Remote Sensing of Alkaline-Saline Lakes: Applications to Flamingo Conservation

EarthzineArticles, Biodiversity, Earth Observation, Original, Water Availability Theme

Photo of lesser flamingos at Lake Bogoria, Kenya

E.J. Tebbs, J.J. Remedios
Department of Physics and Astronomy, University of Leicester
S. Avery
Department of Geography, University of Leicester
D.M. Harper,
Department of Biology, University of Leicester

Photo of lesser flamingos at Lake Bogoria, Kenya

Figure 1. Lesser flamingos at Lake Bogoria, Kenya. Credit: David Harper.

University of Leicester researchers from the Department of Biology and the Earth Observation Science Group have teamed up to work on an interdisciplinary project. The aim is to apply Earth observation data to investigating the connections between ecological and hydrological processes in alkaline-saline lakes in the Eastern Rift Valley (Kenya-Tanzania). This interdisciplinary approach has been adopted to give greater insight into the functioning of these water dependent ecosystems and the results will be used to inform future management strategies. The work will act as a demonstration of how satellite data can contribute to remote monitoring of ecosystems where in situ data are limited. The project forms the basis of a cross-departmental PhD study addressing the sustainability of soda lakes in Kenya and Tanzania critical to the life cycle of lesser flamingos.
Image of arthrospira fusiformis, the dominant phyoplankton species in Lake Bogoria.

Figure 2. Image of Arthrospira fusiformis, the dominant phytoplankton species in Lake Bogoria, enlarged x 100. Credit: Suzanne Mills (2).

A. Motivation – Why Saline Lakes?
Alkaline-saline lakes have a distinct ecology characterized by dense blooms of cyanobacteria (blue-green bacteria). Such blooms are often considered a hazard in freshwater lakes due to the toxins they may produce, but in alkaline-saline lakes they play a vital role in sustaining a population of lesser flamingos, which feed by filtering colonial cyanobacteria from the water of a dozen or so soda lakes in the Rift Valley [1]. Lesser flamingos are classified as a near-threatened species by the International Union for Conservation of Nature due to their decreasing numbers and limited breeding sites. These flamingos are of great economic importance as they attract tourists to the soda lakes of Kenya and Tanzania where they form a globally renowned spectacle; their numbers can reach one million individuals (Figure 1). This study aims to use remote sensing to determine the quantity and distribution of food available to lesser flamingos, thus providing valuable information for their future conservation.
Lesser flamingos feed primarily on cyanobacterium Arthrospira fusiformis (Figure 2) in deep lakes and also on benthic algae, which grow on the bottom of shallower soda lakes. The flamingos move from lake to lake in response to food availability, but little is known about the spatial and temporal distribution of their food supply. Occasionally a drastic reduction in cyanobacterial biomass – known as a “crash” or “die-off event” – is observed in the lakes. The causes of these events are poorly understood. Satellite observations will give insight into how often these crashes occur and how long they last. These lakes are in remote areas and there is no routine in situ monitoring so the ability to monitor these environments with satellite data is urgently needed. The main lake considered in this study is Lake Bogoria, Kenya (Figure 3). It is a key feeding site of lesser flamingos and it is dominated by one species of cyanobacteria, Arthrospira fusiformis (always over 80 percent).
Landsat ETM+ RGB image of Lake Bogoria, Kenya

Figure 3. Landsat ETM+ RGB image (3, 2, 1 band combination) of Lake Bogoria, Kenya. The lake appears green due to high cyanobacterial biomass. Credit: NASA Landsat Program.

B. A Breeding Site under Threat
Another lake of critical importance is Lake Natron as it is the only breeding site for flamingos in East Africa (Figure 4). The unique hydrology of the lake is believed to control the success of flamingo breeding events but the details are unknown. The lake is threatened by two proposed developments: a dam to be built on the Ewaso Ngiro (South) River, which provides 30 percent of the lake’s water, and a soda ash extraction factory that would pump saline water from the lake and extract the salts before returning the water to the lake. Both developments will have a significant effect on the hydrology and ecology of the lake and could potentially be disruptive to the flamingo breeding. Hence another aim of this project is to use archival satellite imagery to establish baseline data about the hydrology of the lake by looking at fluctuations in lake surface area.
Landsat ETM+ RGB image of Lake Natron, Kenya-Tanzania

Figure 4. Landsat ETM+ RGB image (3, 2, 1 band combination) of Lake Natron, Kenya-Tanzania, the sole breeding site for lesser flamingos in East Africa. The red color is due to extremophile bacteria that inhabit the lake’s hypersaline waters. Credit: NASA Landsat Program.

