Habitability Models for Astrobiology
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Where Less May Be More: How the Rare Biosphere Pulls Ecosystems Strings
The ISME Journal (2017) 11, 853–862 OPEN © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej MINI REVIEW Where less may be more: how the rare biosphere pulls ecosystems strings Alexandre Jousset1, Christina Bienhold2,3, Antonis Chatzinotas4,5, Laure Gallien6,7, Angélique Gobet8, Viola Kurm9, Kirsten Küsel10,5, Matthias C Rillig11,12, Damian W Rivett13, Joana F Salles14, Marcel GA van der Heijden15,16,17, Noha H Youssef18, Xiaowei Zhang19, Zhong Wei20 and WH Gera Hol9 1Utrecht University, Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Utrecht, The Netherlands; 2Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; 3Max Planck Institute for Marine Microbiology, Bremen, Germany; 4Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany; 5German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany; 6Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland; 7Center for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Matieland, South Africa; 8Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688, Roscoff Cedex, France; 9Netherlands Institute of Ecology, Department of Terrestrial Ecology, Wageningen, The Netherlands; 10Friedrich Schiller University Jena, Institute of Ecology, Jena, Germany; 11Freie Universtät Berlin, -
Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities
Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities Juan M. Gonzalez1*, Maria C. Portillo1, Pedro Belda-Ferre2, Alex Mira2 1 Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Sevilla, Spain, 2 Genomics and Health Department, Center for Advanced Research in Public Health (CSISP), Valencia, Spain Abstract The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the ‘rare biosphere’. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature. Citation: Gonzalez JM, Portillo MC, Belda-Ferre P, Mira A (2012) Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities. -
Prebiotic Chemistry, Origin, and Early Evolution of Life
Say what you are going to say, say it, say what you said Guiding theory Richard Feynman Polyelectrolytes with uniform structure are universal for Darwinism A specific hypothesis to provide context The polyelectrolyte that supported Earth’s first Darwinism was RNA Focus on paradoxes to constrain human self-deception "Settled science" says that RNA is impossible to form prebiotically Strategies for paradox resolution Mineral-guided processes allow RNA to form nonetheless Natural history context The needed chemistry-mineral combination was transient on Earth Your reward A relatively simple path to form RNA prebiotically A relatively narrow date when life on Earth originated prebiotically A clear statement of the next round of paradoxes Elisa Biondi, Hyo-Joong Kim, Daniel Hutter, Clemens Richert, Stephen Mojzsis, Ramon Brasser, Dustin Trail, Kevin Zahnle, David Catling, Rob Lavinsky Say what you are going to say, say it, say what you said Guiding theory Richard Feynman Polyelectrolytes with uniform structure are universal for Darwinism A specific hypothesis to provide context The polyelectrolyte that supported Earth’s first Darwinism was RNA Focus on paradoxes to constrain human self-deception "Settled science" says that RNA is impossible to form prebiotically Strategies for paradox resolution Mineral-guided processes allow RNA to form nonetheless Natural history context The needed chemistry-mineral combination was transient on Earth Your reward A relatively simple path to form RNA prebiotically A relatively narrow date when life on Earth originated prebiotically A clear statement of the next round of paradoxes Elisa Biondi, Hyo-Joong Kim, Daniel Hutter, Clemens Richert, Stephen Mojzsis, Ramon Brasser, Dustin Trail, Kevin Zahnle, David Catling, Rob Lavinsky What does a repeating backbone charge do for informational molecule? O 1. -
Snowball Earth: a Thin-Ice Solution with Flowing Sea Glaciers’’ by David Pollard and James F
