Fungal extracellular enzyme activity

Extracellular enzymes or exoenzymes are synthesized inside the cell and then secreted outside the cell, where their function is to break down complex macromolecules into smaller units to be taken up by the cell for growth and assimilation.^[1] These enzymes degrade complex organic matter such as cellulose and hemicellulose into simple sugars that enzyme-producing organisms use as a source of carbon, energy, and nutrients.^[2] Grouped as hydrolases, lyases, oxidoreductases and transferases,^[1] these extracellular enzymes control soil enzyme activity through efficient degradation of biopolymers.

Birch polypore (Piptoporus betulinus) - geograph.org.uk - 1553987

Plant residues, animals and microorganisms enter the dead organic matter pool upon senescence^[3] and become a source of nutrients and energy for other organisms. Extracellular enzymes target macromolecules such as carbohydrates (cellulases), lignin (oxidases), organic phosphates (phosphatases), amino sugar polymers (chitinases) and proteins (proteases)^[4] and break them down into soluble sugars that are subsequently transported into cells to support heterotrophic metabolism.^[1]

Biopolymers are structurally complex and require the combined actions of a community of diverse microorganisms and their secreted exoenzymes to depolymerize the polysaccharides into easily assimilable monomers. These microbial communities are ubiquitous in nature, inhabiting both terrestrial and aquatic ecosystems. The cycling of elements from dead organic matter by heterotrophic soil microorganisms is essential for nutrient turnover and energy transfer in terrestrial ecosystems.^[5] Exoenzymes also aid digestion in the guts of ruminants,^[6] termites,^[7] humans and herbivores. By hydrolyzing plant cell wall polymers, microbes release energy that has the potential to be used by humans as biofuel.^[8] Other human uses include waste water treatment,^[9] composting^[10] and bioethanol production.^[11]

Factors influencing extracellular enzyme activity

Extracellular enzyme production supplements the direct uptake of nutrients by microorganisms and is linked to nutrient availability and environmental conditions. The varied chemical structure of organic matter requires a suite of extracellular enzymes to access the carbon and nutrients embedded in detritus. Microorganisms differ in their ability to break down these different substrates and few organisms have the potential to degrade all the available plant cell wall materials.^[12] To detect the presence of complex polymers, some exoenzymes are produced constitutively at low levels, and expression is upregulated when the substrate is abundant.^[13] This sensitivity to the presence of varying concentrations of substrate allows fungi to respond dynamically to the changing availability of specific resources. Benefits of exoenzyme production can also be lost after secretion because the enzymes are liable to denature, degrade or diffuse away from the producer cell.

Enzyme production and secretion is an energy intensive process^[14] and, because it consumes resources otherwise available for reproduction, there is evolutionary pressure to conserve those resources by limiting production.^[15] Thus, while most microorganisms can assimilate simple monomers, degradation of polymers is specialized, and few organisms can degrade recalcitrant polymers like cellulose and lignin.^[16] Each microbial species carries specific combinations of genes for extracellular enzymes and is adapted to degrade specific substrates.^[12] In addition, the expression of genes that encode for enzymes is typically regulated by the availability of a given substrate. For example, presence of a low-molecular weight soluble substrate such as glucose will inhibit enzyme production by repressing the transcription of associated cellulose-degrading enzymes.^[17]

Environmental conditions such as soil pH,^[18] soil temperature,^[19] moisture content,^[20] and plant litter type and quality^[21] have the potential to alter exoenzyme expression and activity. Variations in seasonal temperatures can shift metabolic needs of microorganisms in synchrony with shifts in plant nutrient requirements.^[22] Agricultural practices such as fertilizer amendments and tillage can change the spatial distribution of resources, resulting in altered exoenzyme activity in the soil profile.^[23] Introduction of moisture exposes soil organic matter to enzyme catalysis^[24] and also increases loss of soluble monomers via diffusion. Additionally, osmotic shock resulting from water potential changes can impact enzyme activities as microbes redirect energy from enzyme production to synthesizing osmolytes to maintain cellular structures.

Extracellular enzyme activity in fungi during plant decomposition

 

Plant cell showing primary and secondary wall by CarolineDahl

Most of the extracellular enzymes involved in polymer degradation in leaf litter and soil have been ascribed to fungi.^[25][26][27] By adapting their metabolism to the availability of varying amounts of carbon and nitrogen in the environment, fungi produce a mixture of oxidative and hydrolytic enzymes to efficiently break down lignocelluloses like wood. During plant litter degradation, cellulose and other labile substrates are degraded first^[28] followed by lignin depolymerization with increased oxidative enzyme activity and shifts in microbial community composition.

