Skip to main content
SpringerLink
Log in

Development of soil microbiology methods: from respirometry to molecular approaches

  • Review
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

This review deals with techniques and methods used in the study of the function and development of microorganisms occurring in soil with emphasis on the contributions of Czech Academician Ivan Málek and his coworkers or fellows (Jiří Macura, František Kunc) to the development of basic techniques used in soil microbiology. Early studies, including batch cultivation and respirometric techniques, as well as later developments of percolation and continuous-flow methods of cultivation of soil microorganisms are discussed. Recent developments in the application of analytical chemistry (HPLC or GC) and of molecular biological techniques to ecological questions that have revolutionized concepts in soil microbiology and microbial ecology are also briefly mentioned, including denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), phospholipid fatty acid analysis (PLFA) and others. The shift of soil microbiology from the study of individual microorganisms to entire microbial communities, including nonculturable species, is briefly discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Alef K, Nannipieri P (1998) Methods in applied soil microbiology and biochemistry. Academic, London

    Google Scholar 

  2. Anderson JPE (1982) Soil respiration. In: Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis. Part 2. Chemical and microbiological properties. American Society of Agronomy, Madison, pp 831–871

    Google Scholar 

  3. Audus LJ (1946) A new soil perfusion apparatus. Nature 158:419

    Article  CAS  Google Scholar 

  4. Bååth E, Lundgren B, Sönderström B (1981) Effects of nitrogen fertilization on the activity and biomass of fungi and bacteria in a podzolic soil. Zbl Bakt Hyg I Abt Orig C2:90–98

    Google Scholar 

  5. Baldrian P (2006) Fungal laccases—occurrence and properties. FEMS Microbiol Rev 30:215–242

    Article  CAS  PubMed  Google Scholar 

  6. Baldrian P (2009) Microbial enzyme-catalyzed processes in soils and their analysis. Plant Soil Environ 55:370–378

    CAS  Google Scholar 

  7. Baldrian P, Valášková V (2008) Degradation of cellulose by basidiomycetous fungi. FEMS Microbiol Rev 32:501–521

    Article  CAS  PubMed  Google Scholar 

  8. Banerjee A, Sharma R, Banerjee UC (2002) The nitrile-degrading enzymes: current status and future prospects. Appl Microbiol Biotechnol 60:33–44

    Article  CAS  PubMed  Google Scholar 

  9. Bartholomew WY, Broadbent FE (1949) Apparatus for control of moisture, temperature and air composition in microbiological respiration experiments. Soil Sci Soc Am Proc 14:156–160

    Article  Google Scholar 

  10. Biely P, Puchart V (2006) Recent progress in the assays of xylanolytic enzymes. J Sci Food Agric 86:1636–1647

    Article  CAS  Google Scholar 

  11. Birch HF (1958) The effect of soil drying on humus decomposition and nitrogen availability. Plant Soil 10:9–31

    Article  CAS  Google Scholar 

  12. Birch HF, Friend MT (1956) Humus decomposition in East African soils. Nature 178:500–501

    Article  CAS  Google Scholar 

  13. Bornemann F (1923) Kohlensäure und Pflanzenwachstum. 2. Auflage, Berlin

    Google Scholar 

  14. Bremner JM, Mulvaney RL (1978) Urease activity in soils. In: Burns RG (ed) Soil enzymes. Academic Press, New York, pp 149–196

    Google Scholar 

  15. Brumme R, Beese F (1992) Effects of liming and nitrogen fertilization on emission of CO2 and N2O from a temporate forest. J Geophys Res 97:851–858

    Google Scholar 

  16. Buhler DR (1962) A simple scintillation counting technique for assaying 14CO2 in a Warburg flask. Anal Biochem 4:413–417

    Article  CAS  PubMed  Google Scholar 

  17. Chaloupka J (1984) Regulation of enzyme synthesis and its practical application. In: Krumphanzl V, Řeháček Z (eds) Modern biotechnology. IM ASCR, Prague, pp 248–291

    Google Scholar 

  18. Chase FE, Gray PHH (1953) Use of the Warburg respirometer to study microbial activity in soils. Nature 171:481

    Article  CAS  PubMed  Google Scholar 

  19. Chase FE, Gray PHH (1957) Application of Warburg respirometer in studying respiratory activity in soil. Can J Microbiol 3:335–349

    Article  Google Scholar 

  20. Clarke PH (1970) The aliphatic amidases of Pseudomonas aeruginosa. Adv Microb Physiol 4:179–222

    Article  CAS  Google Scholar 

  21. Collins T, Gerday C, Feller G (2005) Xylanases, xylanase families and extremophilic sylanases. FEMS Microbiol Rev 29:3–23

