Bacterial community structure and its relationship to soil physico-chemical characteristics in alder stands with different management histories

Ecological Engineering

Volumn 49, Issue , 2012, Pages 10-17

  Preem, Jens Konrad ^a   Truu, Jaak ^a   Truu, Marika ^a   Mander, Ülo ^a   Oopkaup, Kristjan ^a   Lõhmus, Krista ^a   Helmisaari, Heljä Sisko ^b   Uri, Veiko ^c   Zobel, Martin ^a  

^a UNIVERSITY OF TARTU   (Estonia)

^b UNIVERSITY OF HELSINKI   (Finland)

^c ESTONIAN UNIVERSITY OF LIFE SCIENCES   (Estonia)

Author keywords

16S rDNA pyrosequencing; Alnus; Land management history; Soil bacterial community; Soil physico chemical characteristics

Indexed keywords

ALNUS; LAND MANAGEMENTS; PHYSICOCHEMICAL CHARACTERISTICS; PYROSEQUENCING; SOIL BACTERIAL COMMUNITY;

ALUMINUM; BORON; CADMIUM; CHEMICAL ANALYSIS; CONSERVATION; FORESTRY; PH EFFECTS; PHOSPHORUS; REGRESSION ANALYSIS; RESTORATION; RNA; SOCIAL SCIENCES; SOIL MOISTURE;

BACTERIA;

AGRICULTURAL LAND; BACTERIUM; BIOMASS; COMMUNITY STRUCTURE; DICOTYLEDON; ENVIRONMENTAL RESTORATION; GEOMORPHOLOGY; HEAVY METAL; MANAGEMENT PRACTICE; PH; PHYSICOCHEMICAL PROPERTY; RENEWABLE RESOURCE; RIPARIAN FOREST; SOIL MICROORGANISM; SOIL ORGANIC MATTER; SOIL TYPE; SPECIES DIVERSITY; STAND STRUCTURE; SUCCESSION; WATER CONTENT;

ALNUS; ALUMINUM; BACTERIA; BORON; CADMIUM; CHEMICAL ANALYSIS; LAND USE; NUCLEIC ACIDS; PH; PHOSPHORUS; REGRESSION ANALYSIS; SOIL;

ACTINOBACTERIA; ALNUS; ALNUS GLUTINOSA; ALNUS INCANA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BRADYRHIZOBIACEAE; PROTEOBACTERIA;

EID: 84866723299     PISSN: 09258574     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecoleng.2012.08.034     Document Type: Article

References (75)

1. Anderson M.J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001, 26:32-46.
2. Anderson M.J. PERMDISP: A FORTRAN Computer Program for Permutational Analysis of Multivariate Dispersions (For Any Two-factor ANOVA Design) Using Permutation Tests 2004, Department of Statistics, University of Auckland, New Zealand.
3. Anderson M.J., Willis T.J. Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 2003, 84:511-525.
4. Baldrian P., Kolařík M., Štursova M., Kopecký J., ValáŠkova V., Větrovský T., Žifčáková L., Šnajdr J., Rídl J., Vlček č., VoříŠková J. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J. 2011, 6:248-258.
5. Bonan G.B. Forests and climate change: forcings, feedbacks, and the climate benefits for forests. Science 2008, 320:1444-1449.
6. Brockett B.F.T., Prescott C.E., Grayston S.J. Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada. Soil Biol. Biochem. 2012, 44:9-20.
7. Bunge J., Woodard L., Böhning D., Foster J.A., Connolly S., Allen H.K. Estimating population diversity with CatchAll. Bioinformatics 2012, 28:1045-1047. 10.1093/bioinformatics/bts075.
8. Busse L.B., Gunkel G. Riparian alder fens - source or sink for nutrients and dissolved organic carbon? 2. Major sources and sinks. Limnologica 2002, 32:44-53.
9. Campbell J.E., Lobell D.B., Genova R.C., Field C.B. The global potential of bioenergy on abandoned agricultural lands. Environ. Sci. Technol. 2008, 42:5791-5794.
10. Chauhan J.S., Rai J.P.N. Phytoextraction of soil cadmium and zinc by microbes-inoculated Indian mustard (Brassica jucea). J. Plant Interact. 2009, 4:279-287.
11. Chu H.Y., Fierer N., Lauber C.L., Caporaso J.G., Knight R., Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 2010, 12:2998-3006.
12. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:141-145.
13. Da Mota F.F., Gomes E.A., Marriel I.E., Paiva E., Seldin L. Bacterial and fungal communities in bulk soil and rhizospheres of aluminium-tolerant and aluminium-sensitive maize (Zea mays L.) lines cultivated in unlimed and limed Cerrado soil. J. Microbiol. Biotechnol. 2008, 18:805-814.
14. Dequiedt S., Thioulouse J., Jolivet C., Nicolas P.A., Saby N.P.A., Lelievre M., Maron P.-A., Manuel P., Martin M.P., Prévost-Bouré N.C., Toutain B., Arrouays D., Lemanceau P., Ranjard L. Biogeographical patterns of soil bacterial communities. Environ. Microbiol. Rep. 2009, 1:251-255.
15. Dilly O. Nitrogen and phosphorous requirement of the microbiota in soils of the Bornhöved Lake district. Plant Soil 1999, 212:175-183.
16. Dilly O., Munch J.C. Ratios between estimates of microbial biomass content and microbial activity in soils. Biol. Fertil. Soils 1998, 27:374-379.
17. Dimitriu P.A., Grayston S.J. Relationship between soil properties and patterns of bacterial beta-diversity across reclaimed and natural boreal forest soils. Microb. Ecol. 2009, 59:563-573.
18. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
19. Edwards U., Rogall T., Blocker H., Emde M., Bottger E. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989, 17:7843-7853.
20. 2 emissions from broadleaved stands growing on abandoned farmland. Silva Fenn. 2006, 40:603-613.
21. Europe's Energy Position - Markets and Supply, 2010. Market Observation for Energy, Report 2009. Publications Office of the European Union, Luxenbourg. ISBN: 978-92-79-14175-1. doi:10.2768/20104.
22. Evans J. Silviculture of broadleaved woodland. UK. Bulletin (FCBU) 1984, 62:187-191.
23. Faoro H., Alves A.C., Souza E.M., Rigo L.U., Cruz L.M., Al-Janabi S.M., Monteiro R.A., Baura V.A., Pedrosa F.O. Influence of soil characteristics on the diversity of bacteria in the Southern Brazilian Atlantic forest. Appl. Environ. Microbiol. 2010, 76:4744-4749.
24. FAO-UNESCO Soil Map of the World. Revised Legend With Corrections 1994, ISRIC, Wageningen.
25. Fierer N., Jackson R.B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:626-631.
26. Fierer N., Strickland M.S., Liptzin D., Bradford M.A., Cleveland C.C. Global patterns in belowground communities. Ecol. Lett. 2009, 12:1238-1249.
27. Giertych M.J., Karolewski P., Zytkowiak R., Oleksyn J. Differences in defence strategies against herbivores between two pioneer tree species: Alnus glutinosa (L.) Gaertn. and Betula pendula Roth. Polish J. Ecol. 2006, 54:181-187.
28. Helingerová M., Frouz J., Šantrůčkova H. Microbial activity in reclaimed and unreclaimed post-mining sites near Sokolov (Czech Republic). Ecol. Eng. 2010, 36:768-776.
29. Holland R.F. Preliminary Descriptions of the Terrestrial Natural Communities of California. State of California, The Resources Agency, Nongame Heritage Program 2004, Dept. Fish & Game, Sacramento, California, 156 pp.
30. Hollister E.B., Engledow A.S., Hammett A.J.M., Provin T.L., Wilkinson H.H., Gentry T.J. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J. 2010, 4:829-838.
31. Hytönen J., Saarsalmi A. Long-term biomass production and nutrient uptake of birch, alder and willow plantations on cut-away peatland. Biomass Bioenerg. 2009, 33:1197-1211.
32. Jones R.T., Robeson M.S., Lauber C.L., Hamady M., Knight R., Fierer N. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 2009, 3:442-453.
33. Kanokratana P., Uengwetwanit T., Rattanachomsri U., Bunterngsook B., Nimchua T., Tangphatsornruang S., Plengvidhya V., Champreda V., Eurwilaichitr L. Insights into the Phyogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microb. Ecol. 2011, 61:518-528.
34. Kuramae E.E., Yergeau E., Wong L.C., Pijl A.S., van Veen J.A., Kowalchuk G.A. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol. Ecol. 2012, 79:12-24.
35. Larsson S., Nilsson C. A remote sensing methodology to assess the costs of preparing abandoned farmland for energy crop cultivation in northern Sweden. Biomass Bioenerg. 2005, 28:1-6.
36. Lauber C.L., Hamady M., Knight R., Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 2009, 75:5111-5120.
37. Lin Y.-T., Jangid K., Whitman W.B., Coleman D.C., Chiu C.-Y. Soil bacterial communities in native and regenerated perhumid montane forest. Appl. Soil Ecol. 2011, 47:111-118.
38. Lindsay W.L. Chemical Equilibria in Soils 1979, Wiley, New York, pp. 450.
39. Lombard N., Prestat E., van Elsas J.D., Simonet P. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol. Ecol. 2011, 78:31-49.
40. Lõhmus K., Kuusemets V., Ivask M., Teiter S., Augustin J., Mander Ü. Budgets of nitrogen fluxes in riparian grey alder forests. Arch. Hydrobiol. Suppl. 2002, 141:321-332.
41. Lõhmus K., Truu J., Truu M., Kaar E., Ostonen I., Alama S., Kuznetsova T., Rosenvald K., Vares A., Uri V., Mander Ü. Black alder as a promising deciduous species for the reclaiming of oil shale mining areas. Brownfields III, Prevention, Assessment, Rehabilitation and Development of Brownfield Sites. WIT Transactions on Ecology and Environment 2006, 87-97. WIT Press, Southampton, Boston. C.A. Brebbia, T. Mander (Eds.).
42. Lõhmus K., Truu M., Truu J., Ostonen I., Vares A., Uri V., Alama S., Kanal A. Functional diversity of culturable bacterial communities in the rhizosphere in relation to fine-root and soil parameters in alder stands on forest, abandoned agricultural and oil-shale mining areas. Plant Soil 2006, 283:1-10.
43. Mander Ü., Hayakawa Y., Kuusemets V. Purification processes, ecological functions, planning and design of riparian buffer zones in agricultural watersheds. Ecol. Eng. 2005, 24:421-432.
44. Mander Ü., Lõhmus K., Teiter S., Uri V., Augustin J. Gaseous nitrogen and carbon fluxes in riparian alder stands. Boreal Env. Res. 2008, 13:231-241.
45. Margulies M., Egholm M., Altman W., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.-J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L.I., Jarvie T.P., Jirage K.B., Kim J.-B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.M., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 43:376-380.
46. McArdle B.H., Anderson M.J. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 2001, 82:290-297.
47. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
48. Nemergut D.R., Costello E.K., Hamady M., Lozupone C., Jiang L., Schmidt S.K., Fierer N., Townsend A.R., Cleveland C.C., Stanish L., Knight R. Global patterns in the biogeography of bacterial axa. Environ. Microbiol. 2011, 13:135-144.
49. Ng W.-L., Bassler B.L. Bacterial quorum-sensing network architectures. Annu. Rev. Genet. 2009, 43:197-222.
50. Orlikowska E.H., Deal R.L., Hennon P.E., Wipfli M. The role of red alder in riparian forest structure along headwater streams in southeastern Alaska. Northwest Sci. 2004, 78:11-123.
51. Pan J., Yu L. Effect of Cd or/and Pb on soil enzyme activities and microbial community structure. Ecol. Eng. 2011, 37:1889-1894.
52. Parameswaran P., Jalili R., Tao L., Shokralla S., Gharizadeh B., Ronaghi M., Fire A.Z. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 2007, 35(19):e130.
