Introduction to integrated methods in the vegetable garden

chapter crop sol

Rhizosphere, mychorizae and suppressive soils

Click on ♦ to go to a page in the chapter

Analysis of the physico-chemical properties of cultivated soils ♦

. Texture and structure of cultivated soils ♦

. Clay-humus complexes and cation exchange capacity ♦

. Other interesting data that may be included in a laboratory analysis ♦

Influence of pH on the fertility potential of cultivated soils ♦

Humus; formation and evolution ♦

Soil fertility: is the apocalypse coming tomorrow? ♦

The microbial world and soil fertility ♦

⇒ Rhizosphere, mychorizae and suppressive soils

Correction of soils that are very clayey, too calcareous or too sandy ♦

Stimation of humus losses in cultivated soil ♦

Compost production for a vegetable garden ♦

Composting with thermophilic phase ♦

Weed management in the vegetable garden ♦

To plow or not to plow? ♦

The rotary tiller, the spade fork, and the broadfork ♦

Please share this website with your friends and family and anyone else who might be interested in integrated farming methods.

Plants host a large number of organisms inside or on the surface of their tissues. These organisms form the plant’s microbiota. Certain microorganisms called endophytes (which live in a plant for at least part of its life), some of which thrive in the root sphere, are of major importance to plants. Knowledge about their diversity and ecological functions is still incomplete. Epiphytic populations live on the surface or near the roots. The rhizosphere refers to the area where soil microorganisms are most concentrated, specifically influenced by the root system, with a high level of taxonomic diversity.

The phyllosphere is home to microorganisms that live on plants above ground. If the nutrient resources on the surface of leaves are limited, it is believed that epiphytic microbiota play an important role in protecting plants against leaf diseases.

Endophytes were discovered only recently, even though they are ubiquitous in plants. It is estimated that most plants live in symbiosis with endophytes, which provide them with various services related to nutrient assimilation and their ability to defend themselves against pests and even physical stress (such as periods of drought).

The rhizosphere :

Bacteria associated with plants are classified into beneficial or harmful groups based on their effects on plant growth. Beneficial soil bacteria are generally referred to as Plant Growth Promoting Rhizobacteria (PGPR). Extracellular PGPRs act on the surface of the roots (called the rhizoplane) or in the spaces between the cells of the root cortex, while intracellular PGPR refers to bacteria that secrete substances targeting root cells to form specialised nodules housing these PGPR (such as rhizobium, which fixes atmospheric nitrogen).

Rhizosphere-specific bacteria

In the rhizosphere, microbial activity is stimulated by organic compounds secreted by the roots. The composition of these root exudates varies greatly from one plant species to another. These root exudates contain various substrates (carbohydrates, mineral salts, amino acids, etc.) that provide a rich source of energy and nutrients for bacteria. It is estimated that approximately 5 to 30% of the substances synthesised by plants are transferred to microorganisms in the rhizosphere via the roots.

This process is called rhizodeposition. The microorganisms that colonise the rhizosphere are called rhizobacteria. It has been established that only 1 to 2% of soil bacteria participate in this process (1), but the number of bacteria found around plant roots is generally 10 to 100 times higher than in soil that is not explored by roots.

This nurturing environment gives an advantage to microorganisms that have the potential to multiply rapidly. Fungal growth is also stimulated, but to a lesser extent. It should be noted that root exudates can inhibit the germination of certain competing plants.

The harmful effects of certain rhizosphere bacteria

Root exudates can promote the emergence of pathogenic soil microorganisms (a) such as Agrobacterium tumefaciens, which causes crown gall (2), Erwinia, which are pathogens of certain fruit trees (fire blight) or vegetable plants, or the fungus Plasmodiophora brassicae, responsible for clubroot in cabbage. Plasmodiophora brassicae persists in the soil in the form of oospores (b). If these pathogenic microorganisms are not controlled by crop rotation and solarisation, they can have significant economic consequences.

RFCPs affect plant growth directly or indirectly.

Indirect promotion of plant growth occurs when RFCPs alter or prevent the harmful effects of one or more phytopathogenic organisms. This can happen by inducing resistance to pathogens in the plant or when the RFCPs themselves produce antagonistic substances. These RFCPs are also considered phytoprotective due to their ability to counteract the activity of pathogens through various processes (production of antibiotics, competition for food, etc.). They are responsible for the properties of “resistant” soils, which are studied in more detail in the article below: “Suppressive soils”.
The direct promotion of plant growth by RFCPs consists either of providing the plant with a compound synthesised by a bacterium, such as phytohormones (auxin, gibberellin, etc.), or, as in the case of azotobacters, helping the plant to acquire certain nutrients such as atmospheric nitrogen. Some bacteria promote the extraction of iron from mineral complexes by siderophores (c), or, as in the case of Bacillus amyloliquefaciens, produce phosphate solubilisation. Other bacteria stimulate root growth.