    Article  CAS  PubMed  Google Scholar 

  22. Cornfield AH (1961) A simple technique for determining mineralization of carbon during incubation of soils treated with organic materials. Plant Soil 14:90–93

    Article  CAS  Google Scholar 

  23. Cripps RE, Norris JR (1969) A soil perfusion apparatus. J Appl Bacteriol 32:259–260

    CAS  PubMed  Google Scholar 

  24. Cuppy D, Crevasse L (1963) An assembly for 14CO2 collection in metabolic studies for liquid scintillation counting. Anal Biochem 5:462–463

    Article  CAS  Google Scholar 

  25. Dean ACR, Ellwood DC, Evans CG-T, Melling J (1976) Continuous culture. 6. Application of new fields. E. Horwood, Chichester

    Google Scholar 

  26. Doelman P, Haanstra L (1986) Short- and long-term effect of heavy metals on urease activity in soils. Biol Fertil Soils 2:213–218

    Article  Google Scholar 

  27. Dohrmann AB, Tebbe CC (2004) Microbial community analysis by PCR-single-strand conformation polymorphism (PCR-SSCP). In: Kowallchuk GA, de Brujin FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Molecular microbial ecology manual. Kluwer Academic, Dordrecht, pp 809–838

    Google Scholar 

  28. Domsch KH (1962) Bodenatmung. Sammelbericht über Methoden und Ergebnisse. Zentralblatt Bakteriol Abt II 116:33–78

    Google Scholar 

  29. Drobník J (1957) Study of biological transformation of organic compounds in soil (in Russian). Potchvovedenije 12:62–71

    Google Scholar 

  30. Drobník J (1957) The use of respirometry in soil microbiology. I. Methodics of macrorespirometry (in Czech). Czechosl Microbiol (since 1959 Folia Microbiol) 2:116–123

    Google Scholar 

  31. Drobník J (1958) A respirometric study of glucose metabolism in soil samples. Folia Biol (Prague) 4:137–146

    Google Scholar 

  32. Drobník J (1958) An apparatus for studying respiration in a soil sample. Folia Biol (Prague) 4:137–146

    Google Scholar 

  33. Drobník J (1960) A Warburg vessel for soil samples. Nature 188:686

    Article  Google Scholar 

  34. Durska G, Kaszubiak H (1980) Occurrence of m-diaminopimelic acid in soil. I. The content of m-diaminopimielic acid in different soils. Pol Ecol Stud 6:189–193

    CAS  Google Scholar 

  35. Durska G, Kaszubiak H (1980) Occurrence of m-diaminopimelic acid in soil. II. Usefulness of m-diaminopimelic acid determination for calculations of the microbial biomass. Pol Ecol Stud 6:195–199

    CAS  Google Scholar 

  36. Durska G, Kaszubiak H (1980) Occurrence of m-diaminopimelic acid in soil. III. m-Diaminopimelic acid as the nutritional component of the soil microorganisms. Pol Ecol Stud 6:201–206

    CAS  Google Scholar 

  37. Durska G, Kaszubiak H (1983) Occurrence of bound muramic acid and m-diaminopimelic acid in soil and comparison of their content with bacterial biomass. Acta Microbiol Pol 3:257–263

    Google Scholar 

  38. Eivazi F, Tabatabai MA (1977) Phosphatases in soils. Soil Biol Biochem 9:167–172

    Article  CAS  Google Scholar 

  39. Fencl Z, Řičica J (1968) Continuous cultivation of microorganisms. Process Biochem 3:41

    CAS  Google Scholar 

  40. Frankenberger WT Jr, Johanson JB (1982) L-Histidine ammonia-lyase activity in soils. Soil Sci Soc Am J 48:943–948

    Article  Google Scholar 

  41. Frankenberger WT Jr, Tabatabai MA (1980) Amidase activity in soils: I. Methods of assay. Soil Sci Soc Am J 44:282–287

    Article  CAS  Google Scholar 

  42. Frankenberger WT Jr, Tabatabai MA (1991) L-Asparaginase activity of soils. Biol Fertil Soils 11:6–12

    Article  CAS  Google Scholar 

  43. Frankenberger WT Jr, Tabatabai MA (1991) Factors affecting L-asparaginase activity in soils. Biol Fertil Soils 11:1–5

    Article  CAS  Google Scholar 

  44. Frankenberger WT Jr, Tabatabai MA (1991) L-Glutaminase activity of soils. Soil Biol Biochem 23:869–874

    Article  CAS  Google Scholar 

  45. Frankenberger WT Jr, Tabatabai MA (1991) Factors affecting L-glutaminase activity of soils. Soil Biol Biochem 23:875–879

    Article  CAS  Google Scholar 

  46. Frankland JC, Lindley DK, Swift MJ (1978) A comparison of two methods for the estimation of mycelial biomass in leaf litter. Soil Biol Biochem 10:323–333

