DOCSLIB.ORG

Carbohydrate Hydrolysis and Transport in the Extreme Thermoacidophile Sulfolobus Solfataricus Sreedevi Lalithambika University of Nebraska-Lincoln

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Carbohydrate Hydrolysis and Transport in the Extreme Thermoacidophile Sulfolobus Solfataricus Sreedevi Lalithambika University of Nebraska-Lincoln University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 2012 Carbohydrate Hydrolysis and Transport in the Extreme Thermoacidophile Sulfolobus solfataricus Sreedevi Lalithambika University of Nebraska-Lincoln Landon Peterson University of Nebraska-Lincoln Karl Dana University of Nebraska-Lincoln Paul H. Blum University of Nebraska - Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/bioscifacpub Part of the Biology Commons Lalithambika, Sreedevi; Peterson, Landon; Dana, Karl; and Blum, Paul H., "Carbohydrate Hydrolysis and Transport in the Extreme Thermoacidophile Sulfolobus solfataricus" (2012). Faculty Publications in the Biological Sciences. 515. http://digitalcommons.unl.edu/bioscifacpub/515 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Carbohydrate Hydrolysis and Transport in the Extreme Thermoacidophile Sulfolobus solfataricus Sreedevi Lalithambika, Landon Peterson, Karl Dana, and Paul Blum Beadle Center for Genetics, University of Nebraska—Lincoln, Lincoln, Nebraska, USA Extremely thermoacidophilic microbes, such as Sulfolobus solfataricus, are strict chemoheterotrophs despite their geologic niche. To clarify their ecophysiology, the overlapping roles of endoglucanases and carbohydrate transporters were examined during growth on soluble cellodextrins as the sole carbon and energy source. Strain-specific differences in genome structure implied a unique role for one of three endogenous endoglucanases. Plasmid-based endoglucanase expression promoted the consumption of oligosaccharides, in- cluding cellohexaose (G6) through cellonanaose (G9). Protein transporters required for cellodextrin uptake were identified through mutagenesis and complementation of an ABC transporter cassette, including a putative oligosaccharide binding protein. In addition, ablation of the binding protein compromised growth on glucose and alpha-linked oligosaccharides while inactivation of a previously described glucose transporter had no apparent impact. These data demonstrate that S. solfataricus employs a redundant mechanism for soluble cellodextrin catabolism having both substrate uptake and extracytoplasmic hydrolytic components. ulfolobus solfataricus is an extremely thermophilic and acido- ries, oligodipeptide transporters and carbohydrate uptake trans- Sphilic organism that thrives in hot acidic habitats, growing porters (2, 3). The oligodipeptide transporters possess a signal optimally between pH values of 3 and 4 at 70 to 90°C (7, 12). S. sequence followed by a catalytic domain, a serine/threonine solfataricus belongs to the archaeal domain and the phylum Cren- linker, and a hydrophobic domain, while sugar transporters con- archaeota (36). It is an obligate aerobe and chemoheterotroph that tain a type III signal sequence followed by a hydrophobic domain, grows on a variety of reduced carbon sources, including simple a serine/threonine linker, and a catalytic domain (2, 35). While sugars and more complex carbohydrates, such as starch (12, 17) these glucose transporter genes were expressed constitutively, and cellulose (38). Even though its native habitat excludes plants, those involved in arabinose uptake were inducible (24). Sso3053 nearby vegetation may be introduced by natural events. Resident (annotated as MalE) was previously reported as a maltose binding conditions are likely to promote chemical transformation of this protein due to the transcription of the gene in the presence of lignocellulosic material, providing carbon for growth. maltose, while Sso2669 (CbtA) bound cellobiose (13). Interest- Glycosyl hydrolase enzymes are classified into 128 families ingly, a recently