The Hidden Microbial Partners of an Invasive Diatom: Uncovering the Ecology of Cymbella janischii Blooms

by Eldrin DLR. Arguelles |

Rivers are among the most dynamic ecosystems on Earth. Beneath the flowing water and seemingly ordinary stones lies an invisible world of microorganisms that drive nutrient cycling, oxygen production, decomposition, and food-web interactions. Diatoms, bacteria, fungi, and other microscopic organisms form complex biofilm communities attached to submerged surfaces, creating ecosystems that are essential for river health. Yet these communities can be dramatically altered when invasive species establish themselves and begin to dominate local habitats.

One such organism is Cymbella janischii, a freshwater diatom native to North America that has become an invasive species in Japan. Since its first documented appearance in the Chikugo River in 2006, C. janischii has rapidly expanded its distribution across multiple prefectures, including Oita, Gunma, Gifu, Kanagawa, Ishikawa, Tochigi, and Shiga. Over the last two decades, the species has become increasingly recognized as a nuisance organism because of its ability to form extensive mats on riverbeds, covering large areas of submerged rocks and altering natural benthic habitats.

Unlike many planktonic algae that drift freely in the water column, C. janischii attaches itself to rocks through long mucilaginous stalks secreted from specialized structures at the tips of its cells. As colonies expand, these stalks intertwine and form thick biofilms that can be several centimeters thick. The resulting mats become highly visible in rivers and may influence ecosystem processes by modifying habitat structure, nutrient dynamics, and microbial community composition. Despite its rapid spread and ecological importance, surprisingly little was known about the microorganisms associated with these blooms or the biological mechanisms that allow this invasive diatom to become so successful.

To better understand the ecology of this invasive species, our research investigated the microbial communities associated with Cymbella janischii blooms across multiple river systems in Japan. Using high-throughput DNA metabarcoding, we simultaneously analyzed three major groups of microorganisms—diatoms, bacteria, and fungi—to determine how riverine microbial communities respond to invasion by C. janischii. The study also sought to identify microorganisms that consistently occur alongside the invasive diatom and to determine whether microbial interactions may contribute to bloom formation.

Field sampling was conducted in fifteen rivers distributed across Japan. At each location, two types of samples were collected: one from cobbles with visible C. janischii mats and another from cobbles lacking visible colonies. By comparing these paired samples, it became possible to assess how the presence of the invasive diatom influences surrounding microbial communities while minimizing environmental differences between sites. A total of thirty samples were analyzed using DNA sequencing technologies targeting diatoms, bacteria, and fungi.

Microscopic observations immediately revealed the remarkable architecture of C. janischii colonies. Thick mat-like growths covered river stones, with cells connected through long stalk structures that anchored them firmly to the substrate. High-resolution scanning electron microscopy provided an even more intriguing discovery: the surfaces of the diatom cells were densely colonized by rod-shaped bacterial cells. This observation suggested that the relationship between the diatom and bacteria may be more than a simple coincidence. Instead, these microorganisms appeared to form a closely associated microbial consortium.

The DNA metabarcoding analysis results revealed that C. janischii blooms significantly altered the diversity of riverine microbial communities. Areas dominated by the invasive diatom showed lower bacterial and diatom diversity compared with nearby non-bloom habitats. In ecological terms, this means that fewer species were able to coexist when C. janischii became dominant. The invasive species effectively reshaped the microbial landscape, creating conditions that favored only a subset of organisms capable of surviving within the dense mats. Interestingly, fungal communities responded differently. Although fungal evenness changed, overall fungal diversity remained relatively stable, indicating that fungi may be more resilient to invasion by C. janischii than bacteria and other diatoms.

These findings demonstrate that the ecological effects of invasive microorganisms extend beyond the invading species itself. Just as invasive plants and animals can transform ecosystems, invasive diatoms can restructure entire microbial communities by altering the availability of space, nutrients, and ecological niches. The decline in bacterial and diatom diversity observed in bloom sites suggests that C. janischii may monopolize resources and suppress competing organisms, ultimately reducing microbial biodiversity within affected rivers.

