The impor­tance of soil micro-organ­isms

“Soil is not a life­less substrate, but an extremely complex, living ecosystem.” So says Professor Alicja Niewiadomska head of the Depart­ment of Soil Science and Micro­bi­ology at the Poznań Univer­sity of Life Sciences in Poland. It is these micro-organ­isms; bacteria, fungi, actin­o­mycetes and protozoa – invis­ible to the naked eye – that are respon­sible for the processes without which soil, could not func­tion. Alicja has been researching the rela­tion­ship between the soil micro­biome, fertility and crop health for many years. “A vast propor­tion of the processes taking place in the soil depend precisely on the activity of micro-organ­isms,” she says. “In 1m² of grass­land, the top 20cm of soil contains around 100bn micro-organ­isms, repre­senting 10,000 species of bacteria. This high­lights the essen­tial, invis­ible role of these organ­isms.”

Soil as a living ecosystem

Soil micro-organ­isms are involved in the decom­po­si­tion of organic matter, forma­tion of humus, the nutrient cycle, and the devel­op­ment of soil struc­ture. “They help main­tain the biolog­ical balance of the envi­ron­ment and are char­ac­terised by a very effi­cient carbon economy – using only as much carbon as they need to func­tion,” explains Alicja.

The problem arises when micro-organ­isms from another envi­ron­ment enter the soil, for example, via poorly fermented manure, slurry, or improp­erly prepared diges­tate from a biogas plant. Such mate­rials may contain path­o­genic micro-organ­isms or microbes with a very wasteful carbon economy. There­fore, after applying organic matter, it is neces­sary to monitor whether the soil is returning to its biolog­ical balance and whether there is any exces­sive growth of non-bene­fi­cial species.

Micro-organ­isms create the soil struc­ture

One of the most impor­tant func­tions of micro-organ­isms is to create the soil crumb struc­ture, which is respon­sible for water reten­tion, aera­tion, and protec­tion against erosion. “The bacteria, actin­o­myce­tota and fungi secrete organic compounds in the form of poly­sac­cha­rides, amino acids and proteins, which act as a natural binder,” explains Alicja.

As a result, the mineral and organic frac­tions of the soil bind together to form soil aggre­gates which are resis­tant to water and wind, helping to prevent soil erosion and improving condi­tions for root system devel­op­ment. Sapro­phytic fungi are also impor­tant. Their hyphae can reach up to 50km/m² of soil. As their diam­eter is up to 10 times smaller than that of root hairs, they can pene­trate very tight soil spaces, gently pushing the soil apart, improving its aera­tion and stability.

Natural produc­tion of nutri­ents

Micro-organ­isms also play a funda­mental role in plant nutri­tion. They are respon­sible for the miner­al­i­sa­tion of organic matter and the conver­sion of nutri­ents to plant-avail­able forms. There is a lot of phos­phorus in the soil, but it is often unavail­able as it is bound in minerals. However, certain bacteria and fungi belonging to the phos­phorus-solu­bil­ising group are able to release it through the produc­tion of organic and mineral acids, and enzymes like phos­phatases. Pseudomonas and Bacillus bacteria and Tricho­derma fungi are partic­u­larly valu­able in this respect.

Micro­bial secre­tions act as a binder, enabling the forma­tion of a crumb struc­ture in the soil.

Alfalfa forms a symbi­otic rela­tion­ship with nitrogen-fixing bacteria, helping to enrich the soil with nitrogen and reduce fertiliser require­ments for subse­quent crops.

Soil cultivation affects both soil struc­ture and micro­bial commu­ni­ties. The extent of this impact depends on the depth and inten­sity of tillage.

Prokary­otic organ­isms, like bacteria, also play their part in the process of fixing the atmos­pheric nitrogen, which is one of the elements crucial for plant growth. In the field, free-living bacteria can fix up to 30kg/ha of nitrogen. In the case of lucerne symbiosis, with appro­priate bacteria, this can be as much as 450kg/ha per year – as obtained in research by Alicja’s team. How effec­tive the symbiosis is, depends on the appro­priate selec­tion of bacte­rial strains for a specific plant species. Every legume requires a compat­ible microsym­biont. The mere pres­ence of root nodules does not neces­sarily indi­cate effec­tive nitrogen fixa­tion, due to the possible occur­rence of so-called inef­fec­tive nodules, colonised by strains that do not produce active nitro­ge­nase.