In plant cell walls, cellulose and hemicellulose is embedded in a pectin scaffold^[29] that requires pectin degrading enzymes, such as polygalacturonases and pectin lyases to weaken the plant cell wall and uncover hemicellulose and cellulose to further enzymatic degradation.^[30] Degradation of lignin is catalyzed by enzymes that oxidase aromatic compounds, such as phenol oxidases, peroxidases and laccases. Many fungi have multiple genes encoding lignin-degrading exoenzymes.^[31]

Most efficient wood degraders are saprotrophic ascomycetes and basidiomycetes. Traditionally, these fungi are classified as brown rot (Ascomycota and Basidiomycota), white rot (Basidiomycota) and soft rot (Ascomycota) based on the appearance of the decaying material.^[2] Brown rot fungi preferentially attack cellulose and hemicellulose;^[32] while white rot fungi degrade cellulose and lignin. To degrade cellulose, basidiomycetes employ hydrolytic enzymes, such as endoglucanases, cellobiohydrolase and β-glucosidase.^[33] Production of endoglucanases is widely distributed among fungi and cellobiohydrolases have been isolated in multiple white-rot fungi and in plant pathogens.^[33] β-glucosidases are secreted by many wood-rotting fungi, both white and brown rot fungi, mycorrhizal fungi^[34] and in plant pathogens. In addition to cellulose, β-glucosidases can cleave xylose, mannose and galactose.^[35]

In white-rot fungi such as Phanerochaete chrysosporium, expression of manganese-peroxidase is induced by the presence of manganese, hydrogen peroxide and lignin,^[36] while laccase is induced by availability of phenolic compounds.^[37] Production of lignin-peroxidase and manganese-peroxidase is the hallmark of basidiomycetes and is often used to assess basidiomycete activity, especially in biotechnology applications.^[38] Most white-rot species also produce laccase, a copper-containing enzyme that degrades polymeric lignin and humic substances.^[39]

Brown-rot basidiomycetes are most commonly found in coniferous forests, and are so named because they degrade wood to leave a brown residue that crumbles easily. Preferentially attacking hemicellulose in wood, followed by cellulose, these fungi leave lignin largely untouched.^[40] The decayed wood of soft-rot Ascomycetes is brown and soft. One soft-rot Ascomycete, Trichoderma reesei, is used extensively in industrial applications as a source for cellulases and hemicellulases.^[41] Laccase activity has been documented in T. reesei, in some species in the Aspergillus genus^[42] and in freshwater ascomycetes.^[43]

Measuring fungal extracellular enzyme activity in soil, plant litter, and other environmental samples

 

Electronic PH meter

Methods for estimating soil enzyme activities involve sample harvesting prior to analysis, mixing of samples with buffers and the use of substrate. Results can be influenced by: sample transport from field-site, storage methods, pH conditions for assay, substrate concentrations, temperature at which the assay is run, sample mixing and preparation.^[44]

For hydrolytic enzymes, colorimetric assays are required that use a p-nitrophenol (p-NP)-linked substrate,^[45] or fluorometric assays that use a 4-methylumbelliferone (MUF)-linked substrate.^[46]

Oxidative enzymes such as phenol oxidase and peroxidase mediate lignin degradation and humification.^[47] Phenol oxidase activity is quantified by oxidation of L-3, 4-dihydoxyphenylalanine (L-DOPA), pyrogallol (1, 2, 3-trihydroxybenzene), or ABTS (2, 2’-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid). Peroxidase activity is measured by running the phenol oxidase assay concurrently with another assay with L-DOPA and hydrogen peroxide (H₂O₂) added to every sample.^[48] The difference in measurements between the two assays is indicative of peroxidase activity. Enzyme assays typically apply proxies that reveal exo-acting activities of enzymes. Exo-acting enzymes hydrolyze substrates from the terminal position. While activity of endo-acting enzymes which break down polymers midchain need to be represented by other substrate proxies. New enzyme assays aim to capture the diversity of enzymes and assess the potential activity of them in a more clear way.^[49][50][51]

With newer technologies available, molecular methods to quantify abundance of enzyme-coding genes are used to link enzymes with their producers in soil environments.^[52][53] Transcriptome analyses are now employed to examine genetic controls of enzyme expression,^[54] while proteomic methods can reveal the presence of enzymes in the environment and link to the organisms producing them.^[55]

Process	Enzyme	Substrate
Cellulose-degradation	Cellobiohydrolase β-glucosidase	pNP, MUF^[33]^[56]
Hemicellulose-degradation	β-glucosidases Esterases	pNP, MUF^[57]^[58]
Polysaccharide-degradation	α-glucosidases N-acetylglucosaminidase	pNP, MUF^[59]
Lignin-degradation	Mn-peroxidase Laccase (polyphenol oxidase) Peroxidase	Pyrogallol, L-DOPA, ABTS^[38] L-DOPA, ABTS^[39]

