Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.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.We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses

Hydrogenation reactions of carbon on Earth: Linking methane, margarine, and life

Hydrogenation 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 implica- tions ranging from the suite of reactions on early Earth to industrial applications like the production of hydrocarbon fuel

How to share underground reservoirs

Many resources, such as oil, gas, or water, are extracted from porous soils and their exploration is often shared among different companies or nations. We show that the effective shares can be obtained by invading the porous medium simultaneously with various fluids. Partitioning a volume in two parts requires one division surface while the simultaneous boundary between three parts consists of lines. We identify and characterize these lines, showing that they form a fractal set consisting of a single thread spanning the medium and a surrounding cloud of loops. While the spanning thread has fractal dimension ${1.55\pm0.03}$, the set of all lines has dimension ${1.69\pm0.02}$. The size distribution of the loops follows a power law and the evolution of the set of lines exhibits a tricritical point described by a crossover with a negative dimension at criticality

Subsurface life can modify volatile cycling on a planetary scale

The past decade of environmental microbiology has revealed that subsurface environments, both marine and continental, harbor one of the largest ecosystems of our planet, with diversity and biomass rivaling those of the surface. In addition, subsurface life has been recently shown to contribute significantly to the planet’s biogeochemistry, with microbial activity potentially playing an important role in controlling the flux and composition of volatiles recycled between the Earth’s surface and interior, which has broad implications for the search for life beyond our planet. Current efforts to discover extraterrestrial life are focused on planetary bodies with largely inhospitable surfaces, such as Mars, Venus, Europa, Titan, and Enceladus. In these locations, subsurface environments might provide niches of habitability, making the study of deep microbial life a priority for future astrobiological missions. Understanding how volatile elements are exchanged between planetary surfaces and interiors and the role of a subsurface biosphere in altering their composition and flux might provide a tractable target for defining planetary habitability and the detection of subsurface life forms.Fil: Giovanelli, D.. Università degli Studi di Napoli Federico II; Italia. Tokyo Institute of Technology; Japón. Rutgers University; Estados Unidos. Consiglio Nazionale delle Ricerche; Italia. Woods Hole Oceanographic Institution; Estados UnidosFil: Barry, P. H.. Woods Hole Oceanographic Institution; Estados UnidosFil: Bekaert, D. V.. Woods Hole Oceanographic Institution; Estados UnidosFil: Chiodi, Agostina Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Cordone, A.. Università degli Studi di Napoli Federico II; ItaliaFil: Covone, G.. Università degli Studi di Napoli Federico II; Italia. Istituto Nazionale di Astrofisica; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Jessen, G.. Universidad Austral de Chile; ChileFil: Lloyd, K.. University of Tennessee; Estados UnidosFil: de Moor, J. M.. Universidad Nacional; Costa RicaFil: Morrison, S. M.. Carnegie Institution For Science; Estados UnidosFil: Schrenk, M. O.. Michigan State University; Estados UnidosFil: Vitale Brovarone, A.. Alma Mater Studiorum Universit`a Di Bologna; Italia. Sorbonne University; Francia. Museum National d’Histoire Naturelle; Franci

Fracturing ranked surfaces

Discretized landscapes can be mapped onto ranked surfaces, where every element (site or bond) has a unique rank associated with its corresponding relative height. By sequentially allocating these elements according to their ranks and systematically preventing the occupation of bridges, namely elements that, if occupied, would provide global connectivity, we disclose that bridges hide a new tricritical point at an occupation fraction $p=p_{c}$, where $p_{c}$ is the percolation threshold of random percolation. For any value of $p$ in the interval $p_{c}< p \leq 1$, our results show that the set of bridges has a fractal dimension $d_{BB} \approx 1.22$ in two dimensions. In the limit $p \rightarrow 1$, a self-similar fracture is revealed as a singly connected line that divides the system in two domains. We then unveil how several seemingly unrelated physical models tumble into the same universality class and also present results for higher dimensions

