Big Tree of Populus Isolates


I had fun putting together a figure this weekend for a proposal. This shows a phylogenetic analysis of partial 16S rRNA genes obtained from over 2400 bacterial isolates we have collected from Populus roots in the past several years. Also I discovered in the process a cool new online tool for making this tree called the “Interactive Tree of Life” (iTOL – iTOL Seems to be pretty user friendly way to display a variety of different types of data on organisms in the context of their phylogeny! Shown here is categorical information around the outside of the tree about the origin of each isolate. However this program is able to display a variety of data types and formats, including continuous information in the form of bar charts and relative abundance data in the form of pie charts.

USDA-DOE Funding Opportunity in Plant Feedstock Genomics for Bioenergy

Woohoo!!! Beneficial Plant Microbe interactions are specifically called out as eligible this year!

Excerpted RFP text below:
The U.S. Department of Energy’s Office of Science, Office of Biological and Environmental Research (BER), and the U.S. Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA), hereby announce their interest in receiving applications for genomics based research that will lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Specifically, applications are sought for fundamental research on plants that will improve biomass characteristics, biomass yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research to predict phenotype from underlying genotype that could lead to improved feedstock characterization and sustainability are also encouraged.

Link to full announcement in PDF format

A universe of soil, rhizosphere and endosphere bacteria

I got this cool figure from my postdoc Mike Robeson to contemplate over the weekend. It shows the Bacterial species network (or OTUs as small white squares) we recovered from bulk soil (orange connections), rhizosphere (blue connections) and root endophyte (green connections) samples from 6 sites taken last fall where we sampled Populus deltoides and surrounding tree species on the Caney Fork River in Tennessee (squares of different colors indicate different riparian sites) as part of our Plant Microbial Interfaces project.  Still not sure exactly what it means, except that it is fun to look at and ponder.  Seems to indicate that the effect of habitat (soil, rhizosphere, endosphere) > site location > tree species.  Anyway, kind of mesmerizing.