ࡱ > y zw bjbj { { To % l l l l l 4 h ' ( " "' $' $' $' $' $' $' $ ( M+ H' l H' l l ]' ! ! ! 2 l l r" ! "' ! ! ! ^ ! ^" s' 0 ' ! 9, 9, ! 9, l ! s ^ ! L H' H' ! ( ' 9, 2 : Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments
Supplementary Material
Etienne Yergeau, Stef Bokhorst, Sanghoon Kang, Jizhong Zhou, Charles W. Greer, Rien Aerts, George A. Kowalchuk
Table S1: qPCR primers and conditions used
Target EnzymePrimersAnneal. T.Reading TStandardStandard curve R2Standard curve efficiencyCt (gene copies1) NTCRef.Ribosomal genesArchaeal 16S-A517F/UA1204R55C82Carchaeal fosmid0.9960.72334.33 (1.21103) ADDIN EN.CITE Baker200322222222217Baker, G. C.Smith, J. J.Cowan, D. A.Cowan, D. A.
Univ Western Cape, Dept Biotechnol, Bellville 7335, Cape Town, South Africa
Univ Western Cape, Dept Biotechnol, Cape Town, South AfricaReview and re-analysis of domain-specific 16S primersJournal of Microbiological MethodsJ Microbiol MethJournal of Microbiological MethodsJ. Microbiol. Methods541555553bacteriaarchaeakorarchaeotananoarchaeota16srrnaprimerribosomal-rna sequencesyellowstone-national-parkpolymerase chain-reactionphylogenetic analysisgene-sequencesphylum nanoarchaeotabacterial diversityarchaeal diversitypcrcommunity2003DECISI:000186823500001<Go to ISI>://000186823500001Lu!Reu ressource lectronique(Baker et al., 2003)Bacterial 16S-Eub338/Eub51853C-unidentified 16S clone0.9990.92727.92 (2.63106) ADDIN EN.CITE Fierer200550750750717Fierer, N.Jackson, J. A.Vilgalys, R.Jackson, R. B.Fierer, N
Univ Calif Santa Barbara, Bren Sch Environm Sci & Management, Bren Hall, Santa Barbara, CA 93106 USA
Duke Univ, Dept Biol, Durham, NC 27708 USA
Duke Univ, Nicholas Sch Environm & Earth Sci, Durham, NC 27708 USAAssessment of soil microbial community structure by use of taxon-specific quantitative PCR assaysApplied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.4117412071716s ribosomal-rnareal-time pcrgradient gel-electrophoresispolymerase-chain-reactionoligonucleotide probesbacterial communitycopy numberdiversityDNAdatabase2005JulISI:000230445700091<Go to ISI>://000230445700091Lu!Reu ressource lectronique(Fierer et al., 2005)Fungal 18S-Fung5f/FF390r48C-unidentified 18S clone0.9970.94727.86 (4.50105) ADDIN EN.CITE Lueders200443043043017Lueders,TillmannManefield,MikeFriedrich,Michael W.Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradientsEnvironmental MicrobiologyEnviron. Microbiol.Environmental MicrobiologyEnviron. Microbiol.Environmental MicrobiologyEnviron. Microbiol.7378612004January 01, 2004http://www.blackwell-synergy.com/links/doi/10.1046/j.1462-2920.2003.00536.x/absLu!Reu ressource lectronique(Lueders et al., 2004)Functional genesArchaeal amoAammonia monooxygenaseamoA19F/CrenamoA616r48x50C-unidentified amoA clone0.9990.96030.13 (2.01103) ADDIN EN.CITE Leininger200674174174117Leininger, S.Urich, T.Schloter, M.Schwark, L.Qi, J.Nicol, G. W.Prosser, J. I.Schuster, S. C.Schleper, C.Univ Bergen, Dept Biol, N-5020 Bergen, Norway. GSF Natl Res Ctr Environm & Hlth, Inst Soil Ecol, D-85764 Neuherberg, Germany. Univ Cologne, Inst Geol & Mineral, D-50674 Cologne, Germany. Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA. Univ Aberdeen, Sch Biol Sci, Aberdeen AB24 3UU, Scotland.Archaea predominate among ammonia-oxidizing prokaryotes in soilsNatureNatureNatureNatureNatureNature80680944271042006AugISI:000239792700044<Go to ISI>://000239792700044 Lu!Reu ressource lectronique(Leininger et al., 2006)Bacterial amoAammonia monooxygenaseamoA-1F/amoA-2R-TC57C81CNitrosomonas europaea0.9940.86329.67 (1.31104) ADDIN EN.CITE Nicolaisen200228928928917Nicolaisen, M. H.Ramsing, N. B.Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteriaJournal of Microbiological MethodsJ. Microbiol. Meth.Journal of Microbiological MethodsJ. Microbiol. Methods189203502Denaturing gradientgel electrophoresisDiversityAmmonia-oxidizing bacteria.16s ribosomal-rnaSingle-base changesClass proteobacteriaBeta-subdivisionDna fragmentsNitrosomonas-europaeaCommunity structureMolecular analysisGc-clampMonooxygenase.Biology in Current Contents(R)/Agricultural, Biology & EnvironmentalSciences. Microbiology in Current Contents(R)/Life Sciences.20022002 week 25Lu!Demand tir--part 25 juillet 2002
