Chris Daum
A5047824262- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Mycorrhizal Fungi and Plant Interactions
- Protist diversity and phylogeny
- Biofuel production and bioconversion
- Plant Pathogens and Fungal Diseases
- Microbial Metabolic Engineering and Bioproduction
- Bioenergy crop production and management
- Plant-Microbe Interactions and Immunity
- Genetic Mapping and Diversity in Plants and Animals
- Legume Nitrogen Fixing Symbiosis
- Food composition and properties
- Fungal Biology and Applications
- Biocrusts and Microbial Ecology
- Enzyme-mediated dye degradation
- Rice Cultivation and Yield Improvement
- Environmental DNA in Biodiversity Studies
- Plant nutrient uptake and metabolism
- Chromosomal and Genetic Variations
- Fungal and yeast genetics research
- Plant Pathogenic Bacteria Studies
- Algal biology and biofuel production
- Coastal wetland ecosystem dynamics
- Metal Extraction and Bioleaching
- Wheat and Barley Genetics and Pathology
Lawrence Berkeley National Laboratory
2016-2025
Joint Genome Institute
2016-2025
United States Department of Energy
2015-2023
Lawrence Livermore National Laboratory
2021
University of California, Berkeley
2019
Los Alamos National Laboratory
2017
KBase
2015
DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies a limited number organisms suggest that also contributes genome regulation, but prevalence and properties such non-restriction-associated systems remain poorly understood. Here, we used single molecule, real-time sequencing map modifications including m6A, m4C, m5C across genomes 230 diverse bacterial archaeal species. We observed nearly all (93%) examined, identified total 834...
Evolution of lignocellulose decomposition was one the most ecologically important innovations in fungi. White-rot fungi Agaricomycetes (mushrooms and relatives) are effective microorganisms degrading both cellulose lignin components woody plant cell walls (PCW). However, precise evolutionary origins poorly understood, largely because certain early-diverging clades its sister group, Dacrymycetes, have yet to be sampled, or been undersampled, comparative genomic studies. Here, we present new...
Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity lifestyles, many which have evolved multiple times. Plant pathogens represent a major ecological niche they are known to infect most food crops feedstocks for biomass biofuel production. Studying ecology evolution has significant implications our fundamental understanding fungal evolution, their adaptation stress host specificity, practical with regard effects climate change on food, feed, livestock...
Section Flavi encompasses both harmful and beneficial Aspergillus species, such as oryzae, used in food fermentation enzyme production, flavus, spoiler mycotoxin producer. Here, we sequence 19 genomes spanning section compare 31 fungal including 23 species. We reassess their phylogenetic relationships show that the closest relative of A. oryzae is not but minisclerotigenes or aflatoxiformans identify high genome diversity, especially sub-telomeric regions. predict abundant CAZymes (598 per...
Abstract Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains Zygnema circumcarinatum . We inferred traits in ancestor and plants that might have ushered conquest by plants: expanded genes signaling cascades, environmental response, multicellular growth. share all major enzymes cell wall synthesis remodifications, gene gains shaped this toolkit. Co-expression network...
Significance The genus of Aspergillus holds fungi relevant to plant and human pathology, food biotechnology, enzyme production, model organisms, a selection extremophiles. Here we present six whole-genome sequences that represent unexplored branches the genus. comparison these genomes with previous genomes, coupled extensive chemical analysis, has allowed us identify genes for toxins, antibiotics, anticancer compounds, as well show novofumigatus is potentially pathogenic fumigatus , an even...
Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This especially true for soil water availability, because drought the greatest abiotic inhibitor worldwide crop yields. Here, we test genetic basis responses in model C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, comparison two complete genomes. While gene expression networks are dominated by local cis-regulatory elements,...
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding generic boundaries and composition this large heterogeneous taxon. Here we used amino acid nucleotide sequences 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which investigate structure sensu lato. These data unambiguously supported five distinct lineages, four correspond stricto newly introduced genera Paraburkholderia, Caballeronia...
The process of crop domestication often consists two stages: initial domestication, where the wild species is first cultivated by humans, followed diversification, when domesticated are subsequently adapted to more environments and specialized uses. Selective pressure increase sugar accumulation in certain varieties cereal Sorghum bicolor an excellent example latter; this has resulted pronounced phenotypic divergence between sweet grain-type sorghums, but genetic mechanisms underlying these...
