We have a new fully funded, two year postdoctoral research position available immediately in our lab to advance methodology in the area of genome-resolved metagenomics of crop microbiomes. The position is suitable for candidates with prior expertise in bioinformatics and/or shotgun metagenomics analysis. Please email firstname.lastname@example.org if interested.
A new article from our lab highlights recent advances in the field of plant microbiome research pertaining to the root microbiome’s response to drought stress. It outlines several hypotheses regarding molecular mechanisms responsible for the observed enrichment of Gram positive bacteria within roots following a plant’s exposure to drought stress, and suggests putative methods for testing the consequence of this enrichment for crop fitness.
Check out the new Book Chapter “Role of the Plant Root Microbiome in Abiotic Stress Tolerance” from Daniel Caddell and Siwen Deng on the impact of root borne microbes on abiotic stress tolerance in plants. The work highlights recent efforts to understand bacterial and fungal contributions to plant fitness under drought, salinity and nutrient stress, and to develop microbial products that can be used in agriculture for boosting yields under challenging environmental conditions.
We are very excited to participate in the inaugural year for the NIFA AFRI Plant Microbiomes program area. This three year funding award will support our ongoing work to characterize the causes and consequences of Actinobacterial enrichment in the root microbiome under drought stress. The project represents our first collaboration with the Deutschbauer lab at UCB, bringing bonafide microbial genomic expertise to our efforts. Welcome Adam! Additionally, this projects reinvests in a long standing collaboration with Jeff Dahlberg at the UC Kearney Agricultural Research Center that will allow us to explore microbial dynamics in agriculturally relevant contexts.
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.
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.
Congratulations to Dan Naylor for publication of his review on the effect of drought on root-associated bacterial communities, published this week in Frontiers in Plant Science.
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.
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.
-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!