Haloterrigena turkmenica

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Haloterrigena turkmenica
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Halobacteria
Order:
Halobacteriales
Family:
Halobacteriaceae
Genus:
Haloterrigena
Species:
H. turkmenica
Binomial name
Haloterrigena turkmenica

Haloterrigena turkmenica is an aerobic chemo organotrophic [1] archeon originally found in Turkish salt lakes. [2]

Contents

Discovery

Haloterrigena turkmenica is a halophilic archeon that was first isolated from sulfate saline soil located in Turkmenistan. [2] However, it wasn't until 2008 that H. turkmenica was successfully grown in the lab on Horikoshi medium. [3]

The Horikoshi medium is composed of yeast extract, glucose, potassium phosphate (KHPO4), peptone, Magnesium sulfate (MgSO4), water, and sodium carbonate (NaCO3). [3]

Haloterrigena turkmenica was initially placed in the family Halobacteriaceae as Halococcus turkmenicus by Zyaginsteva and Tarasov in 1987. [2] In 1999, Ventosa et al. published a proposal that would transfer the following species to Haloterrigena turkmenica, which is a new genera: Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11. [1] The proposal was in response to Ventosa having found significant genetic differences between H. turkmenicus and other organisms in the Halococcus genera. [1] The proposal was accepted and the organism is now classified under this new novel genera. [1]

Etymology

The name Haloterrigena comes from the halos which mean salt and terrigena which means of or from Earth. [2] Turkmenica was proposed by Zvyaginseva and Tarasov in 1987. [2] This name comes from the fact that this species was first collected from the Turkish salt lakes. [1]

Characterization

Haloterrigena turkmenica is a gram-negative organism. Cells are typically found as individuals, but have been seen in the form of pairs and tetrads. Cell shape can be classified as being ovoid to coccoid in shape. The diameter of the cells ranges from 1.5 µm to 2.0 µm. [1]

On growth medium, colonies of H. turkmenica appear elevated, red in color and circular. [3] The red color is due to the presence of C50-carotenoids. [3] There have been conflicting reports on the optimum growth temperature. According to Selim et al., the optimum growth temperature for H. turkmenica is 40 °C, [3] while Saunders et al. reports that the optimum growth temperature is 51 °C. [4] However, both reports state that the temperature growth range is between 29°-57 °C.

H. turkmenica has been documented to best grow at NaCl concentrations around 3.4M. [3] However, it can tolerate salt concentrations from 2-4.5M NaCl. [3] At a pH of 9, H. turkmenica has been shown to grow best. It will tolerate a pH within the range of 8.5 to 11. [3]

Haloterrigena turkmenica is classified as an aerobic chemo-organotroph. [1] This organism uses oxygen its preferred terminal electron acceptor and uses organic compounds for its carbon and energy source. No motility was observed. H. turkmenica tested positive for both oxidase and catalase activity. [3] Also according to Selim et al., H. turkmenica is also able to hydrolyze tweens 80 (a branded version of polysorbate 80), casein, and cellulose. Acid is produced from glucose, mannose, fructose, sucrose, ribose and xylose fermentation. [3] This organism has been found to use the following substrates for growth: glycerol, propionate, citrate, and sodium acetate. [3] Nitrite reduction occurs without the production of gas. [3] H. turkmenica has a generation time of 1.5 hours, under optimal growth conditions, making it the fastest growing member of Halobacteriaceae. [5]

Phylogeny and Genome

Haloterrigena turkmenica is in the domain of Archaea. [1] Archaea are identified as being separate from bacteria and eukaryotes based on ribosomal RNA (rRNA) analysis and certain defining characteristics that separate the three domains of life as described by Woese in 1990. [6]

Rapid Annotation via Subsystems Technology (RAST) is a service that annotates archaeal and bacterial genomes and provides comparison of phylogenetic relationships across a phylogenetic tree. [7] Using RAST, Haloterrrigena turkmenica relatives were determined. [3] Each relative was given a similarity score: higher scores equate to a closer phylogenetic similarity. The scores are based on the number of similar protein-coding genes out of a pool of 2959 protein-coding sequences. [3] The following organisms are the 5 closest relatives to H. turkmenica (similarity scores in bold): [3]

  1. Haloterrigena borinquense DM 11551(515)
  2. Haroarcula marimortui ATCC 43049(506)
  3. Halomicrobium mukohataei DSM 12286(501)
  4. Halorhabdus utahensis DS 12940(497)
  5. Halquadratum walsbyi DSM 1679(488)