The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs preprocessing, error correction, assembly, structural and functional annotation, binning.
Moss sex chromosomes retain thousands of broadly expressed genes despite millions years suppressed recombination.
Abstract Five versions of the Chlamydomonas reinhardtii reference genome have been produced over last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for laboratory strains, CC-503 CC-4532, provide resources plus minus mating-type alleles. We corrected major misassemblies previous validated our via linkage analyses. Contiguity increased ten-fold >80% filled gaps are within...
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how genotype bacterial community composition. Most studies characterizing effect undersample genetic diversity grow plants outside their native ranges, making associations between microbes difficult interpret. Here, we characterized a large panel switchgrass, North American C4 bioenergy crop, three field locations spanning its...
ABSTRACT The filamentous and unicellular algae of the class Zygnematophyceae are closest algal relatives land plants. Inferring properties last common ancestor shared by these plants allows us to identify decisive traits that enabled conquest We sequenced four genomes (three strains Zygnema circumcarinatum one strain Z. cylindricum ) generated chromosome-scale assemblies for all emerging model system . Comparative genomic analyses reveal expanded genes signaling cascades, environmental...
Summary The black morel ( Morchella importuna Kuo, O'Donnell and Volk) was once an uncultivable wild mushroom, until the development of exogenous nutrient bag (ENB), making its agricultural production quite feasible stable. To date, how nutritional acquisition mycelium is fulfilled to trigger fruiting remains unknown. investigate mechanisms involved in ENB decomposition, genome a cultivable strain M . SCYDJ1‐A1) sequenced genes coding for decay apparatus were identified. Expression encoded...
ABSTRACT Microbial fermentation of agro-industrial waste holds great potential for reducing the environmental impact associated with production lipids industrial purposes from plant biomass. However, chemical complexity many residues currently prevents efficient conversion into lipids, creating a high demand strains ability to utilize all energy-rich components agricultural residues. Here, we present results genome and transcriptome analyses Trichosporon oleaginosus . This oil-accumulating...
Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite potential, development engineering methods for these organisms has been slow due complex life cycle, understudied metabolism, challenging culture requirements.
Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity shaped by interactions with prokaryotes as part complex microbiomes. Although differences in their local species have been estimated, we still a limited understanding environmental conditions compositional between communities on large scale from pole to pole. Here, show, based pole-to-pole metatranscriptomes microbial rDNA sequencing, that polar non-polar upper oceans most...
Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing assembly metagenomes from biological soil crusts, group communities that rich BGCs. Taking advantage the unusually long assemblies produced by this approach, recovered nearly 3,000 BGCs for analysis,...
Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing subsequent reconstruction metagenome-assembled genomes (MAGs), this approach yet be applied for complex phytoplankton microbiomes from polar non-polar oceans consisting microbial eukaryotes associated prokaryotes.Here, we have assembled MAGs chlorophyll a maximum...
Abstract Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation xylan in impedes conversion biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved but regulatory mechanism RWAs not fully understood. In this study, we demonstrate overexpression Populus trichocarpa PtRWA-C gene increases level and lignin content S/G ratio, ultimately yielding poplar...
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds soils. We used metatranscriptomics competition for organic resources by fungal groups boreal, temperate, Mediterranean Using a dedicated mRNA annotation pipeline combined with JGI MycoCosm database, we transcripts three targeting enzymes involved C- N mobilization from...
Haliangium ochraceum Fudou et al. 2002 is the type species of genus in myxococcal family 'Haliangiaceae'. Members are first halophilic myxobacterial taxa described. The cells follow a multicellular lifestyle highly organized biofilms, called swarms, they decompose bacterial and yeast as most myxobacteria do. fruiting bodies contain particularly small coccoid myxospores. H. encodes actin homologue identified genome. Here we describe features this organism, together with complete genome...
The genome of Caldithrix abyssi, the first cultivated representative a phylum-level bacterial lineage, was sequenced within framework Genomic Encyclopedia Bacteria and Archaea (GEBA) project. genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or implement nitrate reduction with acetate molecular hydrogen as electron donors. encoded five different [NiFe]- [FeFe]-hydrogenases, one which, group 1 [NiFe]-hydrogenase, is presumably involved in...