Characteristics of Archaea and Bacteria in Rice Rhizosphere Along a Mercury Gradient
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Protein Components of the Microbial Mercury Methylation Pathway
Protein Components of the Microbial Mercury Methylation Pathway ______________________________________________________________ A Dissertation presented to the faculty of the Graduate School at the University of Missouri - Columbia ____________________________________________________ In partial fulfillment of the requirements for the degree Doctor of Philosophy __________________________________________ by Steven D. Smith Dr. Judy D. Wall, Dissertation Supervisor December 2015 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation titled Protein Components of the Microbial Mercury Methylation Pathway Presented by Steven D. Smith, a candidate for the degree of doctor of philosophy, and hereby certify that, in their opinion, it is worthy of acceptance. ____________________________________________ Dr. Judy D. Wall ____________________________________________ Dr. David W. Emerich ____________________________________________ Dr. Thomas P. Quinn ____________________________________________ Dr. Michael J. Calcutt Acknowledgements I would first like to thank my parents and family for their constant support and patience. They have never failed to be there for me. I would like to thank all members of the Wall Lab. At one time or another each one of them has helped me in some way. In particular I would like to thank Barb Giles for her insight into the dynamics of the lab and for her support of me through these years. I am greatly appreciative to Dr. Judy Wall for the opportunity to earn my PhD in her lab. Her constant support and unending confidence in me has been a great source of motivation. It has been an incredible learning experience that I will carry with me and draw from for the rest of my life. Table of Contents Acknowledgements ………………………………………………………………………………………………………… ii List of Figures …………………………………………………………………………………………………………………. -
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. 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 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
Open Thweattetd1.Pdf
The Pennsylvania State University The Graduate School CHARACTERIZATION OF PIGMENT BIOSYNTHESIS AND LIGHT-HARVESTING COMPLEXES OF SELECTED ANOXYGENIC PHOTOTROPHIC BACTERIA A Dissertation in Biochemistry, Microbiology, and Molecular Biology and Astrobiology by Jennifer L. Thweatt 2019 Jennifer L. Thweatt Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2019 ii The dissertation of Jennifer L. Thweatt was reviewed and approved* by the following: Donald A. Bryant Ernest C. Pollard Professor in Biotechnology and Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Squire J. Booker Howard Hughes Medical Investigator Professor of Chemistry and Professor of Biochemistry and Molecular Biology Eberly Distinguished Chair in Science John H. Golbeck Professor of Biochemistry and Biophysics Professor of Chemistry Jennifer L. Macalady Associate Professor of Geosciences Timothy I. Miyashiro Assistant Professor of Biochemistry and Molecular Biology Wendy Hanna-Rose Professor of Biochemistry and Molecular Biology Department Head, Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT This dissertation describes work on pigment biosynthesis and the light-harvesting apparatus of two classes of anoxygenic phototrophic bacteria, namely the green bacteria and a newly isolated purple sulfur bacterium. Green bacteria are introduced in Chapter 1 and include chlorophototrophic members of the phyla Chlorobi, Chloroflexi, and Acidobacteria. The green bacteria are defined by their use of chlorosomes for light harvesting. Chlorosomes contain thousands of unique chlorin molecules, known as bacteriochlorophyll (BChl) c, d, e, or f, which are arranged in supramolecular aggregates. Additionally, all green bacteria can synthesize BChl a, the and green members of the phyla Chlorobi and Acidobacteria can synthesize chlorophyll (Chl) a. -
Edaphobacter Modestus Gen. Nov., Sp. Nov., and Edaphobacter Aggregans Sp
International Journal of Systematic and Evolutionary Microbiology (2008), 58, 1114–1122 DOI 10.1099/ijs.0.65303-0 Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils Isabella H. Koch,1 Frederic Gich,1 Peter F. Dunfield2 and Jo¨rg Overmann1 Correspondence 1Bereich Mikrobiologie, Ludwig-Maximilians-Universita¨t Mu¨nchen, Maria-Ward-Str. 1a, Jo¨rg Overmann D-80638 Mu¨nchen, Germany [email protected] 2Institute of Geological and Nuclear Sciences, Wairakei Research Centre, Wairakei, Private Bag 2000, Taupo, New Zealand The phylum Acidobacteria is currently represented mostly by environmental 16S rRNA gene sequences, and the phylum so far contains only four species with validly published names, Holophaga foetida, Geothrix