Characterizing Methanogen and Methanotroph Diversity, Abundance and Activity Within the Hampshire-Avon Catchment
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Hydrogen Isotope Fractionation in Lipids of the Methane-Oxidizing Bacterium Methylococcus Capsulatus
Geochimica et Cosmochimica Acta, Vol. 66, No. 22, pp. 3955–3969, 2002 Copyright © 2002 Elsevier Science Ltd Pergamon Printed in the USA. All rights reserved 0016-7037/02 $22.00 ϩ .00 PII S0016-7037(02)00981-X Hydrogen isotope fractionation in lipids of the methane-oxidizing bacterium Methylococcus capsulatus 1, 2 3 1 ALEX L. SESSIONS, *LINDA L. JAHNKE, ARNDT SCHIMMELMANN, and JOHN M. HAYES 1Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA 2Exobiology Branch, NASA-Ames Research Center, Moffett Field, CA 94035, USA 3Biogeochemical Laboratories, Department of Geological Sciences, Indiana University, Bloomington, IN 47405, USA (Received December 10, 2001; accepted in revised form June 7, 2002) Abstract—Hydrogen isotopic compositions of individual lipids from Methylococcus capsulatus, an aerobic, methane-oxidizing bacterium, were analyzed by hydrogen isotope-ratio-monitoring gas chromatography–mass spectrometry (GC-MS). The purposes of the study were to measure isotopic fractionation factors between methane, water, and lipids and to examine the biochemical processes that determine the hydrogen isotopic composition of lipids. M. capsulatus was grown in six replicate cultures in which the ␦D values of methane and water were varied independently. Measurement of concomitant changes in ␦D values of lipids allowed estimation of the proportion of hydrogen derived from each source and the isotopic fractionation associated with the utilization of each source. All lipids examined, including fatty acids, sterols, and hopanols, derived 31.4 Ϯ 1.7% of their hydrogen from methane. This was apparently true whether the cultures were harvested during exponential or stationary phase. Examination of the relevant biochemical pathways indicates that no hydrogen is transferred directly (with C-H bonds intact) from methane to lipids. -
Reduced Net Methane Emissions Due to Microbial Methane Oxidation in a Warmer Arctic
LETTERS https://doi.org/10.1038/s41558-020-0734-z Reduced net methane emissions due to microbial methane oxidation in a warmer Arctic Youmi Oh 1, Qianlai Zhuang 1,2,3 ✉ , Licheng Liu1, Lisa R. Welp 1,2, Maggie C. Y. Lau4,9, Tullis C. Onstott4, David Medvigy 5, Lori Bruhwiler6, Edward J. Dlugokencky6, Gustaf Hugelius 7, Ludovica D’Imperio8 and Bo Elberling 8 Methane emissions from organic-rich soils in the Arctic have bacteria (methanotrophs) and the remainder is mostly emitted into been extensively studied due to their potential to increase the atmosphere (Fig. 1a). The methanotrophs in these wet organic the atmospheric methane burden as permafrost thaws1–3. soils may be low-affinity methanotrophs (LAMs) that require However, this methane source might have been overestimated >600 ppm of methane (by moles) for their growth and mainte- without considering high-affinity methanotrophs (HAMs; nance23. But in dry mineral soils, the dominant methanotrophs are methane-oxidizing bacteria) recently identified in Arctic min- high-affinity methanotrophs (HAMs), which can survive and grow 4–7 eral soils . Herein we find that integrating the dynamics of at a level of atmospheric methane abundance ([CH4]atm) of about HAMs and methanogens into a biogeochemistry model8–10 1.8 ppm (Fig. 1b)24. that includes permafrost soil organic carbon dynamics3 leads Quantification of the previously underestimated HAM-driven −1 to the upland methane sink doubling (~5.5 Tg CH4 yr ) north of methane sink is needed to improve our understanding of Arctic 50 °N in simulations from 2000–2016. The increase is equiva- methane budgets. -
Isolation and Characterisation of Methylocystis Spp. for Poly-3
Rumah et al. AMB Expr (2021) 11:6 https://doi.org/10.1186/s13568-020-01159-4 ORIGINAL ARTICLE Open Access Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks Bashir L. Rumah† , Christopher E. Stead† , Benedict H. Claxton Stevens , Nigel P. Minton , Alexander Grosse‑Honebrink and Ying Zhang* Abstract Waste plastic and methane emissions are two anthropogenic by‑products exacerbating environmental pollution. Methane‑oxidizing bacteria (methanotrophs) hold the key to solving these problems simultaneously by utilising otherwise wasted methane gas as carbon source and accumulating the carbon as poly‑3‑hydroxybutyrate, a biode‑ gradable plastic polymer. Here we present the isolation and characterisation of two novel Methylocystis