Changes in methane oxidation activity and methanotrophic community composition in saline alkaline soils
详细信息 查看全文
- 作者：Nancy Serrano-Silva (1)
César Valenzuela-Encinas (2)
Rodolfo Marsch (1)
Luc Dendooven (1)
Rocio J. Alcántara-Hernández (3) - 关键词：Methane oxidation ; Methane monooxygenase ; Saline alkaline soils ; pmoA
- 刊名：Extremophiles
- 出版年：2014
- 出版时间：May 2014
- 年：2014
- 卷：18
- 期：3
- 页码：561-571
- 全文大小：
- 参考文献：1. Altschul SF, Madden TL, Sch?ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25:3389-402 CrossRef
2. Antony CP, Kumaresan D, Ferrando L, Boden R, Moussard H, Scavino AF, Shouche YS, Murrell JC (2010) Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact. ISME J 4:1470-480 CrossRef
3. Antony CP, Kumaresan D, Hunger S, Drake HL, Murrell JC, Shouche YS (2012) Microbiology of Lonar Lake and other soda lakes. ISME J 7:468-76 CrossRef
4. Avnimelech Y, Ritvo G, Meijer LE, Kochba M (2001) Water content, organic carbon and dry bulk density in flooded sediments. Aquac Eng 25:25-3 CrossRef
5. Bárcena TG, Finster KW, Yde JC (2011) Spatial patterns of soil development, methane oxidation, and methanotrophic diversity along a receding glacier forefield, Southeast Greenland. Arct Antarct Alp Res 43:178-88 CrossRef
6. Bedard C, Knowles R (1989) Physiology, biochemistry, and specific inhibitors of CH4, NH4 +, and CO oxidation by methanotrophs and nitrifiers. Microbiol Rev 53:68-4
7. Betancur-Galvis LA, Carrillo H, Luna-Guido M, Marsch R, Dendooven L (2012) Enhanced dissipation of polycyclic aromatic hydrocarbons in the rhizosphere of the Athel Tamarisk ( / Tamarix / aphylla L. Karst.) grown in saline-alkaline soils of the former lake Texcoco. Int J Phytoremediation 14:741-53 CrossRef
8. Bissett A, Abell GCJ, Bodrossy L, Richardson AE, Thrall PH (2012) Methanotrophic communities in Australian woodland soils of varying salinity. FEMS Microbiol Ecol 80:685-95 CrossRef
9. Bodrossy L, Holmes EM, Holmes AJ, Kovács KL, Murrell JC (1997) Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, / Methylocaldum gen. nov. Arch Microbiol 168:493-03 CrossRef
10. Bourne DG, McDonald IR, Murrell JC (2001) Comparison of / pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl Environ Microbiol 67:3802-809 CrossRef
11. Bowman J (2006) The methanotrophs-the families Methylococcaceae and Methylocystaceae Ch. 3.1.14. Prokaryotes 5:266-89 CrossRef
12. Campanella JJ, Bitincka L, Smalley J (2003) MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinform 4:29 CrossRef
13. Ceja-Navarro JA, Rivera FN, Pati?o-Zú?iga L, Govaerts B, Marsch R, Vila-Sanjurjo A, Dendooven L (2010) Molecular characterization of soil bacterial communities in contrasting zero tillage systems. Plant Soil 329:127-37 CrossRef
14. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497-500 CrossRef
15. Conde E, Cardenas M, Ponce-Mendoza A, Luna-Guido ML, Cruz-Mondragón C, Dendooven L (2005) The impacts of inorganic nitrogen application on mineralization of 14C-labelled maize and glucose, and on priming effect in saline alkaline soil. Soil Biol Biochem 37:681-91 CrossRef
16. Conrad R, Frenzel P, Cohen Y (1995) Methane emission from hypersaline microbial mats:?lack of aerobic methane oxidation activity. FEMS Microbiol Ecol 16:297-05 CrossRef
17. Costello AM, Lidstrom ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066-074
18. Cullen DW, Hirsch PR (1998) Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol Biochem 30:983-93 CrossRef
