reply to  ren
June 8, 2021 3:03 am

Perhaps that is why they sampled bare soil, but my guess is they developed their hypothesis post hoc to fish something out of their data.

Reply to  ren
June 8, 2021 5:26 am

I just noticed something like this as I mentioned above. (insert fungi joke here)

June 8, 2021 2:33 am

Bacteria that are in symbiosis with earthworms are excreted by them to form a lumpy highly productive soil.

June 8, 2021 2:57 am

Looks like a plug for more funding to me

Reply to  H B
June 8, 2021 5:27 am

Never ending, until one retires on a nice government pension.

June 8, 2021 3:45 am

Two things:
1) I accept the humble apologies of the crowd who abused me as mentally shortchanged some months ago when I talked about the “subterranean carboniferous ecosystem” as I believe I called it. You now have Authority to confirm the existence of the vast masses of active microbes essential to soil vitality.
2) I would dearly love to see a study comparing the microbial genome of wild, forest, organically farmed, no-till, low-till, and Monsanto Frankendreck fields.
The research to couple soil genome to human culture, tradition and psyche will of course only happen if I pay for it myself, so…. we’ll never know for sure? (Although the vaccinators seem to be doing somewhat similar research for use in their mRNA concoctions, like that “extremism gene”…)

Joao Martins
Reply to  paranoid goy
June 8, 2021 7:03 am

Please elaborate on the objective meaning of “soil vitality”. Using biological terms and concepts would help, on the side of “vitality”. Using geologic and pedological terms and concepts would also be welcome, on the side of “soil”.

Last edited 12 days ago by Joao Martins
Reply to  Joao Martins
June 8, 2021 8:46 am

oh. Sorry. Terms!
Er…Soil. Vitality.
Soil means the stuff where plants like to grow. Tastes a bit like old roots?
Vitality means ‘liveliness’ or ‘aliveness’.
As opposed to an exploitable expanse of inert minerals that needs human aid in the form of poisonous amounts of chemical intervention to grow food-like Frankencrops incapable of scrounging their own living in real soil, where they get scared to death by all the other species that like to hang out around live soil.
For speciality jargon, please refer to any number of sophists disseminating pompously on the settled science from their university-sponsored platforms.

Reply to  paranoid goy
June 8, 2021 4:26 pm

PG & JM:
This reminded me of Jordan Peterson’s Rule #10 – Be precise in your
language (so we are not arguing about everything!). A quick look at Wikipedia on “soil microbiology”: they use nebulous terms such as “health” of the soil.
Two recent books to recommend:
“Tomorrow’s Table” by an organic farmer & his biochemist wife
“Seeds of Science” by an environmental activist [think of a Michael Shellenberger with regard to GMO’s]

Thanks for the quote from the Methods section! I used to (gently!) chastise my medical students if they skipped over the Methods when we’d review a paper.
3 samples from 4 Northern AZ locations, away from plants does not sound like it can be extrapolated very far. And as commented on above, the connection to CO2 is second-order.

Here in central AZ we are having another gorgeous day, completely consistent with ‘climate change’.

Reply to  B. Zipperer
June 8, 2021 11:53 pm

I try to be as precise in my use of language as style, wit and knowledge allows. This does not prevent anyone else from understanding (or not) whatever the hell they wish to extract from any particular phrase.
This stupid thread as example: Demanding the use of “biological terms” when the …person actually just needs to open a friggin’ dictionary.
To yammer on about the meaning of “soil vitality” seems like some sort of intellectual rigour, but it only serves to disrupt the train of thought that might otherwise form around said phrase, such as “what is dead soil then?” or “how do I feed live soil” etc, but instead we get what? “That’s ain’t not sciency enough, that!”
And so an amateur troll kept you and I busy with nonsense…

Geoff Sherrington
June 9, 2021 4:08 am

A common fate of carbon in Nature is to eventually become CO2 gas or a solid carbonate, as these are at the bottom of the energy well in many mechanisms.
Thus, if you add various forms of carbonaceous material to a soil, things like straw, leaf litter, compost, you will likely generate CO2 eventually. Plausibly, some of this will be involved in plant growth, even from the simple mechanism of CO2 outgassing from the soil into the air above and reacting with the leaf growth cycle. This will usually involve bacteria (and fungi).
Geoff S

Rich Lentz
June 9, 2021 10:26 am

If portions of the above are true, would someone explain how mass, industrial sized, hydroponic agriculture will succeed.

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