The spectral signatures of the lakes contain information about the optically active substances in the water column, including dissolved material, cyanobacteria and suspended sediment. A. fusiformis contains photosynthetic pigments, such as chlorophylls and carotenoids, which absorb light in the visible region and give it a characteristic reflectance spectrum. At high biomass concentrations, scattering by cells causes high reflectance in the near infrared region. Due to high biomass concentrations it is likely that the optical properties of Lake Bogoria will be dominated by cyanobacteria.
Chlorophyll retrieval algorithms (as an indicator for cyanobacterial biomass) have been developed for oceanic waters and freshwater lakes [3], but this is the first study to look specifically at remote sensing of chlorophyll in alkaline-saline lakes. Outputs of the project so far include an algorithm for estimating chlorophyll in Lake Bogoria from Landsat ETM+ satellite imagery [4, 5]. The ultimate aim is to develop a set of algorithms for assessing chlorophyll at the landscape scale for a chain of soda lakes in the Rift Valley. The algorithms will be used to recover a long term chlorophyll time series for each lake to assess the stability of the lesser flamingo food supply. Landsat ETM+ has been the focus of work so far because its high resolution imagery (30 m) is necessary due to the small size of the lakes (1-3 km across) and the need to observe small scale variations.
The algorithm was developed using a time series of Landsat ETM+ imagery and in situ chlorophyll measurements. The near infrared band of Landsat was found to be the best predictor of chlorophyll due to the high biomass concentrations (hundreds of µg/l Chl-a). The standard error in the algorithm is relatively large due to the separation between ground and satellite data of up to eight days (to allow matching of a sufficient number of images). The algorithm was applied to Landsat ETM+ images for the period 1999–2010 to produce a long-term chlorophyll time series for Lake Bogoria (Figure 5). The time series show key features such as the die-off event in 2003, which coincided with the in situ study, and other apparent die-offs in early 1999 and in 2005, 2006 and 2007. Large error bars mean, however, that fine variations in chlorophyll cannot be observed. Hence a field spectroscopy study was carried out to aid the development of an improved algorithm and to give a better understanding of other water parameters influencing the optical properties of the lake. Spectral measurements of the lake were made from a boat using a spectroradiometer and, at each site water samples were collected and analyzed for chlorophyll concentration, dissolved organic material and suspended sediment.
Time series for chlorophyll-a in Lake Bogoria showing in site data and satellite estimates

Figure 5. Chlorophyll-a time series for Lake Bogoria showing in situ data and satellite estimates.

A field spectroscopy study allowed the unique spectral properties of Lake Bogoria to be measured for the first time. Three distinct spectral shapes were observed (Figure 6). At one site, within the sediment plume of the Waseges River, a spectral shape typical of suspended sediment was observed; at another site, where cyanobacterial scum (a layer of cyanobacterial cells trapped in the surface tension on the lake surface) was present, a spectral shape similar to that of terrestrial vegetation was observed. At all other sites the shape of the reflectance was characteristic of cyanobacteria mixed in the water column. For these sites the height of the reflectance peak in the near infrared increased with increasing chlorophyll concentration, in agreement with the existing chlorophyll retrieval algorithm.
Image showing different spectral shapes observed at Lake Bogoria (left). Reflectance spectra for sites where cyanobacteria mixed in the water column dominated the optical properties (right).

Figure 6. Different spectral shapes observed at Lake Bogoria (left). Reflectance spectra for sites where cyanobacteria mixed in the water column dominated the optical properties.

Field spectroscopy results showed that the relationship between chlorophyll and near-IR reflectance breaks down in localized regions where scum and sediment are present. Therefore the possibility of masking scum and sediment from the imagery was investigated. Landsat ETM+ Band 3 and Normalized Difference Vegetation Index (NDVI) images were found to be suitable for masking sediment plumes and scum respectively (Figure 7). Masking these regions from the image will give more confidence in the output of the chlorophyll retrieval algorithm; in addition, the ability to monitor areas of scum and sediment will be useful in its own right for the development of additional ecological indicators.
A. Improving the Chlorophyll Algorithm
 Landsat ETM+ band 3 reflectance and NDVI images for Lake Bogoria showing potential for masking sediment and scum.

Figure 7. Landsat ETM+ band 3 reflectance and NDVI images for Lake Bogoria showing potential for masking sediment and scum.

