Person: Stephanie A. Carr

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Abstract

The exploration of Earth’s terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage’s evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Abstract

Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica’s Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ¹³C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ¹³C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.

Abstract

Thanks to C-DEBI’s generous travel support, I traveled to the Joint Genome Institute (JGI) to attend a Microbial Dark Matter (MDM) Meeting and a workshop entitled, “New Lineages of Life” (NeLLi) in April 2017. Both events were focused on JGI’s initiative to characterize yet-to-be-cultivated organisms using single-cell and metagenomic sequencing techniques. Currently, I am working to describe the functional potential of an uncultured archaeal lineage sampled from the Juan de Fuca ridge flank (a project that relates to C-DEBI research theme 2: Activities, Communities, and Ecosystems), and thus most of the content presented throughout the week was applicable to my work. Attending these events allowed me to see how other investigators were approaching the characterization of other new lineages. I was introduced to new open source software and databases (for example, the Genome Taxonomy Database, [http://gtdb.ecogenomic.org, unpublished], GREMLIN, a protein modeling program [http://gremlin.bakerlab.org/index.php] and Data2, a new amplicon pipeline, [https://github.com/benjjneb/dada2]). Being at the NeLLi workshop also gave me the opportunity to meet with my JFR collaborators and share my recent progress. Together we developed a plan for future work and manuscript submission. Additionally, these events provided me with a great networking opportunity, allowing me to meet other scientists with similar interests.

Acquisition Description

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BCO-DMO Project Info

Project Description

Data Project Maintainers

Acquisition Description

Processing Description

Instruments

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Dataset Maintainers

BCO-DMO Project Info

Project Description

Data Project Maintainers

Project Description

Data Project Maintainers

Abstract

Bacteria belonging to the newly classified candidate phylum “Atribacteria” (formerly referred to as “OP9” and “JS1”) are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. In this study of deep sediment from Antarctica’s Adélie Basin, collected during Expedition 318 of the Integrated Ocean Drilling Program (IODP), Atribacteria-related sequences of the 16S rRNA gene were abundant (up to 51% of the sequences) and steadily increased in relative abundance with depth throughout the methane-rich zones. To better understand the metabolic potential of Atribacteria within this environment, and to compare with phylogenetically distinct Atribacteria from non-deep-sea environments, individual cells were sorted for single cell genomics from sediment collected from 97.41 m below the seafloor from IODP Hole U1357C. As observed for non-marine Atribacteria, a partial single cell genome suggests a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol, and CO₂. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments. This first report of a single cell genome from deep sediment broadens the known diversity within the Atribacteria phylum and highlights the potential role of Atribacteria in carbon cycling in deep sediment.

Abstract

A cruise is scheduled for December 5-23, 2013 to visit the Dorado Outcrop, a new Major Program focus site of C-DEBI, with Geoff Wheat from the University of Alaska, Fairbanks as Chief Scientist. I have been given the opportunity to participate aboard this expedition as a shipboard microbiologist. In collaboration with the microbiology team (lead by Dr. B. Orcutt), I will part take in routine microbial and geochemical analyses, which will contribute to the following primary expedition objectives: To determine the ecological and biogeochemical nature of microbial communities in cool crustal fluids from the Dorado Outcrop, and determine the degree to which the communities and chemistry vary by comparison to ridge axis systems; and to determine the influence of cool crustal fluid circulation on sediment and hard-rock microbial ecology and biogeochemistry. These objectives will be further fulfilled post-expedition by various shore-based scientists, using samples that I will help to collect and preserve onboard. As a shipboard scientist, I am also entitled to, and responsible for, contributing to post-expedition research. My specific research plan is to employ single cell genomic techniques to identify the biogeochemical potential of uncultivable heterotrophic organisms present within aerobic marine sediment of the Dorado Outcrop. Revealing the potential functions and life requirements of uncultured organisms will greatly benefit our understanding of elemental cycling in the marine subsurface biosphere.

Abstract

Bacteria belonging to the newly classified candidate phylum “Atribacteria” (formerly referred to as “OP9” and “JS1”) are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. In this study of deep sediment from Antarctica’s Adélie Basin, collected during Expedition 318 of the Integrated Ocean Drilling Program (IODP), Atribacteria-related sequences of the 16S rRNA gene were abundant (up to 51% of the sequences) and steadily increased in relative abundance with depth throughout the methane-rich zones. To better understand the metabolic potential of Atribacteria within this environment, and to compare with phylogenetically distinct Atribacteria from non-deep-sea environments, individual cells were sorted for single cell genomics from sediment collected from 97.41 meters below the seafloor from IODP Hole U1357C. As observed for non-marine Atribacteria, a partial single cell genome suggests a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol and CO₂. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments. This first report of a single cell genome from deep sediment broadens the known diversity within the Atribacteria phylum and highlights the potential role of Atribacteria in carbon cycling in deep sediment.