Reu ressource lectronique (merci...)(Nicolaisen and Ramsing, 2002)chiAChitinaseGA1F/GA1R63C-Streptomyces sp.0.9980.90829.67 (5.78104) ADDIN EN.CITE Williamson200064464464417Williamson, N.Brian, P.Wellington, E. M. H.Molecular detection of bacterial and streptomycete chitinases in the environmentAntonie van Leeuwenhoek International Journal of General & Molecular MicrobiologyAntonie Van LeeuwenhoekAntonie van Leeuwenhoek International Journal of General & Molecular MicrobiologyAntonie Van LeeuwenhoekAntonie van LeeuwenhoekAnton. Leeuw. Int. J. G.315321783-4ActinomyceteChitinaseDggeDiversityDnaPcr.SequencesGeneCommunityDna.Microbiology in Current Contents(R)/Life Sciences.20002001 week 18Reprint available from: Wellington EMH Univ Warwick, Dept Biol Sci Coventry CV4 7AL W Midlands England Univ Warwick, Dept Biol Sci Coventry CV4 7AL W Midlands England TerraGen Discovery Inc Vancouver BC CanadaLu!Reu ressource lectroniqueReu ressource lectronique(Williamson et al., 2000)mcrAmethyl-coenzyme M reductasemcraF/mcraR52C81Cunidentified mrcA clone0.9920.90028.00 (4.14104) ADDIN EN.CITE Radl200796596596517Radl, V.Gattinger, A.Chronakova, A.Nemcova, A.Cuhel, J.Simek, M.Munch, J.C.Schloter, M.Elhottova, D.Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soilsThe ISME JournalISME J.ISME JournalISME J.443452152007http://dx.doi.org/10.1038/ismej.2007.60 (Radl et al., 2007)nirKCu-containing nitrite reductase
F1aCu/R3Cu57C85CPseudomonas sp.0.9940.73334.07 (7.44104) ADDIN EN.CITE Throbck200429229229217Throbck, I.N.Enwall, K.Jarvis, AHallin, S.FEMS Microbiology EcologyFEMS Microbiol. Ecol.Fems Microbiology EcologyFEMS Microbiol. Ecol.Fems Microbiology EcologyFEMS Microbiol. Ecol.401417493diversitydenitrificationsoilpeatactivated sludgefunctional genesenvironmental clonesnitrite reductasenitrous oxide reductaseuncultured bacteria2004Lu!Reu ressource lectronique(Throbck et al., 2004) nirScd1-containing nitrite reductase
cd3aF/R3cd57C83CPseudomonas fluorescens0.9980.79033.92 (4.76106) ADDIN EN.CITE Throbck200429229229217Throbck, I.N.Enwall, K.Jarvis, AHallin, S.FEMS Microbiology EcologyFEMS Microbiol. Ecol.Fems Microbiology EcologyFEMS Microbiol. Ecol.Fems Microbiology EcologyFEMS Microbiol. Ecol.401417493diversitydenitrificationsoilpeatactivated sludgefunctional genesenvironmental clonesnitrite reductasenitrous oxide reductaseuncultured bacteria2004Lu!Reu ressource lectronique(Throbck et al., 2004)pmoAparticulate methane monooxygenasemb661/A18955C82CMethylocystis parvus0.9990.81526.02 (2.75105) ADDIN EN.CITE Kolb200399699699617Kolb, S.Knief, C.Stubner, S.Conrad, R.Conrad, R
Max Planck Inst Terr Microbiol, Karl von Frisch Str, D-35043 Marburg, Germany
Max Planck Inst Terr Microbiol, D-35043 Marburg, GermanyApplied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.24232429695particulate methane monooxygenase16s ribosomal-rnarice field soilmethylococcus-capsulatus bathin-situ hybridizationoxidizing bacteriaoligonucleotide probesmethylocella-palustrisatmospheric methanemolecular analyses2003MayISI:000182808300002<Go to ISI>://000182808300002(Kolb et al., 2003)
1Gene copies in NTC: same calculations as for samples, so values are equivalent to gene copies per gram of soil
Information for standard curves is based on the average of 3-4 different runs.
