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979 results on '"Murrell, J. Colin"'

6. The impacts of ocean acidification on marine trace gases and the implications for atmospheric chemistry and climate

Author

Hopkins, Frances E., Suntharalingam, Parvadha, Gehlen, Marion, Andrews, Oliver, Archer, Stephen D., Bopp, Laurent, Buitenhuis, Erik, Dadou, Isabelle, Duce, Robert, Goris, Nadine, Jickells, Tim, Johnson, Martin, Keng, Fiona, Law, Cliff S., Lee, Kitack, Liss, Peter S., Lizotte, Martine, Malin, Gillian, Murrell, J. Colin, Naik, Hema, Rees, Andrew P., Schwinger, Jörg, and Williamson, Philip

Published
2020

8. Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.

Author

Frindte, Katharina, Kalyuzhnaya, Marina G, Bringel, Françoise, Dunfield, Peter F, Jetten, Mike SM, Khmelenina, Valentina N, Klotz, Martin G, Murrell, J Colin, Op den Camp, Huub JM, Sakai, Yasuyoshi, Semrau, Jeremy D, Shapiro, Nicole, DiSpirito, Alan A, Stein, Lisa Y, Svenning, Mette M, Trotsenko, Yuri A, Vuilleumier, Stéphane, Woyke, Tanja, and Knief, Claudia

Subjects
Biochemistry and Cell Biology, Genetics, Microbiology
Abstract

The genomes of the aerobic methanotrophs "Methyloterricola oryzae" strain 73aT and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73aT represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum.

Published
2017

9. Genetics and Ecology of Isoprene Degradation

Author

Crombie, Andrew T., Mejia-Florez, Nasmille L., McGenity, Terry J., Murrell, J. Colin, Timmis, Kenneth N., Editor-in-Chief, Boll, Matthias, Series Editor, Geiger, Otto, Series Editor, Goldfine, Howard, Series Editor, Krell, Tino, Series Editor, Lee, Sang Yup, Series Editor, McGenity, Terry J., Series Editor, Rojo, Fernando, Series Editor, Sousa, Diana Z, Series Editor, Stams, Alfons J. M., Series Editor, Steffan, Robert, Series Editor, and Wilkes, Heinz, Series Editor

Published
2019
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10. Biochemistry and Molecular Biology of Methane Monooxygenase

Author

Nichol, Tim, Murrell, J. Colin, Smith, Thomas J., Timmis, Kenneth N., Editor-in-Chief, Boll, Matthias, Series Editor, Geiger, Otto, Series Editor, Goldfine, Howard, Series Editor, Krell, Tino, Series Editor, Lee, Sang Yup, Series Editor, McGenity, Terry J., Series Editor, Rojo, Fernando, Series Editor, Sousa, Diana Z, Series Editor, Stams, Alfons J. M., Series Editor, Steffan, Robert, Series Editor, and Wilkes, Heinz, Series Editor

Published
2019
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11. The Methane-Oxidizing Bacteria (Methanotrophs)

Author

Kalyuzhnaya, Marina G., Gomez, Oscar A., Murrell, J. Colin, Timmis, Kenneth N., Editor-in-Chief, Boll, Matthias, Series Editor, Geiger, Otto, Series Editor, Goldfine, Howard, Series Editor, Krell, Tino, Series Editor, Lee, Sang Yup, Series Editor, McGenity, Terry J., Series Editor, Rojo, Fernando, Series Editor, Sousa, Diana Z., Series Editor, Stams, Alfons J. M., Series Editor, Steffan, Robert J., Series Editor, and Wilkes, Heinz, Series Editor

Published
2019
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12. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems

Author

Flynn, James D, Hirayama, Hisako, Sakai, Yasuyoshi, Dunfield, Peter F, Klotz, Martin G, Knief, Claudia, Camp, Huub JM Op den, Jetten, Mike SM, Khmelenina, Valentina N, Trotsenko, Yuri A, Murrell, J Colin, Semrau, Jeremy D, Svenning, Mette M, Stein, Lisa Y, Kyrpides, Nikos, Shapiro, Nicole, Woyke, Tanja, Bringel, Françoise, Vuilleumier, Stéphane, DiSpirito, Alan A, and Kalyuzhnaya, Marina G

Subjects
Microbiology, Biological Sciences, Genetics, Life Below Water
Abstract

The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems.

