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Remote sensing of Indonesian coral reefs

Indonesia has vast areas of coral reefs, and published remote sensing studies describe imageprocessing in several localities. Covering the entire country, national initiative included a COREMAP product derived for Landsat 7 images (2004). The Millennium Mapping Project has released some detailed geomorphological products (Andréfouët et al., 2006), also derived from Landsat 7, after the 2004 Tsunami. Comparison with COREMAP products showed many missing reefs and errors in the COREMAP product (Brian Long and Serge Andréfouët, unpublished data). The fully validated Millennium product is not yet distributed and a simplified, unvalidated version of the Indonesian products have been used by UNEP-WCMC to release a global “coral reef’ product in one single layer without thematical detail. This product also suffers from many errors (Cros et al., 2014). The Table 2 provides recent high spatial resolution studies on Indonesian coral reefs published in the peer-reviewed literature. Other studies can be found in conference proceedings and student thesis. These studies represent a variety of coral reef theme, including change detection (Table 2). These studies looked at SPOT and Landsat imagery, thus analysed changes using 20-30 meter resolution. We did not find example of change detection study using very high spatial resolution images (2-4 m).

Resilience of coral reefs and mapping resilience

Resilience is the ability of a system to absorb or recover from disturbance and change, while maintaining its functions and services (Carpenter et al., 2001): for example a coral reef ’s ability to recover from a hurricane(Grimsditch and Salm, 2006). It is often opposed to resistance, which is the ability of an ecosystem to withstand disturbance without undergoing a phase shift or losing neither structure nor function (Odum, 1989): for example a coral reef ’s ability to withstand bleaching and mortality (Grimsditch and Salm, 2006).
Resilience and the resilience concept have been a significant focus in the past 20 years, triggered by the on-going, obvious, degradation of corals reefs that seemed to be unable to bounce back to their initial state, or even shift to a seemingly different system, for instance dominated by algae. Understanding resilience and managing the resilience capacities of a reef have appeared as new priorities for science and management. The difficulty is that managing resilience implies a holistic, ecosystem, view of how a reef is functioning and the consequences of all interactions between all its diversity of components.
Resilience of coral reefs has been studied as a theoretical concept (Nyström and Folke, 2001), empirically in the field (e.g., Wakeford et al., 2008), and with models (Mumby et al., 2006). Resilience has three critical components (1) biodiversity, (2) connectivity and (3) spatial heterogeneity (Nyström et al., 2008). Biodiversity allows redundancy of important ecosystem functions. Connectivity between reefs allows population flux and population renewal after disturbances. Spatial heterogeneity implies that the resilience factors are variable in space across a reef or series of reef. It is recognized that habitat diversity, connectivity and spatial heterogeneity are important resilience modulators, yet these variables remain poorly quantified for most reefs worlwide.
While there is a general consensus on all the factors, from local to global, that can affect coral reef resilience (McClanahan et al., 2012), which factors are the most important for any given reef remains poorly understood (Obura and Grimsdith, 2009). Some modelling studies suggest universal recipes to manage resilience (e.g., the management of herbivores to limit algal overgrowth), but empirical evidences suggest that these recipes cannot cover the range of situation (e.g., Carassou et al., 2013). Models remain invalidated, non-spatial, with arguable parameterization, and the related sensitivity studies can only show the importance of the pre-selected parameters, not those who have been dismissed or neglected. In practice, little is known on what factors contribute to the resilience of coral reef communities and habitats for a particular reef, before it can be studied intensively.
Considering the most likely factors of resilience, remote sensing has been used to map variables that can affect resilience (Table 3). Both stressors and factors of recovery can be mapped and combined in these approaches. A combined index is then used to define areas prone to resilience or not. This is a fairly pragmatic and common-sense approach that could serve well management due to its spatially-explicit approach, yet it remains also very difficult to validate.

