A pivotal Archaea group

Burggraf, Siegfried; Heyder, P.; Eis, Nicole

doi:10.1038/385780a0

Cited by 40 publications

(22 citation statements)

References 7 publications

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“…Critical improvements in cultivation and in situ identification were necessary to resolve a complete korarchaeal genome. The ultrathin filamentous organisms hybridizing to Korarchaeota-specific probes displayed a thinner and generally longer morphology than described for pJP27-type korarchaeote (38). It is not known whether the morphological discrepancies are because of differences in the enrichment conditions, hence growth rate, or whether variation in cell shape occurs among closely related species.…”

Section: Discussionmentioning

confidence: 76%

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A korarchaeal genome reveals insights into the evolution of the Archaea

Elkins

Podar

Graham

et al. 2008

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

254

193

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The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, ''Candidatus Korarchaeum cryptofilum,'' which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G ؉ C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form. microbial cultivation ͉ genomics ͉ hyperthermophiles ͉ Korarchaeota ͉ phylogeny

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Section: Discussionmentioning

confidence: 76%

“…The cultivation conditions for the Obsidian Pool enrichment culture were similar to those described in ref. 38 FISH Analysis. FISH analysis was performed similar to that described in ref.…”

Section: Methodsmentioning

confidence: 99%

A korarchaeal genome reveals insights into the evolution of the Archaea

Elkins

Podar

Graham

et al. 2008

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

254

193

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“…Among the deep-branching lineages, in particular, Korarchaeota is considered a kingdom that might have diverged very early in the evolution of Archaea (Elkins et al, 2008), even before the Euryarchaeota and Crenarchaeota split (Barns et al, 1994(Barns et al, , 1996. Until recently, the analyses of Korarchaeota were restricted to 16S rRNA-based molecular approaches and a few enrichment cultures (Barns et al, 1994(Barns et al, , 1996Burggraf et al, 1997;Stetter, 2006), as no organisms so far have been obtained in pure laboratory culture. However, most recently Elkins et al (2008) presented the first korarchaeal genome of Candidatus Korarchaeum cryptofilum, being physically isolated from an enrichment culture inoculated with sediments from Obsidian Pool, Yellowstone.…”

Section: Introductionmentioning

confidence: 99%

“…Since the discovery of Korarchaeota more than a decade ago (Barns et al, 1996;Burggraf et al, 1997) several environmental 16S rRNA gene surveys have been conducted, identifying Korarchaeota in terrestrial hot springs (Barns et al, 1994(Barns et al, , 1996Takai and Sako, 1999;Reysenbach et al, 2000;Skirnisdottir et al, 2000;Hjorleifsdottir et al, 2001;Spear et al, 2005;Auchtung et al, 2006;Elkins et al, 2008), in shallow marine hydrothermal vents (Marteinsson et al, 2001a, b), in hydrothermal wells (Rogers and Amend, 2005), in deep-sea hydrothermal vent fluids (Takai and Sako, 1999;Nercessian et al, 2003), sediments (Teske et al, 2002), chimneys (Takai et al, 2004;Auchtung et al, 2006) and on the sea floor of abyssal hills (Ehrhardt et al, 2007a). Korarchaeota 16S rDNA signatures are found in thermal habitats of 55-128 1C and mostly at (sub-) neutral pH.…”

