Microbial Isolation
Our goal is to develop approaches for engineering sulfur cycling microbes. We will use engineering to probe functions of diverse sulfur cycling genes as well as implications of those functions for plant-microbe interactions. With organisms in hand engineered, for example, for enhanced sulfide oxidation, we will grow wild type and engineered representatives with our axenic Sporobolus plants and quantify holobiont growth performance (among other metrics of function.)
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We are isolating bacteria from sediment collected from the rhizosphere of Sporobolus alterniflorus at Little Sippewissett and Great Sippewissett marshes in Falmouth, MA. Suspensions of rhizosphere sediment are plated on diverse media, and resulting colonies are T-struck for purity, identified by 16S, and a subset chosen for whole genome sequencing. The latter step is essential for targeted manipulation of genomes, and we are testing several methods for moving genetic material into sulfur oxidizers.​​
We are also deploying "microbial traps" in salt marsh sediment to selectively culture microbes with particular traits.
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These traps were designed by Dr. Ed Goluch at Northeastern University*, Each trap has 24 wells that can be filled with solutions designed to select for microbes with particular physiological traits. A nanoporous membrane covers the ends of all 24 wells on one side of the block. This membrane allows exchange of solutes with the environment. On the other side of the block, a silicon wafer covers the end of all 24 wells, except that a very small pore (0.25 -1.25 um in size) is drilled in the wafer at the center of each well to allow individual microbes to enter the well. Once inside, if conditions are right, microbes will divide and multiply.
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We are designing traps to isolate sulfate reducing microbes, or sulfur oxidizing microbes, that live around roots of Sporobolus alterniflorus at Little Sippewissett Marsh, Falmouth, MA.
We deploy traps for a week, then bring them back to the lab. The contents of each well are pulled out by piercing the membrane with a syringe needle, then inoculated into a vial holding medium matching that originally added to the well.
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To ease assembly of the parts, we created a 3D printed guide that can align the two adhesive pieces to the polycarbonate block.
*Santiveri CR, Vineis JH, Martins S, Calaza C, Gaspar J, Bowen JL, Goluch ED. Machined silicon traps for capturing novel bacterial communities and strains in situ. In review.
