1 CURRICULUM VITAE William B. Whitman Address
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Cryptic Carbon and Sulfur Cycling Between Surface Ocean Plankton
Cryptic carbon and sulfur cycling between surface ocean plankton Bryndan P. Durhama, Shalabh Sharmab, Haiwei Luob, Christa B. Smithb, Shady A. Aminc, Sara J. Benderd, Stephen P. Dearthe, Benjamin A. S. Van Mooyd, Shawn R. Campagnae, Elizabeth B. Kujawinskid, E. Virginia Armbrustc, and Mary Ann Moranb,1 aDepartment of Microbiology, University of Georgia, Athens, GA 30602; bDepartment of Marine Sciences, University of Georgia, Athens, GA 30602; cSchool of Oceanography, University of Washington, Seattle, WA 98195; dDepartment of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543; and eDepartment of Chemistry, University of Tennessee, Knoxville, TN 37996 Edited by Edward F. DeLong, Univeristy of Hawaii, Manoa, Honolulu, HI, and approved December 2, 2014 (received for review July 12, 2014) About half the carbon fixed by phytoplankton in the ocean is bacterium. As is common among marine eukaryotic phyto- taken up and metabolized by marine bacteria, a transfer that is plankton, T. pseudonana harbors the B12-requiring version of the mediated through the seawater dissolved organic carbon (DOC) methionine synthase gene (metH) yet cannot synthesize B12 (7) pool. The chemical complexity of marine DOC, along with a poor and must obtain it from an exogenous source. The >50 se- understanding of which compounds form the basis of trophic quenced members of the Roseobacter lineage all carry genes for interactions between bacteria and phytoplankton, have impeded B12 biosynthesis (ref. 8; www.roseobase.org). Both groups of efforts to identify key currencies of this carbon cycle link. Here, we organisms are important in the ocean, with diatoms responsible used transcriptional patterns in a bacterial-diatom model system for up to 40% of global marine primary productivity (9) and based on vitamin B12 auxotrophy as a sensitive assay for metabo- roseobacters ubiquitously distributed, metabolically active (10), lite exchange between marine plankton. -
Download Full Article As
Article Genomic Signature Analysis for the Strategic Bioremediation of Polycyclic Aromatic Hydrocarbons in Mangrove Ecosystems in the Gulf of Tonkin Nam H. Dao1, Quan M. Le2, Thang X. Dao3 1The Hill School, USA 2The Loomis Chaffee School, USA 3Unaffiliated SUMMARY processes. Once oil has entered the roots and rhizosphere Current oil spill cleanup methods can be inefficient, (the soil directly influenced by plant roots) of mangrove costly, and have many more downsides. In an effort to trees, they fail to participate in regular salt management and create an efficient, cost-effective, and environmentally- respiration (3). As mangrove trees are responsible for various friendly solution to cleaning oil spills, there has been important functions in this habitat such as protection of soil a flurry of advancements in microbiological vectors. These plasmids confer oil-degrading genes that can be from erosion, improving water quality or helping provide implemented into the native microbial population. For nutrients for microbial communities, the death or failure of this strategy to work, it is critical that an appropriate these trees to function can pose heavy consequences for naturally-found plasmid be picked as a base to local organisms (3). Upon direct contamination by an oil spill, ensure long-term plasmid survival and activation of mangrove trees usually face death within several months, and its genes. To help realize this goal, this study relies other organisms living in the area that depend on a host of on emerging computational technologies to measure benefits provided by mangrove trees are subsequently either genetic similarity between the host chromosome and impacted directly by the influx of oil or indirectly through the the potential plasmid vector, utilizing an algorithm for loss of mangrove trees (3). -
Transcriptome Data for Bacteria Collected Eight Hours After Individual Inoculation Into a Diatom Thalassiosira Psuedonana Culture
Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture Website: https://www.bco-dmo.org/dataset/818765 Data Type: experimental Version: 1 Version Date: 2020-07-16 Project » Metabolic Currencies of the Ocean Carbon Cycle (Metabolic Currencies) Contributors Affiliation Role Moran, Mary Ann University of Georgia (UGA) Principal Investigator Copley, Nancy Woods Hole Oceanographic Institution (WHOI BCO-DMO) BCO-DMO Data Manager Abstract Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168. Table of Contents Dataset Description Acquisition Description Processing Description Related Publications Related Datasets Parameters Instruments Project Information Funding Coverage Temporal Extent: 2017-02 - 2017-12 Dataset Description Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168. Acquisition Description Thalassiosira pseudonana were removed from the co-cultures by pre-filtration through 2.0 µm pore-size filters, and bacteria were collected on 0.2 µm pore-size filters. Filters were incubated in SDS (0.6% final concentration) and proteinase K (120 ng μl –1 final concentration). RNA was extracted from duplicates of each treatment by adding an equal volume of acid phenol:chloroform:isoamyl-alcohol, followed by shaking, centrifugation, and collection of the supernatant. -
Geomicrobiological Processes in Extreme Environments: a Review
202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments. -
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. -
Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
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. -
Draft Genome Sequence of Thalassobius Mediterraneus CECT 5383T, a Poly-Beta-Hydroxybutyrate Producer
Genomics Data 7 (2016) 237–239 Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Data in Brief Draft genome sequence of Thalassobius mediterraneus CECT 5383T, a poly-beta-hydroxybutyrate producer Lidia Rodrigo-Torres, María J. Pujalte, David R. Arahal ⁎ Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain article info abstract Article history: Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an Received 23 December 2015 abundant representative of marine bacteria. T. mediterraneus XSM19T (=CECT 5383T) was isolated from the Received in revised form 8 January 2016 Western Mediterranean coast near Valencia (Spain) in 1989. We present here the draft genome sequence and Accepted 14 January 2016 annotation of this strain (ENA/DDBJ/NCBI accession number CYSF00000000), which is comprised of Available online 15 January 2016 3,431,658 bp distributed in 19 contigs and encodes 10 rRNA genes, 51 tRNA genes and 3276 protein coding fi Keywords: genes. Relevant ndings are commented, including the complete set of genes required for poly-beta- Rhodobacteraceae hydroxybutyrate (PHB) synthesis and genes related to degradation of aromatic compounds. Roseobacter clade © 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license PHB (http://creativecommons.org/licenses/by-nc-nd/4.0/). Aromatic compounds 1. Direct link to deposited data has not been yet validated, and even more recently T. abysii has been Specifications also proposed [6]. Organism/cell line/tissue Thalassobius mediterraneus Strain CECT 5383T Sequencer or array type Illumina MiSeq 2. -
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