Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya
Authors: Hart Lauren N. , Zepernick Brittany N. , Natwora Kaela E. , Brown Katelyn M. , Obuya Julia Akinyi , Lomeo Davide , Barnard Malcolm A. , Okech Eric O. ,   2022-23 NSF-IRES Lake Victoria Research Consortium, Kiledal E. Anders , Den Uyl Paul A. , Olokotum Mark , Wilhelm Steven W. , McKay R. Michael , Drouillard Ken G. , Sherman David H. , Sitoki Lewis , Achiya James , Getabu Albert , Otiso Kefa M. , Bullerjahn George S. , Dick Gregory J. , Achieng Dorine , Barker Katelyn B. , Basweti George M. , Beal Max , Byrne Aidan , Cody William R. , Kiteresi Linet I. , Lawrence Theodore , Miruka Jared B. , Mohney Samantha , Okutoyi Pamela , Otieno Dennis , Owino Omondi A. , Owoko Winnie , Owuor Bethwell , Shitandi Anakalo , Stoll Jordyn , Swaleh Mariam N. , Tebbs Emma J. , Varga Emily , Adem Jack Abibo , Adhikari Anjana , Allan Trinity , Chepkirui Mercy , Khan Nusrat Nasrin , Moseti Martha , Achieng Tonny , Radock Lisa , Njiru James , Omondi Reuben 
Published: January 2025

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.
Dolichospermum
was the dominant bloom-forming cyanobacterium, co-occurring with
Microcystis
at most sites.
Microcystis
and
Planktothrix
were more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) of
Dolichospermum
harbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation of
Dolichospermum
in 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.
Microcystis
MAGs contained
mcy
genes 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.

IMPORTANCE

The Winam Gulf (Kenya) is a vital resource that experiences prolific cyanobacterial harmful algal blooms (cyanoHABs). Bloom-forming cyanobacteria produce cyanotoxins, threatening human and environmental health, recreation, and fishing. However, cyanotoxin production in the gulf has not been linked to a specific type of cyanobacteria. We used DNA sequencing of whole microbial communities to track the species of cyanobacteria present across the gulf and investigate the genes responsible for synthesis of known and novel toxins. Our results reveal
Dolichospermum
as the main bloom-forming cyanobacteria in the gulf, often co-occurring with high abundance of toxigenic
Microcystis.
Over 300 unique gene clusters were found, with most predicted to encode the synthesis of uncharacterized molecules. These results provide initial insights into the diverse biosynthetic potential encoded by cyanobacteria in the Winam Gulf and underscore the need to further elucidate and investigate the effects of known and novel molecules produced in cyanoHABs in this region.