Abstract
Measurement of extracellular enzymic activity in wetland soils can give an indication of the ecosystems biogeochemical processes, and rates of nutrient and carbon cycling. Analysis of these have allowed researchers to gain an understanding of the ecosystems’ microbial ecology and how it can be affected by environmental factors. Here we give a detailed description of the assays necessary to determine the activity of a suite of key hydrolase enzymes and phenol oxidases. These enzymes control the rates of decomposition and consequently the production of biogenic greenhouse gases. Knowing the processes responsible for the breakdown of organic matter is therefore essential if it becomes necessary to curb these emissions. Our protocols allow for cost effective analysis of a large number of samples and provide sufficient accuracy to determine differences between soil types. When coupled with contemporary microbial techniques these enzyme assays permit entire biochemical pathways to be determined, giving unparalleled knowledge on the processes involved in wetland ecosystems.
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References
Bending GD, Read DJ (1997) Lignin and soluble phenolic degradation by ectomycorrhizal and ericoid mycorrhizal fungi. Mycol Res 101
Blank RR, Derner JD (2004) Effects of CO2 enrichment on plant-soil relationships of Lepidium latifolium. Plant Soil 262:159–167
Burke RM, Cairney JWG (2002) Laccases and other polyphenol oxidases in ecto- and ericoid mycorrhizal fungi. Mycorrhiza 12
Burns RG (1982) Enzyme-activity in soil: location and a possible role in microbial ecology. Soil Biol Biochem 14:423–427
Burns A, Ryder DS (2001) Response of bacterial extracellular enzymes to inundation of floodplain sediments. Freshw Biol 46:1299–1307
Corpe WA, Winters H (1972) Hydrolytic enzymes of some periphytic marine bacteria. Can J Microbiol 18:1483–1490
Corstanje R, Reddy KR (2004) Response of biogeochemical indicators to a drawdown and subsequent reflood. J Environ Qual 33:2357–2366
Crawford DL (1978) Lignocellulose decomposition by selected Streptomyces strains. Appl Environ Microbiol 35:1041–1045
Daatselaar MCC, Harder W (1974) Some aspects of regulation of production of extracellular proteolytic-enzymes be a marine bacterium. Arch Microbiol 101:21–34
De Cesare F, Garzillo AMV, Buonocore V, Badalucco L (2000) Use of sonication for measuring acid phosphatase activity in soil. Soil Biol Biochem 32:825–832
Deng S, Popova I (2011) Carbohydrate hydrolases. In: Dick RP (ed) Mehods of soil enzymology. Soil Science Society of America, Inc., Madison, pp 185–209
Dick R, Burns RG (2011) A brief history of soil enzyme research. In: Dick RP (ed) Methods of soil enzymology. Soil Science Society of America, Wisconsin, pp 1–34
Drenovsky RE, Feris KP, Batten KM, Hristova K (2008) New and current microbiological tools for ecosystem ecologists: towards a goal of linking structure and function. Am Midl Nat 160:140–159
Duarte B, Reboreda R, Cacador I (2008) Seasonal variation of extracellular enzymatic activity (EEA) and its influence on metal speciation in a polluted salt marsh. Chemosphere 73:1056–1063
Duckworth W, Coleman JE (1970) Physiochemical and kinetic properties of mushroom tyrosinase. J Biol Chem 245:1613
Duran N, Rosa MA, D’Annibale A, Gianfreda L (2002) Applications of laccases and tyrosinases (phenoloxidases) immobilized on different supports: a review. Enzyme Microb Technol 31:907–931
Endo K, Hayashi Y, Hibi T, Hosono K, Beppu T, Ueda K (2003) Enzymological characterization of EpoA, a laccase-like phenol oxidase produced by Streptomyces griseus. J Biochem 133
Evans CD, Jones TG, Burden A, Ostle N, Zielinski P, Cooper MDA, Peacock M, Clark JM, Oulehle F, Cooper D, Freeman C (2012) Acidity controls on dissolved organic carbon mobility in organic soils. Glob Chang Biol 18:3317–3331
Fenner N, Freeman C (2011) Drought-induced carbon loss in peatlands. Nat Geosci 4:895–900
Fenner N, Freeman C, Reynolds B (2005a) Hydrological effects on the diversity of phenolic degrading bacteria in a peatland: implications for carbon cycling. Soil Biol Biochem 37
Fenner N, Freeman C, Reynolds B (2005b) Observations of a seasonally shifting thermal optimum in peatland carbon-cycling processes; implications for the global carbon cycle and soil enzyme methodologies. Soil Biol Biochem 37:1814–1821
Fenner N, Dowrick DJ, Lock MA, Rafarel CR, Freeman C (2006) A novel approach to studying the effects of temperature on soil biogeochemistry using a thermal gradient bar. Soil Use Manag 22:267–273
