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Advanced Studies Institute on Water Quality and Harmful Algal blooms in lake victoria, Kenya


2022 Program

2022 Program Specifics

Cyanobacteria, commonly referred to as blue-green algae, can grow to dense concentrations in lakes, rivers, ponds and reservoirs across the globe forming what are known as cyanobacterial harmful algal blooms (cyanoHABs; Figure 1; Bullerjahn et al., 2016).  Furthermore, many cyanoHABs can produce toxins that can sicken or kill humans, cattle and other domestic animals.  Indeed, in the last decade major cities in China, the United States, Africa and other parts of the globe have suffered from impaired drinking water due to cyanoHABs (Sitoki et al., 2012; Steffen et al., 2017). Also, many of these cyanoHABs are comprised of the same organism, Microcystis spp., which previous studies have determined to be the most ubiquitous cyanoHAB-forming genus (Harke et al., 2016), and currently it is unclear how Microcystis adjusts its ecological strategies to maintain dominance for long periods of time in lakes from temperate to tropical regions.  Therefore, it is critical to conduct parallel research in comparable lakes from different latitudes to further understand the global ecology of the bloom-forming cyanobacterium, Microcystis spp.

The proposed Advanced Studies Institutes (ASI) will focus on expanding the knowledge of water quality and the Microcystis-dominated cyanoHAB that occurs in Kisumu Bay, Nyanza Gulf, Lake Victoria, Kenya and provide the opportunity for US-based students to expand their research and collaborations into this regionally-important, yet understudied system.  The proposed ASI will leverage current research programs in western Lake Erie, led by Bowling Green State University, and in Kisumu Bay, led by Kisii University, Technical University of Kenya and the

PHOTO - Lake Erie HABs - 06242019 - NASA
The lake is our carwash - Kisumu, Kenya

Left: Satellite image of the annual cyanobacterial (Microcystis spp.) bloom in Lake Erie, USA (Photo: NASA/NOAA). Center: View of Lake Taihu toxic cyanobacterial (Microcystis spp.) bloom during Sept, 2016 (Photo: T. Davis). Right: Microcystis spp. bloom along with daily activities in Kisumu Bay, Nyanza Gulf, Lake Victoria, Kenya (Photo: T. Lawrence).

Kenya Marine and Fisheries Research Institute (KMFRI).  Western Lake Erie and Kisumu Bay are similar in that they are both shallow, eutrophic systems that experience Microcystis-dominated cyanoHABs.  However, they are different in that Lake Erie is a temperate system dominated by non-point nutrient sources, whereas Kisumu Bay is a tropical system that receives a mixture of point source (urban) and non-point source nutrient pollution. 


The proposed Advanced Studies Institute will focus on expanding the knowledge of water quality and the Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) that occur in Kisumu Bay, Nyanza Gulf,  Lake Victoria, Kenya and provide the opportunity for US-based students to expand their research and collaborations into this regionally-important yet, understudied, system.  The proposed ASI will leverage current research programs in western Lake Erie, led by Bowling Green State University, and in Kisumu Bay, led by Kisii University, Technical University of Kenya and Kenya Marine Fisheries Research Institute (KMFRI).


This program’s major component is to go into the field in Eastern Lake Victoria for field research so that students can gain field exposure (sampling techniques), laboratory exposure (sample assessment), expand global view, learn more about HABS, identify similarities and differences of various systems, and work with scientists and students with distinct and various views. In the spirit of scientific inquiry and growth, participants will be paired with a Kenyan counterpart during the field portion of this program and expected to work with that counterpart on subsequent activities, such as data processes, writing papers, and potentially presentations.


Please be mindful that this program, for some, will present uncommon and unconventional situations regarding culture, environment, and politics.

2022 Cohort

2022 Participants


Dorine Achieng

Research Intern

Kenya Marine and Fisheries Research Institute

Kisumu, Kenya, East Africa

Research Title

To assess the socio-economic losess of HABs in the

Lake Dunga Beach, Lake Victoria, Kisumu County

Over the recent months, there has been sudden death of Lates Niloticus in Lake Victoria bordering Uganda and Kenya. Fishermen from these regions were baffled by the sudden deaths and thought the dead fish were harmful if consumed by human. Experts came up and explained the sudden
occurrences as stratification that happened due to climatic changes in the regions bordering the lake, thus causing the death of the fish that were being washed away and deposited at the shoreline. Another cause was due to pollution caused by effluents discharged into the water bodies by industries situated along the Lake region, causing growth of blue-green algae that produces cyanotoxins which is harmful to both human and aquatic lives, resulting in fish kills. 


This study focuses on the growth and introduction of cyanobacteria in Lake Victoria, focusing on Winam Gulf as the study area, to determine their effects on both aquatic and human life. The study will also establish the possible causes of fish loss, economic effects on the fishermen, social effects on the people living around Winam Gulf. On its implementation, the study will recommend possible ways to counter possible spread and growth of blue-green algae and how to limit its growth on other areas of the lake.

