DOCSLIB.ORG

A B Comea Oxaloacetate Decarboxylase, Beta Subunit C ATP

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A B Comea Oxaloacetate Decarboxylase, Beta Subunit C ATP C ATP-binding cassette, subfamily B A ComEA WP 025028831 Bacillus mannanilyticus B oxaloacetate decarboxylase, beta subunit WP 041718914 Alkaliphilus oremlandii PKM81186 Firmicutes bacterium HGW-Firmicutes-14 WP 092588843 Acidaminobacter hydrogenoformans Bacillus spp. MZQ96192 Acidaminobacter sp. Paenibacillus spp. 100% WP 088775865 Carboxydothermus islandicus WP 152967700 Oxobacter pfennigii GAV25686 Carboxydothermus islandicus WP 057983007 Virgibacillus soli 70% WP 146620656 Enterococcus florum WP 049886177 Thermacetogenium phaeum WP 064467709 Bacillus galactosidilyticus WP 126109031 Jeotgalibaca sp. H21T32 WP 090886300 Bacillus caseinilyticus Tree scale: 0.1 Peptoclostridium spp. Trichococcus spp. WP 101330798 Halalkalibacillus sp. B3227 WP 156782411 Geosporobacter ferrireducens WP 078755654 Globicatella sulfidifaciens SFQ43799 Desemzia incerta WP 110940224 Geosporobacter subterraneus WP 051258417 Atopococcus tabaci WP 047393312 Carnobacterium sp. ZWU0011 SHI93557 Geosporobacter subterraneus DSM 17957 WP 156883193 Lacticigenium naphtae WP 051237935 Lacticigenium naphtae 100% Natranaerovirga spp. WP 017470521 Amphibacillus jilinensis WP 097004362 amygdalinum Enterococcus spp. 75% HBG15709 Firmicutes bacterium WP 092653112 Isobaculum melis WP 013780596 Mahella australiensis Thermoanaerobacter spp. WP 126780365 Vagococcus salmoninarum WP 087058768 Marinilactibacillus psychrotolerans WP 084110983 Caldanaerobius fijiensis WP 072693424 Marinilactibacillus sp. 15R 2503533728 Mahella australiensis 50-1 BON Caldicellulosiruptor spp. WP 129721893 Clostridiales bacterium SYSU GA17129 WP 034551516 Carnobacterium funditum WP 085558888 Carnobacterium iners WP 035172562 Caldanaerobius polysaccharolyticus WP 035030695 Carnobacterium mobile WP 148866388 Thermosediminibacter litoriperuensis WP 092091739 Pisciglobus halotolerans Tree scale: 0.1 WP 092479393 Desemzia incerta WP 066355053 Fervidicola ferrireducens WP 047390226 Carnobacterium sp. ZWU0011 WP 073256848 Caldanaerovirga acetigignens WP 129724577 Clostridiales bacterium SYSU GA17129 WP 035618223 Lacticigenium naphtae WP 051258509 Atopococcus tabaci Caldicellulosiruptor spp. WP 013780593 Mahella australiensis WP 161878756 Alkalibacterium sp. MB6 WP 091732591 Proteiniborus ethanoligenes WP 068557831 Thermotalea metallivorans Carnobacterium spp. WP 069981092 Geosporobacter ferrireducens WP 083273835 Geosporobacter ferrireducens SHI50782 Geosporobacter subterraneus DSM 17957 WP 110940295 Geosporobacter subterraneus Marinilactibacillus spp. 100% SHI95638 Geosporobacter subterraneus DSM 17957 WP 068554877 Thermotalea metallivorans 70% WP 053956992 Inediibacterium massiliense TXT49091 Spirochaetes bacterium Coprothermobacter spp. WP 122013730 Christensenella sp. Marseille-P3954 WP 129597337 Clostridiaceae bacterium MJB2 ADM94926 uncultured Candidatus Atribacteria bacterium WP 147518066 Clostridiaceae bacterium Tree scale: 0.1 WP 