Change detection of coral reefs using remote sensing

Habitat mapping is a one-time mapping exercise, but scientists and managers may also want to know how a reef has changed, and if the habitats are stable, degrading, or enhancing in quality. Change detection of habitats using remote sensing has been the subject of several papers, but far less than habitat mapping. Table 4reviews the characteristics of representative studies, published in peer-review journals, and focussing on coral habitats (not on seagrass habitats).
We found methodological papers that look at correction of images, quantify noise, and test various methods of analysis and correction, sometimes using only one pair of images. There are also a number of thematic papers that have tried to understand and explain the causes of the changes that have occurred on a reef, sometimes across several decades and using up to a dozen of images. Various types of images have been used, including aerial photographs (color and black and white) which allow very long time-series, and sometimes with the analysis of multi-sensor series of images. All study sites were shallow, in less than 10 meter deep at the maximum.
The characteristics of change detection analysis, especially for long periods spanning several decades is that the accuracy of the treatment is often difficult to quantify (Scopélitis et al., 2009). Often, no historical data exists to be able to quantify accuracy with a confidence similar to a present-time habitat mapping exercise. Many areas may remain undocumented, hence the level of analysis may be limited to some variables of the habitat that can be photo-interpreted (geomorphology) or related to known unambiguous spectral signatures (cover) while the other variables remain unavailable without historical surveys (architecture, taxonomy).
High thematic richness could be achieved by Scopélitis et al. (2009) even with limited ground-truthing, at least to the point that they could demonstrate, using photo-interpretation techniques that an assemblage of coral communities at Saint-Leu fringing reef in La Reunion has recovered after a hurricane and moderate bleaching event across a 35-year period. In contrast, also using photo-interpretation techniques, Andréfouët et al. (2013) showed for the barrier reef of Toliara in Madagascar that coral communities have steadily decreased due to destructive artisanal fishing, without any signs of recovery. These two Indian Ocean stories highlight two different conclusions in term of resilience: based in the trajectory of their coral habitats, Saint-Leu has been a resilient reef in the face of acute short term disturbance while Toliora appears to be a non-resilient reef in the face of chronic disturbance. Thus, time-series of remote sensing images have the potential to inform on the capacity of a reef to be resilient depending on the type of disturbances the reef had to face during the study period.

General research objective& research questions

The objective of the study is to study for the first time the resilience of an Indonesian coral reef and its habitats, using a multi-sensor time-series of very high spatial resolution (VHR) multispectral satellite images. Bunaken Island, in the Bunaken National park in North Sulawesi, is the study area.
The focus is on thematic interpretation, not image processing method development because the goal is also to provide practical recommendations for Park managers in term of using remote sensing to monitor reefs more effectively, especially the shallow reef flats which have been neglected by monitoring programs.
The INDESO project provides the imagery by purchasing all cloud free images available from the IKONOS, Quickbird, Geoeye and Worldview multispectral archive of images between 2001 and 2015.
The thesis can be divided in 3 series of important questions and steps, inspired by the information presented throughout the previous sections:
1. What are the present day coral reef habitats found in Bunaken National Park and Bunaken Island? How are they distributed? What is the habitat diversity?
2. Can we detect changes in these habitats using a multi-sensor time-series VHR images? Can we reconstruct the recent history of changes around Bunaken Island? Are the habitats resilient?
3. If there are changes on reef habitats after answering Question 2, what are the causes of these changes? If there are no changes after answering Question 2, what resilience factors could be at play?
After answering these questions specific to Bunaken Island, the potential for generalization to other reefs and practical recommendations for mapping and monitoring Indonesian reefs will be discussed.

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Thesis structure

This thesis has been divided into six chapters. Three of them are presented in the form of submitted papers to peer-reviewed journal. We refer to a multi-source approach in the title considering first the use of images acquired by different satellite vectors, but also the use of in situ data, and also the use of altimetry data to explain some of the observed changes.
The current Chapter 1 has presented here the research background and key information used to define the subject, with brief presentation on the INDESO project, Indonesia coral reefs, remote sensing of coral reefs and habitat mapping, remote sensing of Indonesia coral reefs, resilience of coral reefs and its mapping, and change detection of coral reefs. Then the general research objectives and the main research questions are given.
Chapter 2 presents in more detail the field and image processing methods used in the following chapters, and justify the choice of these methods. Bunaken National Park and island are also presented.
Chapter 3 presents the results of the field survey, the creation of a detailed habitat map and the analysis of the map in term of habitat richness and distribution. The chapter is a paper entitled Revisiting Bunaken Island (Indonesia): a habitat stand point using very high spatial resolution remotely sensed, which is submitted to the journal Marine Pollution Bulletin, for a special issue on the project INDESO.
Chapter 4 addresses the mortality of corals related to the 2015-2016 El-Niño that we could witness during the study period. This was an opportunistic event that brought new insights on the processes that control the resilience of Bunaken Island coral reef flats. This chapter is a paper entitled Coral mortality induced by the 2015-2016 El Niño in Indonesia: the effect of rapid sea level fall, which is in press with the journal Biogeosciences and also available as a discussion paper open to comments (DOI:10.5194/bg-2016-375).
Chapter 5 presents the change detection analysis of coral reef habitats in Bunaken National Park using an original scenario-based approach. This chapter is a paper entitled Assessment of the resilience of Bunaken Island coral reefs using 15 years of very high spatial resolution satellite images: a kaleidoscope of habitat trajectories, which is under review with the journal Marine Pollution Bulletin, for a special issue on the project INDESO.
Chapter 6 reviews the results, highlight the main findings and put them in the broader context of understanding the resilience of coral reefs, especially in Indonesia, and make suggestions for the future monitoring of these reefs using a combined remote sensing and monitoring approach.
In this chapter are presented aspects that are general to all the next chapters (Study site, Image data sets, etc.), or additional information not provided in each of the chapter submitted for publications. This includes in particular general methodology information that are often not needed in publications formatted for specialized journals. I also provide here previews of some intermediate results (number of surveyed points, number of mapped polygons, etc.) to illustrate the relevant topics. These results are also provided in greater details in the following chapters.