Katelyn Barker

Masters Candidate

Bowling Green State University

Bowling Green, Ohio


Research Title

Rapid, Portable, Multiplexed Detection of Harmful Algal Toxins

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            Cyanobacterial harmful algal blooms are an issue in lakes and waterways around the globe and can have enormous environmental, economic, and human health impacts. These blooms have the potential to produce various hepatotoxins (microcystin, cylindrospermopsin) and neurotoxins (saxitoxin). The standard method for testing affected waters for toxins is by Enzyme Linked Immunosorbent Assay (ELISA). This method can be time consuming, expensive, and require training and equipment to perform the assay. Recently, a rapid, portable multiplexed assay has been developed by LightDeck Diagnostics to test for toxins quickly and easily in the field, providing results within minutes. This system uses disposable fluidic cartridges containing the assay that can simultaneously detect and quantify microcystin and cylindrospermopsin within minutes. Samples using the LightDeck cartridges will be measured on site using the LightDeck reader and compared to traditional methods to validate the efficacy of the new assay. Currently, a triplex assay which would incorporate saxitoxin detection is being developed and will be used if the technology is ready. While the ELISA assay and HPLC remain the gold standard, the advantages of speed, expense and limited user expertise suggest that the LightDeck assay could play an increasing role in early detection of toxic bloom events.

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George Morara Basweti

Assistant Research Scientist

Kenya Marine and Fisheries Research Institute

Kisumu, Kenya, East Africa

Research Title

Assessment of pollution and their effect in aquatic ecology in Lake Victoria

Water resources plays a key role in the socio economic development and hence contribute immensely to realization of food and nutritional security. However, since the onset of anthropogenic activities, increasing human population created similar increasing demand s in agricultural lands, water
and with expanding settlements. The emerging micropollutants and environmental stressors, all contribute to the multiple environmental pressures which threatens the water quality in lakes, resulting in degradation of fish and other flora and faunal habitats, increasing vulnerability of endangered species, risks to public health and livelihoods. This will push for environmental assessment study of the ecological status of the water quality at selected sites. In situ measuremen t of key water quality parameters will be measured at the identified sites following a given sampling procedure. HANNA HI9829 multi parameter meter will be used to collect the physical chemical variables. Ekman grab will be used to collect triplicate hauls of the benthic macroinvertebrates samples sieved using 500 micron sorted to species level, nutrients and chlorophyll a samples will be collected and analyzed following standard methods of analysis. All physical chemical parameters will be measured for an indication of hypoxic, acidic and toxic environment of pollutants in the water column. Chlorophyll a as primary productivity and algal biomass indicator tool will be recorded as an indication of intense eutrophication. TN: TP ratio will be required for co mparison to a standard of > 15 exhibiting nutrient limitation in the waterbody. The HBI tolerance values >5 in benthic macroinvertebrates is an indicator of highly polluted ecosystem where an organism resides. This endurance to pollutants for a period of t ime in a disturbed environment with poor water quality, needs to be regenerated through policy formulation to stem the menace. Waste water planning and management, long term monitoring needs to be sustained to guide on expanding urban development, anthropo genic pressures and better management of Lake Victoria aquatic ecosystem for harnessing the blue economic growth.

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Max Beal

Ph.D. Candidate

University of Wisconsin - Madison

Madison, Wisconsin


Research Title

Leveraging Local and Global Scale Variables for Season-ahead Forecasting of Lake Water Quality

For decades, cultural eutrophication has posed a threat to the water quality of lakes around the world. In particular, the proliferation of algae in eutrophic lakes has caused concern to grow around potential threats to human health, ecosystems, and the economy. Recurring algae blooms along the western shore of Lake Erie have drawn national attention and highlight the need for novel methods to proactively manage lake water quality. Peak season algae abundance (summer and early fall in the northern hemisphere) typically coincides with the high-use season for lakes across the U.S. and is influenced by an array of pre-season (spring and early summer) local and global scale variables. Currently, little information regarding expected water quality is available prior to the peak season for algae productivity. With sufficient lead time, communicating the likelihood of poor water quality may help proactively manage potential threats to lake health and beach safety. Preliminary results show promise in the application of season-ahead forecasts and remote sensing for water quality management of inland lakes. Selecting inland eutrophic lakes and western Lake Erie as case studies, models of summertime water quality indicators (e.g. chlorophyll-a, secchi depth, and cyanobacteria biomass) conditioned on season-ahead local and global scale predictors are constructed. Additionally, remote sensing methods are employed to enhance the observational record of water quality indicators. This warrants further investigation into the development of seasonal water quality forecast systems, and application to other waterbodies.


Katelyn Brown

Ph.D. Candidate

Bowling Green State University

Bowling Green, Ohio


Research Title

Rapid, portable and multiplexed detection of freshwater harmful algal bloom-forming genera

Harmful algal blooms (HABs) are becoming more common around the world due to excess nutrient loads, eutrophication, and the changing climate. HABs generally occur in systems with high nutrient concentrations, but other factors including lake morphology and temperature also contribute to the growth and development of cyanobacteria. Oftentimes, HABs result in the production of toxins like microcystins, cylindrospermopsins, anatoxins, and saxitoxins, that are harmful to living organisms. To better identify and manage blooms, a multiplexed sandwich hybridization assay (SHA) for use on the Lightdeck system will be developed to quickly recognize 7 prominent genera of cyanobacteria. The genera being targeted for SHA includes Microcystis, Anabaena/Dolichospermum, Aphanizomenon, Planktothrix, Cylindrospermopsis, Lyngbya/Microseira, and Phormidium/Microcoleus. To achieve this multiplexed assay, oligonucleotide probes are designed to target the 16S rRNA. If the target genera are present in a sample, an estimate of cell density will be determined from fluorescence. These probes will also utilize zip codes, an additional oligonucleotide probe that will allow multiplexing and will enhance assay sensitivity. In comparison to traditional methods, the SHA will be able to identify potentially toxin-producing genera more quickly and at a lower cost to lake managers.

