Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle

ISME Journal

Volumn 6, Issue 4, 2012, Pages 802-813

  Bragina, Anastasia ^a,d   Berg, Christian ^b,e   Cardinale, Massimiliano ^b   Shcherbakov, Andrey ^a,f   Chebotar, Vladimir ^c   Berg, Gabriele ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY OF MASSACHUSETTS DARTMOUTH   (United States)

^e EAST CHINA NORMAL UNIVERSITY   (China)

^f Department of Obstetrics Gynecology   (United States)

Author keywords

Crocosphaera; cyanobacteria; group A; nitrogen fixation; qPCR; UCYN A

Indexed keywords

ABUNDANCE; ALPINE ENVIRONMENT; BACTERIUM; BOG; CLONE; COLONIZATION; GAMETOPHYTE; HYBRIDIZATION; LIFE CYCLE; MICROBIAL COMMUNITY; MOSS; NITROGEN FIXATION; PH; PHYLOGENETICS; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY; SPECIES RICHNESS;

ANIMAL; ARTICLE; AUSTRIA; BACTERIUM; CLASSIFICATION; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; LIFE CYCLE STAGE; MICROBIOLOGY; SPHAGNOPSIDA; WETLAND;

ANIMALS; AUSTRIA; BACTERIA; ECOSYSTEM; LIFE CYCLE STAGES; SPHAGNOPSIDA; WETLANDS;

AUSTRIA;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BRYOPHYTA; CROCOSPHAERA; CYANOBACTERIA; EMBRYOPHYTA; GAMMAPROTEOBACTERIA; PLANCTOMYCETES; SPHAGNUM; SPHAGNUM FALLAX; SPHAGNUM MAGELLANICUM; TRACHEOPHYTA; VERRUCOMICROBIA;

EID: 84858866394     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.151     Document Type: Article

References (44)

