BIOCHEMICAL METHODS FOR THE EVALUATION OF THE FUNCTIONAL AND STRUCTURAL DIVERSITY OF MICROORGANISMS IN THE SOIL ENVIRONMENT

Publications

Share / Export Citation / Email / Print / Text size:

Postępy Mikrobiologii - Advancements of Microbiology

Polish Society of Microbiologists

Subject: Microbiology

GET ALERTS

ISSN: 0079-4252
eISSN: 2545-3149

DESCRIPTION

30
Reader(s)
81
Visit(s)
0
Comment(s)
0
Share(s)

SEARCH WITHIN CONTENT

FIND ARTICLE

Volume / Issue / page

Related articles

VOLUME 57 , ISSUE 2 (September 2018) > List of articles

BIOCHEMICAL METHODS FOR THE EVALUATION OF THE FUNCTIONAL AND STRUCTURAL DIVERSITY OF MICROORGANISMS IN THE SOIL ENVIRONMENT

Karolina Furtak * / Anna M. Gajda

Keywords : Biolog ECOplate, enzymatic activity, fatty acid analysis, microbiological activity, proteomic analysis

Citation Information : Postępy Mikrobiologii - Advancements of Microbiology. Volume 57, Issue 2, Pages 194-202, DOI: https://doi.org/10.21307/PM-2018.57.2.194

License : (CC BY-NC-ND 4.0)

Published Online: 23-May-2019

ARTICLE

ABSTRACT

Soil microbiome is composed of groups of microorganisms which are structurally and functionally very different. For many years soil microbiome has been the subject of numerous studies, but still is not fully recognized. It is well known that soil microorganisms play a key role in biogeochemical processes. Knowledge of their structural and functional diversity makes it possible to assess the condition of the soil environment, which is extremely important for agronomy and ecology. The agricultural and industrial activities of humans cause changes in soil activity, which should be monitored. There are many different research methods developed to analyze soil activity and microbiological soil diversity and refined by researchers from around the world in. Biochemical methods used to analyze microbial activity are based on the determination of the ability of microorganisms to synthesize, assimilate or decompose specific chemical compounds, as well as on the analysis of microbial cell components. This study presents the research methods used for the analysis of both: the functionality of microorganisms and their structural diversity.

Content not available PDF Share

FIGURES & TABLES

REFERENCES

1. Błońska E.: Enzymy glebowe i ich znaczenie w ocenie aktywności biologicznej gleb leśnych na przykładzie rezerwatów przyrody nizin i wyżyn Polski. Roczniki Gleboznawcze, Warszawa, LXII, 4, 163–172 (2011)

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

3. 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. 311–315

4. 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. 71–84

5. Ding C.H., He J.: Effect of antibiotics in the environment on microbial populations. Appl. Microbiol. Biotechnol. 87, 925–941 (2010)

6. Dmitrzak-Węglarz M., Hauser J.: Wykorzystanie badań proteomicznych w poszukiwaniu markerów biologicznych dla chorób psychicznych. Via Medica, 3, 118–127 (2006)

7. 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. 557–567

8. Eivazi F., Tabatabai M.A.: Phosphatases in soils. Soil Biol. Biochem. 9, 167–172 (1977)

9. 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. Frankenberger W.T., Tabatabai M.A.: Amidase activity in soils. I. Method of assay. Soil Sci. Soc. Am. J. 44, 282–287 (1980)

11. 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. 129–201

12. 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)

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

14. Furtak K.: Analiza profilu metabolicznego populacji mikroorganizmów 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. 31–37

15. Gajda A.M.: Mikrobiologiczne i biochemiczne wskaźniki jakości gleb pod pszenicą w zależności od systemu uprawy roli. Monografie i Rozprawy Naukowe, IUNG-PIB, 46, Puławy, 2015

16. Gajda A.M., Czyż E.A., Stanek-Tarkowska J., Dexter A.R., Furtak 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)