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Aidan Byrne

Ph.D. Candidate

King's College London


Natural History Museum London

London, England

Research Title

Using Satellite Earth Observation to investigate the impacts of sedimentation on lake ecological states

Catchment degradation has significant impacts on lake water quality and quantity. Land-use intensification leads to the loss of vegetation cover, increasing surface run-off and soil erodibility. Loose soils are washed into rivers where they are transported downstream into lakes, causing visible sediment plumes. High sediment loads impact lake ecosystems in numerous ways, including influencing lake water levels, smothering fish breeding grounds and limiting lake productivity. High turbidity inhibits light penetration through the water column and reduces the photosynthetic activity of the phytoplankton community. Conversely, sediments from agricultural run-off can be nutrient rich and promote cyanobacterial bloom growth in nutrient limited waters. Cyanobacterial species with buoyant gas vesicle are likely to dominate in light-limited water. Similarly, floating vegetation such as the invasive water hyacinth (Pontederia crassipes) could benefit from nutrient-rich turbid water. However, there is limited knowledge on the interactions between sedimentation, cyanobacterial blooms and macrophytes in inland waterbodies and further research is required.


This project will use Satellite Earth Observation to investigate the impacts of catchment degradation on sedimentation and the subsequent effects on lake productivity and ecological states. Catchment degradation will be estimated using vegetation indices applied to satellite imagery. In-situ water samples will be collected simultaneously with spectral reflectance data. This data will be used to develop algorithms for estimating sediment loads, as well as differentiating between cyanobacterial blooms and sediment-dominated water, from satellite imagery. Water hyacinth cover will also be estimated from satellite imagery and results will be combined with cyanobacterial bloom data. These methods will be applied to satellite images over decadal timescales to determine the long-term impacts of catchment degradation on sedimentation, and explore the relationships between sediment loads, lake productivity and ecological states. Methods will also be applied to soda lakes across the Rift Valley where cyanobacterial blooms provide the main food source for the world’s largest population of Lesser Flamingos. Results will improve our understanding of terrestrial-aquatic linkages and explore the threats facing biodiversity in the region.


Linet Kiteresi Imbayi

Research Scientist

Kenya Marine and Fisheries Research Institute

Mombasa, Kenya, East Africa

Research Title

Insights of Toxic Benthic Cyanobacteria of L. Victoria, Kenya

There is minimal focus on benthic cyanobacteria (Oscillatoriales and Nostocales) which produce cyanotoxins that bioaccumulate in organisms such as fish, shrimps, gastropods and bivalves (Ferrão Filho et al., 2014) that biomagnify higher in the trophic levels (Preece e t al., 2017), a process that is not well understood (Quiblier et al., 2013). Cyanotoxins (microcystins, anatoxins, saxitoxins and cylindrospermopsins) result into hepatotoxicity,  neurotoxicity, dermatotoxicity or protein synthesis inhibition. Local communities depend on L. Victoria ecosystem services such as domestic, agricultural water supply, fisheries, aquaculture even with inputs of pollutants and sediment from its watershed and direct discharge of waste. Various studies in L. Victoria have focused on phytoplankton and their toxicity but none on benthic cyanobacteria proliferation and dominance of specific species that could result in alterations of trophic structure and functionality such as loss of biodiversity and dead zones. Overdependence for domestic and agricultural use, cage farming and recreational purposes, there is need for understanding its community structure and potential for toxin production for management purpose. Study area will encompass the shore line areas of L. Victoria that are of aquatic importance and engaged
with human activities. Systematic random sampling in slow flowing shallow water (<3m) for in situ measurement of physiochemical parameter will be done. Filtered water samples will be analyzed for dissolved inorganic nutrients. Benthic cyanobacteria mats will be identified by color and  morphology on bedrocks, scraped off and put in a container whereas sediment samples will be collected using sediment core (50 mm diameter) and transferred to a container and preserved with 10% v/v Lugol’s iodine and observed by inverted light microscopy for enumeration and identification. The Cyanoprokaryota taxonomic keys will be used for species identification (Komarek, 2013). The differences in toxic benthic cyanobacteria composition and substrates will be determined by Principle Component Analysis (PCA). Similarity and diversity using Bray Curtis similarity index and Shannon Weiner diversity index will be used for abundance. The proposed work will generate a baseline information of toxic benthic cyanobacteria community structure and in the understanding the common drivers for their proliferation leading to proper management strategies in its watershed and within the waterbody.

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Davide Lomeo

Ph.D. Candidate

King's College London, Natural History Museum, Plymouth Marine Laboratory

London, England

Research Title

Combining Satellite Earth Observations, long-term climate data and large-scale climate variability phenomena to assess historical cyanobacteria dynamics in Lake Victoria, Kenya

Lakes across the Rift Valley are critical ecosystems that support biodiversity and provide vital ecosystem services to people. However, they are threatened by anthropogenic pressures, including climate change and catchment degradation. Eutrophication and the warming of surface waters increase the risk of harmful algal blooms, which can overtake aquatic environments, suppressing other organisms and threatening the animals that depend on them. In addition, certain environmental conditions can promote toxin production in some bloom-forming species of cyanobacteria, resulting in waters potentially harmful to animals and people. Therefore, it is vital to find ways to predict seasonal cyanobacteria blooms to inform risk management and adaptation. One way of achieving this is to use historical cyanobacteria blooms and climatic variability known to directly impact weather across the country (e.g., Indian Ocean Dipole, ENSO) to assess cyanobacteria dynamics over space and time.


The proposed project will investigate the influence of teleconnections, climate change and local weather on the water quality of Lake Victoria, Kenya. Satellite Earth Observation will provide optimal spatial resolutions to assess and monitor the ecohydrological dynamics of the Lake. The high temporal resolution of long-term climate and climate variability data will help evaluate the predictability potential of large-scale systems.

