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

Sean P Jungbluth,Michael S Rappé,Jan P Amend

doi:10.1038/sdata.2017.37

Abstract

The global deep subsurface biosphere is 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 Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Highlights

Background & SummaryBeneath the sediments of the deep ocean, the subseafloor igneous basement presents a largely unexplored habitat that likely plays a crucial role in global biogeochemical cycling[1]
CORK observatories have been used to collect warm, anoxic crustal fluids originating from boreholes drilled into 1.2 and 3.5 million-year-old ridge flank of the Juan de Fuca Ridge (JdFR)[5]
The sampling and interrogation of raw basement fluids enabled by CORK observatories has revealed the presence of novel microbial lineages that are related to uncultivated candidate microbial phyla with unknown metabolic characteristics[8,9,10,11]

Summary

Introduction

Background & SummaryBeneath the sediments of the deep ocean, the subseafloor igneous basement presents a largely unexplored habitat that likely plays a crucial role in global biogeochemical cycling[1]. Analysis was performed on 98 GFMs that were over 200 Kbp in length, contained marker gene sets identified by CheckM, and were >10% complete (Table 3 and Supplementary Table 1). Scaffold coverage from each metagenome was estimated using the quality-control filtered raw reads as input for mapping using Bowtie[2] version 2.2.3

Results

Conclusion