In 2016, Selim et al. used a Roche DNA sequencer (GS De Novo Assembler V.2.9) to determine the GC (Guanine - Cytosine) content of H. turkmenica's genome. [3] The GC content of H. turkmenica was determined to be 64% for its draft genome with 49 RNA genes predicted using RAST. [3] The protein coding sequences were also digested using RAST. This revealed 193 subsystems including several enzymes encoding genes for carboxylase, cellulase and xylanase enzymes, xylose isomerase, and carboxylesterase. [3] Other genes coding for biosynthesis of peptides and secondary metabolites were also detected. [3]

Importance

Historically the phylogeny of the genera of Haloterrigena has been difficult to classify. [1] Further investigation could help to solidify the phylogeny of this archeon; solidification of the relationships among the members of Haloterrigena and Natrinema will help us to flesh out the Archaea l portion of the tree of life. [1] Investigation of Archaea's extremophile tendencies could lead to insight into novel technologies (such as DNA preservation) and may also provide insight into the biota of early Earth. [8] Methanogenesis is only performed by members of Archea and thus it is important to discover as much as we can about this domain. [8] Haloterrigena turkmenica is a good candidate for research because it has the fastest known generation time within Halobacteriaceae [5] and it can be grown on media. [3]

Related Research Articles

A halophile is an extremophile that thrives in high salt concentrations. In chemical terms, halophile refers to a Lewis acidic species that has some ability to extract halides from other chemical species.

<i>Halobacterium</i> Genus of archaea

Halobacterium is a genus in the family Halobacteriaceae.

Halobacteriaceae is a family in the order Halobacteriales and the domain Archaea. Halobacteriaceae represent a large part of halophilic Archaea, along with members in two other methanogenic families, Methanosarcinaceae and Methanocalculaceae. The family consists of many diverse genera that can survive extreme environmental niches. Most commonly, Halobacteriaceae are found in hypersaline lakes and can even tolerate sites polluted by heavy metals. They include neutrophiles, acidophiles, alkaliphiles, and there have even been psychrotolerant species discovered. Some members have been known to live aerobically, as well as anaerobically, and they come in many different morphologies. These diverse morphologies include rods in genus Halobacterium, cocci in Halococcus, flattened discs or cups in Haloferax, and other shapes ranging from flattened triangles in Haloarcula to squares in Haloquadratum, and Natronorubrum. Most species of Halobacteriaceae are best known for their high salt tolerance and red-pink pigmented members, but there are also non-pigmented species and those that require moderate salt conditions. Some species of Halobacteriaceae have been shown to exhibit phosphorus solubilizing activities that contribute to phosphorus cycling in hypersaline environments. Techniques such as 16S rRNA analysis and DNA-DNA hybridization have been major contributors to taxonomic classification in Halobacteriaceae, partly due to the difficulty in culturing halophilic Archaea.

<span class="mw-page-title-main">Halobacteriales</span> Order of archaea

Halobacteriales are an order of the Halobacteria, found in water saturated or nearly saturated with salt. They are also called halophiles, though this name is also used for other organisms which live in somewhat less concentrated salt water. They are common in most environments where large amounts of salt, moisture, and organic material are available. Large blooms appear reddish, from the pigment bacteriorhodopsin. This pigment is used to absorb light, which provides energy to create ATP. Halobacteria also possess a second pigment, halorhodopsin, which pumps in chloride ions in response to photons, creating a voltage gradient and assisting in the production of energy from light. The process is unrelated to other forms of photosynthesis involving electron transport; however, and halobacteria are incapable of fixing carbon from carbon dioxide.

<span class="mw-page-title-main">Haloarchaea</span> Class of salt-tolerant archaea

Haloarchaea are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea rather than bacteria and are one of the largest groups. The name 'halobacteria' was assigned to this group of organisms before the existence of the domain Archaea was realized, and while valid according to taxonomic rules, should be updated. Halophilic archaea are generally referred to as haloarchaea to distinguish them from halophilic bacteria.

<i>Haloarcula</i> Genus of archaea

Haloarcula is a genus of extreme halophilic Archaea in the class of Halobactaria.

Halobiforma is a genus of halophilic archaea of the family Natrialbaceae.

Halococcus is a genus of the Halococcaceae.

<i>Haloquadratum</i> Genus of archaea

Haloquadratum is a genus of archaean, belonging to the family Haloferacaceae. The first species to be identified in this group, Haloquadratum walsbyi, is unusual in that its cells are shaped like square, flat boxes.

Halorubrum is a genus in the family Halorubraceae. Halorubrum species areusually halophilic and can be found in waters with high salt concentration such as the Dead Sea or Lake Zabuye.

In taxonomy, Halosimplex is a genus of the Halobacteriaceae.

Haloterrigena is a genus of the Natrialbaceae.

In taxonomy, Natrialba is a genus of the Natrialbaceae. The genus consists of many diverse species that can survive extreme environmental niches, especially they are capable to live in the waters saturated or nearly saturated with salt (halophiles). They have certain adaptations to live within their salty environments. For example, their cellular machinery is adapted to high salt concentrations by having charged amino acids on their surfaces, allowing the cell to keep its water molecules around these components. The osmotic pressure and these amino acids help to control the amount of salt within the cell.