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Jared Babu Miruka 

MSc Candidate

Kisii University and Kenya Marine and Fisheries Research Institute

Kisumu, Kenya, East Africa

Research Title

Assessment of cyanobacterial flora and microcystin concentrations in Kisumu Bay

The tropical Lake Victoria supports one of the world’s largest freshwater fisheries. Intensive land use and nutrient runoff, coupled with rapid population growth and climate change ha ve contributed to eutrophication, resulting in proliferation of toxin producing cyanobacterial blooms. In addition, changes in phytoplankton community structure have occurred overtime causing a cascade of trophic changes. Anthropogenic activities in the la ke’s catchment have resulted in increased phytoplankton biomass and a shift in species composition from a moderate mix of diatoms, greens and blue greens to the predominantly bloom forming and nitrogen fixing cyanobacteria. This study aims at determining th e most common cyanobacterial flora and their contribution to cyanotoxicity in Kisumu Bay, Lake Victoria, Kenya. Water samples will be collected in triplicate from each site. Physical chemical parameters such as turbidity, conductivity and pH will be measured insitu. Phytoplankton samples will be transferred to glass vials of 25 mL and fixed with Lugol’s iodine solution then stored in a dark cool box for further analysis. Identification and counting of the cyanobacteria for wet biomass determination will be done under an inverted microscope. Cyanotoxin analysis will be performed using Polyclonal ELISA kits and measured colour-metrically using ELISA plate reader at 450 nm. The research will involve analysing cyanobacterial flora and assess their impact to water resource users and the environment. Both of my research interest are aligned with the main objective of the programme and will provide an opportunity to establish an inventory of the phytoplankton structure and cyanotoxin concentrations, toxin producing cyanobacterial species and prepare a manuscript. I seek to fill a knowledge gap on evaluating the cyanobacterial taxonomy and determine species that are toxin producers. It is anticipated that information generated will be shared to all stakeholders, especially the vulnerable members of the riparian community who have no
other access to clean drinking water other than the contaminated one. Hence data on cyanobacteria flora and cyanotoxins will help in empowering water users to protect their health in regard to public health risks and how they can engage in environmental conservation.

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Samantha Mohney

Ph.D. Candidate

George Mason University

Fairfax, Virginia


Research Title

The physiological and transcriptional response of cHABs to varying environmental conditions

Improvements in federally mandated water quality standards and recent advancements in wastewater treatment methods have played a pivotal role in declining nutrient concentrations being observed in a number of eutrophic lakes and rivers across the United States. These diminishing nutrient levels have triggered a domino-like effect, with noted decreases being observed in turbidity and planktonic cyanobacterial harmful algal bloom (cHAB) occurrence. These events have ultimately resulted in both increased transparency and light penetration, causing multiple waterbodies to subsequently experience both the establishment and proliferation of benthic cHABs. Information and research on benthic cyanobacteria, their associated environmental growth factors, and toxin production has been relatively scarce, especially when compared to their planktonic counterparts. Through a series of field and laboratory experiments, we aim to discern both the environmental conditions and temporal trends that drive benthic cHAB species’ establishment, growth, and toxin production. Data will be collected from three separate areas currently experiencing differing stages of benthic cHAB occurence and dominance. The study areas will include sites from: 1) The Eastern Seaboard (benthic cHAB dominance), 2). The Midwestern U.S. (planktonic cHAB dominance, with rising benthic cHAB occurrence), 3). Lake Victoria (planktonic cHAB dominance, no benthic cHAB occurence). Data will be analyzed in order to evaluate transformations in cHAB dominance type and growth patterns. Ultimately, we will expose and frame relevant trends for the specific purpose of tracking alterations in both bloom formation and toxin production. This will assist in building an initial framework for predicting how shifts in water quality, climate, and policy will shape the future impacts of benthic CHABs on human and ecosystem health.


Kaela Natwora

Ph.D. Candidate

University of Minnesota-Duluth

Duluth, Minnesota


Research Title

The physiological and transcriptional response of cHABs to varying environmental conditions

Cyanobacterial harmful algal blooms (cHABs) are increasing in frequency, duration, and severity in freshwater ecosystems. As of 2018, cHABs have been documented in all five of the Laurentian Great Lakes (LGL). Given the sheer scale of the LGL, employing basin-wide approaches, including spatial and temporal methods, is impractical and restrictive to understanding drivers of cHAB formation and toxicity. With over 10,000 inland lakes spanning broad gradients of latitude, land use, trophic status, and thermal regimes, the state of Minnesota represents a unique natural laboratory for exploring a wide range of potential environmental stressors on cHABs. Using an integrative, multidisciplinary approach, we aim to identity mechanisms and drivers promoting cHAB development and toxicity. Molecular tools including metagenomics and metatranscriptomics, comprehensive environmental surveys, and cyanotoxin profiles will be used to explore relationships between environmental stressors, cHAB composition, and cyanotoxin production. While the inland lakes of Minnesota provide a testing bed to understand broad scale environmental drivers in an ecosystem setting, it is also imperative to understand drivers and processes on the organismal level. Using the N-fixing Dolichospermum, isolated from the Lake Superior bloom in 2018, we determined that it is genetically similar to genomes recovered from Lakes Erie and Ontario. Our previous work shows N-fixing microorganisms are ubiquitous across the LGL, and highly active during algal blooms. Together this emphasizes the ecological heterogeneity of Dolichospermum, and suggests it is phenotypically plastic, as it can persist in a range of ecosystems. The widening of its geographic distribution beyond the LGL and North America suggest the existence of different ecotypes. Thus, we sought to characterize the physiological response of N fixation in Dolichospermum and transcriptional patterns to nutrient conditions similar the LGL and show its variable response across nutrient conditions and temperature regimes. Collectively, the statewide field survey and pure culture laboratory experiments will provide insight to microbial processes and environmental drivers that promote cHABs growth and toxicity.


