Methods for evaluating human impact on soil microorganisms based on their activity, biomass, and diversity in agricultural soils

Journal of Plant Nutrition and Soil Science - Tập 169 Số 3 - Trang 295-309 - 2006
Rainer Georg Joergensen1, Christoph Emmerling2
1Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, D-37213 Witzenhausen, Germany
2Department of Soil Science, Campus II - Behringstr., D-54286 Trier, Germany

Tóm tắt

AbstractThe present review is focused on microbiological methods used in agricultural soils accustomed to human disturbance. Recent developments in soil biology are analyzed with the aim of highlighting gaps in knowledge, unsolved research questions, and controversial results. Activity rates (basal respiration, N mineralization) and biomass are used as overall indices for assessing microbial functions in soil and can be supplemented by biomass ratios (C : N, C : P, and C : S) and eco‐physiological ratios (soil organic C : microbial‐biomass C, qCO2, qNmin). The community structure can be characterized by functional groups of the soil microbial biomass such as fungi and bacteria, Gram‐negative and Gram‐positive bacteria, or by biotic diversity. Methodological aspects of soil microbial indices are assessed, such as sampling, pretreatment of samples, and conversion factors of data into biomass values. Microbial‐biomass C (µg (g soil)–1) can be estimated by multiplying total PLFA (nmol (g soil)–1) by the FPLFA‐factor of 5.8 and DNA (µg (g soil)–1) by the FDNA‐factor of 6.0. In addition, the turnover of the soil microbial biomass is appreciated as a key process for maintaining nutrient cycles in soil. Examples are briefly presented that show the direction of human impact on soil microorganisms by the methods evaluated. These examples are taken from research on organic farming, reduced tillage, de‐intensification of land‐use management, degradation of peatland, slurry application, salinization, heavy‐metal contamination, lignite deposition, pesticide application, antibiotics, TNT, and genetically modified plants.

Từ khóa


Tài liệu tham khảo

10.2136/sssaj1999.03615995006300010014x

10.1016/j.soilbio.2004.02.004

10.1007/BF00424942

10.1139/m75-045

10.1016/0038-0717(78)90099-8

10.1097/00010694-198010000-00008

10.1016/S0167-8809(03)00088-4

10.1016/0038-0717(89)90117-X

10.1016/0038-0717(90)90094-G

10.1016/S0038-0717(97)00011-4

Appuhn A. Joergensen R. G.(2006): Microbial colonisation of roots as a function of plant species.Soil Biol. Biochem. in press.

10.1002/jpln.200321302

10.1016/S0038-0717(03)00154-8

10.1016/S0167-7012(00)00239-6

10.1016/S0167-7012(01)00370-0

10.1016/S0038-0717(02)00033-0

10.1016/S0038-0717(02)00070-6

10.1016/S0929-1393(02)00129-4

10.1016/j.ecoenv.2005.03.024

10.1016/S0038-0717(97)00030-8

10.1016/S0038-0717(98)00050-9

10.1023/B:MICI.0000008379.63620.7b

10.1007/s003740000219

Bloem J. Bohhuis P. R. Veninga M. R. Wieringa J.(1995): Microscopic methods to estimate biomass and activity of soil bacteria and fungi in Alef K. Nannipieri P.: Methods in Applied Soil Microbiology and Biochemistry. Academic Press London pp. 162–173.

Bloem J. Schouten A. J. Sørensen S. J. Rutgers M. Van der Werf A. Breure A. M.(2006): Monitoring and evaluating soil quality in Bloem J. Hopkins D. W. Benedetti A.: Microbiological Methods for Assessing Soil Quality. CABI Wallingford pp. 23–49.

Bölter M. Bloem J. Meiners K. Möller R.(2006): Enumeration and biovolume determination of microbial cells in Bloem J. Hopkins D. W. Benedetti A.: Microbiological Methods for Assessing Soil Quality. CABI Wallingford pp. 93–107.