Applications of fungal extracellular enzymes

Application	Enzymes & their uses
Paper production	Cellulases – improve paper quality and smooth fibers^[60] Laccases – soften paper and improving bleaching^[61]
Biofuel generation	Cellulases – for production of renewable liquid fuels^[62]
Dairy industry	Lactase – part of β-glucosidase family of enzymes and can break down lactose to glucose and galactose Pectinases – in the manufacture of yogurt
Brewing industry   Black Sheep Brewery Tour	Beer production and malting^[63]
Fruit and jam manufacturing	Pectinases, cellulases – to clarify fruit juices and form jams
Bioremediation	Laccases – as biotransformers to remove nonionic surfactants^[64]^[65]
Waste water treatment	Peroxidases - removal of pollutants by precipitation^[66]^[67]
Sludge treatment	Lipases - used in degradation of particulate organic matter^[68]
Phytopathogen management	Hydrolytic enzymes produced by fungi, e.g. Fusarium graminearum, pathogen on cereal grains resulting in economic losses in agriculture ^[69]
Resource management Water retention	Soil aggregates and water infiltration influence enzyme activity^[70]^[71]
Soil fertility and plant production	Use of enzyme activity as indicator of soil quality^[71]^[72]
Composting	Impacts of composting municipal solid waste on soil microbial activity^[10]
Soil organic matter stability	Impact of temperature and soil respiration on enzymatic activity and its effect on soil fertility^[73]
Climate change indicators Impact on soil processes	Potential increase in enzymatic activity leading to elevated CO2 emissions^[74]
Quantifying global warming outcomes	Predictions based on soil organic matter decomposition^[75] and strategies for mitigation^[76]
Impact of elevated CO2 on enzyme activity & decomposition	Understanding the implication of microbial responses and its impact on terrestrial ecosystem functioning^[77]

See also

• Enzymes
• Enzyme kinetics
• Enzyme assay
• List of enzymes
• Decomposition
• Plant litter
• Nutrient cycle

