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Key Points Sirtuins are a critical component of evolutionarily conserved longevity pathways. Sirtuins are nicotinamide adenine dinucleotide (NAD + )-dependent lysine deacylases that promote longevity and healthy ageing. Sirtuin-activating compounds (STACs) bind to and allosterically modulate the affinity of SIRT1 for NAD + and protein substrates, resulting in increased activity. Increasing NAD + levels through various strategies can enhance the activity of all sirtuins and improve metabolic function and increase longevity. Sirtuin overexpression and treatment with naturally occurring and synthetic STACs improves metabolic function and increases longevity in mice. More than 50 clinical trials are currently evaluating the safety and physiological activity of naturally occurring and synthetic STACs for treating human disease. Sirtuins are NAD + -dependent protein deacylases that can reverse various aspects of ageing in model organisms. Trials in non-human primates and humans indicate that sirtuin-activating compounds (STACs) and NAD + precursors are safe and effective in treating inflammatory and metabolic disorders, thereby holding great potential to treat various diseases and to extend lifespan in humans. The sirtuins (SIRT1–7) are a family of nicotinamide adenine dinucleotide (NAD + )-dependent deacylases with remarkable abilities to prevent diseases and even reverse aspects of ageing. Mice engineered to express additional copies of SIRT1 or SIRT6, or treated with sirtuin-activating compounds (STACs) such as resveratrol and SRT2104 or with NAD + precursors, have improved organ function, physical endurance, disease resistance and longevity. Trials in non-human primates and in humans have indicated that STACs may be safe and effective in treating inflammatory and metabolic disorders, among others. These advances have demonstrated that it is possible to rationally design molecules that can alleviate multiple diseases and possibly extend lifespan in humans.

All nutrients that plants absorb have to pass a region of intense interactions between roots, microorganisms and animals, termed the rhizosphere. Plants allocate a great portion of their photosynthetically fixed carbon to root-infecting symbionts, such as mycorrhizal fungi; another part is released as exudates fuelling mainly free-living rhizobacteria. Rhizobacteria are strongly top-down regulated by microfaunal grazers, particularly protozoa. Consequently, beneficial effects of protozoa on plant growth have been assigned to nutrients released from consumed bacterial biomass, that is, the 'microbial loop'. In recent years however, the recognition of bacterial communication networks, the common exchange of microbial signals with roots and the fact that these signals are used to enhance the efflux of carbon from roots have revolutionized our view of rhizosphere processes. Most importantly, effects of rhizobacteria on root architecture seem to be driven in large by protozoan grazers. Protozoan effects on plant root systems stand in sharp contrast to effects of mycorrhizal fungi. Because the regulation of root architecture is a key determinant of nutrient- and water-use efficiency in plants, protozoa provide a model system that may considerably advance our understanding of the mechanisms underlying plant growth and community composition.

Ageing is a degenerative process that leads to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise that disrupts gene expression patterns, leading to decreases in tissue function and regenerative capacity 1 – 3 . Changes to DNA methylation patterns over time form the basis of ageing clocks 4 , but whether older individuals retain the information needed to restore these patterns—and, if so, whether this could improve tissue function—is not known. Over time, the central nervous system (CNS) loses function and regenerative capacity 5 – 7 . Using the eye as a model CNS tissue, here we show that ectopic expression of Oct4 (also known as Pou5f1 ), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice. The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2. These data indicate that mammalian tissues retain a record of youthful epigenetic information—encoded in part by DNA methylation—that can be accessed to improve tissue function and promote regeneration in vivo. Expression of three Yamanaka transcription factors in mouse retinal ganglion cells restores youthful DNA methylation patterns, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice, suggesting that mammalian tissues retain a record of youthful epigenetic information that can be accessed to improve tissue function.

The identification of genes and interventions that slow or reverse aging is hampered by the lack of non-invasive metrics that can predict the life expectancy of pre-clinical models. Frailty Indices (FIs) in mice are composite measures of health that are cost-effective and non-invasive, but whether they can accurately predict health and lifespan is not known. Here, mouse FIs are scored longitudinally until death and machine learning is employed to develop two clocks. A random forest regression is trained on FI components for chronological age to generate the FRIGHT ( Fr ailty I nferred G eriatric H ealth T imeline) clock, a strong predictor of chronological age. A second model is trained on remaining lifespan to generate the AFRAID ( A nalysis of Frai lty and D eath) clock, which accurately predicts life expectancy and the efficacy of a lifespan-extending intervention up to a year in advance. Adoption of these clocks should accelerate the identification of longevity genes and aging interventions. The discovery of interventions that slow aging could be accelerated by employing non-invasive biometrics that predict biological age or life expectancy. Here the authors use longitudinal frailty data from naturally aging mice to develop two such tools, that are responsive to interventions.

Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions. Sustainability in agriculture can be improved harnessing biological N 2 fixation in legumes. Here, the authors combine different crops with peanut plants finding that maize and oilseed rape are the most successful combinations which have potential to enhance rhizosphere microbiota N 2 fixation.

The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

Background Stress-induced hormones are essential for plants to modulate their microbiota and dynamically adjust to the environment. Despite the emphasis of the role of the phytohormone ethylene in the plant physiological response to heterospecific neighbour detection, less is known about how this activated signal mediates focal plant rhizosphere microbiota to enhance plant fitness. Here, using 3 years of peanut ( Arachis hypogaea L.), a legume, and cyanide-containing cassava ( Manihot esculenta Crantz) intercropping and peanut monocropping field, pot and hydroponic experiments in addition to exogenous ethylene application and soil incubation experiments, we found that ethylene, a cyanide-derived signal, is associated with the chemical identification of neighbouring cassava and the microbial re-assemblage in the peanut rhizosphere. Results Ethylene production in peanut roots can be triggered by cyanide production of neighbouring cassava plants. This gaseous signal alters the microbial composition and re-assembles the microbial co-occurrence network of peanut by shifting the abundance of an actinobacterial species, Catenulispora sp., which becomes a keystone in the intercropped peanut rhizosphere. The re-assembled rhizosphere microbiota provide more available nutrients to peanut roots and support seed production. Conclusions Our findings suggest that root ethylene acts as a signal with a dual role. It plays a role in perceiving biochemical cues from interspecific neighbours, and also has a regulatory function in mediating the rhizosphere microbial assembly, thereby enhancing focal plant fitness by improving seed production. This discovery provides a promising direction to develop novel intercropping strategies for targeted manipulations of the rhizosphere microbiome through phytohormone signals. 7bXEfEB7s8fN_xHngDstWf Video abstract.

DNA repair is essential for life, yet its efficiency declines with age for reasons that are unclear. Numerous proteins possess Nudix homology domains (NHDs) that have no known function. We show that NHDs are NAD⁺ (oxidized form of nicotinamide adenine dinucleotide) binding domains that regulate protein-protein interactions. The binding of NAD⁺ to the NHD domain of DBC1 (deleted in breast cancer 1) prevents it from inhibiting PARP1 [poly(adenosine diphosphate–ribose) polymerase], a critical DNA repair protein. As mice age and NAD⁺ concentrations decline, DBC1 is increasingly bound to PARP1, causing DNA damage to accumulate, a process rapidly reversed by restoring the abundance of NAD⁺. Thus, NAD⁺ directly regulates protein-protein interactions, the modulation of which may protect against cancer, radiation, and aging.

This study reveals the diversity and distribution of two major ubiquitous groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes (plasmodial slime-moulds) that are rarely, if ever, recovered in environmental sampling studies. We analyzed 150 grassland soil samples from three Biodiversity Exploratories study regions in Germany. We developed specific primers targeting the V2 variable region in the first part of the small subunit of the ribosomal RNA gene for high-throughput pyrotag sequencing. From ca. 1 million reads, applying very stringent filtering and clustering parameters to avoid overestimation of the diversity, we obtained 273 acanthamoebal and 338 myxomycete operational taxonomic units (OTUs, 96% similarity threshold). This number is consistent with the genetic diversity known in the two investigated lineages, but unequalled to date by any environmental sampling study. Only very few OTUs were identical to already known sequences. Strikingly different OTUs assemblages were found between the three German regions (PerMANOVA p.value = 0.001) and even between sites of the same region (multiple-site Simpson-based similarity indices <0.4), showing steep biogeographical gradients.

Ice-rich Pleistocene-age permafrost is particularly vulnerable to rapid thaw, which may quickly expose a large pool of sedimentary organic matter (OM) to microbial degradation and lead to emissions of climate-sensitive greenhouse gases. Protective physico-chemical mechanisms may, however, restrict microbial accessibility and reduce OM decomposition; mechanisms that may be influenced by changing environmental conditions during sediment deposition. Here we study different OM fractions in Siberian permafrost deposited during colder and warmer periods of the past 55,000 years. Among known stabilization mechanisms, the occlusion of OM in aggregates is of minor importance, while 33-74% of the organic carbon is associated with small, <6.3 µm mineral particles. Preservation of carbon in mineral-associated OM is enhanced by reactive iron minerals particularly during cold and dry climate, reflected by low microbial CO 2 production in incubation experiments. Warmer and wetter conditions reduce OM stabilization, shown by more decomposed mineral-associated OM and up to 30% higher CO 2 production. This shows that considering the stability and bioavailability of Pleistocene-age permafrost carbon is important for predicting future climate-carbon feedback. In ice-rich Siberian permafrost sediments deposited during the Pleistocene, 33-74% of the organic carbon is mineral-bound favoured by the presence of reactive iron, which can reduce microbial CO 2 production after thawing