Work is ongoing to develop improved remote-sensing algorithms and atmospheric correction methods for retrieving chlorophyll concentration from alkaline-saline lakes. Atmospheric correction for turbid (hypereutrophic) water bodies remains an unsolved problem [6]. Since the atmosphere modifies the signal from the surface, atmospheric correction is vital for retrieving quantitative information on biophysical parameters, particularly when observing trends over time. Therefore a field campaign is planned to test the validity of various atmospheric correction methods for improving the accuracy of chlorophyll estimates. Lower spatial resolution sensors will also be considered, such as MODIS and MERIS, because they benefit from shorter revisit times and narrower spectral bands useful for studying dynamic lake processes such as cyanobacterial die-off events.
B. Hydrology of Lake Natron
The hydrology of Lake Natron could be significantly disrupted in the future by two proposed developments. In order to assess the past hydrological variability of Lake Natron a Normalized Difference Water Index will be applied to archival Landsat images of the lake in order to produce a time series of lake surface area. These results will be used in combination with radar altimetry data to determine changes in lake level over time. It is thought that the flamingos only breed at a certain lake level, and in this study we aim to confirm whether this is the case. Our results will inform the future management of the lake.
This work has shown that ecologically useful information about alkaline-soda lakes can be gained from satellite data. Remote sensing can be used to monitor long-term trends in biomass of primary producers in alkaline-saline lakes and assess the sustainability of the lesser flamingo food supply. Work is ongoing to refine the algorithm for Lake Bogoria and to develop algorithms for other lakes. Ultimately the chlorophyll results will be combined with information on lake surface area to determine connections between the hydrological and ecological processes. Our results will contribute to the conservation of lesser flamingos in alkaline-saline lakes within the East African Rift Valley thus preserving the biodiversity and economic value of these unique ecosystems.
[1] C.H. Tuite, “Standing crop densities and distribution of Spirulina and benthic diatoms in East African alkaline saline lakes,” Freshwater Biology, 11: 345–360, 1981.
[2] S. Mills, R. Boar, B. Childress, D.J. White, and D.M. Harper, Foraging by Lesser Flamingos, Phoeniconaias minor, in response to vertically migrating cyanobacterium, Arthrospira fusiformis. Manuscript submitted.
[3] T. Kutser, “Passive optical remote sensing of cyanobacteria and other intense phytoplankton blooms in coastal and inland waters,” International Journal of Remote Sensing, 30(17): 4401–4425, 2009.
[4] E.J. Tebbs, J.J. Remedios, and D.M. Harper, “Remote sensing of chlorophyll a in saline-alkaline lakes using Landsat ETM+, with applications to lesser flamingo (Phoeniconaias minor) ecology,” in preparation.
[5] E.J.Tebbs, Remote Sensing of Chlorophyll in Saline Lakes, with applications to flamingo ecology: A feasibility study, Master’s Thesis, 2009.
[6] M.W. Matthews, S. Bernard, and K. Winter, “Remote sensing of cyanobacteria-dominant algal blooms and water quality parameters in Zeekoevlei, a small hypertrophic lake, using MERIS,” Remote Sensing of Environment, 114 (9): 2070–2087, 2010.
Thanks to the Natural Environment Research Council Field Spectroscopy Facility for providing equipment and training. Emma Tebbs would like to acknowledge the support of the Centre for Interdisciplinary Science at the University of Leicester in funding this PhD study.
Community Links
As well as carrying out scientific research in the area, the University also works with local communities though several projects. Each year the Centre for Interdisciplinary Science runs an undergraduate field course during which students work with members of the local community on sustainability themed projects. Water themed projects are common since clean, safe, fresh water is such a valuable and limited resource in the area. In 2011 a student project on “Reduction of fluoride in drinking water” was particularly successful in raising awareness and transferring knowledge to the community. Although fluoride is added to drinking water in some areas of the world, very high levels of fluoride can have a negative effect on human health. Students found that drinking water from bore holes in the area had fluoride concentrations well above WHO guidelines. They tested and demonstrated a simple method of reducing fluoride concentration in drinking water, using carbonized animal bones. Another project in 2010 investigated the potential of rainwater harvesting. Students found that local people were knowledgeable about the benefits of harvesting rainwater but the main barrier was the cost of purchasing a water storage tank. They devised a method for building a cheap water tank using sticks, concrete and sand. The work done by undergraduate students is complemented by short films about sustainability made by Kenyan and Tanzanian film-makers, trained by a team of British filmmakers under a project funded by the Darwin Initiative. The project is called CBCF (Community-based Biodiversity Conservation Films), and is directed by Dr. David Harper. The films are used to raise awareness of sustainability issues in the area.
Emma Tebbs is a PhD student working on remote sensing for the study of eco-hydrology in East African river basins. She has a Masters in Physics with Space Science and Technology from the University of Leicester. A final year project on remote sensing of chlorophyll in saline lakes led to this PhD project.
Dr. David M. Harper is a Senior Lecturer in Ecology and Conservation Biology in the Biology Department and contributes to the Interdisciplinary Science degree in ecology and sustainability issues. He has conducted scientific research in Kenya and Tanzania for over 25 years, focused upon the sustainability of water – a highly limiting resource in an arid country like Kenya, and which will shortly become limiting in a country like Britain where so much is wasted.
Prof. John J. Remedios is head of the EOS team in the Physics and Astronomy Department at the University of Leicester. He has much experience in infrared radiative transfer, satellite surface temperature measurements, as well as satellite data for atmospheric composition studies of the troposphere and stratosphere, and trace gas profile retrieval using the optimal estimation technique.
Dr. Sean Avery has spent over 30 years working in the water and environmental sectors, initially in South-East Asia and then extensively throughout Africa. He has been resident in East Africa since 1979 and has worked throughout the continent focusing on water resources development. In 2008 he was appointed an Honorary Visiting Fellow of the University of Leicester. His professional field of special expertise is in engineering hydrology. He has a passion for arid lands in particular, and a special interest in Kenya’s conservation areas.