RFCPs can influence plant development by using several of these direct and indirect mechanisms. Mycorrhizal fungi known to provide phosphorus to plants are also capable of strengthening their natural defences against abiotic stress or pests. The filamentous fungus Coniothyrium minitans stimulates root development and destroys the sclerotia of Sclerotinia, a formidable parasite of sunflower crops. Recent studies have demonstrated the suppression of soil-borne fungal pathogens by fluorescent pseudomonads that release iron-chelating siderophores (in soils low in iron), making iron inaccessible to these pathogens (3).

All these data demonstrate the importance of not upsetting the balance of the rhizosphere with toxic substances: industrial or domestic waste disposal; indiscriminate use of synthetic or bio-based persistent pesticides such as copper-containing compounds, etc.

New tools to protect plants.

The significant influence that rhizosphere microorganisms exert on plants is now becoming an important tool for protecting plant health and promoting growth. For several years, research has been conducted on rhizosphere-based plant protection products (RPPs) in the hope that they can complement or replace agrochemicals (fertilizers and pesticides) through various mechanisms involved in humus production, mineral nutrient recycling, strengthening natural plant defenses, and biological pest control.

Mycorrhizae

The role of ectomycorrhizal complexes in plant nutrition

Living in the rhizosphere, fungi are capable of forming symbiotic structures with plant roots called mycorrhizae. It is estimated that 90% of plant species are mycorrhizal. Ectomycorrhizal complexes, which are very common in plants, often incorporate specific endophytic bacteria. Mycorrhizal fungi help their host plants to acquire mineral nutrients from the soil, particularly phosphorus and nitrogen. In return, these fungi receive sugars. This mutualistic association allows for better absorption of trace elements that are not very mobile in the soil. The transfer of sugars to mycorrhizal fungi contributes to an increase in the soil’s carbon reserves. When certain elements are present in large quantities and become toxic, mycorrhization can play a role in protecting the plant by strongly retaining these elements (4).

Arbuscular mycorrhizal fungi

There are three types of fungi capable of forming these associative structures, including arbuscular mycorrhizal fungi (a) (AMF), also known as glomeromycetes. AMF have brush-like structures, which is where the term “arbuscule” comes from. 80% of terrestrial plants are associated with AMF, which account for approximately 20 to 30% of the microbial biomass in the soil.

Almost all cultivated plants are involved in mycorrhizal symbiosis, except for certain members of the Brassicaceae family (formerly known as cruciferous plants, such as cabbage and cauliflower) and the Brassicaceae family, such as canola and crambe (5). This association between plants and fungi allows the fungal mycelium to explore a larger volume of soil by forming filamentous structures called hyphae in areas that are inaccessible to plant roots. For this reason, it is important to remember to water or apply supplementary fertilisers beyond the visible root zone, just as it is important to avoid applying residual fungicides that could have a harmful impact in the area explored by mycorrhizae, which are sensitive to these fungicides.

Glomaline

The filamentous elements of MACs, which are present in large quantities in soils, have the property of strengthening the aggregation of soil constituents by secreting a hydrophobic glycoprotein linked to 9% iron, known as glomalin. Glomalin contains 30 to 40% carbon, and it is estimated that approximately one-third of the carbon in soil is in the form of glomalin (6-7). Glomalin binds to various mineral particles (clay, silt and sand) to form stable agglomerates, which facilitates the absorption of nutrients by fungal hyphae. Clay-humus aggregates are further stabilised when the soil contains glomalin, which acts as a kind of glue. Glomalin is unique among soil components in terms of its resistance and stability.

Other soil components that contain carbon and nitrogen are rapidly decomposed by soil microbes, but this is not the case for glomalin, whose lifespan is estimated to be between 7 and 42 years depending on local conditions..

Suppressive soils

Phytoprotective rhizobacteria are responsible for so-called “resistant” or “suppressive” soils, in which the development of one or more fungal or bacterial soil-borne disease agents is limited despite their presence in the soil. Soil in which certain diseases are easily expressed is called “susceptible” or “permissive”. With regard to market gardening, there is a good example of resistant soil in the PACA region: melons grown in the Châteaurenard region, where Durance alluvial deposits predominate, are known to be little affected by vascular fusarium wilt. Other examples include soils that suppress beet seedling blight caused by the fungus Rhizoctonia solani, and for field crops, soils that suppress wheat seedling blight caused by a fungus of the Gaeumannomyces family, or black root rot in tobacco caused by Tielaviopsis basicola.

Suppressive soils, which are not very common, have been the subject of research for more than twenty years in order to understand the causes of these resistances that prevent the development of certain diseases. The factors are complex and not all known. The addition of organic matter in the form of compost or even sewage sludge containing large amounts of bacterial cell walls (which promote the development of actinomycetes) reduces the virulence of certain soil-dwelling parasites such as rhizoctonia fungi and the fungus that causes damping-off (pythium). Researchers have also found that resistance to Pseudomonas solanacearum, the agent of bacterial wilt, is linked to the presence of certain types of clay. The persistence of the pathogen L Moocytogène in the soil increases 3.5-fold when soil microbial biodiversity is reduced by 30% (8).