Julia Akinyi Obuya

Research Intern

Kenya Marine and Fisheries Research Institute

Kisumu, Kenya, East Africa

Research Title

Characterization of microcystin (mcy) gene in strains of cyanobacterium

genus Microcystis in Lake Victoria, Kenya

Microcystis is one of the most common and dominant cyanobacterial genus found in freshwater and brackish environments worldwide. It contributes to the development of harmful algal blooms in freshwater bodies through the production of a range of hepatotoxin s named microcystins. In Lake
Victoria, Microcystis form blooms together with other genera including Anabaena spp, Nostoc spp, and Planktothrix spp. Lake Victoria is a major source of domestic water use thus the presence of microcystins can be a potential threat to human and animal health. Microcystins occurrence has been reported in colonies of cyanobacterial blooms in various sites of the lake. However, at present little is known about the microcystin producing strains of Microcystis and their associated morphological characteristics (morphospecies) in Lake Victoria. This study aims to investigate the relationship between morphospecies to the occurrence of microcystin (mcy) genes in strains of Microcystis in Lake Victoria Kenya and to test
whether there ar e spatial and temporal variations in morphosphesis specificity and abundance of mcy genes. Molecular identification of microcystin producing strains will be performed using multiplex PCR to detect microcystin biosynthesis genes in samples collected from sp atially distributed sites in the lake. The toxin strains will then be morphologically examined using light microscopy (LM) to identify the Microcystis morphosphesis. Further, DNA sequencing will be performed on the microcystin producing Microcystis strain s to identify the genetic heterogeneities within the strains that would be useful to understand their evolutionary histories. The study is expected to provide information on the distribution of microcystins in Lake Victoria that can efficiently serve in wa ter quality monitoring and risk assessment of microcystin for water management and restoration strategies in the lake.

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Pamela Okutoyi

Sustainability Researcher and Writer

Kenya Climate Innovation Centre Consulting

Nairobi, Kenya, East Africa

Research Title

Assessment of the toxic composition of pollutants on phytoplankton in Lake Victoria

There are four main sources of aquatic pollution: industrial wastes, municipal  wastes, agricultural run off, and accidental spillage. Non point sources, such as automobile exhausts, add appreciable amounts of pollutants to air that may enter aquatic systems in r ainfall or dry fall out. These
sources add pesticides, heavy metals, oil, petroleum products, and a large number of organic and inorganic compounds to water. Lakes and oceans serve as sinks for many pollutants. Plankton comprise a large portion of the livi ng matter in natural waters and function in biogeochemical cycles. They are affected by pollutants, transfer them to sediments and other organisms, and function in their biological transformation. In natural waters, such as oceans, lakes, rivers, and swamp s the greatest amount of biological production is done by the smallest organisms, the plankton. These microscopic plants and animals comprise communities that drift aimlessly with tides and currents, yet they incorporate and cycle large amounts of energy that they pass on to higher trophic levels. Thus communities of plankton, as distinct as those of swamp, forest, or grassland, support other communities of aquatic species and man. Pollution levels in Lake Victoria are increasing. Pollutants from non point sources (NPS) result in lower
dis solved oxygen (DO) concentrations, higher nutrient concentrations and increasing turbidity hence affecting the general health of the lake. Understanding the composition of these toxic pollutants that may cause harmful a lgae bloom (HABs) and impede functioning of the plankton that in turn affects all life depended on the lake, will be key in reducing its production and pollution of the lake in the longer term.

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Mark Olokotum

Research Officer; Ph.D. Candidate

National Fisheries Resources Research Institute; Makerere University

Jinja; Kampala

Uganda, East Africa

Research Title

The dynamics of cyanobacteria and threats of cyanotoxins in Uganda

Lake Victoria is a good example of the huge challenge facing developing countries concerning sustainable management, monitoring and protection of their surface water resources. The lake has suffered human induced eutrophication since the 1950s, leading to recur rent proliferations of water
hyacinth and cyanobacteria blooms. These blooms mainly occur in the numerous bays and gulfs (B&Gs) surrounded by big cities such as Kampala, Kisumu, and Mwanza. Consequently, increasing eutrophication is a major threat to its ecological functioning and support to the growing populations.
Several surveillance programmes have collected data in the past 20 years. However, interests into cyanobacteria and cyanotoxins started in the early 2000s and by late 2000s, there were some break throughs in classification of toxin in water. Based on these background, this study aims to integrate
the current state of knowledge on cyanobacteria, the factors controlling the dynamics of both cyanobacteria and cyanotoxins. The study will further perform experimental mesocosms setups to clarify the environmental factors associated with cyanobacteria dominance and toxin production, transfer and potential biomagnification of cyanotoxins in Nile tilapia. Monthly sampling was done from November 2017 to October 2018. Results from this showed that large differences exist between B&Gs with strong nutrient gradient from the inshore to the offshore areas of hypereutrophic and closed B&Gs. A similar phytoplankton species pool exists in these B&Gs, however, there i s a high dissimilarity in community structure due to turnover shift in the dominant toxigenic cyanobacteria. Further assessment of the dynamics of the toxigenic cyanobacteria revealed significantly high levels of cyanotoxins (microcystins) in the hypereutrophic embayment. The study also assesses other potential exposure routes of toxigenic cyanobacteria such as recreation sites and drinking water production that employ conventional methods of water treatment. Furthermore, the study will assess the concept o f nutrient limitation, control of toxin production, its transfer and potential biomagnification in Nile tilapia using mesocosm experimentation.


