The team aims to understand system-level temporal dynamics of microbial interactions in a synthetic bacterial community. The overarching goal is to understand how the interactions among members of microbial communities determine the emergent properties of the system. Do multi-member microbial communities perform differently, given different membership compositions, then expected by the summation of individual member performances? If…
Genetic Diversity of Shrub Willow Pathogen
This proposal aims to explore the genetic diversity of Melampsora americana willow rust in the Northeast United States by performing full de novo Illumina and PacBio sequencing of a representative isolate to act as a reference genome for future analyses. Melampsora spp. rusts remain the most threatening pathogens of Salicaceae bioenergy crops in the Northern…
Targeting Taxonomic Blind Spots
The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched approximately 10 years ago to systematically fill sequence space in the bacterial and archaeal phylogenetic tree of life. The results from this study had tremendous impact in terms of the reconstruction of phylogenetic histories, the discovery of new protein families, and the prediction of…
Core and Pangenomes of Soil and Plant-associated Prokaryotes
The aim is to determine the pangenomes of 100-200 species of soil or plant-associated prokaryotes. While the genome sequence of the type strain captures much of the genotype of a species, the sequence of any single strain also neglects a large part of the genetic diversity. A more complete description of the species is given by…
Sequencing Zygnematales Algae
The team plans de novo sequencing of the (nuclear and organellar) genomes of two species of Zygnematales: Mesotaenium kramstae and Zygnema circumcarinatum. They also aim to conduct transcriptome sequencing (RNA-seq), to facilitate genome annotation, and small RNA sequencing, to study the potential regulatory roles of miRNAs in green algae and to assess whether miRNAs have conserved…
Gene Atlas for Kalanchoe laxiflora
To better understand the molecular mechanisms underlying environmental response of K. laxiflora, the team will study temporal and tissue specific changes in global gene expression in response to different treatments, including temperature, light intensity, water-deficit stress and nitrogen sources. They also propose to examine the role of circadian and metabolite control over the CAM leaf transcriptome. The…
Fungal Interaction Networks in Soil Crusts
Extremophilic fungi possess adaptations that enable successful colonization of environments characterized by extremes of temperature, water activity, salinity, radiation, and/or pH. As part of a broad emphasis on understanding these adaptations, the long-term objective of the team’s research is to determine how fungi interact with photoautotrophs (algae and cyanobacteria). Their work focuses on fungal interactions…
Microbes’ Role in Plant Fitness Under Induced Drought
The team will investigate the role of root-associated Actinobacteria in promoting host fitness under drought stress in two plants important to the DOE mission of sustainable biofuels. Preliminary data suggest that Actinobacteria are reproducibly more abundant in the roots of drought-treated sorghum and rice than in those of well-watered controls. They hypothesize: 1) that the enriched…
Geo-Metabolomics in a Saltmarsh
Current understanding of how bacteria metabolize plant-derived compounds is surprisingly limited given the importance of these processes to the global carbon cycle. The researchers hypothesize that nominally “recalcitrant” t-DOM in salt marshes is made more reactive by pulses of labile DOM derived from coastal wetland marshes and phytoplankton. Outcomes of their studies have the potential to…
Metagenomics Leads to New CRISPR-Cas Systems
First CRISPR-Cas9 system in archaea discovered The Science Through metagenomic data generated by the DOE Joint Genome Institute, researchers analyzed 155 million protein coding genes from uncultivated microbial communities, leading to the discovery of the first CRISPR-Cas9 protein in the archaeal domain, and of two previously unknown simple bacterial CRISPR-Cas systems. The Impact Microbes play…