described oligodipeptide transporter (16) also (GHF) and 14 clans. Those derived from extremophiles have provides a receptor for virus-host interaction (14). To obtain an gained considerable attention because of their inherent thermo- understanding of the potential overlap between sugar transporters stability and resistance to extremes of pH (5, 6, 10, 15, 19–23, 27, and oligosaccharide hydrolysis, in this study, a genetics-based ap- 31, 32). Three homologous open reading frames (ORFs) have proach was used to examine their impacts on cellodextrin utiliza- been identified in the genome of S. solfataricus strain P2 tion. (DSM1617) as putative extracellular cellulases (35). These genes encode endoglucanases belonging to GHF 12 and lack a cellulose MATERIALS AND METHODS binding domain (CBD). However, an N-terminal signal peptide Archaeal strains and construction. The strains used in this study are listed ranging from 21 to 24 amino acids is present that could guide in Table 1. The strains were grown in modified Allen’s medium in batch membrane targeting and/or secretion. The Sso2534 gene product, culture at 80°C and pH 3.0 with aeration, as described previously (4, 7). Five- identified in the growth medium of S. solfataricus strain MT4, milliliter cultures were cultivated in glass screw-cap test tubes placed in rotary exhibited optimal endoglucanase activity on carboxymethyl cellu- tube-drum agitators mounted in forced-air incubators with external DC mo- lose (CMC) at pH 5.8 and 65°C (23). A recombinant form of tors. A mixture of soluble cellodextrins prepared by dilute acid hydrolysis of Sigmacell (Sigma) was added to modified Allen’s medium at a concentration Sso1949, cloned from S. solfataricus strain P2 (DSM1617) and of 1:4 (vol/vol). Other sugars were added as indicated at 0.2% (wt/vol). For a expressed in Escherichia coli, had optimum activity at pH 1.8 and complex medium, tryptone was added at 0.2% (wt/vol). Growth was moni- 80°C. The enzyme utilized cellotetraose as the smallest substrate tored by absorption at 540 nm. The differences between biological replicates and generated cellobiose and cellotriose as the primary products, are shown in the figures as error bars. Spent culture medium was obtained by indicating it was an endoglucanase (19). Both endoglucanase and successive passages of specific cell lines with cell removal by sterile filtration. A xylanase activities were identified for the native form of Sso1354 solid medium was prepared as described previously (17). (9, 27). The enzyme was purified from S. solfataricus strain O␣ and hydrolyzed CMC, producing cellobiose and cellooligomers under optimal conditions of pH 3.5 and 90°C (27). Received 30 May 2012 Accepted 28 August 2012 The presence of these endoglucanases implies the existence of Published ahead of print 31 August 2012 oligosaccharide transporters that would enable substrate uptake Address correspondence to Paul Blum, [email protected]. and subsequent catabolism. Binding-protein-dependent ABC Copyright © 2012, American Society for Microbiology. All Rights Reserved. transporters are a common transport system in S. solfataricus (2). doi:10.1128/AEM.01758-12 Sugar transporters in these organisms are assigned to two catego- November 2012 Volume 78 Number 22 Applied and Environmental Microbiology p. 7931–7938 aem.asm.org 7931 Lalithambika et al. TABLE 1 Strain list Genomic analysis of S. solfataricus strains. NCBI BLASTp was used Reference(s) to analyze the duplicated region centered around Sso1354 in S. solfataricus Strain Description or source strain P2 (DSM1617). The corresponding but deleted region in strain 98/2 PBL2000 S. solfataricus strain 98/2 (wild type) 30 (PBL2000) (30) was identified by PCR analysis with primers flanking the PBL2025 PBL2000; deletion of Sso3004 to Sso3050 33 deletion region, followed by sequencing and NCBI BLASTn analysis. DSM1617 S. solfataricus P2 (wild type) DSMZ Mixed-acid hydrolysis of cellulose. Generation of mixed soluble