Plant Soil Environ., 2009, 55(9):370-378 | DOI: 10.17221/134/2009-PSE
Microbial enzyme-catalyzed processes in soils and their analysis
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Prague, Czech Republic
Currently, measuring enzyme activities in soils or other lignocellulose-based materials is technically feasible; this measurement is particularly suitable for evaluating soil processes of biopolymer (cellulose, hemicelluloses, lignin, chitin and others) degradation by microbes and for assessing cycling and mobilization of principal nutrients including nitrogen, phosphorus and sulfur. With some considerations, assay methods can provide reliable information on the concentration of enzymes in soil or the rates of enzyme-catalyzed processes. Enzyme analyses in recent studies demonstrated a high level of spatial variability of soil enzyme activity both in depth and in space. The vertical gradients of enzyme activities are most developed in forest soils. Furthermore, enzyme activity in soils is regulated by seasonally-dependent variables such as temperature, moisture and the input of fresh litter. While several enzymes are widely produced by different groups of soil microorganisms, some of them can be used as indicators of the presence or activity of specific microbial taxa.
Keywords: Keywords: assay methods; ecology; extracellular enzymes; fungi; lignocellulose; litter; soil microorganisms
Published: September 30, 2009 Show citation
References
- Alef K., Nannipieri P. (1995): Methods in Applied Soil Microbiology and Biochemistry. Academic Press, London, 1200.
- Andersson M., Kjoller A., Struwe S. (2004): Microbial enzyme activities in leaf litter, humus and mineral soil layers of European forests. Soil Biology and Biochemistry, 36: 1527-1537.
Go to original source...
- Baldrian P. (2006): Fungal laccases - occurrence and properties. FEMS Microbiology Reviews, 30: 215- 242.
Go to original source...
Go to PubMed...
- Baldrian P. (2008a): Enzymes of Saprotrophic Basidiomycetes. In: Boddy L., Frankland J., van West P. (eds.): Ecology of Saprotrophic Basidiomycetes. Academic Press, New York, 19-41.
Go to original source...
- Baldrian P. (2008b): Wood-inhabiting ligninolytic basidiomycetes in soils: ecology and constraints for applicability in bioremediation. Fungal Ecology, 1: 4-12.
Go to original source...
- Baldrian P., Gabriel J. (2002): Copper and cadmium increase laccase activity in Pleurotus ostreatus. FEMS Microbiology Letters, 206: 69-74.
Go to original source...
Go to PubMed...
- Baldrian P., Gabriel J. (2003): Lignocellulose degradation by Pleurotus ostreatus in the presence of cadmium. FEMS Microbiology Letters, 220: 235-240.
Go to original source...
Go to PubMed...
- Baldrian P., Valáąková V. (2008): Degradation of cellulose by basidiomycetous fungi. FEMS Microbiology Reviews, 32: 501-521.
Go to original source...
Go to PubMed...
- Baldrian P., Wiesche C., Gabriel J., Nerud F., Zadrazil F. (2000): Influence of cadmium and mercury on activities of ligninolytic enzymes and degradation of polycyclic aromatic hydrocarbons by Pleurotus ostreatus in soil. Applied and Environmental Microbiology, 66: 2471-2478.
Go to original source...
Go to PubMed...
- Baldrian P., Trögl J., Frouz J., ©najdr J., Valáąková V., Merhautová V., Cajthaml T., Herinková J. (2008): Enzyme activities and microbial biomass in topsoil layer during spontaneous succession in spoil heaps after brown coal mining. Soil Biology and Biochemistry, 40: 2107-2115.
Go to original source...
- Biely P., Puchart V. (2006): Recent progress in the assays of xylanolytic enzymes. Journal of Science in Food and Agriculture, 86: 1636-1647.
Go to original source...
- Bolton H., Elliott L.F., Papendick R.I., Bezdicek D.F. (1985): Soil microbial biomass and selected soil enzyme activities - effect of fertilization and cropping practices. Soil Biology and Biochemistry, 17: 297-302.
Go to original source...
- Bourbonnais R., Paice M.G. (1990): Oxidation of nonphenolic substrates. An expanded role for laccase in lignin biodegradation. FEBS Letters, 267: 99-102.
Go to original source...
Go to PubMed...
- Burns R.G., Dick R.P. (2002): Enzymes in the Environment. Marcel Dekker, New York, 614.
Go to original source...
- Claus H., Filip Z. (1990): Effects of clays and other solids on the activity of phenoloxidases produced by some fungi and actinomycetes. Soil Biology and Biochemistry, 22: 483-488.
Go to original source...
- Collins T., Gerday C., Feller G. (2005): Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiology Reviews, 29: 3-23.
Go to original source...
