RESUMEN
DPANN archaea are a diverse group of microorganisms characterised by small cells and reduced genomes. To date, all cultivated DPANN archaea are ectosymbionts that require direct cell contact with an archaeal host species for growth and survival. However, these interactions and their impact on the host species are poorly understood. Here, we show that a DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. During these interactions, the nanohaloarchaeon appears to enter, or be engulfed by, the host cell. Our results provide experimental evidence for a predatory-like lifestyle of an archaeon, suggesting that at least some DPANN archaea may have roles in controlling host populations and their ecology.
Asunto(s)
Halorubrum , Simbiosis , Halorubrum/genética , Halorubrum/fisiología , Archaea/genética , Archaea/fisiología , Nanoarchaeota/genética , Nanoarchaeota/fisiología , Genoma Arqueal , FilogeniaRESUMEN
Nano-sized archaeota, with their small genomes and limited metabolic capabilities, are known to associate with other microbes, thereby compensating for their own auxotrophies. These diminutive and yet ubiquitous organisms thrive in hypersaline habitats that they share with haloarchaea. Here, we reveal the genetic and physiological nature of a nanohaloarchaeon-haloarchaeon association, with both microbes obtained from a solar saltern and reproducibly cultivated together in vitro. The nanohaloarchaeon Candidatus Nanohalobium constans LC1Nh is an aerotolerant, sugar-fermenting anaerobe, lacking key anabolic machinery and respiratory complexes. The nanohaloarchaeon cells are found physically connected to the chitinolytic haloarchaeon Halomicrobium sp. LC1Hm. Our experiments revealed that this haloarchaeon can hydrolyze chitin outside the cell (to produce the monosaccharide N-acetylglucosamine), using this beta-glucan to obtain carbon and energy for growth. However, LC1Hm could not metabolize either glycogen or starch (both alpha-glucans) or other polysaccharides tested. Remarkably, the nanohaloarchaeon's ability to hydrolyze glycogen and starch to glucose enabled growth of Halomicrobium sp. LC1Hm in the absence of a chitin. These findings indicated that the nanohaloarchaeon-haloarchaeon association is both mutualistic and symbiotic; in this case, each microbe relies on its partner's ability to degrade different polysaccharides. This suggests, in turn, that other nano-sized archaeota may also be beneficial for their hosts. Given that availability of carbon substrates can vary both spatially and temporarily, the susceptibility of Halomicrobium to colonization by Ca Nanohalobium can be interpreted as a strategy to maximize the long-term fitness of the host.
Asunto(s)
Halobacteriaceae/fisiología , Nanoarchaeota/fisiología , Polisacáridos/metabolismo , Simbiosis/fisiología , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Técnicas de Cocultivo , Regulación de la Expresión Génica Arqueal , Genoma Arqueal , Genómica , FilogeniaRESUMEN
In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch's postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships.
Asunto(s)
Halorubrum/fisiología , Metagenoma , Nanoarchaeota/fisiología , Simbiosis/fisiología , Regiones Antárticas , ADN de Archaea/genética , ADN de Archaea/aislamiento & purificación , Citometría de Flujo , Genoma Arqueal/genética , Halorubrum/ultraestructura , Metagenómica , Microscopía Electrónica de Transmisión , Nanoarchaeota/ultraestructura , Filogenia , SalinidadRESUMEN
DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.
Asunto(s)
Archaea/genética , Genoma Arqueal/genética , Metagenoma , Nanoarchaeota/genética , Simbiosis , Archaea/aislamiento & purificación , Archaea/fisiología , Ecosistema , Agua Subterránea , Hibridación Fluorescente in Situ , Nanoarchaeota/aislamiento & purificación , Nanoarchaeota/fisiología , Filogenia , UtahRESUMEN
BACKGROUND: Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity. RESULTS: From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs. CONCLUSIONS: This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.
