NWI-BB036B-2024-KW3-V Applied Ecology
Applied ecology
Lecturers: Quinten Struik, Fritz Christian, Sarian Kosten, Leon Lamers, Tom Heuts, Jack Hemelraad
Course followed in 2025.
All information comes from the lectures provided by the lecturers via BrightSpace, unless otherwise
stated. The student lectures were made by the students that participated in the course.
Table of contents
Water quality assessment ....................................................................................................................... 5
Excursion.................................................................................................................................................. 6
L1 Introduction ...................................................................................................................................... 12
L2 Biogeochemistry ............................................................................................................................... 12
Planetary boundaries ........................................................................................................................ 13
Role of biogeochemistry in ecological science .................................................................................. 13
Key biogeochemical processes important for ecosystem functioning .............................................. 14
Decomposition and mineralization................................................................................................ 14
Carbon and energy flows ............................................................................................................... 14
Reduction and oxidation................................................................................................................ 14
Oxygen ........................................................................................................................................... 16
Carbon (C) ...................................................................................................................................... 17
Nitrogen (N) ................................................................................................................................... 17
Phosphorus (P) .............................................................................................................................. 19
Sulphur (S) ..................................................................................................................................... 20
Iron (Fe) ......................................................................................................................................... 21
Importance of processes for ecological applications, including mitigation strategies, nature
conservation, ecological resoration and water management ........................................................... 21
L4 Climate proof nature management .................................................................................................. 22
Scientific approaches used to assess climate change ....................................................................... 22
Wide-range of ecological responses to climate change .................................................................... 23
Measure to enhance or conserve ...................................................................................................... 24
L5a Air pollution .................................................................................................................................... 27
What is observed? ............................................................................................................................. 27
Sources of N and S deposition ........................................................................................................... 28
Effects of N and S deposition ............................................................................................................. 29
Acidification ....................................................................................................................................... 29
Buffering ............................................................................................................................................ 30
, NWI-BB036B-2024-KW3-V Applied Ecology
Causes of multiple effects of nitrogen in ecosystems ....................................................................... 31
Argue for policy targets for governments to limit N-pollution damage ............................................ 31
Management options to mitigate acidification effects.................................................................. 31
L5b: Critical loads concept and eutrophication ..................................................................................... 32
Critical load ........................................................................................................................................ 32
Effects of increased nitrogen deposition and concentration............................................................. 33
Direct toxicity of ammonia (NH4+) ..................................................................................................... 34
Example of N deposition on mosses ................................................................................................. 34
Eu protection ..................................................................................................................................... 34
L6: Mangroves and blue carbon ............................................................................................................ 35
Identify and distinguish disturbances and stressors for mangrove ecosystems ............................... 35
Describe how resistance and recovery are related to resilience. Explain the effects of disturbance
and stress on the structure of mangrove forests through resilience. ............................................... 36
Restoration of mangroves ................................................................................................................. 37
Explain the similar and distinct processes in blue carbon storage compared to terrestrial carbon
storage (i.e. in peatlands) .................................................................................................................. 37
Argue the differences between ‘Building with nature’ and man-made structures in coastal
protection. ......................................................................................................................................... 37
Link the processes that occur in and affect mangroves to other ecosystems ................................... 38
L7: Water framework directive .............................................................................................................. 38
General water quality and features of the WFD................................................................................ 38
Ecological water quality ..................................................................................................................... 39
