Abstract
A method was designed to simultaneously estimate the diversity of fungal communities and growth-related indices. It is based on cluster analysis of image data of fungal colonies growing in agar plates. A total of 20 features (colony area, mean colours of the upper and lower colony sides as well as features describing the colour distribution) were recorded. The relative differentiating powers of these features were determined. Since the intensity of colours and their ratio to one another were dependent on the camera distance, colours were recorded at a constant distance of 36 cm. In contrast, growth rates were taken at a distance of 68 cm. Identification of a reproducible clustering level was favoured by the fact that, when similarity was reduced in dendrograms, the evenness in type distribution decreased at a higher rate than the number of image types and, in addition, exhibited distinct minima and intermittent maxima. In all data sets examined, abundant and rare image types, including singletons, always occurred at the first evenness minimum. Comparing fungal samples from a metal-contaminated arable soil and the relevant control showed the richness in image types and three growth-related indices (the average and the variation coefficient of growth rates as well as the portion of isolates with growth rates >3 mm day−1) to be greater in the control. Of these four indices, the former was the least sensitive and the latter the most sensitive indicator of metal stress.
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References
Andrews JH (1984) Relevance of r- and K-theory to the ecology of plant pathogens. In: Klug MJ, Reddy CA (eds) Current perspectives in microbial ecology. American Society of Microbiology, Washington DC, pp 1–7
Bjørnsen PK (1986) Automatic determination of bacterioplankton biomass by image analysis. Appl Environ Microbiol 51:1199–1204
Blackburn N, Hagström Å, Wikner J, Cuadros-Hansson R, Bjørnsen PK (1998) Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network-based image analysis. Appl Environ Microbiol 64:3246–3255
Buxton EW (1954) Heterocaryosis and variability in Fusarium oxysporum f. gladioli. J Gen Microbiol 10:71–84
Chaudri AM, McGrath SP, Giller KE, Rietz E, Sauerbeck DR (1993) Enumeration of indigenous Rhizobium leguminosarum biovar trifolii in soils previously treated with metal-contaminated sewage sludge. Soil Biol Biochem 25:301–309
Colin TS (1996) Agar plate colony counting and size determination. Application note, Product, SigmaScan Pro, Labtronics Inc., Jandel Scientific Software
Colin TS (1997) Colony counting and size determination. Application note, Product: Mocha Video Analysis System, Labtronics Inc.
Fließbach A, Martens R, Reber HH (1994) Soil microbial biomass and microbial activity in soils treated with heavy metal contaminated sewage sludge. Soil Biol Biochem 26:1201–1205
Gasol JM, Massana R, Pedrós-Alió C (1997) Bacterial size structure as a method to analyze communities. In: Martins MT, Zanoli Sato MI, Tiedje JM, Hagler LCN, Döbereiner J, Sanchez P (eds) Progress in microbial ecology. Sociedade Brasileira de Microbiologia, São Paulo, pp 155–160
Gottwald S, Germeier C, Ruhmann W, Lorch HJ, Ottow JCG (1996) Einsatz der digitalen Bildanalyse für die Bestimmung von Fusarium spp. 50. Deutsche Pflanzenschutztagung. Mitt Biol Bundesanst Land- Forstwirtsch 321:352
Hoffmann GM (1964) Untersuchungen über die Kernverhältnisse bei Fusarium oxysporum f. callistephi. Arch Mikrobiol 49:51–63
Liu J, Dazzo FB, Glagoleva O, Yu B, Jain AK (2001) CMEIAS: a computer-aided system for the image analysis of bacterial morphotypes in microbial communities. Microb Ecol 41:173–194
Martin JP (1950) Use of acid, rose bengal, and streptomycin in the plate method for estimating soil fungi. Soil Sci 69:215–232
Meijer BC, Kootstra GJ, Wilkinson MHF (1990) A theoretical and practical investigation into the characterization of bacterial species by image analysis. Binary 2:21–31
Møller S, Kristensen CS, Poulsen LK, Carstensen JM, Molin S (1995) Bacterial growth on surfaces: automated image analysis for quantification of growth rate-related parameters. Appl Environ Microbiol 61:741–748
Newton G, Kendrick B (1990) Image processing in taxonomy. Sydowia 42:246–272
Pitt JI (1990) PENNAME, a new computer key to common Penicillium species. In: Samson RA, Pitt JI (eds) Modern concepts in Penicillium and Aspergillus classification. Plenum Press, New York, pp 279–281
Pochon J, Tardieux P (1962) Techniques d’analyse en microbiologie du sol. Editions de la Tourelle, St. Mande (Seine)
Sanders HL (1968) Marine benthic diversity: a comparative study. Am Nat 102:243–282
Simberloff D (1972) Properties of the rarefaction diversity measurement. Am Nat 106:414–418
Stelzer M (2002) Zusammenhang zwischen Stresstoleranz, Diversität und katabolischer Vielseitigkeit schwermetallgestresster Bodenpilze. Thesis, Technische Universität Braunschweig. Published under: http://www.biblio.tu-bs.de/ediss/data/20030210a/20030210a.html
Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58:238–244
Wenderoth DF, Reber HH (1999a) Correlation between structural diversity and catabolic versatility of metal-affected prototrophic bacteria in soil. Soil Biol Biochem 31:345–352
Wenderoth DF, Reber HH (1999b) Development and comparison of methods to estimate the catabolic versatility of metal-affected soil microbial communities. Soil Biol Biochem 31:1793–1802
Wimpenny J, Wilkinson T, Peters A (1995) Monitoring microbial colony growth using image analysis techniques. Binary 7:14–18
Acknowledgements
The authors are grateful to Susanne Behn and Michael Diedrichs for their technical assistance. Technical support from Detlef Pütz of Nikon, Düsseldorf (Germany) is also gratefully acknowledged. Dr. Siegfried Draeger of Braunschweig University provided a collection of fungi. The investigation was supported by a grant from Deutsche Forschungsgemeinschaft (DFG) for two years.
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Stelzer, M., Reber, H.H. Combined method of image and cluster analysis to estimate the structural diversity of fungal communities. Biol Fertil Soils 42, 10–16 (2005). https://doi.org/10.1007/s00374-005-0868-1
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DOI: https://doi.org/10.1007/s00374-005-0868-1