DOCSLIB.ORG

Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV UNLV Theses, Dissertations, Professional Papers, and Capstones 12-2012 Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV Jessica Cole University of Nevada, Las Vegas Follow this and additional works at: https://digitalscholarship.unlv.edu/thesesdissertations Part of the Bacteriology Commons, Biology Commons, and the Environmental Microbiology and Microbial Ecology Commons Repository Citation Cole, Jessica, "Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV" (2012). UNLV Theses, Dissertations, Professional Papers, and Capstones. 1518. http://dx.doi.org/10.34917/4301608 This Thesis is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Thesis in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Thesis has been accepted for inclusion in UNLV Theses, Dissertations, Professional Papers, and Capstones by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. NATURAL AND LIGNOCELLULOSE-ENRICHED MICROBIAL COMMUNITIES IN GREAT BOILING SPRING, NV by Jessica K. Cole Bachelor of Science in Biology University of Nevada - Las Vegas 2010 A thesis submitted in partial fulfillment of the requirements for the Master of Science in Biological Sciences School of Life Sciences College of Sciences The Graduate College University of Nevada, Las Vegas December 2012 Copyright by Jessica K. Cole, 2012 All Rights Reserved THE GRADUATE COLLEGE We recommend the thesis prepared under our supervision by Jessica Cole entitled Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV be accepted in partial fulfillment of the requirements for the degree of Master of Science in Biological Sciences School of Life Sciences Brian Hedlund, Ph.D., Committee Chair Helen Wing Ph.D., Committee Member Eduardo Robleto, Ph.D., Committee Member Ernesto Abel-Santos, Ph.D., Graduate College Representative Tom Piechota, Ph.D., Interim Vice President for Research & Dean of the Graduate College December 2012 ii ABSTRACT Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV by Jessica K. Cole Dr. Brian Hedlund, Committee Chair Professor of Biology University of Nevada, Las Vegas The natural microbial communities present in Great Boiling Spring were investigated and contrasted against those present after in situ enrichment with lignocellulose. High-throughput cultivation-independent DNA sequencing of the V8 region of the small subunit (SSU) rRNA gene generated a total of 274,119 quality-filtered pyrosequencing fragments. Twelve natural spring samples were analyzed, including four high-temperature water samples and eight sediment samples ranging from 87 - 62 °C. Eight lignocellulosic enrichments incubated in the spring sediment and water at two high- temperature sites were analyzed. The natural water communities were found to be extremely uneven but relatively constant throughout time. The natural sediment communities clustered based according to sample temperature and location. This study demonstrates the strong influence of temperature on microbial diversity and composition of both natural and enriched samples, with a negative correlation between temperature and richness. A thermophilic and cellulolytic bacterium was isolated from one of the lignocellulosic enrichments. It was aerobic and able to utilize a wide variety of substrates as sole carbon and energy sources, including both amorphous and crystalline cellulose. iii The results of phylogenetic, chemotaxonomic, and morphological analyses determined the strain to be representative of a new order-level lineage within the class "Chloroflexi". iv ACKNOWLEDGEMENTS I would like to thank Dr. Brian Hedlund for giving me the opportunity to perform such interesting research. I appreciate the guidance and advice he provided throughout the years I spent working in his laboratory. Also, I owe much to David and Sandy Jamieson, who generously allowed access to Great Boiling Spring, making my research possible. My committee members, Drs. Eduardo Robleto, Helen Wing, and Ernesto Abel- Santos, deserve substantial thanks for the consideration and recommendations that they provided. I must thank everyone who provided feedback during my presentations, and Keala Kiko and Nicholle Booker for essential administrative support. My fellow laboratory members were responsible for improving many aspects of my projects and publications with their support and advice. Some of these people include Tara Edwards, Mandy Williams, Jeremy Dodsworth, Joseph Peacock, Brandon Gieler, and Senthil Murugapiran. It was a great pleasure to work with each and every one of you. Thank you. v TABLE OF CONTENTS ABSTRACT ........................................................................................................................ ii ACKNOWLEDGEMENTS ................................................................................................ v LIST OF TABLES ........................................................................................................... viii LIST OF FIGURES ............................................................................................................ x CHAPTER 1 INTRODUCTION ................................................................................... 1 CHAPTER 2 SEDIMENT MICROBIAL COMMUNITIES IN GREAT BOILING SPRING ARE CONTROLLED BY TEMPERATURE AND DISTINCT FROM WATER COMMUNITIES ...................................... 4 Abstract ......................................................................................................................... 4 Introduction ................................................................................................................... 5 Methods......................................................................................................................... 8 Results and Discussion ............................................................................................... 