DOCSLIB.ORG

Consolidated Bioprocessing for Valorization of Pulp And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Consolidated Bioprocessing for Valorization of Pulp And FUNCTIONAL METAGENOMICS AND CONSOLIDATED BIOPROCESSING FOR VALORIZATION OF PULP AND PAPER MILL SLUDGE by Anupama Achal Sharan B.E., Birla Institute of Technology, Mesra, Ranchi, 2015 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF APPLIED SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemical and Biological Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) April 2018 © Anupama Achal Sharan, 2018 i Abstract Biocatalyst discovery is integral to bioeconomy development, enabling design of scalable bioprocesses that can compete with the resource-intensive petrochemical industry. Uncultivated microbial communities within natural and engineered ecosystems provide a near-infinite reservoir of genomic diversity and metabolic potential that can be harnessed for this purpose. To bridge the cultivation gap, functional metagenomic screens have been developed to recover active genes directly from environmental samples. In this thesis, a pipeline for recovery of biomass-deconstructing biocatalysts sourced from pulp and paper mill sludge (PPS) metagenome is described. This environment is targeted given its high composition of cellulose that is hypothesized to direct enrichment of enzymes capable of hydrolysing it. The resulting oligosaccharides represent platform molecules that can be fed to downstream applications using consolidated process design for converting biological waste streams into value-added products. High-molecular weight DNA was extracted from sludge and used to construct a fosmid library containing 15,000 clones using the copy control system in EPI300™-T1 R E.coli. Extracted DNA was also used in whole genome shotgun sequencing to compare the metabolic potential of the sludge community with fosmid screening outcomes as well as other waste biomass environments using MetaPathways v2.5 software pipeline, with specific emphasis on carbohydrate-active enzymes (CAZymes). Metagenomic assembling, open reading frame (ORF) prediction, binning and taxonomic assignment approaches were also used to bring out correlations between function and taxonomy. In total, 32,232 ORF’s were mapped to the CAZy database predicted to encode glycoside hydrolases, glycosyl transferases, and carbohydrate binding module families. The fosmid library was screened for glycosidase hydrolase activities using a pool of sensitive ii fluorogenic glycosides of 6-chloro-4-methylumbelliferone (CMU). A total of 744 clones capable of converting pooled substrates were recovered indicating an extremely high hit rate (1 hit per 43 clones). Following fosmid sequencing and annotation, two of the most promising hits with defined single GH family loci were sub-cloned and overexpressed in E.coli BL21 DE3 strain to conduct basic biochemical characterization. Activity of purified enzymes was demonstrated on model lignocellulosic substrates to evaluate the potential of implementing the proposed circular bioprocess with waste PPS as both the feedstock and source of enriched biocatalysts. iii Lay Summary In an era of growing global consciousness for bioeconomy development, it is ironic that the pulp and paper industry, which is one of the most prominent biomass-based industries in terms of revenue generation, is declining in Canada. The strategic importance of this industry within the bioeconomy and an opportunity to reduce environmental burden by not only remediating but valorising pulp and paper mill waste forms the primary motivation behind this work. This study presents an approach to add value to the solid waste stream, paper sludge, from this industry by unravelling its environmental genome to discover novel genes that produce enzymes capable of breaking down biomass. This was done using both experimental techniques and data analysis that involved high-throughput robotic functional screening and bioinformatics approaches. The findings of this study point to definitive cost-reduction approaches in industrial bioprocessing using cheap, waste biomass feedstocks for reciprocal enzyme discovery and enhanced bioconversion. iv Preface Several sections of this work are being used for composing manuscripts for publication in peer-reviewed journals. The research was conducted under the co-supervision of Dr. Vikramaditya G. Yadav (Chemical and Biological Engineering) and Dr. Steven J. Hallam (Microbiology and Immunology). I conducted the literature review, defined research questions and methodologies, designed and conducted experiments, analysed data and compiled and interpreted results under their guidance and assistance with group members from both Hallam and Yadav lab groups. The thesis is written by me and contains original, unpublished work with inputs from both Dr. Hallam and Dr. Yadav. Several bioinformatics-based workflows included in the thesis as presented in chapters 2- 3, including shotgun metagenome DNA QC, trimming and assembly, binning, EMIRGE and Phylosift taxonomy assignment, positive fosmid clone sequences FabFos pipeline assembly were implemented in collaboration with Connor Morgan-Lang. Small subunit ribosomal RNA (SSU rRNA or 16S) gene pyrotag sequencing and operational taxonomic unit (OTU) data analysis for the metagenomic DNA as presented in chapter 2 was done in collaboration with Ashley Arnold. Annotation of the pulp and paper sludge (PPS) metagenome and other metagenomes included in the comparative analysis presented in chapter 2 was done using Metapathways 2.5, a metagenomic DNA annotation pipeline developed in the Hallam lab (Hanson et al. 2014) with suitable in-house updates. The same pipeline was also used for positive fosmid clone annotations v as presented in chapter 3. The fosmid sequence ORF figure was produced by Kateryna Ievdokymenko and edited by me. The fluorogenic substrates for fosmid library screening as presented in chapter 3, were kindly provided by Zach Armstrong from the Withers lab group at UBC and experiment design for fosmid library screening and biochemical assays and characterization were guided by him. Dr. Aria Hanh and Dr. Keith Mewis also guided several aspects of metagenomic annotation and results interpretations. Compositional analysis of the paper mill sludge as presented in chapter 4 was guided by Dr. Jinguang Hu, Saddler lab group (Forestry) and done in collaboration with Daniela Vargas Figueroa, MASc student in the same group. The Saddler group also provided the Celluclast enzyme used as positive control in enzyme assays. The mutant Chit-O enzyme used for cellulase assaying was kindly provided by the Alessandro R Ferrari from the University of Groningen, Netherlands. Dr. Sandip Pawar and Benson Chang from the Yadav group helped with sub-cloning work presented in this chapter. vi Table of Contents Abstract ............................................................................................................................................ ii Lay summary ................................................................................................................................... iv Preface ............................................................................................................................................. v Table of Contents ........................................................................................................................... vii List of Tables ................................................................................................................................... xi List of Figures ................................................................................................................................ xiii List of Abbreviations…………………………………………………………………………………………………………………xx Acknowledgements ………………………………………………………………………………………………………………xxiii Dedication ……………………………………………………………………………………………………………………………..xxv Chapter 1: Introduction …………………………………………………………………………………………………………….1 1.1 Sustainability and the Circular Economy ………………………………………………………………….1 1.2 The Bioeconomy ……………………………………………………………………………………………………..4 1.2.1 Industrial Biocatalysis ……………………………………………………………………………….9 1.3 Rejuvenating the Paper Industry by Valorising Solid Waste Stream – Pulp and Paper Mill Sludge (PPS) ………………………………………………………………………………………………………….11 1.4 Research Overview ………………………………………………………………………………………………..13 Chapter 2: In-silico Analysis of the Paper Mill Sludge Microbiome……………………………………………16 2.1 Background…………………………………………………………………………………………………………….16 2.1.1 Metagenomics – Unearthing Nature’s Biocatalytic