How to improve water quality and prevent deterioration? .............................................................. 41
Assessment of new activities............................................................................................................. 41
L8: inland waters ................................................................................................................................... 41
Critical factors in determining the effectiveness or the failure of a specific measure in nature
management and environmental management................................................................................ 41
Explain importance of system analysis .............................................................................................. 42
How system analysis works for a real-life case from nature and environmental management........ 43
Critically assess the effectiveness and efficiency of source and effect-oriented measures used in
nature management and environmental management. ................................................................... 47
Formulate adequate measures that can enhance or conserve biological quality in different types of
systems threatened by anthropogenic activities. .............................................................................. 47
Argue in depth how specific ecological feedback mechanisms enhance or decrease the
effectiveness of measures applied in nature and environmental management. .............................. 47
Reason which factors are critical in determining the effectiveness or the failure of a specific
measure in nature management and environmental management. ................................................ 47
, NWI-BB036B-2024-KW3-V Applied Ecology
To explain what biomanipulation and geo-engineering entail and argue under which conditions
these tools may be effective.............................................................................................................. 47
L9: aquaculture ...................................................................................................................................... 47
Explain the key ecological and biogeochemical processes in aquaculture systems .......................... 47
Explain how ecological and biogeochemical knowledge can be applied to make aquaculture more
environmentally sustainable ............................................................................................................. 49
Mechanistically describe the environmental effects of specific aquaculture management options 51
L10: biological water quality assessment .............................................................................................. 51
L11: connecting aquatic ecosystems to the carbon cycle...................................................................... 51
Explain and recognize key pathways of the carbon cycle .................................................................. 51
Explain what makes aquatic ecosystems hotspots for CH4 emissions .............................................. 52
Explain how different environmental parameters affect the C-emissions from aquatic systems ..... 52
Argue why aquatic ecosystem restoration can help reducing aquatic greenhouse gas emissions ... 55
L12: Peatlands ....................................................................................................................................... 55
Peatland functioning ......................................................................................................................... 55
Interactions between peat characteristics, plant communities including peat-forming potential and
hydro-dynamic shaping conditions for peat conservation ................................................................ 57
Restoration of peatlands ................................................................................................................... 59
Plant groups....................................................................................................................................... 60
Peat mosses // Sphagnum ............................................................................................................. 60
Sedges // Carex .............................................................................................................................. 61
Reed and helophytes // Phragmites .............................................................................................. 61
Alder // Alnus - berk ...................................................................................................................... 62
Landscape scale water-carbon connectivity ...................................................................................... 62
L13: Drylands ......................................................................................................................................... 65
Functioning of heathlands and biodiverse acidic grasslands, including heathland pools ................. 65
Deterioration of drylands .................................................................................................................. 66
Restoration of drylands ..................................................................................................................... 68
L14: New nature areas and rewilding .................................................................................................... 70
Different types of nature creation ..................................................................................................... 70
Hydrological, biogeochemical, ecological constraints on transformation of former agricultural lands
to nature ............................................................................................................................................ 70
Hydrology ...................................................................................................................................... 70
Biogeochemical constrains ............................................................................................................ 72
Ecological constraints .................................................................................................................... 73
Hard to reverse but we have to!........................................................................................................ 73
Processes: drought, acidification, eutrophication, toxicity ............................................................... 76
, NWI-BB036B-2024-KW3-V Applied Ecology
Lectures of students .............................................................................................................................. 78
Phosphate eutrophication in nitrate-polluted wetlands (Smolders et al., 2010) .............................. 78
Explain what internal eutrophication is and how it differs from external eutrophication; ........... 78
Explain why phosphorus generally is less mobile in soils and sediments than nitrate; ................ 78
Explain why hydrological models - based on input of nitrogen and transportation only - may in
deeper aquifers; overestimate the nitrate concentration ............................................................. 78