cel- PBL2028 PBL2000; deletion of Sso3017 to Sso3050; IS1::Sso3053 18, 33 lodextrins from hydrolysis of microcrystalline cellulose was as described PBL2091 PBL2025; deletion of Sso0615 to Sso0616 (pyrEF)by This work previously (39) with modifications. Sigmacell in 2-g amounts was gradu- markerless exchange ally added to 16 ml of ice-cold concentrated hydrochloric acid while stir- PBL2092 PBL2091; Sso1949::lacS, Sso2534::pyrEF by linear This work recombination ring. Then, 4 ml of ice-cold concentrated sulfuric acid was gradually PBL2074 PBL2025; Sso1949::lacS by linear recombination This work added, and the flask was capped with a rubber stopper and stirred gently PBL2105 PBL2025; deletion of Sso3052 to Sso3060 using This work for4hatroom temperature. The hydrolysate was then poured into 180 ml plasmid pBN1202 (pUC19; Sso3052::lacS::Sso3060) of Ϫ20°C acetone, chilled at Ϫ20°C for 2 h, and then filtered through a by consecutive single crossover Millipore AP40 glass fiber filter. The filter cake of cellodextrins was PBL2099 PBL2091/pBN1226 (pKlacS; Sso1354::C-His6) This work washed four times with 20 ml Ϫ20°C acetone. The filter cake was resus- PBL2106 PBL2025; deletion of Sso2833 to Sso2850 using This work plasmid pBN1204 (pUC19; Sso2833::lacS::Sso2850) pended with 60 ml of deionized water and stirred overnight in an open by linear recombination container to evaporate residual acetone. The next day, the pH for the PBL2113 PBL2028/pBN1239 (pKlacS; Sso3053) This work hydrolysate was adjusted to 3.0 using potassium hydroxide, and the mix- ture was centrifuged
Load more

Recommended publications
  • 18Th EANA Conference European Astrobiology Network Association
    18th EANA Conference European Astrobiology Network Association 24-28 September 2018 Freie Universität Berlin, Germany Sponsors: Scientific Organizing Committee (EANA Council): Daniela Billi, Italy Oleg Kotsyurbenko, Russia Alexis Brandeker, Sweden Helmut Lammer, Austria John Brucato, Italy Harry Lehto, Finland Barbara Cavalazzi, Italy Kirsi Lehto, Finland Elias Chatzitheodoridis, Greece Zita Martins, Portugal Charles Cockell, UK Nigel Mason, UK Hervé Cottin, France Ralf Möller, Germany Rosa De la Torre, Spain Christine Moissl-Eichinger, Austria Jean-Pierre De Vera, Germany Lena Noack, Germany René Demets, ESA Karen Olsson-Francis, UK Cristina Dobrota, Romania François Raulin, France Pascale Ehrenfreund, The Netherlands Petra Rettberg, Germany Franco Ferrari, Poland Séverine Robert, Belgium Kai Finster, Denmark Gyorgyi Ronto, Hungary Muriel Gargaud, France Dirk Schulze-Makuch, Germany Beda Hofmann, Switzerland Alan Schwartz, The Netherlands Nils Holm, Sweden Ewa Szuszkiewicz, Poland Jan Jehlicka, Czech Republic Ruth-Sophie Taubner, Austria Jean-Luc Josset, Switzerland Jorge Vago, The Netherlands Kensei Kobayashi, Japan Frances Westall, France Local Organizing Committee: Lena Noack (FU) Lutz Hecht (MfN, FU) Jean-Pierre de Vera (DLR, DAbG) Jacob Heinz (TU) Dirk Schulze-Makuch (TU, DAbG) Dennis Höning (VU Amsterdam) Alessandro Airo (TU) Deborah Maus (TU) Felix Arens (FU) Ralf Möller (DLR) Alexander Balduin Carolin Rabethge (FU) Mickael Baqué (DLR) Heike Rauer (DLR, TU, FU) Doris Breuer
    [Show full text]
  • Sulfur Metabolism Pathways in Sulfobacillus Acidophilus TPY, a Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 18 November 2016 doi: 10.3389/fmicb.2016.01861 Sulfur Metabolism Pathways in Sulfobacillus acidophilus TPY, A Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent Wenbin Guo 1, Huijun Zhang 1, 2, Wengen Zhou 1, 2, Yuguang Wang 1, Hongbo Zhou 2 and Xinhua Chen 1, 3* 1 Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China, 2 Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, China, 3 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory forMarine Science and Technology, Qingdao, China Sulfobacillus acidophilus TPY, isolated from a hydrothermal vent in the Pacific Ocean, is a moderately thermoacidophilic Gram-positive bacterium that can oxidize ferrous