10.1016/S0038-0717(03)00235-9

10.1111/j.1469-8137.2004.01066.x

Bossio D. A., 1995, Impact of carbon and flooding on the metabolic diversity of microbial communities in soils., Appl. Environ. Microbiol., 61, 4043, 10.1128/aem.61.11.4043-4050.1995

Brussard L. Kuyper T. W. Didden W. A. M. de Goede R. G. M. Bloem J.(2004): Biological soil quality from biomass to biodiversity – Importance and resilience to management stress and disturbance in Schjønning P. Elmholt S. Christensen B. T.: Challenges in Modern Agriculture. CABI Wallingford pp. 139–161.

Burns R.(1978) Soil Enzymes. Academic Press London.

10.1016/S0038-0717(01)00108-0

10.1007/s003740100406

10.1002/1522-2624(200112)164:6<657::AID-JPLN657>3.0.CO;2-J

10.1007/s00374-002-0443-y

10.1007/s00442-003-1310-8

10.1016/S0038-0717(99)00135-2

10.1007/s00374-003-0646-x

10.1016/S0038-0717(97)00076-X

10.1002/jpln.200321041

Dilly O.(2005): Microbial energetics in soils in Buscot F. Varma A.: Microorganisms in Soils: Roles in Genesis and Functions. Springer Berlin pp. 123–138.

10.1007/s00374‐005‐0021‐1

10.1080/00380768.2004.10408545

10.1007/s003740100375

10.1002/1522-2624(200108)164:4<407::AID-JPLN407>3.0.CO;2-9

10.1023/A:1026271006634

10.1016/S0045-6535(03)00237-6

10.1128/AEM.70.1.468-474.2004

10.1007/BF00334573

10.1007/BF02986478

10.1111/j.1574-6941.1998.tb00549.x

10.1016/S0038-0717(03)00245-1

van Elsas J. D. Top E. M. Smalla K.(2006): Soil microbial community fingerprinting based on total community DNA or RNA in Bloem J. Hopkins D. W. Benedetti A.: Microbiological Methods for Assessing Soil Quality. CABI Wallingford pp. 187–203.

10.1023/A:1004682620283

10.1002/1522-2624(200106)164:3<239::AID-JPLN239>3.0.CO;2-0

10.1016/S1164-5563(01)01095-0

10.1016/S0167-8809(03)00087-2

10.1002/jpln.200290007

10.1016/S0038-0717(01)00143-2

10.1002/1522-2624(200208)165:4<408::AID-JPLN408>3.0.CO;2-3

10.1016/S0016-7061(01)00104-5

Findlay R. H., 1989, Efficacy of phospholipids analysis in determining microbial biomass in sediments., Appl. Environ. Microbiol., 55, 2888, 10.1128/aem.55.11.2888-2893.1989

10.1007/s00374-004-0776-9

10.2136/sssaj1996.03615995006000040025x

10.1016/S0038-0717(01)00016-5

10.1016/S0045-6535(02)00603-3

10.1016/0167-7012(91)90018-L

10.1016/0038-0717(93)90113-P

Garland J. L., 1991, Classification and characterization of hetrotrophic microbial communities on the basis of patterns of community‐level sole‐carbon‐source utilization., Appl. Environ. Microbiol., 57, 2351, 10.1128/aem.57.8.2351-2359.1991

10.1002/1522-2624(200208)165:4<421::AID-JPLN421>3.0.CO;2-N

10.1016/j.soilbio.2003.10.013

10.1128/AEM.69.7.3758-3766.2003

10.1016/S0929-1393(01)00141-X

Guckert J. B., 1985, Phospholipid, ester‐linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments., FEMS Microbiol. Ecol., 31, 147, 10.1111/j.1574-6968.1985.tb01143.x

10.2136/sssaj1999.6351188x

10.1016/j.soilbio.2004.08.023

Hagn A., 2002, Assessment of fungal diversity and community structure in agricultural used soils., Rec. Res. Develop. Microbiol., 6, 551

10.1007/s00374-003-0651-0

10.1016/S0038-0717(99)00145-5

10.1046/j.1351-0754.2003.0559.x

Hartmann A. Pukall R. Rothballer M. Gantner S. Metz S. Schloter M. Mogge B.(2004): Microbial community analysis in the rhizosphere by in situ and ex situ application of molecular probing biomarker and cultivation techniques in Varma A. Abbott L. Werner D. Hampp R.: Plant Surface Microbiology. Springer Berlin pp. 449–469.