strains with the ability to produce up to 55.7 1.9% poly‑3‑hydroxybutyrate of cell dry weight when grown on methane from diferent waste sources such as landfll± and anaerobic digester gas. Methylocystis rosea BRCS1 isolated from a recrea‑ tional lake and Methylocystis parvus BRCS2 isolated from a bog were whole genome sequenced using PacBio and Illumina genome sequencing technologies. In addition to potassium nitrate, these strains were also shown to grow on ammonium chloride, glutamine and ornithine as nitrogen source. Growth of Methylocystis parvus BRCS2 on Nitrate Mineral Salt (NMS) media with 0.1% methanol vapor as carbon source was demonstrated. The genetic tractability by conjugation was also determined with conjugation efciencies up to 2.8 10–2 and 1.8 10–2 for Methylocystis rosea BRCS1 and Methylocystis parvus BRCS2 respectively using a plasmid with ColE1× origin of ×replication. Finally, we show that Methylocystis species can produce considerable amounts of poly‑3‑hydroxybutyrate on waste methane sources without impaired growth, a proof of concept which opens doors to their use in integrated bio‑facilities like landflls and anaerobic digesters. -
Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Methylovulum miyakonense gen. nov., sp. nov., a type I Title methanotroph isolated from forest soil. Author(s) Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi International journal of systematic and evolutionary Citation microbiology (2011), 61(4): 810-815 Issue Date 2011-04 URL http://hdl.handle.net/2433/197236 This is an author accepted manuscript (AAM) that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology that has not been copy-edited, typeset or proofed. The Society for General Microbiology (SGM) does not permit the posting Right of AAMs for commercial use or systematic distribution. SGM disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final version is available athttp://dx.doi.org/10.1099/ijs.0.019604-0 Type Journal Article Textversion author Kyoto University 1 Methylovulum miyakonense gen. nov., sp. nov., a novel 2 type I methanotroph from a forest soil in Japan 3 4 5 6 Hiroyuki Iguchi, Hiroya Yurimoto and Yasuyoshi Sakai 7 8 9 Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto 10 University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan. 11 12 Author for correspondence: Yasuyoshi Sakai. Tel: +81 75 753 6385. Fax: +81 13 75 753 6454. E-mail: [email protected] 14 15 16 Subject category: Proteobacteria. 17 Runnning title: Methylovulum miyakonense gen. nov., sp. -
Fatty Acid 13C-Fingerprinting in Mytilid-Bacteria Symbiosis
Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 7, 3453–3475, 2010 Biogeosciences www.biogeosciences-discuss.net/7/3453/2010/ Discussions BGD doi:10.5194/bgd-7-3453-2010 7, 3453–3475, 2010 © Author(s) 2010. CC Attribution 3.0 License. Fatty acid This discussion paper is/has been under review for the journal Biogeosciences (BG). 13C-fingerprinting in Please refer to the corresponding final paper in BG if available. Mytilid-bacteria symbiosis Tracing carbon assimilation in V. Riou et al. endosymbiotic deep-sea hydrothermal vent Mytilid fatty acids by Title Page 13 C-fingerprinting Abstract Introduction Conclusions References V. Riou1,2, S. Bouillon1,3, R. Serrao˜ Santos2, F. Dehairs1, and A. Colac¸o2 Tables Figures 1Department of Analytical and Environmental Chemistry, Vrije Universiteit Brussel, Brussels, Belgium J I 2Department of Oceanography and Fisheries, IMAR-University of Azores, Horta, Portugal 3Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven, J I Leuven, Belgium Back Close Received: 4 May 2010 – Accepted: 5 May 2010 – Published: 10 May 2010 Full Screen / Esc Correspondence to: V. Riou (virginie [email protected]) Published by Copernicus Publications on behalf of the European Geosciences Union. Printer-friendly Version Interactive Discussion 3453 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract BGD Bathymodiolus azoricus mussels thrive at Mid-Atlantic Ridge hydrothermal vents, where part of their energy requirements -
The Ratio of Methanogens to Methanotrophs and Water-Level Dynamics Drive Methane Exchange Velocity in a Temperate Kettle-Hole Peat Bog