Table S2: Pyrosequencing primers used
Set #Forward primer (5-3)Reverse primer (5-3)MID1-ACGTATCGCCTCCCTCGCGCCATCAGACGAGTGCGTGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID2-ACGTATCGCCTCCCTCGCGCCATCAGACGCTCGACAGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID3-ACGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID4-ACGTATCGCCTCCCTCGCGCCATCAGAGCACTGTAGGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID5-ACGTATCGCCTCCCTCGCGCCATCAGATCAGACACGGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID6-ACGTATCGCCTCCCTCGCGCCATCAGATATCGCGAGGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID7-ACGTATCGCCTCCCTCGCGCCATCAGCGTGTCTCTAGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID8-ACGTATCGCCTCCCTCGCGCCATCAGCTCGCGTGTCGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID9-ACGTATCGCCTCCCTCGCGCCATCAGTAGTATCAGCGAGTTTGATYMTGGCTCCTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGGCMID1-BCTATGCGCCTTGCCAGCCCGCTCAGACGAGTGCGTGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID2-BCTATGCGCCTTGCCAGCCCGCTCAGACGCTCGACAGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID3-BCTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID4-BCTATGCGCCTTGCCAGCCCGCTCAGAGCACTGTAGGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID5-BCTATGCGCCTTGCCAGCCCGCTCAGATCAGACACGGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID6-BCTATGCGCCTTGCCAGCCCGCTCAGATATCGCGAGGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID7-BCTATGCGCCTTGCCAGCCCGCTCAGCGTGTCTCTAGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID8-BCTATGCGCCTTGCCAGCCCGCTCAGCTCGCGTGTCGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGCMID9-BCTATGCGCCTTGCCAGCCCGCTCAGTAGTATCAGCGAGTTTGATYMTGGCTCCGTATCGCCTCCCTCGCGCCATCAGATTACCGCGGCTGCTGGC
Pink: adapter, green: sequencing key, blue: multiplex identifier, red: sequence-specific primer.
Table S3: Mean (standard deviation) bacterial phylum/classe relative abundance in 16S rRNA gene libraries for control and OTC plots at the Falkland, Signy and Anchorage Islands.