148809203 Crassaminicella sp. SY095 SCJ22543 uncultured Clostridium sp. WP 013781790 Mahella australiensis WP 132242701 Marinisporobacter balticus WP 138295909 Clostridium sp. BSD2780061688st1 E8 WP 121958705 Petrotoga sp. 9PWA.NaAc.5.4 PMP78973 Mesoaciditoga sp. WP 074351176 Proteiniborus sp. DW1 WP 113075498 Petrotoga sp. 9PW.55.5.1 BBJ27901 Athalassotoga saccharophila WP 091726468 Proteiniborus ethanoligenes WP 045088399 Defluviitoga tunisiensis WP 161847846 Athalassotoga saccharophila TAH64304 Anaerolineaceae bacterium WP 103077420 Petrotoga mexicana RKX34253 Thermotogae bacterium Tissierellales spp. POZ92254 Petrotoga halophila DSM 16923 RKX43025 Thermotogae bacterium WP 132028356 Keratinibaculum paraultunense WP 103079499 Petrotoga miotherma Pseudothermotoga spp. WP_053963172_unclassified Clostridiales WP 049755351 Petrotoga mobilis WP 132996078 Sporanaerobacter acetigenes Thermotoga spp. WP 103066106 Petrotoga olearia WP 042678573 Anaerosalibacter massiliensis WP 121515169 Petrotoga sp. HKA.pet.4.5 WP 077368902 Anaerosalibacter sp. Marseille-P3206 RKX45149 Thermotogae bacterium WP 032123611 Clostridium amazonitimonense 2572228733 Petrotoga sp. 8T1HF07.NaAc.6.1 HCZ06355 Thermotogae bacterium WP 055665239 Desnuesiella massiliensis WP 121958814 Petrotoga sp. 9T1HF07.CasAA.8.2 WP 138203422 Haloimpatiens lingqiaonensis WP 121567381 Petrotoga sp. Shatin.DS.tank11.9.2.9.3 Mesotoga spp. WP 102399473 Khelaifiella massiliensis WP 103065687 Petrotoga sp. HWHPT.55.6.3 WP 035292670 Clostridium sp. KNHs214 WP 123821425 Petrotoga sp. HWH.PT.55.6.1 Kosmotoga spp. CDF59104 Thermobrachium celere DSM 8682 WP 051150583 Thermobrachium celere HAI87220 Firmicutes bacterium WP 027309049 Caloramator sp. ALD01 Actinobacteria spp. Fervidobacterium spp. SHF07358 Caloramator proteoclasticus DSM 10124 WP 084106657 Caloramator proteoclasticus GAV32211 Coriobacteriaceae bacterium EMTCatB1 Thermosipho spp. WP 094366828 Romboutsia weinsteinii OFW57222 Actinobacteria bacterium RBG 16 64 13 HBK84687 Firmicutes bacterium RKX54855 Thermotoga sp. WP 026485998 Caldanaerobius polysaccharolyticus Chloroflexi bacterium spp. Marinitoga spp. WP 073345650 Caldanaerobius fijiensis WP 096233476 Thermoanaerobacterium sp. RBIITD Chloroflexi bacterium spp. WP 109603821 Oceanotoga teriensis WP 003869068 Thermoanaerobacter ethanolicus WP 135402601 Geotoga petraea WP 074665633 Thermoanaerobacter thermohydrosulfuricus WP 141789874 Oryzihumus leptocrescens WP 091402256 Geotoga petraea WP 042834190 Thermoanaerobacter sp. YS13 WP 022587481 Caldanaerobacter subterraneus WP 139106986 Mumia sp. Z527 WP 045088467 Defluviitoga tunisiensis WP 009610020 Caldanaerobacter subterraneus WP 039348727 Mumia flava WP 068554563 Thermotalea metallivorans WP 141957508 Actinoallomurus bryophytorum WP 113073651 Petrotoga sp. 9PW.55.5.1 WP 103081172 Pseudoclostridium thermosuccinogenes WP 157631242 Catelliglobosispora koreensis WP 121958130 Petrotoga sp. 9PWA.NaAc.5.4 WP 069193962 Clostridiales HCT79401 Micromonosporaceae bacterium PNR94465 Petrotoga sp. 9PWA.NaAc.5.4 WP 038289160 Hungateiclostridium straminisolvens WP 