Otwarty dostęp

Biochemical methods for the evaluation of the functional and structural diversity of microorganisms in the soil environment


Zacytuj

Błońska E.: Enzymy glebowe i ich znaczenie w ocenie aktyw- ności biologicznej gleb leśnych na przykładzie rezerwatów przy- rody nizin i wyżyn Polski. Roczniki Gleboznawcze, Warszawa, LXII, 4, 163–172 (2011)Search in Google Scholar

Casida L.E. Jr., Klein D.A., Santoro T.: Soil dehydrogenase activity. Soil Sci. 98, 371–376 (1964)Search in Google Scholar

Deng S., Kang H., Freeman C.: Microplate Fluorimetric Assay of Soil Enzymes (w) Methods of Soil Enzymology, red. R.P. Dick, Soil Science Society of America, Madison, 2011, s. 311–31510.2136/sssabookser9.c14Search in Google Scholar

Dick W.A.: Development of a Soil Enzyme Reaction Assay (w) Methods of Soil Enzymology, red. R.P. Dick, Soil Science Society of America, Madison, 2011, s. 71–8410.2136/sssabookser9.c4Search in Google Scholar

Ding C.H., He J.: Effect of antibiotics in the environment on microbial populations. Appl. Microbiol. Biotechnol.87, 925–941 (2010)10.1007/s00253-010-2649-5Search in Google Scholar

Dmitrzak-Węglarz M., Hauser J.: Wykorzystanie badań proteo- micznych w poszukiwaniu markerów biologicznych dla chorób psychicznych. Via Medica, 3, 118–127 (2006)Search in Google Scholar

Dunfield K.E.: Lipid-Based Community Analysis (w) Soil Sampling and Methods of Analysis, red. M.R. Carter, E.G. Gregorich, 2nd Edition, CRC Press, Taylor& Francis Group, 2008, s. 557–56710.1201/9781420005271.ch42Search in Google Scholar

Eivazi F., Tabatabai M.A.: Phosphatases in soils. Soil Biol. Bio- chem. 9, 167–172 (1977)Search in Google Scholar

Floch C., Chevremont A.C., Joanico K., Capowiez Y., Criquet S.: Indicators of pesticide contamination: Soil enzyme compared to functional diversity of bacterial communities via Biolog®Ecoplates. Eur. J. Soil Biol.47, 256–263 (2011)10.1016/j.ejsobi.2011.05.007Search in Google Scholar

Frankenberger W.T., Tabatabai M.A.: Amidase activity in soils. I. Method of assay. Soil Sci. Soc. Am. J.44, 282–287 (1980)10.2136/sssaj1980.03615995004400020016xSearch in Google Scholar

Freney J.R., Williams C.H.: The sulphur cycle in soil (w) The global biogeochemical sulfur cycle, red. M.V. Ivanov, J.R. Freney, CSOPE 19, John Wiley& Sons, New York, 1983, s. 129–201Search in Google Scholar

Friedel J.K., Mälter K., Fischer W.R.: Comparison and improvement of methods for determining soil dehydrogenase activity by using triphenyltetrazolium chloride and iodonitrotetrazolium chloride.Biol. Fertil. Soils. 18, 292–296 (1994)Search in Google Scholar

Furtak K., Gajda A.M.: Activity of dehydrogenases as an indicator of soil environment quality. Pol. J. Soil Sci.50, 1, 33– 40 (2017)Search in Google Scholar

Furtak K.: Analiza profilu metabolicznego populacji mikroorga- nizmów z zastosowaniem techniki ECOplate Biolog (w) Badania i Rozwój Młodych Naukowców w Polsce, Nauki Przyrodnicze, red. M. Panfil, Wydawnictwo Młodzi Naukowcy, Poznań, 2017, Część I, s. 31–37Search in Google Scholar

Gajda A.M.: Mikrobiologiczne i biochemiczne wskaźniki jakości gleb pod pszenicą w zależności od systemu uprawy roli. Mono- grafie i Rozprawy Naukowe, IUNG-PIB, 46, Puławy, 2015Search in Google Scholar

Gajda A.M., Czyż E.A., Stanek-Tarkowska J., Dexter A.R., Fur- tak K.M., Grządziel J.: Effects of long-term tillage practices on the quality of soil under winter wheat. Plant Soil Environ.63, 5, 236–242 (2017)Search in Google Scholar

Gałązka A., Łyszcz M., Abrymczyk B., Furtak K., Grządziel J., Czaban J., Pikulicka A.: Bioróżnorodnośćśrodowiska glebowego – przegląd parametrów i metod w analizach różnorodności bio- logicznej gleby. Monografie i Rozprawy Naukowe, IUNG-PIB, 49, Puławy, 2016Search in Google Scholar

Garland J.L., Mills A.: Classification and characterization of heterotrophic microbial communities on the basis or patterns of community level sole carbon source utilization: Appl. Environ. Microbiol.57, 2351 (1991)10.1128/aem.57.8.2351-2359.1991Search in Google Scholar

