Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

M. Ros, B. A. Knapp, U. Peintner, H. Insam

Abstract


Differences in the bacterial community composition of agricultural soils caused by a long-term (12 year) application of different composts were identified by cultivation-dependent and -independent methods (PCR-DGGE and 16S rRNA clone libraries). The number of colony forming units indicated that the successive incorporation of organic amendments increased the bacterial abundance (6.41-5.66 log10 cfu g–1dry soil) compared to control and mineral soils (5.54-3.74 log10 cfu g–1 dry soil). Isolated bacteria were dominated by Actinobacteria, whereby compost-amended soils and green compost-amended soils showed, respectively, higher number of members of Actinobacteria (100% and 64%) than control and mineral soils (50% and 40%). The 16S rRNA clone libraries were dominated by Proteobacteria (43%), Acidobacteria (21%) and Actinobacteria (13%). Proteobacteria and Actinobacteria were most abundant in compost amended soils while Acidobacteria were more frequently found in mineral fertilizer and control soils. Partial 16S rRNA gene clone libraries revealed a higher bacterial diversity than cultivation. In conclusion, we found differences of bacterial community composition with a cultivation approach and clone libraries between compost amended soils and control and mineral soil.


Keywords


16S rRNA clone libraries; fertilizer; isolated bacteria; organic amendments

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References


Chandler D.P., Fredickson J.K., Brockman F.J., 1997. Effect of PCR template concentration on the composition and distribution of total community 16S rRNA clone libraries. Mol Ecol 6, 475-482. http://dx.doi.org/10.1046/j.1365-294X.1997.00205.x PMid:9161015

Cole R., Chai B., Farris R.J., Wang Q., Kulam S.A., Mcgarrell D.M., Garrity G.M., Tiedje J.M., 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33, 294-296. http://dx.doi.org/10.1093/nar/gki038 PMid:15608200 PMCid:539992

Dunbar J., Takala S., Barns S.M., Davis J.A., Kuske C.R., 1999. Levels of bacterial community in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65, 1662-1669. PMid:10103265 PMCid:91235

Feinstein L.M., Sul W.J., Blackwood C.B., 2009. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl Environ Microbiol 75, 5428-5433. http://dx.doi.org/10.1128/AEM.00120-09 PMid:19561189 PMCid:2725469

Felske A., Rheims H., Wolterink A., Stackebrandt E., Akkermans A.D., 1997. Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 143, 2983-2989. http://dx.doi.org/10.1099/00221287-143-9-2983 PMid:9308181

García-Gil J.C., Plaza C., Soler-Rovira P., Polo A., 2000. Long-term effects of municipal solid waste compost application on soil enzyme activities and microbial biomass. Soil Biol Biochem 32, 1907-1913. http://dx.doi.org/10.1016/S0038-0717(00)00165-6

Innerebner G., Knapp B., Vasara T., Romantschuck M., Insam H., 2006. Traceability of ammonia-oxidizing bacteria in compost-treated soils. Soil Biol Biochem 38, 1092-1100. http://dx.doi.org/10.1016/j.soilbio.2005.09.008

Janssen P.H., 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72, 1719-1728. http://dx.doi.org/10.1128/AEM.72.3.1719-1728.2006 PMid:16517615 PMCid:1393246

Kaiser O., Pühler A., Selbitschka W., 2001. Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microb Ecol 42,139-149.

Kersters K., De Vos P., Gillis M., Swings J., Vandamme P., Stackebrandt E., 2006. Introduction to the Proteobacteria. In: Prokaryotes, 3rd ed, vol. 5 (Dwarkin M., Falkow S., Rosenberg E., Schleifer K.H., Stackebrandt E., eds). Springer, NY. pp. 3-37. http://dx.doi.org/10.1007/0-387-30745-1_1

Lalande R., Gagnon B., Simard R.R., Cote D., 2000. Soil microbial biomass and enzyme activity following liquid hog manure application in a long-term trial. Can J Soil Sci 80, 263-269. http://dx.doi.org/10.4141/S99-064

Lynch J.M., Benedetti A., Insam H., Nuti M.P., Smalla K., Torsvik V., Nannipieri P., 2004. Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soils 40, 363-385. http://dx.doi.org/10.1007/s00374-004-0784-9

Marchesi J.R., Sato T., Weightman A.J., Martin T.A., Fry J.C., Hiom S.J., Wade W.G., 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64, 795-799. PMid:9464425 PMCid:106123

Masciandaro G., Ceccanti B., García, C., 2000. In situ vermicomposting of biological sludges and impacts on soil quality. Soil Biol Biochem 32, 1015-1024. http://dx.doi.org/10.1016/S0038-0717(00)00011-0

