New Methods paper in the Journal of Visual Experimentation

Congratulations to Tuesday Simmons, Siwen Deng and Daniel Caddell for their recent publication outlining our protocol for 16S rRNA profiling of plant associated microbial communities from the root endosphere and rhizosphere. The paper includes a video outlining our methodology for field sampling, sample preparation and amplicon library preparation.


New Research from the Coleman-Derr lab published in PNAS

Congratulations to Ling Xu for publication of her recent research article  on the effect of drought on the development of the root-associated bacterial communities of Sorghum bicolor, published this week in Frontiers in the Proceedings of the Natural Academy of Sciences. This work is the first published from our recent DOE funded EPICON Project, exploring the molecular mechanisms of sorghum’s remarkable drought tolerance. This research demonstrates the role of drought in promoting enrichment of gram positive bacteria within the root microbiome, and suggests a potential plant metabolite-mediated mechanism for this restructuring.

New research on the grass root microbiome from Daniel Naylor published in ISME Journal

Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this new study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants. We demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root.

Conservation and Food Health Foundation Funds Research on Phyllosphere Microbiome for Crops of the Developing World

Cassava is considered one of the world’s five major food crops, vital to the food security of more than half a billion people around the globe. While cassava is resistant to drought and pests, pathogens represent an Achilles Heel for an otherwise hearty crop. This research will use metagenomics to investigate the effect of agronomic methods on Cassava health. We anticipate this research will have immediate impact for smallholder farmers by: 1) creating a cassava-specific framework to better anticipate pathogen outbreak in the field; 2) identifying candidate microbial biocontrols of pathogens; and 3) evaluating whether “clean seed” systems currently used by Cassava farmers ultimately help or hurt cassava production.

Alex Styer joins the Coleman-Derr lab, receives NSF-GRFP

-A warm welcome to graduate student Alex Styer, who will be joining the Coleman-Derr lab this summer. Alex Styer joined the UC Berkeley Plant and Microbial Biology Department last Fall after completing his undergraduate work at Georgetown University. Alex was recently awarded an NSF Graduate Research Fellowship related to a project he has started with us on plant microbe interactions in Cassava. Congratulations Alex!

Heidi Wipf Receives NSF-GRFP

Heidi Wipf, a second year graduate student in the Coleman-Derr lab, was awarded an NSF Graduate Research Fellowship for her upcoming work to investigate the effects of polyploidy in plants on the recruitment of beneficial microbes to the root microbiome. Plant growth-promoting microbes (PGPM) show great promise for improving crop yields amidst climate change and rising human population growth, but host traits affecting the recruitment of PGPM are not well characterized. Heidi will use transcriptomics, metabolomics and metagenomics to investigate the impact of whole genome duplication events on the plant microbiome to improve our understanding of plant-microbe signaling and the mechanisms controlling microbial shifts in the rhizosphere, which may reveal candidate PGPM for enhancing drought tolerance and yield. Congratulations Heidi!

Coleman-Derr lab to participate in NASA-funded research as part of the Center for Utilization of Biological Engineering in Space (CUBES)

We are excited to participate in the upcoming CUBES Project funded by NASA. The CUBES institute will advance research into an integrated, multi-function, multi-organism bio-manufacturing system to produce fuel, materials, pharmaceuticals and food. While the research goals of the CUBES institute are to benefit deep-space planetary exploration, these goals also lend themselves to practical Earth-based applications. The CUBES team is led by Adam Arkin, principal investigator at the University of California, Berkeley, in partnership with Utah State University, the University of California, Davis, Stanford University, and industrial partners Autodesk and Physical Sciences, Inc. Our team will focus on improving water and light-use efficiency in crops grown off planet on deep-space missions using CRISPR/Cas9 and microbiome based approaches.

PIECE 2.0: an updated database for plant gene structure comparison and evolution

A new publication from our lab, published in Nucleic Acids Research in October 2016. PIECE is a web-accessible database that houses intron and exon information for plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes.