New radioisotope-free method for measuring bacterial production using [15N5]-2-deoxyadenosine and liquid chromatography mass spectrometry (LC–MS) in aquatic environments
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- 作者：Kenji Tsuchiya ; Tomoharu Sano ; Nobuyuki Kawasaki ; Hideki Fukuda…
- 关键词：Bacterial production ; Stable isotope ; Liquid chromatography mass spectrometry (LC–MS) ; DNA synthesis ; 2-deoxyadenosine
- 刊名：Journal of Oceanography
- 出版年：2015
- 出版时间：December 2015
- 年：2015
- 卷：71
- 期：6
- 页码：675-683
- 全文大小：628 KB
- 参考文献：Auling G, Prelle H, Diekmann H (1982) Incorporation of deoxyribonucleosides into DNA of coryneform bacteria and the relevance of deoxyribonucleoside kinases. Eur J Biochem 121:365-70CrossRef
Azam F (1998) Microbial control of oceanic carbon flux: the plot thickens. Science 280:694-96CrossRef
Azam F, Fenchel T, Field JG, Gray JS, Meyerreil LA, Thingstad F (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10:275-78CrossRef
Bloem J, Ellenbroek FM, B?r-Gilissen MB, Cappenberg TE (1989) Protozoan grazing and bacterial production in stratified lake Vechten estimated with fluorescently labeled bacteria and by thymidine incorporation. Appl Environ Microbiol 55:1787-795
Brittain AM, Karl DM (1990) Catabolism of tritiated thymidine by aquatic microbial communities and incorporation of tritium into RNA and protein. Appl Environ Microbiol 56:1245-254
Camargo APM (2004) An electrochemical study of the adsorption and coadsorption behavior of selected purines, pyrimidines and nucleosides on Au(III). Doctor thesis, Freie Universit?t Berlin, Germany
Davis CL (1989) Uptake and incorporation of thymidine by bacterial isolates from an upwelling environment. Appl Environ Microbiol 55:1267-272
Ducklow HW, Carlson CA (1992) Oceanic bacterial production. Adv Microb Ecol 12:113-81CrossRef
Ebise S (1987) Characteristics of changes in distribution and size composition of particulate matter in Lake Kasumigaura. Jpn J Limnol 48:S85–S97CrossRef
Fuhrman JA, Azam F (1980) Bacterioplankton secondary production estimates for coastal waters of British Clumbia, Antarctica and California. Appl Environ Microbiol 39:1085-095
Fuhrman JA, Azam F (1982) Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: evaluation and field results. Mar Biol 66:109-20CrossRef
Hamasaki K (2006) Comparison of bromodeoxyuridine immunoassay with tritiated thymidine radioassay for measuring bacterial productivity in oceanic waters. J Oceanogr 62:793-99CrossRef
Hollibaugh JT, Fuhrman JA, Azam F (1980) Radioactive labeling of natural assemblages of bacterioplankton for use in trophic studies. Limnol Oceanogr 25:172-81CrossRef
Imai A, Matsushige K, Nagai T (2003) Trihalomethane formation potential of dissolved organic matter in a shallow eutrophic late. Water Res 37:4284-294CrossRef
Ingram LO, Fisher WD (1972) Selective inhibition of deoxyribonucleic acid synthesis by 2-deoxyadenosine in the blue-green bacterium Agmenellum quadruplicatum. J Bacteriol 112:170-75
Jeffrey WH, Paul JH (1990) Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates. Appl Environ Microbiol 56:1367-372
Johnstone BH, Jones RD (1989) A study on the lack of [Methyl-3H] thymidine uptake and incorporation by chemolithotrophic bacteria. Microb Ecol. 18:73-7CrossRef
Karl DM (1982) Selected nucleic acid precursors in studies of aquatic microbial ecology. Appl Environ Microbiol 44:891-02
Kirchman DL, Hoch MP (1988) Bacterial production in the Delaware Bay estuary estimated from thymidine and leucine incorporation rates. Mar Ecol Prog Ser 45:169-78CrossRef
Kirchman D, K’Nees E, Hodson R (1985) Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49:599-07
Legendre P (2001) Model II regression—user’s guide. Département de sciences biologiques, Université de Montréal. <http://?www.?fas.?umontreal.?ca/?biol/?legendre/-/span> >
