8.08 Anaerobic Metabolism: Linkages to Trace Gases and Aerobic Processes J
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Microbial Community Composition and Function Beneath Temperate Trees Exposed to Elevated Atmospheric Carbon Dioxide and Ozone
Oecologia (2002) 131:236–244 DOI 10.1007/s00442-002-0868-x ECOSYSTEMS ECOLOGY Rebecca L. Phillips · Donald R. Zak William E. Holmes · David C. White Microbial community composition and function beneath temperate trees exposed to elevated atmospheric carbon dioxide and ozone Received: 1 August 2001 / Accepted: 13 December 2001 / Published online: 14 February 2002 © Springer-Verlag 2002 Abstract We hypothesized that changes in plant growth activity and microbial metabolism of cellobiose, and that resulting from atmospheric CO2 and O3 enrichment microbial processes under early-successional aspen and would alter the flow of C through soil food webs and birch species were more strongly affected by CO2 and O3 that this effect would vary with tree species. To test this enrichment than those under late-successional maple. idea, we traced the course of C through the soil microbial community using soils from the free-air CO2 and O3 Keywords Soil microorganisms · enrichment site in Rhinelander, Wisconsin. We added Carbon-13-phospholipid fatty acid analysis · either 13C-labeled cellobiose or 13C-labeled N-acetylglu- Elevated carbon dioxide · Elevated ozone · cosamine to soils collected beneath ecologically distinct Soil carbon cycling temperate trees exposed for 3 years to factorial CO2 –1 (ambient and 200 µl l above ambient) and O3 (ambient and 20 µl l–1 above ambient) treatments. For both labeled Introduction substrates, recovery of 13C in microbial respiration increased beneath plants grown under elevated CO2 by Human activity has increased the concentration of CO2 29% compared to ambient; elevated O3 eliminated this and O3 in the earth’s troposphere (Barnola et al. -
Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). -
ORGANIC GEOCHEMISTRY: CHALLENGES for the 21St CENTURY
ORGANIC GEOCHEMISTRY: CHALLENGES FOR THE 21st CENTURY VOL. 2 Book of Abstracts of the Communications presented to the 22nd International Meeting on Organic Geochemistry Seville – Spain. September 12 -16, 2005 Editors: F.J. González-Vila, J.A. González-Pérez and G. Almendros Equipo de trabajo: Rocío González Vázquez Antonio Terán Rodíguez José Mª de la Rosa Arranz Maquetación: Rocío González Vázquez Fotomecánica e impresión: Akron Gráfica, Sevilla © 22nd IMOG, Sevilla 2005 Depósito legal: SE-61181-2005 I.S.B.N.: 84-689-3661-8 COMMITTEES INVOLVED IN THE ORGANIZATION OF THE 22 IMOG 2005 Chairman: Francisco J. GONZÁLEZ-VILA Vice-Chairman: José A. GONZÁLEZ-PÉREZ Consejo Superior de Investigaciones Científicas (CSIC) Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS) Scientific Committee Francisco J. GONZÁLEZ-VILA (Chairman) IRNAS-CSIC, Spain Gonzalo ALMENDROS Claude LARGEAU CCMA-CSIC, Spain ENSC, France Pim van BERGEN José C. del RÍO SHELL Global Solutions, The Netherlands IRNAS-CSIC, Spain Jørgen A. BOJESEN-KOEFOED Jürgen RULLKÖTTER GEUS, Denmark ICBM, Germany Chris CORNFORD Stefan SCHOUTEN IGI, UK NIOZ, The Netherlands Gary ISAKSEN Eugenio VAZ dos SANTOS NETO EXXONMOBIL, USA PETROBRAS RD, Brazil Local Committee José Ramón de ANDRÉS IGME, Spain Mª Carmen DORRONSORO Mª Enriqueta ARIAS Universidad del País Vasco Universidad de Alcalá Antonio GUERRERO Tomasz BOSKI Universidad de Sevilla Universidad do Algarve, Faro, Portugal Juan LLAMAS Ignacio BRISSON ETSI Minas de Madrid Repsol YPF Albert PERMANYER Juan COTA Universidad de Barcelona Universidad de Sevilla EAOG Board Richard L. PATIENCE (Chairman) Sylvie DERENNE (Secretary) Ger W. van GRAAS (Treasurer) Walter MICHAELIS (Awards) Francisco J. GONZALEZ-VILA (Newsletter) C. -
Bioenergetics of Mixotrophic Metabolisms: a Theoretical Analysis
Bioenergetics of mixotrophic metabolisms: A theoretical analysis by Stephanie Slowinski A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Science in Earth Sciences (Water) Waterloo, Ontario, Canada, 2019 © Stephanie Slowinski 2019 Author’s Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Statement of Contributions This thesis consists of two co-authored chapters. I contributed to the study design and execution in chapters 2 and 3. Christina M. Smeaton (CMS) and Philippe Van Cappellen (PVC) provided guidance during the study design and analysis. I co-authored both of these chapters with CMS and PVC. iii Abstract Many biogeochemical reactions controlling surface water and groundwater quality, as well as greenhouse gas emissions and carbon turnover rates, are catalyzed