The Growing Importance of Microbiome Testing
Microbiome testing has emerged as a game-changing tool across multiple scientific fields, unlocking the secrets of microbial communities and their profound impact on ecosystems. In medicine, it has revolutionized our understanding of the human gut microbiome, shedding light on its roles in digestion (1), immunity (2), and even mental health (3). In agriculture and environmental science, microbiome testing offers insights into plant health, soil quality, and sustainable farming practices (4).
When it comes to plants and soil, microbiome analysis plays a crucial role in understanding plant growth, disease resistance, and nutrient absorption. Soil microbiomes, in particular, influence plant health by cycling nutrients, protecting against pathogens, and enhancing resilience to environmental stress. Understanding these microbial communities holds the potential to improve crop productivity and environmental sustainability.
Microbiome Testing in Plants and Soil: Insights from Crotalaria pumila
One example of the relevance of microbiome testing in plants is the study conducted by Leff et al. (5) published in the International Journal of Molecular Sciences. The research explored the seed microbiome of Crotalaria pumila, a plant growing on metalliferous soils, and the role that endophytic microorganisms play if the plant is exposed to metal stress.
By leveraging high-throughput sequencing, after DNA extraction of the surface sterilized seed using the InviSorb Spin Plant Mini Kit, the researchers unveiled the composition of the core microbiome and identified Methylobacterium as the dominant member of the seed microbiome (see Fig. 1). This genus plays an essential role in plant growth promotion by producing phytohormones and facilitating nutrient uptake.
Figure 1: Composition of the core microbiome of Crotalaria pumila seeds throughout three consecutive generations. (Figures from Sánchez-López et al., 2018).
The researchers demonstrated that Methylobacterium sp. Cp3 migrated from the seed-surrounding soil, the so-called rhizosphere, into the seedling under metal stress by colonising the root cortex cells and xylem vessels of the stem, establishing a stable relationship throughout the plant’s life cycle. Once inoculated, the presence of strain Cp3, significantly improves the seed germination and the plantlet survival under cadmium stress (see Fig. 2). Intriguingly, strain Cp3 was detected in C. pumila seeds across three consecutive generations, indicating the endophytic microorganisms are vertically transmitted via the plant seeds to the next generation. Thus, Methylobacterium sp. Cp3 can assist next generations to cope with environmental stresses.
Figure 2: 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).
Exploring the Soil Microbiome: A Crucial Piece of the Puzzle
While analysing the plant microbiome offers valuable insights into plant health and resilience, understanding the microbiome of the soil itself is equally important. Soil is a complex and dynamic environment teeming with diverse microbial communities that directly influence plant growth, nutrient cycling, and disease resistance as shown in the study of Leff et al. above.
By studying the soil microbiome, researchers can uncover the microbial diversity present in the rhizosphere – the soil region surrounding plant roots – and gain a clearer picture of the interactions between plants and their microbial partners. This deeper understanding is crucial for identifying beneficial microbes that promote plant health, enhance nutrient uptake, and protect against pathogens or environmental stress.
Together, plant and soil microbiome analyses provide a more holistic view of plant-microbe relationships and pave the way for sustainable agricultural practices and environmental conservation.
Tailored Solutions for Nucleic Acid Extraction from Plant and Soil
Extracting nucleic acids from plants and soil presents unique challenges, each requiring specialized techniques to ensure high-quality genetic material for microbiome analysis. Plant tissues contain complex cellular structures, including tough cell walls made of cellulose, as well as secondary metabolites that can interfere with the extraction process. In contrast, soil samples are even more complex, with diverse microbial communities embedded in a dense matrix of organic matter, minerals, and potential inhibitors like humic acids.
To overcome these challenges, specialized kits are essential. For DNA extraction, the InviSorb Spin Plant Mini Kit efficiently breaks down plant cell walls and removes contaminants, yielding high-purity DNA for downstream applications like sequencing or qPCR. For soil samples, the InviSorb Spin Soil DNA Kit tackles the unique difficulties of soil extraction, ensuring effective lysis of microbial cells and the removal of inhibitors commonly found in soil.
Additionally, for researchers investigating gene expression, the InviTrap Spin Plant RNA Mini Kit provides a reliable solution for extracting high-quality RNA from plant tissues. Analyzing RNA helps uncover the dynamic responses of plants to environmental stressors, revealing which genes are actively expressed during plant-microbe interactions.
These specialized kits empower researchers to unlock the full potential of plant and soil microbiome and transcriptome, providing deeper insights into their intricate relationship.
Summary
Microbiome testing is revolutionizing our understanding of plant and soil health by revealing the complex interactions between microbial communities, plants, and their environment. Invitek Diagnostics is proud to support this vital research with a range of products tailored for plant and soil microbiome and transcriptome analysis.
References
- Kumar S, Mukherjee R, Gaur P, Leal É, Lyu X, Ahmad S, Puri P, Chang CM, Raj VS, Pandey RP. Unveiling roles of beneficial gut bacteria and optimal diets for health. Front Microbiol. 2025 Feb 18;16:1527755. doi: 10.3389/fmicb.2025.1527755. PMID: 40041870; PMCID: PMC11877911.
- Tuganbaev T, Honda K. Non-zero-sum microbiome immune system interactions. Eur J Immunol. 2021 Sep;51(9):2120-2136. doi: 10.1002/eji.202049065. Epub 2021 Jul 26. PMID: 34242413; PMCID: PMC8457126.
- Foster JA, Baker GB, Dursun SM. The Relationship Between the Gut Microbiome-Immune System-Brain Axis and Major Depressive Disorder. Front Neurol. 2021 Sep 28;12:721126. doi: 10.3389/fneur.2021.721126. PMID: 34650506; PMCID: PMC8508781.
- Sarsaiya S, Jain A, Singh R, Gong Q, Wu Q, Chen J, Shi J. Unveiling the rhizosphere microbiome of Dendrobium: mechanisms, microbial interactions, and implications for sustainable agriculture. Front Microbiol. 2025 Jan 29;16:1531900. doi: 10.3389/fmicb.2025.1531900. PMID: 39944638; PMCID: PMC11814445.
- 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.
