Microbes: the farmer's new friends

In croplands, fungi and bacteria do both good and harm. Using molecular biological methods, researchers are trying to differentiate them from each other. By Florian Fisch

(From "Horizons" no. 110 September 2016)​​​

Die Humanity is facing considerable challenges in that it wants to produce more foodstuffs for the growing global population while causing only the minimum of damage to the environment", says Mark Bailey, who works at the Centre for Ecology and Hydrology in Wallingford, England. He's looking at the big picture – but his actual object of study is too small for the naked eye. He's researching into the community of bacteria, fungi and other microbes found in the soil.

Many specialist articles are talking of a revolution in soil microflora – one on par with the invention of agriculture 10,000 years ago, or the development of high-yield varieties 50 years ago. The current euphoria has been triggered by new molecular biological methods that can analyse whole microbial communities at once (see 'Identifying microbes by the metre').

In another habitat – the intestine – bacteria are already hitting the headlines. They help our digestion, protect us from illnesses and allergies, produce vitamins, and might even have an influence on our emotional state. In the USA, several projects have already been launched to study these communities. The Human Microbiome Project started back in 2008. In 2010, it was the soil that moved into focus with the Earth Microbiome Project. Bailey is participating in it. And in May 2016, the US government invested over USD 100 million in an overarching National Microbiome Initiative.

Dung brings variety

At the Swiss Federal Research Institute 'Agroscope' in Reckenholz, Franco Widmer is one of the experts for microbial diversity in the soil. It's a huge challenge: "A single gram of soil can contain up to ten billion microorganisms belonging to some 7,000 different species". Together with a team from the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) and the Research Institute of Organic Agriculture (FiBL), he has been comparing the microflora in soils that have been cultivated for decades, either for organic or conventional agriculture. (See 'Arable farming in a long-term comparison').

They have thereby discovered that it is the type of fertiliser that has the biggest impact on microbes. Soil that has been fertilised with dung and liquid manure has a greater diversity of microbes than soil that has only been fertilised by minerals. If the soil hasn't been fertilised at all, it becomes home to yet other bacteria and fungi.

In a study that has not yet been published, Widmer and his researchers observed ten different soils in Switzerland for five years – from woodland to arable land and meadows. Here, too, the microbial diversity of species in the soil was seen to be characteristic of how the land was used. "Based on the microflora, we can tell you what type of soil it is", says Widmer. And the composition of the soil barely changed over the period of study.

Bacteria protect against fungi

In her lab at ETH Zurich, Monika Maurhofer is studying the influence of bacteria and fungi on the health of plants. "We know that there are soils that stimulate disease and others that suppress it", she says. The big question, however, is this: which of these many microbes have what function? As part of the National Research Programme 'Soil as a resource' (NRP 68), the researchers wanted to find out whether certain soil bacteria that are known for their antifungal activity – so-called pseudomonads – can indeed protect plants. To this end, they collected soil samples from ten different wheat fields and analysed them to see which of three pseudomonads were present. They determined whether the genes typical of the species were present. Subsequently, the soil samples were planted with wheat again in the laboratory, two pathogenic fungi were added, and the effect of them was measured. As expected, there were big differences between the different soil types. There was also a connection with the presence of the pseudomonads – though it was rather weak.

Diversity isn't everything

"It's obviously not quite so simple", concludes Maurhofer. "It would be ideal if we had indicator organisms to tell us whether a soil is suitable for wheat growing or not". Soil biologists are aware of historical tobacco monocultures in Morens near Payerne in the canton of Vaud where for decades – astonishingly – hardly any problems with pathogenic fungi have occurred. They would love to know what makes this soil so healthy. But one thing is clear to Maurhofer: "It's not a general rule that more diverse microflora necessarily mean healthier soil. A certain diversity is important, but we don't yet know which are the relevant species". So we're still a long way from a molecular-biological classification of the quality of arable land.

Back at the Earth Microbiome Project, Bailey agrees. "It's difficult to manipulate the microbiome by experimental means under field conditions". The role of the total microflora is difficult to determine. Despite the lack of clarity, he insists that "fertile arable surfaces also display the highest degree of bacterial diversity". A greater degree of diversity can bring more protective organisms, yet also more pathogens at the same time.

The health of the soil can certainly be influenced. Working the land by mechanical means brings about a greater compression of the soil and thus less aeration. The concomitant shift in the microflora can be toxic to certain plants. So it's better to work the land without a plough. And varied crop rotation can also prevent a concentration of certain pathogens.

Even adding certain microbes can have a positive effect on the health of plants. For example, insect pests can be combatted biologically by adding threadworms. Good fungi can be used against ladybirds, and pseudomonads against bad fungi.

Cultivating symbiotic fungi

The best-known beneficial microbes are mycorrhizal fungi, which enter into a symbiosis with the roots of plants. In organic farming, the fungus spores have long been sown alongside seeds. Ian Sanders of the University of Lausanne has gone one step further and invented a method by which these fungi can be cultivated specifically. Rice cultures in the laboratory and his initial field trials with cassava cultures have demonstrated impressive increases in yield.

In 2014, Sanders spoke of his dream in the podcast Gastropod: "For millennia, humans have been breeding plants by using natural genetic variations to increase their crop yield. There's no reason why we can't do this with the mycorrhizal fungus too". But this revolution, too, will take many years to come about.

Florian Fisch is a science editor at the SNSF.

Arable farming in a long-term comparison

Since 1978, a unique long-term comparison
has been running in Therwil near Basel,
featuring five different types of farming:
dynamic, bio-organic, conventional/integrated,
conventional with mineral
only, and completely unfertilised.
After running for almost 40 years, this
DOC trial shows that the yield from organic
farming is up to 20% less, depending on the
culture in question. However, up to a total
of 35% less energy has to be expended on
it – including the production of manure and
sprays. The trial is a collaboration between
Agroscope and the research institute FiBL.

Identifying microbes by the metre

Using modern molecular biological methods,
it's possible to identify almost all the
and fungi in different habitats
the space of just a few days – whether
in the human intestine or in the soil. It's
done by searching for specific genes, according
to which the microbes can be allocated
to different groups. The result is an overview
of the whole microbial community – the
microbiome – and its diversity.