Deep Marine Subsurface Eukaryotes

Marine sediments cover more than two thirds of the Earth’s surface and have been estimated to contain as much as one-third of Earth’s prokaryotic biomass (Whitman et al., 1998). Despite this, relatively little is known about this deep biosphere, and essentially nothing is known about the presence of microbial eukaryotes in sediments deeper than a few centimeters. Through consumption of dissolved organic matter and by selective grazing in subsurface horizons where bacterial and/or archaeal numbers are high, protists and/ or fungi may significantly impact carbon and other nutrient cycling in the marine subsurface.

The first analyses of eukaryotic small subunit ribosomal RNA gene (18S rRNA) sequences obtained from deep marine subsurface sediments, the first metagenome, and a cultivation study based on those samples show that fungi dominate eukaryotic life in the buried marine subsurface. Novel fungi continue to be reported from deep marine environments, and and there is fossil evidence of filamentous structures highly suggestive of fungi within carbonate-filled vesicles within the upper oceanic crust. In collaboration with J. Biddle at U.Del, and A. Teske at UNC Chapel Hill, our group used RNA-based approaches to show that fungi are metabolically active in deep subsurface sediment cores. With collaborator Gaetan Burgaud at University of Brest, France, and his postdoc Vanessa Redou we provided a more detailed understanding of the metabolic activities of fungi in marine subsurface sediment cores from various geographic locations using marker genes, metatranscriptome analyses, culture studies, and analysis of metabolic activities of cultured isolates from several oceanic provinces.

Our laboratory led and published the first in-depth investigation of the microbiology of the lower ocean crust using samples collected through the International Ocean Discovery Program (IODP) Expedition 360 from Atlantis Bank, Indian Ocean. In collaboration with Gaetan Burgaud and Maxence Quemener from University of Brest, France, we published the first study of fungal diversity in lower crust samples. The collection of fungal isolates from this study is the subject of ongoing work to search for unique bio signatures of these fungi in collaboration with Florence Schubotz, University of Bremen.

A current study is exploring the thermal limits and the hydrocarbon degradation potential of marine fungi isolated from sediment cores collected from Guaymas Basin hydrothermal vents. This study is combining nutrient and hydrocarbon profiling with marker gene, metatranscriptome, and culture-based studies. New samples from IODP Expedition 385 were collected in 2019 from the deep subsurface below different hydrothermal vent sites in Guaymas Basin as well as cool basin margin sites. We hope to study the distribution of microbiota along temperature and depth profiles as well as the hydrocarbon degradation potential of final isolates.