Soil health - A new challenge for microbiologists and chemists

International Microbiology

Volumn 8, Issue 1, 2005, Pages 13-21

  Arias, M Enriqueta ^a   González Pérez, José A ^b   González Vila, Francisco J ^b   Ball, Andrew S ^c  

^a UNIVERSITY OF ALCALÁ   (Spain)

^b INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SEVILLA   (Spain)

^c UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

Analytical methods; Chemical indicators; Microbial indicators; Molecular methods; Soil health

Indexed keywords

DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; ORGANIC COMPOUND;

BACTERIUM; BIOAVAILABILITY; BIODIVERSITY; GENETIC PROCEDURES; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; POLLUTANT; REVIEW; SOIL; STANDARD;

BACTERIA; BIODIVERSITY; BIOLOGICAL AVAILABILITY; ENVIRONMENTAL POLLUTANTS; GENETIC TECHNIQUES; INDICATORS AND REAGENTS; ORGANIC CHEMICALS; SOIL; SOIL MICROBIOLOGY;

EID: 23844503080     PISSN: 11396709     EISSN: 16181905     Source Type: Journal    
DOI: None     Document Type: Review

References (60)

1. Alef K (1995) Soil respiration. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic Press, New York, pp 214-218
2. Almendros G, González-Vila FJ (1987) Degradative studies on a soil humin fraction. Sequential degradation of inherited humin. Soil Biol Biochem 19:513-520
3. Anderson JPE, Domsch KH (1978) A physiological method for the quantitative measurement of microbial biomass in soils. Soil Biol Biochem 10:215-221
4. Anderson JPE, Domsch KH (1990) Application of echo-physiological quotients (qCO2 and qD) on microbial biomasses from soil of different cropping histories. Soil Biol Biochem 25:393-395
5. Baath E (1998) Growth rates of bacterial communities in soils at varying pH: a comparison of the thymidine and leucine incorporation techniques. Microb Ecol 36:316-327
6. Bajtes NH (1996) Total carbon and nitrogen in the soils of the world. Eur J Soil Sci 47:151-163
7. 13C natural abundance. In: Boutton TW, Yamasaki SI (eds) Mass spectrometry of soil. Marcel Dekker, New York, pp 83-111
8. Bautista JM, González-Vila FJ, Martín F, del Rio JC, Gutierrez A, Verdejo T, Gonzalez AG (1999) Supercritical-carbon-dioxide extraction of lipids from a contaminated soil. J Chromatogr 845:365-371
9. Bennie ATP (1996) Growth and mechanical impedance. In: Waisel Y, Eshel A, Kafkafi U (eds) Plant roots: the hidden half, 2nd edn. Marcel Dekker, New York, pp 453-470
10. Bloem J, Bolhuis PR, Veninga MR, Wieringa J (1995) Microscopic methods for counting bacteria and fungi in soil. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic Press, New York, pp 162-172
11. Bloem J, Breure AM (2003) Microbial indicators. In: Breure AM, Markert B, Zechmeister HG (eds) Bioindicators & biomonitors. Principles, assessment, concepts. Elsevier, Amsterdam, pp. 259-282
12. Bloem J, de Ruiter P, Bouwman LA (1997) Soil food webs and nutrient cycling in agro-ecosystems. In: van Elsas JD, Trevors JT, Wellington HME (eds) Modern soil microbiology. Marcel Dekker, New York, pp 245-278
13. Bossio, DA, Scow, KM, Gunapala, N, Graham, KJ (1998) Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb Ecol 36:1-12
14. Bruggen van A. H. C, Grunwald N J (1996) Tests for risk assessment of root infection by plant pathogens. In: Doran W, Jones AJ (eds) Methods for assessing soil quality. Soil Sci Soc Am, Madison, WI, pp 293-310
15. Buckley DH, Schmidt TM (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42:11-21
16. Campbell JIA, Albrechtsen M, Sorensen J (1995) Large Pseudomonas phages isolated from barley rhizosphere. FEMS Microbiol Ecol 18:63-74
17. Carter MR, Gregorich EG, Angers DA, Beare MH, Sparling GP, Wardle DA, Voroney RP (1999) Interpretation of microbial biomass measurements for soil quality assessment in humid temperate regions. Can J Soil Sci 79:507-520
18. Chan KY, Mullins CE (1994) Slaking characteristics of some Australian and British soils. Eur J Soil Sci 45:273-283
19. Colwell, RR (1997). Microbial biodiversity and biotechnology. In: Reaka-Kudla ML, Wilson DE, Wilson EO (eds) Biodiversity II: Understanding and protecting our biological resources. Joseph Henry Press, University of Washington, Washington, DC, pp. 279-288
20. Dick RP, Breakwell DP, Turco RF (1996) Soil enzyme activities and biodiversity measurements as integrative microbiological indicators. In: Doran JW, Jones AJ (eds) Methods for assessing soil quality. Soil Sci Soc Am, pp 107-121
21. Domínguez J, Negrín MA, Rodríguez CM (2001) Aggregate water-stability, particle-size and soil solution properties in conductive and suppressive soil to Fusarium wilt of banana from Canary Islands (Spain). Soil Biol Biochem 33:449-455
22. Doran JW, Jones AJ (1996) Methods for assessing soil quality. Special publication No 49. Soil Sci Soc Am, American Society of Agronomy, Madison, WI
23. Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3-11
24. Duchaufour Ph, Jacquin F (1975) Comparaison des processus d'humification dans les principaux types d'humus forestiers. Bull Alaska Agric Forest Experim Station 1:29-36 (In French)
25. Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172-178
26. Fitter AH, Hay RKM (1987) Environmental physiology of plants. Academic Press, London, UK