JOURNAL OF GEOPHYSICAL RESEARCH, VOL. 111, C09016, doi:10.1029/2005JC003411, 2006 Click Here for Full Article Comment on ‘‘Snowball Earth: A thin-ice solution with flowing sea glaciers’’ by David Pollard and James F. Kasting Stephen G. Warren1,2 and Richard E. Brandt1 Received 22 November 2005; revised 22 May 2006; accepted 9 June 2006; published 14 September 2006. Citation: Warren, S. G., and R. E. Brandt (2006), Comment on ‘‘Snowball Earth: A thin-ice solution with flowing sea glaciers’’ by David Pollard and James F. Kasting, J. Geophys. Res., 111, C09016, doi:10.1029/2005JC003411. 1. Introduction 2. Choices of Model Variables That Favor [1] Pollard and Kasting [2005] (hereinafter referred to as Thin Ice PK) have coupled an energy-balance climate model to an 2.1. Albedo of Cold Glacier Ice ice-shelf flow model, to investigate the Snowball Earth [2] As sea glaciers flowed equatorward into the tropical episodes of the Neoproterozoic, 600–800 million years region of net sublimation, their surface snow and subsurface ago, when the ocean apparently froze all the way to the firn would sublimate away, exposing bare glacier ice to equator [Hoffman and Schrag, 2002]. PK’s particular con- the atmosphere and solar radiation. This ice would be cern was to investigate the possibility that over a wide freshwater (meteoric) ice, which originated from compres- equatorial band where sublimation exceeded snowfall, the sion of snow, so it would contain numerous bubbles, giving bare ice may have been thin enough to permit transmission a high albedo. The albedo of cold (nonmelting) glacier ice of sunlight to the water below, providing an extensive exposed by sublimation (Antarctic ‘‘blue ice’’) has been refugium for the photosynthetic eukaryotes that survived measured as 0.55–0.65 in four experiments in the Atlantic the Snowball events. -
Westminsterresearch the Astrobiology Primer V2.0 Domagal-Goldman, S.D., Wright, K.E., Adamala, K., De La Rubia Leigh, A., Bond
WestminsterResearch http://www.westminster.ac.uk/westminsterresearch The Astrobiology Primer v2.0 Domagal-Goldman, S.D., Wright, K.E., Adamala, K., de la Rubia Leigh, A., Bond, J., Dartnell, L., Goldman, A.D., Lynch, K., Naud, M.-E., Paulino-Lima, I.G., Kelsi, S., Walter-Antonio, M., Abrevaya, X.C., Anderson, R., Arney, G., Atri, D., Azúa-Bustos, A., Bowman, J.S., Brazelton, W.J., Brennecka, G.A., Carns, R., Chopra, A., Colangelo-Lillis, J., Crockett, C.J., DeMarines, J., Frank, E.A., Frantz, C., de la Fuente, E., Galante, D., Glass, J., Gleeson, D., Glein, C.R., Goldblatt, C., Horak, R., Horodyskyj, L., Kaçar, B., Kereszturi, A., Knowles, E., Mayeur, P., McGlynn, S., Miguel, Y., Montgomery, M., Neish, C., Noack, L., Rugheimer, S., Stüeken, E.E., Tamez-Hidalgo, P., Walker, S.I. and Wong, T. This is a copy of the final version of an article published in Astrobiology. August 2016, 16(8): 561-653. doi:10.1089/ast.2015.1460. It is available from the publisher at: https://doi.org/10.1089/ast.2015.1460 © Shawn D. Domagal-Goldman and Katherine E. Wright, et al., 2016; Published by Mary Ann Liebert, Inc. This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License (http://creativecommons.org/licenses/by- nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. The WestminsterResearch online digital archive at the University of Westminster aims to make the research output of the University available to a wider audience. -
The Rare Bacterial Biosphere
MA04CH18-Pedros-Alio ARI 3 November 2011 17:43 The Rare Bacterial Biosphere Carlos Pedros-Ali´ o´ Institut de Ciencies` del Mar, CSIC, 08003 Barcelona, Spain; email: [email protected] Annu. Rev. Mar. Sci. 2012. 4:449–66 Keywords First published online as a Review in Advance on bacterial diversity, next-generation sequencing, dispersal, dormancy, loss September 19, 2011 mechanisms The Annual Review of Marine Science is online at marine.annualreviews.org Abstract This article’s doi: All communities are dominated by a few species that account for most of the 10.1146/annurev-marine-120710-100948 biomass and carbon cycling. On the other hand, a large number of species Copyright c 2012 by Annual Reviews. are represented by only a few individuals. In the case of bacteria, these rare All rights reserved species were until recently invisible. Owing to their low numbers, conven- 1941-1405/12/0115-0449$20.00 tional molecular techniques could not retrieve them. Isolation in pure culture was the only way to identify some of them, but current culturing techniques Annu. Rev. Marine. Sci. 2012.4:449-466. Downloaded from www.annualreviews.org are unable to isolate most of the bacteria in nature. The recent development by CSIC - Consejo Superior de Investigaciones Cientificas on 12/19/11. For personal use only. of fast and cheap high-throughput sequencing has begun to allow access to the rare species. In the case of bacteria, the exploration of this rare bio- sphere has several points of interest. First, it will eventually produce a reason- able estimate of the total number of bacterial taxa in the oceans; right now, we do not even know the right order of magnitude. -
1 Marine Microbial Diversity and Genomics Frank Oliver Glöckner Seas and Oceans Cover Over 70% of the Earth's Surface And