19. Dalal R, Allen D, Livesley S, Richards G (2008) Magnitude and biophysical regulators of methane emission and consumption in the Australian agricultural, forest, and submerged landscapes: a review. Plant Soil 309:43-6 CrossRef
20. Dedysh SN, Knief C, Dunfield PF (2005) / Methylocella species are facultatively methanotrophic. J Bacteriol 187:4665-670 CrossRef
21. Degelmann DM, Borken W, Drake HL, Kolb S (2010) Different atmospheric methane-oxidizing communities in European beech and Norway spruce soils. Appl Environ Microbiol 76:3228-235 CrossRef
22. Dendooven L, Alcántara-Hernández RJ, Valenzuela-Encinas C, Luna-Guido ML, Perez-Guevara F, Marsch R (2010) Dynamics of carbon and nitrogen in an extreme alkaline saline soil: a review. Soil Biol Biochem 42:865-77 CrossRef
23. D?rr N, Glaser B, Kolb S (2010) Methanotrophic communities in Brazilian ferralsols from naturally forested, afforested, and agricultural sites. Appl Environ Microbiol 76:1307-310 CrossRef
24. Dumont MG, Murrell JC (2005) Community-level analysis: key genes of aerobic methane oxidation. Methods Enzymol 397:413-27 CrossRef
25. Eshinimaev BT, Khmelenina VN, Trotsenko YA (2008) First isolation of a type II methanotroph from a soda lake. Microbiology 77:628-31 CrossRef
26. Fernández-Buces N, Siebe C, Cram S, Palacio JL (2006) Mapping soil salinity using a combined spectral response index for bare soil and vegetation: a case study in the former lake Texcoco, Mexico. J Arid Environ 65:644-67 CrossRef
27. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-48
28. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-04 CrossRef
29. Guo C, Sun W, Harsh JB, Ogram A (1997) Hybridization analysis of microbial DNA from fuel oil-contaminated and non contaminated soil. Microb Ecol 34:178-87 CrossRef
30. Gutiérrez-Castorena MDC, Stoops G, Ortiz-Solorio CA, López-Avila G (2005) Amorphous silica materials in soils and sediments of the Ex-Lago de Texcoco, Mexico: an explanation for its subsidence. Catena 60:205-26 CrossRef
31. Hakemian AS, Rosenzweig AC (2007) The biochemistry of methane oxidation. Annu Rev Biochem 76:223-41 CrossRef
32. Han B, Chen Y, Abell G, Jiang H, Bodrossy L, Zhao J, Murrell JC, Xing XH (2009) Diversity and activity of methanotrophs in alkaline soil from a Chinese coal mine. FEMS Microbiol Ecol 70:196-07 CrossRef
33. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439-71
34. Holmes AJ, Costello A, Lidstrom ME, Murrell JC (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132:203-08 CrossRef
35. Holmes AJ, Roslev P, McDonald IR, Iversen N, Henriksen K, Murrell JC (1999) Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl Environ Microbiol 65:3312-318
36. Horz HP, Rich V, Avrahami S, Bohannan BJM (2005) Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Appl Environ Microbiol 71:2642-652 CrossRef
37. Jensen S, Neufeld JD, Birkeland NK, Hovland M, Murrell JC (2008) Methane assimilation and trophic interactions with marine / Methylomicrobium in deep-water coral reef sediment off the coast of Norway. FEMS Microbiol Ecol 66:320-30 CrossRef
38. Jones RD, Morita RY (1983) Methane oxidation by / Nitrosococcus / oceanus and / Nitrosomonas / europaea. Appl Environ Microbiol 45:401-10
39. Jones BE, Grant WD, Duckworth AW, Owenson GG (1998) Microbial diversity of soda lakes. Extremophiles 2:191-00 CrossRef
40. Khmelenina VN, Kalyuzhnaya MG, Starostina NG, Suzina NE, Trotsenko YA (1997) Isolation and characterization of halotolerant alkaliphilic methanotrophic bacteria from Tuva soda Lakes. Curr Microbiol 35:257-61 CrossRef
41. Khmelenina VN, Eshinimaev BT, Kalyuzhnaya MG, Trotsenko I (2000) Potential activity of methane and ammonia oxidation by methanotrophic communities from soda lakes of the southern Transbaikal. Mikrobiologiia 69:553-58
42. Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol 69:6703-714 CrossRef
43. Levine UY, Teal TK, Robertson GP, Schmidt TM (2011) Agriculture’s impact on microbial diversity and associated fluxes of carbon dioxide and methane. ISME J 5:1683-691 CrossRef
44. Lin JL, Radajewski S, Eshinimaev BT, Trotsenko YA, McDonald IR, Murrell JC (2004) Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing. Environ Microbiol 6:1049-060 CrossRef
45. Lin JL, Joye SB, Scholten JC, Schafer H, McDonald IR, Murrell JC (2005) Analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure. Appl Environ Microbiol 71:6458-462 CrossRef
46. Lüke C, Frenzel P (2011) Potential of / pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl Environ Microbiol 77:6305-309 CrossRef
47. Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P (2010) Biogeography of wetland rice methanotrophs. Environ Microbiol 12:862-72 CrossRef
48. Luna-Guido ML, Beltrán-Hernández RI, Solís-Ceballos NA, Hernández-Chávez N, Mercado-García F, Catt JA, Olalde-Portugal V, Dendooven L (2000) Chemical and biological characteristics of alkaline saline soils from the former Lake Texcoco as affected by artificial drainage. Biol Fertil Soils 32:102-08 CrossRef
49. McDonald IR, Bodrossy L, Chen Y, Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74:1305-315 CrossRef
50. Murrell JC, Gilbert B, McDonald IR (2000) Molecular biology and regulation of methane monooxygenase. Arch Microbiol 173:325-32 CrossRef
51. Nakamura T, Hoaki T, Hanada S, Maruyama A, Kamagata Y, Fuse H (2007) Soluble and particulate methane monooxygenase gene clusters in the marine methanotroph / Methylomicrobium sp. strain NI. FEMS Microbiol Lett 277:157-64 CrossRef
52. Op den Camp H, Islam T, Stott M, Harhangi H, Hynes A, Schouten S, Jetten M, Birkeland N-K, Pol A, Dunfield P (2009) Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep 1:293-06 CrossRef
53. Pester M, Friedrich MW, Schink B, Brune A (2004) / pmoA-based analysis of methanotrophs in a littoral lake sediment reveals a diverse and stable community in a dynamic environment. Appl Environ Microbiol 70:3138-142 CrossRef
54. Rambaut A (2007) FigTree, a graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree/
55. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-541 CrossRef
56. Semrau JD, DiSpirito AA, Yoon S (2010) Methanotrophs and copper. FEMS Microbiol Rev 34:496-31
57. Serrano-Silva N, Luna-Guido M, Fernández-Luque?o F, Marsch R, Dendooven L (2011) Emission of greenhouse gases from an agricultural soil amended with urea: a laboratory study. Appl Soil Ecol 47:92-7 CrossRef
58. Singh BK, Tate KR, Ross DJ, Singh J, Dando J, Thomas N, Millard P, Murrell JC (2009) Soil methane oxidation and methanotroph responses to afforestation of pastures with Pinus radiata stands. Soil Biol Biochem 41:2196-205 CrossRef
59. Smith KA, Ball T, Conen F, Dobbie KE, Massheder J, Rey A (2003) Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes. Eur J Soil Sci 54:779-91 CrossRef
60. Sorokin DY, Kuenen JG (2005) Chemolithotrophic haloalkaliphiles from soda lakes. FEMS Microbiol Ecol 52:287-95 CrossRef
61. Sorokin DY, Jones BE, Kuenen JG (2000) A novel obligately methylotrophic, methane-oxidizing / Methylomicrobium species from a highly alkaline environment. Extremophiles 4:145-55 CrossRef
62. Stoecker K, Bendinger B, Sch?ning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M (2006) Cohn’s / Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci USA 103:2363-367 CrossRef
