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202109 Fresh Quarterly Issue 14 06 Life In Earth
Issue FourteenSeptember 2021

Life in earth

The underground movement that supports orchards. By Anna Mouton.

Plants put a lot of energy into cultivating microbes. A significant portion of the sugars that plants make during photosynthesis is pushed out into the soil in the form of root exudates. Root exudates attract and support microbes. And microbes help to support plants. Some plants even host useful microbes on and in their roots.

What should growers know about the microbes in their soil? Fresh Quarterly spoke to Prof. Karin Jacobs who heads up the Microbial Ecology and Mycology Laboratory in the Department of Microbiology at Stellenbosch University. We were joined by Casper Brink, soil microbiologist with soil-analysis company Sporatec.

Pillars of the soil community

“We never refer to microbes as individuals,” says Jacobs. “We always talk about them collectively, as a colony or a community, and this is how they function.” Jacobs explains that the characteristics of a soil will determine which microbes live there. Factors such as pH, oxygen, water, and nutrient availability all affect the microbial community.

As a microbiologist, Jacobs is particularly interested in bacteria and fungi. Fungi can be single-celled or multicellular. Multicellular fungi typically grow as a network of threadlike hyphae. Fungi are the main decomposers in ecosystems. They have enzymes to break down complex carbohydrates such as the lignin in wood.

Fungi reduce dead plant material to simple sugars which bacteria can use. Bacteria are single-celled organisms that make up the second-largest group of life on earth by mass — readers will be pleased to hear that plants are number one.

“Bacteria can take up certain nutrients, and change them a little bit, so that they can then be used by other organisms,” says Jacobs. Bacteria are essential for recycling organic material, fixing atmospheric nitrogen, and increasing nutrient availability.

“Phosphates are one of the insoluble substrates that farmers struggle to get plants to take up,” says Brink. “Bacteria have phosphatase enzymes that make phosphates soluble, so they become available to plants.”

Bacteria and fungi also serve as prey for other soil organisms, including protozoa, nematodes, collembola, and mites, which get eaten in their turn. At the same time, some bacteria and fungi infect plants and animals – certain fungi even trap and kill nematodes.

A mutually beneficial arrangement

“Plants have, through millennia of evolution, started to select their preferred microbial partners,” says Jacobs. The production of sugary root exudates is one way in which plants entice desirable bacteria. Another is to allow useful bacteria and fungi to take up residence in or on plant roots.

“It’s a mutualistic relationship — give and take — between the plant and the microbe,” clarifies Brink. “The plant gives sugars; the microbe gives some of the other nutrients that the plant can’t get by itself.”

Plants can manipulate the soil and select for their preferred microbes, but the downside is that monocultures can end up with limited microbial diversity. Ecologists have different metrics to assess species communities. Richness is the number of different species, whereas diversity also takes the number of individual members of each species into account.

The problem with low diversity, explains Jacobs, is reduced redundancy. A diverse community has many individuals of many different types that can perform a given function. When conditions change, for example during a drought, chances are that someone will survive to continue performing that function. But if diversity is low, a change might wipe out entire functional groups, leaving no one to do a particular job.

Interactions between plants and soil microbes are concentrated in the thin layer of soil attached to the roots — this is called the rhizosphere. Nutrient levels are elevated in the rhizosphere thanks to all the microbes living there. Resident microbes keep others out through competitive exclusion. This can also protect plants by warding off disease-causing microbes. For their part, many plants will lower the pH of the rhizosphere to facilitate uptake of certain nutrients.

“The rhizosphere is where everything happens,” observes Jacobs. “That’s where farmers need to concentrate if they want to make changes in the plant-soil relationship.”

Getting to the roots of soil health

The key to increasing diversity, says Brink, is to feed the microbes. “Cover crops, for example, stimulate bacteria, because they get the simple sugars from the root exudates, whereas mulching and composting provide more food for fungi, because they break down all the dead material.”

The worst thing, according to Brink, is to have nothing growing in the work rows, thereby starving the microbes. Cover crops and mulches further protect microbes by shading the soil, and preventing large temperature fluctuations of the soil surface. Bare soil tends to dry out, and reduced water equals reduced microbes. Drip irrigation can therefore deliver a twofold blow to microbes — less plant growth and less soil water.

In a water-scarce environment, growers will have to find the balance between water-saving drip irrigation, and microbe-enhancing moisture in the work rows.

Fertilisers are yet another influence on soil microbes. There are both free-living and root-associated bacteria that can fix atmospheric nitrogen, and make it available to plants. Too much nitrogen fertiliser suppresses the ability of these bacteria to fix nitrogen. And remember than, unlike fertiliser, atmospheric nitrogen is free.

Plants can also draw on root-associated fungi — known as mycorrhizae — to aid their nitrogen uptake. But if plants are getting enough nitrogen from fertiliser, they may expel their mycorrhizae, which then start competing with the plants for other nutrients.

Growers who want a better idea of their soil health can turn to companies like Sporatec for specialised testing. Brink has been analysing samples from the cover-crop trials run by Matthew Addison, crop-protection programme manager at Hortgro Science, to assess the impact of increased plant diversity on microbial diversity.

Preliminary results show differences between communities in the tree and the work rows, especially for fungi. Brink speculates that mulching the tree rows is selecting for certain fungi. Analyses of samples from more than one season are needed to see how the different treatments are influencing the soil microbes.

“That’s why most of our samples are submitted,” says Brink. “Growers want to see, am I improving by building soil carbon, increasing microbial activity and diversity, and building resilience in my soil.”

Jacobs and Brink think that the time is ripe for a microbial mind shift in agriculture. Brink explains. “The focus should be more on biology — not just on chemicals and on using the soil just as a growth medium, but on using the microbes to your benefit as well. Because if you keep your microbes happy, then you’re halfway there.”

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