fermentans, Acidobacterium capsulatum and Terriglobus roseus.In the present study, two novel strains of acidobacteria were isolated. High-throughput enrichments were set up with the MicroDrop technique using an alpine calcareous soil sample and a mixture of polymeric carbon compounds supplemented with signal compounds. This approach yielded a novel, previously unknown acidobacterium, strain Jbg-1T. The second strain, Wbg-1T, was recovered from a co-culture with a methanotrophic bacterium established from calcareous forest soil. Both strains represent members of subdivision 1 of the phylum Acidobacteria and are closely related to each other (98.0 % 16S rRNA gene sequence similarity). At a sequence similarity of 93.8–94.7 %, strains Jbg-1T and Wbg-1T are only distantly related to the closest described relative, Terriglobus roseus KBS 63T, and accordingly are described as members of the novel genus Edaphobacter gen. -
Reverse Methanogenesis and Respiration in Methanotrophic Archaea
Hindawi Archaea Volume 2017, Article ID 1654237, 22 pages https://doi.org/10.1155/2017/1654237 Review Article Reverse Methanogenesis and Respiration in Methanotrophic Archaea Peer H. A. Timmers,1,2,3 Cornelia U. Welte,3,4 Jasper J. Koehorst,5 Caroline M. Plugge,1,2 Mike S. M. Jetten,3,4,6 and Alfons J. M. Stams1,3,7 1 Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands 2Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, Netherlands 3Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands 4Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands 5Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands 6TU Delft Biotechnology, Julianalaan 67, 2628 BC Delft, Netherlands 7Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal Correspondence should be addressed to Peer H. A. Timmers; [email protected] Received 3 August 2016; Revised 11 October 2016; Accepted 31 October 2016; Published 5 January 2017 Academic Editor: Michael W. Friedrich Copyright © 2017 Peer H. A. Timmers et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). -
Understanding Mercury Transport and Transformation by Computational Simulations
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2017 Understanding Mercury Transport and Transformation by Computational Simulations Jing Zhou University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Zhou, Jing, "Understanding Mercury Transport and Transformation by Computational Simulations. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4675 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Jing Zhou entitled "Understanding Mercury Transport and Transformation by Computational Simulations." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Life Sciences. Jeremy Smith, Major Professor We have read this dissertation and recommend its acceptance: Jerry Parks, Xiaolin Cheng, Hong Guo, Francisco Barrera Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Understanding Mercury Transport and Transformation by Computational Simulations A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Jing Zhou August 2017 Copyright © 2017 by Jing Zhou All rights reserved. -
Characterizing Restriction-Modification Systems
University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 8-5-2019 Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria Matthew Ouellette University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Ouellette, Matthew, "Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria" (2019). Doctoral Dissertations. 2280. https://opencommons.uconn.edu/dissertations/2280 Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria Matthew Ouellette, Ph.D. University of Connecticut, 2019 Abstract The Halobacteria are a class of archaeal organisms which are obligate halophiles. Several studies have described the Halobacteria as highly recombinogenic, yet members even within the same geographic location cluster into distinct phylogroups, suggesting that barriers exist which limit recombination. Barriers to recombination in the Halobacteria include CRISPRs, glycosylation, and archaeosortases. Another possible barrier which could limit gene transfer might be restriction-modification (RM) systems, which consist of restriction endonucleases (REases) and DNA methyltransferases (MTases) that both target the same sequence of DNA. The REase cleaves the target sequence, whereas the MTase methylates the site and protects it from cleavage. This dissertation examines the role of DNA methylation and RM systems in the Halobacteria and their impact on halobacterial speciation and genetic recombination. Using the model haloarchaeon, Haloferax volcanii, the genomic DNA methylation patterns (methylome) of an archaeal organism was characterized for the first time. Further investigations via gene deletion were used to identify the DNA methyltransferases responsible for the detected methylation patterns in H. volcanii, and experiments were conducted to determine the impact of RM systems on recombination via cell-to-cell mating. -
