Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds

Oh, Dickson; Porter, Kate; Russ, Brendan E.; Burns, David G.; Dyall‐Smith, Mike

doi:10.1007/s00792-009-0295-6

Cited by 97 publications

(103 citation statements)

References 34 publications

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“…For instance, Hqr. walsbyi cultured strains have o1.8% divergence in their 16S rRNA gene sequences (Legault et al, 2006) while environmental phylotypes recovered from highly distant saltern ponds in Spain Legault et al, 2006), Israel (Soerensen et al, 2005), Turkey (Mutlu et al, 2008), Tunisia (Baati et al, 2008), Peru (Maturrano et al, 2006) and Australia (Oh et al, 2010) normally present o1% divergence. In contrast, some Haloquadratum sequences recovered in this work (Table 2 and Figure 2) showed a higher divergence (up to 5%) in the analyzed 16S rRNA gene fragment.…”

Section: Resultsmentioning

confidence: 99%

“…Multi-pond solar salterns consist of a series of interconnected ponds with increasing salinity, from seawater level to sodium chloride saturation Pašić et al, 2005;Oh et al, 2010;Boujelben et al, 2012). In continuously operated salterns, such as the Santa Pola (Spain) facilities studied here, seawater is pumped through a set of shallow ponds where sequential precipitation of calcium carbonate, calcium sulfate and sodium chloride occurs.…”

Section: Introductionmentioning

confidence: 99%

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From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

et al. 2014

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The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to 440%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

et al. 2014

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“…The four DL isolates accounted for a total of ∼72%, averaged across four depths, with the rank and estimated abundance being tADL, first, 43.5%; DL31, second, 18.2%; H. lacusprofundi, fourth, 9.9%; DL1, 17th, 0.3%. The haloarchaeal community composition differs greatly from other hypersaline environments in the world where Haloarcula spp., Haloferax volcanii, Haloquadratum walsbyi, and Halobacterium salinarum are typically found (but are absent in DL) (31)(32)(33).…”

Section: Significancementioning

confidence: 99%

High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake

DeMaere

Williams

Allen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

100

130

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Deep Lake in Antarctica is a globally isolated, hypersaline system that remains liquid at temperatures down to −20°C. By analyzing metagenome data and genomes of four isolates we assessed genome variation and patterns of gene exchange to learn how the lake community evolved. The lake is completely and uniformly dominated by haloarchaea, comprising a hierarchically structured, low-complexity community that differs greatly to temperate and tropical hypersaline environments. The four Deep Lake isolates represent distinct genera (∼85% 16S rRNA gene similarity and ∼73% genome average nucleotide identity) with genomic characteristics indicative of niche adaptation, and collectively account for ∼72% of the cellular community. Network analysis revealed a remarkable level of intergenera gene exchange, including the sharing of long contiguous regions (up to 35 kb) of high identity (∼100%). Although the genomes of closely related Halobacterium, Haloquadratum, and Haloarcula (>90% average nucleotide identity) shared regions of high identity between species or strains, the four Deep Lake isolates were the only distantly related haloarchaea to share long high-identity regions. Moreover, the Deep Lake high-identity regions did not match to any other hypersaline environment metagenome data. The most abundant species, tADL, appears to play a central role in the exchange of insertion sequences, but not the exchange of high-identity regions. The genomic characteristics of the four haloarchaea are consistent with a lake ecosystem that sustains a high level of intergenera gene exchange while selecting for ecotypes that maintain sympatric speciation. The peculiarities of this polar system restrict which species can grow and provide a tempo and mode for accentuating gene exchange. mobile genetic elements | Antarctic haloarchaea | saltern | fragment recruitment | BJ1 virus

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“…Achieving this goal requires coordinated, detailed, accurate measurements of both physical and biological factors, but obtaining this information over temporal and spatial scales relevant to natural microbial communities is challenging. Extreme hypersaline aqueous environments harboring limited phylogenetic diversity provide tractable model ecosystems to confront these challenges (Demergasso et al, 2008;Bodaker et al, 2009;Pagaling et al, 2009;Oh et al, 2010;Boujelben et al, 2012;MakhdoumiKakhki et al, 2012;Oren, 2013). Although overall salt concentrations in these habitats are, by definition, at or exceeding the limits of ionic solubility, geochemical variation in water sources as well as minerals dissolved from surrounding rocks and sediments contribute to variable ratios of different ionic species over space and time (Javor, 1989;Oren, 2013).…”

Section: Introductionmentioning

confidence: 99%

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community

et al. 2013

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Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate, but not sodium, chloride or calcium ions, while relative abundances of Halorubrum, Haloarcula, Halonotius, Halobaculum and Salinibacter-related sequences correlated negatively with Haloquadratum and these same ionic factors. Nanohaloarchaea and Halorhabdus-related sequence abundances were inversely correlated with each other, but not other taxonomic groups. These data, along with predicted gene functions from nearly-complete assembled population metagenomes, suggest different ecological phenotypes for Nanohaloarchaea and Halorhabdus-related strains versus other community members. Nucleotide percent G þ C compositions were consistently lower in community metagenomic reads from summer versus winter samples. The same seasonal G þ C trends were observed within taxonomically binned read subsets from each of seven different genus-level archaeal groups. Relative seasonal abundances were also linked to percent G þ C for assembled population genomes. Together, these data suggest that extreme ionic conditions may exert selective pressure on archaeal populations at the level of genomic nucleotide composition, thus contributing to seasonal successional processes. Despite the unavailability of cultured representatives for most of the organisms identified in this study, effective coordination of physical and biological measurements has enabled discovery and quantification of unexpected taxon-specific, environmentally mediated factors influencing microbial community structure.

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Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds

Cited by 97 publications

References 34 publications

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community

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