Klotz Martin G.

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Klotz
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Martin G.
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  • Article
    Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil
    (BioMed Central, 2016-07-28) Rice, Marlen C. ; Norton, Jeanette M. ; Valois, Frederica ; Bollmann, Annette ; Bottomley, Peter ; Klotz, Martin G. ; Laanbroek, Hendrikus ; Suwa, Yuichi ; Stein, Lisa Y. ; Sayavedra-Soto, Luis ; Woyke, Tanja ; Shapiro, Nicole ; Goodwin, Lynne A. ; Huntemann, Marcel ; Clum, Alicia ; Pillay, Manoj ; Kyrpides, Nikos C. ; Varghese, Neha ; Mikhailova, Natalia ; Markowitz, Victor ; Palaniappan, Krishna ; Ivanova, Natalia N. ; Stamatis, Dimitrios ; Reddy, T. B. K. ; Ngan, Chew Yee ; Daum, Chris
    Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
  • Article
    Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans
    (American Society for Microbiology, 2007-12-07) Sievert, Stefan M. ; Scott, Kathleen M. ; Klotz, Martin G. ; Chain, Patrick S. G. ; Hauser, Loren J. ; Hemp, James ; Hugler, Michael ; Land, Miriam L. ; Lapidus, Alla ; Larimer, Frank W. ; Lucas, Susan ; Malfatti, Stephanie A. ; Meyer, Folker ; Paulsen, Ian T. ; Ren, Qinghu ; Simon, Jörg ; USF Genomics Class
    Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
  • Article
    The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2
    (Public Library of Science (PLoS), 2006-11-14) Scott, Kathleen M. ; Sievert, Stefan M. ; Abril, Fereniki N. ; Ball, Lois A. ; Barrett, Chantell J. ; Blake, Rodrigo A. ; Boller, Amanda J. ; Chain, Patrick S. G. ; Clark, Justine A. ; Davis, Carisa R. ; Detter, Chris ; Do, Kimberly F. ; Dobrinski, Kimberly P. ; Faza, Brandon I. ; Fitzpatrick, Kelly A. ; Freyermuth, Sharyn K. ; Harmer, Tara L. ; Hauser, Loren J. ; Hugler, Michael ; Kerfeld, Cheryl A. ; Klotz, Martin G. ; Kong, William W. ; Land, Miriam L. ; Lapidus, Alla ; Larimer, Frank W. ; Longo, Dana L. ; Lucas, Susan ; Malfatti, Stephanie A. ; Massey, Steven E. ; Martin, Darlene D. ; McCuddin, Zoe ; Meyer, Folker ; Moore, Jessica L. ; Ocampo, Luis H. ; Paul, John H. ; Paulsen, Ian T. ; Reep, Douglas K. ; Ren, Qinghu ; Ross, Rachel L. ; Sato, Priscila Y. ; Thomas, Phaedra ; Tinkham, Lance E. ; Zeruth, Gary T.
    Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
  • Article
    Editorial: The responses of marine microorganisms, communities and ecofunctions to environmental gradients
    (Frontiers Media, 2019-02-08) Dang, Hongyue ; Klotz, Martin G. ; Lovell, Charles R. ; Sievert, Stefan M.
  • Article
    Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)
    (Frontiers Media, 2018-04-18) Waite, David W. ; Vanwonterghem, Inka ; Rinke, Christian ; Parks, Donovan H. ; Zhang, Ying ; Takai, Ken ; Sievert, Stefan M. ; Simon, Jörg ; Campbell, Barbara J. ; Hanson, Thomas E. ; Woyke, Tanja ; Klotz, Martin G. ; Hugenholtz, Philip
  • Article
    Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)
    (Frontiers Media, 2017-04-24) Waite, David W. ; Vanwonterghem, Inka ; Rinke, Christian ; Parks, Donovan H. ; Zhang, Ying ; Takai, Ken ; Sievert, Stefan M. ; Simon, Jörg ; Campbell, Barbara J. ; Hanson, Thomas E. ; Woyke, Tanja ; Klotz, Martin G. ; Hugenholtz, Philip
    The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.