Complete Genome Sequence of the Extremely Halophilic Archaeon Haloarcula hispanica Strain N601

Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina

Diamante Lake located at 4589 m.a.s.l. in the Andean Puna constitutes an extreme environment. It is exposed to multiple extreme conditions such as an unusually high concentration of arsenic (over 300 mg L^-1) and low oxygen pressure. Microorganisms thriving in the lake display specific genotypes that facilitate survival, which include at least a multitude of plasmid-encoded resistance traits. Hence, the genetic information provided by the plasmids essentially contributes to understand adaptation to different stressors. Though plasmids from cultivable organisms have already been analyzed to the sequence level, the impact of the entire plasmid-borne genetic information on such microbial ecosystem is not known. This study aims at assessing the plasmidome from Diamante Lake, which facilitates the identification of potential hosts and prediction of gene functions as well as the ecological impact of mobile genetic elements. The deep-sequencing analysis revealed a large fraction of previously unknown DNA sequences of which the majority encoded putative proteins of unknown function. Remarkably, functions related to the oxidative stress response, DNA repair, as well as arsenic- and antibiotic resistances were annotated. Additionally, all necessary capacities related to plasmid replication, mobilization and maintenance were detected. Sequences characteristic for megaplasmids and other already known plasmid-associated genes were identified as well. The study highlights the potential of the deep-sequencing approach specifically targeting plasmid populations as it allows to evaluate the ecological impact of plasmids from (cultivable and non-cultivable) microorganisms, thereby contributing to the understanding of the distribution of resistance factors within an extremophilic microbial community.

Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica

Gene expression in Haloarcula hispanica cells infected with the gammapleolipovirus His2 was studied using a custom DNA microarray. Total RNA from cells sampled at 0, 1, 2, 3, and 4.5 hr postinfection was reverse‐transcribed into labeled cDNA and hybridized to microarrays, revealing temporal and differential expression in both host and viral genes. His2 gene expression occurred in three main phases (early, middle, and late), and by 4.5 hr p.i. the majority of genes were actively transcribed, including those encoding the major structural proteins. Eighty host genes were differentially regulated ≥twofold postinfection, with most of them predicted to be involved in transport, translation, and metabolism. Differentially expressed host genes could also be grouped into early‐, middle‐, and late‐expressed genes based on the timing of their up‐ and downregulation postinfection. The altered host transcriptional pattern suggests regulation by His2 infection, which may reprogram host metabolism to facilitate its own DNA replication and propagation. This study enhances the characterization of many hypothetical viral genes and provides insights into the interaction between His2 and its host.

Polyhydroxyalkanoate Biosynthesis at the Edge of Water Activitiy-Haloarchaea as Biopolyester Factories

Haloarchaea, the extremely halophilic branch of the Archaea domain, encompass a steadily increasing number of genera and associated species which accumulate polyhydroxyalkanoate biopolyesters in their cytoplasm. Such ancient organisms, which thrive in highly challenging, often hostile habitats characterized by salinities between 100 and 300 g/L NaCl, have the potential to outperform established polyhydroxyalkanoate production strains. As detailed in the review, this optimization presents due to multifarious reasons, including: cultivation setups at extreme salinities can be performed at minimized sterility precautions by excluding the growth of microbial contaminants; the high inner-osmotic pressure in haloarchaea cells facilitates the recovery of intracellular biopolyester granules by cell disintegration in hypo-osmotic media; many haloarchaea utilize carbon-rich waste streams as main substrates for growth and polyhydroxyalkanoate biosynthesis, which allows coupling polyhydroxyalkanoate production with bio-economic waste management; finally, in many cases, haloarchaea are reported to produce copolyesters from structurally unrelated inexpensive substrates, and polyhydroxyalkanoate biosynthesis often occurs in parallel to the production of additional marketable bio-products like pigments or polysaccharides. This review summarizes the current knowledge about polyhydroxyalkanoate production by diverse haloarchaea; this covers the detection of new haloarchaea producing polyhydroxyalkanoates, understanding the genetic and enzymatic particularities of such organisms, kinetic aspects, material characterization, upscaling and techno-economic and life cycle assessment.

