Bryce Foster
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View article: Size-fractionated metagenomic depth profiles from two sulfidic stations in the Chesapeake Bay
Size-fractionated metagenomic depth profiles from two sulfidic stations in the Chesapeake Bay Open
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 potenti…
View article: The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters
The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters Open
Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified…
View article: Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days
Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days Open
In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the i…
View article: First report of Botrytis cinerea in South African blueberry orchards
First report of Botrytis cinerea in South African blueberry orchards Open
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 to grey mould caused by Botrytis cinerea , resulti…
View article: Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert
Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert Open
We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity …
View article: Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting
Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting Open
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 in desert biocrust microbial comm…
View article: Axolotl: a scalable genomics library based on Apache Spark (Axolotl) v1.0.0
Axolotl: a scalable genomics library based on Apache Spark (Axolotl) v1.0.0 Open
Axolotl is a Python library for scalable distributed genome and metagenome data analysis. Existing tools and systems that we rely on are struggling to keep up with the rapid explosion of genomic data. Compounding this issue, developing sca…
View article: First report of potential multiple fungicide resistant Botrytis cinerea in South African blueberry orchards
First report of potential multiple fungicide resistant Botrytis cinerea in South African blueberry orchards Open
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 to grey mould caused by Botrytis cinerea, resultin…
View article: Multiomics in the central Arctic Ocean for benchmarking biodiversity change
Multiomics in the central Arctic Ocean for benchmarking biodiversity change Open
Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable b…
View article: Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria
Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria Open
Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology is from aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cult…
View article: DOE JGI Metagenome Workflow
DOE JGI Metagenome Workflow Open
The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs data preprocessing, error correction, assembly, structural and functional annotation, and binning.
View article: Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil
Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil Open
The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and me…
View article: Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)
Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina) Open
Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and …
View article: The DOE JGI Metagenome Workflow
The DOE JGI Metagenome Workflow Open
The DOE JGI Metagenome Workflow performs metagenome data processing, including assembly, structural, functional, and taxonomic annotation, and binning of metagenomic datasets that are subsequently included into the Integrated Microbial Gen…
View article: Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil
Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil Open
As the world population increases, improvements in crop growth and yield will be needed to meet rising food demands, especially in countries that have not developed agricultural practices optimized for their own soils and crops. In many Af…
View article: Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome
Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome Open
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 soil surface consortium…
View article: Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress
Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress Open
Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, …
View article: Impact of soil salinity on the cowpea nodule-microbiome and the isolation of halotolerant PGPR strains to promote plant growth under salinity stress
Impact of soil salinity on the cowpea nodule-microbiome and the isolation of halotolerant PGPR strains to promote plant growth under salinity stress Open
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 in the rhizosphere and within nodule…
View article: Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials Open
This dataset contains key characteristics about the data described in the Data Descriptor Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Contents: 1. human readable metadata summary table…
View article: Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials Open
This dataset contains key characteristics about the data described in the Data Descriptor Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Contents: 1. human readable metadata summary table…
View article: Illumina Fastq Filtering v1
Illumina Fastq Filtering v1 Open
Method to filter Illumina sequence data by removing low quality reads and reads mapping to artifact and contamination databases using BBTools. DNA sequencing produces low quality reads, reads that contain sequencing artifacts and contamina…