Bacteria and fungi that are intimately associated with plants comprise the plant microbiome . Interest in the role of these organisms in plant health and defense grows as research reveals the importance in modulating responses to defense and abiotic stress. Determining key and conserved nodes within the gene networks underlying these effects in a diverse…

We will dissect the effects of fungi on post-fire soil carbon dynamics by using a systems biology approach that couples small experimental “pyrocosms”, genomics, amplicon metagenomics, transcriptomics, metatranscriptomics, and mass spectrometry. Proposer: Thomas Bruns, University of California, Berkeley

The work continues and expands a previous effort carried out in collaboration with JGI. In the new efforts, we are taking both old and new populations through a total of at least 60 cycles of irradiation and outgrowth to achieve a level of radiation resistance that is the same or greater than that observed in…

Here we propose to expand the search for new lineages of methanotrophs and methanogens by conducting multi-omic (DNA and RNA) sequencing in methane-rich environments enriched in uncultivated microbial “dark matter” (MDM). Specifically, we will focus on: 1) the distribution of methane metabolism in microbial dark matter; 2) capacity for facultative respiration in methanogenic archaea; 3)…

Woody biomass makes up the major portion of terrestrial carbon, and forest ecosystems contain enormous reservoirs of lignocellulose belowground, in dead trees, and litter. Decomposition of this recalcitrant material and mobilization of nutrients are major components of the carbon cycle and essential for forest health. Whether releasing carbon dioxide (CO2) or transforming humic substances, the…

The goal is to establish the common or crystalline ice plant (Mesembryanthemum crystallinum L.) as a DOE Plant Flagship Genome species. The ice plant was the first reported halophytic, facultative crassulacean acid metabolism (CAM) species, meaning that the plant can be induced to switch from C3 photosynthesis to CAM following water-deficit or salinity stress treatment….

We propose a series of comparative genomic analyses with the broad aim of identifying transcripts and putative regulatory control elements (conserved non-coding sequences; CNS) that are associated with the evolutionary transition between annual and perennial life history strategies. We will accomplish this via de novo sequencing of additional perennial Brachypodium species and a new outgroup…

The study of transcription regulatory networks in bacterial communities will greatly benefit our mechanistic understanding of C and N cycling in soil ecosystems and reveal how individual bacterial taxa integrate into whole community responses. Moreover, the study will generate essential information on life-history traits and ecological strategies for hundreds of bacterial taxa, many of which…

The proposed study will answer fundamental questions regarding microbial diversity, metabolism, and growth in one in one of the least understood habitats on Earth. The data will have implications for our understanding of global energy and nutrient cycles, the potential for deep terrestrial disposal of nuclear waste and geo-engineering for CO2 storage, while also providing…

The basic molecular mechanisms by which bacterial endophytes improve plant growth and health and reduce phytotoxic responses and promote remediation are not well understood. To learn more, one approach is to use the RB-TnSeq approach to elucidate which genes are required for N2-fixation by a diazotrophic endophyte of poplar. Using the same approach, researchers then plan…