Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome

Abstract Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co‐dominate: a cyanobacterium, Arthrospira fusiformis , and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell‐sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non‐negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free‐living microbiome (i.e. present in the 3–0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free‐living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.