#seqsAcido.Actino.Kted.Verru.AlphaOthersuncl.FIVegetatedControl13,99128.0 (11.4)35.0 (7.2)0.6
(0.6)1.0
(0.6)27.6 (14.5)2.3 (0.9)5.5
(1.7)OTC12,54023.6 (7.8)37.3 (9.4)0.7
(0.5)1.2
(0.8)30.1 (14.6)2.3 (0.5)4.9
(1.3)Fell-FieldControl3,56929.8 (3.8)33.3 (5.3)0.0
(0.0)0.4
(0.2)19.4 (1.9)4.3 (0.8)12.9
(3.1)OTC2,54320.3 (10.3)46.7 (8.8)0.0
(0.1)0.4
(0.1)15.4 (3.4)4.3 (1.1)12.8
(2.8)SIVegetatedControl13,45239.2 (9.3)25.6 (4.0)5.3
(3.4)1.0
(1.6)16.5 (4.0)4.4 (2.0)8.0
(3.9)OTC11,63530.0 (12.3)29.0 (8.9)6.9
(6.7)1.5
(2.2)19.0 (3.8)5.0 (2.5)8.6
(5.0)Fell-FieldControl7,19620.9 (7.0)28.6 (6.7)6.8
(3.0)0.7
(0.7)16.7 (4.6)5.2 (1.5)21.1
(7.6)OTC8,60315.5 (3.6)31.9 (7.4)9.4
(6.1)0.7
(0.6)17.1 (4.1)4.5 (1.2)21.0
(6.3)AIVegetatedControl6,11618.4 (11.1)23.5 (1.0)11.9
(4.6)2.0
(1.5)19.2 (7.1)5.0 (0.9)19.9
(4.7)OTC10,91911.3 (7.9)17.1 (2.5)14.2
(13.4)2.5
(1.6)30.9 (12.4)6.4 (2.0)17.7
(3.3)Fell-FieldControl5,61510.2 (8.2)28.5 (11.7)21.6
(10.7)1.7
(1.6)12.0 (7.4)7.5 (5.6)18.4
(2.9)OTC7,1397.3 (3.4)32.0 (12.6)14.5
(11.2)2.1
(2.0)16.9 (7.7)9.7 (2.5)17.5
(4.1)all-Control49,93924.6 (12.9)29.4 (7.8)7.7
(9.0)1.2
(1.2)19.3 (10.1)4.6 (3.0)13.3
(7.5)OTC53,37918.3 (10.9)31.5 (11.6)7.6
(9.5)1.5
(1.5)22.9 (11.4)5.2 (3.0)12.9
(7.1)Acido: Acidobacteria; Actino: Actinobacteria; Kted: Ktedonobacteria (this is a class; not classified at the phylum level); Verru: Verrucomicrobia; Alpha: Alphaproteobacteria; uncl: unclassified
Others: All groups that represented less than 1% of the total reads (BRC1, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Nitrospira, OD1, OP10, Planctomycetes, TM7, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria.
Table S4: Mean number of different variants detected on the GeoChip for selected genes of the N- and C-cycles for control and OTC plots at the Falkland (FI), Signy (SI) and Anchorage (AI) Islands.
amoAcell.chit.laccasenifHnirKnirSnosZpmoAureaseFI VControl2.1 (0.7)8.1 (9.9)6.6 (8.7)3.0 (5.0)8.0 (8.9)4.3 (3.5)1.7 (2.5)4.1 (3.1)3.1 (1.8)14.3 (15.5)OTC0.4 (0.5)0.0 (0.0)1.8 (1.2)0.1 (0.4)0.8 (0.7)1.8 (1.3)0.1 (0.4)0.9 (0.8)0.9 (0.8)1.3 (1.0)FFControl4.3 (2.5)11.7 (4.2)7.7 (0.6)5.0 (1.7)14.0 (3.0)3.7 (0.6)2.3 (0.6)3.3 (0.6)4.0 (1.0)22.0 (7.5)OTC0.0 (0.0)4.0 (2.8)0.5 (0.7)0.5 (0.7)0.0 (0.0)1.5 (2.1)0.0 (0.0)0.5 (0.7)1.0 (1.4)1.5 (2.1)SIVControl1.5 (0.5)5.0 (3.5)3.8 (2.9)1.0 (1.5)5.0 (3.2)3.2 (1.0)1.0 (0.9)3.5 (1.4)2.8 (1.2)9.0 (5.8)OTC1.6 (0.9)2.6 (1.1)1.4 (0.5)0.2 (0.4)1.6 (1.1)3.0 (0.0)0.2 (0.4)3.0 (0.0)3.0 (0.7)4.2 (0.8)FFControl5.4 (2.2)14.4 (6.6)7.6 (3.4)4.8 (3.9)10.4 (3.3)4.0 (1.0)2.6 (2.7)3.8 (1.1)5.8 (1.3)20.0 (7.7)OTC1.5 (0.7)2.5 (2.1)1.0 (0.0)0.0 (0.0)1.5 (0.7)2.5 (0.7)0.0 (0.0)2.5 (2.1)2.0 (1.4)2.0 (1.4)AI VControlNANANANANANANANANANAOTC1.0 (0.0)5.5 (5.6)2.5 (1.5)0.0 (0.6)2.0 (1.2)2.5 (0.6)0.0 (0.0)2.0 (1.2)3.5 (0.6)4.5 (2.1)FFControl1.7 (0.6)5.0 (1.7)1.3 (0.6)0.0 (0.0)1.7 (1.5)3.0 (0.0)1.0 (1.0)2.3 (0.6)1.7 (0.6)3.3 (2.1)OTC1.2 (0.5)7.0 (2.8)3.8 (1.0)1.2 (0.5)1.8 (1.4)3.0 (0.0)0.6 (0.5)3.2 (0.5)3.2 (0.5)7.0 (1.4)All-Control2.9 (2.0)8.7 (7.1)5.6 (5.3)2.8 (3.7)7.7 (6.3)3.7 (1.9)1.7 (1.9)3.6 (1.9)3.5 (1.8)13.8 (11.1)OTC0.9 (0.8)3.0 (3.5)2.0 (1.4)0.4 (0.6)1.3 (1.1)2.4 (1.1)0.2 (0.4)2.0 (1.3)2.1 (1.3)3.4 (2.5)Cell.: cellulase; Chit.: chitinase; V: vegetated; FF: fell-field; NA: not available
Table S5: Mean abundance of bacterial and archaeal ammonia monooxygenase (amoA), chitinase (chiA), methyl-coenzyme A reductase (mcrA), nitrite reductase (nirK and nirS and particulate methane monooxygenase (pmoA) in real-time PCR assays for control and OTC plots at the Falkland (FI), Signy (SI) and Anchorage (AI) Islands.
Bact amoAArch amoAchiAmcrAnirKnirSpmoA105 copies g-1 soil FW103 copies g-1 soil FW105 copies g-1 soil FW104 copies g-1 soil FW107 copies g-1 soil FW107 copies g-1 soil FW105 copies g-1 soil FWFI VControl0.8 (0.3)13.2 (12.9)20.8 (19.0)0.2 (0.2)5.4 (5.3)6.7 (4.3)2.9 (0.5)OTC0.7 (0.4)7.6 (9.4)19.8 (21.5)0.3 (0.5)8.9 (13.4)6.1 (4.4)2.2 (0.5)FFControl1.0 (0.5)17.6 (17.8)284.7 (169.3)2.6 (0.7)33.2 (30.0)8.0 (3.3)2.4 (0.8)OTC1.9 (1.6)24.6 (4.9)368.6 (87.7)3.0 (1.4)41.0 (19.9)8.9 (6.5)2.0 (0.3)SIVControl0.4 (0.3)0.9 (1.6)0.2 (0.1)8.2 (5.8)0.1 (0.1)1.1 (0.7)0.2 (0.1)OTC0.8 (0.6)0.1 (0.1)0.4 (0.3)8.0 (5.6)0.1 (0.1)2.6 (1.7)0.3 (0.2)FFControl3.6 (6.5)15.3 (8.7)3.9 (7.4)2.7 (1.7)5.6 (8.5)8.6 (9.8)1.4 (1.0)OTC0.2 (0.2)6.4 (1.7)0.4 (0.4)0.9 (1.1)0.2 (0.2)2.2 (1.7)0.7 (0.4)AI VControl3.5 (1.2)0.3 (0.5)3.2 (1.7)31.8 (31.5)0.1 (0.0)1.4 (1.2)1.1 (0.3)OTC10.3 (6.4)2.8 (2.8)8.9 (5.6)198.5 (324.4)5.0 (NA)3.5 (2.5)2.0 (0.6)FFControl7.8 (3.1)14.4 (11.0)17.3 (10.9)4.9 (2.5)NA11.6 (11.0)2.9 (0.8)OTC11.5 (6.7)24.1 (31.5)25.4 (28.1)21.7 (25.4)NA7.2 (5.0)2.6 (1.0)Bact: bacterial; Arch: archaeal; V: vegetated; FF: fell-field; NA: not available
Fig. S1: Map of the sampling locations
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