Potential……………………16 2.1.1.1 Lignocellulose Hydrolysis and Valorization…………………………………17 2.1.2 In-silico Approaches in Metagenomics – what all can the microbiome map tell us?...................................................................................................................20 2.1.2.1 Bioinformatics Tools – making sense in the noise………………………21 2.1.2.2 Standardizing Data and Streamlining Analysis……………………………23 2.2 Materials and Methods………………………………………………………………………………………….28 2.2.1 Sample Collection and Processing……………………………………………………………28 2.2.2 Whole-metagenome Sequencing, Binning and Assembly…………………………29 vii 2.2.2.1 High Molecular Weight Genomic DNA Extraction………………………29 2.2.2.2 Sequencing………………………………………………………………………………..30 2.2.2.3 Metagenome Assembly and Binning………………………………………….31 2.2.3 Taxonomic Analysis………………………………………………………………………………….32 2.2.3.1 454 16s rRNA gene Pyrotag Sequencing…………………………………….32 2.2.3.2 Expectation Maximization Iterative Reconstruction of Genes from the Environment (EMIRGE) based 16s Prediction………………………………….34
Load more

Recommended publications
  • The Ecology of the Chloroflexi in Full-Scale Activated Sludge 2 Wastewater Treatment Plants
    bioRxiv preprint doi: https://doi.org/10.1101/335752; this version posted May 31, 2018. 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 The ecology of the Chloroflexi in full-scale activated sludge 2 wastewater treatment plants 3 Marta Nierychlo1, Aleksandra Miłobędzka2,3, Francesca Petriglieri1, Bianca 4 McIlroy1, Per Halkjær Nielsen1, and Simon Jon McIlroy1§* 5 1Center for Microbial Communities, Department of Chemistry and Bioscience, 6 Aalborg University, Aalborg, Denmark 7 2Microbial Ecology and Environmental Biotechnology Department, Institute of 8 Botany, Faculty of Biology, University of Warsaw; Biological and Chemical 9 Research Centre, Żwirki i Wigury 101, Warsaw 02-089, Poland 10 3Department of Biology, Faculty of Building Services, Hydro and Environmental 11 Engineering, Warsaw University of Technology, 00-653 Warsaw, Poland 12 * Corresponding author: Simon Jon McIlroy, Center for Microbial Communities, 13 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 14 DK-9220 Aalborg, Denmark; Tel.: +45 9940 3573; Fax: +45 9814 1808; Email: 15 [email protected] 16 § Present address: Australian Centre for Ecogenomics, University of Queensland, 17 Australia 1 bioRxiv preprint doi: https://doi.org/10.1101/335752; this version posted May 31, 2018. 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.
    [Show full text]
  • Special Issue: Significance of Culturing Microbes in the Omics Era
    Microbes Environ. Vol. 24, No. 3, 205–216, 2009 http://wwwsoc.nii.ac.jp/jsme2/ doi:10.1264/jsme2.ME09151S Special issue: Significance of culturing microbes in the omics era Minireview Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi ‘Subphylum I’ with Natural and Biotechnological Relevance Special Issue TAKESHI YAMADA1, and YUJI SEKIGUCHI2* 1Department of Ecological Engineering, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi 441–8580, Japan; and 2Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1–1–1 Higashi, Tsukuba 305–8566, Japan （Received May 31, 2009—Accepted July 30, 2009—Published online August 20, 2009） Cultivation-independent molecular surveys have shown members of the bacterial phylum Chloroflexi to be ubiqui- tous in various natural and artificial ecosystems. Among the subphylum-level taxa of the Chloroflexi known to date, the formerly uncultured ‘subphylum I’ had well been recognized as a typical group that contains a number of environ- mental gene clones with no culture representatives. In order to reveal their ecophysiology, attempts were made over the past decade to domesticate them into laboratory cultures, and significant advances have been made in cultivating strains belonging to the group. The microorganisms characterized so far include seven species in six genera, i.e., Anaerolinea, Levilinea, Leptolinea, Bellilinea, Longilinea, and Caldilinea, and were proposed to represent two classes, Anaerolineae and Caldilineae, providing solid insights into the phenotypic and genetic properties common to the group. Another subphylum-level uncultured group of the Chloroflexi, i.e., the class Ktedonobacteria, has also been represented recently by a cultured strain.
