Created January 28, 2016
Modified August 19, 2016
State Preliminary and in progress
Brief Description

454 pyrotag sequencing of 16S rRNA genes from the Juan de Fuca Ridge.

Acquisition Description

Twelve igneous minerals and glasses were incubated in 3.5 my old basaltic crust in three flow cells (Smith et al., 2011). Each flow cell was connected to an osmotic pump that ensured continuous fluid flow (~ 30 mL per year) for the duration of the experiment (4 years total). Each flow cell contained four mineral chambers arranged in sequence through which fluid flowed. Each chamber contained only one mineral. In the first flow cell, fluid flowed through chambers containing forsterite, Fo90 olivine, fayalite, and then hornblende. The sequence of minerals in the second flow cell was basalt glass, obsidian, augite, and then diopside. In the third flow cell, fluid flowed from anorthite to bytownite, orthoclase, then apatite (Smith et al., 2011).

Each flow cell-pump assembly was placed into IODP Hole 1301A (47 45.210’N, 127 45.833’W) between 275 and 287 meters below sea floor (Smith et al., 2011). Hole 1301A was emplaced in oceanic crust at 2667 meters below sea level and has a CORK (Fisher et al., 2005) designed to seal the observatory system at the seafloor and allow the aquifer to return to native conditions after drilling and CORK insertion. During the first three years of the incubation, bottom seawater leaked into the observatory and mixed with aquifer fluids, providing a cooler, more oxidant-rich environment for aquifer communities (Wheat et al., 2010). In the fourth year of incubation, seawater entrainment became undetectable and the mineral samples were exposed to fluids characteristic of the natural basement aquifer (Wheat et al., 2010). Minerals were retrieved in August 2008 and frozen at – 40 degrees C until extraction with a FastDNA Spin Kit for Soil.

Smith A, Popa R, Fisk M, Nielsen M, Wheat CG, Jannasch HW, et al. 2011. In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device. Geochemistry Geophys Geosystems 12:1–19. doi:10.1029/2010GC003424

Fisher AT, Wheat CG, Becker K, Davis EE, Jannasch H, Schroeder D, et al. 2005. Scientific and technical design and deployment of long-term subseafloor observatories for hydrogeologic and related experiments , IODP Expedition 301 , eastern flank of Juan de Fuca Ridge 1 and general design. Proc Integr Ocean Drill Progr 301. doi:10.2204/iodp.proc.301.103.2005

Wheat CG, Jannasch HW, Fisher AT, Becker K, Sharkey J, Hulme S. 2010. Subseafloor seawater-basalt-microbe reactions: Continuous sampling of borehole fluids in a ridge flank environment. Geochemistry Geophys Geosystems 11:1–18. doi:10.1029/2010GC003057

Processing Description

V4 region 16S rRNA gene amplicons were produced using universal primers for bacteria and archaea and sequenced using 454 FLX pyrosequencing technologies. 



Dataset Maintainers

Radu PopaUniversity of Southern California (USC)
Martin R. FiskUniversity of Southern California (USC)
Gilberto E. FloresOregon State University (OSU-CEOAS)
Amy R. SmithOregon State University (OSU-CEOAS)
Shannon RauchCalifornia State University Northridge (CSU-Northridge)
Shannon RauchCalifornia State University Northridge (CSU-Northridge)
Amy R. SmithOregon State University (OSU-CEOAS)
Amy R. SmithOregon State University (OSU-CEOAS)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Genetic diversity and distribution of microbes colonizing igneous minerals and glasses incubated in IODP Hole 1301A on the eastern flank of the Juan de Fuca Ridge
Acronym Microbe Diversity & Distribution JdFR
Created January 25, 2016
Modified January 25, 2016
Project Description

Project description from C-DEBI:
The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge (JFR) was used as a long term sub-seafloor microbial observatory to determine microbial colonization preferences for twelve silicate minerals and glasses common in igneous rocks. Previous work revealed significant differences in total cell densities, with iron-bearing olivine minerals maintaining the highest densities of total cells, culturable organotrophic mesophiles, and the only culturable organotrophic thermophiles. Since 90% of identified culturable strains were able to oxidize iron in the laboratory, we hypothesized that iron-bearing minerals would support distinct communities from iron-poor minerals. Since most organisms are unculturable, inferences about differences in complexity between microbial communities colonizing minerals could best be made using high-throughput sequencing. We proposed to use 454 pyrosequencing and sequence analysis of the hypervariable V4 region of the SSU rRNA gene for bacteria and archaea using genomic DNA extracted from our mineral samples to test our hypothesis.

Through this work, we found that mineralogy of the crust governed attached community assemblages, diversity, and distribution in deep ocean crust. We discovered that the olivine group of minerals had communities that were unique among igneous minerals and that they were the most diverse. Communities from iron-bearing minerals were more similar to each other than communities from iron-poor minerals, indicating there is an iron-related compositional influence on community development. We compared mineral communities to surrounding aquifer fluid and bottom seawater and found that attached communities differed considerably from their free-living counterparts. Our hypothesis was validated through this work, and the results have significantly increased our understanding of how mineralogy controls micro-scale diversity within igneous rocks. This work has allowed us a glimpse into ecosystem function in the largest habitat on Earth, and will allow us to better model reactive transport, weathering, and biogeochemical cycling in the ocean crust.

Data Project Maintainers
Radu PopaUniversity of Southern California (USC)Lead Principal Investigator
Martin R. FiskOregon State University (OSU-CEOAS)Co-Principal Investigator
Gilberto E. FloresCalifornia State University Northridge (CSU-Northridge)Co-Principal Investigator
Amy R. SmithOregon State University (OSU-CEOAS)Co-Principal Investigator