九州大学 研究者情報
論文一覧
濱村 奈津子(はまむら なつこ) データ更新日:2019.09.18

准教授 /  理学研究院 生物科学部門 動態生態学


原著論文
1. Tatsuya Tsuchiya, Ayaka Ehara, Yasuhiro Kasahara, Natsuko Hamamura, Seigo Amachi, Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-reducing Geobacter sp. OR-1, Applied and environmental microbiology, 10.1128/AEM.00763-19, 2019.05.
2. Takafumi Kataoka, Satoshi Mitsunobu, Natsuko Hamamura, Influence of the chemical form of antimony on soil microbial community structure and arsenite oxidation activity, Microbes and Environments, 10.1264/jsme2.ME17182, 33, 2, 214-221, 2018.01, [URL].
3. Fukushima, K., Huang, H., Hamamura, N., Cellular response of Sinorhizobium sp. strain A2 associated with arsenite oxidation, Microbes and Environment, 10.1264/jsme2.ME15096, 30, 4, 330-334, 2015.12.
4. Kanaly, R.A., Micheletto, R., Matsuda, T., Utsuno, Y., Ozeki, Y., Hamamura, N., Application of DNA adductomics to soil bacterium Sphingobium sp strain KK22, MICROBIOLOGYOPEN, 10.1002/mbo3.283, 4, 5, 841-856, 2015.10.
5. Hamamura, Natsuko; Itai, Takaaki; Liu, Yitai; Reysenbach, Anna-Louise; Damdinsuren, Narantuya; Inskeep, William P., Identification of anaerobic arsenite-oxidizing and arsenate-reducing bacteria associated with an alkaline saline lake in Khovsgol, Mongolia, ENVIRONMENTAL MICROBIOLOGY REPORTS, 10.1111/1758-2229.12144, 6, 5, 476-482, 2014.10.
6. Kanaly, Robert A.; Hamamura, Natsuko, 9,10-Phenanthrenedione biodegradation by a soil bacterium and identification of transformation products by LC/ESI-MS/MS, CHEMOSPHERE, 10.1016/j.chemosphere.2013.03.054, 92, 11, 1442-1449, 2013.09.
7. Mitsunobu, S., Hamamura, N., Kataoka, T., Shiraishi, F., Arsenic attenuation in geothermal streamwater coupled with biogenic arsenic(III) oxidation, Applied Geochemistry, 10.1016/j.apgeochem.2013.04.005, 35, 154-160, 2013.08.
8. Hamamura, N., Ward, D. M., Inskeep, W. P., Effects of petroleum mixture types on soil bacterial population dynamics associated with the biodegradation of hydrocarbons in soil environments, FEMS MICROBIOLOGY ECOLOGY, 10.1111/1574-6941.12108, 85, 1, 168-178, 2013.07.
9. Marie Kunihiro, Yasuhiro Ozeki, Yuichi Nogi, Natsuko Hamamura, Robert A. Kanaly, Benz[a]anthracene biotransformation and production of ring fission products by Sphingobium sp. strain KK22, Applied and Environmental Microbiology, 10.1128/AEM.01129-13, 79, 14, 4410-4420, 2013.07, [URL], A soil bacterium, designated strain KK22, was isolated from a phenanthrene enrichment culture of a bacterial consortium that grew on diesel fuel, and it was found to biotransform the persistent environmental pollutant and high-molecular-weight polycyclic aromatic hydrocarbon (PAH) benz[a]anthracene. nearly complete sequencing of the 16s rRNA gene of strain KK22 and phylogenetic analysis revealed that this organism is a new member of the genus sphingobium. an 8-day time course study that consisted of whole-culture extractions followed by high-performance liquid chromatography (HPLC) analyses with fluorescence detection showed that 80 to 90% biodegradation of 2.5 mg liter-1 benz[a]anthracene had occurred. biodegradation assays where benz[a]anthracene was supplied in crystalline form (100 mg liter-1) confirmed biodegradation and showed that strain KK22 cells precultured on glucose were equally capable of benz[a]anthracene biotransformation when precultured on glucose plus phenanthrene. analyses of organic extracts from benz[a]anthracene biodegradation by liquid chromatography negative electrospray ionization tandem mass spectrometry [LC/ESI(-)-MS/MS] revealed 10 products, including two o-hydroxypolyaromatic acids and two hydroxy-naphthoic acids. 1-hydroxy-2- and 2-hydroxy-3-naphthoic acids were unambiguously identified, and this indicated that oxidation of the benz[a]anthracene molecule occurred via both the linear kata and angular kata ends of the molecule. other two- and single-aromatic-ring metabolites were also documented, including 3-(2-carboxyvinyl)naphthalene-2- carboxylic acid and salicylic acid, and the proposed pathways for benz[a]anthracene biotransformation by a bacterium were extended..
