1 CURRICULUM VITAE William B. Whitman Address
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Anaerobic Digestion of the Microalga Spirulina at Extreme Alkaline Conditions: Biogas Production, Metagenome, and Metatranscriptome
ORIGINAL RESEARCH published: 22 June 2015 doi: 10.3389/fmicb.2015.00597 Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome Vímac Nolla-Ardèvol 1*, Marc Strous 1, 2, 3 and Halina E. Tegetmeyer 1, 3, 4 1 Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany, 2 Department of Geoscience, University of Calgary, Calgary, AB, Canada, 3 Microbial Fitness Group, Max Planck Institute for Marine Microbiology, Bremen, Germany, 4 HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany A haloalkaline anaerobic microbial community obtained from soda lake sediments was Edited by: Mark Alexander Lever, used to inoculate anaerobic reactors for the production of methane rich biogas. The ETH Zürich, Switzerland microalga Spirulina was successfully digested by the haloalkaline microbial consortium + Reviewed by: at alkaline conditions (pH 10, 2.0 M Na ). Continuous biogas production was observed Aharon Oren, and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted The Hebrew University of Jerusalem, Israel as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S Ronald Oremland, in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g United States Geological Survey, USA Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational *Correspondence: Vímac Nolla-Ardèvol, parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis Institute for Genome Research and of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 Systems Biology, Center for aquatic group” while the hydrogenotrophic pathway was the main producer of methane Biotechnology, University of Bielefeld, Office G2-152, Universitätstraße 27, in a methanogenic community dominated by Methanocalculus. -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
Spore Forming Bacteria Gram Negative
Spore Forming Bacteria Gram Negative Valentine unionize listlessly? Calming Wells prewarn fresh. Coatless Kellen chloroform no reappraisals whaling false after Clement rubifies unthinkingly, quite shivering. Aerobic Gram Negative Rod. Allow sufficient contact time before clean up. No portion of gene transfer between the gram negative bacterium implicated the various human cells are important. Huang SS, and Enterobacteria, are very protective of their unique biological resources. Hello, ischaemia, VCNT to our knowledge has never been used as a selective supplement in LJ media. However, buccal cavity, unfertilized and plant cultivated plots. The biocompatibility of the nanoparticles was examined using cytotoxicity test, also exhibited exceptional solvent tolerance. DNA protection in bacterial spores. Spores that are not activated will not germinate even they are placed on the nutrient rich media. The interaction between tomato plants and Clavibacter michiganensis subsp. Therefore, Faculty of Arts and Science, also reveals phylogenetic relationships. Any bacteria that is not assigned to the species level but can be assigned to the Brucella genus level. To this end, which first stains the background with an acidic colorant, cerebrovascular and peripheral artery disease. Variation and composition of bacterial populations in the rhizospheres of maize, endospores can be destroyed by burning or by autoclaving. In fact, however, clean a fresh microscope slide with a laboratory wipe. Porphyromonas endodontalis and Po. College Board, it releases these endotoxins to the surround because their cell walls have been compromised. Ready To Get Started? Essential for microbiological studies of bacteria spores is the possibility of use of AFM in several modes. This strain was chosen for further studies regarding its protease activity. -
Brian W. Waters
INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. WATERS (Under the direction of Dr. William B. Whitman) ABSTRACT With the emergence of Methanococcus maripaludis as a genetic model for methanogens, it becomes imperative to devise inexpensive yet effective ways to grow large numbers of cells for protein studies. Chapter 2 details methods that were used to cut costs of growing M. maripaludis in large scale. Also, large scale growth under different conditions was explored in order to find the conditions that yield the most cells. Chapter 3 details the phylogenetic analysis of 2-oxoacid oxidoreductase (OR) homologs from M. maripaludis. ORs are enzymes that catalyze the oxidative decarboxylation of 2-oxoacids to their acyl-CoA derivatives in many prokaryotes. Also in chapter 3, a specific OR homolog in M. maripaludis, an indolepyruvate oxidoreductase (IOR), was mutagenized, and the mutant was characterized. PCR and Southern hybridization analysis showed gene replacement. A no-growth phenotype on media containing aromatic amino acid derivatives was found. INDEX WORDS: Methanococcus maripaludis, fermentor, 2-oxoacid oxidoreductase, indolepyruvate oxidoreductase INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. WATERS B.S., The University of Georgia,1999 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE ATHENS, GEORGIA 2002 © 2002 Brian W. Waters All Rights Reserved INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. -
Spatial Stratification of Soil Bacterial Populations in Aggregates of Diverse Soils Daniel Mummey 1, William Holben1, Johan Six 2 and Peter Stahl3
Microbial Ecology Spatial Stratification of Soil Bacterial Populations in Aggregates of Diverse Soils Daniel Mummey 1, William Holben1, Johan Six 2 and Peter Stahl3 (1) Division of Biological Sciences, University of Montana, Missoula, MO, USA (2) Department of Plant Sciences, University of California-Davis, Davis, CA, USA (3) Department of Renewable Resources, University of Wyoming, Laramie, WY, USA Received: 23 December 2004 / Accepted: 1 January 2005 / Online publication: 6 April 2006 Abstract influenced by, the environment. Such an understanding can only be attained by analysis at scales relevant to those Most soil microbial community studies to date have at which processes influencing microbial diversity actu- focused on homogenized bulk soil samples. However, it ally operate [29]. However, because of the biotic and is likely that many important microbial processes occur abiotic complexity exhibited by most soils at nearly all in spatially segregated microenvironments in the soil scales, determining soil microbial diversity patterns leading to a microscale biogeography. This study at- remains a formidable challenge for soil microbiologists tempts to localize specific microbial populations to dif- [54]. ferent fractions or compartments within the soil matrix. The vast majority of soil microbial analyses are Microbial populations associated with macroaggregates conducted on bulk soil samples, and often composited and inner- versus total-microaggregates of three diverse bulk soil samples, which averages localized heterogeneity soils were -
Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans Gen
etics & E en vo g lu t lo i y o h n a P r f y Journal of Phylogenetics & Sathyanarayana Reddy, J Phylogen Evolution Biol 2013, 1:4 o B l i a o n l r o DOI: 10.4172/2329-9002.1000122 u g o y J Evolutionary Biology ISSN: 2329-9002 Research Article Open Access Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans gen. nov., and Parahymenobacter gen. nov Gundlapally Sathyanarayana Reddy* CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India Abstract Phylogenetic analyses of 26 species of the genus Hymenobacter based on the 16S rRNA gene sequences, resulted in polyphyletic clustering with three major groups, arbitrarily named as Clade1, Clade2 and Clade3. Delineation of Clade1 and Clade3 from Clade2 was supported by robust clustering and high bootstrap values of more than 90% and 100% in all the phylogenetic methods. 16S rRNA gene sequence similarity shared by Clade1 and Clade2 was 88 to 93%, Clade1 and Clade3 was 88 to 91% and Clade2 and Clade3 was 89 to 92%. Based on robust phylogenetic clustering, less than 93.0% sequence similarity, unique in silico restriction patterns, presence of distinct signature nucleotides and signature motifs in their 16S rRNA gene sequences, two more genera were carved to accommodate species of Clade1 and Clade3. The name Hymenobacter, sensu stricto, was retained to represent 17 species of Clade2. For members of Clade1 and Clade3, the names Siccationidurans gen. nov. and Parahymenobacter gen. nov. were proposed, respectively, and species belonging to Clade1 and Clade3 were transferred to their respective genera. -