Freeman C, Nevison GB (1999) Simultaneous analysis of multiple enzymes in environmental samples using methylumbelliferyl substrates and HPLC. J Environ Qual 28:1378–1380
Freeman C, Liska G, Ostle NJ, Jones SE, Lock MA (1995) The use of fluorogenic substrates for measuring enzyme-activity in peatlands. Plant Soil 175:147–152
Freeman C, Liska G, Ostle NJ, Lock MA, Reynolds B, Hudson J (1996) Microbial activity and enzymic decomposition processes following peatland water table drawdown. Plant Soil 180:121–127
Freeman C, Liska G, Ostle NJ, Lock MA, Hughes S, Reynolds B, Hudson J (1997) Enzymes and biogeochemical cycling in wetlands during a simulated drought. Biogeochemistry 39:177–187
Freeman C, Nevison GB, Hughes S, Reynolds B, Hudson J (1998) Enzymic involvement in the biogeochemical responses of a Welsh peatland to a rainfall enhancement manipulation. Biol Fertil Soils 27:173–178
Freeman C, Evans CD, Monteith DT, Reynolds B, Fenner N (2001a) Export of organic carbon from peat soils. Nature 412:785–785
Freeman C, Ostle N, Kang H (2001b) An enzymic ‘latch’ on a global carbon store—a shortage of oxygen locks up carbon in peatlands by restraining a single enzyme. Nature 409:149–149
Freeman C, Kim SY, Lee SH, Kang H (2004a) Effects of elevated atmospheric CO2 concentrations on soil microorganisms. J Microbiol 42:267–277
Freeman C, Ostle NJ, Fenner N, Kang H (2004b) A regulatory role for phenol oxidase during decomposition in peatlands. Soil Biol Biochem 36:1663–1667
Freeman C, Fenner N, Shirsat AH (2012) Peatland geoengineering: an alternative approach to terrestrial carbon sequestration. Philosophical transactions. Ser A Math Phys Eng Sci 370:4404–4421
Frogbrook ZL, Bell J, Bradley RI, Evans C, Lark RM, Reynolds B, Smith P, Towers W (2009) Quantifying terrestrial carbon stocks: examining the spatial variation in two upland areas in the UK and a comparison to mapped estimates of soil carbon. Soil Use Manag 25:320–332
Gao Y, Mao L, C-Y M, Zhou P, J-J C, Y-E Z, W-J S (2010) Spatial characteristics of soil enzyme activities and microbial community structure under different land uses in Chongming Island, China: geostatistical modelling and PCR-RAPD method. Sci Total Environ 408:3251–3260
Gorham E (1991) Northern Peatlands—role in the carbon-cycle and probable responses to climatic warming. Ecol Appl 1:182–195
Gramss G, Voigt KD, Kirsche B (1999) Oxidoreductase enzymes liberated by plant roots and their effects on soil humic material. Chemosphere 38
Guilbault GG (1990) Practical fluorescence, 2nd edn. Marcel Dekker, New York
Gutknecht JLM, Goodman RM, Balser TC (2006) Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289:17–34
Hullo MF, Moszer I, Danchin A, Martin-Verstraete I (2001) CotA of Bacillus subtilis is a copper-dependent laccase. J Bacteriol 183
Jordan DB, Wagschal K (2010) Properties and applications of microbial beta-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium. Appl Microbiol Biotechnol 86
Kang H, Freeman C, Lock MA (1998) Trace gas emissions from a north Wales fen—role of hydrochemistry and soil enzyme activity. Water Air Soil Pollut 105:107–116
Kang HJ, Freeman C, Ashendon TW (2001) Effects of elevated CO2 on fen peat biogeochemistry. Sci Total Environ 279:45–50
Kang HJ, Freeman C, Park SS, Chun J (2005) N-Acetylglucosaminidase activities in wetlands: a global survey. Hydrobiologia 532
Kim S-Y, Kang H (2008) Effects of elevated CO2 on below-ground processes in temperate marsh microcosms. Hydrobiologia 605:123–130
Klose S, Bilen S, Tabatabai MA, Dick WA (2011) Sulfur cycle enzymes. In: Dick RP (ed) Methods of soil enzymology. Soil Science Society of America, Wisconsin
Kourtev PS, Ehrenfeld JG, Huang WZ (2002) Enzyme activities during litter decomposition of two exotic and two native plant species in hardwood forests of New Jersey. Soil Biol Biochem 34
Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer Science and Business Media, New York
Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368–371
Marx MC, Wood M, Jarvis SC (2001) A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil Biol Biochem 33:1633–1640
Mason HS (1948) The chemistry of melanin; mechanism of the oxidation of dihydroxyphenylalanine by tyrosinase. J Biol Chem 172:83–99
Mentzer JL, Goodman RM, Balser TC (2006) Microbial response over time to hydrologic and fertilization treatments in a simulated wet prairie. Plant Soil 284:85–100
Oshrain RL, Wiebe WJ (1979) Arylsulfatase activity in salt marsh soils. Appl Environ Microbiol 38:337–340
Pelaez F, Martinez MJ, Martinez AT (1995) Screening of 68 species of basidiomycetes for enzymes involved in lignin degradation. Mycol Res 99:37–42