10. Hamamura, N., Fukushima, K., Itai, T., Identification of Antimony- and Arsenic-Oxidizing Bacteria Associated with Antimony Mine Tailing, MICROBES AND ENVIRONMENTS, 10.1264/jsme2.ME12217, 28, 2, 257-263, 2013.06.
11. C. Takacs-vesbach, W. P. Inskeep, Z. J. Jay, M. J. Herrgard, D. B. Rusch, S. G. Tringe, M. A. Kozubal, N. Hamamura, R. E. Macur, B. W. Fouke, A.-L. Reysenbach, T. R. McDermott, R. D. Jennings, N. W. Hengartner, G. Xie, Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three Aquificales lineages, Frontiers in Microbial Physiology, 10.3389/fmicb.2013.00084, 4, 84, 2013.05.
12. Hamamura, Natsuko; Meneghin, Jennifer; Reysenbach, Anna-Louise, Comparative community gene expression analysis of Aquificales-dominated geothermal springs, ENVIRONMENTAL MICROBIOLOGY, 10.1111/1462-2920.12061, 15, 4, 1226-1237, 2013.04.
13. Kanaly, R.A., Maeda, A., Kunihiro, M., Hamamua, N., Application of denaturing gradient gel electrophoresis as an ecotoxicological tool to investigate the effects of aqui-fullerene on a bacterial community, Interdisciplinary Studies on Environmental Chemistry , 6, 79-88, 2012.02.
14. Hamamura N., Liu, Y., Inskeep, W.P., Identification of bacterial community and arsenate-reducing bacteria associated with a soda lake in Khovsgol, Mongolia, Interdisciplinary Studies on Environmental Chemistry, 6, 99-107, 2012.02.
15. Klatt, Christian G.; Wood, Jason M.; Rusch, Douglas B.; Bateson, Mary M.; Hamamura, Natsuko; Heidelberg, John F.; Grossman, Arthur R.; Bhaya, Devaki; Cohan, Frederick M.; Kuhl, Michael; Bryant, Donald A.; Ward, David M., Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential, ISME JOURNAL, 10.1038/ismej.2011.73, 5, 8, 1262-1278, 2011.08.
16. Luis A. Sayavedra-Soto, Natsuko Hamamura, Chih Wen Liu, Jeffrey A. Kimbrel, Jeff H. Chang, Daniel J. Arp, The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family, Environmental Microbiology Reports, 10.1111/j.1758-2229.2010.00239.x, 3, 3, 390-396, 2011.06, [URL], The Gram-positive bacterium Nocardioides sp. strain CF8 uses a membrane-associated monooxygenase (pBMO) to grow on butane. The nucleotide sequences of the genes encoding this novel monooxygenase were revealed through analysis of a de novo assembled draft genome sequence determined by high-throughput sequencing of the whole genome. The pBMO genes were in a similar arrangement to the genes for ammonia monooxygenase (AMO) from the ammonia-oxidizing bacteria and for particulate methane monooxygenase (pMMO) from the methane-oxidizing bacteria. The pBMO genes likely constitute an operon in the order bmoC, bmoA and bmoB. The nucleotide sequence was less than 50% similar to the genes for AMO and pMMO. The operon for pBMO was confirmed to be a single copy in the genome by Southern and computational analyses. In an incubation on butane the increase of transcriptional activity of the pBmoA gene was congruent with the increase of pBMO activity and suggested correspondence between gene expression and the utilization of butane. Phylogenetic comparison revealed distant but significant similarity of all three pBMO subunits to homologous members of the AMO/pMMO family and indicated that the pBMO represents a deeply branching third lineage of this group of particulate monooxygenases. No other bmoCAB-like genes were found to cluster with pBMO lineage in phylogenetic analysis by database searches including genomic and metagenomic sequence databases. pBMO is the first example of the AMO/pMMO-like monooxygenase from Gram-positive bacteria showing similarities to proteobacterial pMMO and AMO sequences..
17. Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary; Geesey, Gill; Frazier, Marvin, Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function, PLOS ONE, 10.1371/journal.pone.0009773, 5, 3, 2010.03.
18. Hamamura, N., Macur, R.E., Liu, Y., Inskeep, W.P., Reysenbach, A-L., Distribution of aerobic arsenite oxidase genes within the Aquificales, Interdisciplinary Studies on Environmental Chemistry , 3, 47-55, 2010.02.
19. Reysenbach, A-L., N. Hamamura, M. Podar, E. Griffiths, S. Fereirra, R. Hochstein, J. Heidelberg, J. A. Johnson, D. Mead, A. Pohorille, M. Sarmiento, K. Schweighofer, R. Seshadri, M. A. Voytek, Complete and draft genome sequences of six members of the Aquificales, Journal of Bacteriology, 10.1128/JB.01645-08, 191, 6, 1992-1993, 2009.03.
20. Hamamura, N.; Macur, R. E.; Korf, S.; Ackerman, G.; Taylor, W. P.; Kozubal, M.; Reysenbach, A. -L.; Inskeep, W. P., Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments, ENVIRONMENTAL MICROBIOLOGY, 10.1111/j.1462-2920.2008.01781.x, 11, 2, 421-431, 2009.02.
21. Hamamura, N., Fukui, M., Ward, D.M., Inskeep, W.P, Assessing Soil Microbial Populations Responding to Crude-Oil Amendment at Different Temperatures Using Phylogenetic, Functional Gene (alkB) and Physiological Analyses, ENVIRONMENTAL SCIENCE & TECHNOLOGY, 10.1021/es800030f, 42, 20, 7580-7586, 2008.10.
22. Reysenbach, A-L., Hamamura, N., A geobiological perspective on metagenomics, Geobiology, 10.1111/j.1472-4669.2008.00169.x, 6, 337-340, 2008.08.
23. Bhaya, Devaki; Grossman, Arthur R.; Steunou, Anne-Soisig; Khuri, Natalia; Cohan, Frederick M.; Hamamura, Natsuko; Melendrez, Melanie C.; Bateson, Mary M.; Ward, David M.; Heidelberg, John F., Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses, ISME JOURNAL, 10.1038/ismej.2007.46, 1, 8, 703-713, 2007.12.
24. Inskeep, William P.; Macur, Richard E.; Hamamura, Natsuko; Warelow, Thomas P.; Ward, Seamus A.; Santini, Joanne M., Detection, diversity and expression of aerobic bacterial arsenite oxidase genes, ENVIRONMENTAL MICROBIOLOGY, 10.1111/j.1462-2920.2006.01215.x, 9, 4, 934-943, 2007.04.
25. Natsuko Hamamura, Sarah H. Olson, David M. Ward, William P. Inskeep, Microbial population dynamics associated with crude-oil biodegradation in diverse soils, Applied and Environmental Microbiology, 10.1128/AEM.01015-06, 72, 9, 6316-6324, 2006.09, [URL], Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populations present during hydrocarbon degradation were analyzed using both 16S rRNA gene sequence analysis and by traditional methods for cultivating hydrocarbon-oxidizing bacteria. After a 50-day incubation, all seven soils showed comparable hydrocarbon depletion, where >80% of added crude oil was depleted and approximately 40 to 70% of added [14C] hexadecane was converted to 14CO2. However, the initial rates of hydrocarbon depletion differed up to 10-fold, and preferential utilization of shorter-chain-length n-alkanes relative to longer-chain-length n-alkanes was observed in some soils. Distinct microbial populations developed, concomitant with crude-oil depletion. Phylogenetically diverse bacterial populations were selected across different soils, many of which were identical to hydrocarbon-degrading isolates obtained from the same systems (e.g., Nocardioides albus, Collimonas sp., and Rhodococcus coprophilus). In several cases, soil type was shown to be an important determinant, defining specific microorganisms responding to hydrocarbon contamination. However, similar Rhodococcus erythropolis-like populations were observed in four of the seven soils and were the most common hydrocarbon-degrading organisms identified via cultivation..
