Selective enrichment on a wide polysaccharide spectrum allowed isolation of novel metabolic and taxonomic groups of haloarchaea from hypersaline lakes

Abstract

Extremely halophilic archaea (haloarchaea) of the class Halobacteria is a dominant group of aerobic heterotrophic prokaryotic communities in salt-saturated habitats, such as salt lakes and solar salterns. Most of the pure cultures of haloarchaea were enriched, isolated, and cultivated on rich soluble substrates such as amino acids, peptides or simple sugars. So far, the evidences on the capability of haloarchaea to use different polysaccharides as growth substrates remained scarce. However, it is becoming increasingly obvious that these archaea can also actively participate in mineralization of complex biopolymers, in particular cellulose and chitin-two dominant biomass polysaccharides on the planet. Here we used an array of commercially available homo- and heteropolysaccharides to enrich hydrolytic haloarchaea from hypersaline salt lakes with neutral pH and from alkaline soda lakes. This resulted in isolation of a range of halo- and natrono-archaea, respectively, belonging to already described taxa as well as several new genus-level lineages. In some cases, the isolates enriched with different polysaccharides happened to be closely related, thus representing generalistic ecotype, while the others were narrow specialists. In general, soda lakes yielded a broader range of polysaccharide-utilizing specialists in comparison to neutral salt lakes. The results demonstrated a significant diversity of halo(natrono)archaea with a previously unrecognized potential for utilization of a broad range of natural polysaccharides in hypersaline habitats.

Keywords: halo(natrono)archaea; hydrolytic; hypersaline lakes; polysaccharides; soda lakes.

FIGURE 1

Schematic representation of selective enrichments of haloarchaea from hypersaline salt lakes on (A) alpha-bonded and (B) beta-bonded polysaccharides. Assignment to the novel genus was based on protein sequence-based phylogenomic analysis and 16S rRNA gene sequence identity values.

FIGURE 2

Schematic representation of selective enrichments of natronoarchaea from hypersaline soda lakes on (A) alpha-bonded and (B) beta-bonded polysaccharides. Assignment to the novel genus was based on protein sequence-based phylogenomic analysis and 16S rRNA gene sequence identity values (for strain AArc-arb3/5 only 16S rRNA gene sequence identity values were used).

FIGURE 3

Maximum likelihood phylogenomic tree showing position of polysaccharide-utilizing halo(natrono)archaea enriched from hypersaline lakes within the class Halobacteria. Sequences of 122 conserved archaeal proteins were used to infer the tree.

FIGURE 4

Sets of GH and PL genes found in the genomes of novel polysaccharidolytic haloarchaea. Size of bubbles indicate number of enzymes; the color of bubbles indicate the prevailing type of glycosidic bonds hydrolyzed by the enzymes (alpha-bonds—green, beta-bonds—blue, both—gray). Color of background indicates these CAZymes families contains the characterized enzyme(s) capable of depolymerization of respective polysaccharides. No color means the activities, characteristic to these families are not directly linked to the substrates used in this work.