Project: Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches

Acronym/Short Name:Subseafloor Lower Crust Microbiology
Project Duration:2017-02 - 2020-01
Geolocation:SW Indian Ridge, Indian Ocean

Description

NSF abstract:

The lower ocean crust has remained largely unexplored and represents one of the last frontiers for biological exploration on Earth. Preliminary data indicate an active subsurface biosphere in samples of the lower oceanic crust collected from Atlantis Bank in the SW Indian Ocean as deep as 790 m below the seafloor. Even if life exists in only a fraction of the habitable volume where temperatures permit and fluid flow can deliver carbon and energy sources, an active lower oceanic crust biosphere would have implications for deep carbon budgets and yield insights into microbiota that may have existed on early Earth. This is all of great interest to other research disciplines, educators, and students alike. A K-12 education program will capitalize on groundwork laid by outreach collaborator, A. Martinez, a 7th grade teacher in Eagle Pass, TX, who sailed as outreach expert on Drilling Expedition 360. Martinez works at a Title 1 school with ~98% Hispanic and ~2% Native American students and a high number of English Language Learners and migrants. Annual school visits occur during which the project investigators present hands on-activities introducing students to microbiology, and talks on marine microbiology, the project, and how to pursue science related careers. In addition, monthly Skype meetings with students and PIs update them on project progress. Students travel to the University of Texas Marine Science Institute annually, where they get a campus tour and a 3-hour cruise on the R/V Katy, during which they learn about and help with different oceanographic sampling approaches. The project partially supports two graduate students, a Woods Hole undergraduate summer student, the participation of multiple Texas A+M undergraduate students, and 3 principal investigators at two institutions, including one early career researcher who has not previously received NSF support of his own.

Given the dearth of knowledge of the lower oceanic crust, this project is poised to transform our understanding of life in this vast environment. The project assesses metabolic functions within all three domains of life in this crustal biosphere, with a focus on nutrient cycling and evaluation of connections to other deep marine microbial habitats. The lower ocean crust represents a potentially vast biosphere whose microbial constituents and the biogeochemical cycles they mediate are likely linked to deep ocean processes through faulting and subsurface fluid flow. Atlantis Bank represents a tectonic window that exposes lower oceanic crust directly at the seafloor. This enables seafloor drilling and research on an environment that can transform our understanding of connections between the deep subseafloor biosphere and the rest of the ocean. Preliminary analysis of recovered rocks from Expedition 360 suggests the interaction of seawater with the lower oceanic crust creates varied geochemical conditions capable of supporting diverse microbial life by providing nutrients and chemical energy. This project is the first interdisciplinary investigation of the microbiology of all 3 domains of life in basement samples that combines diversity and "meta-omics" analyses, analysis of nutrient addition experiments, high-throughput culturing and physiological analyses of isolates, including evaluation of their ability to utilize specific carbon sources, Raman spectroscopy, and lipid biomarker analyses. Comparative genomics are used to compare genes and pathways relevant to carbon cycling in these samples to data from published studies of other deep-sea environments. The collected samples present a rare and time-sensitive opportunity to gain detailed insights into microbial life, available carbon and energy sources for this life, and of dispersal of microbiota and connections in biogeochemical processes between the lower oceanic crust and the overlying aphotic water column.

About the study area:

The International Ocean Discovery Program (IODP) Expedition 360 explored the lower crust at Atlantis Bank, a 12 Ma oceanic core complex on the ultraslow-spreading SW Indian Ridge. This oceanic core complex represents a tectonic window that exposes lower oceanic crust and mantle directly at the seafloor, and the expedition provided an unprecedented opportunity to access this habitat in the Indian Ocean.


DatasetLatest Version DateCurrent State
IODP360 - Raman spectra of a core sample taken at the Atlantis Bank2021-11-08Final no updates expected
Supplementary Table 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values2020-07-01Final no updates expected
Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes2020-06-22Final no updates expected
Supplementary Table 3A: Concentration of archaeal and bacterial lipid biomarkers, ratio of core vs intact polar lipids and average chain length of bacterial dietherglycerol lipids. 2020-06-22Final no updates expected
Supplementary Table 3B: Replicate cell counts for the 11 samples and alkaline phosphatase activity measurements available for any of the 11 samples2020-06-22Final no updates expected
Supplementary Table 4C: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data.2020-05-28Final no updates expected
Supplementary Table 2: Drill fluid contamination testiFMC in drilling. GC mass spectrometry measurements of concentrations of the tracers PFMD and Png fluid and sample materials2020-05-12Final no updates expected
Supplementary Table 1: Results of CHNS analyses in rock samples at different depths and sample images.2020-05-11Final no updates expected
Diversity of archaeal intact polar lipids (IPLs) and changes in relative abundance of bacterial dietherglycerol lipids (DEGs) within the selected 11 samples at different depths2020-02-28Data not available
Archaeal core lipids, intact polar lipids (IPLs), and bacterial dietherglycerol (DEG) lipids in the drilling mud, subsampled from whole round core 29R3 and selected rock samples.2020-02-28Data not available
Relative abundances of the diether lipid archaeol and tetraether lipids with zero, one, two and three rings and crenarchaeol from rock samples at different depths.2020-02-12Data not available

People

Lead Principal Investigator: Virginia P. Edgcomb
Woods Hole Oceanographic Institution (WHOI)

Principal Investigator: Jason Brent Sylvan
Texas A&M University (TAMU)

Co-Principal Investigator: Frieder Klein
Woods Hole Oceanographic Institution (WHOI)

Contact: Virginia P. Edgcomb
Woods Hole Oceanographic Institution (WHOI)


Programs

International Ocean Discovery Program [IODP]


Data Management Plan

DMP_Edgcomb_Klein_Sylvan_OCE-1658031.pdf (293.38 KB)
02/09/2025