Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium

Cui, Heng‐Lin; Zhou, Pengyu; Oren, Aharon; Liu, Shuang‐Jiang

doi:10.1007/s00792-008-0194-2

Cited by 151 publications

(88 citation statements)

References 30 publications

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“…The growth kinetics of Natronomonas has highly unusual temperature requirements for growth, suggesting that the physiology of Natronomonas is different with other halobacteria (Inoue et al 2011). The members of the genus Halomicrobium, i.e., Halomicrobium zhouii, H. katesii, and H. mukohataei, are also halophilic (Cui et al 2009). The genus Halococcus has been found in the rhizosphere of the halophyte Halonemum strobilaceum inhabiting hypersaline coastal areas of the Arabian Gulf, and is known to be an extremely halophilic, oil-utilizing microorganism (AlMailem et al 2010).…”

Section: Archaeamentioning

confidence: 99%

“…Initial studies employed traditional culture-dependent methods and resulted in the discovery of a large number of new bacterial and archaeal taxa (Lefebvre et al 2006). The primary methods in current use are DNA-based molecular biology approaches such as cloning and sequencing of 16S rRNA genes, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (Lefebvre et al 2006;Cui et al 2009;Blum et al 2012). Cloning and sequencing of 16S rRNA genes has been generally favored over other methods because it allows the detection both of known and unknown microbes present in saline soils.…”

Section: Introductionmentioning

confidence: 99%

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A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Gong

2013

World J Microbiol Biotechnol

100

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An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %).Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.

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Section: Archaeamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Gong

2013

World J Microbiol Biotechnol

100

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“…The nine species of the genus Haloarcula and the three species of the genus Halomicrobium also possess multiple heterogeneous 16S rRNA genes. The 16S rRNA genes of the genus Haloarcula are divergent at 4.8-5.6 % (Cui et al, 2009). The ultimate case is the similarity of 90.64 % of Hmc.…”

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confidence: 99%

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

Echigo

Minegishi

Shimane

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan A novel halophilic strain, BNERC31 T , was isolated from solar salt, 'Sel marin de Gué rande', 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. Growth occurred with 20-30 % (w/v) NaCl (optimum, 25 %, w/v), with 0-500 mM MgCl 2 (optimum, 10 mM), at pH 6.0-8.5 (optimum, pH 7.0) and at 25-55 6C (optimum, 40 6C). Growth was dependent on soluble starch, and inhibited completely by 0.5 % organic nutrients, such as Casamino acids or yeast extract. The DNA G+C content was 64.1 mol%. Strain BNERC31 T possessed at least two heterogeneous 16S rRNA genes, and the sequence of the orthologous gene (preceded by the dihydroorotate oxidase gene, pyrD) showed the highest similarity (96.5 %) to that of Haloarcula marismortui JCM 8966 T . The RNA polymerase subunit B9 gene sequence showed the highest similarity (91.7 %) to that of Haloarcula amylolytica JCM 13557 T . The polar lipids of strain BNERC31 T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, diglycosyl diether and sulfated diglycosyl diether, similar to those of species of the genus Halomicrobium. The phenotypic and phylogenetic characteristics showed that strain BNERC31 T differed from species of the genera Haloarcula and Halomicrobium and indicated that it represents a novel species in a new genus, for which the name Halomicroarcula pellucida gen. nov., sp. nov. is proposed. The type strain of the type species is BNERC31 T (5JCM 17820 T 5CECT 7537 T ).This study was initiated several years ago in an attempt to isolate extreme halophiles that produced amylase in simple synthetic media containing 1 % soluble starch. We isolated an extremely halophilic strain, designated BNERC31 T , from a solar salt sample imported from France, which formed nonpigmented transparent colonies on agar containing sodium glutamate as the sole nitrogen source. The strain was extraordinary in requiring soluble starch for growth, and in that growth was inhibited completely by 0.5 % Casamino acids or yeast extract. The 16S rRNA gene sequences indicated that the strain BNERC31 T was closely related to species of the genus Haloarcula of the family Halobacteriaceae, followed by species of the genus Halomicrobium. However, the polar lipid composition of strain BNERC31 T differed from those of Abbreviations: TGD, triglycosyl diether; TMAO, trimethylamine N-oxide.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strain BNERC31 T are AB766179 and AB766180. The GenBank/EMBL/DDBJ accession number f...

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“…Genomic DNA of strain YJ-50-S2 T was extracted and purified using a genomic DNA extraction kit (CW0552; Beijing ComWin Biotech), and the 16S rRNA gene was amplified with the forward primer 0018F and reverse primer 1518R, then cloned and sequenced as described previously (Cui et al, 2009). The rpoB¢ gene was amplified using the primer pair HrpoB2 1420F and HrpoA 153R (Minegishi et al, 2010) and the PCR product was sequenced using the following primers: HrpoB2 1420F, HrpoA 153R and B1-628F (5¢-CCNGCNGSVCAGAACTTC-3¢).…”

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confidence: 99%

Salinigranum salinum sp. nov., isolated from a marine solar saltern

Wang

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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An extremely halophilic archaeal strain YJ-50-S2 T was isolated from Yangjiang marine solar saltern, China. Cells were pleomorphic, stained Gram-negative and formed red-pigmented colonies on agar plates. Strain YJ-50-S2 T was able to grow at 25-50 C (optimum 37 C), with 0.9-4.8 M NaCl (optimum 2.6 M NaCl) and 0-1.0 M MgCl 2 (optimum 0.03 M MgCl 2 ), and at pH 5.0-9.5 (optimum pH 7.5). The cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 5 % (w/v). The 16S rRNA gene and rpoB¢ gene of strain YJ-50-S2 T were phylogenetically related to the corresponding genes of Salinigranum rubrum GX10 T (97.0 % and 90.5 % similarities, respectively). The major polar lipids of strainYJ-50-S2 T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and two major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Several unidentified glycolipids were also detected. The DNA G+C content of strain YJ-50-S2 T was 65.2 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YJ-50-S2 T represents a novel species of the genus Salinigranum, for which the name Salinigranum salinum sp. nov. is proposed. The type strain is

show abstract

Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium

Cited by 151 publications

References 30 publications

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

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

Salinigranum salinum sp. nov., isolated from a marine solar saltern

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