Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis

Haba, Rafael R. de la; Arahal, David R.; Márquez, M. Carmen; Ventosa, António

doi:10.1099/ijs.0.013979-0

Cited by 57 publications

(36 citation statements)

References 72 publications

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“…Halomonas isolates were retrieved from all sample types, assigned to 7 distinct species and clustered within 3 phylogenetic groups: (i) Halomonas group I including H. ventosae ( n = 3), and H. taeanensis ( n = 3); (ii) Halomonas group II represented by H. elongata ( n = 4); and (iii) Halomonas group III constituted by H. boliviensis ( n = 2), H. gomseomensis ( n = 2) and the related species H. janggokensis ( n = 14) and H. subterranea ( n = 1) (Table 1, Figure 2). Considering the nonmonophyletic status of the Halomonas genus and the need of a deep taxonomic revision [65], the number of recovered species indicates high intragenus diversity. In addition, there was no clear correlation between the recovered Halomonas species with their isolation origin, pointing out their adaptation capabilities to harsh conditions.…”

Section: Resultsmentioning

confidence: 99%

“…Within this genus, Halomonas group III includes the 3 closely related species with 6 distinct ITS haplotypes: H. gomseomensis (H7 and H40) , H. janggokensis (H2, H9, and H22) and H. subterranea (H30). Isolates of these species that could be considered as a single one [65, 72] were recovered from all the sites except from Sabkhet El Melah (Table 1, Figure 3). Their high level of microdiversity could contribute to their ecological fitness and their ability to adapt to desert and saline environments.…”

Section: Resultsmentioning

confidence: 99%

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Cultivation-Dependant Assessment, Diversity, and Ecology of Haloalkaliphilic Bacteria in Arid Saline Systems of Southern Tunisia

Hidri

Guesmi

Najjari

et al. 2013

BioMed Research International

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Haloalkaliphiles are polyextremophiles adapted to grow at high salt concentrations and alkaline pH values. In this work, we isolated 122 haloalkaliphilic bacteria upon enrichments of 23 samples from 5 distinct saline systems of southern Tunisia, growing optimally in media with 10% salt and at pH 10. The collection was classified into 44 groups based on the amplification of the 16S–23S rRNA internal transcribed spacers (ITS-PCR). Phylogenetic analysis and sequencing of the 16S rRNA genes allowed the identification of 13 genera and 20 distinct species. Three gram-positive isolates showing between 95 and 96% of 16S rRNA sequence homology with Bacillus saliphilus could represent new species or genus. Beside the difference in bacterial diversity between the studied sites, several species ecological niches correlations were demonstrated such as Oceanobacillus in salt crust, Nesterenkonia in sand, and Salinicoccus in the rhizosphere of the desert plant Salicornia. The collection was further evaluated for the production of extracellular enzymes. Activity tests showed that gram-positive bacteria were mostly active, particularly for protease, lipase, DNase, and amylase production. Our overall results demonstrate the huge phenotypic and phylogenetic diversity of haloalkaliphiles in saline systems of southern Tunisia which represent a valuable source of new lineages and metabolites.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Cultivation-Dependant Assessment, Diversity, and Ecology of Haloalkaliphilic Bacteria in Arid Saline Systems of Southern Tunisia

Hidri

Guesmi

Najjari

et al. 2013

BioMed Research International

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“…Halomonas aquamarina , also in the Gammaproteobacteria, has been described as a slight-to-moderate halophile that produces ectoine as the principle compatible solute and has been isolated from many marine environments including the Pacific Ocean, deep-sea basins, Antarctica, and hypersaline lakes [37,38]. The genus Halomonas has a polyphyletic evolutionary lineage and contains at least 3 main evolutionary branches [38,39]. This may explain, in part, it wide ranging distribution.…”

Section: Discussionmentioning

confidence: 99%

Phenotypic characterization and 16S rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, La Sal del Rey, in extreme South Texas (USA)

Phillips¹,

Zaidan²,

Elizondo³

et al. 2012

Aquat. Biosyst.

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BackgroundLa Sal del Rey ("the King's Salt") is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was estimated by viable plate counts. A collection of isolates was selected, gram-stained, tested for catalase, and characterized using API 20E® test strips. Isolates were putatively identified by sequencing the 16S rDNA. Carbon source utilization by the microbial community from each sample site was examined using EcoPlate™ assays and the carbon utilization total activity of the community was determined.ResultsResults showed that salinity ranged from 4 parts per thousand (ppt) at the lake water source to 420 ppt in water samples taken just along the lake shore. The density of halophilic bacteria in water samples ranged from 1.2 × 102 - 5.2 × 103 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 × 105 - 2.5 × 106 colony forming units per gram (cfu g-1). In general, as salinity increased the density of the bacterial community decreased. Microbial communities from water and soil samples were able to utilize 12 - 31 carbon substrates. The greatest number of substrates utilized was by water-borne communities compared to soil-based communities, especially at lower salinities. The majority of bacteria isolated were gram-negative, catalase-positive, rods. Biochemical profiles constructed from API 20E® test strips showed that bacterial isolates from low-salinity water samples (4 ppt) showed the greatest phenotypic diversity with regards to the types and number of positive tests from the strip. Isolates taken from water samples at the highest salinity (420 ppt) tended to be less diverse and have only a limited number of positive tests. Sequencing of 16S DNA displayed the presence of members of bacterial genera Bacillus, Halomonas, Pseudomonas, Exiguobacterium and others. The genus Bacillus was most commonly identified. None of the isolates were members of the Archaea probably due to dilution of salts in the samples.ConclusionsThe La Sal del Rey ecosystem supports a robust and diverse bacterial community despite the high salinity of the lake and soil. However, salinity does appear to a limiting factor with regards to the density and diversity of the bacterial communities that inhabit the lake and surrounding area.

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“… S. socius SMB35 T (DSM 19940 T ) is the type strain of this species with a well-defined status within the family Halomonadaceae [9, 10], but the taxonomic placement of strains MH3R3–1 and SMB17 was not characterized in details. We compared partial (1333 bp) 16S rDNA sequences of MH3R3–1 and SMB17 to those of type strains ( n = 53) representing main phylogenetic groups recognized within the family Halomonadaceae [10, 11].…”

Section: Organism Informationmentioning

confidence: 99%

“…We compared partial (1333 bp) 16S rDNA sequences of MH3R3–1 and SMB17 to those of type strains ( n = 53) representing main phylogenetic groups recognized within the family Halomonadaceae [10, 11]. Results of the analysis revealed that the strain SMB17 belonged to the genus Chromohalobacter and was closely related to C. japonicus , whereas MH3R3–1 was most similar to Salinicola salarius and S. socius (Fig.…”

Section: Organism Informationmentioning

confidence: 99%

Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia

Olsson

Korsakova

Anan’ina

et al. 2017

Stand in Genomic Sci

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Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75–90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.

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Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis

Cited by 57 publications

References 72 publications

Cultivation-Dependant Assessment, Diversity, and Ecology of Haloalkaliphilic Bacteria in Arid Saline Systems of Southern Tunisia

Cultivation-Dependant Assessment, Diversity, and Ecology of Haloalkaliphilic Bacteria in Arid Saline Systems of Southern Tunisia

Phenotypic characterization and 16S rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, La Sal del Rey, in extreme South Texas (USA)

Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia

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