Dennis Otieno

Research Associate

Kenya Marine and Fisheries Research Institute

Kisumu, Kenya, East Africa

Research Title

Microcystin concentration profile and Vertical heterogeneities of

cyanobacteria in Winam Gulf, Lake Vitoria, Kenya

Cyanobacteria are resilient and ubiquitous planktons that are widely distributed across many lakes of the world including Lake Victoria. Several genera produce toxins that are of concern to human and animal health. Winam Gulf receives nutrients from anthropogenic sources and encounters cyclic cyanobacteria algal bloom which influences the cost of domestic water treatment. Data on the vertical concentrations and potential risks of microcystin are largely lacking to support the decision of locals and the government on domestic water treatment and supply. This paper will explore the vertical concentrations of microcystin and algal genera in Winam Gulf with a focus on areas where the municipal works abstract water for treatment. The study aims to generate information on the best depths within the water column for installing water intake pumps to reduce toxin risks and the cost of water treatment. Water samples will be collected along the littoral zones where communities abstract their water for domestic use and potential municipal water abstraction sites within the Gulf. The samples will be collected using a van don sampler and nutrient analyzed for Ammonium, Soluble Reactive Phosphorus, Nitrates, and Nitrites using the AOC method, 2005. Physio chemical parameters will also be recorded in
situ and the vertical concentration of microcystin determined at different depths. Data will then be analyzed using the R Statistical analysis tool. This paper will contribute to this knowledge gap and provide further insight into the interrelationship between eutrophication and algal toxins for better
management and utilization of Lake Victoria resources.

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Omondi Argwings Owino

Tutorial Fellow of Limnology and Environmental Science

Dept. of Medical and Applied Sciences

Sigalagala National Polytechnic

Kakamega, Kenya, East Africa

Research Title

Diversity, Distribution and Biomass of Phytoplankton in Lake Naivasha, Kenya

Lake Naivasha is a shallow freshwater lake that supports a wide but uneven biodiversity of plants and animals but no native fish as most of the fish species in the lake were introduced. The lake’s ecosystem has been undergoing major changes due to anthropogenic and natural factors that influence its limnology. This study aimed to determine the diversity, distribution, and biomass of the phytoplankton community in this lake. For a period of 6 months from February 2019 to July 2019 covering dry and wet season, water samples from the lake were analyzed to determine the spatio-temporal trends of phytoplankton and associated environmental variables which included nutrients concentrations,  temperature, conductivity, DO, pH and transparency. Monthly samplings were done and samples analyses using the standard procedures. Samples were collected in triplicates for the determination of nitrate nitrogen, soluble reactive phosphorous, total nitrogen, total phosphorous, ammonium nitrogen, silicates, and chlorophyll a. Water temperature, conductivity, DO, and pH were measured in situ using multimeter probe YSI model. The results showed the mean temperature of 22.73 ± 1.6 °C, DO 8.51 ± 0.87 mg/L, conductivity 233.85 ± 26.94 μS/cm, pH 8.13 ± 0.3. TN were 471 ± 170.61 µg/L, PO4-P 5.88 ± 2.12 µg/L, TP 97.97 ± 49.06 µg/L, NO3-N 6.70 ± 3.55 µg/L, NH4-N 18.93 ± 10.91 µg/L and SiO2 3.18 ± 2.99 mg/l and Chlorophyll a 21.51 ± 4.25 mg/m³. Total phosphorous, total nitrogen, silicates, temperature, pH, dissolve oxygen, conductivity, TDS and secchi depth showed significant seasonal differences. A total of one hundred and twenty four (124) species of phytoplankton belonging to six (6) taxonomic families were identified. Chlorophyceae was represented by 43 species consisting of 34.68 % by species composition, Bacillariophyceae was represented by 38 species consisting of 30.65 % by species composition. Cyanophyceae was represented by 24 species leading to 19.35 % species composition. Zygnematophyceae, Euglenophyceae, and Dinophyceae recorded the least species composition. Chlorophyceae recorded the highest total phytoplankton biovolume of 623.41 mm3/L, followed by Bacillariophyceae with 533.16 mm3/L and Cyanophyceae with 114.55 mm3/L. Dinophyceae recorded the least phytoplankton biovolume of 82.36 mm3/L. The total number of algal species was highest at Hippo point sampling site with 72 species, followed closely by 68 species in Crescent Island, then Oserian Bay sampling site with 66 species. Mouth of R. Malewa recorded 59 species, Sher Bay had 58 species, this was followed by Mid Lake station with 56 species, and Sewage Discharge Point had 55 species. Shannon-Wiener diversity (H’) index ranged from 2.0455 at the Mouth of R. Malewa to 2.7077 at Oserian Bay and was highest in July. Lake Naivasha showed a high phytoplankton diversity with significant physico-chemical parameters relationship. There is need for long-term and continuous ecological and hydrological monitoring especially on nutrients seasonal dynamics for proper understanding of seasonal effects of nutrients to algal biomass and diversity, which could be used as an indicator of eutrophication level in the lake.