10.1111/j.1462-2920.2003.00465.x

10.1016/0038-0717(93)90183-C

Höper H.(2006): Substrate‐induced respiration in Bloem J. Hopkins D. W. Benedetti A.: Microbiological Methods for Assessing Soil Quality. CABI Wallingford pp. 84–92.

Höper H. Kleefisch B.(2001): Untersuchung bodenbiologischer Parameter im Rahmen der Boden‐Dauerbeobachtung in Niedersachsen – Bodenbiologische Referenzwerte und Zeitreihen. Arbeitshefte Boden 2001/4 NLfB Hannover.

Jenkinson D. S.(1988): The determination of microbial biomass carbon and nitrogen in soil in Wilson J. R.: Advances in Nitrogen Cycling in Agricultural Ecosystems. CABI Wallingford pp. 368–386.

Jenkinson D. S. Ladd J. N.(1981): Microbial biomass in soil: Measurement and turnover in Paul E. A. Ladd J. N.: Soil Biochemistry Volume 5. Dekker New York pp. 415–471.

10.1016/0038-0717(79)90100-7

10.1016/0038-0717(76)90005-5

Joergensen R. G., 1995, Die quantitative Bestimmung der mikrobiellen Biomasse in Böden mit der Chloroform‐Fumigations‐Extraktions‐Methode., Göttinger Bodenkundl. Ber., 104, 1

10.1016/0038-0717(95)00102-6

10.1016/S0038-0717(99)00191-1

Joergensen R. G. Brookes P. C.(2005): Quantification of soil microbial biomass by fumigation‐extraction in Margesin R. Schinner F.: Manual of Soil Analysis – Monitoring and Assessing Soil Bioremediation. Soil Biology Volume 5. Springer Berlin pp. 283–297.

10.1016/S0038-0717(01)00069-4

10.1016/0038-0717(95)00101-8

10.1002/jpln.1998.3581610109

10.1016/j.soilbio.2004.11.021

10.1016/0038-0717(90)90039-3

10.1007/s00248-004-0135-2

10.1016/0038-0717(92)90046-Z

Khan K. S. Joergensen R. G.(2006): Microbial C N and P relationships in moisture‐stressed soils of Potohar Pakistan.J. Plant Nutr. Soil Sci. in press.

10.1007/BF00335958

10.1016/j.soilbio.2004.10.005

10.1016/j.soilbio.2003.08.019

10.1016/j.soilbio.2004.07.009

10.1016/j.soilbio.2004.05.011

10.1016/S0038-0717(03)00219-0

10.1016/S0269-7491(03)00244-6

10.1002/jpln.200421703

10.1016/S0929-1393(00)00108-6

10.1016/S0016-7061(01)00097-0

10.1007/s003740100340

10.1016/j.soilbio.2003.10.014

10.1078/072320203322346065

10.1016/S0038-0717(01)00133-X

10.1016/j.soilbio.2004.12.009

10.1046/j.1365-2389.2003.00496.x

10.1016/S0016-7061(01)00106-9

10.1126/science.1071148

10.1016/S0038-0717(03)00051-8

10.1007/s003740000316

10.1023/B:PLSO.0000016565.14718.4b

10.1016/S0929-1393(00)00109-8

10.1080/00380768.2004.10408544

10.1016/S0038-0717(02)00297-3

10.1016/S0038-0717(99)00065-6

10.1016/S0038-0717(01)00001-3

10.4141/cjss86-001

10.1016/S0167-7012(03)00089-7

10.1007/s002480000021

10.1007/s11104-005-4906-4

10.1007/s11104-004-0483-1

10.1016/j.soilbio.2003.12.015

10.1016/0038-0717(92)90275-3

10.1007/BF00384450

10.1016/S0304-3800(03)00114-5

Muhammad S. Müller T. Joergensen R. G.(2006): Decomposition of pea and maize straw in Pakistani soils along a gradient in salinity.Biol. Fertil. Soils in press.

