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Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200Arabidopsis thalianagenotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.

Lignocellulose-bearing sediments are legacies of the previously unregulated wastewater discharge from the pulp and paper industry, causing large quantities of toxic organic waste on the Baltic Sea floor and on the bottom of rivers and lakes. Several km2 are covered with deposits of lignocellulosic residues, typically heavily contaminated with complex mixtures of organic and inorganic pollutants, posing a serious threat to human and ecological health. The high toxicity and the large volume of the polluted material are challenges for remediation endeavours. The lignocellulosic material is also a considerable bioresource with a high energy density, and due to its quantity, it could appeal to commercialization as feedstock for various marketable goods. This study sets out to explore the potential of using this polluted material as a resource for industrial production at the same time as it is detoxified. Information about modern production methods for lignocellulosic material that can be adapted to a polluted feedstock is reviewed. Biochemical methods such as composting, anaerobic digestion, as well as, thermochemical methods, for instance, HTC, HTL, pyrolysis, gasification and torrefaction have been assessed. Potential products from lignocellulose-bearing sediment material include biochar, liquid and gaseous biofuels, growing substrate. The use of a contaminated feedstock may make the process more expensive, but the suggested methods should be seen as an alternative to remediation methods that only involve costs. Several experiments were highlighted that support the conception that combined remediation and generation of marketable goods may be an appropriate way to address polluted lignocellulose-bearing sediments. Graphic abstract

In Arabidopsis thaliana, winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor FLOWERING LOCUS C (FLC). Natural Arabidopsis accessions show considerable variation in vernalization. However, which aspect of the FLC repression mechanism is most important for adaptation to different environments is unclear. By analysing FLC dynamics in natural variants and mutants throughout winter in three field sites, we find that autumnal FLC expression, rather than epigenetic silencing, is the major variable conferred by the distinct Arabidopsis FLChaplotypes. This variation influences flowering responses of Arabidopsis accessions resulting in an interplay between promotion and delay of flowering in different climates to balance survival and, through a post-vernalization effect, reproductive output. These data reveal how expression variation through non-coding cis variation at FLC has enabled Arabidopsis accessions to adapt to different climatic conditions and year-on-year fluctuations.

Plants monitor temperatures over long timescales to assess seasons and time developmental transitions. In Arabidopsis thaliana, winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor FLOWERING LOCUS C (FLC). Natural Arabidopsis accessions show considerable variation in vernalization, however which aspect of the FLC repression mechanism is most important for adaptation to different climates is not clear. By analyzing FLC silencing in natural variants throughout winter in three field sites, we find that FLC starting levels and early phases of silencing are the major variables underlying vernalization response, rather than establishment of epigenetic silencing. This results in an intricate interplay between promotion and delay of flowering to balance survival, and through a post-vernalization effect of FLC, reproductive effort via branch production. These data reveal how non-coding FLC variation aligns vernalization response to different climatic conditions and year-on-year fluctuations in natural temperature profiles.Impact StatementAlleles of the major floral repressor vary in their initial expression to underpin the ability of Arabidopsis to survive year-on-year climatic fluctuations.

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Plants integrate widely fluctuating temperatures to monitor seasonal progression. Here, we investigate the temperature signals in field conditions that result in vernalisation, the mechanism by which flowering is aligned with spring. We find that multiple, distinct aspects of the temperature profile contribute to vernalisation. In autumn, transient cold temperatures promote transcriptional shutdown of Arabidopsis FLOWERING LOCUS C (FLC), independently of factors conferring epigenetic memory. As winter continues, expression of VERNALIZATION INSENSITIVE3 (VIN3), a factor needed for epigenetic silencing, is upregulated by at least two independent thermosensory processes. One integrates long-term cold temperatures, while the other requires the absence of daily temperatures above 15 °C. The lack of spikes of high temperature, not just prolonged cold, is thus the major driver for vernalisation. Monitoring of peak daily temperature is an effective mechanism to judge seasonal progression, but is likely to have deleterious consequences for vernalisation as the climate becomes more variable., Plants use multiple cues to monitor seasonal temperatures. Here, the authors show that Arabidopsis requires not only prolonged cold, but the absence of temperature spikes above 15 °C to epigenetically silence FLC during winter.

Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes. Version of record online: 30 May 2017

Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 A. thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial OTU’s. Host genetics disproportionately influenced hubs within the microbial communities, with their impact then percolating through the community, as evidenced by a decline in the heritability of particular OTUs with their distance to the nearest hub. By simultaneously measuring host performance, we found that host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants grown in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins and the immune system. Using untargeted metabolomics, we corroborate the consistent association of variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host natural variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.

Some boreal wood fungi that are associated with forest fire or open dry habitats have an increased resistance to heat in comparison to species associated with a less specific distribution or species found in mesic forests. We hypothesize that extreme temperature-stress experienced during fires will favor species adapted to heat and, ultimately, the composition of species inhabiting logs in such habitats will change. Competitiveness after temperature stress was examined in three fire-associated species – Dichomitus squalens, Gloeophyllum sepiarium and Phlebiopsis gigantea – and three non fire-associated species – Ischnoderma benzoinum, Phellinus pini and Fomitopsis pinicola. There was a difference between the fire-associated species and the non fire-associated species with respect to competitive strength after heat stress. All fire-associated species had an advantage after heat treatment, colonizing a larger volume of wood than any non-fire-associated competitor. Our findings suggest that increased heat tolerance of mycelia can exert a competitive balance shift after forest fire. It shows that a system governed by forest fire will be dominance controlled under certain conditions. Furthermore, from a management perspective, during a prescribed burning, certain species already present in the ecosystem will be favored if the fire is not allowed to totally consume the substrates.

Forest fires have been the major stand-replacing/modifying disturbance in boreal forests. To adapt to fire disturbance, different strategies have evolved. This study focuses on wood fungi, and a specific adaptation to forest fire: increased heat resistance in their mycelia. Fifteen species of wood fungi were selected and a priori sorted in two groups according to their prevalence in fire-affected environments. The fungi were cultivated on fresh wood and exposed to 100, 140, 180, 220 °C for 5, 10, 15, 20 and 25 min. under laboratory conditions. A clear difference was found among the two groups. Species prevalent in fire-affected habitats had a much higher survival rate over all combinations of time and temperature compared to species associated with other environments. Thus, the results indicate that fire adaptation in terms of increased heat resistance in mycelia occurs in some species of wood fungi. Such adaptation will influence the ecology and population dynamics of wood fungi, as well as having implications for best practices during restoration fires.

Summary Many organisms need to respond to complex, noisy environmental signals for developmental decision making. Here, we dissect how Arabidopsis plants integrate widely fluctuating field temperatures over month-long timescales to progressively upregulate VERNALIZATION INSENSITIVE3 (VIN3) and silence FLOWERING LOCUS C (FLC), aligning flowering with spring. We develop a mathematical model for vernalization that operates on multiple timescales—long term (month), short term (day), and current (hour)—and is constrained by experimental data. Our analysis demonstrates that temperature sensing is not localized to specific nodes within the FLC network. Instead, temperature sensing is broadly distributed, with each thermosensory process responding to specific features of the plants’ history of exposure to warm and cold. The model accurately predicts FLC silencing in new field data, allowing us to forecast FLC expression in changing climates. We suggest that distributed thermosensing may be a general property of thermoresponsive regulatory networks in complex natural environments., Graphical Abstract, Highlights • Multiple thermosensory inputs with distinct timescales regulate vernalization • One input identified as a short-term memory of warm temperature spikes • Predictive mathematical model of vernalization in controlled and field conditions • Model predicts future responses to increasingly warm and fluctuating climates, We investigate temperature sensing in the Arabidopsis thaliana vernalization pathway, responsible for accelerated flowering after winter. We uncover multiple thermosensory inputs, each sensing a distinct feature of the temperature signal with a distinct timescale. Such sensing allows the plant to recognize winter cold in a complex and variable environment. We develop a predictive mathematical model for vernalization and find that two predicted features of future climates, higher mean temperatures and larger temperature fluctuations, will both affect the rate of vernalization.

