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Recycling of Archaeal Biomass As a New Strategy for Extreme Life in Dead Sea Deep Sediments

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Recycling of Archaeal Biomass As a New Strategy for Extreme Life in Dead Sea Deep Sediments https://doi.org/10.1130/G45801.1 Manuscript received 12 November 2018 Revised manuscript received 8 March 2019 Manuscript accepted 10 March 2019 © 2019 The Authors. Gold Open Access: This paper is published under the terms of the CC-BY license. Published online 22 March 2019 Recycling of archaeal biomass as a new strategy for extreme life in Dead Sea deep sediments Camille Thomas1*, Vincent Grossi2*, Ingrid Antheaume2, and Daniel Ariztegui1 1Department of Earth Sciences, University of Geneva, Rue des Maraichers 13, 1205 Geneva, Switzerland 2Laboratoire de Géologie de Lyon, Université de Lyon, Centre National de la Recherche Scientifique (CNRS), 69622 Villeurbanne, France ABSTRACT composition of the microbial community and its Archaea and Bacteria that inhabit the deep subsurface (known as the deep biosphere) play potential metabolic strategies to survive the most a prevalent role in the recycling of sedimentary organic carbon. In such environments, this arid periods of the late Quaternary of the Dead process can occur over millions of years and requires microbial communities to cope with Sea basin, we characterized the lipid biomarker extremely limited sources of energy. Because of this scarcity, metabolic processes come at a composition of deep hypersaline halite and gyp- high energetic cost, but the ways heterotrophic microbial communities develop to minimize sum sediments. The good lipid preservation in energy expenses for a maximized yield remain unclear. Here, we report molecular biomarker these extreme horizons gives clues to metabolic evidence for the recycling of archaeal cell wall constituents in extreme evaporitic facies of pathways that allow for the survival of a thus-far- Dead Sea deep sediments. Wax esters derived from the recombination of hydrolyzed products unrecognized deep biosphere. of archaeal membrane lipids were observed in gypsum and/or halite sedimentary deposits down to 243 m below the lake floor, implying the reutilization of archaeal necromass possibly METHODS by deep subsurface bacteria. By recycling the building blocks of putatively better-adapted The material used in this study originated archaea, heterotrophic bacteria may build up intracellular carbon stocks and mitigate osmotic from the International Continental Scientific stress in this energy-deprived environment. This mechanism illustrates a new pathway of Drilling Program (ICDP) Dead Sea Deep Drill- carbon transformation in the subsurface and demonstrates how life can be maintained in ing Project (DSDDP) core 5017–1A retrieved extreme environments characterized by long-term isolation and minimal energetic resources. from the center of the Dead Sea in winter 2010–2011 (Fig. 1). Sediments were sampled INTRODUCTION (Oren, 1999a). The intracellular accumulation on site from core catchers using sterile tools In extreme environments, microbial meta- of ambient organic carbon is a common way and kept in the freezer at –20 °C until further bolic processes that lower the energetic cost of of economizing energy in harsh environments. processing. The main characteristics of samples maintaining life are favored (Hoehler and Jør- For example, under stressed growth conditions, analyzed for lipid biomarkers are given in Table gensen, 2013). Such settings are characterized some Bacteria species are known to accumu- DR1 in the GSA Data Repository1. Samples by low growth rates (Lomstein et al., 2012), and late intracellular lipid droplets (Alvarez et al., were freeze-dried, ground, and extracted using most energy is diverted to maintenance functions 1997; Wältermann and Steinbüchel, 2005) in the multiple sonication cycles (methanol 2×, metha- (van Bodegom, 2007), such as osmotic equilibra- form of polyhydroxyalkanoates, triglycerides, nol/dichloromethane [DCM] [1:1 v/v, 2×], and tion, oxygen stress defense, motility, and more or wax esters (WEs). However, the presence of DCM 3×). Elemental sulfur was removed with sustainable metabolic pathways. These selective such mechanisms in the deep biosphere has not activated copper. Lipid extracts were filtered conditions for life promote the dominance of pro- yet been documented, suggesting that they may and separated using a deactivated silica gel col- karyotes and generally favor Archaea relative to not be sufficiently effective in these low-energy umn (5% H2O) into five fractions of increasing Bacteria (Hoehler and Jørgensen, 2013). This is settings for bacteria to survive. polarity (hexane/DCM [9:1 v/v], hexane/DCM mostly due to the reduced membrane permeabil- The Dead Sea is the most saline lake on Earth [1:1 v/v], DCM, ethyl acetate, and methanol). ity of Archaea, which requires less maintenance and has deposited evaporitic minerals since the Fractions 3 and 4 were silylated with pyridine/ energy with respect to bacterial membranes early Quaternary (Stein, 2001). As a result, its bis(trimethylsilyl) trifluoroacetamide (BSTFA) (Valentine, 2007). This advantage