ESTONIAN ACADEMY
PUBLISHERS
eesti teaduste
akadeemia kirjastus
cover
Estonian Journal of Ecology
Monitoring seasonal changes in microbial populations of spruce forest soil of the Northern Temperate Zone; pp. 190–214
PDF | doi: 10.3176/eco.2012.3.03

Authors
Lelde Grantina, Gunta Bondare, Anna Janberga, Guntis Tabors, Raimonds Kasparinskis, Vizma Nikolajeva, Indrikis Muiznieks
Abstract

Soil microbial populations in the Northern Temperate Zone have been poorly studied in comparison with extreme environments. The aim of the work was to study the seasonal changes in the microbial populations of spruce forest soil of the Northern Temperate Zone using classical methods of microbiology and molecular biology. Upper horizons in two Picea abies stands on sod-podzolic and illuvial humus podzol soil were analysed. Sampling was done monthly over a period of twelve months (May 2009–April 2010). Microbial communities in both experimental plots showed different responses to the analysed environmental factors. In the sod-podzolic soil only the fungal DNA amount was significantly higher in the rest period (October–April) in comparison with the active vegetation period (May–September) and the number of Penicillium spp. colonies was larger in the active vegetation period. In the other soil the number of maltose utilizing bacteria, yeasts, and Penicillium spp. and other culturable filamentous fungi was significantly higher in the active vegetation period, while the fungal DNA amount was elevated in the rest period. Although ARDRA did not reveal differences, sequencing of 84 fungal isolates showed different compositions of the communities. Sørensen’s index between the plots was low (0.29). Comparing the active vegetation period with the rest period, the index was higher (0.48). Although all tested fungal isolates from the rest period were able to grow at 4 °C, none of them showed psychrotrophic growth characters.

References

Bardule, A., Baders, E., Stola, J. & Lazdins, A. 2009. Forest soil characteristic in Latvia according results of the demonstration project BioSoil. Mezzinatne/Forest Science, 20, 105–124 (in Latvian with English summary).

Bergero, R., Girlanda, M., Varese, G. C., Intili, D. & Luppi, A. M. 1999. Psychrooligotrophic fungi from Arctic soils of Franz Joseph Land. Polar. Biol., 21, 361–368.
http://dx.doi.org/10.1007/s003000050374

Brooks, P. D., Williams, M. W. & Schmidt, S. K. 1998. Inorganic N and microbial biomass dynamics before and during spring snowmelt. Biogeochemistry, 43, 1–15.
http://dx.doi.org/10.1023/A:1005947511910

Buss, K. 1997. Forest ecosystem classification in Latvia. Proc. Latvian. Acad. Sci. Sect. B, 51, 204–218.

Carrigg, C., Rice, O., Kavanagh, S., Collins, G. & O’Flaherty, V. 2007. DNA extraction method affects microbial community profiles from soil and sediments. Appl. Microbiol. Biot., 77, 955–964.
http://dx.doi.org/10.1007/s00253-007-1219-y

Cenis, J. L. 1992. Rapid extraction of fungal DNA for PCR amplification. Nucleic Acids Res., 20, 2380.
http://dx.doi.org/10.1093/nar/20.9.2380

Chabrerie, O., Laval, K., Puget, P., Desaire, S. & Alard, D. 2003. Relationship between plant and soil microbial communities along a successional gradient in a chalk grassland in north-western France. Appl. Soil Ecol., 24, 43–56.
http://dx.doi.org/10.1016/S0929-1393(03)00062-3

Danielson, R. M. & Davey, C. B. 1973. Non-nutritional factors affecting the growth of Trichoderma in culture. Soil Biol. Biochem., 5, 495–504.
http://dx.doi.org/10.1016/0038-0717(73)90039-4

Dion, P. 2008. The microbiological promises of extreme soils. In Microbiology of Extreme Soils. Soil Biology 13 (Dion, P. & Nautiyal, C. S., eds), pp. 3–5. Springer-Verlag, Berlin, Heidelberg.
http://dx.doi.org/10.1007/978-3-540-74231-9

Expert Panel on Soil. 2006. Manual on Methods and Criteria for Harmonized Sampling, Assessment, Monitoring and Analysis of the Effects of Air Pollution on Forests. Part IIIa. Sampling and Analysis of Soil. Expert Panel on Soil Forest Soil Co-ordinating Centre, Research Institute for Nature and Forest, Belgium.

FAO WRB. 2006. World Reference Base for Soil Resources 2006: A Framework for International Classification, Correlation and Communication. Food and Agriculture Organization of the United Nations, Rome.

Gabor, E. M., de Vries, E. J. & Janssen, D. B. 2003. Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiol. Ecol., 44, 153–163.
http://dx.doi.org/10.1016/S0168-6496(02)00462-2

Gardes, M. & Bruns, T. D. 1993. ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Mol. Ecol., 2, 113–118.
http://dx.doi.org/10.1111/j.1365-294X.1993.tb00005.x

Grantina, L., Seile, E., Malinovskis, U., Tabors, G., Kasparinskis, R., Nikolajeva, V. & Muiznieks, I. 2010. Particular characteristics of soil microbial communities in forest stands infected with Heterobasidion parviporum and Armillaria spp. In Microorganisms in Industry and Environment. From Scientific and Industrial Research to Consumer Products. Proceedings of the III International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld2009) (Mendez-Vilas, A., ed.), pp. 86–91. World Scientific.

