WHAT CAN LIFE on EARTH TELL US ABOUT LIFE in the UNIVERSE? CHARLES H. LINEWEAVER & ADITYA CHOPRA Planetary Science Institut
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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. -
Growth of Sedimentary Bathyarchaeota on Lignin As an Energy Source
Growth of sedimentary Bathyarchaeota on lignin as an energy source Tiantian Yua,b,1, Weichao Wuc,d,1, Wenyue Lianga,b, Mark Alexander Levere, Kai-Uwe Hinrichsc,d, and Fengping Wanga,b,2 aState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China; bState Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, 200240 Shanghai, China; cOrganic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany; dDepartment of Geosciences, University of Bremen, 28359 Bremen, Germany; and eInstitute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich, 8092 Zurich, Switzerland Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved April 16, 2018 (received for review October 30, 2017) Members of the archaeal phylum Bathyarchaeota are among the other hand, acetogenesis from H2/CO2 has been proposed for most abundant microorganisms on Earth. Although versatile met- some lineages of Bathyarchaeota (3). The reductive acetyl-CoA abolic capabilities such as acetogenesis, methanogenesis, and fer- pathway for carbon fixation has been identified in most of the mentation have been suggested for bathyarchaeotal members, no obtained bathyarchaeotal genomes (3, 12, 14). Among these, direct confirmation of these metabolic functions has been achieved members of the bathyarchaeotal subgroups Bathy-3 and Bathy- through growth of Bathyarchaeota in the laboratory. Here we dem- 8 have been suggested to be capable of methanogenesis (12). All onstrate, on the basis of gene-copy numbers and probing of ar- the above studies indicate great versatility in the metabolic po- chaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in tentials of Bathyarchaeota, with some lineages possibly being enrichments of estuarine sediments with the biopolymer lignin. -
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 -
Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China
Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China Di Wu Northeast Forestry University Caihong Zhao Northeast Forestry University Hui Bai Forestry Science Research Institute of Heilongjiang Province Fujuan Feng Northeast Forestry University Xin Sui Heilongjiang University Guangyu Sun ( [email protected] ) Northeast Forestry University Research article Keywords: Wetlands, Methanogens, Community diversity, Indicator species, Methanogenic metabolic patterns Posted Date: August 12th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-54821/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/18 Abstract Background: Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. Result: The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably inuenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla – Larix gmelinii wetland was relatively different from the structure of the other two wetland types. -
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). -
Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
An Estimate of the Elemental Composition of Luca
Astrobiology Science Conference 2015 (2015) 7328.pdf AN ESTIMATE OF THE ELEMENTAL COMPOSITION OF LUCA. Aditya Chopra1 and Charles H. Lineweaver1, 1Planetary Science Institute, Research School of Earth Sciences and Research School of Astronomy and Astrophysics, Australian National University, [email protected], [email protected] A number of genomic and proteomic features of composition of life, we attempt to account for life on Earth, like the 16S ribosomal RNA gene, have differences in composition between species and other been highly conserved over billions of years. Genetic phylogenetic taxa (Fig. 2) by weighting datasets such and proteomic conservation translates to conservation that the result represents the root of prokaryotic life of metabolic pathways across taxa. It follows that the (LUCA). Variations in composition between data sets stoichiometry of the elements that make up some of that can be attributed to different growth stages or the biomolecules will be conserved. By extension, the environmental factors are used as estimates of the elemental make up of the whole organism is a uncertainty associated with the average abundances for relatively conserved feature of life on Earth [1,2]. each taxa. We describe how average bulk elemental Euryarchaeota 1a Methanococci, Methanobacteria, Methanopyri 7 Euryarchaeota 1b abundances in extant life can yield an indirect estimate 6 Thermoplasmata, Methanomicrobia, Halobacteria, Archaeoglobi Euryarchaeota 2 4 Thermococci of relative abundances of elements in the Last Crenarchaeota Sulfolobus, Thermoproteus ? Thaumarchaeota Universal Common Ancestor (LUCA). The results Cenarchaeum ? Korarchaeota ARMAN could give us important hints about the stoichiometry ? 2 Archaeal Richmond Mine Acidophilic Nanoorganisms Nanoarchaeota of the environment where LUCA existed and perhaps Archaea Terrabacteria clues to the processes involved in the origin and early Actinobacteria, Deinococcus-Thermus, 1 Cyanobacteria, Life Chloroflexi, 9 evolution of life [3]. -
Establishment and Analysis of Microbial Communities Capable of Producing Methane from Grass Waste at Extremely High C/N Ratio