    Article  CAS  Google Scholar 

  47. Freytag HE (1961) Eine Apparatur zur kontinuierlichen Verfolgung der Atmung biologischer objekte. Albrecht-Thaer-Archiv 6:403–420

    Google Scholar 

  48. Freytag HE (1963) On the decomposition of plant matter in soil (in Czech). Rostlinná Výroba 9:798–802

    CAS  Google Scholar 

  49. Frostegard A, Baath E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils 22:59–65

    Article  Google Scholar 

  50. Gaub FB, Dollar AM (1968) Improvement of a continuous-culture apparatus for long-term use. Appl Microbiol 16:232

    Google Scholar 

  51. Gehorn MJ, Davis JD, Glen AS, White DC (1984) Determination of the gram-positive bacterial content of soils and sediments by analysis of teichoic acid components. J Microbiol Meth 2:165–176

    Article  Google Scholar 

  52. Gilmour CM, Allen ON (eds) (1965) Microbiology and soil fertility. In: Papers presented at the 25th annual biology colloquium. Oregon State University Press, Corvallis

  53. Goksøyr J (1962) A Warburg apparatus with automatic recording of respiratory 14CO2. Anal Biochem 3:439–447

    Article  PubMed  Google Scholar 

  54. Gomez-Brandón M, Lores M, Domínguez J (2010) A new combination of extraction and derivatization methods that reduces the complexity and preparation time in determining phospholipid fatty acids in solid environmental samples. Bioresour Technol 101(13):48–54

    Google Scholar 

  55. Goswami KP, Green RE (1971) A simple automatic soil percolator. Soil Biol Biochem 3:389–391

    Article  CAS  Google Scholar 

  56. Grant WD, West AW (1986) Measurement of bound muramic acid and m-diaminopimelic acid and glucosamine in soil: evaluation as indicators of microbial biomass. J Microbiol Meth 6:47–53

    Article  CAS  Google Scholar 

  57. Greenwood DJ, Lees H (1959) Electrolytic rocking percolator. Plant Soil 11:87–92

    Article  CAS  Google Scholar 

  58. Gustavson GG (1890) On microbiological basis of agronomy (O mikrobiologičeskich osnovanijach agronomii). In: VIIIth congress of Russian scientists and physicians, St. Petersburg 1890. According to Fedorov MV, Soil microbiology (in Russian), Sovetskaya Nauka, Moscow 1954

  59. Gyllenberg H, Pessa E (1959) Experiments on artificial propagation of mixed microbial soil populations. Acta Agral Fen 1:1959

    Google Scholar 

  60. Gyorgy P, Rothler H (1926) Conditions for the autolytic formation of ammonia in nature. Series II. Determination of ammonia derived from amino acids and nitrogen containing substances. Biochem Z 173:334–337

    CAS  Google Scholar 

  61. Hayano K (1986) Cellulase complex in tomato field soil: induction, localization and some properties. Soil Biol Biochem 18:215–219

    Article  CAS  Google Scholar 

  62. Hoffmann G (1967) Eine photometrische Methode zur Bestimmung der Phosphatase-aktivität in Boden. Z Pflanernaehr Bodenkd 118:193–198

    Google Scholar 

  63. Hoffmann E, Schmidt W (1953) Über das Enzym-system unserer Kulturböden. II. Urease. Biochem Z 323:125–127

    Google Scholar 

  64. Hofrichter M (2002) Review: lignin conversion by manganese peroxidase (MnP). Enzyme Microb Technol 30:454–466

    Article  CAS  Google Scholar 

  65. Holm-Jensen I (1960) A new gas absorption device. Its application to titrimetric and conductometric microdetermination of carbon-dioxide in air. Anal Chim Acta 23:13–27

    Article  CAS  Google Scholar 

  66. Hynes (1975) Amide utilization in Aspergillus nidulans: evidence for a third amidase enzyme. J Gen Microbiol 91:99–109

    CAS  PubMed  Google Scholar 

  67. Imada A, Igarasi S, Nakahama K, Isono M (1973) Asparaginase and glutaminase activities of microorganisms. J Gen Microbiol 76:85–89

    CAS  PubMed  Google Scholar 

  68. Insam H (2001) Developments in soil microbiology since the mid 1960s. Geoderma 100:389–402

    Article  CAS  Google Scholar 

  69. Isermeyer H (1952) Eine einfache Methode zur Bestimmung der Bodenatmung und der Karbonate im Boden. Zeitschrift Pflanzen Düng Bodenk 56:26–38

    Article  CAS  Google Scholar 

  70. Jansson SL (1958) Tracer studies on nitrogen transformations in soil with special attention to mineralization–immobilization relationships. Kungl Lantbrukshögskolans Annaler 24:101