iron or Edited by: sulfur compounds to obtain energy. In this study, comparative transcriptomic analyses of Jake Bailey, University of Minnesota, USA S. acidophilus TPY were performed under different redox conditions. Based on these Reviewed by: results, pathways involved in sulfur metabolism were proposed. Additional evidence M. J. L. Coolen, was obtained by analyzing mRNA abundance of selected genes involved in the sulfur Curtin University, Australia Karen Elizabeth Rossmassler, metabolism of sulfur oxygenase reductase (SOR)-overexpressed S. acidophilus TPY Colorado State University, USA recombinant under different redox conditions. Comparative transcriptomic analyses of *Correspondence: S. acidophilus TPY cultured in the presence of ferrous sulfate (FeSO4) or elemental Xinhua Chen sulfur (S0) were employed to detect differentially transcribed genes and operons involved [email protected] in sulfur metabolism.
    [Show full text]
  • Extremely Thermophilic Microorganisms As Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals
    REVIEW published: 05 November 2015 doi: 10.3389/fmicb.2015.01209 Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals Benjamin M. Zeldes 1, Matthew W. Keller 2, Andrew J. Loder 1, Christopher T. Straub 1, Michael W. W. Adams 2 and Robert M. Kelly 1* 1 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point Edited by: that the use of these microorganisms as metabolic engineering platforms has become Bettina Siebers, University of Duisburg-Essen, possible. While in its early days, complex metabolic pathways have been altered or Germany engineered into recombinant extreme thermophiles, such that the production of fuels and Reviewed by: chemicals at elevated temperatures has become possible. Not only does this expand the Haruyuki Atomi, thermal range for industrial biotechnology, it also potentially provides biodiverse options Kyoto University, Japan Phillip Craig Wright, for specific biotransformations unique to these microorganisms. The list of extreme University of Sheffield, UK thermophiles growing optimally between 70 and 100◦C with genetic toolkits currently *Correspondence: available includes archaea and bacteria, aerobes and anaerobes, coming from genera Robert M.
    [Show full text]
  • Perspectives
    Copyright 1999 by the Genetics Society of America Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove What Archaea Have to Tell Biologists William B. Whitman,* Felicitas Pfeifer,² Paul Blum³ and Albrecht Klein§ *Department of Microbiology, University of Georgia, Athens Georgia 30602-2605, ²Institut fuer Mikrobiologie und Genetik, Technischen Universitaet, D-64287 Darmstadt Germany, ³School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666 and §Fachbereich Biologie-Genetik, Universitaet Marburg, D-35043 Marburg, Germany E are excited to present the following review and While the study of fascinating microorganisms needs W research articles on archaeal research, and we no special justi®cation, the archaea provide unique op- thank the Genetics Society of America for this opportu- portunities to gain insight into a number of fundamen- nity. In addition, we recognize the contributions of our tal problems in biology. As one of the most ancient colleagues, Charles Daniels (Ohio State University) and lineages of living organisms, the archaea set a boundary Michael Thomm (Universitaet Kiel), who along with for evolutionary diversity and have the potential to offer the authors served as coeditors of papers on archaea in key insights into the early evolution of life, including this volume. the origin of the eukaryotes. Many archaea are also More than two decades after the initial proposal, the extremophiles that ¯ourish at high temperature, low or archaeal hypothesis remains the best explanation for high pH, or high salt and delineate another boundary the unexpected diversity of molecular and biochemical for life, the biochemical and geochemical boundary, properties found in the prokaryotes.
