DOCSLIB.ORG

Marine Microbes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Marine Microbes 11/18/2007 Major Concepts 9 Microbes are small, but incredibly abundant and found Marine Microbes everywhere OCN201 Fall 2007 9 Microbes are genetically and physiologically diverse Zackary Johnson Department of Oceanography 9 Micro bes are responsible for most of the energy and http://www.soest.hawaii.edu/oceanography/zij/education.html mass transformations in the ocean 9 Most microbes have never been cultured and in general microbes are poorly understood Major Concepts What’s in a liter of water? 9 Microbes are small, but incredibly abundant and found 9 Fish none everywhere 9 Copepods 10 Microbes! 9 Microbes are genetically and physiologically diverse 9 Diatoms 10,000 9 Micro bes are responsible for most of the energy and 9 Dinoflagellates 100, 000 mass transformations in the ocean 9 Nanoflagellates 1,000,000 9 Most microbes have never been cultured and in 9 Cyanobacterium 100,000,000 general microbes are poorly understood Archaea/Bacteria 1,000,000,000 Viruses 10,000,000,000 Microbes by Epifluorescence Microscopy Microbes are small #/L diameter Fish none >10‐2 m Copepods 10 10‐3 m Diatoms 10,000 10‐4 m Dinoflagellates 100, 000 10‐5 m nanoflagellate Nanoflagellates 1,000,000 10‐5 m Cyanobacterium 100,000,000 10‐6 m Archaea/Bacteria 1,000,000,000 10‐7 m Viruses 10,000,000,000 10‐8 m ~1 μl 1 11/18/2007 Microbes are found everywhere! •DNA stains (DAPI or Sybr) allow visualization of DNA containing particles (cells) vs. non‐ liv ing partilicles •Most microbes are free living, but they can be attached to particles too (particles are concentrated resources or a home) Distributions of microbes Viruses • Bacteria and Archaea present in significant •Obligate parasites numbers from the surface down to the •No Metabolism bottom of the ocean •No Motility and in the sediments •RNA or DNA viruses • Numbers decrease •Just geneti c i nst ructi ons t o repli cat e, wrapped i n ~exponentially with protective coat depth •A source of mortality (“consumption”) for both • Typically, microbial producers and consumers biomass is about equal to primary •Viruses are about 10X more abundant than all producers other types of microbes (Bacteria/Archaea) Karner et al. 2001 Viruses Infect All Types of Marine Life •Marine mammals •Sea Birds •Fish •Crustaceans •Bivalves •Protozoa •Macroalgae (kelp) •Microalgae (phytoplankton) •Bacteria 2 11/18/2007 Turtle Virus Major Concepts 9 Microbes are small, but incredibly abundant and found everywhere 9 Microbes are genetically and physiologically diverse 9 Micro bes are responsible for most of the energy and Bacterial virus mass transformations in the ocean 9 Most microbes have never been cultured and in general microbes are poorly understood Attachment > Entry > Synthesis > Assembly > Lysis Verrucomicrobia 0.05 vadinBE97 Microbes are diverse Chlamydiae Major Groups of OP3 Planctomycetes WS3 BRC1 Bacteria NKB19 Firmicutes OP9 WS2 Cyanobacteria Fusobacteria OP10 •Highly diverse SC4 Actinobacteria NC10 Bacteroidetes Chlorobi Marine Group A Caldithrix •Not all present in Gemmatimonadetes Fibrobacteres Proteobacteria Deferribacteres marine environments, Chrysiogenes arsenatis SBR1093 Acidobacteria but no exhaustive OP8 OS-K Nitrospira Termite Group 1 search to date TM6 Synergistes OP5 Spirochaetes ABY1 BD1-5 group OP11 WS6 TM7 Guaymas1 WS5 SC3 Chloroflexi Deinococcus-Thermus Thermodesulfobacteria OP1 Thermotogae Coprothermobacter Dictyoglomus Aquificae Desulfurobacterium Rappé and Giovannoni 2003 Heterotrophic Microbes Microbes do many things •No Mouth - digest food outside of the cell Primary producers (Autotrophic = self feeding): •Digest larger molecules and particles with cell- surface enzymes (swimming stomachs) Photosynthetic (use sunlight energy): •Take up small molecules through special channels CO2 + H2O Æ CH2O + O2 (porins, transporters) •Important consumers of Chemosynthetic (use chemical energy): dissolved organic matter + - + 2 NH4 + 3 O2 Æ 2 NO2 + 4 H + 2 H2O - - •Many are motile (they move) 2 NO2 + O2 Æ 2 NO3 2+ + 3+ - flagellum 4 Fe + O2 + 4H Æ 4 Fe + 2 H2O - 2- + HS + 2 O2 Æ SO4 + H •Many (use oxygen and sugars) … just like “higher” organisms, but others have unique metabolisms 3 11/18/2007 Microbes do many things Microbes do many things Consumers: Oxidation of Organic Matter •Conversion of “nutrients” or substrates into different forms - with Different e Acceptors (other than oxygen) “one person’s trash is another person’s treasure” REACTION ΔGo´ (kcal/mole) CH2O + O2 Æ CO2 + H2O ‐686 ‐ ‐ CO2 + H2O Æ CH2O + O2 5 CH2O + 4 NO3 Æ 4 HCO3 + CO2 + 3 H2O + 2 N2 ‐570 2+ CH2O + 3 CO2 + H2O + 2 MnO2 Æ 4 HCO3‐ + 2 Mn ‐349 CH2O + O2 Æ CO2 + H2O 2+ CH2O + 7 CO2 + 4 Fe(OH)3 Æ 8 HCO3‐ + 3 H2O + 4 Fe ‐114 + - + ‐ 2NH2 NH + 3O3 O Æ 2NO2 NO + 4H4 H + 2H2 H O 2CH2O + SO4 Æ 2 HCO3 + H2S ‐77 4 2 2 2 CH O Æ CO + CH ‐58 - - 2 2 4 2 NO2 + O2 Æ 2 NO3 ΔGo´ (kcal/mole) = free energy released per mole of glucose oxidized •Thus, in addition to producing and consuming energy in CONCEPT: Some energetic transformations are more energetically favorable than others. the environment, microbes are also critical in converting These will usually occur first under natural conditions ‐ i.e., the most energetically different chemical constituents for other organisms favorable terminal electron acceptor (O2) will be used until it is no longer available, then the environment will favor organisms (bacteria) capable of utilizing alternative •The vast majority of these transformations in the ocean electron acceptor to oxidize organic matter. are dominated by microbes Verrucomicrobia 0.05 vadinBE97 Chlamydiae Major Groups of Bacteria OP3 Major Concepts Planctomycetes WS3 black – cultured BRC1 NKB19 green – uncultured Firmicutes 9 OP9 Microbes are small, but incredibly abundant and found WS2 red – putative identification Cyanobacteria Fusobacteria everywhere OP10 SC4 Actinobacteria NC10 •Not all present in marine Bacteroidetes Chlorobi environments, but no Marine Group A 9 Microbes are genetically and physiologically diverse Caldithrix Gemmatimonadetes exhaustive search to date Fibrobacteres Proteobacteria Deferribacteres • Highly diverse Chrysiogenes arsenatis SBR1093 Acidobacteria 9 Micro bes are responsible for most of the energy and •Most uncultured OP8 OS-K Nitrospira mass transformations in the ocean •More uncharacterized Termite Group 1 TM6 Synergistes OP5 Spirochaetes ABY1 Thus, our understanding of BD1-5 group 9 Most microbes have never been cultured and in OP11 what bacteria are there and WS6 TM7 Guaymas1 general microbes are poorly understood what they are doing is in its WS5 SC3 Chloroflexi infancy. Same thing for Deinococcus-Thermus Thermodesulfobacteria OP1 archaea and microbial Thermotogae Coprothermobacter eukaryotes. Dictyoglomus Aquificae Desulfurobacterium Rappé and Giovannoni 2003 Plate Count Anomaly Major Concepts – redux Direct Counts Plate Counts 9 Microbes are small, but incredibly abundant and found everywhere 9 Microbes are genetically and physiologically diverse 9 Micro bes are responsible for most of the energy and mass transformations in the ocean 9 Most microbes have never been cultured and in general microbes are poorly understood Staley & Konopka, 1985 Only about ~0.1 to 1% of microbes can be cultured! 4.