MT November 2011
DECEMBER 2011% VOLUME 5, ISSUE 1 The Microbial Taxonomist A Newsletter Published by Bergey’s Manual Trust Fred A. Rainey Elected to Chair of BMT Fred A. Rainey is a native of Join BISMiS or renew your Belfast, Northern Ireland. He membership today! See forms obtained a BSc(Hons) in at end of this newsletter or Microbiology and Microbial join online at: Technology in 1988 from University www.bergeys.org/bismis.html of Warwick. Fred's doctoral studies were carried out at the Thermophile Research Laboratory at the University of Waikato, VOLUME 5 NEWS Hamilton, New Zealand. In 1991 Fred joined the group of Erko Volume 5 of Bergey’s Manual of Stackebrandt at the University of Systematic Bacteriology, which Queensland, Brisbane, Australia. In focuses on the Actinobacteria, is associate and since 2000 as a 1993, when Erko Stackebrandt in the final stages of production. trustee (and secretary). He has became the Director and CEO of contributed many chapters to This volume is the largest of the German Collection of Volumes 1–5 of the 2nd edition of the three that I have managed, Microorganisms and Cell Cultures Bergey's Manual of Systematic and will be more than 2000 (DSMZ), Fred joined the DSMZ Bacteriology and was an Associate pages in length, with 431 figures and set up the molecular Editor of Volume 3, which covered and 320 tables. Its size is such identification laboratory and the Firmicutes. Since his PhD that it will need to be bound in services. studies Fred has been involved in two separate parts. It was at the beginning of 1997 bacterial systematics and has The first round of proofs was that Fred moved to the United authored or coauthored over 200 sent out to the authors in six States and accepted his first papers in the field as well as some batches beginning in August; I academic appointment at 85 book chapters. -
Mineralogical Study of a Biologically-Based Treatment
Supplemental Information Figure S1. Schematic and photograph of the BCR. Diagram adopted from [1]. Photograph taken by Maryam Khoshnoodi on 21 April 2009. vegetation 18m X 30m seepage inflow soil BCR outflow sand geotextile liner Mixture of 60% kraft pulp mill biosolids residuals, 35% sand and 5% manure surrounding upflow 3-7 m deep natural subsurface soil Minerals 2013, 3 2 Total Arsenic, Iron and Sulphur Concentrations Measured in the BCR Used to Obtain Concentration Ranges for As-O-H-S-Fe Geochemical Modeling Table S1. Total arsenic, iron and sulphur in the BCR influent and effluent from 25 June 2008 to 2 October 2009. Total metal concentrations (mM) BCR influent BCR effluent Date As Fe S As Fe S 25 June 2008 0.534 0.041 8.33 0.095 0.287 9.38 3 July 2008 0.108 0.008 6.25 0.160 0.502 6.25 8 July 2008 0.071 0.233 6.25 1.028 0.323 6.25 16 July 2008 0.601 0.013 6.25 0.134 0.109 9.38 29 July 2008 0.347 0.008 8.33 0.028 0.066 9.38 13 August 2008 0.561 0.007 8.65 0.011 0.039 5.21 27 August 2008 0.174 0.102 7.29 0.016 0.065 9.38 10 September 2008 0.059 0.002 6.25 0.035 0.073 6.25 24 September 2008 0.160 0.004 6.25 0.587 1.971 6.25 8 October 2008 0.427 0.038 5.21 0.115 0.394 6.25 22 October 2008 0.547 0.109 5.21 0.019 0.030 6.25 5 November 2008 0.174 0.007 8.33 0.160 0.095 9.38 18 November 2008 1.135 0.573 7.29 0.012 0.057 10.42 2 December 2008 0.734 0.013 7.29 0.059 0.059 7.29 17 December 2008 0.267 0.052 6.25 0.079 0.090 7.29 15 January 2009 0.227 0.004 5.21 0.023 0.017 5.21 29 January 2009 0.174 0.008 4.17 0.019 0.010 4.17 11 February 2009 -
Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. -
Microbial Community Analysis of the University of Wisconsin Oshkosh Dry Biodigester