63. Trotsenko YA, Khmelenina VN (2002) Biology of extremophilic and extremotolerant methanotrophs. Arch Microbiol 177:123-31 CrossRef
64. Trotsenko YA, Murrell JC (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63:183-29 CrossRef
65. Trotsenko YA, Medvedkova KA, Khmelenina VN, Eshinimayev BT (2009) Thermophilic and thermotolerant aerobic methanotrophs. Microbiology 78:387-01 CrossRef
66. Valenzuela-Encinas C, Neria-González I, Alcántara-Hernández R, Enríquez-Aragón J, Estrada-Alvarado I, Hernández-Rodríguez C, Dendooven L, Marsch R (2008) Phylogenetic analysis of the archaeal community in an alkaline–saline soil of the former lake Texcoco (Mexico). Extremophiles 12:247-54 CrossRef
67. Valenzuela-Encinas C, Neria-Gonzalez I, Alcantara-Hernandez RJ, Estrada-Alvarado I, de la Serna FJZD, Dendooven L, Marsch R (2009) Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding. Extremophiles 13:609-21 CrossRef
68. Valenzuela-Encinas C, Alcántara-Hernández RJ, Estrada-Alvarado I, de la Serna FJZD, Dendooven L, Marsch R (2012) The archaeal diversity and population in a drained alkaline saline soil of the former lake Texcoco (Mexico). Geomicrobiology 29:18-2 CrossRef
69. V?lker H, Schweisfurth R, Hirsch P (1977) Morphology and ultrastructure of / Crenothrix polyspora Cohn. J Bacteriol 131:306-13
70. Vorobev AV, Baani M, Doronina NV, Brady AL, Liesack W, Dunfield PF, Dedysh SN (2011) / Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. Int J Syst Evol Microbiol 61:2456-463 CrossRef
71. Zhang J, Li Z, Ning T, Gu S (2011) Methane uptake in salt-affected soils shows low sensitivity to salt addition. Soil Biol Biochem 43:1434-439 CrossRef - 作者单位：Nancy Serrano-Silva (1)
César Valenzuela-Encinas (2)
Rodolfo Marsch (1)
Luc Dendooven (1)
Rocio J. Alcántara-Hernández (3)
1. Laboratory of Soil Ecology, ABACUS, Cinvestav, Campus Zacatenco, 07360, Mexico D.F., Mexico
2. Department of Chemistry, Unidad Profesional Interdisciplinaria de Biotecnologia-IPN (UPIBI), 07340, Mexico D.F., Mexico
3. Laboratorio de Ecología Molecular y Epigenética, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior sn. Ciudad Universitaria, Del. Coyoacán, 04510, Mexico D.F., Mexico - ISSN：1433-4909
文摘
The soil of the former Lake Texcoco is a saline alkaline environment where anthropogenic drainage in some areas has reduced salt content and pH. Potential methane (CH4) consumption rates were measured in three soils of the former Lake Texcoco with different electrolytic conductivity (EC) and pH, i.e. Tex-S1 a >18?years drained soil (EC 0.7?dS?m?, pH 8.5), Tex-S2 drained for ~10?years (EC 9.0?dS?m?, pH 10.3) and the undrained Tex-S3 (EC 84.8?dS?m?, pH 10.3). An arable soil from Alcholoya (EC 0.7?dS?m?, pH 6.7), located nearby Lake Texcoco was used as control. Methane oxidation in the soil Tex-S1 (lowest EC and pH) was similar to that in the arable soil from Alcholoya (32.5 and 34.7?mg CH4?kg? dry soil?day?, respectively). Meanwhile, in soils Tex-S2 and Tex-S3, the potential CH4 oxidation rates were only 15.0 and 12.8?mg CH4?kg? dry soil?day?, respectively. Differences in CH4 oxidation were also related to changes in the methane-oxidizing communities in these soils. Sequence analysis of pmoA gene showed that soils differed in the identity and number of methanotrophic phylotypes. The Alcholoya soil and Tex-S1 contained phylotypes grouped within the upland soil cluster gamma and the Jasper Ridge, California JR-2 clade. In soil Tex-S3, a phylotype related to Methylomicrobium alcaliphilum was detected.