27. Frostegard A, Baath E (1996) The use of phospholipid fatty acids analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils 22:59-65
28. Gardland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community level sole-carbon-source utilization. Appl Environ Microbiol 57:2351-2359
29. Girvan MS, Bullimore J, Ball AS, Pretty JN, Osborn AM (2004) Responses of active bacterial and fungal communities in soils under winter wheat to different fertilizer and pesticide regimens. Appl Environ Microbiol 70:2692-2701.
30. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800-1809
31. González-Pérez JA, González-Vila FJ, Almendros G, Knicker H (2004) The effect of fire on soil organic matter-a review. Environ Int 30:855-870
32. González-Vila FJ, del Río JC, Martín F, Verdejo T (1996) Pyrolytic alkylation-gas chromatography-mass spectrometry of model polymers. Further insights into the mechanism and scope of the technique. J Chromatogr 750:155-160
33. 13C NMR structural features of soil humic acids and their methylated, hydrolyzed and extracted derivatives. Geoderma 31:3-15
34. Harrison AF, Latter TM, Walton DWH (1988) The cotton strip assay: an index of decomposition in soils. In: Institute of Terrestrial Ecology Symposium No. 24, Institute of Terrestrial Ecology, Grange-Over-Sand, UK
35. Heuer H, Smalla K (1997) Application of denaturing gradient gel electrophoresis and temperature gel electrophoresis for studying soil microbial communities. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil microbiology. Marcel Dekker, New York, pp 353-373
36. Hillel D (1982) Introduction to soil physics. 2nd edn. Academic Press, San Diego, CA
37. Kaiser E-A, Muller T, Jorgensen RG, Insam H, Heinemeyer O (1992) Evaluation of methods to estimate the soil microbial biomass and the relationships with soil texture and organic matter. Soil Biol Biochem 24:675-683
38. Kay BD (1998) Soil structure and organic carbon: a review. In: R. Lal, JM Kimble, RF Follett, BA Stewart (eds) Soil processes and carbon cycle. CRC Press, Boca Raton, FL, pp 169-197
39. Killops SD, Killops VJ (1993) An introduction to organic geochemistry. Longman, Harlow, UK
40. Kögel-Knabner I (2000) Analytical approaches for characterizing soil organic matter. Org Geochem 31:609-625
41. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516-4522
42. Lopez-Capel E, Manning DAC (2004) Thermal analysis and isotope ratio mass spectrometry in the evaluation of carbon turnover and SOM characterisation. EUROSOIL 2004. Albert-Ludwigs Universität, Freiburg, Germany
43. Lynch JM, Poole NJ (1979) Microbial ecology: a conceptual approach. John Wiley, New York
44. Moter A, Göbel UB (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms J Microbiol Methods 41:85-112
45. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S ribosomal-RNA. Appl Environ Microbiol 59:695-700
46. Neunlist S, Rodier C, Llopiz P (2002) Isotopic biogeochemistry of the lipids in recent sediments of Lake Bled (Slovenia) and Baldeggersee (Switzerland). Org Geochem 33:1183-1195
47. Pfaffl MW, Hageleit M (2001) Validities of mRNA quantification using recombinant RNA and recombinant DNA external calibration curves in real-time RT-PCR. Biotechnol Lett 23:275-282
48. Prentice IC, Farquhar GD, Fasham MJR, Goulden ML, Heimann M., Jaramillo VJ (2001) The carbon cycle and atmospheric carbon dioxide. In: Houghton JT, Ding Y, Griggs DJ, Noguer M, van der Linden PJ, Dai X, Maskell K, Johson CA (eds) Climate change: the scientific bases. Cambridge University Press, Cambridge, UK, pp 183-237
49. 14C measurements. Forest Ecol Manag 138:19-27
50. Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646-649
51. Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC (2002) Identification of active methylotroph populations in an acidic forest soil by stable isotope probing. Microbiology 148:2331-2342
52. Schnitzer M, Khan UK (1972) Humic substances in the environment. Marcel Dekker, New York
53. Smalla K, Heuer H, Gotz A, Niemeyer D, Krögerrecklenfort E, Tietze E (2000) Exogenous isolation of antibiotic resistance plasmids from piggery manure slurries reveals a high prevalence and diversity of IncQ-like plasmids. Appl Environ Microbiol 66:4854-4862
54. Tate RL (1995) Soil Microbiology. John Wiley, New York
55. Traina SJ, Novak J, Smeck NE (1990) An ultraviolet absorbance method of estimating the percent aromatic carbon content of humic acids. J Environ Qual 19:151-153
56. USDA (1999) Soil quality test kit guide. United States Department of Agriculture, Agricultural Research Service and Natural Resources Conservation Service. Soil Quality Institute, Auburn, AL
57. Verhoef HA (1995) Litter bag method. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic Press, New York, pp 485- 487
58. 13 incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Lett Appl Microbiol 32:398-401
59. Zak JC, Willig MR, Moorhead DL, Wildman HG (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26:1101-1108
60. Zelles L (1999) Fatty acids pattern of phospholipids and polysaccharides in the characterization of microbial communities in soil: a review. Biol Fertil Soils 29:111-129