Peatland succession induces a shift in the community composition of<i>Sphagnum</i>-associated active methanotrophs

FEMS Microbiology Ecology - Tập 88 Số 3 - Trang 596-611 - 2014
Anuliina Putkinen1, Tuula Larmola2, Tero Tuomivirta1, Henri Siljanen3, Levente Bodrossy4, Eeva‐Stiina Tuittila2, Hannu Fritze1
1Southern Finland Regional Unit, Finnish Forest Research Institute, Vantaa, Finland
2Department of Forest Sciences, University of Helsinki, Helsinki, Finland
3Department of Environmental Science, University of Eastern Finland, Kuopio, Finland
4CSIRO Marine and Atmospheric Research and Wealth from Oceans; National Research Flagship; Hobart TAS Australia

Tóm tắt

Từ khóa


Tài liệu tham khảo

Altschul, 1990, Basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2

Auman, 2001, nifH sequences and nitrogen fixation in type I and type II methanotrophs, Appl Environ Microbiol, 67, 4009, 10.1128/AEM.67.9.4009-4016.2001

Basiliko, 2004, Roles of moss species and habitat in methane consumption potential in a northern peatland, Wetlands, 24, 178, 10.1672/0277-5212(2004)024[0178:ROMSAH]2.0.CO;2

Bergmann, 2011, The under-recognized dominance of Verrucomicrobia in soil bacterial communities, Soil Biol Biochem, 43, 1450, 10.1016/j.soilbio.2011.03.012

Bodelier, 2013, Microbial minorities modulate methane consumption through niche partitioning, ISME J, 7, 2214, 10.1038/ismej.2013.99

Bodrossy, 2003, Development and validation of a diagnostic microbial microarray for methanotrophs, Environ Microbiol, 5, 566, 10.1046/j.1462-2920.2003.00450.x

ter Braak, 2012, Canoco Reference Manual and User's Guide: Software for Ordination (version 5.0)

Bragina, 2012a, Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle, ISME J, 6, 802, 10.1038/ismej.2011.151

Bragina, 2012b, Similar diversity of alphaproteobacteria and nitrogenase gene amplicons on two related Sphagnum mosses, Front Microbiol, 2, 275, 10.3389/fmicb.2011.00275

Bragina, 2013, Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning, Sci Rep, 3, 1955, 10.1038/srep01955

Breemen, 1995, How Sphagnum bogs down other plants, Trends Ecol Evol, 10, 270, 10.1016/0169-5347(95)90007-1

Chen, 2008a, Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses, Environ Microbiol, 10, 446, 10.1111/j.1462-2920.2007.01466.x

Chen, 2008b, Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands, Environ Microbiol, 10, 2609, 10.1111/j.1462-2920.2008.01683.x

Dedysh, 2009, Exploring methanotroph diversity in acidic northern wetlands: molecular and cultivation-based studies, Microbiology, 78, 655, 10.1134/S0026261709060010

DeSantis, 2006, NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes, Nucleic Acids Res, 34, W394, 10.1093/nar/gkl244

Drebs, 2002, Climatological Statistics of Finland 1971-2000, 99

Drummond, 2011, Geneious v5.4

Dunfield, 2007, Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia, Nature, 450, 879, 10.1038/nature06411

Graef, 2011, The active methanotrophic community in a wetland from the High Arctic, Environ Microbiol Rep, 3, 466, 10.1111/j.1758-2229.2010.00237.x

Granath, 2010, Rapid ecosystem shifts in peatlands: linking plant physiology and succession, Ecology, 91, 3047, 10.1890/09-2267.1

Grime, 1977, Evidence for the existence of three primary strategies in plants and its relevance to ecological and evolutionary theory, Am Nat, 111, 1169, 10.1086/283244

Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol, 52, 696, 10.1080/10635150390235520

Gupta, 2012, Active methanotrophs in two contrasting north american peatland ecosystems revealed using DNA-SIP, Microb Ecol, 63, 438, 10.1007/s00248-011-9902-z

Hammer, 2001, PAST: paleontological statistics software package for education and data analysis, Palaeontol Electronica, 4, 1

Hanson, 1996, Methanotrophic bacteria, Microbiol Rev, 60, 439, 10.1128/MMBR.60.2.439-471.1996

Henckel, 2000, Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil, Environ Microbiol, 2, 666, 10.1046/j.1462-2920.2000.00149.x

Ho, 2013, Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies, Environ Microbiol Rep, 5, 335, 10.1111/j.1758-2229.2012.00370.x

Huber, 2004, Bellerophon: a program to detect chimeric sequences in multiple sequence alignments, Bioinformatics, 20, 2317, 10.1093/bioinformatics/bth226

Islam, 2008, Methane oxidation at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum, P Natl Acad Sci USA, 105, 300, 10.1073/pnas.0704162105

Jaatinen, 2005, Methane-oxidizing bacteria in a Finnish raised mire complex: effects of site fertility and drainage, Microb Ecol, 50, 429, 10.1007/s00248-005-9219-x

Khadem, 2011, Autotrophic methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicum SolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation, J Bacteriol, 193, 4438, 10.1128/JB.00407-11

Kip, 2010, Global prevalence of methane oxidation by symbiotic bacteria in peat-moss ecosystems, Nat Geosci, 3, 617, 10.1038/ngeo939

Kip, 2011a, Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses, Appl Environ Microbiol, 77, 5643, 10.1128/AEM.05017-11

Kip, 2011b, Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog, Environ Microbiol Rep, 3, 667, 10.1111/j.1758-2229.2011.00260.x

