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Microbiology · Microbial Ecology — Microecology

Plant microflora

Plant microflora includes natural microbiota inhabiting the surface and root zone, as well as phytopathogenic microorganisms. Normal flora protects the plant and assists with nutrition, whereas pathogens cause diseases such as bacterioses, mycoses, and viral infections.

EpiphytesInhabit aerial parts, protect against disease-causing agents
RhizosphereSoil zone near the roots, whose microorganisms nourish the plant
MycotoxicosesPoisoning by toxins of fungi proliferating on moist raw materials
AgrobacteriaCause tumors by integrating their genes into the plant cell
5 min readFor medical studentsUpdated 09/24/2026
Material prepared by WhiteCoat Pro editorial team based on platform study guidesReviewed by medical editor: Aulov A. A., general practitioner · 09/24/2026

Contamination of plant raw materials

Contamination, or contamination, of plant raw materials occurs via two main routes.

Primary (natural) infection implies the presence of normal microflora or phytopathogens on the plant even before harvesting. Secondary (exogenous) contamination occurs during harvesting and processing. Transmission factors include water, production facility air, personnel hands, and non-sterile containers. Improper harvesting creates an ideal breeding ground for bacteria. To prevent their proliferation, the bulk of plant raw materials must be thoroughly dried.

Normal microflora

Natural microbiota is generally divided into two major functional groups depending on localization:

  1. Epiphytic microflora inhabits aerial parts (leaves, stems, seeds). They do not harm the host, instead feeding on organic debris and exudates produced by the plant itself. Epiphytes perform a crucial protective function: they act as antagonists to phytopathogens, preventing them from penetrating tissues, and stimulate a unique form of "immunity". The dominant species is Pantoea agglomerans (an antagonist of soft rot). Pseudomonas fluorescens is also frequently encountered, whereas spore-forming rods (Bacillus mesentericus) and fungi are found in the minority.
  2. Rhizosphere microflora consists of microorganisms in the soil layer directly adjacent to the roots. This includes pseudomonads, mycobacteria, actinomycetes, and fungi. They metabolize soil substrates into a form accessible to the roots and synthesize biologically active substances (vitamins, antibiotics). On the root surface itself (rhizoplane), representatives of the genus Pseudomonas most commonly dominate.
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Phytopathogens and bacterioses

Plant diseases are caused by bacteria, viruses, and microscopic fungi. Bacterial diseases are called bacterioses. They penetrate tissues through mechanical damage or natural openings (such as stomata) and are transmitted via contaminated seeds, soil, water, or insect vectors. Depending on the clinical course, bacterioses can be systemic (affecting vessels or roots, killing the entire plant) or localized (confined to parenchymal areas).

Genus of pathogenType of injuryRepresentative (disease)
ErwiniaBlights, wet rot, wiltE. amylovora (fire blight of apple trees)
PseudomonasBacterial spotP. syringae (leaf spots)
XanthomonasVascular pathologiesX. campestris (black rot)

Pathogenesis of tissue damage

The destruction of plant tissues follows several scenarios. In the parenchymal type, bacteria penetrate intercellularly, causing softening (maceration) and cell detachment. In the vascular type, Gram-positive non-spore-forming rods (e.g., Corynebacterium) release glycopeptides that damage vascular membranes. The bacterial mass clogs the ducts, which, combined with the action of toxins, leads to rapid wilting.

A unique mechanism is demonstrated by the genus Agrobacterium. The bacterium transfers its genetic material (via an oncogenic plasmid) into the plant cell, triggering uncontrolled cell growth and tumor formation (e.g., crown gall). Surprisingly, after the tumor forms, the bacterium itself is usually no longer detectable in the affected tissues.

Medical significance and human risks

Plants from cultivated soils are always more contaminated than wild-growing ones (forest or meadow). The maximum number of microbes accumulates in the root zone. High-risk zones include irrigation fields, pastures, and manure storage sites, where contamination of raw materials with human pathogens is possible.

Phytopathogenic fungi pose a major threat. Consumption of grain affected by them causes severe food poisoning — mycotoxicoses.

  • Cereals are frequently affected by ergot (Claviceps purpurea), which forms characteristic "sclerotia" and causes ergotism.
  • Fungi of the genera Fusarium, Penicillium, and Aspergillus actively proliferate on harvested plants under high humidity and low temperatures, producing toxins that are lethal to humans.

Briefly: answers to topical questions

What types of mycotoxins are produced by fungi of the genera Fusarium, Penicillium, and Aspergillus on plant raw materials?

Fungi of the genera Fusarium, Penicillium, and Aspergillus produce toxins that cause mycotoxicoses; however, the sources detail the spectrum of mycotoxins only for the genus Aspergillus:

  • Aflatoxins (including aflatoxin B1) are produced by molds.
  • Ochratoxins A, B, C (A. ochraceus).
  • Patulin (A. terreus, A. niveus, A. candidum).
  • Gliotoxin (A. giganteus, A. fumigatus).
  • Sterigmatocystin (A. versicolor, A. nidulans).
  • Tremorgen (A. clavatus, A. flavus, A. candidum).
  • Cytochalasins (A. clavatus).
  • Citrinin (A. terreus, A. niveus, A. candidum).

Fungi of the genus Fusarium cause fusariotoxicosis, but the specific names of their toxins, as well as those of Penicillium, are not specified.

What types of bacteria cause the parenchymal type of plant tissue damage?

The parenchymal type of plant tissue damage can be caused by Gram-positive non-spore-forming rods of the genera Corynebacterium, Curtobacterium, and Clavibacter, which cause vascular and parenchymal diseases.

In the parenchymal type, bacteria penetrate into tissues intracellularly and intercellularly, damage cells, and cause their maceration (softening) and detachment.

Which representatives of Gram-positive non-spore-forming rods cause the vascular type of plant tissue damage?

The vascular type of plant tissue damage can be caused by Gram-positive non-spore-forming rods of the genera Corynebacterium, Curtobacterium, and Clavibacter, which cause vascular and parenchymal diseases.

Bacteria release glycopeptides that damage vascular membranes. This leads to vascular occlusion; combined with the action of bacterial toxins, this results in wilting and death of the plant. Vascular occlusion by bacterial mass is also characteristic of the vascular type.

How to memorize

To easily remember the pathogenesis of vascular bacterioses, draw an analogy with human thrombosis: bacteria release glycopeptides that damage the walls of the plant's "vessels". The accumulating bacterial mass acts as a thrombus, blocking the flow of water and nutrients, which causes the plant to wilt.

Class and exam questions

What is the essence and significance of mycorrhiza?

Mycorrhiza (fungus root) is a symbiosis between the mycelium of microscopic fungi and the roots of higher plants. The fungi help the plant better absorb nutrients from the soil, which significantly stimulates its growth.

How do viruses and viroids infect plants?

Viruses cause mosaic disease (mottled leaf coloration) or yellows (shoot deformation, dwarfism). Viroids are circular RNA molecules without a protein coat that also lead to dwarfism, chlorotic spotting, and flowering disorders.

What environmental factors influence the abundance of epiphytes?

The main abiotic factor is humidity: as it increases, the bacterial count on the plant surface grows, and as it decreases, it falls. Ambient temperature, soil type, and the species and age of the plant itself also have an effect.

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What else to study on this topic

  • Metabolic and synthetic functions of rhizosphere microorganisms
  • Dynamics of microflora proliferation depending on the integrity of seed coats
  • Specific toxins of fungi of the genera Fusarium and Aspergillus
  • Agrotechnical methods of prevention and soil decontamination
  • Structure and genetic features of the oncogenic plasmid of Agrobacterium

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