003518007 Hungateiclostridium thermocellum WP 109133197 Cellulomonas sp. WB94 WP 103067232 Petrotoga olearia WP 013779695 Mahella australiensis Cellulomonas spp. KUK82010 Petrotoga mobilis WP 068749207 Thermovenabulum gondwanense WP 103876932 Petrotoga WP 144016950 Beutenbergia cavernae WP 120766489 Thermoanaerobacterales WP 103076743 Petrotoga mexicana WP 013276302 Thermosediminibacter oceani Cellulomonas spp. WP 103079102 Petrotoga PZN04256 Firmicutes bacterium WP 066350690 Fervidicola ferrireducens WP 115850749 Thermasporomyces composti WP 012209049 Petrotoga mobilis RKX64439 candidate division TA06 bacterium WP 030918385 Streptosporangium amethystogenes WP 121567249 Petrotoga sp. Shatin.DS.tank11.9.2.9.3 PKN79773 Candidatus Cloacimonetes bacterium HGW-Cloacimonetes-1 RQV92520 bacterium Rhodococcus spp. 2572229732 Petrotoga sp. 8T1HF07.NaAc.6.1 WP 144683200 Desulfobotulus alkaliphilus NDL60863 Phytoactinopolyspora sp. XMNu-373 WP 139447101 Desulfobotulus sp. PAR22N WP 103064872 unclassified Petrotoga RKX56515 Thermotoga sp. WP 026875417 Jiangella gansuensis WP 121514761 Petrotoga sp. 9T1HF07.CasAA.8.2 WP 036223367 Mesoaciditoga lauensis WP 015746133 Nakamurella multipartita Kosmotoga spp. and Mesotoga spp. Microbacterium spp. RKX54619 Thermotoga sp. ODU65792 Leifsonia sp. SCN 70-46 HCZ06801 Thermotogae bacterium RKX45705 Thermotogae bacterium Agromyces spp. RKX57037 Thermotoga sp. Thermotoga spp. Thermosipho spp. Fervidobacterium spp. Pseudothermotoga spp. Marinitoga spp. WP 109604002 Oceanotoga teriensis WP 091403634 Geotoga petraea WP 135403012 Geotoga petraea WP 121957003 Petrotoga sp. 9PWA.NaAc.5.4 WP 045087964 Defluviitoga tunisiensis WP 113075352 Petrotoga sp. 9PW.55.5.1 POZ88140 Petrotoga sibirica DSM 13575 WP 103877284 Petrotoga WP 103067341 Petrotoga olearia WP 103079010 Petrotoga 2572229017 Petrotoga sp. 8T1HF07.NaAc.6.1 WP 103077838 Petrotoga mexicana WP 121515358 unclassified Petrotoga 2558333798 Petrotoga sp. 9T1HF07.CasAA.8.2 WP 012209457 Petrotoga 641302858 Petrotoga mobilis SJ95.
Load more

Recommended publications
  • Mannoside Recognition and Degradation by Bacteria Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese
    Mannoside recognition and degradation by bacteria Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese To cite this version: Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese. Mannoside recognition and degradation by bacteria. Biological Reviews, Wiley, 2016, 10.1111/brv.12316. hal- 01602393 HAL Id: hal-01602393 https://hal.archives-ouvertes.fr/hal-01602393 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Biol. Rev. (2016), pp. 000–000. 1 doi: 10.1111/brv.12316 Mannoside recognition and degradation by bacteria Simon Ladeveze` 1, Elisabeth Laville1, Jordane Despres2, Pascale Mosoni2 and Gabrielle Potocki-Veron´ ese` 1∗ 1LISBP, Universit´e de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France 2INRA, UR454 Microbiologie, F-63122, Saint-Gen`es Champanelle, France ABSTRACT Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein–protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them.
