Microbes are associated with every plant tissue: they are found in the stems, leaves, and seeds (where they are known as endophytes), and on the surfaces of these same tissues (where they are known as epiphytes). The most studied agricultural microbiome is the plant’s rhizosphere: the bacteria, archaea, and fungi (such as mycorrhizal fungi) living in and around the plant’s root system. Whereas the rhizosphere is mainly recruited from the soil to provide support to the growing plant, the seeds containing their own microbiomes provide support for the plant’s next generation.
Microbiome Insights has decades of experience working with Bill Mohn’s lab in microbial ecology to develop best practices for sequencing soil and plant microbiomes. Our lab has extensive knowledge of these microbial ecosystems and can advise on a workflow that meets your needs.
Our expertise includes:
- Advanced extraction methods for consideration of particularly robust microbes in the system
- Inclusion of negative controls to eliminate confounding results
- rRNA gene sequencing to determine, at a high level, the role of various microbes including fungi
- Shotgun metagenome sequencing for a higher resolution of both taxonomic and functional outputs
- Bioinformatic analysis with a firm understanding of environmental ecosystems
Services We Offer
- rRNA Gene Sequencing of 16S, 18S, ITS2 and archaeal V4-V5
- Total Bacterial Quantification via qPCR (quantitative PCR) for total bacterial content
- Shotgun Metagenome Sequencing