The various forms of resistance acquired or inherent in suppressive soils

Either through antagonism by producing hydrolytic enzymes, such as proteases, chitinases, lipases, lucanases, which can lyse the cells of pathogenic fungi, or antibiotics and bacteriocides (b) that inhibit the growth or metabolic activities of other microorganisms.
Either by interference, reducing the action of molecules involved in the growth of pathogenic organisms.
Either by activating the internal resistance of plants.

Other acquired or inherent resistances are involved due to the presence in the soil of certain antagonistic microorganisms such as Pseudomonas spp fluorescens, Fusarium oxysporum, etc. These microorganisms reduce the severity of various soil-borne diseases through several processes:

With regard to the induction of resistance mechanisms in plants, also known as Induced Systemic Resistance (ISR), it is interesting to cite the example of cucumbers. It has been found that strains of rhizobacteria protect leaves against anthracnose caused by the fungus Colletotrichum orbiculare (9).

Studies have shown that resistance can also be the result of competition between microorganisms to absorb nutrients present in the soil. Pathogenic microorganisms cannot compete with beneficial microorganisms when the latter are predominant. In general, competition for nutrients is more intense in resistant soil than in susceptible soil, which shows that the amount of microbial biomass in resistant soil plays an important role.

In constitutive resistance, the soil environment opposes the expression of the pathogenic power of the introduced or pre-existing infectious agent. Acquired resistance develops gradually, year after year, following the use of certain cultivation techniques or, more frequently, which may seem strange at first glance, through the repeated cultivation of the host plant on the same plot.

The biological resistance of soils to certain diseases has been demonstrated by the disappearance of this resistance in a soil sample when it is sterilised. Researchers at INRA have shown that there are 10 times more wild Fusarium spp. in resistant soil in Châteaurenard than in susceptible soil in Ouroux (Rhône department), even though the pathogen, Fusarium vascular, establishes itself at comparable levels in both soils. In the absence of susceptible plants, the pathogen population changes little over time in both resistant and susceptible soils and persists for more than a year after its introduction. In the presence of a susceptible plant, the pathogen population tends to increase in susceptible soil in line with the progression of the disease (10).

Cultivation practices adapted to promote soil resistance

In the past, the fight against soil-borne pathogens involved the use of substances that were toxic to the environment. Today, these substances are mostly banned. In integrated agriculture, they are replaced by the implementation of appropriate cultural practices such as crop rotation, which breaks the development cycle of certain pathogens, or increasing the pH by liming acidic soils, which reduces the severity of fusarium wilt. Efforts are being made to increase microbial biodiversity by adding composted organic amendments. Studies have shown that a 30% loss in soil microbial diversity increases the residence time of pathogenic microorganisms in the soil by 3 to 5 times (11). Efforts are also being made to introduce preparations containing spores of bacterial agents such as Pseudomonas or Coniothyrium minitans. In integrated agriculture, maintaining soil biomass through the consistent and permanent addition of organic matter that promotes beneficial microflora has become essential as a complementary means of controlling plant diseases.

a) Arbuscules: fungal mycelium growths present in the cells of the host’s underground parts, shaped like small trees.

b) Bacteriocides differ from antibiotics in that they have a relatively narrow spectrum and are toxic only to the bacteria that produce them.

1) Antoun et Kloepper, 2001
2) Sol : interface fragile P. Stengel, S. Gelin INRA 1998.
3) Loper, 1988 , Paulitz et Loper, 1991 , Dwivedi et Johri, 2003
4) La Mycorhize à arbuscules : quels bénéfices pour l’homme et son environnement dans un contexte de développement durable – Anissa Lounès-Hadj Sahraoui. Synthèse Revue des Sciences et de la Technologie N° 26 avril 2013 – Université Badji Mokhtar Annaba – Algérie.
5) Gouvernement du Canada ; Agriculture et agroalimentaire Canada Les champignons mycorhiziens arbusculaires et leur symbiose végétale
6) La symbiose mycorhizienne – une association entre les plantes et les champignons – Jean Carbaye (Directeur de recherche INRA)
7) United States Department of Agriculture AgResearch Magazine ; Glomalin: Hiding Place for a Third of the World’s Stored Soil Carbon ♦
8) Vivant et al. 2013
9) Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents – genetic and molecular biology – dec 2012 – Anelise Beneduzi , Adriana Ambrosini , and Luciane MP Passaglia
10) Recherches sur la résistance des sols aux maladies. IX. – Dynamique des populations du Fusarium spp. et de Fusarium oxysporum f. sp. melonis dans un sol résistant et dans un sol sensible aux fusarioses vasculaires – Claude ALABOUVETTE, Yvonne COUTEAUDIER Jean LOUVET Marie-Louise SOULAS I.N.R. A., Station de Recherches sur la Flore pathogène dans le Sol, Dijon – agronomie 1984
11) Vivant et all – 2013 ; signalé dans l’atlas français des bactéries du sol.