    CAS  Google Scholar 

  71. Jeffreys EG, Smith WK (1951) A new type of soil percolator. Proc Soc Appl Bacteriol 14:169–170

    Google Scholar 

  72. Johnson BN, McGill WB (1990) Comparison of ergosterol and chitin as quantitative estimates of mycorrhizal infection and Pinus contora seedling response to inoculation. Can J Forest Res 20:1125–1131

    Article  CAS  Google Scholar 

  73. Joshi JG, Handler P (1962) Purification and properties of nicotinamidase from Torula cremoris. J Biol Chem 237:929–935

    CAS  PubMed  Google Scholar 

  74. Kandeler E, Gerber H (1988) Short-term assay of soil urease activity using colorimetric determination of ammonium. Biol Fertil Soils 6:68–72

    Article  CAS  Google Scholar 

  75. Kato T (1986) Sterol-biosynthesis in fungi, a target for broad spectrum fungicides. In: Haug G, Hoffman H (eds) Sterol biosynthesis inhibitors and anti-feeding compounds. Springer, Berlin, pp 1–25

    Google Scholar 

  76. Kleinzeller A, Málek I, Vrba R (1954) Manometric methods and their application for biology and biochemistry (in Czech). SZN Praha

  77. Kozlovsky SA, Zaitsev GM, Kunc F (1993) Degradation of 2-chlorobenzoic and 2,5-dichlorobenzoic acids in soil columns by Pseudomonas stutzeri. Folia Microbiol 38:376–378

    Article  CAS  Google Scholar 

  78. Kunc F, Macura J (1966) Oxidation of aromatic compounds in soil. Folia Microbiol 11:248–256

    Article  CAS  Google Scholar 

  79. Kunc F (1988) Three decades of heterocontinuous flow cultivation method in soil microbiology. In: Kyslík P, Dawes EA, Krumphanzl V, Novák M (eds) Continuous culture. Academic Press, London, pp 43–55

    Google Scholar 

  80. Ladd JN, Butler JHA (1972) Short-term assays of soil proteolytic enzyme activities using protein and dipeptide derivatives as substrates. Soil Biol Biochem 4:19–30

    Article  CAS  Google Scholar 

  81. Lee C, Howarth RW, Howes BL (1980) Sterols in decomposing Spartina alterniflora and the use of ergosterol in estimating the contribution of fungi to detrital nitrogen. Limnol Ocean 25:290–303

    Article  CAS  Google Scholar 

  82. Lee DH, Zo YG, Kim SJ (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 62:3112–3120

    CAS  PubMed  Google Scholar 

  83. Lees H (1947) A simple automatic percolator. J Agric Sci 37:27–28

    Article  Google Scholar 

  84. Lees H (1949) The soil percolation technique. Plant Soil 1:221–239

    Article  CAS  Google Scholar 

  85. Lees H (1949) A simple apparatus for measuring the oxygen uptake of soils. Plant Soil 2:123–128

    Article  CAS  Google Scholar 

  86. Lees H, Quastel JH (1944) Chem Ind 26:238 (according to [87])

  87. Lees H, Quastel JH (1946) Biochemistry of nitrification in soil. 1. Kinetics of, and the effects of poisons on, soil nitrification, as studied by a soil perfusion technique. Addendum by Lees H (1946) A soil perfusion apparatus. Biochem J 40:803–815

    Google Scholar 

  88. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522

    CAS  PubMed  Google Scholar 

  89. Loll MJ, Bollag JM (1983) Protein transformation in soil. Adv Agron 36:351–358

    Article  CAS  Google Scholar 

  90. Longden AR, Claridge CA (1976) Easily constructed soil percolation apparatus. Appl Environ Microbiol 32:188–189

    CAS  PubMed  Google Scholar 

  91. Lundegardh H (1924) Der Kreislauf der Kohlensäure in der Natur. G. Fischer, Jena

    Google Scholar 

  92. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506–577

    Article  CAS  PubMed  Google Scholar 

  93. Macura J (1961) Continuous flow method in soil microbiology. I. Apparatus. Folia Microbiol 6:28–334

    Google Scholar 

  94. Macura J (1961) The use of continuous flow method for studying soil metabolism. In: Transactions of the VIIth international congress on soil science, Madison, Wisconsin, USA, III-29:664–671 (cf. [94])

  95. Macura J (1974) Trends and advances in soil microbiology from 1924 to 1974. Geoderma 12:311–329

    Article  CAS  Google Scholar 

  96. Macura J, Kunc F (1961) Continuous flow method in soil microbiology. II. Observations on glucose metabolism. Folia Microbiol 6:398–407

