Beyond Archaea: The Table Salt Bacteriome

Abstract

Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.

Keywords: 16S rRNA gene sequencing analysis; haloarchaea; halophilic bacteria; halotolerant bacteria; table salt microbiome.

FIGURE 1

Bacterial and archaeal genera from table salts recovered on culture media with different salt concentrations and nutritional compositions. SMM and saline R2A are supplemented with 10% w/v total salt, while their nutritional compositions are different. SM15 contains 17% w/v total salt. Modified DBCM2 and DBCM2 have 2.5% w/v total salt, 25% w/v total salt, respectively. MGM was also especially used for the isolation of archaea, supplemented with 23 and 25% w/v total salt. The color code indicates the number of microorganisms isolated on each medium.

FIGURE 2

Microbial profiles of six table salt samples based on the identification of culturable isolates. The percentage indicates that the value was calculated based on the total number of isolates in each table salt. The abbreviation is correlated to the genus name: Ac, Acinetobacter; Al, Alkalihalobacillus; Aq, Aquibacillus; Ba, Bacillus; Br, Brevundimonas; Cy, Cytobacillus; De, Dermacoccus; Eu, EU817569_g; Fi, Fictibacillus; Gr, Gracilibacillus; Ha, Haloarcula; Hba, Halobacillus; Hbu, Halobacterium; Hr, Halorubrum; Le, Lentibacillus; Mes, Mesobacillus; Met, Metabacillus; Mi, Micrococcus; Oc, Oceanobacillus; Pe, Peribacillus; Pi, Piscibacillus; Po, Pontibacillus; Sbu, Salibacterium; Sbr, Salinibacter; St, Staphylococcus; Te, Terribacillus; Th, Thalassobacillus; Vi, Virgibacillus.

FIGURE 3

(A) Microbial composition of table salt samples after 16S rRNA gene sequencing. The abbreviation is correlated to the genus name and highlighted the most frequent genera: Su, Sulfitobacter; Ba, Bacillus; En, Enterococcus; Hr, Halorubrum; Hb, Halobellus; Hl, Halolamina; Hp, Haloplanus; Fl, Flavobacterium; Na, Natronomonas; Sbr, Salinibacter; Hq, Haloquadratum; Ch, chloroplast; Mi, mitochondria; Yo, Yoonia_Loktanella; Hn; Halonotius. (B) Beta diversity (PCoA) based on Bray–Curtis dissimilarity metric. Distances to the linear statistical correlation indicate the similarity of the microbial diversity of each sample affected by the origin of those salts.

FIGURE 4

Main archaeal composition (A) and bacterial composition (B) of each table salt sample based on the 16S rRNA gene metagenomic analyses with archaea-specific primers. Only values higher than 1% are shown to explain the biodiversity of the samples.