Schrenk
Matthew O.
Schrenk
Matthew O.
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ArticleIdentification and removal of contaminant sequences from ribosomal gene databases : lessons from the Census of Deep Life(Frontiers Media, 2018-04-30) Sheik, Cody S. ; Kiel Reese, Brandi ; Twing, Katrina I. ; Sylvan, Jason B. ; Grim, Sharon L. ; Schrenk, Matthew O. ; Sogin, Mitchell L. ; Colwell, Frederick S.Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
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ArticleHydrogenation reactions of carbon on Earth: linking methane, margarine, and life(GeoScienceWorld, 2020-05-01) McGlynn, Shawn E. ; Glass, Jennifer B. ; Johnson-Finn, Kristin ; Klein, Frieder ; Sanden, Sebastian A. ; Schrenk, Matthew O. ; Ueno, Yuichiro ; Vitale-Brovarone, AlbertoHydrogenation reactions are a major route of electron and proton flow on Earth. Interfacing geology and organic chemistry, hydrogenations occupy pivotal points in the Earth’s global geochemical cycles. Some examples of hydrogenation reactions on Earth today include the production and consumption of methane in both abiotic and biotic reactions, the reduction of protons in hydrothermal settings, and the biological synthesis and degradation of fatty acids. Hydrogenation reactions were likely important for prebiotic chemistry on the early Earth, and today serve as one of the fundamental reaction classes that enable cellular life to construct biomolecules. An understanding and awareness of hydrogenation reactions is helpful for comprehending the larger web of molecular and material inter-conversions on our planet. In this brief review we detail some important hydrogenation and dehydrogenation reactions as they relate to geology, biology, industry, and atmospheric chemistry. Such reactions have implications ranging from the suite of reactions on early Earth to industrial applications like the production of hydrocarbon fuel.
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ArticleMetabolic strategies shared by basement residents of the lost city hydrothermal field(American Society for Microbiology, 2022-09-13) Brazelton, William J. ; McGonigle, Julia M. ; Motamedi, Shahrzad ; Pendleton, H. Lizethe ; Twing, Katrina I. ; Miller, Briggs C. ; Lowe, William J. ; Hoffman, Alessandrina M. ; Prator, Cecilia A. ; Chadwick, Grayson L. ; Anderson, Rika E. ; Thomas, Elaina ; Butterfield, David A. ; Aquino, Karmina A. ; Fruh-Green, Gretchen L. ; Schrenk, Matthew O. ; Lang, Susan Q.Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth’s mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions.
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ArticleCarbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer(American Society for Microbiology, 2020-03-10) Seyler, Lauren M. ; Brazelton, William J. ; McLean, Craig ; Putman, Lindsay I. ; Hyer, Alex ; Kubo, Michael D. Y. ; Hoehler, Tori M. ; Cardace, Dawn ; Schrenk, Matthew O.Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.
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ArticleHigh (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume(National Academy of Sciences, 2021-11-23) Bekaert, David V. ; Gazel, Esteban ; Turner, Stephen ; Behn, Mark D. ; de Moor, J. Maarten ; Zahirovic, Sabin ; Manea, Vlad C. ; Hoernle, Kaj A. ; Fischer, Tobias P. ; Hammerstrom, Alexander ; Seltzer, Alan M. ; Kulongoski, Justin T. ; Patel, Bina S. ; Schrenk, Matthew O. ; Halldórsson, Saemundur ; Nakagawa, Mayuko ; Ramírez, Carlos J. ; Krantz, John A. ; Yucel, Mustafa ; Ballentine, Christopher J. ; Giovannelli, Donato ; Lloyd, Karen G. ; Barry, Peter H.It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (>1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He >10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
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ArticleThe helium and carbon isotope characteristics of the Andean Convergent Margin(Frontiers Media, 2022-06-13) Barry, Peter H. ; de Moor, J. Maarten ; Chiodi, Agostina ; Aguilera, Felipe ; Hudak, Michael R. ; Bekaert, David V. ; Turner, Stephen ; Curtice, Joshua ; Seltzer, Alan M. ; Jessen, Gerdhard L. ; Osses, Esteban ; Blamey, Jenny M. ; Amenabar, Maximiliano J. ; Selci, Matteo ; Cascone, Martina ; Bastianoni, Alessia ; Nakagawa, Mayuko ; Filipovich, Rubén ; Bustos, Emilce ; Schrenk, Matthew O. ; Buongiorno, Joy ; Ramirez, Carlos J. ; Rogers, Timothy J. ; Lloyd, Karen G. ; Giovannelli, DonatoSubduction zones represent the interface between Earth’s interior (crust and mantle) and exterior (atmosphere and oceans), where carbon and other volatile elements are actively cycled between Earth reservoirs by plate tectonics. Helium is a sensitive tracer of volatile sources and can be used to deconvolute mantle and crustal sources in arcs; however it is not thought to be recycled into the mantle by subduction processes. In contrast, carbon is readily recycled, mostly in the form of carbon-rich sediments, and can thus be used to understand volatile delivery via subduction. Further, carbon is chemically-reactive and isotope fractionation can be used to determine the main processes controlling volatile movements within arc systems. Here, we report helium isotope and abundance data for 42 deeply-sourced fluid and gas samples from the Central Volcanic Zone (CVZ) and Southern Volcanic Zone (SVZ) of the Andean Convergent Margin (ACM). Data are used to assess the influence of