    Article  CAS  Google Scholar 

  97. Macura J, Kunc F (1965) Continuous flow method in soil microbiology. III. Biological immobilization of nitrogen and phosphorus. Folia Microbiol 10:36–43

    Article  CAS  Google Scholar 

  98. Macura J, Kunc F (1965) Continuous flow method in soil microbiology. IV. Decomposition of glycine. Folia Microbiol 10:115–124

    Article  CAS  Google Scholar 

  99. Makarov BH (1959) Determination of carbon dioxide and oxygen in soil air (in Russian). Potchvovedenije 1:121–125

    Google Scholar 

  100. Málek I (1968) Continuous cultivation as a model for studies of biological systems. Scripta Med 41:205

    Google Scholar 

  101. Málek I, Fencl Z (1961) Continuous cultivation of microorganisms. A review. Folia Microbiol 6:192–209

    Article  Google Scholar 

  102. Málek I, Beran K (1962) Continuous cultivation of microorganisms. A review. Folia Microbiol 7:388–411

    Article  Google Scholar 

  103. Málek I, Hospodka J (1960) Continuous cultivation of microorganisms. A review. Folia Microbiol 5:120–139

    Article  Google Scholar 

  104. Málek I, Macura J (1958) Continuous-flow method for the study of microbiological processes in soil samples. Nature 182:1796–1797

    Article  PubMed  Google Scholar 

  105. Málek I, Řičica J (1965) Continuous cultivation of microorganisms. A review. Folia Microbiol 10:302–323

    Article  Google Scholar 

  106. Málek I, Řičica J (1966) Continuous cultivation of microorganisms. A review. Folia Microbiol 11:479–535

    Article  Google Scholar 

  107. Málek I, Řičica J (1968) Continuous cultivation of microorganisms. A review. Folia Microbiol 13:46

    Article  Google Scholar 

  108. Málek I, Řičica J (1970) Continuous cultivation of microorganisms. A review. Folia Microbiol 15:129–149

    Article  Google Scholar 

  109. Martínez AT, Speranza M, Ruiz-Duenas FJ, Ferreira P, Guillén F, Martínez MJ, Gutiérrez A, del Rio CJ (2005) Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int Microbiol 8:195–204

    PubMed  Google Scholar 

  110. McCarty GW, Bremner JM, Chac HS (1989) Effects of N-(n-butyl)thiophosphorictriamide on hydrolysis of urea by plant, microbial and soil urease. Biol Fertil Soils 8:123–127

    CAS  Google Scholar 

  111. McGarity JW, Gilmour CM, Bollen WB (1958) Use of an electrolytic respirometer to study denitrification in soil. Can J Microbiol 4:303–316

    Article  CAS  PubMed  Google Scholar 

  112. McKhann GM, Tower DB (1960) Modified manometric vessel for special studies on tissue metabolism. Anal Biochem 1:511–516

    Article  CAS  PubMed  Google Scholar 

  113. Millar WN, Cassida LE (1970) Evidence for muramic acid in the soil. Can J Microbiol 18:299–304

    Article  Google Scholar 

  114. Miller M, Palojarvi A, Rangger A, Reeslev M, Kjoller A (1998) The use of fluorogenic substrates to measure fungal presence and activity in soil. Appl Environ Microbiol 64:613–617

    CAS  PubMed  Google Scholar 

  115. Miller RH, Schmidt EL (1963) Manometric study of nitrogen utilisation during early stages of cellulose decomposition in soils. Soil Sci Soc Am Proc 27:374–377

    Article  CAS  Google Scholar 

  116. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturating gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S ribosomal RNA. Appl Environ Microbiol 59:695–700

    CAS  PubMed  Google Scholar 

  117. Muyzer G, Brinkhoff T, Nubel U, Santegoeds C, Schafer H, Wawer C (2004) Denaturating gradient gel electrophoresis (DGGE) in microbial ecology. In: Kowallchuk GA, de Brujin FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Molecular microbial ecology manual. Kluwer, Dordrecht, pp 743–769

    Google Scholar 

  118. Müller D, Gabriel J (1999) Bacterial degradation of the herbicide bromoxynil by Agrobacterium radiobacter in biofilm. Folia Microbiol 44:377–379

    Article  Google Scholar 

  119. Nannipieri P, Ceccanti B, Cervelli S, Matarese E (1980) Extraction of phosphatase, urease, protease, organic carbon and nitrogen from soil. Soil Sci Soc Am J 44:1011–1016

    Article  CAS  Google Scholar 

  120. Nannipieri P, Ceccanti B, Bianchi B (1988) Characterization of humus–phosphate complexes extracted from soil. Soil Biol Biochem 20:683–691

