Introductory Chapter: Brief Overview of the Diversity of Secondary Metabolite in Extreme Environment – The Case of Halobacteria Based on Genome Sequence Mining

1. Introduction

Secondary metabolites (SMs) are a range of bioactive compounds yielded by several microorganisms, such as bacteria, fungi, and archaea [1]. They are not directly involved in basic life processes, such as growth, cell division, and respiration [2]. However, they are thought to be important components of the innate immune system against other organisms and also play essential roles in enhancing tolerance to environmental stress for some microbes, such as Haloarchaea domain [3]. Members of Halorarchaea are reported to generate various types of molecules, such as terpenes, polyketides, alkaloids, and archaeocins, which can be exploited for biotechnological purposes [1]. Halobacteria constitute an evolutionary distinct salt-tolerant microorganism and are known as Haloarchaea that require a minimum of 8% salt concentration to grow [4]. Actually, Haloarchaea is divided into three orders: Halobacteriales, Haloferacales, and Natrialbales consisting currently of 48 genera [5]. It is worth noting that compared with bacteria or plants, SMs in Haloarchaea have been far less researched. Here, we aimed to predict the SMs of genomes sequences of 48 genera genus available in the IMG database [5] using antiSMASH version 6.0 with default parameters [6]. Indeed, computation of strain similarities based on SMs production profile was conducted with MVSP (Multi-Variate Statistical Package) software. The similarity of SMs profiles among genera was calculated using Pearson’s product correlation coefficient. The clustering of strains was based on the unweighted pair group method with an arithmetic average [7].

2. Results

Results showed that nine (n = 9) SBs were identified within 46 (of 48) genome sequences (Figure 1):

Figure 1.

Unweighted pair group method with arithmetic mean (UPGMA) dendrogram derived from similarity coefficients calculated by Pearson’s product moment, showing the relationship among Haloarchaeal genera analyzed by presence or absence of secondary metabolites types. The different color refers to the nine secondary metabolites identified.

1. Terpenes are a major class of biological compounds usually found in the plant known to protect the plant against and in bacteria [8]. Here, the analysis showed that almost all genomes could produce terpenes (Figure 1);

2. Siderophore are organic compounds with low molecular masses that are produced by microorganisms and plants growing under low iron conditions [9, 10]. There are only very few studies on siderophores reported on Haloarchaea [9]. Here, the analysis showed that 18 genera could produce siderophores (Figure 1);

3. Ribosomally synthesized and posttranslational modification modified peptides with antibiotic potential found in Archaea [11], including (i) Lantipeptide [12], here, genomes mining showed that Natrarchaeobaculum, Natronorubrum, and Halobiforma could produce Lantipeptides (ii) Thiopetide [13] identified in three genera Halorubrum, Halobiforma, and Halobacterium(ii) Lasso peptide, recently detected across some archaeal genomes [14], here identified in Halorubrum, Halosimplex, Halomicrobium, Natrarchaeobaculum, and Candidatus Halobonum(iv) Linaridin with antibiotic potential [15] was found within Natronoarchaeum, Haloterrigena, and Natronorubrum(v) Linear azol(in)e-containing peptides [16] identified in Haloterrigena and Halovivax.

4. The remaining SMs, including acyl homoserine lactones (AHLs) [17], metabolites controlling a range of quorum sensing phenotypes in bacteria was identified in Halorientalis and Haloferax. The betalactone [18] was identified only in two genera, Halococcus and Haloterrigena.

On the basis of our in silico analyses, we can conclude that Haloterregina represents a good candidate for SMs production profile (terpene, siderophore, betalactone, linaridin, and Linear azol(in)e-containing peptides), followed by Natronorubrum (terpene, siderophore, betalactone, and Lantipeptide). This chapter will open new research lines that will shed light on metabolites in extreme environments and their biotechnological potential.