PHOTOSYNTHETICA

Photosynthetica X:X | DOI: 10.32615/ps.2026.013

What's in your pellet? 16S rRNA V4 amplicon-profiling reveals persistent microbiomes in laboratory cyanobacterial cultures

M.S. RAO¹, J. MONDAL^{1, 2}, B.D. BRUCE^{1, 3, 4}

¹ Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, USA

² Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

³ Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, Tennessee, USA

⁴ Microbiology Department, University of Tennessee, Knoxville, Tennessee, USA

Cyanobacterial laboratory cultures are widely assumed to be axenic, yet the diversity and associated microorganisms are rarely examined. In this study, 16S rRNA V4 amplicon sequencing was used to characterize microbial communities associated with multiple cyanobacterial strains maintained in laboratory cultures and large-scale photobioreactors. Analysis of 24 samples revealed persistent, culture-specific microbiomes dominated by heterotrophic bacteria. Distinct ecological patterns were observed, including consistent differences between thermophilic and mesophilic cyanobacterial cultures and repeated detection of taxa linked to geothermal or freshwater environments. Despite more than 14 years of cultivation and shared bioreactor infrastructure, no evidence of cross-contamination between cyanobacterial hosts was detected, suggesting that many associated organisms derive from original culture stocks or environmental recruitment. Although none of the detected taxa were oxygenic phototrophs, their presence may influence genomic, transcriptomic, metabolomic, and lipidomic analyses. These findings indicate that many laboratory cyanobacterial cultures represent stable microbial consortia rather than strictly axenic systems.

Additional key words: 16S rRNA; cyanobacterium; microbiome; monoculture; photobioreactor; thermophile.

Received: April 7, 2026; Revised: June 3, 2026; Accepted: June 4, 2026; Prepublished online: June 16, 2026