Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts

Abstract

Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument. The results indicated that these microbial communities contained 48.22-61.4% Bacteria, 37.72-51.26% Archaea, 0.51-0.86% Eukarya, and 0.005-0.009% unclassified reads. Among bacteria, the communities in these salts were dominated by the phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. Of the archaea, 91.58% belonged to the class Halobacteria, whereas the remaining 7.58, 0.83, and 0.01% were Nanoarchaea, Methanobacteria, and Thermococci, respectively. This comparison of microbial diversity in salts from two countries showed the presence of many archaeal and bacterial genera that occurred in salt samples from one country but not the other. The bacterial genera Enterobacter and Halovibrio were found only in Korean and Ethiopian salts, respectively. This study indicated the occurrence and diversity of halophilic bacteria and archaea in commercial salts that could be important in the gastrointestinal tract after ingestion.

Keywords: Ethiopia; Korea; commercial salts; diversity; halophilic archaea; halophilic bacteria.

Figure 1

Average composition of selected communities of metagenomically identified bacterial and archaeal genera of salt samples.

Figure 2

Heat map showing the relative abundances and distribution of representative 16S rRNA gene tag sequences classified at the genus level. The color code indicates the differences in the relative abundance from the mean, ranging from red (negative) through black (the mean) to the green (positive).

Figure 3

The rarefaction curves of pyrosequenced bacteria (upper panel) and archaea (bottom panel) communities of the four salts.

Figure 4

Clustering analysis for the samples classified as archaea and bacteria using the UniFrac service after genome sequencing. The scale bar indicates the distance between clusters in UniFrac units (data generated with CL community, Chun Lab Inc.).

Figure 5

UniFrac distance-based Jackknife clustering of bacteria and archaea communities associated with difference salts. Asian seawater (SWA) and Europian seawater (SWE) samples as the control were also included in this analysis. Unifrac PCoA image were captured from 3D UniFrac PCoA to illustrate differences in the microbiota among the different salts. The following UniFrac analysis were based on the OTU data, with the first three principal coordinates (PCs) shown: unweighted UNiFrac with PC1 (66.71%, 35.71%), PC2 (0.00, 0.00), and PC3 (9.23, 9.23).