1. Belyea LR, Malmer N. (2004). Carbon sequestration in peatland: patterns and mechanisms of response to climate change. Glob Change Biol 10: 1043-1052. (Pubitemid 38964499)
2. Berg G, Krechel A, Ditz M, Sikora RA, Ulrich A, Hallman J. (2005). Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51: 215-229. (Pubitemid 40038381)
3. Berg G, Smalla K. (2009). Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68, 1-13.
4. Binladen J, Gilbert MTP, Bollbacj JP, Panitz F, Bendixen C, Nielsen R et al. (2007). The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2: 1-9.
5. Blackwood CB, Adam O, Buyer JS. (2005). Phylum- and class-specific PCR primers for general microbial community analysis. Appl Environ Microbiol 71: 6193-6198. (Pubitemid 41456918)
6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
7. Chelius MK, Triplett EW. (2001). The diversity of archaea and bacteria in association with roots of Zea mays L. Microb Ecol 41: 252-263. (Pubitemid 32540516)
8. Daniels RE, Eddy A. (1985). Handbook of Europaen Sphagna. Institute of Terrestrial Ecology, Natural Environment Research Council. Cambrian News: Aberystwyth, UK, pp 262.
9. Dedysh SN, Panikov NS, Tiedje JM. (1998). Acidophilic methanotrophic communities from Sphagnum peat bogs. Appl Environ Microbiol 64: 922-929. (Pubitemid 28108466)
10. Dedysh SN, Derakshani M, Liesack W. (2001). Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris. Appl Environ Microbiol 67: 4850-4857. (Pubitemid 33646121)
11. Dise NB. (2009). Environmental science. Peatland response to global change. Science 326: 810-811.
12. Ellenberg H, Weber HE, Dull R, Wirth V, Werner W. (1991). Zeigerwerte von Pflanzen in Mitteleuropa. Verlag Erich Goltze KG: Goettingen, p 248.
13. Felsenstein J. (1989). PHYLIP - phylogeny inference package (version 3.2). Cladistics 5: 164-166.
14. Garbeva P, van Jeen JA, van Elsas JD. (2004). Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42: 243-270. (Pubitemid 39308513)
15. Granath G, Wiedermann MM, Strengbom J. (2009). Physiological responses to nitrogen and sulphur addition and raised temperature in Sphagnum balticum. Oecologia 161: 481-490.
16. Grube M, Cardinale M, Vieira de Castro Junior J, Muller H, Berg G. (2009). Species-specific structural and functional diversity of bacterial communities in lichen symbiosis. ISME J 3: 1105-1115.
17. Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW. (1997). Endophytic bacteria in agricultural crops. Can J Microbiol 43: 5-914.
18. Horn MA, Matthies C, Kusel K, Schramm A, Drake HL. (2003). Hydrogenotrophic methanogenesis by moderately acid-tolerant methanogens of a methane-emitting acidic peat. Appl Environ Microbiol 69: 74-83. (Pubitemid 36077459)
19. Huber T, Faulkner G, Hugenholtz P. (2004). Bellerophon: a program to detect chimeric sequences I multiple sequence alignments. Bioinformatics 20: 2317-2319. (Pubitemid 39341624)
20. Hur I, Chun J. (2004). A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J Microbiol 42: 9-13. (Pubitemid 38639037)
21. Jassey VEJ, Gilbert D, Binet P, Toussaint M, Chiapusioa G. (2011). Effect of a temperature gradient on Sphagnum fallax and its associated living microbial communities: a study under controlled conditions. Can J Microbiol 57: 226-235.
22. Joosten H, Couwenberg J. (2009). Are emissions reductions from peatlands MRV- able? Report in: Wetlands International, Ede. p 14.
23. Kropf S, Läuter J, Eszlinger M, Krohn K, Paschke R. (2004). Nonparametric multiple test procedures with datadriven order of hypotheses and with weighted hypotheses. J Stat Plan Infer 125: 31-47. (Pubitemid 39072452)
24. Lane DJ. (1991). 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley: New York, pp. 115-175.
25. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. (Pubitemid 350162903)
26. Larmola T, Tuittila ES, Tiirola M, Nykänen H, Martikainen PJ, YrjälaK et al. (2010). The role of Sphagnum mosses in the methane cycling of a boreal mire. Ecology 91: 2356-2365.
27. Lauber CL, Hamady M, Knight R, Fierer N. (2009). Pyrosequencing- based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
28. Leps J, Smilauer P. (2003). Multivariate analysis of ecological data using Canoco. Cambridge University Press: Cambridge, UK, p 282.
29. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G et al. (2001). DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67: 2354-2359. (Pubitemid 33641427)
30. Opelt K, Berg C, Berg G. (2007b). The bryophyte genus Sphagnum is a reservoir for powerful and extraordinary antagonists and potentially facultative human pathogens. FEMS Microbiol Ecol 61: 38-53. (Pubitemid 46889826)
31. Opelt K, Berg C, Schönmann S, Eberl L, Berg G. (2007c). High specificity but contrasting biodiversity of Sphagnum- associated bacterial and plant communities in bog ecosystems independent of the geographical region. ISME J 1: 502-516. (Pubitemid 47530656)
32. Opelt K, Berg G. (2004). Diversity and antagonistic potential of bacteria associated with bryophytes from nutrient-poor habitats of the Baltic Sea Coast. Appl Environ Microbiol 70: 6569-6579. (Pubitemid 39518565)
33. Opelt K, Chobot V, Hadacek F, Schönmann S, Eberl L, Berg G. (2007a). Investigations of the structure and function of bacterial communities associated with Sphagnum mosses. Environ Microbiol 91: 2795-2809. (Pubitemid 47547547)
34. Pankratov TA, Serkebaeva YM, Kulichevskaya IS, Liesack W, Dedysh SN. (2008). Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat. ISME J 2: 551-560. (Pubitemid 351666974)
35. Raghoebarsing AA, Smolders AJP, Schmid MC, Rijpstra WIC, Wolters-Arts M, Derksen JM et al. (2005). Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436: 1153-1156. (Pubitemid 41232292)
36. Rahman T, Crombie A, Chen Y, Stralis-Pavese N, Bodrossy L, Meir P et al. (2010). Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J 5: 1061-1066.
37. Schaffers AP, Sỳkora KV. (2000). Reliability of Ellenberg indicator values for moisture, nitrogen and soil reaction: a comparison with field measurements. J Veg Sci 11: 225-244. (Pubitemid 30368916)
38. Schloss PD, Handelsman J. (2006). Toward a census of bacteria in soil. PLoS Comput Biol 2: 786-793.
39. Schwieger F, Tebbe CC. (1998). A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64: 4870-4876. (Pubitemid 28557853)
40. Soudzilovskaia NA, Cornelissen JHC, During HJ, van Logtestijn RSP, Lang SI, Aerts R. (2010). Similar cation exchange capacities among bryophyte species refute a presumed mechanism of peatland acidification. Ecology 91: 2716-2726.
41. Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W. (2008). Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55: 415-424. (Pubitemid 351421331)
42. Theurillat JP, Guisan A. (2001). Potential impact of climate change on vegetation in the European Alps: A review. Climatic Change 50: 77-109. (Pubitemid 32665125)
43. Whinam J, Copson G. (2006). Sphagnum moss: an indicator of climate change in the sub-Antarctic. Polar Record 42: 43-49. (Pubitemid 43125670)
44. Van Overbeek L, Franke AC, Nijhuis EHM, Groeneveld RMW, Nunes da Rocha U, Lotz LAP. (2011). Bacterial communities associated with Chenopodium album and Stellaria media seeds from arable soils. Microb Ecology 62: 257-264.