Marine Microbial Diversity and Genomics Frank Oliver Glöckner Seas and oceans cover over 70% of the Earth’s surface and account for 97 percent of the biosphere. Marine ecosystems provide energy resources, and the basis for maritime transport, and recreation. The oceans contain the highest biological diversity on Earth; marine organisms live throughout the water column, to an extreme depth of up to 11 km, and in ocean sediments up to a further 400 mbelow the seafloor. Marine microorganisms in particular play a central role in the global cycling of matters and energy, for they are both a driver and indicator of global climate change. Furthermore, they are an inevitable genetic resource for new enzymes and reactions which can be used for pharmaceutical and industrial applications. Current estimates show that a millilitre of sea water hosts around 1 million cells. In sediments total cell numbers of up to 1 billion per gram can be reached. Microorganisms' total biomass represented as fixed carbon is currently estimated to be more than 300 gigatonnes (14). But apart from the huge total numbers, their diversity is also quite impressive. Although no exact numbers exist, our studies infer that around 1000 different active microorganisms persist per millilitre (1). Additionally, oceans act as a seed bank hosting a “rare biosphere” of hundreds of thousands of distinct microorganisms which become active in response to seasonal or environmental changes (9, 11). The more than 500 microbial genome projects carried out over the last 10 years have shown that each bacterium contributes around 4000 genes (http://www.genomesonline.org/). -
The First Billion Years: Warm and Wet Or Cold and Icy? Robert M
The First Billion Years: Warm and Wet or Cold and Icy? Robert M. Haberle Space Science and Astrobiology Division NASA/Ames Research Center July 15, 2014 Mars 8 Meeting Acknowledgements: Mike Carr, David Catling, and Kevin Zahnle Haberle, 8th Mars Conference Evidence for a Different Valley Networks Climate Isotopic Heavy Isotopes Aqueous Minerals 14N/15N 170±15 (Viking) 20Ne/22Ne ~10 (Meteorites) 36Ar/38Ar 4.2±0.2 (MSL) δ13C 46±4‰ (MSL) Elmann and Edwards (2014) 129Xe/132Xe ~ 2.5 (Viking) Haberle, 8th Mars Conference The First Billion Years Haberle, 8th Mars Conference Faint Young Sun Problem Noachian Haberle, 8th Mars Conference Atmospheric Redox and Outgassing The oxidation state of volcanic gases (principally H2/H2O) is governed by the oxidation state (fO2) of the upper mantle. During core(a) formation After core(b) formation Since core formation was fast (< 10 My), the mantle was likely weakly reducing and Outgassing products were mostly CO2, H2O, and N2 Haberle, 8th Mars Conference 1-D Calculations of Pollack et al. (1987) Main Conclusion: Early Mars was Continuously Warm and Wet - 5 bars of CO2 maintained against carbonate loss by impact recycling Haberle, 8th Mars Conference Problems With This Model Haberle, 8th Mars Conference 1. CO2 condenses in the atmosphere reducing the greenhouse effect. Latent heat release warms the upper atmosphere Kasting (1991) Haberle, 8th Mars Conference 2. Collision Induced Absorption Overestimated We now have more accurate absorption data based on theoretical and experimental data Old parameterizations overestimated induced-dipole absorption -1 in the 250-500 cm region Haberle, 8th Mars Conference Wordsworth et al. -
Habitable Zone
How to Find a Habitable Planet James Kasting Department of Geosciences Penn State University The search for other habitable worlds is ancient “There are infinite worlds both like and unlike this world of ours...”--- Epicurus (c. 300 BCE) (died painfully 269 BCE) “… false and "There are countless suns and damnable ...” countless earths …” G. Galilei (b. 1564) Giordano Bruno (b. 1584) in De L'infinito Universo E Mondi From Mike Devirian, (life imprisonment JPL (burned at the stake in Campo 1633) dei Fiore, Rome, 1600) • Even today, opinions differ widely as to whether other Earth-like planets exist… The Gaia hypothesis First presented in the 1970s by James Lovelock 1979 1988 http://www.ecolo.org/lovelock Gaia—The Greek goddess • According to this hypothesis, life creates and maintains conditions for its own existence by stabilizing Earth’s climate and other aspects of the Earth system • If this idea is correct, then only planets that are already inhabited would be habitable http://www.paleothea.com/Majors.html The Medea and Rare Earth hypotheses Peter Ward 2009 2000 Medea hypothesis: Life is harmful to the Earth! Rare Earth hypothesis: Complex life (animals, including humans) is rare in the universe The latest addition to this literature Me My new book (Princeton University Press, 2010) • As you will see, I am more optimistic than either Peter Ward or Jim Lovelock Talk outline • Introduction (which you heard already) • Part 1: What makes Earth unique, and what is life? • Part 2: Can we find Earth-like planets around other stars, and can -