Pind A, Freeman C, Lock MA (1994) Enzymatic degradation of phenolic materials in peatlands—measurement of Phenol Oxidase activity. Plant Soil 159:227–231
Pomerantz SH, Murthy VV (1974) Purification and properties of tyrosinases from vibrio-tyrosinaticus. Arch Biochem Biophys 160
Press MC, Henderson J, Lee JA (1985) Arylsulfatase activity in peat in relation to acidic deposition. Soil Biol Biochem 17:99–103
Prosser JA, Speir TW, Stott DE (2011) Soil oxidoreductases and FDA hydrolysis. In: Dick RP (ed) Methods of soil enzymology. Soil Science Society of America Inc., Wisconsin, pp 103–124
Siciliano SD, Lean DRS (2002) Methyltransferase: an enzyme assay for microbial methylmercury formation in acidic soils and sediments. Environ Toxicol Chem 21:1184–1190
Sinsabaugh RL (1994) Enzymatic analysis of microbial pattern and process. Biol Fertil Soils 17:69–74
Sinsabaugh RL, Findlay S (1995) Microbial-production, enzyme-activity, and carbon turnover in surface sediments of the Hudson River Estuary. Microbial Ecol 30:127–141
Sinsabaugh RL, Linkins AE (1990) Enzymatic and chemical-analysis of particulate organic-matter from a boreal river. Freshw Biol 23:301–309
Sinsabaugh RL, Antibus RK, Linkins AE, McClaugherty CA, Rayburn L, Repert D, Weiland T (1992) Wood decomposition over a 1st-order watershed—mass-loss as a function of lignocellulase activity. Soil Biol Biochem 24:743–749
Sinsabaugh RL, Osgood MP, Findlay S (1994) Enzymatic models for estimating decomposition rates and particulate detritus. J N Am Benthol Soc 13:160–169
Sinsabaugh RL, Klug MJ, Collins HP, Yeager PE, Peterson SO (1999) Characterizing soil microbial communities. In: Robertson GP, Coleman DC, Bledsoe CS, Sollins P (eds) Standard soil methods for long-term ecological research. Oxford University Press, New York
Sinsabaugh, R. L., Lauber, C. L., Weintraub, M. N., Ahmed, B., Allison, S. D., Crenshaw, C., Contosta, A. R., Cusack, D., Frey, S., Gallo, M. E., Gartner, T. B., Hobbie, S. E., Holland, K., Keeler, B. L., Powers, J. S., Stursova, M., Takacs-Vesbach, C., Waldrop, M. P., Wallenstein, M. D., Zak, D. R. and Zeglin, L. H. (2008), Stoichiometry of soil enzyme activity at global scale. Ecology Letters, 11:1252–1264. doi: 10.1111/j.1461-0248.2008.01245.x
Sinsabaugh RL, Hill BH, Shah JJF (2009) Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature 462:795–798
Song K-Y, Zoh K-D, Kang H (2007) Release of phosphate in a wetland by changes in hydrological regime. Sci Total Environ 380:13–18
Tallis, J H, (1987) Fire and flood at Holme Moss: Erosion processes in an upland blanket mire. Journal of Ecology. 75:(4)1099–1129
Thomas VK, Kuehn KA, Francoeur SN (2009) Effects of UV radiation on wetland periphyton: algae, bacteria, and extracellular polysaccharides. J Freshw Ecol 24:315–326
Turner BL, Baxter R, Whitton BA (2002) Seasonal phosphatase activity in three characteristic soils of the English uplands polluted by long-term atmospheric nitrogen deposition. Environ Pollut 120
Whitehead PG, Crossman J (2012) Macronutrient cycles and climate change: key science areas and an international perspective. Sci Total Environ 434:13–17
Williams CJ, Shingara EA, Yavitt JB (2000) Phenol oxidase activity in peatlands in New York State: response to summer drought and peat type. Wetlands 20
Williamson J, Mills G, Freeman C (2010) Species-specific effects of elevated ozone on wetland plants and decomposition processes. Environ Pollut 158:1197–1206
Wittmann C, Kahkonen MA, Ilvesniemi H, Kurola J, Salkinoja-Salonen MS (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 Biol Biochem 36
Woods AF (1899) The destruction of chlorophyll by oxidizing enzymes
Ye R, Wright AL, Inglett K, Wang Y, Ogram AV, Reddy KR (2009) Land-use effects on soil nutrient cycling and microbial community dynamics in the Everglades Agricultural Area, Florida. Commun Soil Sci Plant Anal 40:2725–2742
Acknowledgments
This research was funded by the Knowledge and Economy Skills Scholarship, which is part funded by the European Social Fund through the European Union’s Convergence programme and administered by the Welsh Assembly Government. We would also like to thank George Meyrick of Energy and Environment Business Services for supporting this research.
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Dunn, C., Jones, T.G., Girard, A. et al. Methodologies for Extracellular Enzyme Assays from Wetland Soils. Wetlands 34, 9–17 (2014). https://doi.org/10.1007/s13157-013-0475-0
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DOI: https://doi.org/10.1007/s13157-013-0475-0