Asunto(s)
Especificidad del Huésped , Nanoarchaeota/genética , Simbiosis , Archaea/aislamiento & purificación , Archaea/fisiología , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Genoma Arqueal , Genómica , Manantiales de Aguas Termales/microbiología , Nanoarchaeota/clasificación , Nanoarchaeota/aislamiento & purificación , Nanoarchaeota/fisiología , Filogenia , Análisis de la Célula IndividualRESUMEN
Biosynthesis of L-tyrosine (L-Tyr) and L-phenylalanine (L-Phe) is directed by the interplay of three enzymes. Chorismate mutase (CM) catalyzes the rearrangement of chorismate to prephenate, which can be either converted to hydroxyphenylpyruvate by prephenate dehydrogenase (PD) or to phenylpyruvate by prephenate dehydratase (PDT). This work reports the first characterization of a trifunctional PD-CM-PDT from the smallest hyperthermophilic archaeon Nanoarchaeum equitans and a bifunctional CM-PD from its host, the crenarchaeon Ignicoccus hospitalis. Hexa-histidine tagged proteins were expressed in Escherichia coli and purified by affinity chromatography. Specific activities determined for the trifunctional enzyme were 21, 80, and 30 U/mg for CM, PD, and PDT, respectively, and 47 and 21 U/mg for bifunctional CM and PD, respectively. Unlike most PDs, these two archaeal enzymes were insensitive to regulation by L-Tyr and preferred NADP(+) to NAD(+) as a cofactor. Both the enzymes were highly thermally stable and exhibited maximal activity at 90 °C. N. equitans PDT was feedback inhibited by L-Phe (Ki = 0.8 µM) in a non-competitive fashion consistent with L-Phe's combination at a site separate from that of prephenate. Our results suggest that PD from the unique symbiotic archaeal pair encompass a distinct subfamily of prephenate dehydrogenases with regard to their regulation and co-substrate specificity.
Asunto(s)
Proteínas Arqueales/metabolismo , Corismato Mutasa/metabolismo , Desulfurococcaceae/enzimología , Nanoarchaeota/enzimología , Prefenato Deshidratasa/metabolismo , Prefenato Deshidrogenasa/metabolismo , Aminoácidos Aromáticos/biosíntesis , Proteínas Arqueales/química , Proteínas Arqueales/genética , Corismato Mutasa/química , Corismato Mutasa/genética , Desulfurococcaceae/fisiología , Estabilidad de Enzimas , Calor , Nanoarchaeota/fisiología , Nitrosaminas/metabolismo , Prefenato Deshidratasa/química , Prefenato Deshidratasa/genética , Prefenato Deshidrogenasa/química , Prefenato Deshidrogenasa/genética , Especificidad por Sustrato , SimbiosisRESUMEN
Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in high-temperature (â¼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.
Asunto(s)
Manantiales de Aguas Termales/microbiología , Nanoarchaeota/fisiología , Nanoarchaeota/virología , Sulfolobales/fisiología , Manantiales de Aguas Termales/virología , Metagenómica , Nanoarchaeota/clasificación , Nanoarchaeota/genética , Parques Recreativos , ARN Ribosómico 16S/genética , Análisis de la Célula Individual , Sulfolobales/genética , WyomingRESUMEN
I reply to the suggestion of Podar et al. (2013) that the split genes of Nanoarchaeun equitans are a derived character, showing that their analysis is mistaken. In particular, I show that the split genes both proteins and tRNAs have not been split in N. equitans and have been on the contrary merged in the nanoarchaeon sequenced recently by Podar et al. (2013). This implies that the main argument of Podar et al. (2013) that there should be: "a unique propensity for splitting in the Nanoarchaeota that is most dramatically manifested in the Nanoarchaeum equitans lineage" is false. On the other hand, the analysis seems to favor the hypothesis that the split genes are an ancestral character. This would strengthen to greater extent a model for the origin of the tRNA molecule.
Asunto(s)
Proteínas Arqueales/genética , Genoma Arqueal , Nanoarchaeota/fisiología , Sulfolobales/fisiología , SimbiosisRESUMEN
BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.
