1 introduction ............................................... 1
1.1 Biodegradation in soil ..................................... 1
1.1.1 Pollution of soil ................................... l
1.1.2 Bacterial degradation as ecosystem service .......... 2
1.1.3 Soil as heterogeneous environment ................... 3
1.1.4 Fungal networks ..................................... 4
1.2 Environmental disturbances ................................. 4
1.2.1 Disturbance in ecology .............................. 4
1.2.2 Microbial response to disturbances .................. 5
1.3 Microbial simulation models ................................ 6
1.4 Aim of research ............................................ 7
1.4.1 Research objectives ................................. 8
1.5 Chapters overview .......................................... 8
2 The modelling framework ecolony .......................... 11
2.1 Base model ................................................ 11
2.1.1 Model validation ................................... 12
2.2 Extended model............................................. 13
2.2.1 Disturbance events.................................. 13
2.2.2 Substrate input..................................... 13
2.3 Scenarios.................................................. 14
2.3.1 Initial conditions ................................. 14
2.3.2 Disturbance regimes ................................ 15
2.3.3 Parameterization ................................... 16
2.3.4 Analyses ........................................... 16
3 functional resilience to single disturbance events ........ 19
3.1 Introduction .............................................. 19
3.2 Methods ................................................... 20
3.2.1 Scenarios .......................................... 20
3.2.2 Analysis ........................................... 21
3.3 Results and Discussion .................................... 21
3.3.1 Spatiotemporal dynamics of recovery ................ 21
3.3.2 Relevance of processes ............................. 24
3.3.3 Relevance of spatial disturbance pattern ........... 26
3.3.4 Implications for general ecological theory ......... 29
3.3.5 Implications for natural systems and applications .. 29
3.3.6 Potentials and restrictions of the presented
modelling approach ................................. 30
3.4 Conclusion ................................................ 31
4 functional resistance to recurrent disturbance events ..... 33
4.1 Introduction .............................................. 33
4.2 Methods ................................................... 34
4.2.1 Scenarios .......................................... 34
4.2.2 Analysis ........................................... 35
4.2.3 Classification of habitat types .................... 36
4.3 Results ................................................... 36
4.3.1 Relevance of spatial disturbance pattern ........... 36
4.3.2 Relevance of disturbance return interval ........... 40
4.4 Discussion ................................................ 42
4.4.1 Factors controlling functional resistance .......... 42
4.4.2 Relevance of dispersal networks .................... 44
4.4.3 Relevance for natural systems ...................... 45
4.4.4 Model potentials and limitations ................... 45
5 Emergence of functional collapse and its prevention ....... 47
5.1 Introduction .............................................. 47
5.2 Methods ................................................... 48
5.3 Results ................................................... 49
5.3.1 Relevance of disturbance characteristics ........... 49
5.3.2 Relevance of ecological processes .................. 53
5.3.3 Relevance of dispersal networks .................... 56
5.4 Discussion ................................................ 56
5.4.1 Thresholds for functional collapse ................. 56
5.4.2 Key factors for functional resistance .............. 60
5.4.3 Implications for management strategies ............. 61
6 Synthesis and outlook ..................................... 63
6.1 Main results .............................................. 63
6.1.1 Key factors for functional stability ............... 63
6.1.2 Influence of dispersal networks .................... 66
6.1.3 A question of scale ................................ 66
6.2 Implications for natural systems and management
applications .............................................. 67
6.3 Applied methodology ....................................... 68
6.3.1 Model potentials ................................... 68
6.3.2 Model limitations .................................. 69
6.3.3 Outcome visualization .............................. 70
6.4 Outlook ................................................... 70
6.4.1 Bacteria ........................................... 70
6.4.2 Fungal networks .................................... 71
6.4.3 Soil environment ................................... 73
6.4.4 Disturbances ....................................... 75
A Appendix .................................................. 77
List of Figures ................................................ 83
List of Tables ................................................. 89
List of Symbols ................................................ 90
bibliography ................................................... 93
acknowledgements .............................................. 107
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