Haack S.K., Garchow H., Odelson D.A., Forney L.J., Klug M.J.: Accuracy, reproducibility, and interpretation of Fatty Acid methyl ester profiles of model bacterial communities. Appl. Environ. Microbial. 60, 7, 2483–2493 (1994)Search in Google Scholar

Hames D.B., Hooper N.M.: Biochemia-krótkie wykłady. Wyd. Naukowe PWN, 2009, s. 68–71Search in Google Scholar

Hatzinger P.B., Palmer P., Smith R.L., Pe Arrieta C.T., Yoshi- nari T.: Applicability of tetrazolium salts for the measurement of respiratory activity and viability of groundwater bacteria. J. Microbiol. Meth.52, 47–58 (2003)10.1016/S0167-7012(02)00132-XSearch in Google Scholar

Hoffman G., Teicher K.: Ein kolorimetrisches Verfahren zur Bestimmung der Ureaseaktivität in Böden. Zeit. Pflanzenerna- ehr. Dung. Bodenkunde, 95, 55–63 (1961)10.1002/jpln.19610950107Search in Google Scholar

Killham K., Rashid M.A.: Assay of activity of a soil deaminase. Plant Soil, 92, 15–21 (1986)10.1007/BF02372261Search in Google Scholar

Kim M.R., Kim C.W.: Human blood plasma preparation for two-dimensional gel electrophoresis. J. Chromatogr.849, 203–210 (2007)10.1016/j.jchromb.2006.11.046Search in Google Scholar

Kozdrój J.: Metagenom –źródło nowej informacji o mikroorga- nizmach glebowych. Post. Mikrobiol.52, 2, 185–200 (2013)Search in Google Scholar

Ladd J.N., Butler J.H.A.: Short-term assays of soil proteolytic enzyme activities using proteins and dipeptide derivatives as substrate. Soil Biol. Biochem. 4, 19–30 (1972)Search in Google Scholar

Ladd J.N., Jackson R.B.: Biochemistry of ammonification (w) Nitrogen in agricultural soils red. F.J. Stevenson, Am. Soc. Agron. Madison, 1982, s. 173–22810.2134/agronmonogr22.c5Search in Google Scholar

Lechevalier M.P.: Lipids in bacterial taxonomy (w) Practical handbook of microbiology, red. O’Leary W.M., CRC, Boca Raton, 1989, s. 455–561Search in Google Scholar

Liu F., Wu J., Ying G.G., Luo Z., Feng H.: Changes in functional diversity of soil microbial community with addition of antibiotics sulfamethoxazole and chlortetracycline. Appl. Microbiol. Biotechnol.95, 1615–1623 (2012)10.1007/s00253-011-3831-0Search in Google Scholar

Lv T., Zhang Y., Carvalho P.N., Zhang L., Button M., Arias C.A., Weber K.P., Brix H.: Microbial community metabolic function in constructed wetland mesocosms treating the pesticides ima- zalil and tebuconazole. Ecol. Eng.98, 378–387 (2017)10.1016/j.ecoleng.2016.07.004Search in Google Scholar

Malosso E., English L., Hopkins D.W., O’Donnell A.G.: Community level physiological profile response to plant residue additions in Antarctic soils. Biol. Fertil. Soils. 42, 60–65 (2005)Search in Google Scholar

Marchut-Mikołajczyk O., Kwapisz E., Antczak T.: Enzymatyczna bioremediacja ksenobiotyków. Inżynieria i Ochrona Środowiska, 16, 39– 55 (2013)Search in Google Scholar

Mocek-Płóciniak A.: Wykorzystanie aktywności enzymatycznej do oceny wpływu antropogenicznych zmian wywołanych przez metale ciężkie w środowisku glebowym. Nauka Przyr. Technol. 4, 86 (2010)Search in Google Scholar

Nannipieri P., Ascher J. Ceccherini M.T.; Landi L., Pietra- mellara G., Renella G.: Microbial diversity and soil function. Eur. J. Soil Sci.54, 655–670 (2003)Search in Google Scholar

O’Farrell P.H.: High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem.250, 4007–4021 (1975)10.1016/S0021-9258(19)41496-8Search in Google Scholar

Olsson P.A., Larsson L., Bago B., Wallander H., van Aarle I.M.: Ergosterol and fatty acids for biomass estimation of mycorrhizal fungi. New Phytologist, 159, 1, 7–10 (2003)10.1046/j.1469-8137.2003.00810.xSearch in Google Scholar

Olsson S., Persson P.: The composition of bacterial populations in soil fractions differing in their degree an adherence to barley roots. Appl. Soil. Ecol.12, 205–215 (1999)10.1016/S0929-1393(99)00010-4Search in Google Scholar

Pennanen T., Perkiomaki J., Kiikkila O., Vanhala P., Neuvonen S., Fritze H: Prolonged, simulated acid rain and heavy metal deposition: separated and combined effects on forest soil microbial community structure. FEMS Microbiol. Ecol.27, 291–300 (1998)10.1111/j.1574-6941.1998.tb00545.xSearch in Google Scholar