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Winiie Owoko

Research Intern; MS Candidate

Kenya Marine and Fisheries Research Institute; Kisii University

Kisumu; Kisii

Kenya, East Africa

Research Title

Spatial Modelling of cyanobacteria toxin composition and abundance

in Winam Gulf, Lake Victoria, Kenya

Rapid increase in human population in riparian cities around Lake Victoria has brought about urbanization and industrialization. Increase in human population brings about increasing demands on energy, increasing use of fertilizer containing nitrogen (N) and phosphorus (P) for agriculture, poor sewage waste management and increasing industrial activities hence emissions that leads to eutrophication and nutrient pollution. Increased effluent into Lake Victoria has altered the magnitude and composition of nutrient load in the lake therefore creating a favorable environment for harmful algal species to bloom.  The lake is highly depended upon for various domestic and industrial use. Harmful Algal Blooms (HABs) which has a lot of concomitant economic and ecological effects therefore presents a great risk to the health of the people using the water. The HABs produce toxins which have negative impacts on the socioeconomic and ecological well-being of the population dependent on the lake. This study aims to map species composition, diversity, distribution and abundance in the algal blooms. Focus will be on both toxic and non-toxic HABs traversing horizontally on the lake’s surface. A remote sensing Landsat image showing the occurrence of HABs on the lake will also be used to corroborate the findings of the in-situ measurements. The study will map the different concentration of algal bloom toxin levels and spatial analysis of the physico-chemical parameters using G.I.S and R tool analysis. Findings from this study will give resource managers and biologist insight in better tools to forecast HAB events and to predict the composition of algal species and assemblages that may occur under conditions of changing nutrient loads.


Jordyn Stoll

Ph.D. Candidate

Kent State University

Kent, Ohio


Research Title

Investigating the role of macro and micronutrients on algal community processes

With global anthropogenic nutrient enrichment of aquatic systems accelerating, a holistic view of nutrient influence on primary producers is needed to inform management decisions and ultimately protect aquatic resources. By conducting nutrient enrichment experiments, ecologists can begin to determine the degree of effect various nutrients inflict on community processes. While the effect of macronutrients (N, P) on aquatic primary producer community processes is well studied, and the role of micronutrients (Fe, trace metals) is known, the magnitude that micronutrients affect primary producers in freshwater ecosystems is severely understudied. Furthermore, many nutrient enrichment experiments only quantify the effect of nutrients on growth, ignoring processes related to toxin production, metabolism and other key ecosystem processes that may provide insight into the underlying physiological pathways that are nutrient limited. Eutrophication has been linked to the global increase in harmful cyanobacterial blooms in lentic systems; however, there are conflicting findings regarding what nutrient is driving bloom formation. While macronutrients are essential for primary producers, there are roughly 25 other elements (micronutrients) that are utilized for various metabolic processes. Micronutrients act as gatekeepers, as they are essential cofactors in metalloenzymes and can directly limit the metabolic processes they are involved in when at limiting concentrations in the environment.

My dissertation is focused on the direct and indirect effects of micronutrients and macronutrients on algal community composition, growth, toxin production and enzyme (alkaline phosphatase & urease) activity in lakes and streams. To assess the effect of nutrients on phytoplankton and biofilm community functions, a series of nutrient enrichment experiments have been used both in situ and within mesocosms. Quantification of enzyme activity, community composition and metabolic processes alongside growth allows me to tease apart what processes are limited or driven by nutrients, and determine if nutrients interact to influence these processes. By determining the magnitude of effect micronutrient enrichment has on various aquatic primary producer community processes, my dissertation work will help fill the micronutrient knowledge gap in aquatic ecology and expand our understanding of the underlying physiological mechanisms controlling community and ecosystem level responses.

Mariam Maku Swaleh

Ph.D. Candidate

Technical University of Mombasa


Kenya, East Africa

Research Title

Marine Microalgae Potential in Simultaneous Wastewater Treatment

and Low-Cost Biofuel Feedstock

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With rapid increase in urban population, depletion of oil resources as well as the negative environmental impact associated with industrialization and us e of fossil fuels, has spurred interest in seeking sustainable solutions. Biofuel derived from oil crops has been viewed as a potential renewable
replacement for our fossil fuel needs. However, concern has grown that the use of food crops for biofuel will increase food prices while having little impact on greenhouse gas emissions. On the other hand, wastewater discharged by industries introduces high levels of nutrients which cause eutrophication in receiving water bodies leading to irreversible ecological degradation. Microalgae offer a sustainable solution for wastewater treatment and low cost alternative renewable source of energy. Like plants, microalgae are capable of sequestering greenhouse gas using sunlight and incorporating nutrients such as nitrogen and phosphorus to produce potentially valuable biomass, which can be used for biofuel. The biofuel produced can replace a significant fraction of our fossil fuel consumption. The goal of this study is therefore to develop an integrated system for algae b ased biofuel production and wastewater treatment. In this study growth of microalgae in wastewater will be monitored with simultaneous removal of dissolved nutrients such as nitrogen and phosphorus. The microalgae biomass will then be used as feedstock for biofuel production. Overall, the waste to biofuel approach of this study will be effective in addressing energy insecurity, environmental remediation and mitigate global warming in Kenya as envisaged in Vision 2030 and Sustainable Development Goals (SDGs) 7 and 13.


Emily Varga

Ph.D. Candidate

University of Windsor

Windsor, Ontario


Research Title

Reciprocal learning to understand the environmental drivers of cyanoHABs in large lakes. 