Published
2016

18. Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase

Author

Dedysh, Svetlana N, Naumoff, Daniil G, Vorobev, Alexey V, Kyrpides, Nikos, Woyke, Tanja, Shapiro, Nicole, Crombie, Andrew T, Murrell, J Colin, Kalyuzhnaya, Marina G, Smirnova, Angela V, and Dunfield, Peter F

Subjects
Microbiology, Biological Sciences, Genetics, Biochemistry and Cell Biology
Abstract

Methyloferula stellata AR4 is an aerobic acidophilic methanotroph, which, in contrast to most known methanotrophs but similar to Methylocella spp., possesses only a soluble methane monooxygenase. However, it differs from Methylocella spp. by its inability to grow on multicarbon substrates. Here, we report the draft genome sequence of this bacterium.

Published
2015

19. Bacteria are important dimethylsulfoniopropionate producers in coastal sediments

Author

Williams, Beth T., Cowles, Kasha, Bermejo Martínez, Ana, Curson, Andrew R. J., Zheng, Yanfen, Liu, Jingli, Newton-Payne, Simone, Hind, Andrew J., Li, Chun-Yang, Rivera, Peter Paolo L., Carrión, Ornella, Liu, Ji, Spurgin, Lewis G., Brearley, Charles A., Mackenzie, Brett Wagner, Pinchbeck, Benjamin J., Peng, Ming, Pratscher, Jennifer, Zhang, Xiao-Hua, Zhang, Yu-Zhong, Murrell, J. Colin, and Todd, Jonathan D.

Published
2019
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20. Genomic Insights into Moderately Thermophilic Methanotrophs of the Genus Methylocaldum.

Author

Delherbe, Nathalie A., Pearce, David, But, Sergey Y., Murrell, J. Colin, Khmelenina, Valentina N., and Kalyuzhnaya, Marina G.

Subjects
METHANOTROPHS, OXIDATION of methanol, HIGH temperatures, POLYHYDROXYALKANOATES, GLYCOGEN, METHANOL
Abstract

Considering the increasing interest in understanding the biotic component of methane removal from our atmosphere, it becomes essential to study the physiological characteristics and genomic potential of methanotroph isolates, especially their traits allowing them to adapt to elevated growth temperatures. The genetic signatures of Methylocaldum species have been detected in many terrestrial and aquatic ecosystems. A small set of representatives of this genus has been isolated and maintained in culture. The genus is commonly described as moderately thermophilic, with the growth optimum reaching 50 °C for some strains. Here, we present a comparative analysis of genomes of three Methylocaldum strains—two terrestrial M. szegediense strains (O-12 and Norfolk) and one marine strain, Methylocaldum marinum (S8). The examination of the core genome inventory of this genus uncovers significant redundancy in primary metabolic pathways, including the machinery for methane oxidation (numerous copies of pmo genes) and methanol oxidation (duplications of mxaF, xoxF1-5 genes), three pathways for one-carbon (C1) assimilation, and two methods of carbon storage (glycogen and polyhydroxyalkanoates). We also investigate the genetics of melanin production pathways as a key feature of the genus. [ABSTRACT FROM AUTHOR]

Published
2024
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36. The effect of methane and methanol on the terrestrial ammonia oxidising archaeon 'Candidatus Nitrosocosmicus franklandus C13'

Author

Oudova‐Rivera, Barbora, Wright, Chloe L., Crombie, Andrew T., Murrell, J. Colin, and Lehtovirta‐Morley, Laura E.

Subjects
Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract

The ammonia monooxygenase (AMO) is a key enzyme in ammonia oxidising archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper-containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co-oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well-established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia oxidising archaeon 'Ca. Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (K

Published
2022

43. Hydrazines as Substrates and Inhibitors of the Archaeal Ammonia Oxidation Pathway

Author

Schatteman, Arne, Wright, Chloë L., Crombie, Andrew T., Murrell, J. Colin, and Lehtovirta-Morley, Laura E.