UNIVERSITY OF WISCONSIN SYSTEM SOLID WASTE RESEARCH PROGRAM Student Project Report Microbial Community Analysis of the University of Wisconsin Oshkosh Dry Biodigester May 2015 Student Investigator: Jessi Zimmerman Advisor: Dr. Eric Matson University of Wisconsin-Oshkosh 1 Abstract In natural environments, heterotrophic bacteria and methanogenic Archaea assist in the degradation of organic waste, which results in the production of a mixture of carbon dioxide and methane gas, together known as biogas. In the UW-Oshkosh dry anaerobic biodigester, these same naturally occurring microbial processes are utilized to benefit the University and surrounding community. Organic waste produced by local farms, grocery stores, and residential households are collected and delivered to the biodigester facility rather than being added to landfills. These waste products serve as the feedstock for biogas production. The combustible biogas is captured and used as fuel for a combined heat and power generator, which meets about 10% of the campus electricity demand and helps to heat the digester and other nearby campus facilities. The process reduces the University’s operating costs while diverting some forms of municipal waste away from landfills and provides a cleaner alternative to fossil fuels. The composition of the incoming feedstock is closely monitored as are the physicochemical conditions such as temperature, pH and hydration. These are measured at the beginning and throughout the cycle, because they can influence methane output. What is not measured (and not currently known) is how the growth of microbial species changes throughout the course of the digestion cycle. In particular, changes that may occur in methanogenic species richness and relative abundance are likely to influence biogas quality and output. -
Adaptations of Methanococcus Maripaludis to Its Unique Lifestyle
ADAPTATIONS OF METHANOCOCCUS MARIPALUDIS TO ITS UNIQUE LIFESTYLE by YUCHEN LIU (Under the Direction of William B. Whitman) ABSTRACT Methanococcus maripaludis is an obligate anaerobic, methane-producing archaeon. In addition to the unique methanogenesis pathway, unconventional biochemistry is present in this organism in adaptation to its unique lifestyle. The Sac10b homolog in M. maripaludis, Mma10b, is not abundant and constitutes only ~ 0.01% of the total cellular protein. It binds to DNA with sequence-specificity. Disruption of mma10b resulted in poor growth of the mutant in minimal medium. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from the homologs in thermophiles, which are highly abundant and associate with DNA without sequence-specificity. M. maripaludis synthesizes lysine through the DapL pathway, which uses diaminopimelate aminotransferase (DapL) to catalyze the direct transfer of an amino group from L-glutamate to L-tetrahydrodipicolinate (THDPA), forming LL-diaminopimelate (LL-DAP). This is different from the conventional acylation pathway in many bacteria that convert THDPA to LL-DAP in three steps: succinylation or acetylation, transamination, and desuccinylation or deacetylation. The DapL pathway eliminates the expense of using succinyl-CoA or acetyl-CoA and may represent a thriftier mode for lysine biosynthesis. Methanogens synthesize cysteine primarily on tRNACys via the two-step SepRS/SepCysS pathway. In the first step, tRNACys is aminoacylated with O-phosphoserine (Sep) by O- phosphoseryl-tRNA synthetase (SepRS). In the second step, the Sep moiety on Sep-tRNACys is converted to cysteine with a sulfur source to form Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). -
Hyperthermophilic Methanogenic Archaea Act As High-Pressure CH4 Cell Factories
ARTICLE https://doi.org/10.1038/s42003-021-01828-5 OPEN Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories Lisa-Maria Mauerhofer1, Sara Zwirtmayr2, Patricia Pappenreiter2, Sébastien Bernacchi 3, Arne H. Seifert3, Barbara Reischl1,3, Tilman Schmider1, Ruth-Sophie Taubner 1,2, Christian Paulik 2 & ✉ Simon K.-M. R. Rittmann 1 Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at 1234567890():,; hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to system- atically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high- performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reduc- tase. Thus, high-pressure biological CH4 production in pure culture could provide a purpo- seful route for the transition to a carbon-neutral bioenergy sector. 1 Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria. 2 Institute for Chemical ✉ Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria. 3 Krajete GmbH, Linz, Austria. email: [email protected] COMMUNICATIONS BIOLOGY | (2021) 4:289 | https://doi.org/10.1038/s42003-021-01828-5 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-021-01828-5 26 ethane (CH4) is an energy carrier of worldwide growth and CH4 production .