    [Show full text]
  • Temperature Control As Key Factor for Optimal Biohydrogen
    Temperature control as key factor for optimal biohydrogen production from thermomechanical pulping wastewater Paolo Dessì a,*, Estefania Porca b, Aino–Maija Lakaniemi a, Gavin Collins b, Piet N. L. Lens a,c a Tampere University of Technology, Faculty of Natural Sciences, P.O. Box 541, FI-33101 Tampere, Finland bMicrobial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland cUNESCO–IHE, Institute for Water Education, Westvest 7, 2611AX Delft, The Netherlands Manuscript submitted to: Biochemical Engineering Journal *Corresponding author: Phone: +358 417239696, e-mail: [email protected], mail: Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland Estefania Porca: [email protected] Aino-Maija Lakaniemi: [email protected] Gavin Collins: [email protected] Piet N.L. Lens: [email protected] 1 Abstract This study evaluates the use of non-pretreated thermo-mechanical pulping (TMP) wastewater as a potential substrate for hydrogen production by dark fermentation. Batch incubations were conducted in a temperature gradient incubator at temperatures ranging from 37 to 80 °C, using an inoculum from a thermophilic, xylose-fed, hydrogen-producing fluidised bed reactor. The aim was to assess the short-term response of the microbial communities to the different temperatures with respect to both hydrogen yield and composition of the active microbial community. High throughput sequencing (MiSeq) of the reversely transcribed 16S rRNA showed that Thermoanaerobacterium sp. dominated the active microbial community at 70 °C, resulting in the -1 highest H2 yield of 3.6 (± 0.1) mmol H2 mol CODtot supplied.
    [Show full text]
  • Genomic Insights from Monoglobus Pectinilyticus: a Pectin-Degrading Specialist Bacterium in the Human Colon
    The ISME Journal (2019) 13:1437–1456 https://doi.org/10.1038/s41396-019-0363-6 ARTICLE Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon 1,2 1,3 4 2 2 5 Caroline C. Kim ● Genelle R. Healey ● William J. Kelly ● Mark L. Patchett ● Zoe Jordens ● Gerald W. Tannock ● 6 6 1 7,8,9 1 Ian M. Sims ● Tracey J. Bell ● Duncan Hedderley ● Bernard Henrissat ● Douglas I. Rosendale Received: 19 April 2018 / Revised: 7 January 2019 / Accepted: 19 January 2019 / Published online: 6 February 2019 © International Society for Microbial Ecology 2019 Abstract Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate- 1234567890();,: 1234567890();,: active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M.
    [Show full text]
  • Development of a Thermophilic Coculture for Corn Fiber Conversion
    ARTICLE https://doi.org/10.1038/s41467-020-15704-z OPEN Development of a thermophilic coculture for corn fiber conversion to ethanol ✉ Dhananjay Beri 1,2, William S. York 2,3,4, Lee R. Lynd1,2,5,6 , ✉ Maria J. Peña 2,3 & Christopher D. Herring1,2,5 The fiber in corn kernels, currently unutilized in the corn to ethanol process, represents an opportunity for introduction of cellulose conversion technology. We report here that Clostridium 1234567890():,; thermocellum can solubilize over 90% of the carbohydrate in autoclaved corn fiber, including its hemicellulose component glucuronoarabinoxylan (GAX). However, Thermoanaerobacterium thermosaccharolyticum or several other described hemicellulose-fermenting thermophilic bacteria can only partially utilize this GAX. We describe the isolation of a previously undescribed organism, Herbinix spp. strain LL1355, from a thermophilic microbiome that can consume 85% of the recalcitrant GAX. We sequence its genome, and based on structural analysis of the GAX, identify six enzymes that hydrolyze GAX linkages. Combinations of up to four enzymes are successfully expressed in T. thermosaccharolyticum. Supplementation with these enzymes allows T. thermosaccharolyticum to consume 78% of the GAX compared to 53% by the parent strain and increases ethanol yield from corn fiber by 24%. 1 Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA. 2 Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA. 3 Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA. 4 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. 5 Enchi Corporation, Lebanon, NH 03766, USA. 6 Department of Biological Sciences, Dartmouth ✉ College, Hanover, NH 03755, USA.
