Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

Sean P Jungbluth; Jan P Amend; Michael S Rappé

doi:10.7287/peerj.preprints.2613v1

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

Sean P Jungbluth ^1,2, Jan P Amend^2,3,4, Michael S Rappé ⁵

1 Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States

2 Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, United States

3 Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States

4 Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States

5 Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, United States

DOI: 10.7287/peerj.preprints.2613v1

Published: 2016-12-01
Accepted: 2016-12-01

Subject Areas: Bioinformatics, Environmental Sciences, Genomics, Microbiology
Keywords: Juan de Fuca Ridge, Deep Biosphere, Genomes from Metagenomes, Genome Binning, Microbial Diversity, Phylogenomics, Subseafloor, Basalt

Copyright: © 2016 Jungbluth et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.

Cite this article: Jungbluth SP, Amend JP, Rappé MS. 2016. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. PeerJ Preprints 4:e2613v1 https://doi.org/10.7287/peerj.preprints.2613v1

Abstract

The global deep subsurface biosphere is thought to be one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the subseafloor of the Juan de Fuca Ridge. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs) with completeness > 10%. Of the GFMs, 31 were estimated to be > 90% complete, while an additional 17 were > 70% complete. In most instances, estimated redundancy in the GFMs was < 10%. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs and nearly all were distantly related to known cultivates. In the GFMs, abundant bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria and abundant archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). In this study, we identified the first near-complete genomes from archaeal and bacterial lineages THSCG, MBG-E, and EM3 and, based on the warm, subsurface and hydrothermally-associated from which these groups tend to be found, propose the names, Geothermarchaeota, Hydrothermarchaeota, and Hydrothermae, respectively. The data set presented here are the first description of Juan de Fuca igneous basement microbial GFMs reported and will provide a platform by which one can perform a higher level interrogation of the many uncultivated lineages presented herein.