The FungiResp method: An application of the MicroResp™ method to assess fungi in microbial communities as soil biological indicators

Ecological Indicators

Volumn 23, Issue , 2012, Pages 482-490

  Sassi, Meriem Ben ^a   Dollinger, Jeanne ^a   Renault, Pierre ^a   Tlili, Ahmed ^b   Bérard, Annette ^a  

^a UAPV   (France)

^b LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES   (Germany)

Author keywords

MicroResp ; Selective inhibition; Soil fungal catabolic structure; Soil microbial catabolic structure; Substrate induced respiration

Indexed keywords

AS-SOILS; BIOLOGICAL INDICATORS; BRONOPOL; COMPLEX SUBSTRATES; DECOMPOSERS; ECOSYSTEM SERVICES; FUNCTIONAL DIVERSITY; FUNGAL BIOMASS; FUNGAL COMMUNITY; MICROBIAL COMMUNITIES; NUTRIENT CYCLING; ORGANIC MATTER DECOMPOSITION; OXYTETRACYCLINES (OTC); SELECTIVE INHIBITION; SOIL FUNCTION; SOIL MICROBIAL COMMUNITY; SOIL QUALITY; SUBSTRATE UTILIZATION; SUBSTRATE-INDUCED RESPIRATIONS;

BACTERICIDES; DECOMPOSITION; ECOSYSTEMS; FUNGI; MICROORGANISMS; SUBSTRATES;

SOILS;

ANTIMICROBIAL ACTIVITY; BIOINDICATOR; CATABOLISM; CONCENTRATION (COMPOSITION); DECOMPOSITION; ECOSYSTEM SERVICE; FUNCTIONAL ROLE; FUNGUS; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; NONTARGET ORGANISM; NUTRIENT CYCLING; SOIL ECOSYSTEM; SOIL MICROORGANISM; SOIL ORGANIC MATTER; SOIL QUALITY; SPECIES DIVERSITY; SUBSTRATE;

FUNGI;

EID: 84861678091     PISSN: 1470160X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolind.2012.05.002     Document Type: Article

References (57)