    [Show full text]
  • Expansion Segments in Bacterial and Archaeal 5S Ribosomal Rnas
    Downloaded from rnajournal.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press BIOINFORMATICS Expansion segments in bacterial and archaeal 5S ribosomal RNAs VICTOR G. STEPANOV and GEORGE E. FOX Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA ABSTRACT The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural var- iability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bac- terial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales. When sev- eral copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases. Keywords: ribosome; 5S rRNA; expansion segment; archaea; bacteria INTRODUCTION Expansion segments in 5S rRNAs can certainly be re- garded as a very exotic structural abnormality that deserves 5S ribosomal RNA (5S rRNA) is a small RNA that is an inte- special attention.
    [Show full text]
  • Mesophilic and Thermophilic Biohydrogen and Bioelectricity Production from Real and Synthetic Wastewaters Paolo Dessi
    Mesophilic and thermophilic biohydrogen and bioelectricity production from real and synthetic wastewaters Paolo Dessi To cite this version: Paolo Dessi. Mesophilic and thermophilic biohydrogen and bioelectricity production from real and synthetic wastewaters. Environmental Engineering. Université Paris-Est; Tampereen yliopisto, 2018. English. NNT : 2018PESC2056. tel-02373735 HAL Id: tel-02373735 https://tel.archives-ouvertes.fr/tel-02373735 Submitted on 21 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Joint PhD degree in Environmental Technology Docteur de l’Université Paris-Est Spécialité : Science et Technique de l’Environnement Dottore di Ricerca in Tecnologie Ambientali Degree of Doctor in Environmental Technology Thesis for the degree of Doctor of Philosophy in Environmental Technology Tesi di Dottorato – Thèse – PhD thesis – Väitöskirja Paolo Dessì Mesophilic and thermophilic biohydrogen and bioelectricity production from real and synthetic wastewaters 23/05/2018, Tampere In front of the PhD evaluation committee Prof. Alan Guwy Reviewer Dr. Serge Hiligsmann Reviewer Prof. Jóhann Örlygsson Reviewer Prof. Piet N.L. Lens Promotor Prof. Giovanni Esposito Co-Promotor Prof. Hab. Eric D. van Hullebusch Co-Promotor Asst. Prof. Aino-Maija Lakaniemi Co-Promotor Prof. Jukka Rintala Chair Marie Sklodowska-Curie European Joint Doctorate, Advanced Biological Waste-to-Energy Technologie Evaluation committee Chair Prof.