subduction parameters (e.g., crustal thickness, subduction inputs, and convergence rate) on the composition of volatiles in surface volcanic fluid and gas emissions. He isotopes from the CVZ backarc range from 0.1 to 2.6 RA (n = 23), with the highest values in the Puna and the lowest in the Sub-Andean foreland fold-and-thrust belt. Atmosphere-corrected He isotopes from the SVZ range from 0.7 to 5.0 RA (n = 19). Taken together, these data reveal a clear southeastward increase in 3He/4He, with the highest values (in the SVZ) falling below the nominal range associated with pure upper mantle helium (8 ± 1 RA), approaching the mean He isotope value for arc gases of (5.4 ± 1.9 RA). Notably, the lowest values are found in the CVZ, suggesting more significant crustal inputs (i.e., assimilation of 4He) to the helium budget. The crustal thickness in the CVZ (up to 70 km) is significantly larger than in the SVZ, where it is just ∼40 km. We suggest that crustal thickness exerts a primary control on the extent of fluid-crust interaction, as helium and other volatiles rise through the upper plate in the ACM. We also report carbon isotopes from (n = 11) sites in the CVZ, where δ13C varies between −15.3‰ and −1.2‰ [vs. Vienna Pee Dee Belemnite (VPDB)] and CO2/3He values that vary by over two orders of magnitude (6.9 × 108–1.7 × 1011). In the SVZ, carbon isotope ratios are also reported from (n = 13) sites and vary between −17.2‰ and −4.1‰. CO2/3He values vary by over four orders of magnitude (4.7 × 107–1.7 × 1012). Low δ13C and CO2/3He values are consistent with CO2 removal (e.g., calcite precipitation and gas dissolution) in shallow hydrothermal systems. Carbon isotope fractionation modeling suggests that calcite precipitation occurs at temperatures coincident with the upper temperature limit for life (122°C), suggesting that biology may play a role in C-He systematics of arc-related volcanic fluid and gas emissions.
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ArticleSampling across large-scale geological gradients to study geosphere–biosphere interactions(Frontiers Media, 2022-10-31) Giovannelli, Donato ; Barry, Peter H. ; de Moor, J. Maarten ; Jessen, Gerdhard L. ; Schrenk, Matthew O. ; Lloyd, Karen G.Despite being one of the largest microbial ecosystems on Earth, many basic open questions remain about how life exists and thrives in the deep subsurface biosphere. Much of this ambiguity is due to the fact that it is exceedingly difficult and often prohibitively expensive to directly sample the deep subsurface, requiring elaborate drilling programs or access to deep mines. We propose a sampling approach which involves collection of a large suite of geological, geochemical, and biological data from numerous deeply-sourced seeps—including lower temperature sites—over large spatial scales. This enables research into interactions between the geosphere and the biosphere, expanding the classical local approach to regional or even planetary scales. Understanding the interplay between geology, geochemistry and biology on such scales is essential for building subsurface ecosystem models and extrapolating the ecological and biogeochemical roles of subsurface microbes beyond single site interpretations. This approach has been used successfully across the Central and South American Convergent Margins, and can be applied more broadly to other types of geological regions (i.e., rifting, intraplate volcanic, and hydrothermal settings). Working across geological spatial scales inherently encompasses broad temporal scales (e.g., millions of years of volatile cycling across a convergent margin), providing access to a framework for interpreting evolution and ecosystem functions through deep time and space. We propose that tectonic interactions are fundamental to maintaining planetary habitability through feedbacks that stabilize the ecosphere, and deep biosphere studies are fundamental to understanding geo-bio feedbacks on these processes on a global scale.
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ArticleHelium, inorganic and organic carbon isotopes of fluids and gases across the Costa Rica convergent margin(Nature Research, 2019-11-25) Barry, Peter H. ; Nakagawa, Mayuko ; Giovannelli, Donato ; de Moor, J. Maarten ; Schrenk, Matthew O. ; Seltzer, Alan M. ; Manini, Elena ; Fattorini, Daniele ; di Carlo, Marta ; Regoli, Francesco ; Fullerton, Katherine ; Lloyd, Karen G.In 2017, fluid and gas samples were collected across the Costa Rican Arc. He and Ne isotopes, C isotopes as well as total organic and inorganic carbon concentrations were measured. The samples (n = 24) from 2017 are accompanied by (n = 17) samples collected in 2008, 2010 and 2012. He-isotopes ranged from arc-like (6.8 RA) to crustal (0.5 RA). Measured dissolved inorganic carbon (DIC) δ13CVPDB values varied from 3.55 to −21.57‰, with dissolved organic carbon (DOC) following the trends of DIC. Gas phase CO2 only occurs within ~20 km of the arc; δ13CVPDB values varied from −0.84 to −5.23‰. Onsite, pH, conductivity, temperature and dissolved oxygen (DO) were measured; pH ranged from 0.9–10.0, conductivity from 200–91,900 μS/cm, temperatures from 23–89 °C and DO from 2–84%. Data were used to develop a model which suggests that ~91 ± 4.0% of carbon released from the slab/mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition with an additional 3.3 ± 1.3% incorporated into autotrophic biomass.