Award: OCE-1658031

Award Title: Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches
Funding Source: NSF Division of Ocean Sciences (NSF OCE)
Program Manager: David L. Garrison

Outcomes Report

The lower oceanic crust is one of the last biological frontiers for exploration of life on Earth. Samples of lower oceanic crustal rocks were obtained during IODP Expedition 360 at Atlantis Bank from Hole U1473A down to ~800 meters below the seafloor (mbsf) (Figure 1). Analyses of enzyme activities, marker genes, lipid biomarkers, and microscopy counts of cells revealed heterogeneously-distributed, ultra-low cell densities (<2000 cells/cm3), some fraction of which are active. Messenger RNA recovered from these rocks provides evidence for heterotrophic activities of bacteria, archaea and fungi, including use of polyhydroxyalkanoates as carbon storage molecules (likely under long periods of austerity), degradation of polyaromatic hydrocarbons, and recycling of different amino acids for use in redox reactions, energy production and storage. These findings all provide insights into how microorganisms are able to survive in such an inhospitable environment where sources of carbon and energy are limited. Active carbon cycling in this extensive realm is likely unevenly distributed and occurs at extremely slow rates, Nonetheless, subsurface fluid circulation connects activities in the lower crust with the deep ocean, so detected activities have implications for carbon and other nutrient cycling in the deep sea. The results of this study extend what we know as the habitable biosphere on Earth. They also have implications for our understanding of the evolution of life on Earth. Since this realm provides an analog environment for certain extraterrestrial environments, our results also provide possible biomarkers to use in future searches for life elsewhere. Analyses of lipid biomarkers reveal little accumulation of fossil material in these samples, archaeal intact polar lipids that are distinct from those observed in typical deep biosphere settings, and the presence of bacterial diether glycerol lipids. Raman spectroscopy of a sample from 182 mbsf shows filamentous inclusions of organic compounds consistent with those found in microbial cells, inter-grown with the calcite host rock, evidence of their in situ origin. Marker genes reveal low diversity microbial communities including heterotrophs and chemoautotrophic taxa, many described from dee-sea and polyextreme habitats. Significant correlations were found between detection of biomarkers/cells and the presence of veins and fractures in the host rock. Local faulting and fractures in the rocks provide conduits for the circulation of fluids through the crust at this site, providing sources of carbon and energy to sustain life, and likely cells entrained in those fluids from the seafloor. In addition to recovery of expressed genes from microbial fungi, further evidence for viable (and some fraction active) fungi comes from a collection of fungal isolates cultured from these samples, most of which are closely-related to ubiquitous terrestrial and deep-sea taxa. This project provided opportunities for participation and training of twelve individuals, including undergraduate and graduate students, postdocs, and two visiting sabbatical professors. Talks at (inter)national meetings and posters were delivered by team members, and an education and outreach program involving primary school students from under-represented communities in Texas was conducted. The outreach program provided an immersive full-day experience for these students in coastal oceanography, hands-on experience with basic oceanography sampling gear on a coastal research ship, and classroom/school visits to engage students in our research. Last Modified: 03/22/2021 Submitted by: Virginia P Edgcomb
DatasetLatest Version DateCurrent State
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
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
Supplementary Table 1: Results of CHNS analyses in rock samples at different depths and sample images.2020-05-11Final 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 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 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 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
IODP360 - Raman spectra of a core sample taken at the Atlantis Bank2021-11-08Final no updates expected

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

Co-Principal Investigator: Frieder Klein