Mid Sweden University

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: [Figure not available: see fulltext.] 

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 Arabidopsis thaliana genotypes 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. 

Fiberbanksfrom the pulp and paper industry are typically contaminated with a wide range ofchlorinated aromatic and aliphatic toxins such as HCB and other chlorinated benzenes, PCB,HCH, DDT, PCDD, PCDF and Chlorophenols. This poses a formidable challenge for theanalyst to develop appropriate analytical methodology for the monitoring of the progress ofremediation.In preparation to this undertaking, an examination of a practical analytical method using oneextraction method, one clean-up and one analysis method for the aforementioned targetcompounds found in the fibrous sediment. This method was performed using acceleratedsolvent extraction (ASE), a modified silica gel column and GC-FID/ECD. 

Additionally,an assessment of the levels of organic pollutants was conducted,with the purposeofmeasuringthe potential alteration in contaminantswhenfreeze-drying, air-drying andautoclavingpretreatments are applied to the sediment samples, prior to be used as a media forbiological remediation.The results showed that the ASE is a very fast and reliable method of extraction, with yieldscomparableorhigher than the reference Soxhlet extraction method. Theactivatedsilica gelcolumn demonstrated adequate purification of the sediment extract for analysisusingthe twodetectors, FID and ECD, whichwere able to identify the target analytes fromonlyone purifiedextract. The method employed in this study has the potentialto reduceboth processing timeand materialusedfor analytical sample preparation. Lastly, some modifications inconcentrations anddistribution of target analyteswere revealedin thesediments pre-treated byautoclave and air-driedwhencompared withthefreeze-dried sediments, which can helpunderstanding the development of the biological remediation process.

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. 

Fiberbanks and fiber-rich sediments are legacies of the previously unregulated wastewater discharge from the pulp and paper industry that have accumulated 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 fibrous residues that are, typically, heavily polluted with a number of organic and inorganic substances, posing a serious threat to human and ecological health. High toxicity and the large volume of the polluted material are challenges for remediation endeavors. However, since the fibrous material is a bioresource with a high energy density, the sheer quantity of it could appeal to commercialization as feedstock for various marketable products. This study sets out to explore the potential of using this polluted material as a resource for industrial production, by reviewing and synthesizing data about modern production methods or reuse alternatives for lignocellulose material that can be adapted to a polluted feedstock. Biochemical methods such as composting, anaerobic digestion, as well as, thermochemical methods, for instance, HTC, HTL, pyrolysis, gasification etc. have been assessed. Potential end products from fiber bank material include biochar, liquid and gaseous biofuels, growth media, and fatty acids and proteins produced by white-rot fungi.

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. 

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. 

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.

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-offunction 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.