Genomics, transcriptomics, and laboratory experiments link bioconvection to nitrogen fixation

Lake Cadagno is a meromictic lake characterized by a stable euxinic chemocline that hosts a diverse community of anoxygenic phototrophic sulfur bacteria, among the earliest photosynthetic organisms on Earth. These microorganisms are key to understanding the evolution of photosynthesis; however, due to the rarity of permanently anoxic environments, their genetic and ecophysiological traits remain poorly characterized.

We generated four high-quality genomes (>93% completeness, < 2% contamination), including two purple sulfur bacteria (PSB; Chromatium okenii LaCa and Thiodictyon syntrophicum Cad16T) and two green sulfur bacteria (GSB; Chlorobium phaeobacteroides 1VII D7 and Chlorobium clathratiforme Cad4DE). Using an improved C. okenii genome, we analyzed chemocline transcriptomes under conditions with and without bioconvection. Nitrogen fixation potential was assessed through comparative genomic analyses of nif gene content and organization, complemented by laboratory growth experiments under nitrogen-limited conditions.

Nitrogen fixation (nif) genes were significantly upregulated in the chemocline, particularly in September, indicating a potential link between nitrogen fixation and bioconvection. Comparative genomic analyses revealed a higher abundance and diversity of nif genes in PSBs than in GSBs. Laboratory experiments demonstrated that PSBs (C. okenii, T. syntrophicum) and the GSB C. phaeobacteroides can grow using atmospheric nitrogen as the sole nitrogen source. Light intensity had minimal effects on overall biomass yield but influenced growth rates, while GSBs exhibited reduced performance relative to PSBs under nitrogen limitation.

Collectively, genomic, transcriptomic, and experimental evidence confirms active nitrogen fixation in dominant phototrophic sulfur bacteria of Lake Cadagno. The upregulation of nif genes and their association with bioconvection suggest a functional coupling between nitrogen cycling and physical mixing processes, potentially mediated by C. okenii. These findings provide new insights into the ecological role of anoxygenic phototrophs in stratified anoxic systems and their contribution to biogeochemical cycling.