Load more

Recommended publications
  • The Great Oxidation Event Expanded the Genetic Repertoire of Arsenic Metabolism and Cycling
    The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling Song-Can Chena,b,c,1, Guo-Xin Suna,1, Yu Yand, Konstantinos T. Konstantinidise,f, Si-Yu Zhange, Ye Denga, Xiao-Min Lia,c, Hui-Ling Cuia,c, Florin Musatb, Denny Poppg, Barry P. Rosenh,2, and Yong-Guan Zhua,i,2 aState Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; bDepartment of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, 04318 Leipzig, Germany; cCollege of Resources and Environment, University of Chinese Academy of Sciences, 100049 Beijing, China; dDepartment of Environmental Science and Engineering, Huaqiao University, 361021 Xiamen, China; eSchool of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332; fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332; gDepartment of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, 04318 Leipzig, Germany; hDepartment of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199; and iKey Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China Edited by Donald E. Canfield, Institute of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense M., Denmark, and approved March 20, 2020 (received for review January 25, 2020) The rise of oxygen on the early Earth about 2.4 billion years ago under an atmosphere with very low oxygen levels (<<0.001% reorganized the redox cycle of harmful metal(loids), including that compared with present atmospheric level) (9).
    [Show full text]
  • Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
    ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
    [Show full text]
  • Geomicrobiological Processes in Extreme Environments: a Review
    202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments.
    [Show full text]
  • Intra-Field Variation of Prokaryotic Communities on and Below the Seafloor 24 in the Back-Arc Hydrothermal System of the Southern Mariana Trough
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor 24 in the Back-Arc Hydrothermal System of the Southern Mariana Trough Shingo Kato, Moriya Ohkuma, and Akihiko Yamagishi Abstract Deep-sea hydrothermal vents harbor diverse prokaryotes. There are a variety of habitat types in a deep-sea hydrothermal field, e.g., active and inactive chimneys, iron-rich mats, venting fluid and hydrothermal plume. Numerous studies have shown the diversity and composition of prokaryotic communities in individual habitats. However, it is still unclear whether and how the characteristics of prokaryotic communities in their respective habitats are different. Previously, we reported 16S rRNA genes in a variety of habitats, i.e., hydrothermally active and inactive chimneys, iron-rich mats, a vent fluid, crustal fluids from boreholes, as well as ambient seawater in a back-arc basin hydrothermal field of the Southern Mariana Trough. Here we summarize the prokaryotic communities in the col- lected samples at higher taxonomic resolution (up to family level) using the detected 16S rRNA gene sequences and compare them using recently developed bioinformatics tools. The comparative analysis clearly highlights differences in prokaryotic communities among the habitat types on and below the seafloor in the Southern Mariana Trough. Furthermore, descriptions of cultured species and environmental clones close to the detected sequences provide valuable information for understanding of their distribution and potential of ecological roles in deep-sea hydrothermal fields. Keywords 16S rRNA gene Archaea Back-arc basin Bacteria Chemosynthetic ecosystem Deep- sea hydrothermal vents Prokaryotic community 24.1 Introduction The online version of this chapter (doi:10.1007/978-4-431-54865-2_24) Deep-sea hydrothermal vents are oases for organisms on the contains supplementary material, which is available to authorized users.
    [Show full text]
  • Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. 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 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. 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 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria.
    [Show full text]
  • The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide
    The ISME Journal (2012) 6, 259–272 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide Zhili He1, Yvette Piceno2, Ye Deng1, Meiying Xu1,3, Zhenmei Lu1,4, Todd DeSantis2, Gary Andersen2, Sarah E Hobbie5, Peter B Reich6 and Jizhong Zhou1,2 1Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA; 2Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China; 4College of Life Sciences, Zhejiang University, Hangzhou, China; 5Department of Ecology, Evolution, and Behavior, St Paul, MN, USA and 6Department of Forest Resources, University of Minnesota, St Paul, MN, USA One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies.
    [Show full text]
  • Thermophilic Lithotrophy and Phototrophy in an Intertidal, Iron-Rich, Geothermal Spring 2 3 Lewis M
    bioRxiv preprint first posted online Sep. 27, 2018; doi: http://dx.doi.org/10.1101/428698. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-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.