10.1128/AEM.69.5.2816-2824.2003

10.1016/j.soilbio.2003.12.010

10.1016/S0953-7562(09)80723-5

10.1046/j.1469-8137.2003.00810.x

Paetz A. Wilke B.‐M.(2005): Soil sampling and storage in Margesin R. Schinner F.: Manual of Soil Analysis – Monitoring and Assessing Soil Bioremediation. Soil Biology Volume 5. Springer Berlin pp. 1–46.

10.1016/j.soilbio.2004.11.022

Potthoff M. Steenwerth K. L. Jackson L. E. Drenovsky R. E. Scow K. M. Joergensen R. G.(2006): Soil microbial community composition as affected by restoration practices in California grassland.Soil Biol. Biochem. in press.

10.1016/0038-0717(87)90076-9

10.1016/j.mimet.2004.04.001

Quintern M. Joergensen R. G. Wildhagen H.(2006): Permanent soil monitoring sites for documentation of soil fertility development after changing from conventional to organic farming.J. Plant Nutr. Soil Sci. in press.

10.1016/S0038-0717(02)00016-0

10.1002/1522-2624(200208)165:4<435::AID-JPLN435>3.0.CO;2-3

10.1016/j.soilbio.2005.04.034

Rothballer M., 2003, In situ localization and PGPR‐effect of Azospirillum brasilense strains colonizing roots of different wheat varieties., Symbiosis, 34, 261

10.1016/S0167-8809(03)00086-0

10.1016/S0929-1393(02)00091-4

10.1016/S0929-1393(03)00027-1

10.1007/BF00418670

10.1016/S0167-8809(03)00085-9

10.1016/S0167-8809(03)00089-6

10.1016/S0038-0717(99)00207-2

10.1016/S0016-7061(01)00101-X

10.1016/j.pedobi.2004.10.003

10.1128/AEM.71.1.175-184.2005

10.1007/s11104-005-7077-4

10.1016/0038-0717(73)90020-5

Smalla K., 1998, Analysis of BIOLOG GN substrate utilization patterns by microbial communities., Appl. Environ. Microbiol., 64, 1220, 10.1128/AEM.64.4.1220-1225.1998

10.1002/(SICI)1522-2624(199908)162:4<385::AID-JPLN385>3.0.CO;2-O

10.1016/0038-0717(85)90060-4

10.1016/j.soilbio.2005.02.035

10.1111/j.1574-6941.2001.tb00829.x

10.1002/jpln.1998.3581610309

10.1016/j.soilbio.2004.05.015

10.1016/j.chemosphere.2005.01.023

Tscherko D., 1999, Classification and monitoring of soil microbial biomass, N‐mineralization and enzyme activities to indicate environmental changes., Bodenkultur, 50, 215

10.1016/j.soilbio.2004.07.004

10.1016/j.baae.2005.02.004

10.1016/0038-0717(87)90052-6

10.1007/BF02205585

10.1023/B:PLSO.0000016553.49882.9e

10.1016/j.soilbio.2005.02.014

10.1016/j.soilbio.2005.02.039

10.1016/S0929-1393(03)00097-0

10.1007/s00374-004-0727-5

10.1016/0038-0717(89)90183-1

10.1016/S0038-0717(01)00006-2

Wiemken V., 2001, Effects of elevated carbon dioxide and nitrogen fertilization on mycorrhizal fine roots and the soil microbial community in beech‐spruce ecosystems on siliceous and calcareous soil., Microb. Ecol., 42, 126, 10.1007/s002480000080

10.1016/j.soilbio.2003.12.003

10.1016/j.ecoenv.2005.03.026

10.1016/0038-0717(94)90203-8

10.1016/S0045-6535(97)00155-0

10.1016/S0038-0717(97)00062-X

10.1016/0038-0717(96)00117-4

10.1016/j.soilbio.2004.07.041

10.1007/s10438-005-0093-6