    [Show full text]
  • Towards a Metagenomic Understanding on Enhanced
    Wong et al. Biotechnology for Biofuels 2013, 6:38 http://www.biotechnologyforbiofuels.com/content/6/1/38 RESEARCH Open Access Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment Mabel Ting Wong1, Dong Zhang2, Jun Li1, Raymond Kin Hi Hui1, Hein Min Tun1, Manreetpal Singh Brar1, Tae-Jin Park1, Yinguang Chen2* and Frederick C Leung1,3* Abstract Background: Understanding the effects of pretreatment on anaerobic digestion of sludge waste from wastewater treatment plants is becoming increasingly important, as impetus moves towards the utilization of sludge for renewable energy production. Although the field of sludge pretreatment has progressed significantly over the past decade, critical questions concerning the underlying microbial interactions remain unanswered. In this study, a metagenomic approach was adopted to investigate the microbial composition and gene content contributing to enhanced biogas production from sludge subjected to a novel pretreatment method (maintaining pH at 10 for 8 days) compared to other documented methods (ultrasonic, thermal and thermal-alkaline). Results: Our results showed that pretreated sludge attained a maximum methane yield approximately 4-fold higher than that of the blank un-pretreated sludge set-up at day 17. Both the microbial and metabolic consortium shifted extensively towards enhanced biodegradation subsequent to pretreatment, providing insight for the enhanced methane yield. The prevalence of Methanosaeta thermophila and Methanothermobacter thermautotrophicus, together with the functional affiliation of enzymes-encoding genes suggested an acetoclastic and hydrogenotrophic methanogenesis pathway. Additionally, an alternative enzymology in Methanosaeta was observed. Conclusions: This study is the first to provide a microbiological understanding of improved biogas production subsequent to a novel waste sludge pretreatment method.
    [Show full text]
  • Chloroflexi: the Alet of a Bacterium Present in Human and Environmental Habitats
    San Jose State University SJSU ScholarWorks Master's Theses Master's Theses and Graduate Research Fall 2015 Chloroflexi: the aleT of a Bacterium Present in Human and Environmental Habitats Jayashree Sanjeeviraman San Jose State University Follow this and additional works at: https://scholarworks.sjsu.edu/etd_theses Recommended Citation Sanjeeviraman, Jayashree, "Chloroflexi: the aleT of a Bacterium Present in Human and Environmental Habitats" (2015). Master's Theses. 4664. DOI: https://doi.org/10.31979/etd.a5ab-5k4u https://scholarworks.sjsu.edu/etd_theses/4664 This Thesis is brought to you for free and open access by the Master's Theses and Graduate Research at SJSU ScholarWorks. It has been accepted for inclusion in Master's Theses by an authorized administrator of SJSU ScholarWorks. For more information, please contact [email protected]. CHLOROFLEXI THE TALE OF A BACTERIUM PRESENT IN HUMAN AND ENVIRONMENTAL HABITATS A Thesis Presented to The Faculty of Department of Biological Sciences San Jóse State University In Partial Fulfillment of the Requirements for the Degree Master of Science by Jayashree Sanjeeviraman December 2015 i © 2015 Jayashree Sanjeeviraman ALL RIGHTS RESERVED ii The Designated Thesis Committee Approves the Thesis Titled CHLOROFLEXI THE TALE OF A BACTERIUM PRESENT IN HUMAN AND ENVIRONMENTAL HABITATS by Jayashree Sanjeeviraman APPROVED FOR THE DEPARTMENT OF BIOLOGICAL SCIENCES SAN JÓSE STATE UNIVERSTY December 2015 Dr. Cleber Ouverney Department of Biological Sciences Dr. Miri VanHoven Department of Biological Sciences Dr. Rachael French Department of Biological Sciences iii ABSTRACT CHLOROFLEXI THE TALE OF A BACTERIUM PRESENT IN HUMAN AND ENVIRONMENTAL HABITATS by Jayashree Sanjeeviraman The phylum Chloroflexi is relatively unexplored, with the majority of its representatives being uncultivable.
    [Show full text]
  • Preservation of Microbial Communities Enriched on Lignocellulose Under Thermophilic and High‑Solid Conditions Chaowei Yu1, Amitha P
    Yu et al. Biotechnol Biofuels (2015) 8:206 DOI 10.1186/s13068-015-0392-y Biotechnology for Biofuels RESEARCH Open Access Preservation of microbial communities enriched on lignocellulose under thermophilic and high‑solid conditions Chaowei Yu1, Amitha P. Reddy1,2, Christopher W. Simmons2,3, Blake A. Simmons2,4, Steven W. Singer2,5 and Jean S. VanderGheynst1,2* Abstract Background: Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were com- pleted in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. Results: High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of domi- nant organisms.