Micro-organ­isms protect plants

Soil micro-organ­isms can also support plant resis­tance and miti­gate the devel­op­ment of pathogens. “Some bacteria and fungi produce antibi­otic-like substances and lytic enzymes that destroy the cells of path­o­genic fungi,” explains Alicja. Among the most impor­tant micro-organ­isms with protec­tive prop­er­ties are bacteria of the genera Pseudomonas, Bacillus and Azoto­bacter. Some micro-organ­isms also produce siderophores, which are iron-binding compounds. Micro-organ­isms like Pseudomonas fluo­rescens, Pseudomonas putida or Tricho­derma fungi can sequester iron from the soil very quickly and transfer it to the plant, while simul­ta­ne­ously limiting its avail­ability to pathogens.

Support during periods of water scarcity

With increasing pres­sures from climate change, the ability to miti­gate envi­ron­mental stress using micro-organ­isms is becoming partic­u­larly impor­tant. Mycor­rhizal fungi increase the absorp­tive surface area of roots and can trans­port water from deeper soil layers. This helps plants to cope better in drought condi­tions. Equally impor­tant is the produc­tion of growth hormones, like auxins, gibberellins, and cytokinins, by micro-organ­isms known as plant growth-promoting rhizobac­teria, fungi or bacteria.

The impact of agri­cul­ture on the soil micro­biome

Alicja points out that cultivation method has a huge impact on the biolog­ical health of the soil. Ploughing causes the break­down of soil aggre­gates, soil desic­ca­tion and an increase in the popu­la­tion of actin­o­mycetes, which often domi­nate under condi­tions of water scarcity. Simpli­fied and no-till systems yield signif­i­cantly better results. Strip-till and no-till promote the growth of the nitri­fying and nitrogen-fixing bacteria, while simul­ta­ne­ously limiting the exces­sive growth of actin­o­mycetes asso­ci­ated with soil desic­ca­tion. 

Catch crops and cover crops are also of great impor­tance. One study conducted by Alicja’s team on preventing soil fatigue in orchards showed that the use of plants like French marigolds, radish and mustard reduced soil desic­ca­tion and promoted the devel­op­ment of the desired taxo­nomic group of proteobac­teria. This includes bacteria essen­tial for agri­cul­tural produc­tion, like nitri­fying and nitrogen-fixing bacteria, etc.

Bioprepa­ra­tions – the future of modern agri­cul­ture?

The Depart­ment of Soil Science and Micro­bi­ology is conducting in-depth research into modern micro­bi­o­log­ical prepa­ra­tions. The consortia of bene­fi­cial bacteria and fungi are being devel­oped to support soil fertility and plant growth. However, Alicja points out that it is crucial the indi­vidual strains used to create consortia are not antag­o­nistic towards each other. 

Modern agri­cul­ture should learn to work with micro-organ­isms, rather than against them.

Prof. Alicja Niewiadomska

A team of scien­tists has devel­oped, prepa­ra­tions containing bacteria of the genera Bacillus, Pseudomonas and Azoto­bacter, and has also patented the formu­la­tion and soil appli­ca­tion of an organic fertiliser based on biochar derived from organic waste. However, Alicja advises against prepa­ra­tions with uncon­firmed effec­tive­ness. The label should include the full species name, its concen­tra­tion, and a detailed descrip­tion of the prepa­ra­tion and appli­ca­tion method. The mere infor­ma­tion that a product contains nitrogen-fixing bacteria is insuf­fi­cient.

How should soil micro-organ­isms be main­tained?

According to Alicja, improving soil’s biolog­ical quality primarily requires limiting activ­i­ties that degrade the micro­biome. “Modern agri­cul­ture should learn to work with micro-organ­isms, rather than against them,” she says. “They are the crucial factor of soil fertility, plant health and yield stability.”