Kip, 2012, Methanotrophic activity and diversity in different Sphagnum magellanicum dominated habitats in the southernmost peat bogs of Patagonia, Biogeoscience, 9, 47, 10.5194/bg-9-47-2012

Knief, 2005, Response and adaptation of different methanotrophic bacteria to low methane mixing ratios, Environ Microbiol, 7, 1307, 10.1111/j.1462-2920.2005.00814.x

Laine, 2011a, Sphagnum growth and ecophysiology during mire succession, Oecologia, 167, 1115, 10.1007/s00442-011-2039-4

Laine J Harju P Timonen T Laine A Tuittila E-S Minkkinen K Vasander H 2011b The intricate beauty of Sphagnum mosses - a Finnish guide to identification 191

Lane, 1991, Nucleic Acid Techniques in Bacterial Systematics, 115

Larmola, 2010, The role of Sphagnum mosses in the methane cycling of a boreal mire, Ecology, 91, 2356, 10.1890/09-1343.1

Larmola, 2014, Methanotrophy induces nitrogen fixation during peatland development, P Natl Acad Sci USA, 111, 734, 10.1073/pnas.1314284111

Leppälä, 2008, Seasonal dynamics of CO2 exchange during primary succession of boreal mires as controlled by phenology of plants, Ecoscience, 15, 460, 10.2980/15-4-3142

Leppälä, 2011a, Methane flux dynamics during mire succession, Oecologia, 165, 489, 10.1007/s00442-010-1754-6

Leppälä, 2011b, Differences in CO2 dynamics between successional mire plant communities during wet and dry summers, J Veg Sci, 22, 357, 10.1111/j.1654-1103.2011.01259.x

Lin, 2004, Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing, Environ Microbiol, 6, 1049, 10.1111/j.1462-2920.2004.00635.x

Lüke, 2011, Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies, Appl Environ Microbiol, 77, 6305, 10.1128/AEM.05355-11

Lüke, 2010, Biogeography of wetland rice methanotrophs, Environ Microbiol, 12, 862, 10.1111/j.1462-2920.2009.02131.x

Marchesi, 1998, Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA, Appl Environ Microbiol, 64, 795, 10.1128/AEM.64.2.795-799.1998

McAuliffe, 1971, GC determination of solutes by multiple phase equilibration, Chem Technol, 1, 46

McDonald, 2005, Stable isotope probing of nucleic acids in methanotrophs and methylotrophs: a review, Org Geochem, 36, 779, 10.1016/j.orggeochem.2005.01.005

Merilä, 2006, Methanogen communities along a primary succession transect of mire ecosystems, FEMS Microbiol Ecol, 55, 221, 10.1111/j.1574-6941.2005.00030.x

Morris, 2002, Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing, Appl Environ Microbiol, 68, 1446, 10.1128/AEM.68.3.1446-1453.2002

Moussard, 2009, Identification of active methylotrophic bacteria inhabiting surface sediment of a marine estuary, Environ Microbiol Rep, 1, 424, 10.1111/j.1758-2229.2009.00063.x

Nazaries, 2013, Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions, Environ Microbiol, 15, 2395, 10.1111/1462-2920.12149

Nykänen, 1998, Methane fluxes on boreal peatlands of different fertility and the effect of long-term experimental lowering of the water table on flux rates, Global Biogeochem Cycles, 12, 53, 10.1029/97GB02732

Parmentier, 2011, The role of endophytic methane-oxidizing bacteria in submerged Sphagnum in determining methane emissions of Northeastern Siberian tundra, Biogeoscience, 8, 1267, 10.5194/bg-8-1267-2011

Pol, 2007, Methanotrophy below pH1 by a new Verrucomicrobia species, Nature, 450, 874, 10.1038/nature06222

Putkinen, 2012, Water dispersal of methanotrophic bacteria maintains functional methane oxidation in Sphagnum mosses, Front Microbiol, 3, 15, 10.3389/fmicb.2012.00015

Radajewski, 2002, Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing, Microbiology, 148, 2331, 10.1099/00221287-148-8-2331

Raghoebarsing, 2005, Methanotrophic symbionts provide carbon for photosynthesis in peat bogs, Nature, 436, 1153, 10.1038/nature03802

Rahman, 2011, Environmental distribution and abundance of the facultative methanotroph Methylocella, ISME J, 5, 1061, 10.1038/ismej.2010.190

Sharp, 2012, Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing, Front Microbiol, 3, 303, 10.3389/fmicb.2012.00303

Steenbergh, 2010, Biphasic kinetics of a methanotrophic community is a combination of growth and increased activity per cell, FEMS Microbiol Ecol, 71, 12, 10.1111/j.1574-6941.2009.00782.x

Stoecker, 2006, Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase, P Natl Acad Sci USA, 103, 2363, 10.1073/pnas.0506361103

Stralis-Pavese, 2004, Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers, Environ Microbiol, 6, 347, 10.1111/j.1462-2920.2004.00582.x

Stralis-Pavese, 2011, Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray, Nat Protoc, 6, 609, 10.1038/nprot.2010.191

Tuittila, 2013, Wetland chronosequence as a model of peatland development: vegetation succession, peat and carbon accumulation, Holocene, 23, 25, 10.1177/0959683612450197

Vorobev, 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, 10.1099/ijs.0.028118-0

Wang, 2007, Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl Environ Microbiol, 73, 5261, 10.1128/AEM.00062-07

Yimga, 2003, Wide distribution of a novel pmoA-like gene copy among type II methanotrophs, and its expression in Methylocystis strain SC2, Appl Environ Microbiol, 69, 5593, 10.1128/AEM.69.9.5593-5602.2003