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

Abstract

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.

Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea

“…Thus, the biosynthesis of this wide variety of secondary metabolites by strains of the genus Halomicroarcula suggests the versatility of members of this genus, which have developed several ecological advantages such as a great adaptability to extreme conditions or defense mechanisms. In addition, our results brought to light their possible applications on the biotechnological field as a source of new natural compounds, also recently proposed for other novel haloarchaeal taxa (Durán-Viseras et al, 2021).…”

“…Previous metagenomic studies on prokaryotic diversity of hypersaline soils showed a large proportion of haloarchaea, with a high percentage not closely related to any previously described taxa. For that reason, we isolated a large collection of strains from the Odiel saltmarsh hypersaline soils located in Huelva, South-west Spain, using different complex oligotrophic media and culture conditions, based on culturomics techniques as previously detailed ( Durán-Viseras et al, 2021 ). Partial sequencing of the 16S rRNA gene permitted us to preliminary delineate the taxonomic position of the isolates.…”

“…Purified agar (2%; Oxoid) was used as solidifying agent, when needed. For long term maintenance, cultures were preserved at –80°C in this medium containing 20% (v/v) glycerol ( Durán-Viseras et al, 2021 ).…”

“…With the purpose of isolating such of these metabolically diverse groups not isolated to date, we focused on these habitats by using culture-dependent methods. For that purpose, we used the current “culturomics” approach ( Durán-Viseras et al, 2019a , 2021 ), in order to isolate new haloarchaeal groups taking advantage of the previous metagenomic studies, that showed an unexpected large proportion of haloarchaea in these hypersaline soils ( Vera-Gargallo and Ventosa, 2018 ). As a result, four haloarchaeal strains phylogenetically related to the genus Halomicroarcula were isolated in pure culture.…”

Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments

“…The recent successes with cultivating Candidatus Nanohaloarchaeota as co-cultures with Halobacteria opens up an exciting new hot spot in the field of halophilic archaea research. It is anticipated that improvements in cultivation technology (also termed 'culturomics' (Durán-Viseras et al 2020;Greub 2012), such as the use of robotics and highthroughput microchambers (Nichols et al 2010) will greatly increase the ability to cultivate diverse halophilic archaea from different hypersaline environments, so that many thousands of isolates can be recovered and analyzed simultaneously (Berdy et al 2017).…”