Where Less May Be More: How the Rare Biosphere Pulls Ecosystems Strings
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Experimental and Statistical Analysis of Nutritional Requirements for the Growth of the Extremophile Deinococcus Geothermalis DSM 11300
Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300 Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gorret To cite this version: Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gor- ret. Experimental and statistical analysis of nutritional requirements for the growth of the ex- tremophile Deinococcus geothermalis DSM 11300. Extremophiles, Springer Verlag, 2014, 18 (6), pp.1009-1021. 10.1007/s00792-014-0671-8. hal-01268947 HAL Id: hal-01268947 https://hal.archives-ouvertes.fr/hal-01268947 Submitted on 11 Mar 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible This is an author’s version published in: http://oatao.univ-toulouse.fr/22999 Official URL: https://doi.org/10.1007/s00792-014-0671-8 To cite this version: Bornot, Julie and Aceves-Lara, César-Arturo and Molina-Jouve, Carole and Uribelarrea, Jean-Louis and Gorret, Nathalie Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300. -
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. -
Science and Innovation: the Under-Fueled Engine of Prosperity
Science and Innovation: The Under-Fueled Engine of Prosperity JULY 14, 2021 AUTHOR Benjamin F. Jones* ABSTRACT Science and innovation are central to human progress and national economic success. Currently, the United States invests 2.8% of GDP in research and development, which is supported by a range of public policies. This paper asks whether the United States invests enough. To answer that question, the conceptual case for government intervention and skepticism about that case are reviewed. The paper then turns to systematic evidence, including the very latest evidence, regarding the operation of the science and innovation system and its social returns. This evidence suggests a clear answer: We massively underinvest in science and innovation, with implications for our standards of living, health, national competitiveness, and capacity to respond to crisis. * Kellogg School of Management and National Bureau of Economic Research. Email: [email protected]. 1. Introduction Scientific and technological advances have long been recognized as engines of economic growth and rising prosperity. The fruits of these advances—instantaneous global communications, vaccines, airplanes, heart surgery, computers, skyscrapers, industrial robots, on-demand entertainment, to name a few—might seem almost magical to our ancestors from not-too-many generations ago. The power of this progress has been broadly evident since the Industrial Revolution and was recognized at the time, including by political leaders. As the British Prime Minister Benjamin Disraeli noted in 1873, “How much has happened in these fifty years … I am thinking of those revolutions of science which … have changed the position and prospects of mankind more than all the conquests and all the codes and all the legislators that ever lived.” Disraeli was talking of things like the steam engine, the telegraph, and textile manufacturing. -
Arxiv.Org | Cornell University Library, July, 2019. 1
arXiv.org | Cornell University Library, July, 2019. Extremophiles: a special or general case in the search for extra-terrestrial life? Ian von Hegner Aarhus University Abstract Since time immemorial life has been viewed as fragile, yet over the past few decades it has been found that many extreme environments are inhabited by organisms known as extremophiles. Knowledge of their emergence, adaptability, and limitations seems to provide a guideline for the search of extra-terrestrial life, since some extremophiles presumably can survive in extreme environments such as Mars, Europa, and Enceladus. Due to physico-chemical constraints, the first life necessarily came into existence at the lower limit of it‟s conceivable complexity. Thus, the first life could not have been an extremophile, furthermore, since biological evolution occurs over time, then the dual knowledge regarding what specific extremophiles are capable of, and to the analogue environment on extreme worlds, will not be sufficient as a search criterion. This is because, even though an extremophile can live in an extreme environment here-and-now, its ancestor however could not live in that very same environment in the past, which means that no contemporary extremophiles exist in that environment. Furthermore, a theoretical framework should be able to predict whether extremophiles can be considered a special or general case in the galaxy. Thus, a question is raised: does Earth‟s continuous habitability represent an extreme or average value for planets? Thus, dependent on whether it is difficult or easy for worlds to maintain the habitability, the search for extra- terrestrial life with a focus on extremophiles will either represent a search for dying worlds, or a search for special life on living worlds, focusing too narrowly on extreme values. -
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. -
Extremely Thermophilic Microorganisms As Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals
REVIEW published: 05 November 2015 doi: 10.3389/fmicb.2015.01209 Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals Benjamin M. Zeldes 1, Matthew W. Keller 2, Andrew J. Loder 1, Christopher T. Straub 1, Michael W. W. Adams 2 and Robert M. Kelly 1* 1 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point Edited by: that the use of these microorganisms as metabolic engineering platforms has become Bettina Siebers, University of Duisburg-Essen, possible. While in its early days, complex metabolic pathways have been altered or Germany engineered into recombinant extreme thermophiles, such that the production of fuels and Reviewed by: chemicals at elevated temperatures has become possible. Not only does this expand the Haruyuki Atomi, thermal range for industrial biotechnology, it also potentially provides biodiverse options Kyoto University, Japan Phillip Craig Wright, for specific biotransformations unique to these microorganisms. The list of extreme University of Sheffield, UK thermophiles growing optimally between 70 and 100◦C with genetic toolkits currently *Correspondence: available includes archaea and bacteria, aerobes and anaerobes, coming from genera Robert M. -