    [Show full text]
  • 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
    [Show full text]
  • Pdf Accessed 2013 Feb 25
    Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment Joseph P. Peacock1,2, Jessica K. Cole1, Senthil K. Murugapiran1, Jeremy A. Dodsworth1, Jenny C. Fisher2, Duane P. Moser1,2, Brian P. Hedlund1* 1 School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America, 2 Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, Nevada, United States of America Abstract To characterize high-temperature cellulolytic microbial communities, two lignocellulosic substrates, ammonia fiber- explosion-treated corn stover and aspen shavings, were incubated at average temperatures of 77 and 85uC in the sediment and water column of Great Boiling Spring, Nevada. Comparison of 109,941 quality-filtered 16S rRNA gene pyrosequences (pyrotags) from eight enrichments to 37,057 quality-filtered pyrotags from corresponding natural samples revealed distinct enriched communities dominated by phylotypes related to cellulolytic and hemicellulolytic Thermotoga and Dictyoglomus, cellulolytic and sugar-fermenting Desulfurococcales, and sugar-fermenting and hydrogenotrophic Archaeoglobales. Minor enriched populations included close relatives of hydrogenotrophic Thermodesulfobacteria, the candidate bacterial phylum OP9, and candidate archaeal groups C2 and DHVE3. Enrichment temperature was the major factor influencing community composition, with a negative correlation between temperature and richness, followed by lignocellulosic substrate composition. This study establishes the importance of these groups in the natural degradation of lignocellulose at high temperatures and suggests that a substantial portion of the diversity of thermophiles contributing to consortial cellulolysis may be contained within lineages that have representatives in pure culture. Citation: Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, et al.
    [Show full text]
  • Characterization of an Adapted Microbial Population to the Bioconversion of Carbon Monoxide Into Butanol Using Next-Generation Sequencing Technology
    Characterization of an adapted microbial population to the bioconversion of carbon monoxide into butanol using next-generation sequencing technology Guillaume Bruant Research officer, Bioengineering group Energy, Mining, Environment - National Research Council Canada Pacific Rim Summit on Industrial Biotechnology and Bioenergy December 8 -11, 2013 Butanol from residue (dry): syngas route biomass → gasification → syngas → catalysis → synfuels (CO, H2, CO2, CH4) (alcohols…) Biocatalysis vs Chemical catalysis potential for higher product specificity may be less problematic when impurities present less energy intensive (low pressure and temperature) Anaerobic undefined mixed culture vs bacterial pure culture mesophilic anaerobic sludge treating agricultural wastes (Lassonde Inc, Rougemont, QC, Canada) PRS 2013 - 2 Experimental design CO Alcohols Serum bottles incubated at Next Generation RDP Pyrosequencing mesophilic temperature Sequencing (NGS) pipeline 35°C for 2 months Ion PGMTM sequencer http://pyro.cme.msu.edu/ sequences filtered CO continuously supplied Monitoring of bacterial and to the gas phase archaeal populations RDP classifier atmosphere of 100% CO, http://rdp.cme.msu.edu/ 1 atm 16S rRNA genes Ion 314TM chip classifier VFAs & alcohol production bootstrap confidence cutoff low level of butanol of 50 % Samples taken after 1 and 2 months total genomic DNA extracted, purified, concentrated PRS 2013 - 3 NGS: bacterial results Bacterial population - Phylum level 100% 80% Other Chloroflexi 60% Synergistetes %
    [Show full text]
  • The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Minnesota Digital Conservancy The ISME Journal (2012) 6, 259–272 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide Zhili He1, Yvette Piceno2, Ye Deng1, Meiying Xu1,3, Zhenmei Lu1,4, Todd DeSantis2, Gary Andersen2, Sarah E Hobbie5, Peter B Reich6 and Jizhong Zhou1,2 1Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA; 2Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China; 4College of Life Sciences, Zhejiang University, Hangzhou, China; 5Department of Ecology, Evolution, and Behavior, St Paul, MN, USA and 6Department of Forest Resources, University of Minnesota, St Paul, MN, USA One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2.
    [Show full text]
  • 1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
    Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds.
    [Show full text]