NASA Astrobiology Institute 2018 Annual Science Report
A National Aeronautics and Space Administration 2018 Annual Science Report Table of Contents 2018 at the NAI 1 NAI 2018 Teams 2 2018 Team Reports The Evolution of Prebiotic Chemical Complexity and the Organic Inventory 6 of Protoplanetary Disk and Primordial Planets Lead Institution: NASA Ames Research Center Reliving the Past: Experimental Evolution of Major Transitions 18 Lead Institution: Georgia Institute of Technology Origin and Evolution of Organics and Water in Planetary Systems 34 Lead Institution: NASA Goddard Space Flight Center Icy Worlds: Astrobiology at the Water-Rock Interface and Beyond 46 Lead Institution: NASA Jet Propulsion Laboratory Habitability of Hydrocarbon Worlds: Titan and Beyond 60 Lead Institution: NASA Jet Propulsion Laboratory The Origins of Molecules in Diverse Space and Planetary Environments 72 and Their Intramolecular Isotope Signatures Lead Institution: Pennsylvania State University ENIGMA: Evolution of Nanomachines in Geospheres and Microbial Ancestors 80 Lead Institution: Rutgers University Changing Planetary Environments and the Fingerprints of Life 88 Lead Institution: SETI Institute Alternative Earths 100 Lead Institution: University of California, Riverside Rock Powered Life 120 Lead Institution: University of Colorado Boulder NASA Astrobiology Institute iii Annual Report 2018 2018 at the NAI In 2018, the NASA Astrobiology Program announced a plan to transition to a new structure of Research Coordination Networks, RCNs, and simultaneously planned the termination of the NASA Astrobiology Institute -
Ultradeep Microbial Communities at 4.4 Km Within Crystalline Bedrock: Implications for Habitability in a Planetary Context
life Article Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context Lotta Purkamo 1,2,* , Riikka Kietäväinen 2,3, Maija Nuppunen-Puputti 4, Malin Bomberg 4 and Claire Cousins 1 1 School of Earth and Environmental Sciences, University of St Andrews, St Andrews KY16 9AL, UK; [email protected] 2 Geological Survey of Finland, 02151 Espoo, Finland; riikka.kietavainen@gtk.fi 3 Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland 4 VTT Technical Research Centre of Finland, 02044 VTT, Finland; maija.nuppunen-puputti@vtt.fi (M.N.-P.); malin.bomberg@vtt.fi (M.B.) * Correspondence: lotta.purkamo@gtk.fi; Tel.: +358-44-322-9432 Received: 1 November 2019; Accepted: 1 January 2020; Published: 4 January 2020 Abstract: The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. -
Archaea and Bacteria with Surprising Microdiversity Show Shifts in Dominance Over 1,000-Year Time Scales in Hydrothermal Chimneys
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys William J. Brazeltona,1, Kristin A. Ludwiga,2, Mitchell L. Soginb, Ekaterina N. Andreishchevab, Deborah S. Kelleya, Chuan-Chou Shenc, R. Lawrence Edwardsd, and John A. Barossa aSchool of Oceanography and Center for Astrobiology and Early Evolution, University of Washington, Seattle, WA 98195; bJosephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, Woods Hole, MA 02543; cDepartment of Geosciences, National Taiwan University, Taipei 106, Taiwan; and dDepartment of Geology and Geophysics, University of Minnesota, Minneapolis, MN 55455 Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved December 11, 2009 (received for review May 18, 2009) The Lost City Hydrothermal Field, an ultramafic-hosted system known as serpentinization (1). These reactions commonly occur in located 15 km west of the Mid-Atlantic Ridge, has experienced at ultramafic environments on Earth where water reacts with the least 30,000 years of hydrothermal activity. Previous studies have mineral olivine, and they are expected to occur on other planetary shown that its carbonate chimneys form by mixing of ∼90 °C, pH 9– bodies hosting aqueous fluids (7). Serpentinization of subsurface fl 11 hydrothermal uids and cold seawater. Flow of methane and ultramafic minerals is one of the most likely sources of CH4 on hydrogen-rich hydrothermal fluids in the porous interior chimney Mars (8). At the LCHF, serpentinization reactions produce alka- walls supports archaeal biofilm communities dominated by a single line (pH 9–11) fluids that are rich in calcium (up to 30 mmol/kg), Methanosarcinales phylotype of .