CD Genomics Blog

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The importance of microbiology in crop yield

Plants, bacteria, and fungi have coexisted in soil in a symbiosis for millions of years, and they both benefit greatly from symbiosis. Healthy microbial communities perform a variety of vital ecosystem functions, such as pathogen suppression and regulation of nutrient availability. For example, microorganisms make essential elements such as nitrogen and phosphorus available in exchange for carbon provided by plants. In plant-microbe interactions, two symbiotic systems have been extensively studied and well understood: arbuscular mycorrhizal (AM) symbiosis and root nodule (RN) symbiosis. Microorganisms also do many other things, like decomposing organic matter such as crop residues and releasing the nutrients, plant growth control, as well as maintaining soil structure and good hydrology.

Microbial genomics methods to promote crop production

The productivity of plants largely depends on the soil quality, in which microorganisms play a major role. One way to develop improved sustainable crop yield is to enhance the beneficial plant-associated microbiome. And microbial genomics represents a series of powerful tools to differentiate beneficial, neutral, and harmful microorganisms. The common microbial genomics technologies include 16S/18S/ITS amplicon sequencing, metagenomics, metatranscriptomics, microbial whole genome sequencing, complete plasmid sequencing, and microbial single-cell sequencing. The first three methods are genetic investigations into microbial communities, while the last three methods represent genetic studies of individual microorganisms.

Microbial genomics approaches can promote crop yield through soil microbial diversity analysis, functional microbial genomics, biological products development, and bacterial genome modification by utilizing high-throughput and high-resolution genomics technology platforms. Both next-generation sequencing (such as illumina HiSeq/MiSeq and Roche 454) and PacBio SMRT sequencing systems are excellent platform for microbial research. In addition to generating long-length reads, PacBio SMRT systems are able to characterize methylation with PacBio analytical tools.

Figure 1. Sustainable increase in crop productivity by harnessing microbial technologies (Trivedi et al. 2017). SDGs: Sustainable Development Goals (SDGs).

  • Microbial diversity analysis

The abundance and diversity of soil microbial communities are indicators of crop health. A healthy soil microbial community support a balanced and sustainable ecosystem. The 16S/18S/ITS sequencing is a powerful and common method. It can explore soil microbial abundance and diversity quickly and efficiently. After generating various isoforms of targeted genes, you are able to determine taxonomic composition of soil microbial communities and understand the probable cause of low crop yield by comparing microbiomes between high-yield and low-yield crops. Artificial manipulation of soil microbial community composition may increase crop yield, such as addition of beneficial microbial strains or removal of pathogenic microbes.

  • Functional microbial genomics

Understanding the taxonomic composition of soil microbial communities is far from enough. Functional microbial genomics is crucial to elucidate microbiome functions, differentiate beneficial, neutral, and pathogenic microbes, as well as provide insights into improvement of soil quality and bacterial strains, and biological products development. Functional microbial genomics allows researchers and farmers to select important microbial strains that play important roles in achieving the maximum yield potential of a crop.

  • Microbial products development

Metagenomics, metatranscriptomics, microbial whole genome sequencing, and single-cell sequencing help scientists to develop microbial products, such as probiotics. Probiotics represent living bacteria or yeast that are good for environment or human health. Microbial products have been used for sustainable agriculture, contributing to increase crop yield by optimizing beneficial bacteria or protecting plants from pests and disease. Compared with inorganic/organic fertilizers and pesticides, microbial products are more effective and environmental-friendly.

  • Microbial genome modification

After characterizing microbiome functions and genomes by high-throughput sequencing and phenotype analysis, the appropriate microbial strains with activities of interest can be selected and their genomes can be altered in a very targeted manner, with the power of genetic engineering. Compared with traditional random methods, it is more efficient and sometimes necessary to use targeted techniques for strains modification to improve the relevant characteristics of the strain.


Trivedi P, Schenk P M, Wallenstein M D, et al. Tiny Microbes, Big Yields: enhancing food crop production with biological solutions. Microbial Biotechnology, 2017, 10(5):999-1003.

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