International Journal of New Technology and Research (IJNTR) ISSN:2454-4116, Volume-2, Issue-9, September 2016 Pages 81-86 Establishment and Analysis of Microbial Communities Capable of Producing Methane from Grass Waste at Extremely High C/N Ratio S. Matsuda, T. Ohtsuki* Anaerobic digestion is a conventional method for biomass Abstract— Acclimation of microbial communities, aiming to utilization [8]. Despite the fact that a great deal of research methane production from grass as a sole substrate at extremely for methane production from grass has been conducted high carbon-to-nitrogen (C/N) ratio, was conducted. In a series especially in recent years, almost processes need supply of of experiments with various sizes of added grass, two microbial communities showing high methane production were obtained abundant sludge source such as sewage and manure [9, 10]. with powdered grass. In the two microbial communities Many studies indicated that the optimal carbon-to-nitrogen designated NR and RP, Bacteroidia including genera (C/N) ratio in methane fermentation were 25-30, and the C/N Bacteroides, Dysgonomonas, Proteiniphilum, and Alistipes were ratio higher than 40 are not generally suitable [11]. The C/N detected as dominant members in eubacteria. It was also shown ration of raw grass shows a wide range; wild grassy weed is at that Methanomicrobia and Methanobacteria including genera relatively high (>59) while lawn grass is at low (<29) [12]. Methanomassiliicoccus and Methanobacterium were found as dominant members in methanogen. It is noteworthy that Therefore, it is difficult to conduct methane fermentation nitrogen fixation were observed both in NR and RP, suggesting with wild grass-only, also being due to less degradability of that insufficiency of nitrogen sources would be complemented lignocellulose [13]. -
Supplementary Information
Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation Po-Hsiang Wang, Yi-Lung Chen, Sean Ting-Shyang Wei, Kan Wu, Tzong-Huei Lee, Tien-Yu Wu, and Yin-Ru Chiang Supplementary Information Table of Contents Dataset Dataset S1. Genome annotation of strain DHT3 and transcriptomic analysis (RNA-Seq) of bacterial cells grown anaerobically with testosterone or estradiol. SI Tables Table S1. Oligonucleotides used in this study. Table S2. Selection of housekeeping genes of strain DHT3 used for constructing the linear regression line in the global gene expression profiles (RNA-Seq). Table S3. Selection of the cobalamin-dependent methyltransferases used for the un-rooted maximum likelihood tree construction. Table S4. UPLC–APCI–HRMS data of the intermediates involved in anaerobic estrone catabolism by strain DHT3. Table S5. 1H- (600 MHz) and 13C-NMR (150 MHz) spectral data of the HPLC-purified metabolite (AND2) and the authentic standard 5-androstan-3,17-diol Table S6. Selection of the bacteria used for comparative analysis of the gene organization for HIP degradation. SI Figures Fig. S1 Scanning electron micrographs of strain DHT3 cells. Fig. S2 Cobalamin as an essential vitamin during the anaerobic growth of strain DHT3 on estradiol. Fig. S3 Arrangement and expression analysis of the emt genes in strain DHT3. Fig. S4 The anaerobic growth of the wild type (A) and the emtA-disrupted mutant (B) of strain DHT3 with testosterone and estradiol. Fig. S5 APCI–HRMS spectrum of the HIP produced by estrone-fed strain DHT3. 1 Fig. S6 UPLC–APCI–HRMS spectra of two TLC-purified androgen metabolites, 17β-hydroxyandrostan-3-one (A) and 3β,17β-dihydroxyandrostane (B). -
Universidad Politécnica De Madrid Escuela Técnica Superior De Ingeniería Agronómica Alimentaria Y De Biosistemas Departamento De Biotecnología-Biología Vegetal
UNIVERSIDAD POLITÉCNICA DE MADRID ESCUELA TÉCNICA SUPERIOR DE INGENIERÍA AGRONÓMICA ALIMENTARIA Y DE BIOSISTEMAS DEPARTAMENTO DE BIOTECNOLOGÍA-BIOLOGÍA VEGETAL TESIS DOCTORAL Caracterización de una nueva proteína hipertermófila NifB y su papel en el mecanismo de síntesis de NifB-co, precursor del grupo metálico de FeMo-co Author: Alessandro Scandurra Director: Prof. Luis Manuel Rubio Herrero Co-director: Dr. Simon Jean Marius Arragain i ii UNIVERSIDAD POLITÉCNICA DE MADRID ESCUELA TÉCNICA SUPERIOR DE INGENIERÍA AGRONÓMICA ALIMENTARIA Y DE BIOSISTEMAS DEPARTAMENTO DE BIOTECNOLOGÍA-BIOLOGÍA VEGETAL Memoria presentada por D. Alessandro Scandurra para optar al grado de Doctor Director Dr. Luis Manuel Rubio Herrero Profesor Titular UPM Madrid, 2017 © This copy oF the thesis has been supplied on condition that anyone who consults it is understood to recognize that its copyright rest with the author and that no quotation From the thesis, or any inFormation derived therefrom may be published without the author’s prior, written consent. I II AcKnowledgments As each journey, also this one has an end (Thanks goodness). It was a long trip, with several changes oF direction. Like For many other people, the PhD adventure was not easy, but I have to admit that I was lucky enough to meet really unique people, that became special Friendships. First oF all, I want to thank my Family, especially my mother and my Father, who always push me to go Forward in my life and to Follow my dreams, ready to pay the sacrifice oF the distance. This expirience has helped me to understand how easy is to be a son and how challenging is to be a parent. -
Lifestyle Preferences Drive the Structure and Diversity of Bacterial and Archaeal Communities in a Small Riverine Reservoir
www.nature.com/scientificreports OPEN Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir Carles Borrego1,2, Sergi Sabater1,3* & Lorenzo Proia1,4 Spatial heterogeneity along river networks is interrupted by dams, afecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil diferences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Diferences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir. Spatial heterogeneity of river networks results from the sequence of lotic segments—which promote the transport and quick transformation of materials—and lentic segments such as large pools and wetlands—which mostly contribute to the process and storage of organic matter 1,2.