A5070241316- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Legume Nitrogen Fixing Symbiosis
- Biocrusts and Microbial Ecology
- Coastal wetland ecosystem dynamics
- Environmental DNA in Biodiversity Studies
- Plant Pathogens and Fungal Diseases
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
- Hydrocarbon exploration and reservoir analysis
- Fungal Plant Pathogen Control
- Climate change and permafrost
- Geological Studies and Exploration
- Peatlands and Wetlands Ecology
- Gene expression and cancer classification
- Trace Elements in Health
- Polar Research and Ecology
- Soil Carbon and Nitrogen Dynamics
- Bacteriophages and microbial interactions
- Diatoms and Algae Research
- Mine drainage and remediation techniques
- Algal biology and biofuel production
- Microbial Natural Products and Biosynthesis
- Aquatic Ecosystems and Phytoplankton Dynamics
Joint Genome Institute
2019-2025
Lawrence Berkeley National Laboratory
2019-2025
Stellenbosch University
2023-2024
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.
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...
Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory bacterial archaeal community genes, transcripts, taxonomy during intense dinoflagellate bloom Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 88 16S rRNA amplicon libraries from samples collected on 41 dates. also includes 18S libraries, characterizing eukaryotic bloom. Accompanying sequence are chemical biological...
Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions clinical and environmental relevance. metabolite biosynthetic gene clusters (BGCs) can be identified within DNA sequences various sequence similarity tools, but determining the exact genes in pathway predicting their chemical products only done careful, manual comparative analysis. To facilitate this, we report first release secondary metabolism collaboratory (SMC), which...
ABSTRACT We present 45 size-fractionated metagenomes collected from two stratified Chesapeake Bay mainstem stations during bottom water sulfidic conditions. This data set enables investigations into shifts in community structure and genomic potential across redox gradients particle associations (free-living [0.2–3 µm], small [3–30 medium [30–180 large [>180 µm] fractions).
Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology relates to aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cultures. These data will support phylogenomic studies evolutionary relationships and gene content among these unique algae relatives.
Abstract In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours 22 days. This high temporal resolution sampling effort captured the last 3 days a Rhizosolenia sp. bloom, initiation complete bloom cycle Chaetoceros socialis (8 days), following bacterial (2 days). Metagenomes completed on time series, dataset includes 128 size-fractionated (0.22–1.2 µm), providing gene abundances dominant members bacteria, archaea, viruses. also...
Cowpea is one of the major legumes cultivated in arid and semiarid regions world. Four soil-microbial samples (SS-1 through SS-4) collected from soils Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which grown under salinity stress to analyze bacterial composition rhizosphere within nodules using cultivation-dependent -independent methods. Two varieties, 603 salt-tolerant CB 46, each inoculated or without four different native soil medium either N-deficient (−N)...
The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species a dominant plant family, Velloziaceae, are highly specialized to low-nutrient seasonal water availability this environment, where phosphorus (P) is key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, contribution these interactions remains poorly studied. Here we present first microbiome...
Multiomics approaches need to be applied in the central Arctic Ocean benchmark biodiversity change and identify novel species their genes. As part of MOSAiC, EcoOmics will therefore essential for conservation sustainable bioprospecting one least explored ecosystems on Earth.
In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours 22 days. This high temporal resolution sampling effort captured the last 3 days a
Abstract Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these to atmospheric oxygen, iron minerals soils rapidly oxidized. This process turns potential acid sulfate into actual and mobilizes large quantities of acidity leachable toxic metals that cause severe environmental problems. It is known acidophilic microorganisms living catalyze mineral oxidation. However, only a few studies regarding...
Abstract As the world population increases, improvements in crop growth and yield will be needed to meet rising food demands, especially countries that have not developed agricultural practices optimized for their own soils crops. In many African countries, farmers improve productivity by applying synthetic fertilizers pesticides crops, but continued use over years has had serious environmental consequences including air water pollution as well loss of soil fertility. To reduce overuse...
We present eight metatranscriptomic datasets of light algal and cyanolichen biological soil crusts from the Mojave Desert in response to wetting. These data will help us understand gene expression patterns desert biocrust microbial communities after they have been reactivated by addition water.
ABSTRACT We present six whole community shotgun metagenomic sequencing data sets of two types biological soil crusts sampled at the ecotone Mojave Desert and Colorado in California. These will help us understand diversity function biocrust microbial communities, which are essential for desert ecosystems.
Abstract The South African blueberry industry has grown consistently over the past few years due to an increase in local and international demand. Like many other crops, blueberries are susceptible grey mould caused by Botrytis cinerea , resulting significant reductions yield. In this study, isolates were recovered from symptomatic fruit, flowers, leaves undifferentiated buds, but not found as endophytes healthy tissues. Phylogenetic analysis of concatenated glyceraldehyde-3-phosphate...
ABSTRACT The DOE JGI Metagenome Workflow performs metagenome data processing, including assembly, structural, functional, and taxonomic annotation, binning of metagenomic datasets that are subsequently included into the Integrated Microbial Genomes Microbiomes (IMG/M) comparative analysis system (I. Chen, K. Chu, Palaniappan, M. Pillay, A. Ratner, J. Huang, Huntemann, N. Varghese, White, R. Seshadri, et al, Nucleic Acids Rsearch, 2019) provided for download via Joint Genome Institute (JGI)...
The addition of glucose to soil has long been used study the metabolic activity microbes in soil; however, response microbial ecophysiology remains poorly characterized. To address this, we sequenced metagenomes and metatranscriptomes glucose-amended communities a laboratory incubation.
Abstract Four soil samples (SS-1—SS-4) isolated from semi-arid soils in Punjab, Pakistan were used as inocula for cowpea (V igna unguiculata L.) grown under salinity stress to analyze the composition of bacteria rhizosphere and within nodules through cultivation-dependent cultivation-independent methods. Two varieties, 603 salt-tolerant CB 46, each inoculated with four different native samples, data showed that plants SS-2 SS-4 grew better than SS-1 SS-3. Bacteria both nodules, 34 51...
Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based consortium, in the presence absence an underlying microbiome and/or urea.
Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater experiment which manipulated hydrologic conditions plant presence. These soil will deepen our understanding of how hydrology vegetation influence functional diversity.