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-116 Manuscript under review for journal Biogeosciences Discussion started: 23 April 2019 c Author(s) 2019. CC BY 4.0 License. The ratio of methanogens to methanotrophs and water-level dynamics drive methane exchange velocity in a temperate kettle-hole peat bog Camilo Rey-Sanchez1,4, Gil Bohrer1, Julie Slater2, Yueh-Fen Li3, Roger Grau-Andrés2, Yushan Hao2, 5 Virginia I. Rich3, & G. Matt Davies2 1Department of Civil and Environmental Engineering and Geodetic Science, The Ohio State University, Columbus, Ohio, 43210, USA 2School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio, 43210, USA 3Department of Microbiology, The Ohio State University, Columbus, Ohio, 43210, USA 10 4Current address, Department of Environmental Science, Management and Policy, University of California- Berkeley, California, 94720, USA Correspondence to: Camilo Rey-Sanchez ([email protected]) 15 Abstract. Peatlands are a large source of methane (CH4) to the atmosphere, yet the uncertainty around the estimates of CH4 flux from peatlands is large. To better understand the spatial heterogeneity in temperate peatland CH4 emissions and their response to physical and biological drivers, we studied CH4 dynamics throughout the growing seasons of 2017 and 2018 in Flatiron Lake Bog, a kettle-hole peat bog in Ohio. The site is composed of six different hydro-biological zones: an open water zone, four concentric vegetation zones surrounding the open water, and a restored zone connected to the main bog by a narrow 20 channel. At each of these locations, we monitored water level (WL), CH4 pore-water concentration at different peat depths, CH4 fluxes from the ground and from representative plant species using chambers, and microbial community composition with focus here on known methanogens and methanotrophs. -
Methane Utilization in Methylomicrobium Alcaliphilum 20ZR: a Systems Approach Received: 8 September 2017 Ilya R
www.nature.com/scientificreports OPEN Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach Received: 8 September 2017 Ilya R. Akberdin1,2, Merlin Thompson1, Richard Hamilton1, Nalini Desai3, Danny Alexander3, Accepted: 22 January 2018 Calvin A. Henard4, Michael T. Guarnieri4 & Marina G. Kalyuzhnaya1 Published: xx xx xxxx Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confrmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efcient tool for metabolic engineering or ecosystem modeling. Climate change concerns linked to increasing concentrations of anthropogenic methane have spiked inter- est in biological methane utilization as a novel platform for improving ecological and human well-being1–4. -
(Antarctica) Glacial, Basal, and Accretion Ice
CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa. -
Large Scale Biogeography and Environmental Regulation of 2 Methanotrophic Bacteria Across Boreal Inland Waters
1 Large scale biogeography and environmental regulation of 2 methanotrophic bacteria across boreal inland waters 3 running title : Methanotrophs in boreal inland waters 4 Sophie Crevecoeura,†, Clara Ruiz-Gonzálezb, Yves T. Prairiea and Paul A. del Giorgioa 5 aGroupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), 6 Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada 7 bDepartment of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, 8 Catalunya, Spain 9 Correspondence: Sophie Crevecoeur, Canada Centre for Inland Waters, Water Science and Technology - 10 Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, 11 Burlington, Ontario, Canada, e-mail: [email protected] 12 † Current address: Canada Centre for Inland Waters, Water Science and Technology - Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, Ontario, Canada 1 13 Abstract 14 Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby 15 mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and 16 phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain 17 the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here we used high 18 throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic 19 community composition and the environmental factors that influence their distribution and relative 20 abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal 21 landscape. Within one region, soil and soil water samples were additionally taken from the surrounding 22 watersheds in order to cover the full terrestrial-aquatic continuum. -
Nitrification 31