    Article  CAS  Google Scholar 

  121. Naumann K (1963) Bodenatmungsmessungen mit der Warburg Apparatur. Zentralblatt Bakteriol 116:502–511

    Google Scholar 

  122. Novák B (1956) Die Kohlensäurentwicklung als Indikator für die Humusbildung im Wirtschaftsdüngers. Za socialisticeskuju selsko-chozjajsvtennuju nauku, 278–282 (according to [123])

  123. Novák B (1960) Microbiology in the study of soil genesis (in Czech). Rostlinná Výroba 6:1029–1032

    Google Scholar 

  124. Novák B, Apfelthaler R (1964) Contribution to the methodics of respiration determination as indicator of microbiological processes in soil (in Czech). Rostlinná Výroba 10:145–150

    Google Scholar 

  125. Parkinson D (1982) Filamentous fungi. In: Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis. Part 2. Chemical and microbiological properties. American Society of Agronomy, Madison, pp 949–967

    Google Scholar 

  126. Parkinson D, Coups E (1962) Microbial activity in a podzol. Soil organisms. In: Proceedings of the colloquium on soil fauna, soil microflora and their relationships. Oosterbeck, The Netherlands, pp 258–265

  127. Payne TMB, Gray PHH (1952) Apparatus for soils of a high organic matter content. Nature 170:325

    Article  Google Scholar 

  128. Perfilev BV (1959) Theory and technique of continuous-flow cultivation of bacteria. Ordena Lenina Gosudarstvennyj Universitet imeni (in Russian). A.A. Zhdanova, Leningrad

    Google Scholar 

  129. Perfilev BV (1960) Theory and technique of continuous-flow cultivation of bacteria. In: Continuous fermentation and growth of microorganisms (in Russian). In: Yerusalimsky ND (ed) Pischchepromizdat, Moscow, p 28 (in Russian)

  130. Petersen SO, Debosz K, Schjonning P, Christensen BT, Elmholt S (1997) Phospholipid fatty acid profiles and C availability in wet-stable macro-aggregates from conventionally and organically farmed soils. Geoderma 78:181–196

    Article  CAS  Google Scholar 

  131. Rao MB, Tanksale AM, Fhatge MS, Deshpande VV (1998) Molecular and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 62:597–635

    CAS  PubMed  Google Scholar 

  132. Richter J (1972) Zur Methodik des Bodengashaushaltes. II. Ergebnisse und Diskussion. Z Pflanzenernähr Bodenkd 132:220–239

    Article  CAS  Google Scholar 

  133. Riesner D, Henco K, Steger G (1990) Temperature-Gradient Gel Electrophoresis: a method for the analysis of conformational transitions and mutations in nucleic acids and protein. In: Chrambach AM, Dunn MJ, Radola BJ (eds) Advances in electrophoresis, vol 4. VCH Verlagsgesselschaft, Weinheim, pp 169–250

    Google Scholar 

  134. Rinnan R, Bååth E (2009) Differential utilization of carbon substrates by bacteria and fungi in tundra soil. Appl Environ Microbiol 75:3611–3620

    Article  CAS  PubMed  Google Scholar 

  135. Rovira AD (1953) Use of Warburg apparatus in soil metabolism studies. Nature 172:29–30

    Article  CAS  PubMed  Google Scholar 

  136. Russel EJ (1905) Oxidation in soils and its connection with fertility. J Agric Sci 1:261–279

    Article  Google Scholar 

  137. Ruzicka S, Edgerton D, Norman M, Hill T (2000) The utility of ergosterol as a bioindicator of fungi in temperature soils. Soil Biol Biochem 32:989–1006

    Article  CAS  Google Scholar 

  138. Sarkar JM, Batistic L, Mayaudon J (1980) Les hydrolases du sol et leur association avec les hydrates de carbone. Soil Biol Biochem 12:325–328

    Article  CAS  Google Scholar 

  139. Sarkar JM, Leonowicz A, Bollag JM (1989) Immobilization of enzymes on clays and soils. Soil Biol Biochem 21:223–230

    Article  CAS  Google Scholar 

  140. Schloesing T, Müntz A (1877) CR Acad Sci 84:301 According to Payne a Gray, Nature (1952)

  141. Seidel V (2008) Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. Fungal Biol Rev 22:36–42

    Article  Google Scholar 

  142. Seitz LM, Mohr HE, Burroughs R, Sauer DB (1977) Ergosterol as an indicator of fungal invasion in grains. Cereal Chem 54:1207–1217

    CAS  Google Scholar 

  143. Seitz LM, Sauer DB, Burroughs R, Mohr HE, Hubbard ID (1979) Ergosterol as a measure of a fungal growth. Phytopathology 69:1201–1203

    Article  Google Scholar 

  144. Sharp RF, Taylor BP (1969) A new soil percolator for the effective culture of soil organisms. Soil Biol Biochem 1:191–194