    [Show full text]
  • Enhancing the Performance of Anaerobic Bioreactors for The
    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 8-29-2017 Enhancing the Performance of Anaerobic Bioreactors for the Biological Degradation of Volatiles Organic Compounds in Groundwater Using Alternate Electron Acceptors Leslie Michele Pipkin Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Environmental Engineering Commons Recommended Citation Pipkin, Leslie Michele, "Enhancing the Performance of Anaerobic Bioreactors for the Biological Degradation of Volatiles Organic Compounds in Groundwater Using Alternate Electron Acceptors" (2017). LSU Doctoral Dissertations. 4106. https://digitalcommons.lsu.edu/gradschool_dissertations/4106 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. ENHANCING THE PERFORMANCE OF ANAEROBIC BIOREACTORS FOR THE BIOLOGICAL DEGRADATION OF VOLATILE ORGANIC COMPOUNDS IN GROUNDWATER USING ALTERNATE ELECTRON ACCEPTORS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Civil and Environmental Engineering by Leslie Michele Pipkin B.S., Florida State University, 2010 M.S., Florida State University, 2012 December 2017 ACKNOWLEDGEMENTS I would like to recognize those who have encouraged, directed, and supported me during my studies at Louisiana State University leading to my doctoral degree and this dissertation. I am forever grateful for my major advisor Dr.
    [Show full text]
  • Genomic and in Situ Investigations of the Novel Uncultured Chloroflexi Associated with 0092 Morphotype Filamentous Bulking in Activated Sludge
    The ISME Journal (2016) 10, 2223–2234 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge Simon Jon McIlroy1, Søren Michael Karst1, Marta Nierychlo1, Morten Simonsen Dueholm1, Mads Albertsen1, Rasmus Hansen Kirkegaard1, Robert James Seviour2 and Per Halkjær Nielsen1 1Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark and 2Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. Filaments with the Eikelboom 0092 morphotype are commonly associated with such bulking episodes. Members of the uncultured B45 phylotype, which is embraced within the phylum Chloroflexi, were recently shown to exhibit this morphology. Although these organisms are among the most abundant populations recorded in activated sludge processes, nothing is known about their metabolic characteristics. In this study, a genome sequence, representing the B45 phylotype, was retrieved from a metagenome generated from an activated sludge WWTP. The genome consisted of two chromosomes and one plasmid, which were 4.0, 1.0 and 0.04 Mbps in size, respectively. A metabolic model was constructed for this organism, based on annotation of its genome, showing its ability to generate energy by respiration, utilizing oxygen, nitrite or nitrous oxide as electron acceptors, or by fermentation of sugars. The ability of B45 members to ferment sugars under anaerobic conditions was validated in situ with microautoradiography—fluorescence in situ hybridization.
    [Show full text]
  • Thermoflexus Hugenholtzii Gen. Nov., Sp. Nov., a Thermophilic
    International Journal of Systematic and Evolutionary Microbiology (2014), 64, 2119–2127 DOI 10.1099/ijs.0.055855-0 Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov. Jeremy A. Dodsworth,1 Jonathan Gevorkian,1 Fairuz Despujos,1 Jessica K. Cole,1* Senthil K. Murugapiran,1 Hong Ming,2,3 Wen-Jun Li,3,4 Gengxin Zhang,5 Alice Dohnalkova6 and Brian P. Hedlund1 Correspondence 1School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA Jeremy A. Dodsworth 2Department of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China [email protected] 3Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China 4Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, U¨ ru¨mqi 830011, PR China 5Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 10085, PR China 6Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Mail Stop K8-93, Richland, WA 99352, USA A thermophilic, filamentous, heterotrophic bacterium, designated strain JAD2T, a member of an as-yet uncultivated lineage that is present and sometimes abundant in some hot springs worldwide, was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had a mean diameter of 0.3 mm and length of 4.0 mm, and formed filaments that typically ranged in length from 20 to 200 mm.