    [Show full text]
  • ELBA BIOFLUX Extreme Life, Biospeology & Astrobiology International Journal of the Bioflux Society
    ELBA BIOFLUX Extreme Life, Biospeology & Astrobiology International Journal of the Bioflux Society A short review on tardigrades – some lesser known taxa of polyextremophilic invertebrates 1Andrea Gagyi-Palffy, and 2Laurenţiu C. Stoian 1Faculty of Environmental Sciences and Engineering, Babeş-Bolyai University, Cluj- Napoca, Romania; 2Faculty of Geography, Babeş-Bolyai University, Cluj-Napoca, Romania. Corresponding author: A. Gagyi-Palffy, [email protected] Abstract. Tardigrades are polyextremophilic small organisms capable to survive in a variety of extreme conditions. By reversibly suspending their metabolism (cryptobiosis – tun state) tardigrades can dry or freeze and, thus, survive the extreme conditions like very high or low pressure and temperatures, changes in salinity, lack of oxygen, lack of water, some noxious chemicals, boiling alcohol, even the vacuum of the outer space. Despite their peculiar morphology and amazing diversity of habitats, relatively little is known about these organisms. Tardigrades are considered some lesser known taxa. Studying tardigrades can teach us about the evolution of life on our planet, can help us understand what extremophilic evolution and adaptation means and they can show us what forms of life may develop on other planets. Key Words: tardigrades, extremophiles, extreme environments, adaptation. Rezumat. Tardigradele sunt mici organisme poliextremofile capabile să supraviețuiască într-o varietate de condiţii extreme. Suspendandu-şi reversibil metabolismul (criptobioză) tardigradele pot să se usuce sau să îngheţe şi, astfel, să supravieţuiască unor condiţii extreme precum presiuni şi temperaturi foarte scăzute sau crescute, variaţii de salinitate, lipsă de oxygen, lipsă de apă, unele chimicale toxice, alcool în fierbere, chiar şi vidul spaţiului extraterestru. În ciuda morfologiei lor deosebite şi a diversittii habitatelor lor, se cunosc relativ puţine aspecte se despre aceste organisme.
    [Show full text]
  • Deep-Sea Hydrothermal Vent Euryarchaeota 2”
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE ORIGINAL RESEARCH ARTICLE published: 20 February 2012provided by PubMed Central doi: 10.3389/fmicb.2012.00047 Distribution, abundance, and diversity patterns of the thermoacidophilic “deep-sea hydrothermal vent euryarchaeota 2” Gilberto E. Flores†, Isaac D. Wagner,Yitai Liu and Anna-Louise Reysenbach* Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, USA Edited by: Cultivation-independent studies have shown that taxa belonging to the “deep-sea Kirsten Silvia Habicht, University of hydrothermal vent euryarchaeota 2” (DHVE2) lineage are widespread at deep-sea Southern Denmark, Denmark hydrothermal vents. While this lineage appears to be a common and important mem- Reviewed by: Kuk-Jeong Chin, Georgia State ber of the microbial community at vent environments, relatively little is known about their University, USA overall distribution and phylogenetic diversity. In this study, we examined the distribu- Elizaveta Bonch-Osmolovskyaya, tion, relative abundance, co-occurrence patterns, and phylogenetic diversity of cultivable Winogradsky Institute of Microbiology thermoacidophilic DHVE2 in deposits from globally distributed vent fields. Results of quan- Russian Academy of Sciences, Russia titative polymerase chain reaction assays with primers specific for the DHVE2 and Archaea *Correspondence: Anna-Louise Reysenbach, demonstrate the ubiquity of the DHVE2 at deep-sea vents and suggest that they are sig- Department of Biology, Center for nificant members of the archaeal communities of established vent deposit communities. Life in Extreme Environments, Local similarity analysis of pyrosequencing data revealed that the distribution of the DHVE2 Portland State University, PO Box was positively correlated with 10 other Euryarchaeota phylotypes and negatively correlated 751, Portland, OR 97207-0751, USA.