    Article  Google Scholar 

  145. Steffen KT, Cajthaml T, Šnajdr J, Baldrian P (2007) Differential degradation of oak (Quercus petrea) leaf litter by litter-decomposing basidiomycetes. Res Microbiol 158:447–455

    Article  CAS  PubMed  Google Scholar 

  146. Steubing L (1970) Chemische Methoden zur Bewertung des mengenmässgen Vorkommens von Bakterien und Algen im Boden. Zentralbl Bakteriol Parasitenk Abt 2 124:245–249

  147. Stevens RJ, Cornforth IS (1975) An all-glass closed system soil percolation apparatus for gas and liquid. Plant Soil 43:327–335

    Article  CAS  Google Scholar 

  148. Stevenson IL (1956) Some observations on the microbial activity in remoistened air dried soils. Plant Soil 8:170–182

    Article  Google Scholar 

  149. Stewart DG, Warner RG, Seeley HW (1961) Continuous culture as a method for studying rumen fermentation. Appl Microbiol 9:150

    CAS  PubMed  Google Scholar 

  150. Stoklasa J (1911) Methoden zur Bestimmung der Atmungsintensität der Bakterien im Boden. Z Landv Versuchsw Österreich 14:1243–1279

    Google Scholar 

  151. Stoklasa J (1922) Biochemische Methoden zur Bestimmung der Fruchtbarkeit des Bodens. Chemiker Ztg 46:681–683

    CAS  Google Scholar 

  152. Stotzky G (1960) A simple method for the determination of the respiratory quotient of soils. Can J Microbiol 6:439–452

    Article  CAS  PubMed  Google Scholar 

  153. Swaby RJ, Passey BI (1953) A simple macro-respirometer for studies in soil microbiology. Austral J Agric Res 4:334–339

    Article  CAS  Google Scholar 

  154. Szolnoki J, Kunc F, Macura J, Vančura V (1963) Effect of glucose on the decomposition of organic materials added to soil. Folia Microbiol 8:356–361

    Article  CAS  Google Scholar 

  155. Symposium on continuous cultivation of microorganisms. Málek I (ed) (1958) Publishing House of the Czechoslovak Academy of Sciences, Prague

  156. Šimek I (1958) A simple time switch (in Czech). Chem Zvesti 10:632

    Google Scholar 

  157. Šnajdr J, Valášková V, Merhautová V, Cajthaml T, Baldrian P (2008) Activity and spatial distribution of lignocellulose-degrading enzymes during forest soil colonization by saprotrophic basidiomycetes. Enzyme Microb Technol 43:186–192

    Article  CAS  Google Scholar 

  158. Tabatabai MA, Bremner JM (1972) Assay of urease activity in soil. Soil Biol Biochem 4:479–487

    Article  CAS  Google Scholar 

  159. Takai T, Macura J, Kunc F (1969) Anaerobic decomposition of glucose continuously added to the soil. Folia Microbiol 14:327–333

    Article  CAS  Google Scholar 

  160. Temple KL (1951) A modified design of the Lees soil percolation apparatus. Soil Sci 71:209–210

    Article  CAS  Google Scholar 

  161. Ton SJ, Gander JE (1979) Biosynthesis of polysaccharides by prokaryotes. Ann Rev Microbiol 33:169–199

    Article  Google Scholar 

  162. Trasar-Cepeda MC, Gil-Sotres F (1988) Kinetics of acid phosphatase activity in various soils of Galicia (NW Spain). Soil Biol Biochem 20:275–280

    Article  CAS  Google Scholar 

  163. Trevors J (1984) Dehydrogenase activity in soil: a comparison between the INT and TTC assay. Soil Biol Biochem 16:673–674

    Article  CAS  Google Scholar 

  164. Tunlid A, White DC (1992) Biochemical analysis of biomass, community structure, nutritional status, and metabolic activity of microbial communities in soil. In: Stotzky G, Bollag J-M (eds) Soil biochemistry, vol 7. Marcel Dekker, New York, pp 229–262

    Google Scholar 

  165. Vacek J, Drobník J (1962) Apparatus for the determination of soil respiration (in Czech). Rostlinná Výroba 8:773–780

    Google Scholar 

  166. Vacek J (1963) Experiences obtained in the respiration measurements of forest soil in macrorespirometer (in Czech). Rostlinná Výroba 9:818–820

    Google Scholar 

  167. Van Bruggen JT, Scott JC (1962) Microdetermination of carbon dioxide. Anal Biochem 3:464–471

    Article  Google Scholar 

  168. Van Elsas JD, Trevors JT, Wellington EMH (1997) Modern soil microbiology. Marcel Dekker, New York, Basel

    Google Scholar 

  169. Valášková V, Baldrian P (2009) Denaturating gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities. Plant Soil Environ 55:413–423