References

1. Sinsabaugh, R. S. (1994). "Enzymic analysis of microbial pattern and process". Biology and Fertility of Soils. 17 (1): 69–74. doi:10.1007/BF00418675. ISSN 0178-2762. S2CID 20188510.
2. Burns, Richard G.; DeForest, Jared L.; Marxsen, Jürgen; Sinsabaugh, Robert L.; Stromberger, Mary E.; Wallenstein, Matthew D.; Weintraub, Michael N.; Zoppini, Annamaria (2013). "Soil enzymes in a changing environment: Current knowledge and future directions". Soil Biology and Biochemistry. 58: 216–234. doi:10.1016/j.soilbio.2012.11.009. ISSN 0038-0717.
3. Cebrian, Just (1999). "Patterns in the Fate of Production in Plant Communities". The American Naturalist. 154 (4): 449–468. doi:10.1086/303244. ISSN 0003-0147. PMID 10523491. S2CID 4384243.
4. Allison, S.D.; et al. (2007). "Soil enzymes: linking proteomics and ecological processes". In Hurst, CJ.; Crawford, RL.; Garland, JL.; Lipson DA.; Mills, AL; Stetzenbach, LD (eds.). Manual of environmental microbiology (3rd ed.). Washington, DC: ASM. pp. 704–711. ISBN 978-1-55581-379-6.
5. Gessner, Mark O.; Swan, Christopher M.; Dang, Christian K.; McKie, Brendan G.; Bardgett, Richard D.; Wall, Diana H.; Hättenschwiler, Stephan (2010). "Diversity meets decomposition". Trends in Ecology & Evolution. 25 (6): 372–380. doi:10.1016/j.tree.2010.01.010. ISSN 0169-5347. PMID 20189677.
6. Krause, Denis O; Denman, Stuart E; Mackie, Roderick I; Morrison, Mark; Rae, Ann L; Attwood, Graeme T; McSweeney, Christopher S (2003). "Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics". FEMS Microbiology Reviews. 27 (5): 663–693. doi:10.1016/S0168-6445(03)00072-X. ISSN 0168-6445. PMID 14638418.
7. Warnecke, F; et al. (2007). "Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite" (PDF). Nature. 450 (7169): 560–565. Bibcode:2007Natur.450..560W. doi:10.1038/nature06269. PMID 18033299. S2CID 4420494.
8. Ragauskas, A. J. (2006). "The Path Forward for Biofuels and Biomaterials". Science. 311 (5760): 484–489. Bibcode:2006Sci...311..484R. doi:10.1126/science.1114736. ISSN 0036-8075. PMID 16439654. S2CID 9213544.
9. Shackle, V.; Freeman, C.; Reynolds, B. (2006). "Exogenous enzyme supplements to promote treatment efficiency in constructed wetlands". Science of the Total Environment. 361 (1–3): 18–24. Bibcode:2006ScTEn.361...18S. doi:10.1016/j.scitotenv.2005.09.032. ISSN 0048-9697. PMID 16213577.
10. Crecchio, Carmine; Curci, Magda; Pizzigallo, Maria D.R.; Ricciuti, Patrizia; Ruggiero, Pacifico (2004). "Effects of municipal solid waste compost amendments on soil enzyme activities and bacterial genetic diversity". Soil Biology and Biochemistry. 36 (10): 1595–1605. doi:10.1016/j.soilbio.2004.07.016. ISSN 0038-0717.
11. Wackett, Lawrence P (2008). "Biomass to fuels via microbial transformations". Current Opinion in Chemical Biology. 12 (2): 187–193. doi:10.1016/j.cbpa.2008.01.025. ISSN 1367-5931. PMID 18275861.
12. Allison, Steven D.; LeBauer, David S.; Ofrecio, M. Rosario; Reyes, Randy; Ta, Anh-Minh; Tran, Tri M. (2009). "Low levels of nitrogen addition stimulate decomposition by boreal forest fungi". Soil Biology and Biochemistry. 41 (2): 293–302. doi:10.1016/j.soilbio.2008.10.032. ISSN 0038-0717.
13. Klonowska, Agnieszka; Gaudin, Christian; Fournel, André; Asso, Marcel; Le Petit, Jean; Giorgi, Michel; Tron, Thierry (2002). "Characterization of a low redox potential laccase from the basidiomycete C30". European Journal of Biochemistry. 269 (24): 6119–6125. doi:10.1046/j.1432-1033.2002.03324.x. ISSN 0014-2956. PMID 12473107.
14. Schimel, J (2003). "The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model". Soil Biology and Biochemistry. 35 (4): 549–563. doi:10.1016/S0038-0717(03)00015-4. ISSN 0038-0717.
15. Allison, Steven D.; Weintraub, Michael N.; Gartner, Tracy B.; Waldrop, Mark P. (2010). "Evolutionary-Economic Principles as Regulators of Soil Enzyme Production and Ecosystem Function". Soil Enzymology. Soil Biology. Vol. 22. pp. 229–243. CiteSeerX 10.1.1.689.2292. doi:10.1007/978-3-642-14225-3_12. ISBN 978-3-642-14224-6. ISSN 1613-3382.
16. Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina; Kopecký, Jan; Valášková, Vendula; Větrovský, Tomáš; Žifčáková, Lucia; Šnajdr, Jaroslav; Rídl, Jakub; Vlček, Čestmír; Voříšková, Jana (2011). "Active and total microbial communities in forest soil are largely different and highly stratified during decomposition". The ISME Journal. 6 (2): 248–258. doi:10.1038/ismej.2011.95. ISSN 1751-7362. PMC 3260513. PMID 21776033.
