Halobacteriales

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Halobacteriales
Haloarcula quadrata.png
SEM image of Haloarcula quadrata.
Scientific classification
Domain:
Kingdom:
Phylum:
Class:
Order:
Halobacteriales

Grant & Larsen, 1989
Families
Synonyms
  • "Haloarchaeales" (sic) DasSarma & DasSarma 2008

Halobacteriales are an order of the Halobacteria, [1] 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.

Contents

Halobacteria can exist in salty environments because although they are aerobes they have a separate and different way of creating energy through photosynthesis. Parts of the membranes of halobacteria are purplish in color. These parts conduct photosynthetic reactions with retinal pigment rather than chlorophyll. This allows them to create a proton gradient across the membrane of the cell which can be used to create ATP for their own use. Some species in this order are used as model organisms to study how some microorganisms can survive in hypersaline environments, understand cellular processes and to research their physiology. [2]

Ecology

Habitats

Usually, Halobacteriales grow in aerobic and high salinity environments. [3] Halobacteriales have been found in salt lakes, marine salterns, seawater, solar salts and salted food products. [4] Mostly, members of the order Halobacteriales can be located in environments where concentration of salt (NaCl) exceeds 25%. [2] However, they can also survive in environments with low concentrations of salt, between 1 and 3.5%. [2] Studies show Halobacteriales can also be found in environments where sulfur reduction takes part as well as in salinity salterns,, seawater black smoker, coastal salt marshes and chimney structures. [3] This results show Halobacteriales only need the enough amount of salt to prevent their lysis and thus can grow in environments with low salinity concentration. [3]

Current taxonomy

Halobacteriales was a large phylogenetically diverse lineage encompassing all Halobacteria species. [4] The wide variety of biochemical characteristics and different ecological niches of the class Haloarchaea proved to be an unreliable tool in clarifying the evolutionary relationships of Halobacteria above the genus level. [4]

In 2015, Gupta et al. proposed the division of class Halobacteria into three orders, Halobacteriales, Haloferacales and Natrialbales based on comparative genomic analyses and the branching pattern of various phylogenetic trees constructed from several different datasets of conserved proteins and 16S rRNA sequences. [5] This division greatly restricted the membership of the order Halobacteriales to include only species which were closely related to the type genus, Halobacterium.

A subsequent study examining higher taxonomic relationships within the order Halobacteriales resulted in the division of the order into three families, Halobacteriaceae , Haloarculaceae and Halococcaceae, each of which can be distinguished from each other and all other species through the presence of multiple highly specific molecular signatures, known as conserved signature indels. [6]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [7] and National Center for Biotechnology Information (NCBI). [8]

16S rRNA based LTP_06_2022 [9] [10] [11] 53 marker proteins based GTDB 08-RS214 [12] [13] [14]

Halobacteriaceae 2 *

Halobacteriaceae 3 *

Haloarculaceae

Halobacteriaceae *

"Haladaptaceae" *

Halostella {QS-9-68-17} *

Halalkalicoccus {"Halalkalicoccaceae"} *

Halococcus {Halococcaceae}

Halobacteriaceae 4 *

Natronoarchaeum {"Natronoarchaeaceae"} *

Salinarchaeum {"Salinarchaeaceae"}

Natrialbaceae

Salinirubrum *

Haloferacaceae (incl. Halorubraceae)

Halobacteriales

"Haladaptaceae" *

Halobacteriaceae *

Salinarchaeum {"Salinarchaeaceae"}

Halostella {QS-9-68-17} *

Natronoarchaeum {"Natronoarchaeaceae"} *

Natrialbaceae

Halococcus {Halococcaceae}

Haloarculaceae

Halalkalicoccus {"Halalkalicoccaceae"} *

Haloferacaceae (incl. Halorubraceae)

Note: * paraphyletic Halobacteriaceae

See also

Related Research Articles

In taxonomy, the Halobacteriaceae are a family of the Halobacteriales in 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">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.

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

In taxonomy, the Acidilobales are an order of the Thermoprotei.

The Pyrodictiaceae are a family of disc-shaped anaerobic microorganisms belonging to the order Desulfurococcales, in the domain Archaea. Members of this family are distinguished from the other family (Desulfurococcaceae) in the order Desulfurococcales by having an optimal growth temperature above 100 °C, rather than below 100 °C.

<i>Methanohalophilus</i> Genus of archaea

In taxonomy, Methanohalophilus is a genus of the Methanosarcinaceae.

Haladaptatus is a genus of halophilic archaea in the family of Halobacteriaceae. The members of Haladaptatus thrive in environments with salt concentrations approaching saturation

Halalkalicoccus is a genus of the Halobacteriaceae.

