BioBead is a hydrogel microbial delivery system designed to support plant-microbe symbioses in dynamic soil environments. It serves as both a carrier and a living interface, delivering beneficial fungal, bacterial, or mycorrhizal consortia in bead form to plant roots. As part of my PhD research in CEE, I am expanding into greenhouse and field trials with BioBead.
BioBead enables precise, tunable inoculation strategies in ecological restoration and sustainable agriculture. Each bead can be customized to deliver targeted microbial consortia.
We are analyzing the metagenomes from 2 (out of 48) soil samples that were used in a greenhouse study prior to biofertilizer treatment. These will give us a sense of resident microbial (fungal and bacterial) communities residing in them.
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F1B-KM40 - bulk field soil
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F2R-KM41 - rhizosphere soil
The goal is to generate phylogenetic trees of bacteria and fungi in these samples, and analyze them for nitrogenase gene (nif) abundance. We expect there to be a more diverse commmunity of microbes in the rhizosphere (root zone), and for there to be more nif gene activity.
Characterizing microbial activity across soil types and host plant interfaces using isotopic C/N tracing, -omics approaches, and plant growth responses.
- Alginate-based encapsulation with fungal and bacterial consortia
- Microscopy, FISH, and bioinformatics tools (e.g., PEAR, Megahit, Megan, HMMER, Prodigal)
This repository serves as an open, evolving pipeline for metagenome analysis of greenhouse soil samples from BioBead trials.
Slide deck: https://rpubs.com/reneedavis/nifhunt
Compendium: http://rpubs.com/reneedavis/1311624