Mumy KL, Findlay RH (2004) Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative competitive PCR. J Microbiol Meth 57:259-68CrossRef
Nelson CE, Carlson CA (2005) A nonradioactive assay of bacterial productivity optimized for oligotrophic pelagic environments. Limnol Oceanogr Methods 3:211-20CrossRef
Nemtseva YuA, Rasskazov VA, Terent’eva NA, Terent’ev LL, Shevchenko LS, Mikhailov VV (2006) Heterogeneity of nucleoside kinases in marine microorganism cells. Russian J Mar Biol 32:55-3CrossRef
Nohara K, Baba T, Murai H, Kobayashi Y, Suzuki T, Tateishi Y, Matsumoto M, Nishimura N, Sano T (2011) Global DNA methylation in the mouse liver is affected by methyl deficiency and arsenic in a sex-dependent manner. Arch Toxicol 85:653-61CrossRef
Ogura N (1975) Further studies on decomposition of dissolved organic matter in coastal seawater. Mar Biol 31:101-11CrossRef
Pedrós-Alió C, Newell SY (1989) Microautoradiographic study of thymidine uptake in brackish waters around Sapelo Island, Georgia. USA Mar Ecol Prog Ser 55:83-4CrossRef
Pérez MT, H?rtnagl P, Sommaruga R (2010) Contrasting ability to take up leucine and thymidine among freshwater bacterial groups: implications for bacterial production measurements. Environ Microbiol 12:74-2CrossRef
Petit M, Servais P, Lavandier P (1999) Bacterial producti - 作者单位：Kenji Tsuchiya (1)
Tomoharu Sano (2)
Nobuyuki Kawasaki (2) (3)
Hideki Fukuda (4)
Noriko Tomioka (2)
Koji Hamasaki (4)
Yuya Tada (4) (5)
Shinji Shimode (6)
Tatsuki Toda (1)
Akio Imai (2)
1. Faculty of Science and Engineering, Soka University, 1-236, Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
2. National Institute for Environmental Studies, 16-2, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
3. Universiti Selangor, Jalan Timur Tambahan, 45600, Bestari Jaya, Salangor, Malaysia
4. Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
5. Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
6. Graduate School of Environment and Information Science, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa, 240-8501, Japan - 刊物类别：Earth and Environmental Science
- 刊物主题：Earth sciences
Oceanography
Hydrobiology - 出版者：Springer Netherlands
- ISSN：1573-868X
文摘
This study proposed a non-radioactive quantitative measurement of bacterial production using stable isotope nitrogen-15-labeled deoxyadenosine ([15N5]-2-deoxyadenosine; 15N-dA) by liquid chromatography mass spectrometry (LC–MS). The method of preparing 5N-dA described in this study included incubation of seawater or lake water with 15N-dA for 5-4 h, filtration onto a membrane filter, DNA extraction, enzymatic hydrolysis of DNA to nucleosides and quantification of 15N-dA by LC–MS. In the DNA extraction, the silica beads method was examined first, but a large amount of salts and enzymatic inhibitors used in the method caused failure of subsequent procedures, such as enzymatic hydrolysis and LC–MS analysis. On the other hand, the magnetic beads method showed much better results for the extraction. The incorporation rate of 15N-dA was significantly positively correlated to that of tritium-labeled thymidine (3H-TdR) in samples of coastal seawaters and lake waters. The average 15N-dA: 3H-TdR incorporation ratio for the seawater sample was 0.55 with 2.5 and 97.5 % confidence intervals of 0.51 and 0.58, respectively; the average ratio for the lake water sample was 0.28 with 2.5 and 97.5 % confidence intervals of 0.23 and 0.34, respectively. The results suggest that the 15N-dA method can be applied to the measurement of bacterial production in aquatic ecosystems, and that this method can accurately predict the DNA synthesis rates measured by the conventional method. Keywords Bacterial production Stable isotope Liquid chromatography mass spectrometry (LC–MS) DNA synthesis 2-deoxyadenosine