1. J.P. Anderson, and K.H. Domsch Quantification of bacterial and fungal contributions to soil respiration Arch. Mikrobiol. 93 1973 113 127
2. J.P.E. Anderson, and K.H. Domsch Measurements of bacterial and fungal contribution to respiration of selected agricultural and forest soils Can. J. Microbiol. 21 1975 314 322
3. J.P.E. Anderson, and K.H. Domsch A physiological method for the quantitative measurement of microbial biomass in soil Soil Biol. Biochem. 10 1978 215 221
4. T.-H. Anderson, and K.H. Domsch Determination of ecophysiological maintenance carbon requirements of soil microorganisms in a dormant state Biol. Fertil. Soils 1 1985 81 89
5. V.L. Bailey, J.L. Smith, and H. Bolton Fungal to bacterial ratios in soil investigated for enhanced C sequestration Soil Biol. Biochem. 34 2002 997 1007
6. V.L. Bailey, J.L. Smith, and H. Bolton Novel antibiotics as inhibitors for the selective respiratory inhibition method of measuring fungal: bacterial ratios in soil Biol. Fertil. Soils 38 2003 154 160
7. G. Barcela-Moreno, and E. Bååth Bacterial and fungal growth in soil heated at different temperatures to simulate a range of fire intensities Soil Biol. Biochem. 41 2009 2517 2526
8. R.D. Bardgett, P.J. Hobbs, and A. Frostegard Changes in soil fungal: bacterial biomass ratios following reductions in the intensity of management of an upland grassland Biol. Fertil. Soils 22 1996 261 264
9. T. Bell, J.A. Newman, B.W. Silverman, S.L. Turner, and A.K. Lilley The contribution of species richness and composition to bacterial services Nature 436 2005 1157 1160
10. A. Bérard, M. Ben Sassi, P. Renault, and R. Gros Severe drought-induced community tolerance to heat wave. An experimental study on soil microbial processes J. Soils Sci. 2012 10.1007/s11368-012-0469-1
11. A. Bérard, T. Bouchet, G. Sévenier, A.L. Pablo, and R. Gros Resilience of soil microbial communities impacted by severe drought and high temperature in the context of Mediterranean heat-waves Eur. J. Soil Biol. 47 2011 333 342
12. A. Bérard, F. Rimet, Y. Capowiez, and C. Leboulanger Procedures for determining the pesticide sensitivity of indigenous soil algae - a possible bioindicator of soil contamination? Arch. Environ. Contam. Toxicol. 46 2004 24 31
13. S.A. Boyle, R.R. Yarwood, P.J. Bottomley, and D.D. Myrold Bacterial and fungal contributions to soil nitrogen cycling under Douglas fir and red alder at two sites in Oregon Soil Biol. Biochem. 40 2008 443 451
14. E. Branson Efficacy of bronopol against infection of rainbow trout (Oncorhynchus mykiss) with the fungus Saprolegnia species Vet. Rec. 151 2002 539 541
15. J.S. Buyer, D.P. Roberts, P. Millner, and E. Russek-Cohen Analysis of fungal communities by sole carbon source utilization profiles J. Microbiol. Meth. 45 2001 53 60
16. R. Calbrix, S. Barray, and K. Laval Analysis of potential functional diversity of soil bacterial community using sole-carbon-source utilization profiles: a reproducible procedure Eur. J. Soil Biol. 41 2005 11 20
17. C.D. Campbell, S.J. Chapman, C.M. Cameron, M.S. Davidson, and J.M. Potts A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil Appl. Environ. Microbiol. 69 2003 3593 3599
18. C.D. Campbell, S.J. Graystona, and D.J. Hirst Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities J. Microbiol. Meth. 30 1997 33 41
19. S.J. Chapman, C.D. Campbell, and R.R.E. Artz Assessing CLPPs using MicroResp™. A comparison with biolog and multi-SIR J. Soil Sediment 7 2007 406 410
20. Commission of the European Communities, 2002. Towards a Thematic Strategy for Soil Protection. 179 Final. p. 35.
21. W.R. Cookson, M.H. Beare, and P.E. Wilson Effects of prior crop residue management on microbial properties and crop residue decomposition Appl. Soil Ecol. 7 1998 179 188
22. W.R. Cookson, D.V. Murphy, and M.M. Roper Characterizing the relationships between soil organic matter components and microbial function and composition along a tillage disturbance gradient Soil Biol. Biochem. 40 2008 763 777
23. B.P. Degens, and J.A. Harris Development of a physiological approach to measuring the catabolic diversity of soil microbial communities Soil Biol. Biochem. 29 1997 1309 1320
24. J.K. Dobranic, and J.C. Zak A microtiter plate procedure for evaluating fungal functional diversity Mycologia 91 1999 756 765
25. J.W. Doran, and M.R. Zeiss Soil health and sustainability: managing the biotic component of soil quality Appl. Soil Ecol. 15 2000 3 11
26. S.D. Frey, E.T. Elliott, and K. Paustian Bacterial and fungal abundance and biomass in conventional and no-tillage agroecosystems along two climatic gradients Soil Biol. Biochem. 31 1999 573 585
27. B.M. Gómez, M. Lores, and J. Domínguez 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 2010 1348 1354
28. J.G. Hardman, L.E. Limbird, and A.G. Gilman Goodman and Gilman's. The Pharmacological Basis of Therapeutics 10th ed. 2001 McGraw-Hill New York, NY p. 2045
29. Z. Hossain, and S. Sugiyama Geographical structure of soil microbial communities in northern Japan: effects of distance land use type and soil properties Eur. J. Soil Biol. 47 2011 88 94
