Carbon in the Deep Biosphere: Forms, Fates, and Biogeochemical Cycling

Building on the synthesis of carbon reservoirs in Earth\u27s subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of carbon in the deep biosphere

Carbon in the Deep Biosphere: Forms, Fates, and Biogeochemical Cycling

Building on the synthesis of carbon reservoirs in Earth\u27s subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of carbon in the deep biosphere

Genomic Evidence for Formate Metabolism by as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems

The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City , but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by populations. Additionally, we present evidence for metabolically diverse, formate-utilizing populations and new genomic and phylogenetic insights into the unique Lost City Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor

14C contamination testing in natural abundance laboratories: a new preparation method using wet chemical oxidation and some experiences

Substances enriched with radiocarbon can easily contaminate samples and laboratories used for natural abundance measurements. We have developed a new method using wet chemical oxidation for swabbing laboratories and equipment to test for 14C contamination. Here, we report the findings of 18 months’ work and more than 800 tests covering studies at multiple locations. Evidence of past and current use of enriched 14C was found at all but one location and a program of testing and communication was used to mitigate its effects. Remediation was attempted with mixed success and depended on the complexity and level of the contamination. We describe four cases from different situations

Habitability of the Oceanic Alkaline Serpentinite Subsurface: A Case Study of the Lost City Hydrothermal Field

The Lost City hydrothermal field is a dramatic example of the biological potential of serpentinization. Microbial life is prevalent throughout the Lost City chimneys, powered by the hydrogen gas and organic molecules produced by serpentinization and its associated geochemical reactions. Microbial life in the serpentinite subsurface below the Lost City chimneys, however, is unlikely to be as dense or active. The marine serpentinite subsurface poses serious challenges for microbial activity, including low porosities, the combination of stressors of elevated temperature, high pH and a lack of bioavailable ∑CO2. A better understanding of the biological opportunities and challenges in serpentinizing systems would provide important insights into the total habitable volume of Earth\u27s crust and for the potential of the origin and persistence of life in Earth\u27s subsurface environments. Furthermore, the limitations to life in serpentinizing subsurface environments on Earth have significant implications for the habitability of subsurface environments on ocean worlds such as Europa and Enceladus. Here, we review the requirements and limitations of life in serpentinizing systems, informed by our research at the Lost City and the underwater mountain on which it resides, the Atlantis Massif. This article is part of a discussion meeting issue ‘Serpentinite in the Earth System’

Isotopic (δ13C, Δ14C) Analysis of Organic Acids in Marine Samples Using Wet Chemical Oxidation

We present a method for the isolation and off-line isotope analysis of formate and acetate in marine samples. Organic acids are separated by high performance liquid chromatography and collected in glass Exetainer® screw-capped vials that have been prespiked with an oxidant and flushed with helium. The vials are subsequently heated to convert the organic compounds to CO2 for radiocarbon and δ13C analysis. Small aliquots are sampled for measurement of δ13C by isotope ratio mass spectrometry, whereas the majority of the CO2 is saved for radiocarbon analysis by accelerator mass spectrometry using a gas ion source. Accurate δ13C and radiocarbon values were obtained for formate and acetate standards spiked into deep seawater and saline Milli-Q water at concentrations of 25 to 1000 µM C. The process blank associated with the isolation of formate for radiocarbon analysis was ~1.5 µg C and stable over time. Accurate results could be obtained for marine samples with only 25 µM formate. The radiocarbon analysis of acetate showed significantly higher and more variable extraneous carbon contributions, particularly for samples spiked into seawater. Potential improvements that may make the method appropriate for the radiocarbon analysis of acetate in seawater are discussed. The blanks associated with the wet chemical oxidation were assessed independently and found to be small and consistent (\u3c0.3 µg C), potentially making this approach feasible for a broader set of compounds separated by HPLC for radiocarbon analysis