In taxonomy, Natronococcus is a genus of the Natrialbaceae.

Halocins are bacteriocins produced by halophilic Archaea and a type of archaeocin.

Halobacterium noricense is a halophilic, rod-shaped microorganism that thrives in environments with salt levels near saturation. Despite the implication of the name, Halobacterium is actually a genus of archaea, not bacteria. H. noricense can be isolated from environments with high salinity such as the Dead Sea and the Great Salt Lake in Utah. Members of the Halobacterium genus are excellent model organisms for DNA replication and transcription due to the stability of their proteins and polymerases when exposed to high temperatures. To be classified in the genus Halobacterium, a microorganism must exhibit a membrane composition consisting of ether-linked phosphoglycerides and glycolipids.

<i>Haloferax mediterranei</i> Species of bacterium

Haloferax mediterranei is a species of archaea in the family Haloferacaceae.

Halorhabdus utahensis is a halophilic archaeon isolated from the Great Salt Lake in Utah.

Halococcaceae is a family of halophilic and mostly chemoorganotrophic archaea within the order Halobacteriales. The type genus of this family is Halococcus. Its biochemical characteristics are the same as the order Halobacteriales.

Natronolimnohabitans innermongolicus is a species of archaea in the family Natrialbaceae. It has been proposed that Haloterrigena turkmenica be reclassified as Natronolimnohabitans innermongolicus due to the genome sequence of Haloterrigena turkmenica being contaminated in a previous study.

References

  1. 1 2 3 4 5 6 7 8 9 10 Ventosa, Antonio; Gutiérrez, M. Carmen; Kamekura, Masahiro; Dyall-Smith, Michael L. (1999-01-01). "Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov". International Journal of Systematic and Evolutionary Microbiology. 49 (1): 131–136. doi: 10.1099/00207713-49-1-131 . PMID   10028254.
  2. 1 2 3 4 5 Zvyagintseva, IS; Tarasov, AL (1987). "Extreme halophilic bacteria saline soils". Mikrobiologiia. 56: 839–844.
  3. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Selim, Samy; Hagagy, Nashwa (2016-03-01). "Genome sequence of carboxylesterase, carboxylase and xylose isomerase producing alkaliphilic haloarchaeon Haloterrigena turkmenica WANU15". Genomics Data. 7: 70–72. doi:10.1016/j.gdata.2015.11.031. PMC   4778622 . PMID   26981365.
  4. ↑ Saunders, Elisabeth; Tindall, Brian J.; Fähnrich, Regine; Lapidus, Alla; Copeland, Alex; Rio, Tijana Glavina Del; Lucas, Susan; Chen, Feng; Tice, Hope (2010-02-28). "Complete genome sequence of Haloterrigena turkmenica type strain (4k T )". Standards in Genomic Sciences. 2 (1): 107–16. doi:10.4056/sigs.681272. ISSN   1944-3277. PMC   3035258 . PMID   21304683.
  5. 1 2 Robinson, Jessie L.; Pyzyna, Brandy; Atrasz, Rachelle G.; Henderson, Christine A.; Morrill, Kira L.; Burd, Anna Mae; DeSoucy, Erik; Fogleman, Rex E.; Naylor, John B. (2005-02-01). "Growth Kinetics of Extremely Halophilic Archaea (Family Halobacteriaceae) as Revealed by Arrhenius Plots". Journal of Bacteriology. 187 (3): 923–929. doi:10.1128/JB.187.3.923-929.2005. ISSN   0021-9193. PMC   545725 . PMID   15659670.
  6. ↑ Woese, C R; Kandler, O; Wheelis, M L (1990-06-01). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–4579. doi: 10.1073/pnas.87.12.4576 . ISSN   0027-8424. PMC   54159 . PMID   2112744.
  7. ↑ Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.; DeJongh, Matthew; Disz, Terrence; Edwards, Robert A.; Formsma, Kevin; Gerdes, Svetlana; Glass, Elizabeth M. (2008-01-01). "The RAST Server: Rapid Annotations using Subsystems Technology". BMC Genomics. 9: 75. doi: 10.1186/1471-2164-9-75 . ISSN   1471-2164. PMC   2265698 . PMID   18261238.
  8. 1 2 Gribaldo, Simonetta; Brochier-Armanet, Celine (2006-06-29). "The origin and evolution of Archaea: a state of the art". Philosophical Transactions of the Royal Society of London B: Biological Sciences. 361 (1470): 1007–1022. doi:10.1098/rstb.2006.1841. ISSN   0962-8436. PMC   1578729 . PMID   16754611.
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