17. Gałązka A., Łyszcz M., Abrymczyk B., Furtak K., Grządziel J., Czaban J., Pikulicka A.: Bioróżnorodność środowiska glebowego – przegląd parametrów i metod w analizach różnorodności biologicznej gleby. Monografie i Rozprawy Naukowe, IUNG-PIB, 49, Puławy, 2016

18. 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)

19. 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)

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

21. Hatzinger P.B., Palmer P., Smith R.L., Pe Arrieta C.T., Yoshinari T.: Applicability of tetrazolium salts for the measurement of respiratory activity and viability of groundwater bacteria. J. Microbiol. Meth. 52, 47–58 (2003)

22. Hoffman G., Teicher K.: Ein kolorimetrisches Verfahren zur Bestimmung der Ureaseaktivität in Böden. Zeit. Pflanzenernaehr. Dung. Bodenkunde, 95, 55–63 (1961)

23. Killham K., Rashid M.A.: Assay of activity of a soil deaminase. Plant Soil, 92, 15–21 (1986)

24. Kim M.R., Kim C.W.: Human blood plasma preparation for two-dimensional gel electrophoresis. J. Chromatogr. 849, 203–210 (2007)

25. Kozdrój J.: Metagenom – źródło nowej informacji o mikroorganizmach glebowych. Post. Mikrobiol. 52, 2, 185–200 (2013)

26. 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)

27. Ladd J.N., Jackson R.B.: Biochemistry of ammonification (w) Nitrogen in agricultural soils red. F.J. Stevenson, Am. Soc. Agron. Madison, 1982, s. 173–228

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

29. 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)

30. 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 imazalil and tebuconazole. Ecol. Eng. 98, 378–387 (2017)

31. 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)

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

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

34. Nannipieri P., Ascher J. Ceccherini M.T.; Landi L., Pietramellara G., Renella G.: Microbial diversity and soil function. Eur. J. Soil Sci. 54, 655–670 (2003)

35. O’Farrell P.H.: High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021 (1975)

36. 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)

37. 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)

38. 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)

39. 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)

40. 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

41. Protein Data Bank (PDB): Protein-only Structures Released Per Year, https://www.rcsb.org/pdb (18.01.2018)

42. Rocha E.P.: The organization of the bacterial genome. Annu Rev. Genet. 42, 211–223 (2008)

43. 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)

44. 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)

45. Smithwick E.A.H., Turner M.G., Metzger K.L., Balser T.C.: Variation in NH4+ mineralization and microbial communities with stand age in lodgepole pine (Pinus contorta) forests, Yellowstone National Park (USA). Soil Biol. Biochem. 37, 1546–1559 (2005)

46. Sonck K.A., Kint G., Schoofs G., Vander Wauven C., Vanderleyden J., De Keersmaecker S.C.: The proteome of Salmonella typhimurium grown under in vivo-mimicking conditions. Proteomics, 9, 565–579 (2009)

47. Tabatabai M.A., Bremner J.M.: Factors affecting soil arylsulfatase activity. Soil Sei. Soc. Amer. Proc. 34, 427–429 (1970)

48. Tabatabai M.A., Bremner J.M.: Use of p-nitrophenyl phosphate for assay of soil phosphatase activity. Soil Biol. Biochem. 1, 301–307 (1969)

49. 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. 567–996

50. 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)

51. Weber K.P., Legge R.L.: Community-level physiological profiling. Methods Mol Biol. 599, 263–281 (2010)

52. 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)

53. Welker M.: Proteomics for routine identification of microorganisms. Proteomics, 11, 3143–3153 (2011)

54. Wolff S., Otto A., Albrecht D., Zeng J.S., Buttner K., Gluckmann M., Hecker M., Becher D.: Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study. Mol. Cell Proteomics, 5, 1183–1192 (2006)

55. Wu W., Zhang H.H.: Analysis of gene expression at the proteomic level (w) Gene Biotechnology, red. W. Wu, M.J. Welsh, P.B. Kaufman, H.H. Zhang, CRC Press LLC, 2004, s. 265–287

56. 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)

57. 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)

58. Zhang W., Li F., Nie L.: Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology, 156, 287–301 (2010)

EXTRA FILES

COMMENTS