Thread by @Danidiin

I'm excited to share my first postdoc manuscript (and first-ever preprint!) from Dianne Newman’s lab @caltech. This was a wonderful collaboration with Linda Thomashow and David Weller @USDA_ARS. tinyurl.com/ydynmqhq.

#microbialecology #plantmicrobe #genomics

Metabolite-mediated interactions shape microbial communities and can inhibit pathogen invasion. We focused on the ecology of phenazines, a family of bacterially produced redox-active antibiotics that can protect major crops from disease-causing microbes.

Phenazines are chemically diverse but are all derived from the same precursors, which are synthesized by conserved genes. We leveraged this knowledge to find which bacteria can make phenazines and to measure their abundance in the environment.

We developed a simple computational process that outputs an ecologically intuitive metric: percent phenazine producers/degraders out of all bacteria in a given microbiome.

We built a reference db of single-copy genes that appear in every bacterial genome and used it to measure a "total-bacteria" signal in shotgun-metagenomes. We then used this measure to normalize our phenazine gene counts and extracted the % producer levels.

We validated our approach in commercial dryland wheat fields, where phenazines are known to provide protection from disease-causing fungi, and where their producers (pseudomonads) can be directly enumerated via cultivation.

We analyzed >800 publicly available soil and plant metagenomes and found that phenazine biosynthesis is a very common trait that is preferentially enriched in rhizospheres (how come?). In contrast, biodegradation was quite rare.

We also found new producer-crop associations...

For example, Dyella japonica, a putative producer recently isolated from Arabidopsis, was the most abundant species in our global analysis (up to 2.7% of all bacteria in maize) and was enriched in the rhizospheres several major crops.

We wanted to know more about this bug...

So I got to work on a bench!😆

We found several bioactive phenazines that D. japonica produces. Their biosynthesis was upregulated during phosphate limitation, an environmental stress that is expected to become more common (P-fertilizer going scarce).

I also got to grow corn! (: 🌽🤠🌽

We set up and characterized a laboratory model for D. japonica–maize interaction. We think this bug is a very efficient root colonizer that likes the root interior compartment and root-hair tips (a major source of root exudates).

This work was only possible because of my wonderful PI, which is a supportive and generous mentor, and our fantastic lab members.

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