Go to PubMed...
- Criquet S., Farnet A.M., Tagger S., Le Petit J. (2000): Annual variations of phenoloxidase activities in an evergreen oak litter: influence of certain biotic and abiotic factors. Soil Biology and Biochemistry, 32: 1505-1513.
Go to original source...
- Criquet S., Tagger S., Vogt G., Le Petit J. (2002): Endoglucanase and beta-glycosidase activities in an evergreen oak litter: annual variation and regulating factors. Soil Biology and Biochemistry, 34: 1111-1120.
Go to original source...
- Criquet S., Ferre E., Farnet A.M., Le Petit J. (2004): Annual dynamics of phosphatase activities in an evergreen oak litter: influence of biotic and abiotic factors. Soil Biology and Biochemistry, 36: 1111-1118.
Go to original source...
- de Boer W., Folman L.B., Summerbell R.C., Boddy L. (2005): Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiology Reviews, 29: 795-811.
Go to original source...
Go to PubMed...
- Dick R.P. (1994): Soil enzyme activity as indicators of soil quality. In: Doran J.W., Coleman D.C., Bezdicek D.F., Stewart B.A. (eds.): Defining Soil Quality for a Sustainable Environment. Soil Science Society of America, Madison, 107-124.
Go to original source...
- Dick R.P., Breakwell D.P., Turco R.F. (1996): Soil enzyme activities and biodiversity measurements as integrative microbiological indicators. In: Doran J.W., Jones A.J. (eds.): Methods for Assessing Soil Quality. Soil Science Society of America, Madison, 247-271.
Go to original source...
- Dilly O., Munch J.C. (1996): Microbial biomass content, basal respiration and enzyme activities during the course of decomposition of leaf litter in a black alder (Alnus glutinosa (L) Gaertn) forest. Soil Biology and Biochemistry, 28: 1073-1081.
Go to original source...
- Effron D., de la Horra A.M., Defrieri R.L., Fontanive V., Palma R.M. (2004): Effect of cadmium, copper, and lead on different enzyme activities in a native forest soil. Communications in Soil Science and Plant Analysis, 35: 1309-1321.
Go to original source...
- Garland J.L., Mills A.L. (1991): Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Applied and Environmental Microbiology, 57: 2351-2359.
Go to original source...
Go to PubMed...
- Gianfreda L., Bollag M.J. (1996): Influence of natural and anthropogenic factors on enzyme activity in soil. In: Stotzky G., Bollag J.M. (eds.): Soil Biochemistry, Vol. 9, Marcel Dekker, New York, 123-193.
- Gruner E., von Graevenitz A., Altwegg M. (1992): The API ZYM system: a tabulated review from 1977 to date. Journal of Microbiological Methods, 16: 101-118.
Go to original source...
- Hassett J., Zak D., Blackwood C., Pregitzer K. (2009): Are basidiomycete laccase gene abundance and composition related to reduced lignolytic activity under elevated atmospheric NO3- deposition in a northern hardwood forest? Microbial Ecology, 57: 728-739.
Go to original source...
Go to PubMed...
- Hättenschwiler S., Tiunov A.V., Scheu S. (2005): Biodiversity and litter decomposition in terrestrial ecosystems. Annual Reviews of Ecology, Evolution and Systematics, 36: 191-218.
Go to original source...
- Hayano K. (1977): Extraction and properties of phosphodiesterase from a forest soil. Soil Biology and Biochemistry, 9: 221-223.
Go to original source...
- Hayes J.E., Richardson A.E., Simpson R.J. (2000): Components of organic phosphorus in soil extracts that are hydrolysed by phytase and acid phosphatase. Biology and Fertility of Soils, 32: 279-286.
Go to original source...
- He Z.L., Gentry T.J., Schadt C.W., Wu L.Y., Liebich J., Chong S.C., Huang Z.J., Wu W.M., Gu B.H., Jardine P., Criddle C., Zhou J. (2007): GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. International Society for Microbial Ecology Journal, 1: 67-77.
Go to original source...
Go to PubMed...
- Hildén K.S., Bortfeldt R., Hofrichter M., Hatakka A., Lundell T.K. (2008): Molecular characterization of the basidiomycete isolate Nematoloma frowardii b19 and its manganese peroxidase places the fungus in the corticioid genus Phlebia. Microbiology, 154: 2371-2379.
Go to original source...
Go to PubMed...
- Hofrichter M. (2002): Review: lignin conversion by manganese peroxidase (MnP). Enzyme and Microbial Technology, 30: 454-466.
Go to original source...
- Chapman S.J., Campbell C.D., Artz R.R. (2007): Assessing CLPPs Using MicroResp™: a comparison with Biolog and multi-SIR. Journal of Soils and Sediments, 7: 406-410.