    [Show full text]
  • Cultivation of Uncultured Bacteria of the Class Ktedonobacteria in the Phylum Chloroflexi
    Makara Journal of Science 16/1 (2012) 1-8 1 MINI-REVIEW Cultivation of Uncultured Bacteria of the Class Ktedonobacteria in the Phylum Chloroflexi Akira Yokota Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia E-mail: [email protected] Abstract The class Ktedonobacteria in the phylum Chloroflexi is known to contain a large number of uncultured, environmental 16S rRNA gene clones, and cultured representatives are a limited number. In this review, recent findings on the taxonomical and ecological significance of the class Ktedonobacteria in the phylum Chloroflexi are discussed based on the findings from both the characteristics of the cultured Ktedonobacteria and molecular-based analysis. The microorganisms characterized so far include four species in three genera, Ktedonobacter, Thermosporothrix and Thermogemmatispora, and were proposed to represent three families, Ktedonobacteraceae, Thermosporotricaceae, and Thermogemmatisporaceae, and two orders, Ktedonobacterales and Thermogemmatisporales. Ktedonobacteria strains showed a common property of gram-positive, aerobic organisms that produce branched vegetative mycelia and form spores by budding. Abstrak Kultivasi Bakteri yang tidak dapat Dikultur dari Kelas Ktedonobacteria pada Filum Chloroflexi. Kelas Ktedonobacteria dari filum Chloroflexi terdiri atas sejumlah besar taksa yang tidak dapat dikultur, klona-klona gen 16S rRNA yang berasal dari lingkungan, dan sejumlah kecil taksa yang dapat dikultur. Tulisan ini mengulas temuan terakhir mengenai taksonomi dan ekologi kelas Ktedonobacteria dari filum Chloroflexi berdasarkan karateristik yang ditemukan pada biakan Ktedonobacteria dan analisis molekuler. Sejauh ini, mikroorganisme yang telah dikarakterisasi mencakup empat spesies dari tiga marga, yaitu Ktedonobacter, Thermosporothrix, dan Thermogemmatispora. Ketiga marga tersebut diusulkan untuk mewakili tiga famili, yaitu Ktedonobacteraceae, Thermosporotricaceae, dan Thermogemmatisporaceae, dan dua bangsa, Ktedonobacterales dan Thermogemmatisporales.
    [Show full text]
  • A Journey to the Center of a Bacterial Organelle by Onur Erbilgin A
    A Journey to the Center of a Bacterial Organelle By Onur Erbilgin A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Cheryl A. Kerfeld, Co-Chair Professor Arash Komeili, Co-Chair Professor Kathleen R. Ryan Professor David F. Savage Spring 2015 Copyright 2015 Onur Erbilgin All rights reserved Abstract A Journey to the Center of a Bacterial Organelle by Onur Erbilgin Doctor of Philosophy in Microbiology University of California, Berkeley Professors Cheryl A. Kerfeld and Arash Komeili, Co-Chairs Cellular compartmentalization is a fundamental strategy through which complex tasks can be carried out, where each compartment carries out a specialized function. Compartmentalization strategies in the bacteria have (relatively) recently been discovered and are not present across the entire domain; they instead seem to be tied to niche specialization of the host species. For example, carboxysomes are necessary for all cyanobacteria to fix carbon dioxide in present-day atmospheric conditions. Carboxysomes are part of a larger family of bacterial organelles termed bacterial microcompartments (BMCs), which are all related by the proteinaceous shell that bounds the compartment. Many different metabolic functions have been attributed to BMCs, such as carbon fixation, propanediol metabolism, and ethanolamine metabolism, and cursory genome gazing had hinted that there may be several more functional types of these organelles in a vast number of bacteria. In order to survey the functional and phylogenetic diversity of BMCs, a bioinformatic algorithm was developed to predict and categorize genetic loci that encode genes that can construct a complete organelle.
    [Show full text]