17. Hanif, A (2004). "Induction, production, repression, and de-repression of exoglucanase synthesis in Aspergillus niger". Bioresource Technology. 94 (3): 311–319. doi:10.1016/j.biortech.2003.12.013. ISSN 0960-8524. PMID 15182839.
18. DeForest, Jared L.; Smemo, Kurt A.; Burke, David J.; Elliott, Homer L.; Becker, Jane C. (2011). "Soil microbial responses to elevated phosphorus and pH in acidic temperate deciduous forests". Biogeochemistry. 109 (1–3): 189–202. doi:10.1007/s10533-011-9619-6. ISSN 0168-2563. S2CID 97965526.
19. Wallenstein, Matthew D.; Haddix, Michelle L.; Lee, Daniel D.; Conant, Richard T.; Paul, Eldor A. (2012). "A litter-slurry technique elucidates the key role of enzyme production and microbial dynamics in temperature sensitivity of organic matter decomposition". Soil Biology and Biochemistry. 47: 18–26. doi:10.1016/j.soilbio.2011.12.009. ISSN 0038-0717.
20. Fioretto, A.; Papa, S.; Curcio, E.; Sorrentino, G.; Fuggi, A. (2000). "Enzyme dynamics on decomposing leaf litter of Cistus incanus and Myrtus communis in a Mediterranean ecosystem". Soil Biology and Biochemistry. 32 (13): 1847–1855. doi:10.1016/S0038-0717(00)00158-9. ISSN 0038-0717.
21. Waldrop, Mark P.; Zak, Donald R. (2006). "Response of Oxidative Enzyme Activities to Nitrogen Deposition Affects Soil Concentrations of Dissolved Organic Carbon". Ecosystems. 9 (6): 921–933. doi:10.1007/s10021-004-0149-0. ISSN 1432-9840. S2CID 10919578.
22. Finzi, Adrien C; Austin, Amy T; Cleland, Elsa E; Frey, Serita D; Houlton, Benjamin Z; Wallenstein, Matthew D (2011). "Responses and feedbacks of coupled biogeochemical cycles to climate change: examples from terrestrial ecosystems". Frontiers in Ecology and the Environment. 9 (1): 61–67. doi:10.1890/100001. hdl:11336/84335. ISSN 1540-9295. S2CID 2862965.
23. Poll, C.; Thiede, A.; Wermbter, N.; Sessitsch, A.; Kandeler, E. (2003). "Micro-scale distribution of microorganisms and microbial enzyme activities in a soil with long-term organic amendment". European Journal of Soil Science. 54 (4): 715–724. doi:10.1046/j.1351-0754.2003.0569.x. ISSN 1351-0754. S2CID 97005809.
24. Fierer, N; Schimel, JP (2003). "A proposed mechanism for the pulse of carbon dioxide production commonly observed following the rapid rewetting of a dry soil". Soil Science Society of America Journal. 67 (3): 798–805. Bibcode:2003SSASJ..67..798F. doi:10.2136/sssaj2003.0798. S2CID 2815843.
25. Boer, Wietse de; Folman, Larissa B.; Summerbell, Richard C.; Boddy, Lynne (2005). "Living in a fungal world: impact of fungi on soil bacterial niche development". FEMS Microbiology Reviews. 29 (4): 795–811. doi:10.1016/j.femsre.2004.11.005. ISSN 0168-6445. PMID 16102603.
26. Hättenschwiler, Stephan; Tiunov, Alexei V.; Scheu, Stefan (2005). "Biodiversity and Litter Decomposition in Terrestrial Ecosystems". Annual Review of Ecology, Evolution, and Systematics. 36 (1): 191–218. doi:10.1146/annurev.ecolsys.36.112904.151932. ISSN 1543-592X.
27. Baldrian, P (2009). "Microbial enzyme-catalyzed processes in soils and their analysis". Plant, Soil and Environment. 55 (9): 370–378. doi:10.17221/134/2009-PSE.
28. Berg, Björn (2000). "Litter decomposition and organic matter turnover in northern forest soils". Forest Ecology and Management. 133 (1–2): 13–22. doi:10.1016/S0378-1127(99)00294-7. ISSN 0378-1127.
29. Ridley, Brent L; O'Neill, Malcolm A; Mohnen, Debra (2001). "Pectins: structure, biosynthesis, and oligogalacturonide-related signaling". Phytochemistry. 57 (6): 929–967. Bibcode:2001PChem..57..929R. doi:10.1016/S0031-9422(01)00113-3. ISSN 0031-9422. PMID 11423142.
30. Lagaert, Stijn; Beliën, Tim; Volckaert, Guido (2009). "Plant cell walls: Protecting the barrier from degradation by microbial enzymes". Seminars in Cell & Developmental Biology. 20 (9): 1064–1073. doi:10.1016/j.semcdb.2009.05.008. ISSN 1084-9521. PMID 19497379.
31. Courty, P. E.; Hoegger, P. J.; Kilaru, S.; Kohler, A.; Buée, M.; Garbaye, J.; Martin, F.; Kües, U. (2009). "Phylogenetic analysis, genomic organization, and expression analysis of multi-copper oxidases in the ectomycorrhizal basidiomyceteLaccaria bicolor". New Phytologist. 182 (3): 736–750. doi:10.1111/j.1469-8137.2009.02774.x. ISSN 0028-646X. PMID 19243515. S2CID 23324645.