Summary Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes., Graphical Abstract, Highlights • The genomes of 1,135 naturally inbred lines of Arabidopsis thaliana are presented • Relict populations that continue to inhabit ancestral habitats were discovered • The last glacial maximum was important in structuring the distribution of relicts • This collection will connect genotypes and phenotypes on a species-wide level, Genomic sequencing analysis of over 1,000 natural inbred lines of Arabidopsis thaliana reveals its global population structure, migration patterns, and evolutionary history and provides a rich genetic resource for studying phenotypic variation and adaptation.

The potential role of tributaries as seed sources to an impoundment in northern Sweden : a field experiment with seed mimics

The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection., Nature Genetics, 48 (9), ISSN:1061-4036, ISSN:1546-1718

The requirement for vernalization, a need for prolonged cold to trigger flowering, aligns reproductive development with favorable spring conditions. In Arabidopsis thaliana vernalization depends on the cold-induced epigenetic silencing of the floral repressor locus FLC. Extensive natural variation in vernalization response is associated with A. thaliana accessions collected from different geographical regions. Here, we analyse natural variation for vernalization temperature requirement in accessions, including those from the northern limit of the A. thaliana range. Vernalization required temperatures above 0°C and was still relatively effective at 14°C in all the accessions. The different accessions had characteristic vernalization temperature profiles. One Northern Swedish accession showed maximum vernalization at 8°C, both at the level of flowering time and FLC chromatin silencing. Historical temperature records predicted all accessions would vernalize in autumn in N. Sweden, a prediction we validated in field transplantation experiments. The vernalization response of the different accessions was monitored over three intervals in the field and found to match that when the average field temperature was given as a constant condition. The vernalization temperature range of 0–14°C meant all accessions fully vernalized before snowfall in N. Sweden. These findings have important implications for understanding the molecular basis of adaptation and for predicting the consequences of climate change on flowering time. DOI: http://dx.doi.org/10.7554/eLife.06620.001, eLife digest Plants are not able to move around and so they need to be able to adapt their growth and development to seasonal changes in their environment. For example, prolonged exposure to cold temperatures during winter can prime some plants to flower when temperatures increase in the spring—a process called vernalization. In these plants, extended periods of cold temperatures lead to lower activity of a gene called FLC, which normally inhibits flowering. In the plant Arabidopsis thaliana, vernalization requires several months of exposure to temperatures between 0–6°C. Recently, A. thaliana plants from southern Europe were found to vary in the temperature requirements for vernalization, responding to temperatures higher than 6°C. This suggested that plants from northern Europe might vernalize preferentially at lower temperatures. Here, Duncan et al. compared vernalization in a collection of A. thaliana plants (or ‘accessions’) sampled from different regions of Sweden and the UK. The experiments show that all the accessions needed temperatures above 0°C to vernalize and that vernalization still worked relatively well at temperatures as high as 14°C. The optimal temperature range for vernalization differed between the accessions, but plants from more northern areas did not necessarily vernalize at lower temperatures. For example, for one particular accession from northern Sweden, the temperature that is optimum for vernalization was 8°C, a notably higher temperature than expected. Historical local climate records suggested that this accession would vernalize before the first snowfall of the winter in North Sweden. Duncan et al. confirmed this proposal with field experiments. Plants were grown in natural field sites in September and then moved into a greenhouse. The experiments show that the plants complete vernalization by November, which strongly suggests that FLC is silenced during autumn rather than during winter, as previously thought. This changed temperature response is due, in part, to a small number of tiny genetic differences in regions of the FLC gene that do not code for protein. These findings have important implications for future studies of vernalization and flowering time, and for understanding how plants will adapt to on going and future climate change. The next step is to understand what causes these changed temperature responses at a molecular level, which should enable selective breeding for flowering and harvest date in a range of crops. DOI: http://dx.doi.org/10.7554/eLife.06620.002

