Unlocking the Secrets of Plants and Soil: The Power of Microbiome Testing

The Growing Importance of Microbiome Testing

Microbiome testing has become a game‑changing tool across medicine, agriculture, and environmental science - but in plants and soils, its real power lies in revealing the underground relationships that drive resilience. Beyond listing microbial species, modern testing illuminates how plants actively shape their local microbiomes through root exudates - sugars, amino acids, organic acids, and secondary metabolites that recruit and steer beneficial microbes. These interactions help plants access nutrients, prime immunity, and tolerate stress. In other words, plant microbiomes aren’t just passengers; they’re an extended plant trait that directly contributes to growth, nutrition, and health.

Understanding the Plant Microbiome

Plants are not solitary organisms - they live in close association with diverse microbial communities that include bacteria, fungi, archaea, and protists. Collectively, these microbes form the plant microbiome, an extended trait of the plant that contributes directly to nutrition, growth, and immunity.

The plant microbiome is organized into distinct compartments:

• Phyllosphere: microbial communities on leaves and stems.
• Endosphere: microbes living inside plant tissues, both above and below ground.
• Rhizosphere: the soil surrounding roots, rich in microbial activity shaped by root exudates.

Figure 1: A general overview of plant microbiome interaction zones (left) and selected beneficial functions reported (right). (Figure from Santoyo, 2025)

Each compartment hosts unique microbial populations, selectively recruited by plants through chemical signals. For example, root exudates - sugars, amino acids, organic acids, and secondary metabolites - act as both food sources and communication molecules, attracting microbes that can mobilize nutrients or protect against pathogens.

By viewing the microbiome as part of the plant’s biology rather than just its environment, researchers can better understand how plants adapt to stress, thrive in poor soils, and maintain health across generations.

The Rhizosphere Soil Microbiome

The rhizosphere - the narrow zone of soil directly influenced by plant roots - is one of the most biologically active interfaces in terrestrial ecosystems. It is shaped by a constant flux of water, oxygen, and metabolites released from roots, which create steep gradients of nutrients and signalling molecules that distinguish it from bulk soil. This microenvironment is where plants and microbes engage in a continuous exchange of resources and information (see Figure 2 below).

Figure 2: Components of the rhizosphere. Especially microbes in this narrow soil zone around roots play a fundamental role in nutrient cycling and plant health. (Figure from Pan, 2025)

Microbial diversity in the rhizosphere is immense. Bacterial groups such as Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Acidobacteria are particularly abundant, while fungal communities are dominated by Ascomycota and Basidiomycota. In addition to these well‑studied groups, archaea, protists, nematodes, and other soil microfauna play important roles in nutrient cycling and microbial population control. Mycorrhizal fungi extend the effective root system, enhancing nutrient and water uptake while mediating plant signalling.

The rhizosphere is not only biological but also chemical and physical. Root exudates alter local pH, redox conditions, and mineral solubility, while root hairs physically restructure soil pores and influence water distribution. These changes create a dynamic interface where microbial communities are actively recruited or excluded by plants through chemical cues and immune filtering.

Because the rhizosphere integrates soil properties, plant genotype, and microbial activity, its composition is highly dynamic across environments and over time. This complexity makes the rhizosphere a critical target for microbiome testing, as it reveals not only which organisms are present but also how they function in sustaining plant growth, resilience, and ecosystem stability.

Nutrient Exchange Between Plants and the Rhizosphere Microbiome

The rhizosphere is not only a reservoir of microbial diversity but also a dynamic interface of nutrient exchange. Plants invest a significant fraction of their photosynthetically fixed carbon into root exudates, releasing sugars, amino acids, organic acids, flavonoids, coumarins, and triterpenes into the surrounding soil. These compounds act as both substrates and chemical cues, selectively enriching microbial taxa that provide functional benefits.

Recent studies have shown that nutrient deprivation triggers the release of specialized metabolites that directly shape microbial recruitment (3). For example, coumarins such as fraxetin are secreted under iron deficiency to attract iron‑reducing bacteria, flavones like apigenin enrich Oxalobacteraceae under nitrogen limitation, and organic acids mobilize phosphorus by stimulating siderophore‑producing microbes. In return, these microbes solubilize nutrients, produce phytohormones, and activate plant immune responses.

Figure 1 (see below) illustrates this reciprocal dialogue. It shows how nutrient stress induces the secretion of specific metabolites from roots, which then act as signals or resources for rhizosphere microorganisms. The enriched microbial communities mediate nutrient availability and display growth‑promoting traits, effectively extending the plant’s physiological capacity to acquire nitrogen, phosphorus, and iron.

By combining microbiome testing with metabolite profiling, researchers can capture this two‑way exchange: plants provide carbon‑rich exudates, and microbes return essential nutrients and protective functions. This perspective reframes the rhizosphere not as passive soil but as a biochemical negotiation zone, where plant survival and productivity are co‑engineered by microbial partners.