Pritsch K., Raidl S., Marksteiner E., Blaschke H., Agerer R., Schloter M., Hartmann A.: A rapid and highly sensitive method for measuring enzyme activities in single mycorrhizal tips using 4-methylumbelliferone-labelled fluorogenic substrates in a microplate system. J. Microbiol. Methods.58, 233–241 (2004)10.1016/j.mimet.2004.04.00115234521Search in Google Scholar

Prosser J.A., Speir T.W., Stott D.E.: Soil Oxidoreductases and FDA Hydrolysis (w) Methods of Soil Enzymology, red. R.P. Dick, SSSA Book Series, no. 9, Soil Science Society of Amercica, Madison, USA, 2011, s. 103–124 4.1 Protein Data Bank (PDB): Protein-only Structures Released Per Year, https://www.rcsb.org/pdb (18.01.2018)10.2136/sssabookser9.c6Search in Google Scholar

Rocha E.P.: The organization of the bacterial genome. Annu Rev. Genet.42, 211–223 (2008)10.1146/annurev.genet.42.110807.091653Search in Google Scholar

Ross M., Goberna M., Pascual J.A., Klammer S., Insam H.: 16S rDNA analysis reveals low microbial diversity in community level physiological profile assays. J. Microb. Meth.72, 221–226 (2008)10.1016/j.mimet.2008.01.003Search in Google Scholar

Scherer-Lorenzen M., Palmborg C., Prinz A., Schulze E.D.: The role of plant diversity and composition for nitrate leaching in grasslands. Ecology, 84, 6, 1539–1552 (2003)10.1890/0012-9658(2003)084[1539:TROPDA]2.0.CO;2Search in Google Scholar

Smithwick E.A.H., Turner M.G., Metzger K.L., Balser T.C.: Variation in NH + mineralization and microbial communities 4 with stand age in lodgepole pine (Pinus contorta) forests, Yellowstone National Park (USA). Soil Biol. Biochem.37, 1546–1559 (2005)10.1016/j.soilbio.2005.01.016Search in Google Scholar

Sonck K.A., Kint G., Schoofs G., Vander Wauven C., Vander- leyden J., De Keersmaecker S.C.: The proteome of Salmonella typhimurium grown under in vivo-mimicking conditions. Proteomics, 9, 565–579 (2009)10.1002/pmic.200700476Search in Google Scholar

Tabatabai M.A., Bremner J.M.: Factors affecting soil arylsulfatase activity. Soil Sei. Soc. Amer. Proc.34, 427–429 (1970)10.2136/sssaj1970.03615995003400030023xSearch in Google Scholar

Tabatabai M.A., Bremner J.M.: Use of p-nitrophenyl phosphate for assay of soil phosphatase activity. Soil Biol. Biochem.1, 301– 307 (1969)10.1016/0038-0717(69)90012-1Search in Google Scholar

Tabatabai M.A., Dick W.A.: Enzymes in soil: Research and developments in measuring activities (w) Enzymes in the Environment, red. R.G. Bums, R.P. Dick, Marcel Dekker, New York, 2002, 21, s. 567–996Search in Google Scholar

Wagg C., Bender S.F., Widmerc F., van der Heijdena M.G.A.: Soil biodiversity and soil community composition determine ecosystem multifunctionality. P. Natl. Acad. Sci. USA, 111, 14, 5266–5270 (2014)Search in Google Scholar

Weber K.P., Legge R.L.: Community-level physiological profiling. Methods Mol Biol. 599, 263–281 (2010)10.1007/978-1-60761-439-5_16Search in Google Scholar

Weber K.P., Legge R.L.: One-dimensional metric for tracking bacterial community divergence using sole carbon source utilization patterns, J. Microbiol. Meth.79, 55–61 (2009)10.1016/j.mimet.2009.07.020Search in Google Scholar

Welker M.: Proteomics for routine identification of microorganisms. Proteomics, 11, 3143–3153 (2011)10.1002/pmic.201100049Search in Google Scholar

Wolff S., Otto A., Albrecht D., Zeng J.S., Buttner K., Gluck- mann M., Hecker M., Becher D.: Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study. Mol. Cell Proteomics, 5, 1183–1192 (2006)10.1074/mcp.M600069-MCP20016552027Search in Google Scholar

Wu W., Zhang H.H.: Analysis of gene expression at the proteo- mic level (w) Gene Biotechnology, red. W. Wu, M.J. Welsh, P.B. Kaufman, H.H. Zhang, CRC Press LLC, 2004, s. 265–28710.1201/9780203489277Search in Google Scholar

Zarag S.M., Gupta N., Mir R.A., Rai V.: Shift from Gel Based to Gel Free Proteomics to Unlock Unknown Regulatory Network in Plants: A Comprehensive Review. J. Adv. Res. Biotech. 1, 2, 19 (2016)10.15226/2475-4714/1/2/00107Search in Google Scholar

Zelles L.: Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fert. Soils.29, 111–129 (1999)10.1007/s003740050533Search in Google Scholar

Zhang W., Li F., Nie L.: Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology, 156, 287–301 (2010)10.1099/mic.0.034793-019910409Search in Google Scholar

eISSN:
2545-3149
Języki:
Angielski, Polski
Częstotliwość wydawania:
4 razy w roku
Dziedziny czasopisma:
Life Sciences, Microbiology and Virology