Mayrhofer S., Mikoviny T., Waldhuber S.,Wagner A.O., Innerebner G., Franke-Whittle I.H., Märk T.D., Hansel A., Insam H., 2006. Microbial community related to volatile organic compound (VOC) emission in household biowaste. Environ Microbiol 8, 1960-1974. http://dx.doi.org/10.1111/j.1462-2920.2006.01076.x PMid:17014495

Mccaig A.E., Glover L.A., Prosser J.I., 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures.Appl Environ Microbiol 65, 1721-1730. PMid:10103273 PMCid:91243

Pascual J.A., Hernández T., Ayuso M., García C., 1997. Changes in the microbial activity of arid soils amended with urban organic wastes. Biol Fertil Soils 24, 429-434. http://dx.doi.org/10.1007/s003740050268

Pascual J.A., García C., Hernández T., Moreno J.L., Ros M., 2000. Soil microbial activity as a biomarker of degradation and remediation processes. Soil Biol Biochem 32, 1877-1883. http://dx.doi.org/10.1016/S0038-0717(00)00161-9

Peacock A.D., Mullen M.D., Ringelberg D.B., Tyler D.D., Hedrick D.B., Gale P.M., White D.C., 2001. Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33, 1011-1019. http://dx.doi.org/10.1016/S0038-0717(01)00004-9

Rheims H., Felske A., Seufert S., Stackebrandt E., 1999. Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments. J Microbiol Methods 36, 65-75. http://dx.doi.org/10.1016/S0167-7012(99)00012-3

Ros M., Hernández M.T., García C., 2003. Soil microbial activity after restoration of a semiarid soil by organic amendments. Soil Biol Biochem 35, 463-469. http://dx.doi.org/10.1016/S0038-0717(02)00298-5

Ros M., Klammer S., Knapp B., Aichberger K., Insam H., 2006a. Long-term effects of compost amend-ment of soils on functional and structural diversity and microbial activity. Soil Use Manage 22, 209-218. http://dx.doi.org/10.1111/j.1475-2743.2006.00027.x

Ros M., Pascual J.A., García C., Hernández M.T., Insam H., 2006b. Hydrolase activities, microbial biomass and bacterial community in a soil after long-term amendment with different composts. Soil Biol Biochem 38, 3443-3452. http://dx.doi.org/10.1016/j.soilbio.2006.05.017

Saison C., Degrange V., Oliver R., Millard P., Commeaux C., Montange D., Le Roux X., 2006. Alteration and resilence of the microbial community following compost amendment: effects of compost level and compost-borne microbial community. Environ Microbiol 8, 247-257. http://dx.doi.org/10.1111/j.1462-2920.2005.00892.x PMid:16423013

Seewald M., Bonfanti M., Singer W., Knapp B.A., Hansel A., Franke-Whittle I.H., Insam H., 2009. Substrate-induced volatile organic compound emissions from compost-amended soils. Biol Fertil Soils 46, 371-382. http://dx.doi.org/10.1007/s00374-010-0445-0

Sessitsch A., Weilharter A., Gerzabek M.H., Kirchmann H., Kandeler E., 2001. Microbial population structures in soil particle size fractions of longterm fertilizer field experiment. Appl Environ Microbiol 67, 2284-2291. http://dx.doi.org/10.1128/AEM.67.9.4215-4224.2001 PMCid:93150

Smit E., Leeflang P., Gommans S., Van Den Broek J., Van Mil S., Wernars K., 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67, 2284-2291. http://dx.doi.org/10.1128/AEM.67.5.2284-2291.2001 PMid:11319113 PMCid:92868

Sun H.Y., Deng S.P., Raun W.R., 2004. Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl Environ Microbiol 70, 5868-5874. http://dx.doi.org/10.1128/AEM.70.10.5868-5874.2004 PMid:15466526 PMCid:522114

Suzuki M.T., Rappé M.S., Haimberger Z.W., Winfield H., Adair N., Ströbel J., Giovannoni S.J., 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl Environ Microbiol 63, 983-989. PMid:9055415 PMCid:168390

Toyota K., Kuninaga S., 2006. Comparison of soil microbial community between soils amended with or without farmyard manure. Appl Soil Ecol 33, 39-48. http://dx.doi.org/10.1016/j.apsoil.2005.09.002

Valinsky L., Vedova G.D., Scupham A.J., Alvey S., Figueroa A., Yin B., Hartin R.J., Chrobak M., Crowley D.E., Jiang T., Borneman J., 2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl Environ Microbiol 68, 3243-3250. http://dx.doi.org/10.1128/AEM.68.7.3243-3250.2002 PMid:12089000 PMCid:126790




DOI: 10.5424/sjar/20110901-118-10