Halococcus is a genus of the Halococcaceae.

<i>Haloferax</i> Genus of archaea

In taxonomy, Haloferax is a genus of the Haloferacaceae.

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, Halovivax is a genus of the Natrialbaceae. Some species of Halovivax are halophiles and have been found in Iran's Aran-Bidgol hypersaline lake.

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.

Natronorubrum is a genus in the family Halobacteriaceae.

The Selenomonadales are an order of bacteria within the class Negativicutes; unlike most other members of Bacillota, they are Gram-negative. The phylogeny of this order was initially determined by 16S rRNA comparisons. More recently, molecular markers in the form of conserved signature indels (CSIs) have been found specific for all Selenomonadales species. On the basis of these markers, the Selenomonadales are inclusive of two distinct families, and are no longer the sole order within the Negativicutes. Several CSIs have also been found specific for both families, Sporomusaceae and Selenomonadceae. Samples of bacterial strains within this order have been isolated from the root canals of healthy human teeth.

<span class="mw-page-title-main">Haloferacaceae</span> Family of bacteria

Haloferacaceae is a family of halophilic, chemoorganotrophic or heterotrophic archaea within the order Haloferacales. The type genus of this family is Haloferax. Its biochemical characteristics are the same as the order Haloferacales.

Natrialbales is an order of halophilic, chemoorganotrophic archaea within the class Haloarchaea. The type genus of this order is Natrialba.

Haloferacales is an order of halophilic, chemoorganotrophic or heterotrophic archaea within the class Haloarchaea. The type genus of this order is Haloferax.

Halorubraceae is a family of halophilic, chemoorganotrophic or heterotrophic archaea within the order Haloferacales. The type genus of this family is Halorubrum. Its biochemical characteristics are the same as the order Haloferacales.

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

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.

References

  1. See the NCBI webpage on Halobacteriales. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information . Retrieved 2007-03-19.
  2. 1 2 3 Youssef NH, Ashlock-Savage KN, Elshahed MS (March 2012). "Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats". Applied and Environmental Microbiology. 78 (5): 1332–44. doi:10.1128/AEM.07420-11. PMC   3294467 . PMID   22179255.
  3. 1 2 3 Elshahed MS, Najar FZ, Roe BA, Oren A, Dewers TA, Krumholz LR (April 2004). "Survey of archaeal diversity reveals an abundance of halophilic Archaea in a low-salt, sulfide- and sulfur-rich spring". Applied and Environmental Microbiology. 70 (4): 2230–9. doi:10.1128/AEM.70.4.2230-2239.2004. PMC   383155 . PMID   15066817.
  4. 1 2 3 Oren A, Ventosa A, Kamekura M (2017-09-15). "Halobacteriales". In Whitman WB, Rainey F, Kämpfer P, Trujillo M (eds.). Bergey's Manual of Systematics of Archaea and Bacteria. Chichester, UK: John Wiley & Sons, Ltd. pp. 1–3. doi:10.1002/9781118960608.obm00048.pub2. ISBN   978-1-118-96060-8.
  5. Gupta, Radhey S.; Naushad, Sohail; Baker, Sheridan (2015-03-01). "Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov". International Journal of Systematic and Evolutionary Microbiology. 65 (Pt_3): 1050–1069. doi: 10.1099/ijs.0.070136-0 . ISSN   1466-5026. PMID   25428416.
  6. Gupta, Radhey S.; Naushad, Sohail; Fabros, Reena; Adeolu, Mobolaji (April 2016). "A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov". Antonie van Leeuwenhoek. 109 (4): 565–587. doi:10.1007/s10482-016-0660-2. ISSN   0003-6072. PMID   26837779. S2CID   254231068.
  7. J.P. Euzéby. "Halobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-11-17.
  8. Sayers; et al. "Halobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-06-05.
  9. "The LTP" . Retrieved 10 May 2023.
  10. "LTP_all tree in newick format" . Retrieved 10 May 2023.
  11. "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.
  12. "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  13. "ar53_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  14. "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.

Further reading

Journals

Books

  • Grant WD, Kamekura M, McGenity TJ, Ventosa A (2001). "Class III. Halobacteria class. nov." . In DR Boone, RW Castenholz (eds.). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria (2nd ed.). New York: Springer Verlag. p.  169. ISBN   978-0-387-98771-2.
  • Grant WD, Larsen H (1989). "Group III. Extremely halophilic archaeobacteria. Order Halobacteriales ord. nov.". In JT Staley, MP Bryant, N Pfennig, JG Holt (eds.). Bergey's Manual of Systematic Bacteriology, Volume 3 (1st ed.). Baltimore: The Williams & Wilkins Co. p. 169.