NITROGEN IN SOILS/Nitrification 31 See also: Eutrophication; Greenhouse Gas Emis- Powlson DS (1993) Understanding the soil nitrogen cycle. sions; Isotopes in Soil and Plant Investigations; Soil Use and Management 9: 86–94. Nitrogen in Soils: Cycle; Nitrification; Plant Uptake; Powlson DS (1999) Fate of nitrogen from manufactured Symbiotic Fixation; Pollution: Groundwater fertilizers in agriculture. In: Wilson WS, Ball AS, and Hinton RH (eds) Managing Risks of Nitrates to Humans Further Reading and the Environment, pp. 42–57. Cambridge: Royal Society of Chemistry. Addiscott TM, Whitmore AP, and Powlson DS (1991) Powlson DS (1997) Integrating agricultural nutrient man- Farming, Fertilizers and the Nitrate Problem. Wallingford: agement with environmental objectives – current state CAB International. and future prospects. Proceedings No. 402. York: The Benjamin N (2000) Nitrates in the human diet – good or Fertiliser Society. bad? Annales de Zootechnologie 49: 207–216. Powlson DS, Hart PBS, Poulton PR, Johnston AE, and Catt JA et al. (1998) Strategies to decrease nitrate leaching Jenkinson DS (1986) Recovery of 15N-labelled fertilizer in the Brimstone Farm experiment, Oxfordshire, UK, applied in autumn to winter wheat at four sites in eastern 1988–1993: the effects of winter cover crops and England. Journal of Agricultural Science, Cambridge unfertilized grass leys. Plant and Soil 203: 57–69. 107: 611–620. Cheney K (1990) Effect of nitrogen fertilizer rate on soil Recous S, Fresnau C, Faurie G, and Mary B (1988) The fate nitrate nitrogen content after harvesting winter wheat. of labelled 15N urea and ammonium nitrate applied to a Journal of Agricultural Science, Cambridge 114: winter wheat crop. -
Large D/H Variations in Bacterial Lipids Reflect Central Metabolic Pathways
Large D/H variations in bacterial lipids reflect central metabolic pathways Xinning Zhanga, Aimee L. Gillespieb, and Alex L. Sessionsa,b,1 aEnvironmental Science and Engineering Program and bDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 This Feature Article is part of a series identified by the Editorial Board as reporting findings of exceptional significance. Edited by John M. Hayes, Woods Hole Oceanographic Institution, Woods Hole, MA, and approved May 29, 2009 (received for review March 19, 2009) Large hydrogen-isotopic (D/H) fractionations between lipids and compositions. Jones et al. (17) measured fatty acids extracted growth water have been observed in most organisms studied to from coastal marine particulate organic matter (POM) and date. These fractionations are generally attributed to isotope found ␦D values ranging from Ϫ73 to Ϫ237‰. Measurements effects in the biosynthesis of lipids, and are frequently assumed to of lipids from marine sediments have extended this range from be approximately constant for the purpose of reconstructing cli- Ϫ32 to Ϫ348‰ for lipids with n-alkyl skeletons and Ϫ148 to matic variables. Here, we report D/H fractionations between lipids Ϫ469‰ for those with isoprenoid skeletons (18). Because the and water in 4 cultured members of the phylum Proteobacteria, lipids measured by both studies likely derive from marine and show that they can vary by up to 500‰ in a single organism. organisms inhabiting seawater of essentially constant ␦D value The variation cannot be attributed to lipid biosynthesis as there is (Ϸ0‰), such differences cannot be due to varying environmen- no significant change in these pathways between cultures, nor can tal water. -
Ethane-Dependent Synthesis of Polyhydroxyalkanoates By
bioRxiv preprint doi: https://doi.org/10.1101/307108; this version posted April 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Ethane-dependent synthesis of polyhydroxyalkanoates by 2 the obligate methanotroph Methylocystis parvus OBBP 3 Jaewook Myunga,e#, James C. A. Flanaganb,f, Wakuna M. Galegaa, Robert M. Waymouthb, Craig 4 S. Criddlea,c,d 5 a Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, 6 USA 7 b Department of Chemistry, Stanford University, Stanford, California 94305, USA 8 c Woods Institute for the Environment, Stanford, CA 94305, USA 9 d William and Cloy Codiga Resource Recovery Center, Stanford, CA 94305, USA 10 e Current address: Department of Civil and Environmental Engineering, Southern Methodist 11 University, Dallas, TX 75205, USA 12 f Current address: Brighton College, Eastern Road, Brighton, BN2 0AL, United Kingdom 13 14 Running title: Methanotrophic synthesis of PHAs using ethane 15 16 # Address correspondence to: Jaewook Myung, [email protected] 17 Phone: (+1) 214-768-4229 1 bioRxiv preprint doi: https://doi.org/10.1101/307108; this version posted April 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 18 ABSTRACT (250 words) 19 Under conditions of nutrient-limited growth, Type II obligate methanotrophs oxidize C1 20 compounds, such as methane or methanol and accumulate intracellular granules of poly(3- 21 hydroxybutyrate) (P3HB). Here, we report that, under same nutrient-limited conditions, the Type 22 II obligate methanotroph Methylocystis parvus OBBP can use ethane as its sole carbon and 23 energy source for synthesis P3HB granules, accumulating up to 35 ± 4 wt% P3HB.