Abstract
The diversity of soil proteolytic community encoding for subtilisin (sub) was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. A terminal restriction fragment length polymorphism (T-RFLP) analysis of subtilisin gene (sub) was applied to study dynamic of the sub gene pool. The aim of the present study was to relate differences in sub community structure to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. A significant spatial variability in the community structure of sub-containing bacteria was observed. The richness of sub proteolytic bacterial population decreased with increasing soil depth, revealing the highest values in upper layers. A similar trend was observed among the different sites; the highest diversity was noticed at the site with the highest silt and nutrient content. The reasons behind the observed patterns in the community structure might be varying water amount and spatial isolation along the soil profile as well as variability of the quantity and quality of available substrates among different depths and different sites.
Similar content being viewed by others
References
Agnelli A, Ascher J, Corti G, Ceccherini MT, Nannipieri P, Pietramellara G (2004) Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol Biochem 36:859–868 doi:10.1016/j.soilbio.2004.02.004
Asmar F, Eiland F, Nielsen NE (1994) Effect of extracellular-enzyme activities on solubilization rate of soil organic nitrogen. Biol Fertil Soils 17:32–38 doi:10.1007/BF00418669
Bach HJ, Munch JC (2000) Identification of bacterial sources of soil peptidases. Biol Fertil Soils 31:219–224 doi:10.1007/s003740050648
Bach HJ, Hartmann A, Schloter M, Munch JC (2001) PCR primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil. J Microbiol Methods 44:173–182 doi:10.1016/S0167-7012(00)00239-6
FAO (1976) FAO–Unesco Soil Map of the World Legend. Unesco, Paris 1
Fedi S, Tremaroli V, Scala D, Perez-Jimenez JR, Fava F, Young L et al (2005) T-RFLP analysis of bacterial communities in cyclodextrin-amended bioreactors developed for biodegradation of polychlorinated biphenyls. Res Microbiol 156:201–210
Hayano K, Takeuchi M, Ichishima E (1987) Characterization of a metalloproteinase component extracted from soil. Biol Fertil Soils 4:179–183 doi:10.1007/BF00270938
Kamimura Y, Hayano K (2000) Properties of protease extracted from tea-field soil. Biol Fertil Soils 30:351–355 doi:10.1007/s003740050015
Kandeler E, Tscherko D, Bruce KD, Stemmer M, Hobbs PJ, Bardgett RD et al (2000) The structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biol Fertil Soils 32:390–400 doi:10.1007/s003740000268
Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66:1328–1333 doi:10.1128/AEM.66.4.1328-1333.2000
Kloos K, Husgen U, Bothe H (1998) DNA-probing for genes coding for denitrification, N2-fixation and nitrification in bacteria isolated from different soils. Z Naturforsch 53:69–81
Kumar K, Rosen CJ, Russelle MP (2006) Enhanced protease inhibitor expression in plant residues slows nitrogen mineralization. Agron J 98:514–521 doi:10.2134/agronj2005.0261
Ladd JN, Butler JHA (1972) Short-term assays of soil proteolytic enzyme activities using proteins and dipeptide derivatives as substrates. Soil Biol Biochem 4:19–30 doi:10.1016/0038-0717(72)90038-7
Ladd JN, Jackson RB (1982) Biochemistry of ammonification. In: Stevenson FJ (ed) Nitrogen in agricultural soils. American Society of Agronomy, Madison, pp 173–228
Langer U, Böhme L, Böhme F (2004) Classification of soil microorganisms based on growth properties: a critical view of some commonly used terms. J Plant Nutr Soil Sci 167:267–269 doi:10.1002/jpln.200421362
Lipson D, Näsholm T (2001) The unexpected versatility of plants: organic nitrogen use and availability in terrestrial ecosystems. Oecologia 128:305–316 doi:10.1007/s004420100693
Loll MJ, Bollag JM (1983) Protein transformation in soil. Adv Agron 36:351–382 doi:10.1016/S0065-2113(08)60358-2
Marx MC, Kandeler E, Wood M, Wermbter N, Jarvis SC (2005) Exploring the enzymatic landscape: distribution and kinetics of hydrolytic enzymes in soil particle-size fractions. Soil Biol Biochem 37:35–48 doi:10.1016/j.soilbio.2004.05.024
Mrkonjic Fuka M, Engel M, Gattinger A, Bausenwein U, Sommer M, Munch JC et al (2008a) Factors influencing variability of proteolytic genes and activities in arable soils. Soil Biol Biochem 40:1646–1653 doi:10.1016/j.soilbio.2008.01.028
Mrkonjic Fuka M, Engel M, Hagn A, Munch JC, Sommer M, Schloter M (2008b) Changes of diversity pattern of proteolytic bacteria over time and space in an agricultural soil. Microb Ecol doi:10.1007/s00248-008-9416-5
Nannipieri P, Badalucco L, Landi L (1994) Holistic approaches to the study of populations nutrient pools and fluxes: limits and future research needs. In: Ritz K, Dighton J, Giller KE (eds) Beyond the biomass. Wiley, New York, pp 231–238
Paul EA, Clark FE (1996) Ammonification and nitrification. In: Paul EA, Clark FE (eds) Soil microbiology and biochemistry. Academic, San Diego, pp 182–183
Rao MB, Tanksale AM, Ghatge MS, Deshpande VV (1998) Molecular and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 62:597–635
Sakurai M, Suzuki K, Onodera M, Shinano T, Osaki M (2007) Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes. Soil Biol Biochem 39:2777–2784 doi:10.1016/j.soilbio.2007.05.026
Schulten HR, Schnitzer M (1998) The chemistry of soil organic nitrogen: a review. Biol Fertil Soils 26:1–15 doi:10.1007/s003740050335
Sims GK, Wander MM (2002) Proteolytic activity under nitrogen or sulfur limitation. Appl Soil Ecol 19:217–221 doi:10.1016/S0929-1393(01)00192-5
Sommer M, Weherhan M, Zipprich M, Weller U, zuCastell W, Ehrich S et al (2003) Hierarchical data fusion for mapping soil units at field scale. Geoderma 112:179–196 doi:10.1016/S0016-7061(02)00305-1
Team RDC (2005) A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria URL http://www.R-project.org.: ISBN 3-900051-07-0
Watanabe K, Hayano K (1994) Estimate of the source of soil protease in upland fields. Biol Fertil Soils 18:341–346 doi:10.1007/BF00570638
Watanabe K, Sakai J, Hayano K (2003) Bacterial extracellular protease activities in field soils under different fertilizer managements. Can J Microbiol 49:305–312 doi:10.1139/w03-040
WRB (2006) World Reference Base for Soil Resources 2006. World Soil Resources Reports 103. FAO, Rome
Zhou J, Xia B, Huang H, Palumbo AV, Tiedje JM (2004) Microbial diversity and heterogeneity in sandy subsurface soils. Appl Environ Microbiol 70:1723–1734 doi:10.1128/AEM.70.3.1723-1734.2004
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fuka, M.M., Engel, M., Haesler, F. et al. Diversity of proteolytic community encoding for subtilisin in an arable field: spatial and temporal variability. Biol Fertil Soils 45, 185–191 (2008). https://doi.org/10.1007/s00374-008-0319-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00374-008-0319-x