26. Hosoda, A., Kasai, Y., Hamamura, N., Takahata, Y., Watanabe, K., Development of a PCR method for the detection and quantification of benzoyl-CoA reductase genes and its application to monitored natural attenuation, Biodegradation, 10.1007/s10532-005-0826-5, 16, 6, 591-601, 2005.12.
27. Hamamura, N., Olson, S. J., Ward, D.M., Inskeep, W.P., Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park, Applied and Environmental Microbiology, 10.1128/AEM.71.10.5943-5950.2005, 71, 10, 5943-5950, 2005.10.
28. Watanabe, K., Hamamura, N., Molecular and physiological approaches to understanding the ecology of pollutant degradation, Current Opinion in Biotechnology, 10.1016/S0958-1669(03)00059-4, 14, 289-295, 2003.06.
29. Kazuya Watanabe, Yumiko Kodama, Natsuko Hamamura, Nobuo Kaku, Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity, Applied and Environmental Microbiology, 10.1128/AEM.68.8.3899-3907.2002, 68, 8, 3899-3907, 2002.08, [URL], Fluorescence in situ hybridization has shown that cells labeled with an Archaea-specific probe (ARCH915) accounted for approximately 10% of the total cell count in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Although chemical analyses have revealed vigorous consumption of nitrate in cavity groundwater, the present study found that the methane production rate was higher than the nitrate consumption rate. To characterize the likely archaeal populations responsible for methane production in this system, fragments of 16S ribosomal DNA (rDNA) were amplified by PCR using eight different combinations of universal and Archaea-specific primers. Sequence analysis of 324 clones produced 23 different archaeal sequence types, all of which were affiliated with the kingdom Euryarchaeota. Among them, five sequence types (KuA1, KuA6, KuA12, KuA16, and KuA22) were obtained in abundance. KuA1 and KuA6 were closely related to the known methanogens Methanosaeta concilii (99% identical) and Methanomethylovorans hollandica (98%), respectively. Although no closely related organism was found for KuA12, it could be affiliated with the family Methanomicrobiaceae. KuA16 and KuA22 showed substantial homology only to some environmental clones. Both of these branched deeply in the Euryarchaeota, and may represent novel orders. Quantitative competitive PCR showed that KuA12 was the most abundant, accounting for ∼50% of the total archaeal rDNA copies detected. KuA1 and KuA16 also constituted significant proportions of the total archaeal rDNA copies (7 and 17%, respectively). These results suggest that limited species of novel archaea were enriched in the oil storage cavity. An estimate of specific methane production rates suggests that they were active methanogens..
30. Natsuko Hamamura, Chris M. Yeager, Daniel J. Arp, Two Distinct Monooxygenases for Alkane Oxidation in Nocardioides sp. Strain CF8, Applied and Environmental Microbiology, 67, 3-12, 4992-4998, 2001, Alkane monooxygenases in Nocardioides sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C2, to C16. Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne did not affect growth on octane or decane. A specific 30-kDa acetylene-binding polypeptide was observed for butane-, hexane-, octane-, and decane-grown cells but was absent from cells grown with octane or decane in the presence of 1-hexyne. These results suggest the presence of two monooxygenases in strain CF8. Degenerate primers designed for PCR amplification of genes related to the binuclear-iron-containing alkane hydroxylase from Pseudomonas oleovorans were used to clone a related gene from strain CF8. Reverse transcription-PCR and Northern blot analysis showed that this gene encoding a binuclear-iron-containing alkanc hydroxylase was expressed in cells grown on alkanes above C6. These results indicate the presence of two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8..