Extreme Organisms on Earth Show Us Just How Weird Life Elsewhere Could Be. by Chris Impey Astrobiology
Astrobiology Extreme organisms on Earth show us just how weird life elsewhere could be. by Chris Impey How life could thrive on hostile worlds Humans have left their mark all over Earth. We’re proud of our role as nature’s generalists — perhaps not as swift as the gazelle or as strong as the gorilla, but still pretty good at most things. Alone among all species, technology has given us dominion over the planet. Humans are endlessly plucky and adaptable; it seems we can do anything. Strain 121 Yet in truth, we’re frail. From our safe living rooms, we may admire the people who conquer Everest or cross deserts. But without technology, we couldn’t live beyond Earth’s temperate zones. We cannot survive for long in temperatures below freezing or above 104° Fahrenheit (40° Celsius). We can stay underwater only as long as we can hold our breath. Without water to drink we’d die in 3 days. Microbes, on the other hand, are hardy. And within the microbial world lies a band of extremists, organisms that thrive in conditions that would cook, crush, smother, and dissolve most other forms of life. Collectively, they are known as extremophiles, which means, literally, “lovers of extremes.” Extremophiles are found at temperatures above the boiling point and below the freezing point of water, in high salinity, and in strongly acidic conditions. Some can live deep inside rock, and others can go into a freeze-dried “wait state” for tens of thousands of years. Some of these microbes harvest energy from meth- ane, sulfur, and even iron. -
Marine Extremophiles: a Source of Hydrolases for Biotechnological Applications
Mar. Drugs 2015, 13, 1925-1965; doi:10.3390/md13041925 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Extremophiles: A Source of Hydrolases for Biotechnological Applications Gabriel Zamith Leal Dalmaso 1,2, Davis Ferreira 3 and Alane Beatriz Vermelho 1,* 1 BIOINOVAR—Biotechnology laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] 2 Graduate Program in Plant Biotechnology, Health and Science Centre, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil 3 BIOINOVAR—Biotechnology Laboratories: Virus-Cell Interaction, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +55-(21)-3936-6743; Fax: +55-(21)-2560-8344. Academic Editor: Kirk Gustafson Received: 1 December 2014 / Accepted: 25 March 2015 / Published: 3 April 2015 Abstract: The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. -
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 Resolved Mystery of Tardigrades
Journal of Investigative Genomics Mini review Open Access The resolved mystery of tardigrades Abstract Volume 4 Issue 2 - 2017 Tardigrades, also known as ‘Water bears’ or ‘Space Bears’ are famous for their ability to survive in extreme environmental conditions. With incredible ability to survive at a range Oisorjo Chakraborty, Pranab Roy Department of Biotechnology, Haldia Institute of Technology, of temperature between -272˚C to 150˚C, these small eight legged animals are considered India as one of the toughest organisms of the world. There are several records of survival of these animals under high pressure, UV exposure and even in space under cosmic radiation. For Correspondence: Pranab Roy, Department of Biotechnology, decades it remained a mystery how tardigrades can tolerate the extreme environmental Haldia Institute of Technology, India, Tel 9933037099, conditions. Afteryears of research, it was found that tardigrades dry out and turn their entire Email [email protected] body into a glass like structure at very low temperature, termed as “Bio-glass” to shut Oisorjo Chakraborty, Department of Biotechnology, Haldia down all their metabolic processes. Later by rehydrating, the creatures bring back life in Institute of Technology, India, Email [email protected] them. Finally researchers have identified the key protein in tardigrades which helps them to survive at extreme low temperature. The genome of several tardigrades species has been Received: April 21, 2017 | Published: May 19, 2017 sequenced like ‘Ramazzottius varieornatus’, ‘Hypsibius dujardini’. The sequenced genome provides evidences of expression of tolerance related genes and horizontal gene transfer in the animals helping them to survive in extreme environmental conditions with these key genes. -
EXTREMOPHILES – Vol
EXTREMOPHILES – Vol. I - Extremophiles: Basic Concepts - Charles Gerday EXTREMOPHILES: BASIC CONCEPTS Charles Gerday Laboratory of Biochemistry, University of Liège, Belgium Keywords: extremophiles, thermophiles, halophiles, alkaliphiles, acidophiles, metallophiles, barophiles, psychrophiles, piezophiles, extreme conditions Contents 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Acknowledgments Glossary Bibliography Biographical Sketch Summary Extremophiles are organisms which permanently experience environmental conditions which mayUNESCO be considered as extreme –in comparisonEOLSS to the physico-chemical characteristics of the normal environment of human cells: the latter belonging to the mesophile or temperate world. Some eukaryotic organisms such as fishes, invertebrates, yeasts, fungi, and plants have partially colonized extreme habitats characterized by low temperature and/orSAMPLE of elevated hydrostatic pressure. CHAPTERS In general, however, the organisms capable of thriving at the limits of temperature, pH, salt concentration and hydrostatic pressure, are prokaryotic. In fact, some organisms depend on these extreme conditions for survival and have therefore developed unique adaptations, especially at the level of their membranes and macromolecules, and affecting proteins and nucleic acids in particular. The molecular bases of the various adaptations are beginning to be understood and are briefly described. The study of the extremophile world has contributed greatly to defining, in more precise terms, fundamental concepts such as macromolecule stability and protein folding. -
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.