is particu- subsurface environment constitutes one of the at 2:1 (v/v). Fraction 5 was trans-esterified by larly striking in environments characterized by most extreme ecosystems on the planet. The overnight incubation with 0.5 mL of toluene and high osmotic stress such as hypersaline environ- extreme chemistry of the water allows only for the 2 mL of 2% H2SO4 in methanol at 60 °C. Fol- ments. There, bacteria may use alternative strate- survival of halophilic archaea in the water column lowing the addition of NaCl (5%), the organic gies that allow competition with the putatively and recent halite sediments (Bodaker et al., 2010; phase was extracted with hexane:DCM (4:1 v/v, better-adapted archaea, for example, by recycling Thomas et al., 2015). Bacteria have rarely been 3×), washed with NaHCO3 (2%), and dried with available organic molecules as osmotic solutes observed in the most extreme sedimentary facies sodium sulfate before silylation. of the Dead Sea (halite or gypsum), suggesting All fractions were analyzed by gas chroma- *E-mails: camille .thomas@ unige .ch; vincent that these harsh conditions limit their growth tography mass spectrometry (GC-MS) on an HP .grossi@ univ -lyon1.fr (Thomas et al., 2015). To further investigate the 6890 Series Plus gas chromatograph equipped 1GSA Data Repository item 2019179, supplementary Figures DR1 and DR2 and Tables DR1 and DR2, is available online at http://www .geosociety .org /datarepository /2019/, or on request from editing@ geosociety .org. CITATION: Thomas, C., Grossi, V., Antheaume, I., and Ariztegui, D., 2019, Recycling of archaeal biomass as a new strategy for extreme life in Dead Sea deep sediments: Geology, v. 47, p. 479–482, https:// doi .org /10 .1130 /G45801.1 Geological Society of America | GEOLOGY | Volume 47 | Number 5 | www.gsapubs.org 479 Downloaded from http://pubs.geoscienceworld.org/gsa/geology/article-pdf/47/5/479/4680560/479.pdf by guest on 24 September 2021 depth (mblf) ARCHAEAL BACTERIAL 34° 36° O WEST 050100 150200 250300 350400 450 plasma membrane plasma membrane 32° BANK Dead Sea lithology MEDITERRANEAN (North SEA Basin) GAZA STRIP 0.6 Drilling close-up of 0.4 TOC site (%) plasma membrane 0.2 structure 31° 5017-1 0 polar head polar head 30 intact ISRAEL archaeal glycerol & phospholipids glycerol & EGYPT 20 core lipids ether linkages ester linkages (µg/g TOC) 10 JORDAN 0 core lipids 6 hydrolyzed 4 archaeal core lipids isoprenoid linear 2 (µg/g TOC) 50 km chains chains RED SEA 0 hydrolyzed Figure 1. Localization of Dead Sea cores. 0.2 isoprenoid core lipids wax esters Material used in this study originated from 0.1 (µg/g TOC) International Continental Scientific Drill- 0 ing Program (ICDP) Dead Sea Deep Drilling 10 Project (DSDDP) drilling site 5017–1. bacterial wax ester 5 fatty acids biosynthesis ratio with a cool on-column injector, and coupled to 0 ester linkage bromide an Agilent 5975C (VL MSD) mass spectrom- 0.06 concentration eter. The GC was equipped with an HP5 column 0.02 (mol.L-1) 0255075100 125150 175200 (30 m × 0.25 mm × 0.25 µm, RESTEK). Samples age (ka) WAX ESTER-PRODUCING BACTERIA were injected at 60 °C (held for 30 s), and the Figure 2. Occurrence of wax esters (WEs) and other lipid biomarkers in Dead Sea core 5017–1 oven temperature was increased to 130 °C at a (gypsum and halite intervals are shown in black; dashed lines indicate position of samples rate of 20 °C/min, then to 250 °C (5 °C/min) and analyzed). “Hydrolyzed core lipids” refer to degradation products of archaeol and extended 300 °C (3 °C/min), and finally held isothermal for archaeol, which are presented as alkyl chains. TOC—total organic carbon; mblf—meters below 45 min. Stepwise dilution of external standards lake floor. Bacterial fatty acids ratio (sum of methyl-branched C15 and C17 over sum of linear C15 and C fatty acids) indicates presence of bacteria potentially involved in WE production. Sampled allowed quantification. Isoprenoid fatty acids 17 layers are compared to bromide concentration in sediment pore waters (used as a proxy for are less polar than linear acids and partly eluted lake-water dilution/concentration; Levy et al., 2017) and fitted to 14C ages (Kitagawa et al., 2016) in fraction F4. A ratio based on specific bacte- and U/Th ages (Torfstein et al., 2015). Formation of WE building blocks is schematized on right- rial fatty acids was calculated using the sum of hand side of figure. Red items indicate an archaeal origin; blue items indicate a bacterial origin. methyl-branched C15 and C17 fatty acids over the sum of linear C15 and C17 fatty acids. Changes in so far (Wang et al., 2019). WEs are formed by sediments (Thomas et al., 2015), was also found to this ratio indicate a shift in bacterial community. condensation of fatty acids and alcohols available be enriched in halite and gypsum facies. In most Compound-specific carbon isotope (δ13C) in the environment and provide easily accessible of the sedimentary intervals where WEs occurred, analyses were done using a HP7890B GC (intracellular) sources of carbon (Wältermann archaeol and extended archaeol were found in coupled to an Isoprime visION isotope ratio mass and Steinbüchel, 2005).
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