An Artificial Habitat Increases the Reproductive Fitness of a Range-shifting Species within a Newly Colonized Ecosystem

When a range-shifting species colonizes an ecosystem it has not previously inhabited, it may experience suboptimal conditions that challenge its continued persistence and expansion. Some impacts may be partially mitigated by artificial habitat analogues: artificial habitats that more closely resemble a species\u27 historic ecosystem than the surrounding habitat. If conditions provided by such habitats increase reproductive success, they could be vital to the expansion and persistence of range-shifting species. We investigated the reproduction of the mangrove tree crab Aratus pisonii in its historic mangrove habitat, the suboptimal colonized salt marsh ecosystem, and on docks within the marsh, an artificial mangrove analogue. Crabs were assessed for offspring production and quality, as well as measures of maternal investment and egg quality. Aratus pisonii found on docks produced more eggs, more eggs per unit energy investment, and higher quality larvae than conspecifics in the surrounding salt marsh. Yet, crabs in the mangrove produced the highest quality larvae. Egg lipids suggest these different reproductive outcomes result from disparities in the quality of diet-driven maternal investments, particularly key fatty acids. This study suggests habitat analogues may increase the reproductive fitness of range-shifting species allowing more rapid expansion into, and better persistence in, colonized ecosystems

Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer

Hyperthermophilic methanogens are often H2 limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H2 conditions and interspecies H2 transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80 to 83 μM) and low (15 to 27 μM) aqueous H2 concentrations and in coculture with the hyperthermophilic H2 producer Thermococcus paralvinellae. The purpose was to measure changes in growth and CH4 production kinetics, CH4 fractionation, and gene expression in M. jannaschii with changes in H2 flux. Growth and cell-specific CH4 production rates of M. jannaschii decreased with decreasing H2 availability and decreased further in coculture. However, cell yield (cells produced per mole of CH4 produced) increased 6-fold when M. jannaschii was grown in coculture rather than monoculture. Relative to high H2 concentrations, isotopic fractionation of CO2 to CH4(εCO2-CH4) was 16‰ larger for cultures grown at low H2 concentrations and 45‰ and 56‰ larger for M. jannaschii growth in coculture on maltose and formate, respectively. Gene expression analyses showed H2-dependent methylene-tetrahydromethanopterin (H4MPT) dehydrogenase expression decreased and coenzyme F420-dependent methylene-H4MPT dehydrogenase expression increased with decreasing H2 availability and in coculture growth. In coculture, gene expression decreased for membrane-bound ATP synthase and hydrogenase. The results suggest that H2 availability significantly affects the CH4 and biomass production and CH4 fractionation by hyperthermophilic methanogens in their native habitats

Particulate and Dissolved Organic Matter in Stormwater Runoff Influences Oxygen Demand in Urbanized Headwater Catchments

Increasing inputs of organic matter (OM) are driving declining dissolved oxygen (DO) concentrations in coastal ecosystems worldwide. The quantity, source, and composition of OM transported to coastal ecosystems via stormwater runoff have been altered by land use changes associated with urbanization and subsequent hydrologic flows that accompany urban stormwater management. To elucidate the role of stormwater in the decline of coastal DO, rain event sampling of biochemical oxygen demand (BOD) in samples collected from the outfall of stormwater ponds and wetlands, as well as samples of largely untreated runoff carried by stormwater ditches, was conducted across a range of urban and suburban development densities. Sampling also included measurements of particulate and dissolved carbon and nitrogen, carbon and nitrogen stable isotopes, and chlorophyll-a. Results suggest stormwater may be a significant source of labile OM to receiving waters, especially during the first flush of runoff, even though BOD concentrations vary both among and within sites in response to rain events. BOD variability was best predicted by particulate OM (POM) and chlorophyll-a, rather than the larger pool of dissolved OM. These findings demonstrate the importance of managing episodic stormwater discharge, especially POM, from urbanized areas to mitigate DO impairment in larger downstream systems