32. Martinez, AT; et al. (2005). "Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin". International Microbiology. 8 (3): 195–204. PMID 16200498.
33. Baldrian, Petr; Valášková, Vendula (2008). "Degradation of cellulose by basidiomycetous fungi". FEMS Microbiology Reviews. 32 (3): 501–521. doi:10.1111/j.1574-6976.2008.00106.x. ISSN 0168-6445. PMID 18371173.
34. Kusuda, Mizuho; Ueda, Mitsuhiro; Konishi, Yasuhito; Araki, Yoshihito; Yamanaka, Katsuji; Nakazawa, Masami; Miyatake, Kazutaka; Terashita, Takao (2006). "Detection of β-glucosidase as saprotrophic ability from an ectomycorrhizal mushroom, Tricholoma matsutake". Mycoscience. 47 (4): 184–189. doi:10.1007/s10267-005-0289-x. ISSN 1340-3540. S2CID 84906200.
35. Valaskova, V.; Baldrian, P. (2006). "Degradation of cellulose and hemicelluloses by the brown rot fungus Piptoporus betulinus - production of extracellular enzymes and characterization of the major cellulases". Microbiology. 152 (12): 3613–3622. doi:10.1099/mic.0.29149-0. ISSN 1350-0872. PMID 17159214.
36. Li D, Alic M, Brown JA, Gold MH (January 1995). "Regulation of manganese peroxidase gene transcription by hydrogen peroxide, chemical stress, and molecular oxygen". Appl. Environ. Microbiol. 61 (1): 341–5. Bibcode:1995ApEnM..61..341L. doi:10.1128/AEM.61.1.341-345.1995. PMC 167287. PMID 7887613.
37. Leonowicz, A; et al. (2001). "Fungal laccases: properties and activity on lignin". Journal of Basic Microbiology. 41 (3–4): 185–227. doi:10.1002/1521-4028(200107)41:3/4<185::aid-jobm185>3.0.co;2-t. PMID 11512451. S2CID 23523898.
38. Hofrichter, Martin (2002). "Review: lignin conversion by manganese peroxidase (MnP)". Enzyme and Microbial Technology. 30 (4): 454–466. doi:10.1016/S0141-0229(01)00528-2. ISSN 0141-0229.
39. Baldrian, Petr (2006). "Fungal laccases – occurrence and properties". FEMS Microbiology Reviews. 30 (2): 215–242. doi:10.1111/j.1574-4976.2005.00010.x. ISSN 0168-6445. PMID 16472305.
40. Hammel, Kenneth E.; Kapich, Alexander N.; Jensen, Kenneth A.; Ryan, Zachary C. (2002). "Reactive oxygen species as agents of wood decay by fungi". Enzyme and Microbial Technology. 30 (4): 445–453. doi:10.1016/S0141-0229(02)00011-X. ISSN 0141-0229. S2CID 96847091.
41. Kumar, Raj; Singh, Sompal; Singh, Om V. (2008). "Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives". Journal of Industrial Microbiology & Biotechnology. 35 (5): 377–391. doi:10.1007/s10295-008-0327-8. ISSN 1367-5435. PMID 18338189. S2CID 4830678.
42. Tamayo-Ramos, Juan Antonio; van Berkel, Willem JH; de Graaff, Leo H (2012). "Biocatalytic potential of laccase-like multicopper oxidases from Aspergillus niger". Microbial Cell Factories. 11 (1): 165. doi:10.1186/1475-2859-11-165. ISSN 1475-2859. PMC 3548707. PMID 23270588.
43. Junghanns, C. (2005). "Degradation of the xenoestrogen nonylphenol by aquatic fungi and their laccases". Microbiology. 151 (1): 45–57. doi:10.1099/mic.0.27431-0. ISSN 1350-0872. PMID 15632424.
44. German, Donovan P.; Weintraub, Michael N.; Grandy, A. Stuart; Lauber, Christian L.; Rinkes, Zachary L.; Allison, Steven D. (2011). "Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies". Soil Biology and Biochemistry. 43 (7): 1387–1397. doi:10.1016/j.soilbio.2011.03.017. ISSN 0038-0717.
45. Sinsabaugh, Robert L.; Linkins, Arthur E. (1990). "Enzymic and chemical analysis of particulate organic matter from a boreal river". Freshwater Biology. 23 (2): 301–309. doi:10.1111/j.1365-2427.1990.tb00273.x. ISSN 0046-5070.
46. 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 (12–13): 1633–1640. doi:10.1016/S0038-0717(01)00079-7. ISSN 0038-0717.
47. Sinsabaugh, Robert L. (2010). "Phenol oxidase, peroxidase and organic matter dynamics of soil". Soil Biology and Biochemistry. 42 (3): 391–404. doi:10.1016/j.soilbio.2009.10.014. ISSN 0038-0717.
48. DeForest, Jared L. (2009). "The influence of time, storage temperature, and substrate age on potential soil enzyme activity in acidic forest soils using MUB-linked substrates and l-DOPA". Soil Biology and Biochemistry. 41 (6): 1180–1186. doi:10.1016/j.soilbio.2009.02.029. ISSN 0038-0717.