Describe in detail two different processes through which an increased availability of sulphate in
aquatic sediments can increase internal eutrophication. Explain in detail how nitrate pollution of
groundwater can result in an increase in sediment phosphorus release...................................... 79
Nature based solutions to climate changes and other global challenges (Seddon et al., 2020) ....... 79
Explain what Nature-based solutions are...................................................................................... 79
Give examples of NbS aiming at reducing exposure, reducing sensitivity and supporting adaptive
capacity related to ecosystems and to socioeconomic systems; Mention and explain trade-offs
related to specific NbS; .................................................................................................................. 80
Mention and explain challenges related to the evaluation of the effectiveness of NbS ............... 81
Aquatic ecosystems and their connection to carbon cycle (Aben et al., 2022)................................. 81
Explain the interactions between climate change and regime shifts in shallow waters; .............. 81
b) Explain what climate-ecosystem feedbacks are and illustrate this using shallow waters as an
example; ........................................................................................................................................ 82
c) Describe in detail how and through which processes a shift from submerged macrophytes to
algae or free-floating plant dominance may alter diffusive and ebullitive CH4 emissions. .......... 82
d) Explain why CH4 ebullition tends to respond much stronger to warming than CH4 diffusion to
the atmosphere ............................................................................................................................. 83
Peatlands and wetscapes (Temmink et al., 2023) ............................................................................. 83
a) Explain what wetscapes are (types); ......................................................................................... 83
b) Explain what wetscapes include and what their potentials are; d) Explain what paludiculture is
and how paludiculture can be implemented in wetscapes ........................................................... 84
c) Argue why wetscapes a more sustainable alternative for drainage-based peatland use; ........ 85
Cases and solutions for eutrophication in inland waters (Lürling & Mucci, 2020) ............................ 86
a) Explain which processes are responsible for the hysteresis between nutrient loading and
water transparency in shallow waters. .......................................................................................... 86
b) Discuss pro’s and cons of at least two different physical methods used to combat
cyanobacterial blooms and explain the processes they aim to tackle; ......................................... 86
c) Discuss pro’s and cons of at least two different chemical methods used to combat
cyanobacterial blooms and explain the processes they aim to tackle; ......................................... 87
d) Explain why in many (Dutch) systems within-lake measures are inevitable ............................. 88
Coastal waters, seagrass restoration (Cronau et al., 2023) ............................................................... 89
a) Explain what bottom-up (resource-driven) and top-down (consumer-driven) trophic, and non-
trophic interactions are; ................................................................................................................ 89
Applied ecology
Lecturers: Quinten Struik, Fritz Christian, Sarian Kosten, Leon Lamers, Tom Heuts, Jack Hemelraad
Course followed in 2025.
All information comes from the lectures provided by the lecturers via BrightSpace, unless otherwise
stated. The student lectures were made by the students that participated in the course.
Table of contents
Water quality assessment ....................................................................................................................... 5
Excursion.................................................................................................................................................. 6
L1 Introduction ...................................................................................................................................... 12
L2 Biogeochemistry ............................................................................................................................... 12
Planetary boundaries ........................................................................................................................ 13
Role of biogeochemistry in ecological science .................................................................................. 13
Key biogeochemical processes important for ecosystem functioning .............................................. 14
Decomposition and mineralization................................................................................................ 14
Carbon and energy flows ............................................................................................................... 14
Reduction and oxidation................................................................................................................ 14
Oxygen ........................................................................................................................................... 16
Carbon (C) ...................................................................................................................................... 17
Nitrogen (N) ................................................................................................................................... 17
Phosphorus (P) .............................................................................................................................. 19
Sulphur (S) ..................................................................................................................................... 20
Iron (Fe) ......................................................................................................................................... 21
Importance of processes for ecological applications, including mitigation strategies, nature
conservation, ecological resoration and water management ........................................................... 21
L4 Climate proof nature management .................................................................................................. 22
Scientific approaches used to assess climate change ....................................................................... 22
Wide-range of ecological responses to climate change .................................................................... 23
Measure to enhance or conserve ...................................................................................................... 24
L5a Air pollution .................................................................................................................................... 27