    [Show full text]
  • © 2016 Hans Müller Paul
    © 2016 Hans Müller Paul BIOCHEMICAL CHARACTERIZATION OF FIVE GH130-FAMILY ENZYMES FROM Caldanaerobius polysaccharolyticus ATCC BAA-17 AND INSIGHTS ON THEIR METABOLIC ROLE AND REACTION MECHANISMS BY HANS MÜLLER PAUL THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Animal Sciences in the Graduate College of the University of Illinois at Urbana-Champaign, 2016 Urbana, Illinois Master's Adviser: Professor Isaac Cann ABSTRACT Proteins in the glycoside hydrolase family 130 (GH130, CAZy database) have been proposed to perform the phosphorolysis of β-1,2 and β-1,4-mannosyl linkages between the mannose at the non-reducing end of substrates and mannose, glucose or N-acetylglucosamine residues, with the subsequent release of α-mannose-1-phosphate. In this study, we compare five different GH130 enzymes (CpMan130 A-E) encoded within the genome of Caldanaerobius polysaccharolyticus, a thermophilic anaerobic bacterium able to ferment mannan as the sole carbon source. Analysis of substrate specificity and end product release allowed for the identification of pathways involving GH130 enzymes in the metabolism of mannans with different structures by this organism. Mechanistic studies involving the binding order and amino acid mapping on a three-dimensional model of Man130B helped to elucidate the ordered sequential bi-bi mechanism utilized by these enzymes. Phylogenetic analysis of over 950 sequences assigned to the GH130 family, combined with differences in amino acid conservation and substrate specificity, revealed a new subgroup for this family, GH130_3, consisting of thermostable enzymes that act on β- 1,2-linked manno-oligosaccharides. The genomic context of all genes in the proposed subgroup GH130_3 suggests that they appear in pairs, preceded by an ABC-like transporter.
    [Show full text]
  • Fermentation of Mannitol Extracts from Brown Macro Algae by Thermophilic Clostridia
    fmicb-09-01931 August 16, 2018 Time: 19:14 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Opin visindi ORIGINAL RESEARCH published: 20 August 2018 doi: 10.3389/fmicb.2018.01931 Fermentation of Mannitol Extracts From Brown Macro Algae by Thermophilic Clostridia Theo Chades, Sean M. Scully, Eva M. Ingvadottir and Johann Orlygsson* Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland Mannitol-containing macro algae biomass, such as Ascophyllum nodosum and Laminaria digitata, are a potential feedstock for the production of biofuels such as bioethanol. The purpose of this work was to evaluate the ability of thermophilic anaerobes within Class Clostridia to ferment mannitol and mannitol-containing algal extracts. Screening of the type strains of six genera, Caldanaerobius, Caldanaerobacter, Caldicellulosiruptor, Thermoanaerobacter, Thermobrachium, and Thermoanaerobacterium) was conducted on 20 mM mannitol and revealed that 11 of 41 strains could utilize mannitol with ethanol being the dominant end-product. Mannitol utilization seems to be most common within the genus of Thermoanaerobacter (7 of 16 strains) with yields up to 88% of the theoretical yield in the case of Thermoanaerobacter pseudoethanolicus. Six selected mannitol-degrading strains (all Thermoanaerobacter Edited by: species) were grown on mannitol extracts prepared from A. nodosum and L. digitata. Nils-Kaare Birkeland, Five of the strains produced similar amounts of ethanol as compared with ethanol University of Bergen, Norway yields from mannitol only. Finally, T. pseudoethanolicus was kinetically monitored using Reviewed by: Hugh Morgan, mannitol and mannitol extracts made from two macro algae species, A. nodosum and University of Waikato, New Zealand L.
    [Show full text]
  • Ph and Phosphate Induced Shifts in Carbon Flow and Microbial Community During Thermophilic Anaerobic Digestion
    microorganisms Article pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion Nina Lackner * , Andreas O. Wagner , Rudolf Markt and Paul Illmer Department of Microbiology, Universität Innsbruck, 6020 Innsbruck, Austria; [email protected] (A.O.W.); [email protected] (R.M.); [email protected] (P.I.) * Correspondence: [email protected] Received: 21 January 2020; Accepted: 17 February 2020; Published: 20 February 2020 Abstract: pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0–8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values 5.5, with the maximum ≤ CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.