Grantina, L., Seile, E., Kenigsvalde, K., Kasparinskis, R., Tabors, G., Nikolajeva, V., Jungerius, P. & Muiznieks, I. 2011. The influence of the land use on abundance and diversity of soil fungi: comparison of conventional and molecular methods of analysis. Env. Exp. Biol., 9, 9–21.

Hagn, A., Wallisch, S., Radl, V., Munch, J. C. & Schloter, M. 2007. A new cultivation independent approach to detect and monitor common Trichoderma species in soils. J. Microbiol. Meth., 69, 86–92.
http://dx.doi.org/10.1016/j.mimet.2006.12.004

Hartmann, M. & Widmen, F. 2006. Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl. Environ. Microbiol., 72, 7804–7812.
http://dx.doi.org/10.1128/AEM.01464-06

Izzo, A., Nguyen, D. T. & Bruns, T. D. 2006. Spatial structure and richness of ectomycorrhizal fungi colonizing bioassay seedlings from resistant propagules in a Sierra Nevada forest: comparisons using two hosts that exhibit different seedling establishment patterns. Mycologia, 98, 374–383.
http://dx.doi.org/10.3852/mycologia.98.3.374

Karklins, A., Gemste, I., Mezals, H., Nikodemuss, O. & Skujans, R. 2009. Taxonomy of Latvian Soils. LLU, Jelgava (in Latvian).

Korhonen, K. & Stenlid, J. 1998. Biology of Heterobasidion annosum. In Heterobasidion annosum: Biology, Ecology, Impact and Control (Woodward, S., Stenlid, J., Karjalainen, R. & Huutermann, A., eds), pp. 43–70. CAB International, UK.

Lipson, D. A., Schmidt, S. K. & Monson, R. K. 1999. Links between microbial population dynamics and nitrogen availability in an alpine ecosystem. Ecology, 80, 1623–1631.
http://dx.doi.org/10.1890/0012-9658(1999)080[1623:LBMPDA]2.0.CO;2

Lipson, D. A., Schmidt, S. K. & Monson, R. K. 2000. Carbon availability and temperature control the post-snowmelt decline in alpine soil microbial biomass. Soil Biol. Biochem., 32, 441–448.
http://dx.doi.org/10.1016/S0038-0717(99)00068-1

Lipson, D. A., Schadt, C. W. & Schmidt, S. K. 2002. Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt. Microbial. Ecol., 43, 307–314.
http://dx.doi.org/10.1007/s00248-001-1057-x

Nemergut, D. R., Costello, E. K., Meyer, A. F., Pescador, M. Y., Weintraub, M. N. & Schmidt, S. K. 2005. Structure and function of alpine and arctic soil microbial communities. Res. Microbiol., 156, 775–784.
http://dx.doi.org/10.1016/j.resmic.2005.03.004

Ning, J., Liebich, J., Kästner, M., Zhou, J., Schäffer, A. & Burauel, P. 2009. Different influence of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl. Microbiol. Biot., 82, 983–993.
http://dx.doi.org/10.1007/s00253-009-1912-0

R Development Core Team. 2009. R: A language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org (visited 05.05.2010).

Schmidt, S. K. & Lipson, D. A. 2004. Microbial growth under the snow: implications for nutrient and allelochemical availability in temperate soils. Plant Soil, 259, 1–7.
http://dx.doi.org/10.1023/B:PLSO.0000020933.32473.7e

Schmidt, S. K., Lipson, D. A, Ley, R. E., Fisk, M. C. & West, A. E. 2004. Impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils. Biogeochemistry, 69, 1–17.
http://dx.doi.org/10.1023/B:BIOG.0000031028.53116.9b

Staddon, W. J., Trevors, J. T., Duchesne, L. C. & Colombo, C. A. 1998. Soil microbial diversity and community structure across a climatic gradient in Western Canada. Biodivers. Conserv., 7, 1081–1092.
http://dx.doi.org/10.1023/A:1008813232395

Thakuria, D., Schmidt, O., Mac Siúrtáin, M., Egan, D. & Doohan, F. M. 2008. Importance of DNA quality in comparative soil microbial community structure analysis. Soil Biol. Biochem., 40, 1390–1403.
http://dx.doi.org/10.1016/j.soilbio.2007.12.027

Waldrop, M. P., Zak, D. R. & Sinsabaugh, R. L. 2004. Microbial community response to nitrogen deposition in northern forest ecosystems. Soil Biol. Biochem., 36, 1443–1451.
http://dx.doi.org/10.1016/j.soilbio.2004.04.023

Widden, P. & Abitbol, J. J. 1980. Seasonality of Trichoderma species in a spruce forest soil. Mycologia, 72, 775–784.
http://dx.doi.org/10.2307/3759770

Yeates, C., Gillings, M. R., Davison, A. D., Altavilla, N. & Veal, D. A. 1998. Methods for microbial DNA extraction from soil for PCR amplification. Biol. Proc. Online, 1, 40–47.
http://dx.doi.org/10.1251/bpo6

Zimov, S. A., Semietov, I. P., Davidov, S. P., Voropaev, I. V., Prosyannikov, S. F., Wong, C. S. & Chan, Y. H. 1993. Wintertime CO2 emissions from soils of northeastern Siberia. Arctic, 46, 197–204.

Back to Issue

Back issues