Microbes measure ecological restoration success

The researchers used next generation sequencing of the DNA in soil from samples taken across the site that had a range of plantings between six and 10 years old.

The technique – high-throughput amplicon sequencing of environmental DNA (eDNA), otherwise known as eDNA metabarcoding – identifies and quantifies the different species of bacteria in a sample.

The researchers – students Nick Gellie and Jacob Mills, Dr Martin Breed and Professor Lowe – analysed soil samples at the restoration site at Mt Bold Reservoir in the Adelaide Hills, South Australia, and compared them with neighbouring wilderness areas as ‘reference sites’.

“We showed that the bacterial community of an old field which had been grazed for over 100 years had recovered to a state similar to the natural habitat following native plant revegetation – an amazing success story,” says Dr Breed, Research Fellow in the Environment Institute.

“A dramatic change in the bacterial community were observed after just eight years of revegetation. The bacterial communities in younger restoration sites were more similar to cleared sites, and older sites were more similar to the remnant patches of woodland.”

Revegetation rewilds the soil bacterial microbiome of an old field – Gellie – 2017 – Molecular Ecology – Wiley Online Library

Oxygen during inflammation helps E. coli thrive in an inflamed gut.


The mechanisms driving gut bacterial imbalance.

During episodes of intestinal inflammation – which can occur during IBD and gastrointestinal infections and cancers – the composition of these gut microbial communities is radically disturbed.

“Beneficial bacteria begin to dwindle in numbers as less beneficial, or even harmful, bacteria flourish,” said Ms. Hughes. “This imbalance of microbiota is believed to exacerbate the inflammation.”

A healthy gut is devoid of oxygen. The beneficial bacteria that live there are well-adapted to the low-oxygen environment and break down fiber through fermentation. Unlike these beneficial bacteria, potentially harmful E. coli grow better in high-oxygen environments.

“Inflammation changes the environment so that it is no longer perfect for the commensal anaerobes, but perfect for opportunistic E. coli, which basically wait for an ‘accident’ like inflammation to happen,” Dr. Winter explained.

The increased availability of oxygen during inflammation helps E. coli thrive in an inflamed gut through a metabolic “trick,” Ms. Hughes said.

“Through respiration, the abundant waste products generated by the beneficial microbes can be ‘recycled’ by commensal E. coli – which do not grow well on fiber – and turned into valuable nutrients, thus fueling a potentially harmful bloom of the E. coli population,” she explained.

“If we interfere with the production of waste products by the beneficial commensal bacteria, then we impede their metabolism, which causes them to grow more slowly and throw off the entire ecosystem,” Dr. Winter said. “The most effective strategy may be to inhibit commensal E. coli‘s unique metabolism to avoid the bloom and negative impacts.”

Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis: Cell Host & Microbe

Ideal Soil Element Ratios

There’s no such thing as ideal. Or is there?

While calculating the ratios of soil elements I made an interesting observation about carbon. Both plant and soil.

We know from previous studies that about 8% soil organic carbon (SOC) is optimum for yield. It turns out that’s about the same amount of carbon in most plants. Coincidence? I think not.

Optimum soil carbon for yield likely correlates with actual plant carbon.

If I take that and assume an 8% SOC 10cm topsoil and a linear decline over 60cm depth, I get 15.75% Total SOC. You see these levels in some forests and Terra Preta.

I wonder what percentage of fungi and bacteria is carbon?… Just checked… and it turns out fungi are about 8%!

*Mind Blown*

Spirulina, a cyanobacteria? 3.12%. If you divide 8% by 3.12% you get a Fungal to Bacteria ratio of 2.56:1.

Meaning you’d need 2.56 fungi to 1 bacteria to get the equivalent of 8% carbon.

What did David Johnson say was ideal Fungi:Bacteria ratio? Well, will you look at that, 2.56 is pretty darn close to the productivity maxima.

So, depending on what you are growing, it could well dictate the ideal soil organic carbon and the bacteria:fungi ratio.

FWIW, if you’re growing a human, then we’re 18.5% carbon… and a vegetarian would need to consume something like 2.3x the amount of food as a carnivore. This is below the bifurcation growth rate of chaos theory at 3.0.
Fungi:Bacteria Ratio.png

15.875% Total SOC.png