    [Show full text]
  • Resolving a Piece of the Archaeal Lipid Puzzle COMMENTARY Ann Pearsona,1
    COMMENTARY Resolving a piece of the archaeal lipid puzzle COMMENTARY Ann Pearsona,1 Lipid membranes are common to all cells, despite archaea, in which it is observed that a higher fractional occurring in many different forms across Earth’s great abundance of cyclopentane rings is associated with biotic diversity. Among the most distinctive mem- higher growth temperature (1, 11). Refined calibra- branes are those formed by the archaea, whose lipids tions of the TEX86 index and its response to upper are characterized by sn-2,3-glycerol stereochemistry ocean temperatures have made it a key tool for the (in contrast to sn-1,2-glycerol in bacteria and eukarya), paleoclimate community (12). isoprenoid rather than acetyl hydrophobic chains, and However, archaeal groups in addition to Thaumarch- frequent occurrence as membrane-spanning macrocycle aeota also make cyclopentane-containing GDGTs, includ- structures (1). The membrane-spanning lipids consist ing the Crenarchaeota and many divisions of Euryarchaeota of mixed assemblages of structural isomers contain- (Fig. 1A). In particular, the surface-dwelling Marine ingupto8internalcyclopentanerings(GDGT-0 Group II (MG-II) Euryarchaeota have been suggested through GDGT-8 [glycerol dibiphytanyl glycerol tet- to be GDGT sources (13). This would affect TEX86 raethers with zero to 8 rings]) (Fig. 1). Many aspects of signals if their ring distributions have different physio- the biosynthesis of these unusual structures remain un- logical controls compared to Thaumarchaeota. Such known, but, in PNAS, Zeng et al. (2) take an important differences in lipid response might be expected, be- step forward by revealing genes encoding for 2 enzymes cause, to date, the known ammonia-oxidizing Thau- involved in synthesis of the cyclopentane moieties.
    [Show full text]
  • Experimental Microbial Evolution of Extremophiles Paul H
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 2016 Experimental Microbial Evolution of Extremophiles Paul H. Blum University of Nebraska-Lincoln, [email protected] Deepak Rudrappa University of Nebraska–Lincoln, [email protected] Raghuveer Singh University of Nebraska - Lincoln, [email protected] Samuel McCarthy University of Nebraska-Lincoln, [email protected] Benjamin J. Pavlik University of Nebraska- Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/bioscifacpub Part of the Biology Commons Blum, Paul H.; Rudrappa, Deepak; Singh, Raghuveer; McCarthy, Samuel; and Pavlik, Benjamin J., "Experimental Microbial Evolution of Extremophiles" (2016). Faculty Publications in the Biological Sciences. 623. http://digitalcommons.unl.edu/bioscifacpub/623 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published (as Chapter 22) in P. H. Rampelotto (ed.), Biotechnology of Extremophiles, Grand Challenges in Biology and Biotechnology 1, pp. 619–636. DOI 10.1007/978-3-319-13521-2_22 Copyright © 2016 Springer International Publishing Switzerland. digitalcommons.unl.edu Used by permission. Experimental Microbial Evolution of Extremophiles Paul Blum,1 Deepak Rudrappa,1 Raghuveer Singh,1 Samuel McCarthy,1 and Benjamin Pavlik2 1 School of Biological Science, University of Nebraska–Lincoln, Lincoln, NE, USA 2 Department of Chemical and Biomolecular Engineering, University of Nebraska–Lincoln, Lincoln, NE, USA Corresponding author — P.