Temperature-dependent expression of different guanine-plus-cytosine content 16S rRNA genes in Haloarcula strains of the class Halobacteria

Haloarcula strains, which are halophilic archaea, harbour two to three copies of 16S rRNA genes (rrsA, rrsB and rrsC) in their genomes. While rrsB and rrsC (rrsBC) show almost identical sequences, rrsA shows 4–6% sequence difference and 1–3% guanine-plus-cytosine content (P_GC) difference compared to rrsBC. Based on the strong correlation between the P_GC of 16S rRNA genes and the growth temperatures of the prokaryotes, we hypothesised that high-P_GCrrsA and low-P_GCrrsBC are expressed at high and low temperatures, respectively. To verify the hypothesis, we performed sequence analyses and expression surveys of each 16S rRNA gene in eight Haloarcula strains. The secondary structure prediction of the 16S rRNA via computer simulation showed that the structural stability of 16S rRNAs transcribed from rrsA was higher than that of 16S rRNAs transcribed from rrsBC. We measured expression levels of rrsA and rrsBC under various temperature conditions by reverse-transcriptase quantitative PCR. The expression ratio of high-P_GCrrsA to low-P_GCrrsBC increased with cultivation temperatures in seven of eight Haloarcula strains. Our results suggest that the transcription of high-P_GCrrsA and low-P_GCrrsBC may be regulated in response to environmental temperature, and that 16S rRNAs transcribed from high-P_GCrrsA function under high temperature conditions close to the maximum growth temperature.

Expression and Function of Different Guanine-Plus-Cytosine Content 16S rRNA Genes in Haloarcula hispanica at Different Temperatures

The halophilic archaeon Haloarcula hispanica harbors three ribosomal RNA (rRNA) operons (rrnA, rrnB, and rrnC) that contain the 16S rRNA genes rrsA, rrsB, and rrsC, respectively. Although rrsB and rrsC (rrsBC) have almost identical sequences, the rrsA and rrsBC sequences differ by 5.4%, and they differ by 2.5% with respect to guanine-plus-cytosine content (P_GC). The strong correlation between the typical growth temperatures of archaea and P_GC of their 16S rRNA genes suggests that H. hispanica may harbor different 16S rRNA genes having different P_GC to maintain rapid growth in a wide range of temperatures. We therefore performed reverse transcription-coupled quantitative PCR to assess expression levels of rrsA (P_GC, 58.9%) and rrsBC (P_GC, 56.4-56.5%) at various temperatures. The expression ratio of rrsA to rrsBC increased with culture temperature. Mutants with complete deletions of one or two of the three rRNA operons were constructed and their growth rates at different temperatures compared to that of the wild-type. The growth characteristics of the rRNA operon single-mutant strains were indistinguishable from the wild-type. The rRNA operon double-mutant strains maintained the same temperature range as wild-type but displayed reduced growth rates. In particular, the double-mutant strains grew much slower than wild-type at low temperature related to minimum growth temperature of the wild-type. On the other hand, at physiologically high temperatures the wild-type and the double-mutant strain which harbors only rrnA with high-P_GCrrsA grew significantly faster than the double-mutant strain which harbors only rrnC with low-P_GCrrsC. These findings suggest the importance of 16S rRNAs transcribed from rrsA with high-P_GC in maintaining rapid growth of this halophilic archaeon at raised growth temperatures.

Glycerol metabolism of haloarchaea

Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.

Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1-lysogenic archaeal strain

Proviral regions have been identified in the genomes of many haloarchaea, but only a few archaeal halophilic temperate viruses have been studied. Here, we report a new virus, SNJ2, originating from archaeal strain Natrinema sp. J7-1. We demonstrate that this temperate virus coexists with SNJ1 virus and is dependent on SNJ1 for efficient production. Here, we show that SNJ1 is an icosahedral membrane-containing virus, whereas SNJ2 is a pleomorphic one. Instead of producing progeny virions and forming plaques, SNJ2 integrates into the host tRNA(Met) gene. The virion contains a discontinuous, circular, double-stranded DNA genome of 16 992 bp, in which both nicks and single-stranded regions are present preceded by a 'GCCCA' motif. Among 25 putative SNJ2 open reading frames (ORFs), five of them form a cluster of conserved ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. Two structural protein encoding genes in the conserved cluster were verified in SNJ2. Furthermore, SNJ2-like proviruses containing the conserved gene cluster were identified in the chromosomes of archaea belonging to 10 different genera. Comparison of SNJ2 and these proviruses suggests that they employ a similar integration strategy into a tRNA gene.

