How can soil microbiomes be measured?

1 DNA extraction

One of the most common ways to measure soil microbiomes is to extract their DNA from soil samples and analyze it using molecular techniques. DNA extraction involves breaking open the cells of the microbes and isolating their genetic material. There are different methods and kits for DNA extraction, depending on the type and quality of the soil, the amount and diversity of the microbes, and the desired output. DNA extraction can be done in the lab or in the field, using manual or automated procedures.

2 DNA sequencing

After extracting the DNA from the soil samples, you can sequence it to identify the types and abundance of the microbes. DNA sequencing is the process of reading the order of the nucleotides that make up the DNA molecules. There are different types of DNA sequencing, such as shotgun metagenomics, 16S rRNA gene sequencing, and functional gene sequencing. Each type has its own advantages and limitations, depending on the research question, the budget, and the computational resources.

3 Bioinformatics analysis

Once you have the DNA sequences from the soil samples, you need to analyze them using bioinformatics tools and software. Bioinformatics is the application of computer science, mathematics, and statistics to biological data. Bioinformatics analysis can help you compare the soil microbiomes across different samples, sites, or treatments, and reveal their taxonomic and functional diversity, composition, and structure. You can also use bioinformatics to infer the interactions, networks, and pathways of the soil microbes.

4 Microbial activity assays

Another way to measure soil microbiomes is to assess their activity, or how they perform various functions in the soil. Microbial activity assays are tests that measure the rates or levels of certain processes or products that are mediated by the microbes. For example, you can measure the microbial activity by monitoring the soil respiration, enzyme activity, nutrient cycling, or greenhouse gas emissions. Microbial activity assays can provide insights into the metabolic potential and performance of the soil microbes.

5 Microscopy and imaging

A more direct way to measure soil microbiomes is to observe them under a microscope or an imaging device. Microscopy and imaging can help you visualize the morphology, size, shape, and distribution of the microbes in the soil. You can also use microscopy and imaging to detect specific microbes or groups of microbes by using stains, probes, or markers that bind to their cell walls or DNA. Some examples of microscopy and imaging techniques are light microscopy, fluorescence microscopy, electron microscopy, and X-ray microtomography.

6 Cultivation and isolation

The last method to measure soil microbiomes is to cultivate and isolate them in the lab. Cultivation and isolation involve growing the microbes in artificial media or conditions that mimic their natural environment. This way, you can obtain pure cultures of individual microbes or consortia of microbes that work together. Cultivation and isolation can help you identify, characterize, and manipulate the soil microbes. However, this method is limited by the fact that only a small fraction of the soil microbes can be cultured in the lab.

7 Here’s what else to consider

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