14 Conclusions ................................................................................................................. 22 CHAPTER 3 PYROSEQUENCING ANALYSIS OF HIGH-TEMPERATURE CELLULOLYTIC MICROBIAL CONSORTIA DEVELOPED IN GREAT BOILING SPRING AFTER IN SITU LIGNOCELLULOSE ENRICHMENT ..................................................................................... 32 Abstract ....................................................................................................................... 32 Introduction ................................................................................................................. 32 Methods....................................................................................................................... 36 Results and Discussion ............................................................................................... 43 Conclusions ................................................................................................................. 58 CHAPTER 4 KALLOTENUE PAPYROLYTICUM GEN. NOV., SP. NOV., A CELLULOLYTIC AND FILAMENTOUS THERMOPHILE ISOLATED FROM GREAT BOILING SPRING THAT REPRESENTS A NOVEL LINEAGE (KALLOTENUACEAE ORD. NOV., KALLOTENUALES FAM. NOV.) WITHIN THE CLASS CHLOROFLEXI .................................................................................... 66 Abstract ....................................................................................................................... 66 Introduction ................................................................................................................. 67 Methods....................................................................................................................... 67 Results and Discussion ............................................................................................... 73 Conclusions ................................................................................................................. 75 CHAPTER 5 CONCLUSIONS ................................................................................... 82 APPENDIX A ADDITIONAL TABLES ...................................................................... 85 APPENDIX B ADDITIONAL FIGURES................................................................... 101 APPENDIX C EXCEL FILE CONTAINING ALPHA DIVERSITY METRICS PLOTTED AGAINST PHYSICOCHEMICAL MEASUREMENTS. 115 vi REFERENCES ............................................................................................................... 116 VITA .............................................................................................................................. 130 vii LIST OF TABLES Table 2.1. Physical, chemical, and mineralogical data and sequencing statistics ..... 24 Table 2.2. SIMPER analysis results displaying top ten 97% OTUs responsible for dissimilarity between water and sediment samples. ................................. 25 Table 2.3. SIMPER analysis results displaying top ten 97% OTUs responsible for dissimilarity between high temperature (A,B) vs. medium temperature (C) vs. low temperature (E) sediment. ...........................................................
Load more

Recommended publications
  • Arthrobacter Paludis Sp. Nov., Isolated from a Marsh
    TAXONOMIC DESCRIPTION Zhang et al., Int J Syst Evol Microbiol 2018;68:47–51 DOI 10.1099/ijsem.0.002426 Arthrobacter paludis sp. nov., isolated from a marsh Qi Zhang,1 Mihee Oh,1 Jong-Hwa Kim,1 Rungravee Kanjanasuntree,1 Maytiya Konkit,1 Ampaitip Sukhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A novel Gram-stain-positive, strictly aerobic, non-endospore-forming bacterium, designated CAU 9143T, was isolated from a hydric soil sample collected from Seogmo Island in the Republic of Korea. Strain CAU 9143T grew optimally at 30 C, at pH 7.0 and in the presence of 1 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain CAU 9143T belonged to the genus Arthrobacter and was closely related to Arthrobacter ginkgonis SYP-A7299T (97.1 % T similarity). Strain CAU 9143 contained menaquinone MK-9 (H2) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and two unidentified phospholipids as the major polar lipids. The whole-cell sugars were glucose and galactose. The peptidoglycan type was A4a (L-Lys–D-Glu2) and the major cellular fatty T acid was anteiso-C15 : 0. The DNA G+C content was 64.4 mol% and the level of DNA–DNA relatedness between CAU 9143 and the most closely related strain, A. ginkgonis SYP-A7299T, was 22.3 %. Based on phenotypic, chemotaxonomic and genetic data, strain CAU 9143T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter paludis sp. nov. is proposed. The type strain is CAU 9143T (=KCTC 13958T,=CECT 8917T).
    [Show full text]
  • Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman
    University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2015 Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes Daniel Colman Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Colman, Daniel. "Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes." (2015). https://digitalrepository.unm.edu/biol_etds/18 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Daniel Robert Colman Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach , Chairperson Robert Sinsabaugh Laura Crossey Diana Northup i Diversity of understudied archaeal and bacterial populations from Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico, 2009 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July 2015 ii DEDICATION I would like to dedicate this dissertation to my late grandfather, Kenneth Leo Colman, associate professor of Animal Science in the Wool laboratory at Montana State University, who even very near the end of his earthly tenure, thought it pertinent to quiz my knowledge of oxidized nitrogen compounds. He was a man of great curiosity about the natural world, and to whom I owe an acknowledgement for his legacy of intellectual (and actual) wanderlust.