Go to original source...
- Kandeler E., Tscherko D., Spiegel H. (1999): Long-term monitoring of microbial biomass, N mineralisation and enzyme activities of a Chernozem under different tillage management. Biology and Fertility of Soils, 28: 343-351.
Go to original source...
- Kilcawley K.N., Wilkinson M.G., Fox P.F. (2002): Determination of key enzyme activities in commercial peptidase and lipase preparations from microbial or animal sources. Enzyme and Microbial Technology, 31: 310-320.
Go to original source...
- Klose S., Tabatabai M.A. (1999a): Urease activity of microbial biomass in soils. Soil Biology and Biochemistry, 31: 205-211.
Go to original source...
- Klose S., Tabatabai M.A. (1999b): Arylsulfatase activity of microbial biomass in soils. Soil Science Society of America Journal, 63: 569-574.
Go to original source...
- Lang E., Eller G., Zadrazil F. (1997): Lignocellulose decomposition and production of ligninolytic enzymes during interaction of white rot fungi with soil microorganisms. Microbial Ecology, 34: 1-10.
Go to original source...
Go to PubMed...
- Lauber C., Sinsabaugh R., Zak D. (2009): Laccase gene composition and relative abundance in oak forest soil is not affected by short-term nitrogen fertilization. Microbial Ecology, 57: 50-57.
Go to original source...
Go to PubMed...
- Luis P., Kellner H., Martin F., Buscot F. (2005a): A molecular method to evaluate basidiomycete laccase gene expression in forest soils. Geoderma, 128: 18-27.
Go to original source...
- Luis P., Kellner H., Zimdars B., Langer U., Martin F., Buscot F. (2005b): Patchiness and spatial distribution of laccase genes of ectomycorrhizal, saprotrophic, and unknown basidiomycetes in the upper horizons of a mixed forest cambisol. Microbial Ecology, 50: 570-579.
Go to original source...
Go to PubMed...
- Lynd L.R., Weimer P.J., van Zyl W.H., Pretorius I.S. (2002): Microbial cellulose utilization: fundamentals and biotechnology. Microbiology and Molecular Biology Reviews, 66: 506-577.
Go to original source...
Go to PubMed...
- Martínez A.T., Speranza M., Ruiz-Duenas F.J., Ferreira P., Guillén F., Martínez M.J., Gutiérrez A., del Rio C.J. (2005): Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. International Microbiology, 8: 195-204.
- Marx M.C., Wood M., Jarvis S.C. (2001): A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil Biology and Biochemistry, 33: 1633-1640.
Go to original source...
- Miller M., Palojarvi A., Rangger A., Reeslev M., Kjoller A. (1998): The use of fluorogenic substrates to measure fungal presence and activity in soil. Applied and Environmental Microbiology, 64: 613-617.
Go to original source...
Go to PubMed...
- Ngo T.T., Lenhoff H.M. (1980): A sensitive and versatile chromogenic assay for peroxidase and peroxidasecoupled reactions. Analytical Biochemistry, 105: 389-397.
Go to original source...
Go to PubMed...
- Niemi R.M., Vepsäläinen M. (2005): Stability of the fluorogenic enzyme substrates and pH optima of enzyme activities in different Finnish soils. Journal of Microbiological Methods, 60: 195-205.
Go to original source...
Go to PubMed...
- Niemi R.M., Vepsäläinen M., Wallenius K., Simpanen S., Alakukku L., Pietola L. (2005): Temporal and soil depth-related variation in soil enzyme activities and in root growth of red clover (Trifolium pratense) and timothy (Phleum pratense) in the field. Applied Soil Ecology, 30: 113-125.
Go to original source...
- Preston-Mafham J., Boddy L., Randerson P.F. (2002): Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. FEMS Microbiology Ecology, 42: 1-14.
Go to original source...
Go to PubMed...
- Prietzel J. (2001): Arylsulfatase activities in soils of the Black Forest/Germany - seasonal variation and effect of (NH 4) 2 SO 4 fertilization. Soil Biology and Biochemistry, 33: 1317-1328.
Go to original source...
- Quiquampoix H., Staunton S., Baron M.H., Ratcliffe R.G. (1993): Interpretation of the pH dependence of protein adsorption on clay mineral surfaces and its relevance to the understanding of extracellular enzyme activity in soil. Colloids and Surfaces A - Physicochemical Engineering Aspects, 75: 85-93.
Go to original source...
- Rao M.B., Tanksale A.M., Ghatge M.S., Deshpande V.V. (1998): Molecular and biotechnological aspects of microbial proteases. Microbiology and Molecular Biology Reviews, 62: 597-635.
