Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis

Environ Microbiol. 2021 Jul;23(7):3418-3434. doi: 10.1111/1462-2920.15082. Epub 2020 Jun 15.


The development of culture-independent techniques has revolutionized our understanding of microbial ecology, especially through the illustration of the vast gap between the environmentally abundant microbial diversity and that accessible through cultivation. However, culture-based approaches are not only crucial for understanding the evolutionary, metabolic and ecological milieu of microbial diversity but also for the development of novel biotechnological applications. In this study, we used a culturomics-based approach in order to isolate novel microbial taxa from hypersaline environments (i.e. Isla Cristina and Isla Bacuta salterns in Huelva, Spain). We managed to obtain axenic cultures of four haloarchaeal strains that belong to a new haloarchaeal genus and to obtain their genomic sequences. The phylogenomic and phylogenetic analyses (together with AAI, ANI and digital DDH indices) showed that the isolates constitute two new species, for which we propose the names Halosegnis longus sp. nov. and Halosegnis rubeus sp. nov. The genomic-based metabolic reconstructions indicated that members of this new haloarchaeal genus have photoheterotrophic aerobic lifestyle with a typical salt-in signature. 16S rRNA gene sequence reads abundance profiles and genomic recruitment analyses revealed that the Halosegnis genus has a worldwide geographical distribution, reaching high abundance (up to 8%) in habitats with intermediate salinities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial
  • Genomics*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Salinity*


  • DNA, Bacterial
  • RNA, Ribosomal, 16S