The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes ...mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.
ADP- dependent glucokinase (ADPGK) is a glycolytic enzyme catalyzing the reaction of glucoseglucose 6-P by using ADP instead of ATP. ADPGK is remarkably conserved across various phyla from archaea to ...humans. Despite an important role priming glycolysis in conditions of metabolic stress in extremophile organisms, human ADPGK does not contribute to glycolysis. Recent work shows that ADPGK is essential for ROS generation during T-cell activation. Intriguingly, ADPGK protein levels are upregulated across a panel of cancer cell lines and primary tumors. Hereby we hypothesized that the increase of cellular ROS in response to mild (1 O2) hypoxia is dependent on ADPGK therefore contributing to the stabilization of hypoxia- inducible factor (HIF)-1, a central regulator of the transcriptional response of cancer cells to hypoxia.
In recent years, there has been a major expansion of dairy farming in New Zealand, largely as a result of land use change from forestry and sheep farming to dairy farming. Possible impacts of ...different land uses and land use change on ammonia oxidising bacteria (AOB) and archaea (AOA) and N sub(2)O emissions are not well understood. A field study was carried out to determine the effects on AOB and AOA abundance by three long-term different land uses, pine tree plantation (30+ years), sheep farming (30+ years) and dairy farming (12+ years), located in close proximity on the same soil type. A laboratory incubation study was carried out to determine the impact of dairy cow urine application (simulating the deposition of dairy cattle urine after the conversion of tree plantation and sheep farming to dairy farming) on AOB and AOA growth and N sub(2)O emissions. The results showed that AOB abundance was higher in the dairy and sheep farm soils (P < 0.05) than in the pine tree soil but that the AOA abundance was higher in the sheep farm soil than in the dairy and pine tree soils (P < 0.05). When dairy cow urine was applied in the incubation study, the AOB growth was initially faster in the dairy, followed by sheep and then followed by the pine tree soil, but the growth continued for an extended period in the pine tree soil with the amoA gene copy numbers eventually exceeding those in the sheep and dairy pasture soils. AOA grew following urine application in the sheep soil but did not change in the other soils. Total N sub(2)O emissions in the pine tree soil was more than twice those from the dairy and sheep farm soils. These results demonstrate the significant impact of land use and land use change on ammonia oxidiser communities and subsequent impacts on nitrogen transformations and N sub(2)O emissions. Further research is needed to verify these results in the field.
In recent years, identification of the microbial sources responsible for soil N sub(2)O production has substantially advanced with the development of isotope enrichment techniques, selective ...inhibitors, mathematical models and the discoveries of specific N-cycling functional genes. However, little information is available to effectively quantify the N sub(2)O produced from different microbial pathways (e.g. nitrification and denitrification). Here, a super(15)N-tracing incubation experiment was conducted under controlled laboratory conditions (50, 70 and 85% water-filled pore space (WFPS) at 25 and 35 degree C). Nitrification was the main contributor to N sub(2)O production. At 50, 70 and 85% WFPS, nitrification contributed 87, 80 and 53% of total N sub(2)O production, respectively, at 25 degree C, and 86, 74 and 33% at 35 degree C. The proportion of nitrified N as N sub(2)O (P sub(N2O)) increased with temperature and moisture, except for 85% WFPS, when P sub(N2O) was lower at 35 degree C than at 25 degree C. Ammonia-oxidizing archaea (AOA) were the dominant ammonia oxidizers, but both AOA and ammonia-oxidizing bacteria (AOB) were related to N sub(2)O emitted from nitrification. AOA and AOB abundance was significantly influenced by soil moisture, more so than temperature, and decreased with increasing moisture content. These findings can be used to develop better models for simulating N sub(2)O from nitrification to inform soil management practises for improving N use efficiency.
Marine ammonia-oxidizing archaea (AOA) are among the most abundant of marine microorganisms, spanning nearly the entire water column of diverse oceanic provinces. Historical patterns of abundance are ...preserved in sediments in the form of their distinctive glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids. The correlation between the composition of GDGTs in surface sediment and the overlying annual average sea surface temperature forms the basis for a paleotemperature proxy (TEX...) that is used to reconstruct surface ocean temperature as far back as the Middle Jurassic. However, mounting evidence suggests that factors other than temperature could also play an important role in determining GDGT distributions. We here use a study set of four marine AOA isolates to demonstrate that these closely related strains generate different TEX...-temperature relationships and that oxygen (O...) concentration is at least as important as temperature in controlling TEX... values in culture. All of the four strains characterized showed a unique membrane compositional response to temperature, with TEX...-inferred temperatures varying as much as 12 ...C from the incubation temperatures. In addition, both linear and nonlinear TEX...-temperature relationships were characteristic of individual strains. Increasing relative abundance of GDGT-2 and GDGT-3 with increasing O... limitation, at the expense of GDGT-1, led to significant elevations in TEX...-derived temperature. Although the adaptive significance of GDGT compositional changes in response to both temperature and O... is unclear, this observation necessitates a reassessment of archaeal lipid-based paleotemperature proxies, particularly in records that span low-oxygen events or underlie oxygen minimum zones. (ProQuest: ... denotes formulae/symbols omitted.)
Subsurface microbial life contributes significantly to biogeochemical cycling, yet it remains largely uncharacterized, especially its archaeal members. This 'microbial dark matter' has been explored ...by recent studies that were, however, mostly based on DNA sequence information only. Here, we use diverse techniques including ultrastuctural analyses to link genomics to biology for the SM1 Euryarchaeon lineage, an uncultivated group of subsurface archaea. Phylogenomic analyses reveal this lineage to belong to a widespread group of archaea that we propose to classify as a new euryarchaeal order ('Candidatus Altiarchaeales'). The representative, double-membraned species 'Candidatus Altiarchaeum hamiconexum' has an autotrophic metabolism that uses a not-yet-reported Factor420-free reductive acetyl-CoA pathway, confirmed by stable carbon isotopic measurements of archaeal lipids. Our results indicate that this lineage has evolved specific metabolic and structural features like nano-grappling hooks empowering this widely distributed archaeon to predominate anaerobic groundwater, where it may represent an important carbon dioxide sink.
N
-acetylcytidine (ac
C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA
. However, the distribution, ...dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac
C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac
C at single-nucleotide resolution. In human and yeast mRNAs, ac
C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac
C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac
C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac
C and its potential thermoadaptive role. Our studies quantitatively define the ac
C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease
.
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a ...provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms. In order to fully realize this potential, standards and guidelines on how to perform these descriptions are needed. Here we aimed to outline these standards and draw the roadmap for a new genome-based taxonomy that, at least initially, would be parallel but highly convergent to the one in existence for isolates. In particular, we recommend the use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for (i) identification and phylogenetic placement, (ii) bioinformatics-based functional and thus phenotypic predictions, as well as (iii) type material. We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the 'uncultivated majority', but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system.
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