The methylaspartate cycle in haloarchaea and its possible role in carbon metabolism

Haloarchaea (class Halobacteria) live in extremely halophilic conditions and evolved many unique metabolic features, which help them to adapt to their environment. The methylaspartate cycle, an anaplerotic acetate assimilation pathway recently proposed for Haloarcula marismortui, is one of these special adaptations. In this cycle, acetyl-CoA is oxidized to glyoxylate via methylaspartate as a characteristic intermediate. The following glyoxylate condensation with another molecule of acetyl-CoA yields malate, a starting substrate for anabolism. The proposal of the functioning of the cycle was based mainly on in vitro data, leaving several open questions concerning the enzymology involved and the occurrence of the cycle in halophilic archaea. Using gene deletion mutants of H. hispanica, enzyme assays and metabolite analysis, we now close these gaps by unambiguous identification of the genes encoding all characteristic enzymes of the cycle. Based on these results, we were able to perform a solid study of the distribution of the methylaspartate cycle and the alternative acetate assimilation strategy, the glyoxylate cycle, among haloarchaea. We found that both of these cycles are evenly distributed in haloarchaea. Interestingly, 83% of the species using the methylaspartate cycle possess also the genes for polyhydroxyalkanoate biosynthesis, whereas only 34% of the species with the glyoxylate cycle are capable to synthesize this storage compound. This finding suggests that the methylaspartate cycle is shaped for polyhydroxyalkanoate utilization during carbon starvation, whereas the glyoxylate cycle is probably adapted for growth on substrates metabolized via acetyl-CoA.

Complete genome sequence of Haloarcula sp. CBA1115 isolated from non-purified solar salts

Haloarcula sp. CBA1115, isolated from non-purified solar salts from South Korea, is a halophilic archaeon belonging to the family Halobacteriaceae. Here, we present the complete genome sequence of the strain Haloarcula sp. CBA1115 (4,225,046bp, with a G+C content of 61.98%), which is distributed over one chromosome and five plasmids. A comparison of the genome sequence of Haloarcula sp. CBA1115 with those of members of its closely related taxa showed that the closest neighbor is Haloarcula hispanica Y27, a popular model organism for archaeal studies. The strain was found to possess a number of genes predicted to be involved in osmo-regulatory strategies and metal regulation, suggesting that it might be useful for bioremediation in extreme environments.

Association between the dynamics of multiple replication origins and the evolution of multireplicon genome architecture in haloarchaea

Haloarchaeal genomes are generally composed of multiple replicons, and each replicon has a single or multiple replication origin(s). The comparative genomic analysis of replication origins from closely related species can be used to reveal the evolutionary mechanisms that account for the development of multiple origin systems. Multiple replication origins have been in silico and experimentally investigated in Haloarcula hispanica, which raise the possibility for comparisons of multiple replication origins in Haloarcula species. Thus, we performed a comparison of H. hispanica replication origins with those from five additional Haloarcula species. We demonstrated that the multiple replication origins in the chromosome were evolved independently multiple times from the oriC1-dependent ancestral chromosome. Particularly, the two origins oriC1 and oriC2 were conserved in location, and both of them were adjacent to an rRNA operon, suggestive of correlations in replication and expression of surrounding genes that may promote the conservation of these two origins. Some chromosomal variable regions were used as hotspots for origin evolution in which replication origins were continually being acquired, lost, and disrupted. Furthermore, we demonstrated that autonomously replicating sequence plasmids with H. hispanica minichromosomal replication origins were extremely unstable. Because both organization and replication origins of minichromosomes were not conserved, we proposed an association between the evolution of extrachromosomal replicons and origin variation. Taken together, we provided insights into the evolutionary history of multiple replication origins in Haloarcula species, and proposed a general model of association between the dynamics of multiple replication origins and the evolution of multireplicon genome architecture in haloarchaea.