Freshwater resources around the world have been threatened by cyanobacterial harmful algal blooms for decades. Surveys of these blooms in western Lake Erie have shown that they are dominated by hepatotoxin-producing Microcystis and by various filamentous forms in agriculturally influenced embayments and tributaries to these lakes. It has been shown that rivers contribute to the formation of cyanoHABs in lakes mainly by serving as conduits delivering nutrients to promote the blooms. Only recently has a systems biology approach been adopted for in-depth study of these blooms, combining environmental chemistry, ecology and molecular biology. The goals of this study are to gain an understanding of the factors that contribute to the formation of distinct cyanoHABs in rivers compared to the lakes into which they flow. Our surveys will focus on the Thames River and the receiving waters of Lake St. Clair and will address which environmental factors promote proliferation of algal blooms. We will also investigate the dominant algal taxa found in these systems and the prevalence of toxin production. Methods which we will employ to achieve these goals include analysis of water chemistry, microscopy to identify cyanobacterial taxa, transcriptome analysis to assess cyanobacterial response to environmental influence, quantitative PCR (qPCR) and RT-qPCR to determine prevalence of toxin-producing taxa and in-situ mesocosms in which we will attempt to assess the influence of physico-chemical factors (e.g. light and nutrients) on promoting the growth of cyanobacteria. Our project will likewise include use of remote data collection using water quality sondes to monitor in real-time changes in physico-chemical parameters and algal community dynamics. It has been shown that the cyanobacterial community will shift with nutrient limitation and as such, we hypothesize that the dominant taxa within the mesocosms will also vary with respect to changes in the nitrogen to phosphorus ratio, light penetration and temperature as the communities respond to differences in nutrient limitation. We also hypothesize that there will be variation in taxa with respect to light penetration and temperature. This study will provide us with the tools to not only predict the composition and quantity of future blooms in terms of taxonomy and potential toxin-production but also to plan appropriate means to mitigate future bloom events. This would be beneficial at many levels of public health concerns.


Ryan Wagner

Masters Candidate

Bowling Green State University

Bowling Green, Ohio


Research Title

Abiotic Factors limiting Chytridiomycota infecting Planktothrix in Sandusky Bay lake Erie

Sandusky Bay, Lake Erie has frequent and often toxic cyanobacterial blooms that are dominated by filamentous Planktothrix species. Chytridiomycota known as chytrids are fungal parasites that are capable of infecting cyanobacteria. In Sandusky Bay the chytrid Rhizophydium sp. has been known to infect Planktothrix. Chytrids are an overlooked aspect of cyanobacterial blooms and the effect they have on naturally controlling cyanobacteria blooms. Biotic and abiotic factors limiting these epidemics are important for understanding the role in controlling cyanobacterial blooms. Chytrids serve as a parasite and as a food source for other organisms. Zoospores, a flagellated infectious life stage, can break apart long less edible filamentous cyanobacteria causing a trophic upgrading for zooplankton. Additionally, the sporangia stage which is attached to a cyanobacteria removes nutrients from the inside of the cyanobacteria. This stage then produced more zoospores which are released along with the nutrients to make them. Due to the small nature of zoospores it is likely that abiotic factors like depth and the amount of water movement play a large role in chytrids ability to find and infect their obligate hosts. I propose that water circulation with significantly lessen the severity of infections and that infections will vary with depth.


Brittany Zepernick

Ph.D. Candidate

University of Tennessee Knoxville

Knoxville, Tennessee


Research Title

Investigating drivers of Lake Erie algal blooms

In Lake Erie, a seasonal pattern of algal succession occurs: diatom blooms dominate winter-spring, and Microcystis blooms dominate summer-fall. My research aims to assess the drivers of these blooms and their succession in Lake Erie. Our first driver of focus was pH, as studies indicate Microcystis blooms inc. water column pH to ≥ 9.2. We used culture assays to assess Microcystis’s response to N sources on a pH gradient, demonstrating M. aeruginosa utilizes urea during pH-induced nutrient limitation “Urea is both a carbon and nitrogen source for Microcystis aeruginosa: Tracking 13C Incorporation at bloom pH conditions” (Krausfeldt, Zepernick, et al., 2019). This work suggests high pH is a positive feedback loop for Microcystis blooms. Yet, there is little work on the effects of high pH on Microcystis’s competitors (diatoms). We predicted due to the pH-dependency of biosilicification, diatoms can’t deposit silica (Si) cell walls at pH ≥ 9.2. Serendipitously, troubleshooting this project led to a paper “Flaming as part of aseptic technique increases CO2 and decreases pH in freshwater culture media” (Zepernick et al., 2020).  After which, I assessed the effects of pH on the relevant diatom Fragilaria crotonensis in vitro, and a Lake Erie diatom community in situ. These studies indicated high pH negatively affects growth and Si deposition, serving as a competitive disadvantage “Elevated pH conditions associated with Microcystis spp. blooms decrease viability of the cultured diatom Fragilaria crotonensis and natural diatoms in Lake Erie” (Zepernick et al., 2021 accepted). Cumulatively, these results suggest pH plays a role in taxa succession, creating a potential to prolong summer Microcystis blooms and constrain diatom fall resurgence. In addition to my work on urea and pH, I took part in a field study at OSU’s Stone Lab (July 2019), assessing short-term responses of Microcystis to episodic nutrient pulses (Pound, Zepernick et al., 2021in prep). During this, I also led my first field study assessing the effects of pH on natural diatoms (to be published in Zepernick et al., 2021). While my work thus far focused on drivers of summer-fall HAB succession, there is a lack of research on problematic, albeit non-toxic, diatom blooms in Lake Erie. I received an Illumina Grant (2020) to sequence the genome of the diatom F. crotonensis, which will facilitate future bioinformatic studies of diatoms. Currently, I am processing Lake Erie winter diatom metatranscriptomes.

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