Nanoparticles coated with single stranded DNA have been shown to efficiently hybridize to targets of complementary DNA. This property might be used to implement programmable (or algorithmic) self-assembly to build nanoparticle structures. However, we argue that a DNA coated nanoparticle by itself cannot be used as a programmable self-assembly building block since it does not have directed bonds. A general scheme for assembling and purifying nanoparticle eight-mers with eight geometrically well-directed bonds is presented together with some preliminary experimental work.

Forty populations of Potentilla argentea L. (sensu lato) from southern Sweden were investigated to determine the pattern of genetic variation. Since the diploid form of Potentilla argentea has been reported to produce seeds apomictically, the intention was, in particular, to investigate whether the variation pattern indicated a purely asexual mode of reproduction in nature. The investigated populations were chosen to represent the diploid form of Potentilla argentea. Nevertheless, sympatry between diploid and hexaploid forms was found in 14 out of 40 populations sampled. Two samples contained only hexaploid plants, and 24 only diploid plants. The ploidy level was determined by chromosome counting or by morphological analysis of greenhouse grown plants. The mean number of leaves was higher and the size of the largest leaf was greater in hexaploid than in diploid offspring plants grown in the greenhouse. Among the diploids, significant variation was found for both traits between populations as well as within populations. Genetic variation was also detected with the RAPD method. To work, the method required a number of modifications of the standard protocol for DNA-purification, but it then gave clear and reproducible results. The RAPD variation was evenly distributed within and among the investigated diploid populations. The level of variation was comparable to the level found in selfing plants, but the pattern of variation was more as expected from outbreeding plants. The conclusion is drawn that Potentilla argentea may well have a variable breeding system. In nature, it does not, however, behave in a predominantly asexual manner.

Thirty-six crosses between plants of the putative facultative apomictic diploid Pofentilkz argentea L. (s.l.) from southern Sweden led to the production of hybrid offspring, as determined by isozyme analysis. Forty-three crosses with diploid P. argentea as mother plants and hexaploid P. argenrea L. (s. l.) or hexaploid P. collina Wib. as pollen donors resulted in normal-looking seeds but with no, or only low, rates of germination. Among the few offspring obtained, two were found to be tetraploid as determined by Row cytometry. Offspring plants with non-hybrid genotypes were occasionally obtained in the crosses, which in all cases could be explained as being due to selfing resulting from incomplete emasculations or unwanted insect pollinations. We conclude that, on the basis of currently available information, diploid Potentilla argentea is not a facultative apomict.

Hexaploid Potentilla argentea L. (s.l.) plants from twelve populations in southern Sweden were investigated with RAPD to determine the pattern of genetic variability. The ploidy level of the plants was ascertained by flow cytometry. Thirteen different RAPD band patterns (genotypes) were found among 64 plants investigated. Nine of the populations had unique band patterns, two populations shared the same, and in one population three different patterns were found among three plants. Also a small isozyme investigation detected genetic variability, again distributed primarily between populations. Analyses with RAPD of offspring derived from bagged flower-stalks and from artificial crosses between different hexaploid genotypes, showed that seeds are normally produced by apomixis. However, one hybrid offspring with a nonoploid (9x) ploidy level was found, proving that pollen produced by hexaploid P. argentea is capable of fertilization, and that sexually derived seeds can develop and mature on hexaploid plants. The broad genetic variability found in the RAPD and isozyme investigations indicates that gamete production after reduction division may also occur on the female side, though at a low frequency. Judging from its isozyme patterns, hexaploid P. argentea is an allopolyploid having diploid P. argentea as one of its parents.

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual—a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.