Reddy, T. B. K. | bioRxiv Science

bioRxiv2020

The DOE JGI Metagenome Workflow

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 Genomes and Microbiomes (IMG/M) comparative analysis system (I. Chen, K. Chu, K. Palaniappan, M. Pillay, A. Ratner, J. Huang, M. Huntemann, N. Varghese, J. White, R. Seshadri, et al, Nucleic Acids Rsearch, 2019) and provided for download via the Joint Genome Institute (JGI) Data Portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here we describe the different tools, databases, and parameters used at different steps of the workflow, to help with interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a Workflow Description Language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl.git). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, H. Katta, A. Mojica, I Chen, and N. Kyrpides, and T. Reddy, Nucleic Acids Research, 2018). IMPORTANCEThe DOE JGI Metagenome Workflow is designed for processing metagenomic datasets starting from Illumina fastq files. It performs data pre-processing, error correction, assembly, structural and functional annotation, and binning. The results of processing are provided in several standard formats, such as fasta and gff and can be used for subsequent integration into the Integrated Microbial Genome (IMG) system where they can be compared to a comprehensive set of publicly available metagenomes. As of 7/30/2020 7,155 JGI metagenomes have been processed by the JGI Metagenome Workflow.

bioinformatics↗

bioRxiv2020

Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil

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 African countries, farmers improve agricultural productivity by applying synthetic fertilizers and pesticides to crops, but their continued use over the years has had serious environmental consequences including air and water pollution as well as loss of soil fertility. To reduce the overuse of synthetic amendments, we are developing inocula for crops that are based on indigenous soil microbes, especially those that enhance plant growth and improve agricultural productivity in a sustainable manner. We first isolated environmental DNA from soil samples collected from an agricultural region to study the composition of the soil microbiomes and then used Vigna unguiculata (cowpea), an important legume crop in Botswana and other legumes as "trap" plants using the collected soil to induce nitrogen-fixing nodule formation. We have identified drought-tolerant bacteria from Botswana soils that stimulate plant growth; many are species of Bacillus and Paenibacillus. In contrast, the cowpea nodule microbiomes from plants grown in these soils house mainly rhizobia particularly Bradyrhizobium, but also Methylobacterium spp. Hence, the nodule microbiome is much more limited in non-rhizobial diversity compared to the soil microbiome, but also contains a number of potential pathogenic bacteria.

microbiology↗