    [Show full text]
  • Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes
    microorganisms Article Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes Charlotte M. van der Graaf 1,* , Javier Sánchez-España 2 , Iñaki Yusta 3, Andrey Ilin 3 , Sudarshan A. Shetty 1 , Nicole J. Bale 4, Laura Villanueva 4, Alfons J. M. Stams 1,5 and Irene Sánchez-Andrea 1,* 1 Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; [email protected] (S.A.S.); [email protected] (A.J.M.S.) 2 Geochemistry and Sustainable Mining Unit, Dept of Geological Resources, Spanish Geological Survey (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain; [email protected] 3 Dept of Mineralogy and Petrology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; [email protected] (I.Y.); [email protected] (A.I.) 4 NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Landsdiep 4, 1797 SZ ‘t Horntje, The Netherlands; [email protected] (N.J.B.); [email protected] (L.V.) 5 Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal * Correspondence: [email protected] (C.M.v.d.G.); [email protected] (I.S.-A.) Received: 30 June 2020; Accepted: 14 August 2020; Published: 21 August 2020 Abstract: Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)—highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ).
    [Show full text]
  • Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes
    bioRxiv preprint doi: https://doi.org/10.1101/766709; this version posted September 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes 2 3 Medina-Chávez Nahui Olin1, Viladomat-Jasso Mariette2, Olmedo-Álvarez Gabriela3, Eguiarte Luis 4 E2, Souza Valeria2, De la Torre-Zavala Susana1,4 5 6 1Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de 7 Biotecnología. Av. Pedro de Alba S/N Ciudad Universitaria. San Nicolás de los Garza, Nuevo León, 8 México. C.P. 66455. 9 2Instituto de Ecología, UNAM, Circuito Exterior S/N anexo Jardín Botánico exterior. Ciudad 10 Universitaria, Ciudad de México, C.P. 04500 11 3Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. 12 Campus Guanajuato, AP 629 Irapuato, Guanajuato 36500, México 13 14 4Correspondence should be addressed to Susana De la Torre-Zavala; 15 [email protected]. 16 17 18 19 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/766709; this version posted September 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 23 Abstract 24 Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), 25 Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that 26 can form small domes where their anoxic inside reminds us of the characteristics of the Archaean 27 Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD).
    [Show full text]
  • 4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
    Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists.
    [Show full text]
  • Genome Sequence of Picrophilus Torridus and Its Implications for Life Around Ph 0
    Genome sequence of Picrophilus torridus and its implications for life around pH 0 O. Fu¨ tterer*, A. Angelov*, H. Liesegang*, G. Gottschalk*, C. Schleper†, B. Schepers‡, C. Dock‡, G. Antranikian‡, and W. Liebl*§ *Institut of Microbiology and Genetics, University of Goettingen, Grisebachstrasse 8, D-37075 Goettingen, Germany; †Institut of Microbiology and Genetics, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 D-Darmstadt, Germany; and ‡Technical Microbiology, Technical University Hamburg–Harburg, Kasernenstrasse 12, 21073 D-Hamburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 20, 2004 (received for review February 26, 2004) The euryarchaea Picrophilus torridus and Picrophilus oshimae are (4–6). After analysis of a number of archaeal and bacterial ge- able to grow around pH 0 at up to 65°C, thus they represent the nomes, it has been argued that microorganisms that live together most thermoacidophilic organisms known. Several features that swap genes at a higher frequency (7, 8). With the genome sequence may contribute to the thermoacidophilic survival strategy of P. of P. torridus, five complete genomes of thermoacidophilic organ- torridus were deduced from analysis of its 1.55-megabase genome. isms are available, which allows a more complex investigation of the P. torridus has the smallest genome among nonparasitic aerobic evolution of organisms sharing the extreme growth conditions of a microorganisms growing on organic substrates and simulta- unique niche in the light of horizontal gene transfer. neously the highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over ATP-consuming primary Methods transport systems demonstrates that the high proton concentra- Sequencing Strategy.
    [Show full text]