49. Arnosti, C.; Bell, C.; Moorhead, D. L.; Sinsabaugh, R. L.; Steen, A. D.; Stromberger, M.; Wallenstein, M.; Weintraub, M. N. (January 2014). "Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs". Biogeochemistry. 117 (1): 5–21. doi:10.1007/s10533-013-9906-5. ISSN 0168-2563. S2CID 83660222.
50. Arnosti, Carol (2011-01-15). "Microbial Extracellular Enzymes and the Marine Carbon Cycle". Annual Review of Marine Science. 3 (1): 401–425. Bibcode:2011ARMS....3..401A. doi:10.1146/annurev-marine-120709-142731. ISSN 1941-1405. PMID 21329211.
51. Obayashi, Y; Suzuki, S (2008-03-26). "Occurrence of exo- and endopeptidases in dissolved and particulate fractions of coastal seawater". Aquatic Microbial Ecology. 50: 231–237. doi:10.3354/ame01169. ISSN 0948-3055.
52. Hassett, John E.; Zak, Donald R.; Blackwood, Christopher B.; Pregitzer, Kurt S. (2008). "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 (4): 728–739. doi:10.1007/s00248-008-9440-5. ISSN 0095-3628. PMID 18791762. S2CID 39272773.
53. Lauber, Christian L.; Sinsabaugh, Robert L.; Zak, Donald R. (2008). "Laccase Gene Composition and Relative Abundance in Oak Forest Soil is not Affected by Short-Term Nitrogen Fertilization". Microbial Ecology. 57 (1): 50–57. doi:10.1007/s00248-008-9437-0. ISSN 0095-3628. PMID 18758844. S2CID 15755901.
54. Morozova, Olena; Hirst, Martin; Marra, Marco A. (2009). "Applications of New Sequencing Technologies for Transcriptome Analysis". Annual Review of Genomics and Human Genetics. 10 (1): 135–151. doi:10.1146/annurev-genom-082908-145957. ISSN 1527-8204. PMID 19715439. S2CID 26713396.
55. Wallenstein, Matthew D.; Weintraub, Michael N. (2008). "Emerging tools for measuring and modeling the in situ activity of soil extracellular enzymes". Soil Biology and Biochemistry. 40 (9): 2098–2106. doi:10.1016/j.soilbio.2008.01.024. ISSN 0038-0717.
56. 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 (3): 506–577. doi:10.1128/MMBR.66.3.506-577.2002. ISSN 1092-2172. PMC 120791. PMID 12209002.
57. Collins, Tony; Gerday, Charles; Feller, Georges (2005). "Xylanases, xylanase families and extremophilic xylanases". FEMS Microbiology Reviews. 29 (1): 3–23. doi:10.1016/j.femsre.2004.06.005. ISSN 0168-6445. PMID 15652973.
58. Biely, Peter; Puchart, Vladimír (2006). "Recent progress in the assays of xylanolytic enzymes". Journal of the Science of Food and Agriculture. 86 (11): 1636–1647. Bibcode:2006JSFA...86.1636B. doi:10.1002/jsfa.2519. ISSN 0022-5142.
59. Seidl, Verena (2008). "Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions". Fungal Biology Reviews. 22 (1): 36–42. doi:10.1016/j.fbr.2008.03.002. ISSN 1749-4613.
60. Ravalason, Holy; Jan, Gwénaël; Mollé, Daniel; Pasco, Maryvonne; Coutinho, Pedro M.; Lapierre, Catherine; Pollet, Brigitte; Bertaud, Frédérique; Petit-Conil, Michel; Grisel, Sacha; Sigoillot, Jean-Claude; Asther, Marcel; Herpoël-Gimbert, Isabelle (2008). "Secretome analysis of Phanerochaete chrysosporium strain CIRM-BRFM41 grown on softwood". Applied Microbiology and Biotechnology. 80 (4): 719–733. doi:10.1007/s00253-008-1596-x. ISSN 0175-7598. PMID 18654772. S2CID 24813930.
61. Witayakran, Suteera; Ragauskas, Arthur J. (2009). "Modification of high-lignin softwood kraft pulp with laccase and amino acids". Enzyme and Microbial Technology. 44 (3): 176–181. doi:10.1016/j.enzmictec.2008.10.011. ISSN 0141-0229.
62. Wilson, David B (2009). "Cellulases and biofuels". Current Opinion in Biotechnology. 20 (3): 295–299. doi:10.1016/j.copbio.2009.05.007. ISSN 0958-1669. PMID 19502046.
63. Lalor, Eoin; Goode, Declan (2009). Brewing with Enzymes. pp. 163–194. doi:10.1002/9781444309935.ch8. ISBN 9781444309935. {{cite book}}: |journal= ignored (help)
64. Martin, C.; Corvini, P. F. X.; Vinken, R.; Junghanns, C.; Krauss, G.; Schlosser, D. (2009). "Quantification of the Influence of Extracellular Laccase and Intracellular Reactions on the Isomer-Specific Biotransformation of the Xenoestrogen Technical Nonylphenol by the Aquatic Hyphomycete Clavariopsis aquatica". Applied and Environmental Microbiology. 75 (13): 4398–4409. Bibcode:2009ApEnM..75.4398M. doi:10.1128/AEM.00139-09. ISSN 0099-2240. PMC 2704831. PMID 19429559.
65. Strong, P. J.; Claus, H. (2011). "Laccase: A Review of Its Past and Its Future in Bioremediation". Critical Reviews in Environmental Science and Technology. 41 (4): 373–434. Bibcode:2011CREST..41..373S. doi:10.1080/10643380902945706. ISSN 1064-3389. S2CID 96397441.