    Google Scholar 

  170. Věková J, Pavlů L, Vosáhlo J, Gabriel J (1995) Degradation of Bromoxynil by resting and immobilized cells of Agrobacterium radiobacter 8/4-strain. Biotechnol Lett 17:449–452

    Article  Google Scholar 

  171. Vokounová M (1990) Microbial degradation of the herbicide Bromoxynil (in Czech). PhD Thesis, Institute of Microbiology, ASCR, Prague

  172. Vokounová M, Vacek O, Kunc F (1992) Effect of glucose and ribose on microbial degradation of the herbicide Bromoxynil continuously added to soil. Folia Microbiol 37:128–132

    Article  Google Scholar 

  173. Vokounová M, Vacek O, Kunc F (1992) Degradation of the herbicide Bromoxynil in Pseudomonas putida. Folia Microbiol 37:122–127

    Article  Google Scholar 

  174. Waksman SA (1952) Soil microbiology. Wiley, New York. Chapman and Hall, London

  175. Wang CH, Stern J, Gilmur CM, Klungsoyr S, Reed DJ, Bialy JJ, Christensen BE, Cheldelin VH (1958) Comparative study of glucose catabolism by the radiorespirometric method. J Bacteriol 76:207–216

    CAS  PubMed  Google Scholar 

  176. Ward JB (1981) Teichoic acid and chichuronic acids: biosynthesis, assembly and location. Microbiol Rev 45:211–243

    CAS  PubMed  Google Scholar 

  177. Weeraratne CS (1975) A simple instrument for soil perfusion. Plant Soil 42:709–710

    Article  Google Scholar 

  178. Wolf JM, Brown AH, Goddard DR (1952) An improved electrical conductivity method for accurately following changes in the respiratory quotient of a single biological sample. Plant Physiol 27:70–80

    Article  CAS  PubMed  Google Scholar 

  179. Wieringa KT, Mogot MFK (1957) Apparatus for the determination of the respiration process in soil samples. Plant Soil 8:395–396

    Article  Google Scholar 

  180. Wriston JC Jr (1971) L-Asparaginase. In: Boyer PD (ed) The enzymes, vol 4. Academic Press, New York, pp 101–102

    Google Scholar 

  181. Zelles L (1988) The simultaneous determination of muramic acid and glucosamine in soil by high-performance liquid chromatography with percolumn fluorescence derivatization. Biol Fertil Soils 6:125–130

    Article  CAS  Google Scholar 

  182. Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indication of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317–323

    Article  CAS  Google Scholar 

  183. Zelles L, Alef K (1995) Biomarkers. In: Methods in applied soil microbiology and biochemistry. Academic Press, London, pp 422–423

  184. Zöttl H (1960) Dynamik der Stickstoffmineralization im organischen Waldbodenmaterial. I. Beziehung zwischen Bruttomineralization und Nettomineralization. Plant Soil 13:166–182

    Article  Google Scholar 

  185. Zöttl H (1960) Dynamik der Stickstoffmineralization im organischen Waldbodenmaterial. II. Einfluss der Stickstoffgehaltes auf die Mineralstickstoff-Nachlieferung. Plant Soil 13:183–206

    Article  Google Scholar 

  186. Zöttl H (1960) Dynamik der Stickstoffmineralization im organischen Waldbodenmaterial. III. pH-wert und Mineralstickstoff-Nachlieferung. Plant Soil 13:207–223

    Article  Google Scholar 

  187. Zöttl H (1960) Methodische Untersuchungen zur Bestimmung der Mineralstickstoffnachlieferung des Waldbodens. Forstw Cbl 79:72–90

    Article  Google Scholar 

  188. Zöttl H (160) Die Mineral-stickstoff-anlieferung im Fichten- und Kieferbeständen Bayerns. Forstw Cbl 79:221–236

    Google Scholar 

  189. Zöttl H (160) Beziehung zwischen Mineralstickstoff-Anhäufung und Kohlendioxyd-Produktion von Waldhumusproben im Brutversuch. Zeitschr Pflanzern Düng Bodenk 90:132–138

    Google Scholar 

Download references

Acknowledgment

Supported by Institutional Research Concept AV0Z50200510.

Author information

Authors and Affiliations

  1. Institute of Microbiology, ASCR, v.v.i., Vídeňská 1083, 142 20, Prague 4-Krč, Czech Republic

    Jiří Gabriel

Authors
  1. Jiří Gabriel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jiří Gabriel.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gabriel, J. Development of soil microbiology methods: from respirometry to molecular approaches. J Ind Microbiol Biotechnol 37, 1289–1297 (2010). https://doi.org/10.1007/s10295-010-0866-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10295-010-0866-7

Keywords

Search

Navigation