Phylogenomics of Haloarchaea: The Controversy of the Genera .

The haloarchaeal genera and were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either or , mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned.

sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt.

A mannan-degrading halophilic archaeal strain, MD130-1, was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented.

Salinarchaeum chitinilyticum sp. nov., a chitin-degrading haloarchaeon isolated from commercial salt.

Two chitin-degrading halophilic archaeal strains, MC-74T and MC-23, were isolated from commercial salt samples. Cells were motile, rod-shaped and stained Gram-negative. Colonies were vermillion-pigmented.

Haloparvum alkalitolerans sp. nov., alkali-tolerant haloarchaeon isolated from commercial salt.

A Gram-stain-negative, rod-pleomorphic, aerobic, halophilic archaeon, strain MK62-1T, was isolated from commercial salt made from seawater in the Philippines. Strain MK62-1T was able to grow at 2.1-4.

Halopiger thermotolerans sp. nov., a thermo-tolerant haloarchaeon isolated from commercial salt.

Three thermo-tolerant halophilic archaeal strains, SR-441T, SR-412 and SR-188, were isolated from commercial salt samples. Cells were non-motile pleomorphic rod-shaped, and stained Gram-negative. Colonies were pink-pigmented.

Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample.

Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6, were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic and stained Gram-negative. Colonies of the strains were orange-red-pigmented.

Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt.

A Gram-stain-negative, non-motile, pleomorphic rod-shaped, orange-red-pigmented, facultatively aerobic and haloalkaliphilic archaeon, strain MK13-1T, was isolated from commercial rock salt imported from Pakistan. The NaCl, pH and temperature ranges for growth of strain MK13-1T were 3.0-5.

Halocalculus aciditolerans gen. nov., sp. nov., an acid-tolerant haloarchaeon isolated from commercial salt.

Three halophilic archaeal strains, MH2-243-1(T), MH2-93-1 and MH2-91-1 were isolated from commercial salt samples from Japan, Australia, and Bolivia. Strain MH2-243-1(T) was able to grow in the presence of 12-30% (w/v) NaCl (optimum, 18% NaCl), at pH 4.5-7.

Halococcus agarilyticus sp. nov., an agar-degrading haloarchaeon isolated from commercial salt.

Two agar-degrading halophilic archaeal strains, 62 E(T) and 197 A, were isolated from commercial salt samples. Cells were non-motile cocci, approximately 1.2-2.

Thermophilic and halophilic β-agarase from a halophilic archaeon Halococcus sp. 197A.

An agar-degrading archaeon Halococcus sp. 197A was isolated from a solar salt sample. The agarase was purified by hydrophobic column chromatography using a column of TOYOPEARL Phenyl-650 M.

Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt.

Two halophilic moderately acidophilic archaeal strains, MH1-136-2(T) and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2(T) was pink pigmented, while MH1-370-1 was orange-red pigmented.

Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt.

A novel halophilic strain, BNERC31(T), was isolated from solar salt, 'Sel marin de Guérande', imported from France. Colonies on agar medium containing soluble starch, sodium citrate, sodium glutamate and inorganic salts were non-pigmented and transparent, while cells obtained by centrifuging liquid cultures were red-pigmented. Cells of strain BNERC31(T) were non-motile, pleomorphic, stained Gram-negative and lysed in distilled water.

Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples.

Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative.

Natronoarchaeum philippinense sp. nov., a haloarchaeon isolated from commercial solar salt.

A Gram-staining-negative, pleomorphic, aerobic, halophilic archaeon, designated strain 294-194-5(T), was isolated in Japan from commercial solar salt imported from the Philippines. Colonies of strain 294-194-5(T) were translucent and red. Strain 294-194-5(T) was able to grow at 20-50 °C (optimum, 37-45 °C), with 14-30 % (w/v) NaCl (optimum, 18 %), and at pH 6.

Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt.

Two extremely halophilic archaea, strains MGY-184(T) and MGY-205, were isolated from sea salt produced in Japan and rock salt imported from Bolivia, respectively. Both strains were pleomorphic, non-motile, Gram-negative and required more than 5 % (w/v) NaCl for growth, with optimum at 9-12 %, in the presence of 2 % (w/v) MgCl2 . 6H2O.

Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957.

Halobacterium piscisalsi was proposed by Yachai et al. (2008), with a single strain, HPC1-2(T) (= BCC 24372(T) = JCM 14661(T) = PCU 302(T)), which was isolated from fermented fish (pla-ra) in Thailand. According to Yachai et al.

Natribacillus halophilus gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium isolated from soil.

A moderately halophilic and alkalitolerant bacterium, designated strain HN30(T), was isolated from garden soil in Japan. Cells of strain HN30(T) were motile, endospore-forming, aerobic, rod-shaped and gram-positive, and contained A1γ meso-diaminopimelic acid-type murein. Growth occurred in 7-23 % (w/v) NaCl (optimum, 10-15 %, w/v), at pH 6.

Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups.

In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to concerted evolution. At the time of writing, the genus Haloarcula of the family Halobacteriaceae comprises nine species with validly published names, all of which possess two to four highly heterogeneous 16S rRNA genes. Existence of multiple heterogeneous 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequence data.

Halostagnicola alkaliphila sp. nov., an alkaliphilic haloarchaeon from commercial rock salt.

A Gram-negative, pleomorphic, aerobic, haloalkaliphilic archaeon, strain 167-74(T), was isolated from commercial rock salt imported into Japan from China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain 167-74(T) is closely related to Halostagnicola larsenii XH-48(T) (98.3 %) and Halostagnicola kamekurae 194-10(T) (97.

Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt.

A novel halophilic archaeon, strain MH1-52-1(T), was isolated from solar salt imported from Australia. Cells were pleomorphic, non-motile and Gram-negative. Strain MH1-52-1(T) required at least 3.

Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene.

A considerable number of species of the Halobacteriaceae possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera Haloterrigena and Natrinema show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus Natrialba form definitely separate clusters in neighbour-joining trees, suggesting that these two clusters could be separated into two genera. In an attempt to solve these problems, the RNA polymerase B' subunit has been used as an additional target molecule for phylogenetic analysis, using partial sequences of 1305 bp.

Natronomonas moolapensis sp. nov., non-alkaliphilic isolates recovered from a solar saltern crystallizer pond, and emended description of the genus Natronomonas.

Two isolates of non-alkaliphilic, extremely halophilic archaea, with very similar characteristics, were recovered from a marine solar saltern crystallizer. Cells were pleomorphic, motile and Gram-stain-negative and grew on a limited range of carbon sources, with pyruvate being the best substrate. Optimum growth occurred at 18-20 % (w/v) NaCl, pH 6.

Halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer.

Strains 1.15.5(T), 2.