53. Piccolo J.J., Wipfli M.S. Does red alder (Alnus rubra) in upland riparian forests elevate macroinvertebrate and detritus export from headwater streams to downstream habitats in southeastern Alaska?. Can. J. Fish. Aquat. Sci. 2002, 59:503-513.
54. Piña R.G., Cervantes C. Microbial interactions with aluminium. Biometals 1996, 9:311-326.
55. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal. RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
56. Rasche F., Rasche F., Knapp D., Kaiser C., Koranda M., Kitzler B., Zechmeister-Boltenstern S., Richter A., Sessitsch A. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME J. 2010, 5:389-402.
57. Rasmussen J.J., Baattrup-Pedersen A., Wiberg-Larsen P., McKinght U.S., Kronvang B. Buffer strip width and agricultural pesticide contamination in Danish lowland streams: implication for stream and riparian management. Ecol. Eng. 2011, 37:1990-1997.
58. Rounsevell M.D.A., Reginster I., Araújo M.B., Carter N., Dendoncker F., Ewert J.I., House S., Kankaanpää R., Leemans M.J., Metzger C., Schmit P., Smith G., Tuck A. A coherent set of future land use change scenarios for Europe. Agric. Ecosyst. Environ. 2006, 114:57-68.
59. Rousk J., Bååth E., Brookes P.C., Lauber C.L., Lozupone C., Caporaso J.G., Knight R., Fierer N. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010, 4:1340-1351.
60. Rytter L., Slapokas T., Granhall U. Woody biomass and litter production of fertilized grey alder plantations on a low-humified peatbog. For. Ecol. Manage. 1989, 28:161-176.
61. Schloss P.D., Westcott S.L. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl. Environ. Microbiol 2011, 77:3219-3226.
62. Schloss P.D., Westcott S.L., Ryabin T., Hall J.L., Hartmann M., Hollister E.B., Lesniewski L.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.J. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
63. Shade A., Handelsman J. Beyond the Venn diagram: the hunt for a core microbiome. Environ. Microbiol. 2012, 14:4-12.
64. Singh B.K., Munro S., Potts J.M., Millard P. Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl. Soil Ecol. 2007, 36:147-155.
65. Stres B., Danevcic T., Pal L., Fuka M.M., Resman L., Leskovec S., Hacin J., Stopar D., Mahne I., Mandic-Mulec I. Influence of temperature and soil water content on bacterial, archaeal and denitrifying microbial communities in drained fen grassland soil microcosms. FEMS Microbiol. Ecol. 2008, 66:110-122.
66. Szukics U., Abell G.C.J., Hodl V., Mitter B., Sessitsch A., Hackl E., Zechmeister-Boltenstern S. Nitrifiers and denitrifiers respond rapidly to changed moisture and increasing temperature in a pristine forest soil. FEMS Microbiol. Ecol. 2010, 72:395-406.
67. Uri V., Lõhmus K., Mander Ü., Ostonen I., Aosaar J., Maddison M., Helmisaari H.-S., Augustin J. Long-term effect on nitrogen budget of a short-rotation grey alder (Alnus incana (L.) Moench) forest on abandoned agricultural land. Ecol. Eng. 2011, 37:920-930.
68. Uri V., Tullus H., Lõhmus K. Biomass production and nutrient accumulation in short-rotation grey alder (Alnus incana (L.) Moench) plantation on abandoned agricultural land. For. Ecol. Manage. 2002, 161:169-179.
69. Uroz S., Buee M., Murat C., Frey-Klett P., Martin F. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ. Microbiol. Rep. 2010, 2:281-288.
70. van Elsas J.D., Boersma F.G.H. A review of molecular methods to study the microbiota of soil and the mycosphere. Eur. J. Soil Biol. 2011, 47:77-87.
71. Vares A., Lõhmus K., Truu M., Truu J., Tullus H., Kanal A. Productivity of Black alder (Alnus glutinosa (L.) Gaerttn.) on reclaimed oil - shale mining detritus and mineral soils in relation to rhizosphere conditions. Oil Shale 2004, 21:47-62.
72. Vig K., Megharaj M., Sethunathan N., Naidu R. Bioavailability and toxicity of cadmium to microorganisms and their activities in soil: a review. Adv. Environ. Res. 2003, 8:121-135.
73. Wackett L.P., Dodge A.G., Ellis L.B.M. Microbial genomics and the periodic table. Appl. Environ. Microbiol. 2004, 70:647-655.
74. Yarwood S.A., Bottomley P.J., Myrold D.D. Soil microbial communities associated with Douglas-fir and Red Alder stands at high- and low-productivity forest sites in Oregon, USA. Microb. Ecol. 2010, 60:606-617.
75. Yarwood S.A., Myrold D.D., Hogberg M.N. Termination of belowground C allocation by trees alters soil fungal and bacterial communities in a boreal forest. FEMS Microbiol. Ecol. 2009, 70:151-162.