30. R.G. Joergensen, P.C. Brookes, and D.S. Jenkinson Survival of the soil microbial biomass at elevated temperatures Soil Biol. Biochem. 22 1990 1129 1136
31. M. Klamer, and E. Bååth Microbial community dynamics during composting of straw material studied using phospholipid fatty acid analysis FEMS Microbiol. Ecol. 27 1998 9 20
32. Q. Lin, and P.C. Brookes An evaluation of the substrate-induced respiration method Soil Biol. Biochem. 31 1999 1969 1983
33. Q. Lin, and P.C. Brookes Comparison of substrate induced respiration, selective inhibition and biovolume measurments of microbial biomass and its community structure in unamended, ryegrass-amended, fumigated and pesticide-treated soils Soil Biol. Biochem. 31 1999 1999 2014
34. E.J. Lundquist, L.E. Jackson, and K.M. Scow Wet-dry cycles affect dissolved organic carbon in two California agricultural soils Soil Biol. Biochem. 31 1999 1031 1038
35. P. Millard, and B.K. Singh Does grassland vegetation drive soil microbial diversity? Nutr. Cycl. Agroecosyst. 88 2010 147 158
36. Millennium Ecosystem Assessment Ecosystems and Human Well-being: Synthesis 2005 Island Press Washington, DC
37. T. Nakamoto, and S. Wakahara Development of substrate induced respiration (SIR) method combined with selective inhibition for estimating fungal and bacterial biomass in Humic Andosols Plant Prod. Sci. 7 2004 70 76
38. D. Or, B.F. Smets, J.M. Wraith, A. Deschesne, and S.P. Friedman Physical constraints affecting bacterial habitats and activity in unsaturated porous media - a review Adv. Water Res. 30 2007 1505 1527
39. A. Oren, and Y. Steinberger Catabolic profiles of soil fungal communities along a geographic climatic gradient in Israel Soil Biol. Biochem. 40 2008 2578 2587
40. Z. Piotrowska-Seget, R. Engel, E. Nowak, and J. Kozdro Successive soil treatment with captan or oxytetracycline affects non-target microorganisms World J. Microbiol. Biotechnol. 24 2008 2843 2848
41. R.M.C.P. Rajapaksha, M.A. Tobor-Kapłon, and E. Bååth Metal toxicity affects fungal and bacterial activities in soil differently Appl. Environ. Microbiol. 70 2004 2966 2973
42. H.L. Reynolds, A. Packer, J.D. Bever, and K. Clay Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics Ecology 84 2003 2281 2291
43. K. Ritz, H.I.J. Black, C.D. Campbell, J.A. Harris, and C. Wood Selecting biological indicators for monitoring soils: a framework for balancing scientific and technical opinion to assist policy development Ecol. Indic. 9 2009 1212 1221
44. R. Romaniuk, L. Giuffre, A. Costantini, and P. Nannipieri Assessment of soil microbial diversity measurements as indicators of soil functioning in organic and conventional horticulture systems Ecol. Indic. 11 2011 1345 1353
45. J. Rousk, P.C. Brookes, and E. Bååth Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil Soil Biol. Biochem. 42 2010 926 934
46. J. Rousk, P.C. Brookes, and E. Bååth Contrasting soil pH effects on fungal and bacterial growth suggests functional redundancy in carbon mineralisation Appl. Environ. Microbiol. 75 2009 1589 1596
47. J. Rousk, L.A. Demoling, and E. Bååth Contrasting short-term antibiotic effects on respiration and bacterial growth compromises the validity of the selective respiratory inhibition technique to distinguish fungi and bacteria Microb. Ecol 58 2009 75 85
48. V. Saul-Tcherkas, and Y. Steinberger Substrate utilization patterns of desert soil microbial communities in response to xeric and mesic conditions Soil Biol. Biochem. 41 2009 1882 1893
49. M.E. Schutter, and R.P. Dick Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities Soil Sci. Soc. Am. J. 64 2000 1659 1668
50. J.A. Shepherd, D. Roger, R.D. Waigh, and P. Gilbert Antibacterial action of 2-bromo-2-nitropropane-1,3-diol(bronopol) Antimicrob. Agents Chemother. 32 1988 1693 1698
51. J. Six, S.D. Frey, R.K. Thiet, and K.M. Batten Bacterial and fungal contributions to carbon sequestration in agroecosystems Soil Sci. Soc. Am. J. 70 2006 555 569
52. M.S. Strickland, and J. Rousk Considering fungal:bacterial dominance in soils - methods controls, and ecosystem implications Soil Biol. Biochem. 42 2010 1385 1395
53. C.J.F. Ter Braak, and P. Smilauer CANOCO Reference Manual and User's Guide to Canoco for Windows: Software for Canonical Community Ordination (Version 4) 1998 Microcomputer Power Ithaca, New York p. 352
54. S. Thiele-Bruhn, and I.-C. Beck Effects of sulfonamide and tetracycline antibiotics on soil microbial activity and microbial biomass Chemosphere 59 2005 457 465
55. A. Tlili, M. Marechal, B. Montuelle, B. Volat, U. Dorigo, and A. Bérard Use of the MicroResp™ method to assess pollution-induced community tolerance for lotic biofilms Environ. Pollut. 159 2011 18 24
56. E. Uhlirova, J. Elhottova, J. Triska, and H. Santruckova Physiology and microbial community structure in soil at extreme water content Folia Microbiol. 50 2005 161 166
57. G. Welp, and G.W. Brummer Microbial toxicity of Cd and Hg in different soils related to total and water-soluble contents Ecotoxicol. Environ. Saf. 38 1997 200 220