Category Archives: Microbe Sampling Kits

Preprint Available: Global-scale structure of the eelgrass microbiome

Bioinformatics, Microbe Sampling Kits, Papers, Project Updates, ZEN

Abstract

Plant-associated microorganisms are essential for their hosts’ survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of their surrounding seawater and sediment communities, we uncovered the structure, composition and variability of microbial communities associated with Z. marina. We also investigated hypotheses about the mechanisms driving assembly of the eelgrass microbiome using a whole-genomic metabolic modeling approach. Our results reveal aboveground leaf communities displaying high variability and spatial turnover, that strongly mirror their adjacent coastal seawater microbiomes. In contrast, roots showed relatively low spatial turnover and were compositionally distinct from surrounding sediment communities – a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Metabolic modeling of enriched taxa was consistent with an assembly process whereby similarity in resource use drives taxonomic co-occurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core Z. marina root microbiome with putative functional roles and highlights potentially disparate processes influencing microbiome assembly on different plant compartments.

 

http://biorxiv.org/content/early/2016/11/28/089797

Seagrass Microbe Sampling Kit

Microbe Sampling Kits, ,

Here’s the version of the sampling kit that’s being sent to 25 ZEN partner sites throughout the world:

Photo: Madison Dunitz
Photo: Madison Dunitz

Each ZEN partner (site) is working in two Zostera marina beds (subsites.) At each subsite, the partners will take three water, sediment, and plant (root+leaf tissue) samples.

On the left, is the AeroPress coffee maker that will function as a water filtration device. The plunger is hollow, so inside of that, I put plastic forceps and 6 gloves. A piece of tape over the top will make sure that it doesn’t all slide out.

On the right is a 500mL plastic bottle for water collection.

In the middle is a plastic, hinged tube storage box. There are 30 2mL tubes inside. The tops of the tubes are pre-labeled:

Lavender: R1.1, R1.2, R1.3 for the three root collections at subsite 1.

Lavender: R2.1, R2.2, R2.3 for the three root collections at subsite 2.

Green: L1.1, L1.2, L1.3 for the three leaf collections at subsite 1.

Green: L2.1, L2.2, L2.3 for the three root collections at subsite 2.

Orange: S1.1, S1.2, S1.3 for the three sediment collections at subsite 1.

Orange: S2.1, S2.2, S2.3 for the three sediment collections at subsite 2.

Blue (2 of each): W1.1, W1.2, W1.3 for the three water collections at subsite 1.

Blue (2 of each): W2.1, W2.2, W2.3 for the three water collections at subsite 2.

There are two blue tubes for each water collection because the filter is to be cut in half and put into two tubes. There are also 30 Tough Tag labels for the sides of the tubes that are to be filled out by the ZEN partners with their site ID, subsite ID, plot ID, and date.

Also, six 0.22micron filters that have been LASER cut to fit the AeroPress, a small pair of scissors for cutting leaves and roots and water filters, a 6mL syringe (top cut off) for taking sediment cores, plastic spatulas for scooping a little bit of sediment out of the corer, a Sharpie, 24 individually-wrapped alcohol swabs, and the 3D-printed stand for the Aeropress.

Pretty cool, huh? Hope I didn’t forget anything!!

I will update with the sampling protocol when it has been finalized.

3D printed AeroPress base

Microbe Sampling Kits, , , ,

While in Cocoa Beach, waiting for the rocket to launch, we decided to test out Russell Neches’s idea for filtering seawater with an AeroPress coffee maker. We were also shooting the instructional video for the Seagrass Microbiome sampling kits that include the AeroPress for this purpose.

Forcing water through a 0.2 micron filter with the AeroPress was easier than I thought it would be, but pretty awkward. It would have been much easier to put that thing over something like – oh I don’t know – a coffee cup to hold it in place while pressing down. I’d decided that if I put a 500mL wide-mouth plastic collection bottle (for the seawater collections) in the kit, that they might also be able to use the bottle for that purpose. But, I was having a hard time figuring out if the mouth of the bottle would be wide enough. So, I went next door to complain to Russell Neches and David Coil. And David said, “you should just have Russell 3D print something,” and Russell said, “Sure, I can do that!” and then 30 minutes later an email had been sent to Madison Dunitz, an undergrad in the lab, and within a couple of hours, it’s done! It’s really simple, just a ring that serves the same purpose as the rim of the coffee cup, with channels in the sides for the water to go through, that is just tall enough to keep the bottom of the AeroPress off the table (or whatever surface.)

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