Figure 3: The role of root exudates on the recruitment of rhizosphere bacteria to improve the plants nutrient acquisition: plants supply carbon-rich root exudates to the soil, while microbes return essential nutrients, like nitrogen, phosphorus, and iron. Identified metabolites and associated bacterial taxa are shown. (Figure from Pantigoso et al., 2022)

Case Study: The Crotalaria Pumila Seed Microbiome

The principles of rhizosphere microbiome diversity and nutrient exchange are exemplified in the case of Crotalaria pumila, a legume adapted to metalliferous mine soils. A detailed study by Sánchez‑López et al. (2018) in the International Journal of Molecular Sciences investigated the seed microbiome of this plant and its role in coping with metal stress.

The researchers implemented the following experimental workflow:

• Seed Collection & Sterilization: Closed pods of Crotalaria pumila were collected from metalliferous soils. Seeds were cleaned and surface-sterilized. Sterilization was confirmed by plating and PCR.
• DNA Extraction & Sequencing: Genomic DNA was extracted from sterilized seeds using the InviSorb Spin Plant Mini Kit (Invitek Diagnostics). The bacterial 16S rRNA gene was amplified and sequenced.
• Data Analysis: Sequencing data were processed to identify microbial taxa, cluster them into groups, and determine the core microbiome. Functional potential was predicted based on gene profiles.
• Colonization Assays: Methylobacterium Cp3 was inoculated into soil and tracked through the plant using molecular fingerprinting and microscopy to study its movement and localization.
• Microscopy & Imaging: Confocal laser scanning microscopy was used to visualize Cp3 in roots and stems.

Most strikingly, Cp3 was consistently detected in seeds across three consecutive generations, demonstrating vertical transmission of endophytic microorganisms via seeds. This finding shows that beneficial microbes are not only recruited from the rhizosphere but also inherited by progeny, equipping future generations with microbial allies to withstand environmental challenges.

Figure 4: Composition of the core microbiome of Crotalaria pumila seeds throughout three consecutive generations. (Figures from Sánchez-López et al., 2018).

Microscopy images confirmed Cp3 colonization within the root cortex and vascular tissues, validating its role as a true endophyte. Quantitative assays under cadmium stress further demonstrated its impact: germination rates increased to 90% compared with 75% in controls; seedling survival rate increased by approximately 40%; and both fresh biomass and dry biomass were significantly enhanced (Figure 5). Together, these results provide compelling evidence that Cp3 bridges the rhizosphere and seed microbiome, establishing a heritable endophytic partnership that translates into measurable improvements in plant resilience and growth.

 Figure 5: Left: Confocal images of combined m-Cherry fluorescence (red) and plant autofluorescence (green) showing root colonisation by Methylobacterium strain Cp3. Right: seedlings of Crotalaria pumila either inoculated with Methylobacterium sp. Cp3 (B) or non-inoculated (A, control). Percentage of germination (C), survival rate (D), and fresh (E) and dry biomass (F) of inoculated plants were significantly higher. (Figures from Sánchez-López et al., 2018). 

Summary

Microbiome testing is transforming our understanding of plant-soil interactions by uncovering the hidden networks that sustain plant health and resilience. Plants actively shape their microbiomes through root exudates, creating dynamic zones like the rhizosphere where microbes and roots exchange nutrients and signals. These microbial partners enhance nutrient acquisition, stress tolerance, and immunity, making the microbiome an integral plant trait rather than a passive environmental factor. Advances in sequencing and metabolite profiling now allow researchers to map these interactions in detail, revealing strategies for sustainable agriculture and ecosystem stability.

Unlock Insights from Plant and Soil Microbiomes with Invitek Diagnostics

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References

1. Santoyo, G. Advances in the Plant Microbiome: Rhizosphere, Endosphere, and Phyllosphere. Microorganisms2025, 13, 2581. https://doi.org/10.3390/microorganisms13112581
2. Pan, S. (2025, July 27). Components of the rhizosphere [Diagram]. BiologyNotesOnline.com. https://biologynotesonline.com/wp-content/uploads/2025/03/Components-of-the-Rhizosphere.png
3. Pantigoso HA, Newberger D, Jorge M. Vivanco, The rhizosphere microbiome: Plant–microbial interactions for resource acquisition, Journal of Applied Microbiology, Volume 133, Issue 5, 1 November 2022, Pages 2864–2876, https://doi.org/10.1111/jam.15686
4. Sánchez-López AS, Pintelon I, Stevens V, Imperato V, Timmermans JP, González-Chávez C, Carrillo-González R, Van Hamme J, Vangronsveld J, Thijs S. Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria. Int J Mol Sci. 2018 Jan 19;19(1):291. doi: 10.3390/ijms19010291. PMID: 29351192; PMCID: PMC5796236.