The Genome Sequence of Methanohalophilus Mahii SLPT
Hindawi Publishing Corporation Archaea Volume 2010, Article ID 690737, 16 pages doi:10.1155/2010/690737 Research Article TheGenomeSequenceofMethanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments Stefan Spring,1 Carmen Scheuner,1 Alla Lapidus,2 Susan Lucas,2 Tijana Glavina Del Rio,2 Hope Tice,2 Alex Copeland,2 Jan-Fang Cheng,2 Feng Chen,2 Matt Nolan,2 Elizabeth Saunders,2, 3 Sam Pitluck,2 Konstantinos Liolios,2 Natalia Ivanova,2 Konstantinos Mavromatis,2 Athanasios Lykidis,2 Amrita Pati,2 Amy Chen,4 Krishna Palaniappan,4 Miriam Land,2, 5 Loren Hauser,2, 5 Yun-Juan Chang,2, 5 Cynthia D. Jeffries,2, 5 Lynne Goodwin,2, 3 John C. Detter,3 Thomas Brettin,3 Manfred Rohde,6 Markus Goker,¨ 1 Tanja Woyke, 2 Jim Bristow,2 Jonathan A. Eisen,2, 7 Victor Markowitz,4 Philip Hugenholtz,2 Nikos C. Kyrpides,2 and Hans-Peter Klenk1 1 DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5 Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA 6 HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 7 Davis Genome Center, University of California, Davis, CA 95817, USA Correspondence should be addressed to Stefan Spring, [email protected] and Hans-Peter Klenk, [email protected] Received 24 August 2010; Accepted 9 November 2010 Academic Editor: Valerie´ de Crecy-Lagard´ Copyright © 2010 Stefan Spring et al. -
Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other
Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other Archaea;Crenarchaeota;South;Other;Other Archaea;Crenarchaeota;terrestrial;Other;Other Archaea;Euryarchaeota;Halobacteria;Halobacteriales;Miscellaneous Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae Archaea;Euryarchaeota;Methanomicrobia;Methanocellales;Methanocellaceae Archaea;Euryarchaeota;Methanomicrobia;Methanosarcinales;Methanosarcinaceae Archaea;Euryarchaeota;Thermoplasmata;Thermoplasmatales;Marine Bacteria;Acidobacteria;Acidobacteria;11-24;uncultured Bacteria;Acidobacteria;Acidobacteria;Acidobacteriales;Acidobacteriaceae Bacteria;Acidobacteria;Acidobacteria;BPC102;uncultured Bacteria;Acidobacteria;Acidobacteria;Bryobacter;uncultured Bacteria;Acidobacteria;Acidobacteria;Candidatus;Other Bacteria;Acidobacteria;Acidobacteria;DA023;uncultured Bacteria;Acidobacteria;Acidobacteria;DA023;unidentified Bacteria;Acidobacteria;Acidobacteria;DS-100;uncultured Bacteria;Acidobacteria;Acidobacteria;PAUC26f;uncultured Bacteria;Acidobacteria;Acidobacteria;RB41;uncultured Bacteria;Acidobacteria;Holophagae;32-20;uncultured Bacteria;Acidobacteria;Holophagae;43F-1404R;uncultured Bacteria;Acidobacteria;Holophagae;Holophagales;Holophagaceae Bacteria;Acidobacteria;Holophagae;NS72;uncultured Bacteria;Acidobacteria;Holophagae;SJA-36;uncultured Bacteria;Acidobacteria;Holophagae;Sva0725;uncultured Bacteria;Acidobacteria;Holophagae;iii1-8;uncultured Bacteria;Acidobacteria;RB25;uncultured;Other Bacteria;Actinobacteria;Actinobacteria;Actinobacteridae;Actinomycetales -
Bacterial Community in Soils Following Century-Long Application of Organic Or Inorganic Fertilizers Under Continuous Winter Wheat Cultivation
agronomy Article Bacterial Community in Soils Following Century-Long Application of Organic or Inorganic Fertilizers under Continuous Winter Wheat Cultivation Xiufen Li 1,2 , Shiping Deng 1,*, William R. Raun 1, Yan Wang 1 and Ying Teng 3 1 Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA; [email protected] (X.L.); [email protected] (W.R.R.); [email protected] (Y.W.) 2 Texas A&M AgriLife Research Center at Beaumont, Texas A&M University System, Beaumont, TX 77713, USA 3 Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; [email protected] * Correspondence: [email protected]; Tel.: +1-405-744-9591 Received: 30 July 2020; Accepted: 29 September 2020; Published: 1 October 2020 Abstract: Fertilization is one of the most common agricultural practices to achieve high yield. Although microbes play a critical role in nutrient cycling and organic matter decomposition, knowledge of the long-term responses of the soil bacterial community to organic and inorganic fertilizers is still limited. This study was conducted to evaluate the effects of century-long organic (manure), inorganic (NPK), and no fertilization (control) treatments on soil bacterial community structure under continuous winter wheat (Triticum aestivum L.) cultivation. Fertilization treatments altered the richness, diversity and composition of the soil bacterial community. Compared with the control, manure significantly increased the operational taxonomic units (OTUs), Chao 1 and Shannon indices, and taxonomic groups, while NPK significantly decreased these parameters. Fertilization treatments did not alter the types of dominant phyla but did significantly affect their relative abundances.