What is observed? ............................................................................................................................. 27
Sources of N and S deposition ........................................................................................................... 28
Effects of N and S deposition ............................................................................................................. 29
Acidification ....................................................................................................................................... 29
Buffering ............................................................................................................................................ 30
, NWI-BB036B-2024-KW3-V Applied Ecology
Causes of multiple effects of nitrogen in ecosystems ....................................................................... 31
Argue for policy targets for governments to limit N-pollution damage ............................................ 31
Management options to mitigate acidification effects.................................................................. 31
L5b: Critical loads concept and eutrophication ..................................................................................... 32
Critical load ........................................................................................................................................ 32
Effects of increased nitrogen deposition and concentration............................................................. 33
Direct toxicity of ammonia (NH4+) ..................................................................................................... 34
Example of N deposition on mosses ................................................................................................. 34
Eu protection ..................................................................................................................................... 34
L6: Mangroves and blue carbon ............................................................................................................ 35
Identify and distinguish disturbances and stressors for mangrove ecosystems ............................... 35
Describe how resistance and recovery are related to resilience. Explain the effects of disturbance
and stress on the structure of mangrove forests through resilience. ............................................... 36
Restoration of mangroves ................................................................................................................. 37
Explain the similar and distinct processes in blue carbon storage compared to terrestrial carbon
storage (i.e. in peatlands) .................................................................................................................. 37
Argue the differences between ‘Building with nature’ and man-made structures in coastal
protection. ......................................................................................................................................... 37
Link the processes that occur in and affect mangroves to other ecosystems ................................... 38
L7: Water framework directive .............................................................................................................. 38
General water quality and features of the WFD................................................................................ 38
Ecological water quality ..................................................................................................................... 39
How to improve water quality and prevent deterioration? .............................................................. 41
Assessment of new activities............................................................................................................. 41
L8: inland waters ................................................................................................................................... 41
Critical factors in determining the effectiveness or the failure of a specific measure in nature
management and environmental management................................................................................ 41
Explain importance of system analysis .............................................................................................. 42
How system analysis works for a real-life case from nature and environmental management........ 43
Critically assess the effectiveness and efficiency of source and effect-oriented measures used in
nature management and environmental management. ................................................................... 47
Formulate adequate measures that can enhance or conserve biological quality in different types of
systems threatened by anthropogenic activities. .............................................................................. 47
Argue in depth how specific ecological feedback mechanisms enhance or decrease the
effectiveness of measures applied in nature and environmental management. .............................. 47
Reason which factors are critical in determining the effectiveness or the failure of a specific
measure in nature management and environmental management. ................................................ 47
, NWI-BB036B-2024-KW3-V Applied Ecology
To explain what biomanipulation and geo-engineering entail and argue under which conditions
these tools may be effective.............................................................................................................. 47
L9: aquaculture ...................................................................................................................................... 47
Explain the key ecological and biogeochemical processes in aquaculture systems .......................... 47
Explain how ecological and biogeochemical knowledge can be applied to make aquaculture more
environmentally sustainable ............................................................................................................. 49
Mechanistically describe the environmental effects of specific aquaculture management options 51
L10: biological water quality assessment .............................................................................................. 51
L11: connecting aquatic ecosystems to the carbon cycle...................................................................... 51
Explain and recognize key pathways of the carbon cycle .................................................................. 51
Explain what makes aquatic ecosystems hotspots for CH4 emissions .............................................. 52
Explain how different environmental parameters affect the C-emissions from aquatic systems ..... 52
Argue why aquatic ecosystem restoration can help reducing aquatic greenhouse gas emissions ... 55
L12: Peatlands ....................................................................................................................................... 55
Peatland functioning ......................................................................................................................... 55
Interactions between peat characteristics, plant communities including peat-forming potential and