    [Show full text]
  • Relative Contributions of Archaea and Bacteria to Aerobic Ammonia Oxidation in the Environment
    Environmental Microbiology (2008) 10(11), 2931–2941 doi:10.1111/j.1462-2920.2008.01775.x Minireview Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment James I. Prosser* and Graeme W. Nicol in linking specific microbial groups to ecosystem Institute of Biological and Environmental Sciences, function and the limitations of reliance on laboratory University of Aberdeen, Cruickshank Building, St. cultures. Machar Drive, Aberdeen AB24 3UU, UK. Introduction Summary The accumulation of evidence for the existence and Traditionally, organisms responsible for major importance of mesophilic archaea in ammonia oxidation biogeochemical cycling processes have been deter- has had a significant impact on the contemporary view of mined by physiological characterization of environ- nitrification (Francis et al., 2007). Since the isolation of mental isolates in laboratory culture. Molecular autotrophic prokaryotes in the late 19th century, it has techniques have, however, confirmed the widespread been assumed that all autotrophic ammonia oxidizers are occurrence of abundant bacterial and archaeal bacteria. Early isolates are presumed to have been groups with no cultivated representative, making it bacterial and, until recently, all cultivated, aerobic, difficult to determine their ecosystem function. Until autotrophic ammonia oxidizers were betaproteobacteria recently, ammonia oxidation, the first step in the glo- or gammaproteobacteria (Koops et al., 2003). This article bally important process of nitrification, was thought assesses the current evidence for the role of mesophilic to be performed almost exclusively by bacteria. archaeal ammonia oxidizers in terrestrial, marine and Metagenome studies, followed by laboratory isola- wastewater treatment environments, in comparison with tion, then demonstrated the potential for significant that of bacteria.
    [Show full text]
  • Assessing the Use of Archaeal Lipids As Marine Environmental Proxies
    EA41CH14-Ingalls ARI 30 April 2013 15:56 Assessing the Use of Archaeal Lipids as Marine Environmental Proxies Ann Pearson1 and Anitra E. Ingalls2 1Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 02138; email: [email protected] 2School of Oceanography, University of Washington, Seattle, Washington 98195; email: [email protected] Annu. Rev. Earth Planet. Sci. 2013. 41:359–84 Keywords First published online as a Review in Advance on paleothermometry, lipid biomarkers, TEX86, Thaumarchaeota, March 7, 2013 Euryarchaeota, marine prokaryotes The Annual Review of Earth and Planetary Sciences is online at earth.annualreviews.org Abstract by Harvard University on 12/05/13. For personal use only. This article’s doi: Archaea are abundant in marine and terrestrial aquatic environments, sed- 10.1146/annurev-earth-050212-123947 iments, and soils. They inhabit at least an 85◦C temperature range from Copyright c 2013 by Annual Reviews. the polar ocean to hydrothermal springs. Many Archaea produce membrane All rights reserved lipids called glycerol dialkyl glycerol tetraethers (GDGTs). Experiments on Annu. Rev. Earth Planet. Sci. 2013.41:359-384. Downloaded from www.annualreviews.org pure and enrichment cultures as well as an empirical correlation for ma- rine sediments (the TEX86 index) together show positive relationships be- tween temperature and the number of cyclopentane or cyclohexane rings in GDGTs. The resulting TEX86 paleotemperature proxy has been applied across a wide range of geologic history and depositional settings. The ex- act relationship between TEX86 and temperature, however, remains poorly understood. Environmental systems and cultures have different temperature dependencies, and the ecological niche(s) of aquatic Archaea are still a sub- ject of active investigation.
    [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]
  • Archaeology of Eukaryotic DNA Replication
    Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Archaeology of Eukaryotic DNA Replication Kira S. Makarova and Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Correspondence: [email protected] Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously un- characterized archaeal proteins involved in replication and currently reveal a nearly com- plete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were compa- rable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionali- zation of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific dupli- cations of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal rep- lication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages. ouble-stranded DNA is the molecule that Okazaki fragments (Kornberg and Baker 2005; Dcarries genetic information in all cellular Barry and Bell 2006; Hamdan and Richardson life-forms; thus, replication of this genetic ma- 2009; Hamdan and van Oijen 2010).
    [Show full text]
  • Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
    Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA.
