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Insight into Cyanobacterial Microbiome Interactions and Cyanotoxin Biosynthesis

Cyanobacteria are a group of photosynthetic bacteria that are widespread in virtually every environment and play an important role in freshwater aquatic ecosystems as hotspots for primary production and nutrient cycling and as foundational members of aquatic food webs. As a primary producer, they provide a perfect microenvironment in their proximity called a cyanosphere. The cyanosphere is a term equivalent to the phycosphere coined already by Bell and Mitchell in 1972 that represents microorganisms interacting with photosynthetic organisms and is an aquatic analog to the widely studied rhizosphere. We use genome-resolved metagenomics to investigate the microbial ecology of freshwater planktonic and benthic cyanobacteria and their complex interactions with the cyanosphere microbiome. Both planktonic and benthic cyanobacteria can produce cyanotoxins that negatively impact water quality and aquatic organisms and can have strong impacts on human and community health. There are diverse types of cyanotoxins depending on their mode of action, and their list keeps expanding.


The Eel River watershed in Northern California is recognized for the yearly occurrence of cyanobacterial mats on the riverbed dominated by cyanobacteria Microcoleus spp. that can form mats several square meters in size. Using genome-resolved metagenomics, we discovered the first anatoxin-a biosynthesis gene cluster in the Microcoleus genus, and its production seems to be correlated not only with the environmental factors but also with the associated microbes. Furthermore, we investigate the genomic content and organization of these organisms and how spatial distances and environmental variation across the watershed affect the Microcoleus genomes and gene flow between strains and species. This work was supported by an NSF Division of Environmental Biology grant, and experiments were performed at the Angelo Coast Range Reserve.

Microcoleus mats

Field collection


The Sacramento-San Joaquin Delta has been experiencing toxic freshwater cyanobacterial blooms (cyanoHABs) since 1999 as a yearly summer occurrence. The emergence of cyanoHABs dominated by novel cyanobacterial taxa with the concurrent emergence and detection of several previously unobserved cyanotoxins has been recently observed. We are going to combine the extensive water quality monitoring data collected across the Delta with actual cyanotoxins measurements and genome-resolved metagenomic methods to understand and characterize the cyanobacterial taxa, their potential for the biosynthesis of cyanotoxins, and the impact of their associated microbial communities present in Delta CyanoHABs. This effort will address key knowledge gaps regarding which emerging cyanobacterial species can produce which toxins, as well as how changing environmental and ecological factors may be contributing to the observation of these emerging Delta threats. This work is supported by the Delta Science Fellowship.

Relevant publications

Bouma-Gregson, K., Crits-Christoph A., Olm M.R., Power, M.E., Banfield J.F. 2021, Microcoleus

(Cyanobacteria) form watershed-wide populations without strong gradients in population structure.

Molecular Ecology 31(1):86-103. 10.1111/mec.16208

Bouma-Gregson K., Olm M.R., Probst A.J., Anantharaman K., Power M.E., Banfield J.F. 2019,

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a

producing cyanobacteria within a river network. ISME Journal, 13:1618-1634,

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