Asunto(s)
Proteínas Arqueales/genética , Genoma Arqueal , Nanoarchaeota/fisiología , Sulfolobales/fisiología , Simbiosis , Proteínas Arqueales/metabolismo , Evolución Biológica , Evolución Molecular , Datos de Secuencia Molecular , Nanoarchaeota/genética , Filogenia , Reacción en Cadena de la Polimerasa , Homología de Secuencia , Sulfolobales/genética , WyomingRESUMEN
BACKGROUND: The minimal genome of the tiny, hyperthermophilic archaeon Nanoarchaeum equitans contains several fragmented genes and revealed unusual RNA processing pathways. These include the maturation of tRNA molecules via the trans-splicing of tRNA halves and genomic rearrangements to compensate for the absence of RNase P. RESULTS: Here, the RNA processing events in the N. equitans cell are analyzed using RNA-Seq deep sequencing methodology. All tRNA half precursor and tRNA termini were determined and support the tRNA trans-splicing model. The processing of CRISPR RNAs from two CRISPR clusters was verified. Twenty-seven C/D box small RNAs (sRNAs) and a H/ACA box sRNA were identified. The C/D box sRNAs were found to flank split genes, to form dicistronic tRNA-sRNA precursors and to be encoded within the tRNAMet intron. CONCLUSIONS: The presented data provide an overview of the production and usage of small RNAs in a cell that has to survive with a highly reduced genome. N. equitans lost many essential metabolic pathways but maintains highly active CRISPR/Cas and rRNA modification systems that appear to play an important role in genome fragmentation.
Asunto(s)
Genoma Arqueal , Nanoarchaeota/genética , Procesamiento Postranscripcional del ARN , ARN de Archaea/análisis , Proteínas Arqueales/metabolismo , Sistemas CRISPR-Cas , Evolución Molecular , Secuenciación de Nucleótidos de Alto Rendimiento , Modelos Moleculares , Datos de Secuencia Molecular , Nanoarchaeota/metabolismo , Nanoarchaeota/fisiología , ARN de Archaea/química , ARN de Archaea/metabolismo , ARN de Transferencia/química , ARN de Transferencia/metabolismo , Análisis de Secuencia de ARN , Trans-EmpalmeRESUMEN
Nanoarchaeum equitans, the only cultured representative of the Nanoarchaeota, is dependent on direct physical contact with its host, the hyperthermophile Ignicoccus hospitalis. The molecular mechanisms that enable this relationship are unknown. Using whole-cell proteomics, differences in the relative abundance of >75% of predicted protein-coding genes from both Archaea were measured to identify the specific response of I. hospitalis to the presence of N. equitans on its surface. A purified N. equitans sample was also analyzed for evidence of interspecies protein transfer. The depth of cellular proteome coverage achieved here is amongst the highest reported for any organism. Based on changes in the proteome under the specific conditions of this study, I. hospitalis reacts to N. equitans by curtailing genetic information processing (replication, transcription) in lieu of intensifying its energetic, protein processing and cellular membrane functions. We found no evidence of significant Ignicoccus biosynthetic enzymes being transported to N. equitans. These results suggest that, under laboratory conditions, N. equitans diverts some of its host's metabolism and cell cycle control to compensate for its own metabolic shortcomings, thus appearing to be entirely dependent on small, transferable metabolites and energetic precursors from I. hospitalis.
Asunto(s)
Proteínas Arqueales/metabolismo , Desulfurococcaceae/metabolismo , Nanoarchaeota/metabolismo , Proteómica/métodos , Desulfurococcaceae/fisiología , Nanoarchaeota/fisiologíaRESUMEN
This month's Genome Watch looks at the publication of four hyperthermophilic archaeal genomes, three of which belong to the Crenarchaeota phylum and one of which belongs to the newly defined Nanoarchaeota phylum.