31. Natsuko Hamamura, Daniel J. Arp, Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8, FEMS microbiology letters, 10.1016/S0378-1097(00)00109-9, 186, 1, 21-26, 2000.05, [URL], A butane-utilizing bacterial strain CF8 was isolated and identified as a member of the genus Nocardioides from chemotaxonomic and 16S rDNA sequence analysis. Strain CF8 grew on alkanes ranging from C2 to C16 in addition to butane and various other substrates including primary alcohols, carboxylic acids, and phenol. Butane degradation by strain CF8 was inactivated by light, a specific inactivator of copper-containing monooxygenases. The unique thermal aggregation phenomenon of acetylene-binding polypeptides was also observed for strain CF8. These results suggest that butane monooxygenase in strain CF8 is a third example of the copper-containing monooxygenases previously described in ammonia oxidizers and methanotrophs. Copyright (C) 2000 Federation of European Microbiological Societies..
32. Natsuko Hamamura, Ryan T. Storfa, Lewis Semprini, Daniel J. Arp, Diversity in butane monooxygenases among butane-grown bacteria, Applied and Environmental Microbiology, 65, 10, 4586-4593, 1999, Butane monooxygenases of butane-grown Pseudomonas butanovora, Mycobacterium vaccae JOB5, and an environmental isolate, CF8, were compared at the physiological level. The presence of butane monooxygenases in these bacteria was indicated by the following results. (i) O2 was required for butane degradation. (ii) 1-Butanol was produced during butane degradation. (iii) Acetylene inhibited both butane oxidation and 1-butanol production. The responses to the known monooxygenase inactivator, ethylene, and inhibitor, allyl thiourea (ATU), discriminated butane degradation among the three bacteria. Ethylene irreversibly inactivated butane oxidation by P. butanovora but not by M. vaccae or CF8. In contrast, butane oxidation by only CF8 was strongly inhibited by ATU. In all three strains of butane-grown bacteria, specific polypeptides were labeled in the presence of [14C]acetylene. The [14C]acetylene labeling patterns were different among the three bacteria. Exposure of lactate-grown CF8 and P. butanovora and glucose-grown M. vaccae to butane induced butane oxidation activity as well as the specific acetylene-binding polypeptides. Ammonia was oxidized by all three bacteria. P. butanovora oxidized ammonia to hydroxylamine, while CF8 and M. vaccae produced nitrite. All three bacteria oxidized ethylene to ethylene oxide. Methane oxidation was not detected by any of the bacteria. The results indicate the presence of three distinct butane monooxygenases in butane-grown P. butanovora, M. vaccae, and CF8..
33. Natsuko Hamamura, Cynthia Page, Tulley Long, Lewis Semprini, Daniel J. Arp, Chloroform cometabolism by butane-grown CF8, Pseudomonas butanovora, and Mycobacterium vaccae JOB5 and methane-grown Methylosinus trichosporium OB3b, Applied and Environmental Microbiology, 63, 9, 3607-3613, 1997.09, Chloroform (CF) degradation by a butane-grown enrichment culture, CF8, was compared to that by butane-grown Pseudomonas butanovora and Mycobacterium vaccae JOB5 and to that by a known CF degrader Methylosinus trichosporium OB3b. All three butane-grown bacteria were able to degrade CF at rates comparable to that of M. trichosporium. CF degradation by all four bacteria required O2. Butane inhibited CF degradation by the butane-grown bacteria, suggesting that butane monooxygenase is responsible for CF degradation. P. butanovora required exogenous reductant to degrade CF, while CF8 and M. vaccae utilized endogenous reductants. Prolonged incubation with CF resulted in decreased CF degradation. CF8 and P. butanovora were more sensitive to CF than either M. trichosporium or M. vaccae. CF degradation by all three butane-grown bacteria was in-activated by acetylene, which is a mechanism- based inhibitor for several monooxygenases. Butane protected all three butane-grown bacteria from inactivation by acetylene, which indicates that the same monooxygenase is responsible for both CF and butane oxidation. CF8 and P. butanovora were able to degrade other chlorinated hydrocarbons, including trichloroethylene, 1,2-cis-dichloroethylene, and vinyl chloride. In addition, CF8 degraded 1,1,2-trichloroethane. The results indicate the potential of butane-grown bacteria for chlorinated hydro-carbon transformation..

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