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ABSTRACT We report 40 metagenomic libraries collected from the Winam Gulf of Lake Victoria during May–July of 2022–2023 and an additional eight opportunistic libraries from adjacent Lakes Simbi, Naivasha, and regional river systems. The sampling period captured cyanobacterial bloom events – shedding insight onto community composition and genomic potential. 

ABSTRACT The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf’s cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf’s cyanobacterial composition, function, and biosynthetic potential.Dolichospermumwas the dominant bloom-forming cyanobacterium, co-occurring withMicrocystisat most sites.MicrocystisandPlanktothrixwere more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) ofDolichospermumharbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation ofDolichospermumin the nitrogen-limited gulf. Over 300 biosynthetic gene clusters (BGCs) putatively encoding the synthesis of toxins and other secondary metabolites were identified across the gulf, even at sites where there were no visible cyanoHAB events. Almost all BGCs identified had no known synthesis product, indicating a diverse and novel biosynthetic repertoire capable of synthesizing harmful or potentially therapeutic metabolites.MicrocystisMAGs containedmcygenes encoding the synthesis of hepatotoxic microcystins which are a concern for drinking water safety. These findings illustrate the spatial variation of bloom-forming cyanobacteria in the Winam Gulf and their available strategies to dominate different ecological niches. This study underscores the need for further use of genomic techniques to elucidate the dynamics and mitigate the potentially harmful effects of cyanoHABs and their associated toxins on human, environmental, and economic health. 

Abstract The Winam Gulf (Kenya) is frequently impaired by cyanobacterial harmful algal blooms (cHABs) due to inadequate wastewater treatment and excess agricultural nutrient input. While phytoplankton in Lake Victoria have been characterized using morphological criteria, our aim is to identify potential toxin‐producing cyanobacteria using molecular approaches. The Gulf was sampled over two successive summer seasons, and 16S and 18S ribosomal RNA gene sequencing was performed. Additionally, key genes involved in production of cyanotoxins were examined by quantitative PCR. Bacterial communities were spatially variable, forming distinct clusters in line with regions of the Gulf. Taxa associated with diazotrophy were dominant near Homa Bay. On the eastern side, samples exhibited elevatedcyrAabundances, indicating genetic capability of cylindrospermopsin synthesis. Indeed, near the Nyando River mouth in 2022,cyrAexceeded 10 million copies L⁻¹where there were more than 6000Cylindrospermopsisspp. cells mL⁻¹. In contrast, the southwestern region had elevatedmcyEgene (microcystin synthesis) detections near Homa Bay whereMicrocystisandDolichospermumspp. were observed. These findings show that within a relatively small embayment, composition and toxin synthesis potential of cHABs can vary dramatically. This underscores the need for multifaceted management approaches and frequent cyanotoxin monitoring to reduce human health impacts. 

Components of the lower food web (mussels, Caridina and Omena) were collected from stations from Winam Gulf, Lake Victoria, Kenya in 2022 and 2023 to analyze for stable isotopes and total mercury (THg). Temporal comparisons were made with data generated for the same species in 1998. Values of δ15N in mussels and Caridina were similar (6.89‰ vs. 6.78 ± 0.13‰), while Omena occupied an elevated trophic position (9.97 ± 0.24‰) with minor shifts in δ15N over time. All species had elevated δ13C values in 2022–2023 versus 1998 supportive of enhanced eutrophication in the Gulf. THg concentrations exhibited modest spatial differences between sites (< 2.6 fold), but not between Caridina and Omena. Larger temporal differences were apparent relative to spatial patterns with THg concentrations decreasing in study species by 2.8 to 4.1-fold between years. An exposure assessment indicated that Omena, commonly found in local markets, can be consumed up to 0.74 kg/month without generating excess THg exposures. 

Metagenome-assembled genomes were generated for two xenic cyanobacterial strains collected from aquatic sources in Kenya and sequenced by NovaSeq S4. Here, we report the classification and genome statistics of Microcystis panniformis WG22 and Limnospira fusiformis. 

The Nile perch (Lates niloticus L.) commercial fishery for Lake Victoria in East Africa is an important source of revenue and employment. We focused on shifts in food web structure and total mercury (THg) bioaccumulation and biomagnification in Nile perch, and lower food web items collected from Winam Gulf (Kenya) sampled 24 years apart (1998 and 2022). Stable isotope carbon (δ13C) values were higher in all species from 2022 compared to 1998. Stable nitrogen isotope (δ15N) values in baseline organisms were lower in 2022 compared to 1998. In Nile perch, δ15N values were correlated with total length, but the δ15N-length regressions were steeper in 1998 compared to 2022 except for one large (158 cm) Nile perch from 1998 with an uncharacteristically low δ15N value. Total Hg concentrations were lower in lower trophic species from 2022 compared to 1998. However, the THg bioaccumulation rate (as a function of fish length) in Nile perch was greater in 2022 compared to 1998 resulting in 24.2 % to 42.4 % higher wet weight dorsal THg concentrations in 2022 Nile perch for market slot size (50 to 85 cm) fish. The contrasting observations of increased THg bioaccumulation with size in 2022 against decreases in the rate of trophic increase with size and lower THg concentrations of lower food web items imply reduced fish growth and potential bioenergetic stressors on Winam Gulf Nile perch. All samples except 1 large Nile perch (139 cm total length collected in 2022) had THg concentrations below the European Union trade limit (500 ng/g wet weight). However, for more vulnerable individuals (women, children and frequent fish eaters), we recommend a decrease in maximum monthly meal consumption for 55–75 cm Nile perch from 16 meals per month calculated for 1998 to a limit of 8 meals per month calculated for 2022. 

A learning module for middle school science students created by an NSF-IRES funded program facilitated by BGSU, KiSII University, Technical University of Kenya, Kenya Marine Fisheries Research Institute and the African Center for Aquatic Research and Education 

Lake Victoria has experienced progressive eutrophication which has exacerbated the proliferation of cyanobacterial harmful algal blooms (cHABs). Fueled by anthropogenic nutrient loadings and climate change, these cHABs are increasing in distribution, duration, and frequency, particularly in areas such as the Winam Gulf. With limited resources and infrastructure, local communities have been left vulnerable as they rely on the lake for water for domestic use. Our study presents the results of a localized survey on how small-scale fishing communities perceive and respond to the threat of cHABs in the Winam Gulf of Lake Victoria, Kenya. We used a mixed-methods approach of quantitative and qualitative data-gathering techniques to elucidate the perceptions and consequences of cHABs in local communities. Our results demonstrate most (93.67%) respondents were aware of cHABs in the lake, but were not knowledgeable of cHAB threats to human and animal health. Respondents noted that fish catches decreased during cHABs, with this economic consequence serving as a primary concern of communities. Notably, respondents altered their use of lake water during perceived cHAB events and relied on other means of water treatment or alternative water sources. Overall, cHAB information was selfsourced or passed on from community elders, with no public mechanism for adequate cHAB risk communication. Lake Victoria serves as a critical resource to the Eastern African region and requires a concerted cHAB response effort. Therefore, we recommend the development of a public awareness program to reduce cHAB exposure in these at-risk communities.