Microbes Persist: Building a KBase Foundation for Microbial and Viral Ecogenomics in Soil

Abstract

A science focus area (SFA) is a research project funded by the Department of Energy (DOE) to further scientific advancement and support the DOE’s Office of Science mission. The LLNL Soil Microbiome SFA led by Henry Shaw at Lawrence Livermore National Laboratory aims to understand the critical role that microbes play in the stabilization and persistence of soil carbon. It does so by studying microbial biochemistry, functional potential, and physiology of the soil microbiome. This SFA is producing hundreds of soil genome-resolved metagenomes and will be implementing new tools in KBase to tackle the bioinformatic challenges associated with the corresponding data analysis. The Banfield group is leading the microbial metagenome efforts and the Sullivan group is working on porting iVirus tools to KBase.

Collaborative Development Object

New Metagenomic Functionality:

  • A new suite of tools for automated curation of metagenomes and more confident binning
  • Scripts that integrate multiple assembly outcomes and long read data to convert bins into essentially complete genomic sequences
  • Production of higher quality and refined metagenome-assembled genomes (MAGs)

New Viral Tools:

  • Two tools from iVirus, a tool designed to explore viral ecology and bring bioinformatic analyses to the study of viral genomes
  • Additional capabilities will be added to iVirus within KBase including assessing viral genome completion and distinguishing free lytic phages from prophages
  • PhATE, a phage functional annotation pipeline developed at LLNL

Additional Information

Meet the Members

SFA Manager for LLNL: Henry Shaw1
Lead Investigator: Jennifer Pett-Ridge1
SFA Contact: Jennifer Pett-Ridge1Jill Banfield2,3, and Matthew B. Sullivan3
KBase Contact: Paramvir Dehal2,7 and Dylan Chivian2,7
Lead Developers: Rohan Sachdeva3 and Ben Bolduc5
LLNL SFA Team: Steve Blazewicz1, Yongqin Jiao1, Stephanie Malfatti1, Karis McFarlane1, Erin Nuccio1, Brian Souza1, Ben Stewart1, Rhona Stuart1, Peter Weber1, Mavrik Zavarin1
Collaborators: Eoin Brodie2, Peter Nico2, Jinyun Tang2, Mary Firestone3, Bruce Hungate4, Paul Dijkstra4, Christina Schaedel4, Ben Koch4, Ljiljana Paša-Tolić6
Postdocs/Students: Rachel Neurath1,3, Keith Morrison1, Evan Starr3, Alexa Nicholas3
Affiliations: 1Lawrence Livermore National Lab, 2Lawrence Berkeley National Lab, 3University of California Berkeley, 4Northern Arizona University, 5The Ohio State University, 6Environmental and Molecular Sciences Laboratory/Pacific Northwest National Lab, 7KBase

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