Go to original source...
Go to PubMed...
- Roy S., Bhattacharyya P., Ghosh A.K. (2004): Influence of toxic metals on activity of acid and alkaline phosphatase enzymes in metal-contaminated landfill soils. Australian Journal of Soil Research, 42: 339-344.
Go to original source...
- Seidl V. (2008): Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. Fungal Biology Reviews, 22: 36-42.
Go to original source...
- Schinner F., Öhlinger R., Kandeler E., Margesin R. (1996): Methods in Soil Biology. Springer Verlag, Berlin.
Go to original source...
- Schlosser D., Grey R., Fritsche W. (1997): Patterns of ligninolytic enzymes in Trametes versicolor. Distribution of extra- and intracellular enzyme activities during cultivation on glucose, wheat straw and beech wood. Applied Microbiology and Biotechnology, 47: 412-418.
Go to original source...
- Schomburg D., Schomburg I. (2007): Springer Handbook of Enzymes. Springer, Berlin.
Go to original source...
- Steffen K.T., Cajthaml T., ©najdr J., Baldrian P. (2007): Differential degradation of oak (Quercus petraea) leaf litter by litter-decomposing basidiomycetes. Research in Microbiology, 158: 447-455.
Go to original source...
Go to PubMed...
- ©najdr J., Valáąková V., Merhautová V., Cajthaml T., Baldrian P. (2008a): Activity and spatial distribution of lignocellulose-degrading enzymes during forest soil colonization by saprotrophic basidiomycetes. Enzyme and Microbial Technology, 43: 186-192.
Go to original source...
- ©najdr J., Valáąková V., Merhautová V., Herinková J., Cajthaml T., Baldrian P. (2008b): Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil. Soil Biology and Biochemistry, 40: 2068-2075.
Go to original source...
- Tabatabai M.A. (1994): Soil enzymes. In: Weaver R.V., Angle S., Bottomley P.J., Bezdicek D.F., Smith S., Tabatabai M.A. (eds.): Methods of Soil Analysis: Part 2 Microbiological and Chemical Properties. Soil Science Society of America, Madison, 903-947.
Go to original source...
- Tabatabai M.A., Bremner J.M. (1970): Arylsulfatase activity of soils. Soil Society of America Proceedings, 34: 225-229.
Go to original source...
- Toberman H., Evans C.D., Freeman C., Fenner N., White M., Emmett B.A., Artz R.R.E. (2008): Summer drought effects upon soil and litter extracellular phenol oxidase activity and soluble carbon release in an upland Calluna heathland. Soil Biology and Biochemistry, 40: 1519-1532.
Go to original source...
- Trasar-Cepeda C., Leiros M.C., Gil-Sotres F. (2000): Biochemical properties of acid soils under climax vegetation (Atlantic oakwood) in an area of the European temperate-humid zone (Galicia, NW Spain): specific parameters. Soil Biology and Biochemistry, 32: 747-755.
Go to original source...
- Valáąková V., Baldrian P. (2006): Estimation of bound and free fractions of lignocellulose-degrading enzymes of wood-rotting fungi Pleurotus ostreatus, Trametes versicolor and Piptoporus betulinus. Research in Microbiology, 157: 119-124.
Go to original source...
Go to PubMed...
- Valáąková V., ©najdr J., Bittner B., Cajthaml T., Merhautová V., Hoffichter M., Baldrian P. (2007): Production of lignocellulose-degrading enzymes and degradation of leaf litter by saprotrophic basidiomycetes isolated from a Quercus petraea forest. Soil Biology and Biochemistry, 39: 2651-2660.
Go to original source...
- Vepsäläinen M. (2001): Poor enzyme recovery by extraction from soils. Soil Biology and Biochemistry, 33: 1131-1135.
Go to original source...
- Vepsäläinen M., Kukkonen S., Vestberg M., Sirvio H., Niemi R.M. (2001): Application of soil enzyme activity test kit in a field experiment. Soil Biology and Biochemistry, 33: 1665-1672.
Go to original source...
- Wittmann C., Kahkonen M.A., Ilvesniemi H., Kurola J., Salkinoja-Salonen M.S. (2004): Areal activities and stratification of hydrolytic enzymes involved in the biochemical cycles of carbon, nitrogen, sulphur and phosphorus in podsolized boreal forest soils. Soil Biology and Biochemistry, 36: 425-433.
Go to original source...
- Zavarzina A.G., Leontievsky A.A., Golovleva L.A., Trofimov S.Y. (2004): Biotransformation of soil humic acids by blue laccase of Panus tigrinus 8/18: an in vitro study. Soil Biology and Biochemistry, 36: 359-369.
Go to original source...
This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.