Study site: Bunaken National Park and Bunaken Island

Bunaken National Park (BNP) is located at the northwest tip of Sulawesi, Indonesia (Figure 4). The location is at the core of the Coral Triangle, a vast area spanning Malaysia to Solomon Island, where the number of marine species is maximum (Hoeksema, 2007).
The BNP is one of the flagships of coral reef conservation in Indonesia. The park has been created in 1991 by decree of national government (Erdmann et al., 2004). The area includes part of the coastline around the nearby city of Manado, and five islands: Bunaken, Manado Tua, Siladen, Nain, and Mantehage (Figure 4). Since 1991 the Park is ruled by a zoning plan that has been designed using socio-economic constraints with the participation of numerous stakeholders for a better compliance.
Bunaken Island (BI) is located by 1.62379°N, 124.76114°E. It is surrounded by a simple fringing reef system, comprising reef flats, several small enclosed lagoons, and forereefs. At low tide, the reef flats are sometimes dry, and the maximum depth can reach above 2m at spring high tide conditions. Most of the time, depth would be between 40 and 1.50 meter. The tide regime is semi-diurnal, but with marked diurnal inequalities (Ray et al., 2005), with a maximum spring tidal range that can reach 2.52 m.
BI is famous for his wall dives that attract a high number of divers. Tourism is one the main activity in the park. The reef flats themselves are seldom visited by tourists, except one location dedicated to snorkelling activities. However, reef flats are systematically combed by the resident population at low tide to harvest crustaceans, molluscs and small fishes living in corals and seagrass beds. The gleaning activity occurs mostly on the south and east reef flats (personal observations). A survey of 7 fishermen suggested that destructive dynamite fishing is not occurring anymore around BI, since more than 20 years (personal data).

Table of contents :

1.1. The INDESO project
1.2. Coral reefs of Indonesia
1.3. Remote sensing of coral reef habitats and habitat mapping
1.4. Remote sensing of Indonesian coral reefs
1.5. Resilience of coral reefs and mapping resilience
1.6. Change detection of coral reefs using remote sensing
1.7. General research objective& research questions
1.8. Thesis structure
2.1. Introduction
2.2. Study site: Bunaken National Park and Bunaken Island
2.3. Field work method for habitat typology
2.4. Training and accuracy assessment points
2.5. Photo-interpretation, digitization, thematic simplification, and final typology of mapped habitats
2.6. Accuracy assessment for habitat mapping
2.7. Multi-sensor image data sets for change detection analysis
3.1. Introduction
3.2. Material and Methods
3.2.1. VHR Image
3.2.2. Habitat typology
3.2.3. Habitat mapping for a very high thematic resolution of habitats
3.2.4. Accuracy assessment for a very high thematic resolution of habitats
3.4. Results
3.4.1. Habitat typology
3.4.2. Habitat mapping
3.4.3. Accuracy assessment
3.5. Discussion and conclusion
4.1. Introduction
4.2. Material and Methods
4.3. Results
4.3.1. Mortality rates per dominant coral genus
4.3.2. Map of occurrences of mortality
4.3.3. Absolute Dynamic Topography time series
4.3.4. Sea Level Anomaly trends
4.4. Discussion
4.5. Conclusion
5.1. Introduction
5.2. Material and methods
5.2.1. Study site
5.2.2. Remote sensing data set
5.2.3. Mining georeferenced historical in situ data
5.2.4. Image and habitat-scenario analyses
5.2.5. Interpretation of changes
5.3. Results
5.3.1. Image time-series quality and correction
5.3.2. Historical data search
5.3.3. Changes for selected polygons
5.4. Discussion
5.4.1. Towards an ecological view of changes using VHR images
5.4.2. A kaleidoscope of habitat trajectories
5.4.3. A kaleidoscope of processes difficult to reconcile
5.4.4. The influence of management and recommendations
5.4.5. Methods for change detection beyond a scenario-based approach
5.4.6. Bunaken, a resilient reef?
5.5. Conclusion
CONCLUSION (in French)


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