Asunto(s)
Genoma Arqueal/genética , Crenarchaeota/genética , Crenarchaeota/crecimiento & desarrollo , Crenarchaeota/fisiología , Crenarchaeota/ultraestructura , Nanoarchaeota/genética , Nanoarchaeota/crecimiento & desarrollo , Nanoarchaeota/fisiología , Nanoarchaeota/ultraestructuraRESUMEN
The complete genome sequence of the crenarchaeon Ignicoccus hospitalis published recently in Genome Biology provides a great leap forward in the dissection of its unique association with another hyperthermophilic archaeon, Nanoarchaeum equitans.
Asunto(s)
Desulfurococcaceae/genética , Genoma Arqueal , Nanoarchaeota/genética , Simbiosis , Desulfurococcaceae/fisiología , Transferencia de Gen Horizontal , Genómica , Familia de Multigenes , Nanoarchaeota/fisiología , FilogeniaRESUMEN
BACKGROUND: The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship. RESULTS: We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources. CONCLUSIONS: A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.
Asunto(s)
Desulfurococcaceae/genética , Nanoarchaeota/genética , Transporte Biológico , Desulfurococcaceae/fisiología , Metabolismo Energético , Transferencia de Gen Horizontal , Genoma Arqueal , Nanoarchaeota/fisiología , Filogenia , SimbiosisRESUMEN
A novel chemolithoautotrophic and hyperthermophilic member of the genus Ignicoccus was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland. The new isolate showed high similarity to the two species described to date, Ignicoccus islandicus and Ignicoccus pacificus, in its physiological properties as well as in its unique cell architecture. However, phylogenetic analysis and investigations on the protein composition of the outer membrane demonstrated that the new isolate was clearly distinct from I. islandicus and I. pacificus. Furthermore, it is the only organism known so far which is able to serve as a host for 'Nanoarchaeum equitans', the only cultivated member of the 'Nanoarchaeota'. Therefore, the new isolate represents a novel species of the genus Ignicoccus, which we name Ignicoccus hospitalis sp. nov. (type strain KIN4/I(T)=DSM 18386(T)=JCM 14125(T)).
Asunto(s)
Desulfurococcaceae/clasificación , Desulfurococcaceae/fisiología , Nanoarchaeota/fisiología , Composición de Base , Crecimiento Quimioautotrófico , Desulfurococcaceae/citología , Desulfurococcaceae/aislamiento & purificación , Islandia , Proteínas de la Membrana/química , Datos de Secuencia Molecular , FilogeniaRESUMEN
Active deep-sea hydrothermal vents are areas of intense mixing and severe thermal and chemical gradients, fostering a biotope rich in novel hyperthermophilic microorganisms and metabolic pathways. The goal of this study was to identify the earliest archaeal colonizers of nascent hydrothermal chimneys, organisms that may be previously uncharacterized as they are quickly replaced by a more stable climax community. During expeditions in 2001 and 2002 to the hydrothermal vents of the East Pacific Rise (EPR) (9 degrees 50'N, 104 degrees 17'W), we removed actively venting chimneys and in their place deployed mineral chambers and sampling units that promoted the growth of new, natural hydrothermal chimneys and allowed their collection within hours of formation. These samples were compared with those collected from established hydrothermal chimneys from EPR and Guaymas Basin vent sites. Using molecular and phylogenetic analysis of the 16S rDNA, we show here that at high temperatures, early colonization of a natural chimney is dominated by members of the archaeal genus Ignicoccus and its symbiont, Nanoarchaeum. We have identified 19 unique sequences closely related to the nanoarchaeal group, and five archaeal sequences that group closely with Ignicoccus. These organisms were found to colonize a natural, high temperature protochimney and vent-like mineral assemblages deployed over high temperature outflows within 92 h. When compared phylogenetically, several of these colonizing organisms form a unique clade independent of those found in mature chimneys and low-temperature mineral chamber samples. As a model ecosystem, the identification of pioneering consortia in deep-sea hydrothermal vents may help advance the understanding of how early microbial life forms gained a foothold in hydrothermal systems on early Earth and potentially on other planetary bodies.