    [Show full text]
  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Archaeal Lipid-Inferred Paleohydrology and Paleotemperature of Lake
    1 Archaeal lipid-inferred paleohydrology and paleotemperature of 2 Lake Chenghai during the Pleistocene-Holocene transition 3 Weiwei Sun a, Enlou Zhang a, b, *, Jie Chang a, James Shulmeister c, d, Michael I. Bird e, 4 f, Cheng Zhao a, b, Qingfeng Jiang g, Ji Shen a 5 a State Key Laboratory of Lake Science and Environment, Nanjing Institute of 6 Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China 7 b Center for Excellence in Quaternary Science and Global Change, Chinese Academy 8 of Science, Xian 710061, China 9 c School of Earth and Environmental Sciences, The University of Queensland, St 10 Lucia, Brisbane, Qld, 4072, Australia 11 d School of Earth and Environment, University of Canterbury, Private Bag 4800, 12 Christchurch, New Zealand 13 e ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook 14 University, PO Box 6811, Cairns, Queensland, 4870, Australia 15 f College of Science and Engineering, James Cook University, PO Box 6811, Cairns, 16 Queensland, 4870, Australia 17 g School of Geography Sciences, Nantong University, Nantong, 226007, China 18 * Corresponding authors. [email protected]. State Key Laboratory of Lake 19 Science and Environment, Nanjing Institute of Geography and Limnology, Chinese 20 Academy of Sciences, Nanjing 210008, China 21 22 23 24 1 25 ABSTRACT 26 Over the past decades, paleoenvironmental studies in the Indian Summer 27 Monsoon (ISM) region have mainly focused on precipitation change, with few 28 published terrestrial temperature records from the region. We analyzed the distribution 29 of isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) in the sediments of 30 Lake Chenghai in southwest China across the Pleistocene–Holocene transition, to 31 extract both regional hydrological and temperature signals for this important transition 32 period.
    [Show full text]
  • The Enigmatic Structure of the Crenarchaeol Isomer ⇑ Jaap S
    Organic Geochemistry 124 (2018) 22–28 Contents lists available at ScienceDirect Organic Geochemistry journal homepage: www.elsevier.com/locate/orggeochem The enigmatic structure of the crenarchaeol isomer ⇑ Jaap S. Sinninghe Damsté a,b, , W. Irene C. Rijpstra a, Ellen C. Hopmans a, Mimi J. den Uijl c, Johan W.H. Weijers c, Stefan Schouten a,b a NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands b Utrecht University, Faculty of Geosciences, Department of Earth Sciences, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands c Shell Global Solutions International B.V., Grasweg 31, 1031 HW Amsterdam, The Netherlands article info abstract Article history: Isolation of crenarchaeol and its isomer from marine surface sediments, followed by ether cleavage and Received 30 March 2018 GC–MS characterization using supersonic molecular beam (SMB) ionization of the biphytanes formed, Received in revised form 12 June 2018 revealed that the crenarchaeol isomer comprises a tricyclic biphytane that is stereochemically different Accepted 12 June 2018 from the tricyclic biphytane of crenarchaeol. This isomeric tricyclic biphytane was also released from the Available online 15 June 2018 crenarchaeol isomer in extant Thaumarchaeotal biomass. Reinterpretation of previously obtained 13C NMR data of the crenarchaeol isomer suggested that the cyclopentane moiety adjacent to the cyclohexyl Keywords: moiety of the tricyclic biphytane of the crenarcheaol isomers possesses the unusual cis stereochemistry in Crenarchaeol comparison to the trans stereochemistry of all cyclopentane moieties in crenarchaeol. This stereochem- Structural determination ical difference likely affects the packing of lipid membranes of Thaumarchaeota and therefore provides a TEX86 Archaea biophysical explanation for the role of the crenarchaeol isomer in the TEX86 palaeothermometer based on Thaumarchaeota fossilized Thaumarcheotal lipids.
    [Show full text]
  • Benthic Archaea As Potential Sources of Tetraether Membrane Lipids in Sediments Across an Oxygen Minimum Zone” by Marc A
    Biogeosciences Discuss., https://doi.org/10.5194/bg-2017-289-RC1, 2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 4.0 License. Interactive comment on “Benthic Archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone” by Marc A. Besseling et al. Anonymous Referee #1 Received and published: 30 September 2017 The manuscript by Besseling et al. describes the distribution of archaeal intact po- lar tetraether lipids and their covariation with archaeal 16S rRNA genes in the Ara- bian Sea. Given the ever-expanding diversity of uncultivated archaea discovered by next-gen sequencing, “next gen” lipidomics techniques such as UHPLC-high-resolution mass spectrometry techniques need to be further developed and applied to allow lipid source assignments that in turn will improve the use of intact polar lipid biomarkers and improve our understanding of the mechanisms of, and problems with, proxies such as TEX86. The high-throughput sequencing methods used by the authors are state of the art. However, the methodology for intact polar lipid analysis employed by the authors is sub-par. While I agree that the use of high-resolution mass spectrometry represents C1 a significant improvement over previous analyses on the same samples, the chromato- graphic method used by the authors does not satisfy this potential. In fact, I have reason to believe that the results of this study are severely flawed by the choice of chromatographic method. Thus, I cannot recommend publication of this work in Bio- geosciences in the current form. I urge the authors to re-analyze their data using more appropriate reversed phase HPLC-MS methods.
    [Show full text]