Subjects
Ecology, Bacteria, Hydroxylamines, Applied Microbiology and Biotechnology, Archaea, Nitrification, Phenylhydrazines, Adenosine Triphosphate, Hydrazines, Ammonia, Humans, Soil Microbiology, Food Science, Biotechnology
Abstract

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) perform key steps in the global nitrogen cycle, the oxidation of ammonia to nitrite. While the ammonia oxidation pathway is well characterized in AOB, many knowledge gaps remain about the metabolism of AOA. Hydroxylamine is an intermediate in both AOB and AOA, but homologues of hydroxylamine dehydrogenase (HAO), catalyzing bacterial hydroxylamine oxidation, are absent in AOA. Hydrazine is a substrate for bacterial HAO, while phenylhydrazine is a suicide inhibitor of HAO. Here, we examine the effect of hydrazines in AOA to gain insights into the archaeal ammonia oxidation pathway. We show that hydrazine is both a substrate and an inhibitor for AOA and that phenylhydrazine irreversibly inhibits archaeal hydroxylamine oxidation. Both hydrazine and phenylhydrazine interfered with ammonia and hydroxylamine oxidation in AOA. Furthermore, the AOA "

Published
2022

48. Additional file 1 of Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater

Author

Liu, Jingli, Xue, Chun-Xu, Wang, Jinyan, Crombie, Andrew T., Carrión, Ornella, Johnston, Andrew W. B., Murrell, J. Colin, Liu, Ji, Zheng, Yanfen, Zhang, Xiao-Hua, and Todd, Jonathan D.

Abstract

Additional file 1: Figure S1. Microbial taxonomic profiles of seawater samples at the domain, phylum and class levels. Figure S2. Potential eukaryotic sources of DMSP in the natural (T0) coastal seawater. Figure S3. Potential prokaryotic sources of DMSP in the natural (T0) coastal seawater. Figure S4. Maximum likelihood phylogenetic tree of DmdA proteins. Figure S5. Maximum likelihood phylogenetic tree of DddP proteins. Figure S6. Maximum likelihood phylogenetic trees of DddQ, DddL, DddK, DddY, DddW and DddX proteins. Figure S7. 16S rRNA gene profiles of seawater samples enriched with DMSP analysed by DGGE. Figure S8. Bacterial community profiles of coastal seawater samples analysed by 16S rRNA gene sequencing. Figure S9. Relative abundance and taxonomy of ancillary genes from the DMSP demethylation pathway in coastal seawater samples. Figure S10. Relative abundance and taxonomic affiliation of ancillary genes from the DMSP cleavage pathway in coastal seawater metagenomes. Figure S11. Relative abundance and taxonomic affiliation of DMS cycling genes in coastal seawater samples. Table S1. Relative abundance of genes encoding proteins involved in the cycling of DMSP, DMS and related compounds in metagenomes from seawater samples. Table S2. Relative abundance (RA) of main bacterial genera from seawater samples analysed by 16S rRNA gene amplicon (16S) and metagenomics (MG) sequencing. Table S3. Dominant bacterial genera in T0 seawater samples analysed by 16S rRNA gene amplicon sequencing. Table S4. Relative abundance (RA) of main bacterial orders from seawater samples analysed by 16S rRNA gene amplicon (16S) and metagenomics (MG) sequencing. Table S5. Metagenome-assembled genomes (MAGs) with homologous sequences to genes involved in DMSP cycling reconstructed from metagenomes from seawater samples. Table S6. Characteristics of bacterial strains with DMSP-degrading activity isolated from seawater incubations with DMSP. Table S7. 16S rRNA gene amplicon sequencing results for coastal seawater samples. Table S8. Statistics for metagenomic sequencing and assemblies. Table S9. Accession numbers of previously ratified enzymes involved in the cycling of DMSP and related compounds.

Published
2022
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50. A four-helix bundle stores copper for methane oxidation

Author

Vita, Nicolas, Platsaki, Semeli, Basle, Arnaud, Allen, Stephen J., Paterson, Neil G., Crombie, Andrew T., Murrell, J. Colin, Waldron, Kevin J., and Dennison, Christopher

Subjects
Copper in the body -- Physiological aspects, Methane -- Physiological aspects, Methanotrophs -- Physiological aspects, Microbiological research, Oxidation-reduction reaction -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase (1,2). Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper (3,4). Methane monooxygenases are nature's primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock (5,6). Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location., Biology exploits copper to catalyse a range of important reactions, but use of this metal has been influenced by its availability and potential toxicity (7-9). In eukaryotes, excess copper is [...]

Published
2015

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