66. Durán, Nelson; Esposito, Elisa (2000). "Potential applications of oxidative enzymes and phenoloxidase-like compounds in wastewater and soil treatment: a review". Applied Catalysis B: Environmental. 28 (2): 83–99. doi:10.1016/S0926-3373(00)00168-5. ISSN 0926-3373.
67. M., Kissi; M., Mountadar; O., Assobhei; E., Gargiulo; G., Palmieri; P., Giardina; G., Sannia (2001). "Roles of two white-rot basidiomycete fungi in decolorisation and detoxification of olive mill waste water". Applied Microbiology and Biotechnology. 57 (1–2): 221–226. doi:10.1007/s002530100712. ISSN 0175-7598. PMID 11693925. S2CID 1662318.
68. Whiteley, C.G.; Burgess, J.E.; Melamane, X.; Pletschke, B.; Rose, P.D. (2003). "The enzymology of sludge solubilisation utilising sulphate-reducing systems: the properties of lipases". Water Research. 37 (2): 289–296. Bibcode:2003WatRe..37..289W. doi:10.1016/S0043-1354(02)00281-6. ISSN 0043-1354. PMID 12502058.
69. Kikot, G.E.; et al. (2009). "Contributions of cell wall degrading enzymes to pathogenesis of Fusarium graminearum: a review". Journal of Basic Microbiology. 49 (3): 231–241. doi:10.1002/jobm.200800231. PMID 19025875. S2CID 45168988.
70. Udawatta, Ranjith P.; Kremer, Robert J.; Garrett, Harold E.; Anderson, Stephen H. (2009). "Soil enzyme activities and physical properties in a watershed managed under agroforestry and row-crop systems". Agriculture, Ecosystems & Environment. 131 (1–2): 98–104. doi:10.1016/j.agee.2008.06.001. ISSN 0167-8809.
71. Powlson, D.S.; Gregory, P.J.; Whalley, W.R.; Quinton, J.N.; Hopkins, D.W.; Whitmore, A.P.; Hirsch, P.R.; Goulding, K.W.T. (2011). "Soil management in relation to sustainable agriculture and ecosystem services". Food Policy. 36: S72–S87. doi:10.1016/j.foodpol.2010.11.025. ISSN 0306-9192.
72. Trasar-Cepeda, C.; Leirós, M.C.; Gil-Sotres, F. (2008). "Hydrolytic enzyme activities in agricultural and forest soils. Some implications for their use as indicators of soil quality". Soil Biology and Biochemistry. 40 (9): 2146–2155. doi:10.1016/j.soilbio.2008.03.015. hdl:10261/49118. ISSN 0038-0717.
73. Jones, Chris D.; Cox, Peter; Huntingford, Chris (2003). "Uncertainty in climate-carbon-cycle projections associated with the sensitivity of soil respiration to temperature". Tellus B. 55 (2): 642–648. Bibcode:2003TellB..55..642J. doi:10.1034/j.1600-0889.2003.01440.x. ISSN 0280-6509.
74. Kirschbaum, Miko U. F. (2004). "Soil respiration under prolonged soil warming: are rate reductions caused by acclimation or substrate loss?". Global Change Biology. 10 (11): 1870–1877. Bibcode:2004GCBio..10.1870K. doi:10.1111/j.1365-2486.2004.00852.x. ISSN 1354-1013. S2CID 86293310.
75. Gillabel, Jeroen; Cebrian-Lopez, Beatriz; Six, Johan; Merckx, Roel (2010). "Experimental evidence for the attenuating effect of SOM protection on temperature sensitivity of SOM decomposition". Global Change Biology. 16 (10): 2789–2798. Bibcode:2010GCBio..16.2789G. doi:10.1111/j.1365-2486.2009.02132.x. ISSN 1354-1013. S2CID 86672269.
76. Macías, Felipe; Camps Arbestain, Marta (2010). "Soil carbon sequestration in a changing global environment". Mitigation and Adaptation Strategies for Global Change. 15 (6): 511–529. doi:10.1007/s11027-010-9231-4. ISSN 1381-2386. S2CID 153406514.
77. Zak, Donald R.; Pregitzer, Kurt S.; Burton, Andrew J.; Edwards, Ivan P.; Kellner, Harald (2011). "Microbial responses to a changing environment: implications for the future functioning of terrestrial ecosystems". Fungal Ecology. 4 (6): 386–395. doi:10.1016/j.funeco.2011.04.001. ISSN 1754-5048.

Further reading

• Enzyme nomenclature
• Richard P. Dick (ed.) 2011. Methods in Soil Enzymology. Soil Science Society of America, Wisconsin, USA ISBN 978-0-89118-854-4

External links

• ExplorEnz- searchable enzyme database to access the IUBMB Enzyme Nomenclature List
• BRENDA – database and related literature of known enzymes
• Enzyme structures
• ExPASy database for sequence data
• KEGG: Kyoto Encyclopedia of Genes and Genomes biochemical pathways and enzymes database
• MycoCLAP searchable database of fungal enzyme genes
• MetaCyc metabolic pathways of different organisms
• Pectinase 2019-09-15 at the Wayback Machine database for pectinase enzymes and their inhibitors