To identify microorganisms most closely associated with C. janischii, co-occurrence network analyses were performed. These analyses revealed that certain microorganisms consistently occurred alongside the invasive diatom. Among the most important were the diatom Nitzschia paleacea and bacteria belonging to the genus Flavobacterium. Their repeated association across multiple river systems suggests that they may participate in ecological interactions that help maintain or enhance C. janischii blooms. Conversely, several native diatom species exhibited negative associations with C. janischii, indicating possible competition for resources and habitat space.

Particularly noteworthy was the dominance of bacterial taxa belonging to the phylum Bacteroidota. Members of this group are well known for their ability to degrade complex polysaccharides and other organic compounds. Because C. janischii produces abundant extracellular mucilage and polysaccharide-rich stalk material, these bacteria may benefit from the organic-rich environment created by the diatom. In return, they may provide nutrients, vitamins, or growth-promoting compounds that support the persistence of the bloom. Such mutually beneficial relationships between bacteria and algae have been reported in other aquatic systems and may represent an important but often overlooked driver of invasive species success.

To explore this possibility further, predictive metagenomic analyses were used to infer the metabolic capabilities of bacterial communities associated with C. janischii mats. The results showed enrichment of pathways related to carbohydrate metabolism, amino acid metabolism, nucleotide metabolism, and the biosynthesis of secondary metabolites. Among these pathways, one stood out: zeatin biosynthesis. Zeatin is a cytokinin, a class of phytohormones traditionally known for regulating growth and development in higher plants. The discovery of enhanced zeatin-related pathways within bacterial communities associated with C. janischii suggested a possible link between bacterial activity and bloom formation.

This observation raised an intriguing question: Could bacteria be producing growth hormones (zeatin) that stimulate the invasive diatom?

To test this hypothesis, laboratory experiments were conducted using cultures of Cymbella janischii exposed to varying concentrations of zeatin. The results were striking. Compared with untreated controls, zeatin-treated cultures exhibited enhanced cell growth and increased stalk formation. Both responses are biologically significant because they directly contribute to the formation of dense benthic mats. At moderate concentrations, zeatin stimulated rapid proliferation and the production of longer stalks, whereas very high concentrations resulted in reduced growth, suggesting an optimal hormonal range for bloom development.

These experiments provided the first direct evidence that zeatin can promote the growth of C. janischii. More importantly, they suggest that bacteria living within the mats may influence bloom dynamics through the production of signaling molecules and growth-promoting compounds. Rather than acting as passive inhabitants of the biofilm, bacterial communities may actively contribute to the success of the invasive diatom through chemical interactions that stimulate growth, attachment, and colony expansion.

The implications of this discovery extend far beyond a single species. Traditionally, studies of invasive algae have focused on environmental factors such as nutrient availability, water temperature, and hydrology. Our findings demonstrate that microbial interactions must also be considered. The success of invasive species may depend not only on their own biological traits but also on the support they receive from associated microbial partners. Understanding these hidden relationships could provide new perspectives on bloom ecology and may ultimately contribute to the development of more effective management strategies for invasive microorganisms.

This study represents one of the first comprehensive investigations of the microbiome associated with Cymbella janischii blooms. By integrating metabarcoding, microbial network analysis, predictive metagenomics, microscopy, and laboratory experimentation, the research reveals a complex ecological story in which diatoms, bacteria, and fungi interact to shape river ecosystems. The work highlights how microscopic organisms influence one another through networks of physical associations and chemical signaling, ultimately affecting biodiversity and ecosystem function at much larger scales.

As invasive microorganisms continue to spread globally through natural and human-mediated pathways, understanding their interactions with native microbial communities will become increasingly important. The hidden microbial world surrounding Cymbella janischii demonstrates that even the smallest organisms can have profound impacts on ecosystem health, and that some of the most important ecological relationships occur beyond the limits of what we can see with the naked eye.

Reference:

Arguelles, E. D. L. R., Mugikura, K., & Sato, S. (2026). Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin. Journal of phycology, 62(4), 1221–1239. https://doi.org/10.1111/jpy.70195