by microorganisms. Representing the thermodynamic (or bioenergetic) constraints on the reduction-oxidation reactions carried out by microorganisms in the subsurface is essential to understand and predict how microbial activity affects the environmental fate and transport of chemicals. While organic compounds are often considered to be the primary electron donors (EDs) in the subsurface, many microorganisms use inorganic EDs and are capable of autotrophic carbon fixation. Furthermore, many microorganisms and communities are likely capable of mixotrophy, switching between heterotrophic and autotrophic metabolisms according to the environmental conditions and energetic substrates available to them. -
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene -
Thermophilic Lithotrophy and Phototrophy in an Intertidal, Iron-Rich, Geothermal Spring 2 3 Lewis M
bioRxiv preprint doi: https://doi.org/10.1101/428698; this version posted September 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Thermophilic Lithotrophy and Phototrophy in an Intertidal, Iron-rich, Geothermal Spring 2 3 Lewis M. Ward1,2,3*, Airi Idei4, Mayuko Nakagawa2,5, Yuichiro Ueno2,5,6, Woodward W. 4 Fischer3, Shawn E. McGlynn2* 5 6 1. Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138 USA 7 2. Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan 8 3. Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 9 91125 USA 10 4. Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, 11 Japan 12 5. Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Meguro, Tokyo, 13 152-8551, Japan 14 6. Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth 15 Science and Technology, Natsushima-cho, Yokosuka 237-0061, Japan 16 Correspondence: [email protected] or [email protected] 17 18 Abstract 19 Hydrothermal systems, including terrestrial hot springs, contain diverse and systematic 20 arrays of geochemical conditions that vary over short spatial scales due to progressive interaction 21 between the reducing hydrothermal fluids, the oxygenated atmosphere, and in some cases 22 seawater. At Jinata Onsen, on Shikinejima Island, Japan, an intertidal, anoxic, iron- and 23 hydrogen-rich hot spring mixes with the oxygenated atmosphere and sulfate-rich seawater over 24 short spatial scales, creating an enormous range of redox environments over a distance ~10 m. -
Limits of Iron Fertilization
LIMITS OF IRON FERTILIZATION Anand Gnanadesikan1, John P. Dunne1 and Irina Marinov2 1: NOAA Geophysical Fluid Dynamics Laboratory, PO Box 308, Princeton, NJ 08542 [email protected], [email protected] 2: Department of Earth, Atmosphere and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, [email protected] ABSTRACT Iron fertilization has been proposed as a cheap, controllable, and environmentally benign method for removing carbon dioxide from the atmosphere. While this is in fact the case in simple, 3-box models of the carbon cycle, more realistic models show that these claims fall short of reality. The fact that the efficiency of iron fertilization depends on the long term fate of the added iron and on the carbon associated with it makes tracking the effects of iron fertilization much more difficult and expensive than has been asserted. Additionally, advection of low nutrient water away from iron-rich areas can result in lowering production remotely, with potentially serious consequences. INTRODUCTION The idea of offsetting anthropogenic carbon dioxide emissions by fertilizing the ocean with iron has a number of superficially attractive features. A host of iron fertilization experiments have demonstrated that adding iron to surface waters leads to a local increase in productivity [see for example Coale et al., 1996]. Our own survey of the literature [Dunne et al. subm.] shows that this should be expected to lead to a local increase in particle export. It is claimed however, that this local increase in particle export would necessarily lead to an easily verifiable drawdown in atmospheric carbon dioxide. It is further claimed that the increase in export is controllable and environmentally benign, implying that the effects cease as soon as the fertilization stops. -
Aerobic Respiration