Impacts of deep-sea mining on microbial ecosystem services

© 2020 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography. Interest in extracting mineral resources from the seafloor through deep-sea mining has accelerated in the past decade, driven by consumer demand for various metals like zinc, cobalt, and rare earth elements. While there are ongoing studies evaluating potential environmental impacts of deep-sea mining activities, these focus primarily on impacts to animal biodiversity. The microscopic spectrum of seafloor life and the services that this life provides in the deep sea are rarely considered explicitly. In April 2018, scientists met to define the microbial ecosystem services that should be considered when assessing potential impacts of deep-sea mining, and to provide recommendations for how to evaluate and safeguard these services. Here, we indicate that the potential impacts of mining on microbial ecosystem services in the deep sea vary substantially, from minimal expected impact to loss of services that cannot be remedied by protected area offsets. For example, we (1) describe potential major losses of microbial ecosystem services at active hydrothermal vent habitats impacted by mining, (2) speculate that there could be major ecosystem service degradation at inactive massive sulfide deposits without extensive mitigation efforts, (3) suggest minor impacts to carbon sequestration within manganese nodule fields coupled with potentially important impacts to primary production capacity, and (4) surmise that assessment of impacts to microbial ecosystem services at seamounts with ferromanganese crusts is too poorly understood to be definitive. We conclude by recommending that baseline assessments of microbial diversity, biomass, and, importantly, biogeochemical function need to be considered in environmental impact assessments of deep-sea mining

Deeply-Sourced Formate Fuels Sulfate Reducers but Not Methanogens at Lost City Hydrothermal Field

Hydrogen produced during water-rock serpentinization reactions can drive the synthesis of organic compounds both biotically and abiotically. We investigated abiotic carbon production and microbial metabolic pathways at the high energy but low diversity serpentinite-hosted Lost City hydrothermal field. Compound-specific 14C data demonstrates that formate is mantle-derived and abiotic in some locations and has an additional, seawater-derived component in others. Lipids produced by the dominant member of the archaeal community, the Lost City Methanosarcinales, largely lack 14C, but metagenomic evidence suggests they cannot use formate for methanogenesis. Instead, sulfate-reducing bacteria may be the primary consumers of formate in Lost City chimneys. Paradoxically, the archaeal phylotype that numerically dominates the chimney microbial communities appears ill suited to live in pure hydrothermal fluids without the co-occurrence of organisms that can liberate CO2. Considering the lack of dissolved inorganic carbon in such systems, the ability to utilize formate may be a key trait for survival in pristine serpentinite-hosted environments

The Helium and Carbon Isotope Characteristics of the Andean Convergent Margin

Subduction 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.Fil: Barry, P. H.. Woods Hole Oceanographic Institution; Estados UnidosFil: De Moor, J. M.. University of New Mexico; Estados Unidos. UNIVERSIDAD NACIONAL DE COSTA RICA (UNA);Fil: Chiodi, Agostina Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Aguilera, F.. Universidad Católica del Norte; ChileFil: Hudak, M. R.. Woods Hole Oceanographic Institution; Estados UnidosFil: Bekaert, D. V.. Woods Hole Oceanographic Institution; Estados UnidosFil: Turner, S. J.. University of Massachussets; Estados UnidosFil: Curtice, J.. Woods Hole Oceanographic Institution; Estados UnidosFil: Seltzer, A. M.. Woods Hole Oceanographic Institution; Estados UnidosFil: Jessen, G. L.. Universidad Austral de Chile; ChileFil: Osses, E.. Universidad Austral de Chile; ChileFil: Blamey, J. M.. Universidad de Santiago de Chile; ChileFil: Amenábar, M. J.. Universidad de Santiago de Chile; ChileFil: Selci, M.. University Of Naples Federico Ii; ItaliaFil: Cascone, M.. University Of Naples Federico Ii; ItaliaFil: Bastianoni, A.. University Of Naples Federico Ii; ItaliaFil: Nakagawa, M.. Tokyo Institute Of Technology; JapónFil: Filipovich, Ruben Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Bustos, Emilce. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Schrenk, M. O.. Michigan State University; Estados UnidosFil: Buongiorno, J.. Maryville College; Estados UnidosFil: Ramírez, C. J.. Servicio Geológico Ambiental (segeoam); Costa RicaFil: Rogers, T. J.. University of Tennessee; Estados UnidosFil: Lloyd, K. G.. University of Tennessee; Estados UnidosFil: Giovannelli, D.. Institute Of Marine Biological Resources And Biotechno; Itali

On Component Forces in Physics: A Pragmatic View

Do component forces exist? I argue that the answer lies in the affirmative, on historical and operational grounds

Axillary sentinel lymph node biopsy after mastectomy: a case report

<p>Abstract</p> <p>Background</p> <p>Sentinel lymph node biopsy has been established as the preferred method for staging early breast cancer. A prior history of mastectomy is felt to be a contraindication.</p> <p>Case presentation</p> <p>A patient with recurrent breast cancer in her skin flap was discovered to have positive axillary sentinel nodes by sentinel lymph node biopsy five years after mastectomy for ductal carcinoma in situ.</p> <p>Conclusion</p> <p>A prior history of mastectomy may not be an absolute contraindication to sentinel lymph node biopsy.</p