    [Show full text]
  • Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria
    ORIGINAL RESEARCH published: 18 November 2016 doi: 10.3389/fmicb.2016.01854 Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria Olga L. Mayorga 1 †, Alison H. Kingston-Smith 1, Eun J. Kim 2, Gordon G. Allison 1, Toby J. Wilkinson 1, Matthew J. Hegarty 1, Michael K. Theodorou 3, Charles J. Newbold 1 and Sharon A. Huws 1* 1 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK, 2 Department of Animal Science, Kyungpook National University, Sangju, Korea, 3 Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, UK Edited by: Understanding the relationship between ingested plant material and the attached Zhongtang Yu, Ohio State University, USA microbiome is essential for developing methodologies to improve ruminant nutrient use Reviewed by: efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial Suzanne Lynn Ishaq, colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based Montana State University, USA Seungha Kang, on the differences in diversity of the attached bacteria. In this study, we investigated Commonwealth Scientific and temporal niche specialization of primary and secondary populations of attached rumen Industrial Research Organisation microbiota using metagenomic shotgun sequencing as well as monitoring changes in the (CSIRO), Australia plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation *Correspondence: Sharon A. Huws using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic [email protected] sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, † Present Address: and Selenomonas dominated the attached microbiome irrespective of time.
    [Show full text]
  • Original Paper Development of Polymerase Chain Reaction And
    _ Food Science and Technology Research, 21 (4), 531 536, 2015 Copyright © 2015, Japanese Society for Food Science and Technology doi: 10.3136/fstr.21.531 http://www.jsfst.or.jp Original paper Development of Polymerase Chain Reaction and Multiplex Polymerase Chain Reaction for Simple Identification of Thermoanaerobic Spore-forming Bacteria *1, 2 3 Fuyuki AOYAMA and Takahisa MIYAMOTO 1Technology Research & Development Laboratory, Research & Development Headquarters, Asahi Soft Drinks Co., Ltd., 1-1- 21 Midori, Moriya-shi, Ibaraki Prefecture 302-0106, Japan 2Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki Higashi-ku Fukuoka Prefecture 812-8581, Japan 3Division of Food Science & Biotechnology, Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu university, 6-10-1 Hakozaki Higashi-ku Fukuoka Prefecture 812-8581, Japan Received February 17, 2015 ; Accepted April 10, 2015 Thermoanaerobic spore-forming bacteria such as Thermoanaerobacter, Moorella, Thermoanaerobacterium, and Caldanaerobius produce spores with extremely high heat resistance. They are known to spoil various sealed, sterile drinks; in particular, low-acid drinks distributed at high temperatures, such as canned coffee containing milk. These bacteria are difficult to culture and identify on the basis of traditional biochemical characteristics. We developed novel primers for single and multiplex PCR methods for simple identification of these bacteria at the genus level. Bacteria were correctly identified approximately 2 h after DNA extraction among 86 strains of 35 species of Gram-positive and -negative bacteria including various spore-forming bacilli. Furthermore, new Loop- Mediated Isothermal Amplification (LAMP) primers were designed to develop a specific detection method for Thermoanaerobacter mathranii and Thermoanaerobacter thermocopriae, highly problematic microbes in the food industry due to their extremely high resistance to heat and various antibacterial agents.
    [Show full text]
  • Expansion Segments in Bacterial and Archaeal 5S Ribosomal Rnas
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.02.233163; this version posted August 2, 2020. 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. Expansion Segments in Bacterial and Archaeal 5S Ribosomal RNAs Victor G. Stepanov, George E. Fox Department of Biology and Biochemistry, 3369 Cullen Blvd., University of Houston, Houston, TX 77204-5001, USA Corresponding author: Dr. George E. Fox, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA, tel. no. 713-743-8363, fax. no. 713-743-8351, e-mail: [email protected] Running Title: Expansion Segments in Prokaryotic 5S rRNAs Keywords: ribosome, 5S rRNA, expansion segment, archaea, bacteria bioRxiv preprint doi: https://doi.org/10.1101/2020.08.02.233163; this version posted August 2, 2020. 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. ABSTRACT The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs.
    [Show full text]