Life is based on redox • All energy generation in biological systems is due to redox (reduction-oxidation) reactions Aerobic Respiration: + - C6H12O6 + 6 H2O ==> 6 CO2 + 24 H +24 e oxidation electron donor (aka energy source) + - (O2+ 4H + 4e ==> 2H2O) x6 reduction electron acceptor --------------------------------------- C6H12O6 + 6 O2 ==> 6 CO2 + 6 H2O overall reaction (24 electrons) Types of bacterial metabolisms • While eukaryotes only reduce O2 and oxidize organic compounds, prokaryotes can use a variety of electron donors and acceptors, organic and inorganic. - • Aerobic respiration: e acceptor is O2 - • Anaerobic respiration: e acceptor is not O2 • Fermentation: e- donor and acceptor are organic molecules • Chemolithotrophy: e- donor and acceptor are inorganic molecules • Phototrophy: e- donor is light and e- acceptor is either organic or inorganic all microorganisms energy source? chemical light chemotroph phototroph carbon source? carbon source? organic organic CO CO compound 2 compound 2 chemoheterotroph chemoautotroph photoheterotroph photoautotroph e- acceptor? Nitrifying and sulfur- use H O to reduce CO ? oxidizing bacteria 2 2 green non-sulfur and O Other than O 2 2 purple non-sulfur bacteria anoxygenic oxygenic photosynthesis: photosynthesis: green sulfur and most bacteria Organic Inorganic cyanobacteria compound compound purple sulfur bacteria fermentative organism anaerobic respiration: nitrate, sulfate, Fe(III) Aerobic or anaerobic respiration Chemolithotrophy Important molecules Redox Electron Carrier: for example the -
An Iron Cycle Cascade Governs the Response of Equatorial Pacific Ecosystems to Climate Change
Received: 19 June 2020 | Revised: 7 August 2020 | Accepted: 9 August 2020 DOI: 10.1111/gcb.15316 PRIMARY RESEARCH ARTICLE An iron cycle cascade governs the response of equatorial Pacific ecosystems to climate change Alessandro Tagliabue1 | Nicolas Barrier2 | Hubert Du Pontavice3,4 | Lester Kwiatkowski5 | Olivier Aumont5 | Laurent Bopp6 | William W. L. Cheung4 | Didier Gascuel3 | Olivier Maury2 1School of Environmental Sciences, University of Liverpool, Liverpool, UK Abstract 2MARBEC (IRD, Univ. Montpellier, CNRS, Earth System Models project that global climate change will reduce ocean net pri- Ifremer), Sète, France mary production (NPP), upper trophic level biota biomass and potential fisheries 3ESE, Ecology and Ecosystem Health, Institut Agro, Rennes, France catches in the future, especially in the eastern equatorial Pacific. However, projec- 4Nippon Foundation-Nereus Program, tions from Earth System Models are undermined by poorly constrained assumptions Institute for the Oceans and Fisheries, regarding the biological cycling of iron, which is the main limiting resource for NPP University of British Columbia, Vancouver, BC, Canada over large parts of the ocean. In this study, we show that the climate change trends 5LOCEAN, Sorbonne Université-CNRS-IRD- in NPP and the biomass of upper trophic levels are strongly affected by modifying MNHN, Paris, France assumptions associated with phytoplankton iron uptake. Using a suite of model ex- 6ENS-LMD, Paris, France periments, we find 21st century climate change impacts on regional NPP range from Correspondence −12.3% to +2.4% under a high emissions climate change scenario. This wide range Alessandro Tagliabue, School of Environmental Sciences, University of arises from variations in the efficiency of iron retention in the upper ocean in the Liverpool, Liverpool, UK. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Revised Supplement 1: Reference List for Figure 1
Revised Supplement 1: Reference list for Figure 1. Manuscript title: Process disturbances in agricultural biogas production – causes, mechanisms and effects on the biogas microbiome: A review Susanne Theuerl 1,*, Johanna Klang 1, Annette Prochnow 1,2 1 Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Exth-Allee 100, 14469 Potsdam, Germany, [email protected] (ST), [email protected] (JK), [email protected] (AP) 2 Humboldt-Universität zu Berlin, Albrecht-Daniel-Thaer-Institute for Agricultural and Horticultural Sciences, Hinter der Reinhardtstr. 6-8, 10115 Berlin, Germany * Correspondence: [email protected] Tel.: +49-331-5699-900 References of Figure 1 1Abt et al. 2010, 2Parizzi et al. 2012, 3Hahnke et al. 2016 and Tomazetto et al. 2018, 4Ueki et al. 2006 and Gronow et al. 2011, 5Grabowski et al. 2005, 6Chen and Dong 2005, 7Avgustin et al. 1997 and Purushe et al. 2010, 8Yamada et al. 2006 and Matsuura et al. 2015, 9Yamada et al. 2007 and Matsuura et al. 2015, 10Sun et al. 2016, 11Suen et al. 2011, 12Hahnke et al. 2014 and Tomazetto et al. 2016, 13Mechichi et al. 1999, 14Koeck et al. 2015a and 2015b, 15Tomazetto et al. 2017, 16Fonknechten et al. 2010, 17Chen et al. 2010, 18Nishiyama et al. 2009, 19Sieber et al. 2010, 20Plerce et al. 2008, 21Westerholm et al. 2011 and Müller et al. 2015, 22Ueki et al. 2014, 23Jackson et al. 1999 and McInerney et al. 2007, 24Ma et al. 2017, 25Harmsen et al. 1998 and Plugge et al. 2012, 26Menes and Muxi 2002, Mavromatis et al. 2013 and Hania et al.