Section: Introductionmentioning

confidence: 99%

Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka

2009

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Korarchaeota constitute a recently proposed and little characterized kingdom of Archaea that might have diverged before the lineages of Crenarchaeota and Euryarchaeota split. To assess the diversity, distribution and abundance of Korarchaeota, we analysed 19 terrestrial hot springs in Hveragerdi and Krysuvik, Iceland, and in Kamchatka, Russia. The springs were 70-97 1C with pH 2.5-6.5. Out of 19 springs, 12 tested positive for Korarchaeota with specific primers. A Korarchaeota 16S rDNA library was made from each of these. From the 301 clones sequenced, 87 unique sequences were obtained from Iceland and 33 from Kamchatka. The similarity between Kamchatkan and Icelandic 16S rDNA sequences and that of Candidatus Korarchaeum cryptofilum was p93.5%. Phylogenetic analyses revealed a clear separation between sequences retrieved from terrestrial and marine habitats. Within the terrestrial sequences, four clusters could be recognized showing a geographic distribution with surprisingly low diversity. Furthermore, the abundance of Korarchaeota 16S rDNA in the 12 environmental samples was analysed using quantitative PCR (qPCR), showing that Korarchaeota represent only a minor fraction of the microbial community in hot springs; however, in some cases they constitute up to 7% of all Archaea. Taxonomic profiling of an Icelandic Korarchaeota-positive habitat revealed an Aquificales-dominated community. In fact, Aquificales were dominating or present in high numbers in all 12 positive sites. Chemical analyses of three Korarchaeota-positive hot springs showed their occurrence in variable water chemistry. Our data provide new information on Korarchaeota habitats and shed light on their abundance, diversity, distribution and coexisting organisms.

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“…This information can be used to gain insight into the intracellular organization of the chromosome DNA, the morphological features of the nucleoid partition process, and the temporal stage in the cell cycle at which different nucleoid processing events take place. Such studies have not been performed with archaea, although reports exist in which in situ DNA staining has been used for other purposes (8,16,18,20). Although nucleoid conformation may also be studied by electron microscopy, the significance is difficult to estimate since the structure of the nucleoids may alter during sample preparation (5,26).…”

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confidence: 99%

Nucleoid structure and distribution in thermophilic Archaea

Poplawski

Bernander

1997

J Bacteriol

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Nucleoid structure and distribution in thermophilic organisms from the Archaea domain were studied. Combined phase-contrast and fluorescence microscopy of DAPI (4,6-diamidino-2-phenylindole)-stained Sulfolobus acidocaldarius and Sulfolobus solfataricus cells revealed that the nucleoids were highly structured. Different nucleoid distribution within the cells, representing different partition stages, was observed. The conformation of the nucleoids differed between exponentially growing and stationary-phase cells. Also, the stationary-phase cells contained two chromosomes, and the nucleoids occupied a larger part of the interior of the cells than in the exponentially growing cells. The part of the cell cycle during which fully separated nucleoids could be detected was short. Since the postreplication period is long in these organisms, there was a considerable time interval between termination of chromosome replication and completion of nucleoid separation, similar to the G 2 phase in eukaryotic cells. The length of the visible cell constriction period was found to be in the same range as that of eubacteria. Finally, cell-cell connections were observed under certain conditions. Possible eubacterial, eukaryotic, and unique features of nucleoid processing and cell division in thermophilic archaea are discussed.Chromosome replication, segregation of the replicated genomes, and cell division are key processes in the cell cycle of any organism. The mechanistic and regulatory features of these processes have been extensively studied in eukaryotes and eubacteria. In contrast, little is known about the cell cycle in organisms from the third major evolutionary lineage of life on earth, the archaea (24).When the complete genome sequence of the archaeon Methanococcus jannaschii become available (7), several genes that may be involved in replication, partition, and cell division (called cell cycle genes in this work) in archaeal cells were found. Genes similar to cell cycle genes of organisms from both the Bacteria (e.g., ftsZ, minD, and soj) and the Eukarya (e.g., CBF5, cdc21, CDC54, and X.MCM4) domains were identified, which indicates that insights into the cell cycle of archaea may also help to increase the understanding of the cell cycle in organisms from the other two domains (see discussion in reference 3).Insight into the cell cycle features of archaea can be obtained not only from the M. jannaschii gene repertoire. Cell morphology has been used to draw conclusions about the mode of growth and division of different archaea (reference 13 and references therein). The genus studied in this report, Sulfolobus, was first described morphologically by Brock et al. (6).By staining the chromosome DNA (the nucleoids) in situ, nucleoid structure and distribution may be studied by light microscopy. This information can be used to gain insight into the intracellular organization of the chromosome DNA, the morphological features of the nucleoid partition process, and the temporal stage in the cell cycle at which different nucleoid pro...

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A pivotal Archaea group

Cited by 40 publications

References 7 publications

A korarchaeal genome reveals insights into the evolution of the Archaea

A korarchaeal genome reveals insights into the evolution of the Archaea

Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka

Nucleoid structure and distribution in thermophilic Archaea

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