hydro-dynamic shaping conditions for peat conservation ................................................................ 57
Restoration of peatlands ................................................................................................................... 59
Plant groups....................................................................................................................................... 60
Peat mosses // Sphagnum ............................................................................................................. 60
Sedges // Carex .............................................................................................................................. 61
Reed and helophytes // Phragmites .............................................................................................. 61
Alder // Alnus - berk ...................................................................................................................... 62
Landscape scale water-carbon connectivity ...................................................................................... 62
L13: Drylands ......................................................................................................................................... 65
Functioning of heathlands and biodiverse acidic grasslands, including heathland pools ................. 65
Deterioration of drylands .................................................................................................................. 66
Restoration of drylands ..................................................................................................................... 68
L14: New nature areas and rewilding .................................................................................................... 70
Different types of nature creation ..................................................................................................... 70
Hydrological, biogeochemical, ecological constraints on transformation of former agricultural lands
to nature ............................................................................................................................................ 70
Hydrology ...................................................................................................................................... 70
Biogeochemical constrains ............................................................................................................ 72
Ecological constraints .................................................................................................................... 73
Hard to reverse but we have to!........................................................................................................ 73
Processes: drought, acidification, eutrophication, toxicity ............................................................... 76
, NWI-BB036B-2024-KW3-V Applied Ecology
Lectures of students .............................................................................................................................. 78
Phosphate eutrophication in nitrate-polluted wetlands (Smolders et al., 2010) .............................. 78
Explain what internal eutrophication is and how it differs from external eutrophication; ........... 78
Explain why phosphorus generally is less mobile in soils and sediments than nitrate; ................ 78
Explain why hydrological models - based on input of nitrogen and transportation only - may in
deeper aquifers; overestimate the nitrate concentration ............................................................. 78
Describe in detail two different processes through which an increased availability of sulphate in
aquatic sediments can increase internal eutrophication. Explain in detail how nitrate pollution of
groundwater can result in an increase in sediment phosphorus release...................................... 79
Nature based solutions to climate changes and other global challenges (Seddon et al., 2020) ....... 79
Explain what Nature-based solutions are...................................................................................... 79
Give examples of NbS aiming at reducing exposure, reducing sensitivity and supporting adaptive
capacity related to ecosystems and to socioeconomic systems; Mention and explain trade-offs
related to specific NbS; .................................................................................................................. 80
Mention and explain challenges related to the evaluation of the effectiveness of NbS ............... 81
Aquatic ecosystems and their connection to carbon cycle (Aben et al., 2022)................................. 81
Explain the interactions between climate change and regime shifts in shallow waters; .............. 81
b) Explain what climate-ecosystem feedbacks are and illustrate this using shallow waters as an
example; ........................................................................................................................................ 82
c) Describe in detail how and through which processes a shift from submerged macrophytes to
algae or free-floating plant dominance may alter diffusive and ebullitive CH4 emissions. .......... 82
d) Explain why CH4 ebullition tends to respond much stronger to warming than CH4 diffusion to
the atmosphere ............................................................................................................................. 83
Peatlands and wetscapes (Temmink et al., 2023) ............................................................................. 83
a) Explain what wetscapes are (types); ......................................................................................... 83
b) Explain what wetscapes include and what their potentials are; d) Explain what paludiculture is
and how paludiculture can be implemented in wetscapes ........................................................... 84
c) Argue why wetscapes a more sustainable alternative for drainage-based peatland use; ........ 85
Cases and solutions for eutrophication in inland waters (Lürling & Mucci, 2020) ............................ 86
a) Explain which processes are responsible for the hysteresis between nutrient loading and
water transparency in shallow waters. .......................................................................................... 86
b) Discuss pro’s and cons of at least two different physical methods used to combat
cyanobacterial blooms and explain the processes they aim to tackle; ......................................... 86
c) Discuss pro’s and cons of at least two different chemical methods used to combat
cyanobacterial blooms and explain the processes they aim to tackle; ......................................... 87
d) Explain why in many (Dutch) systems within-lake measures are inevitable ............................. 88
Coastal waters, seagrass restoration (Cronau et al., 2023) ............................................................... 89
a) Explain what bottom-up (resource-driven) and top-down (consumer-driven) trophic, and non-
trophic interactions are; ................................................................................................................ 89
