Umeå Plant Science Centre

Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.

Abstract Understanding how plant-associated microbiomes interact with host genome variation to influence agronomic traits is essential for advancing microbiome⍰assisted crop improvement. In this study, we characterized the phyllosphere and rhizosphere microbiomes of 164 diverse Nicotiana tabacum accessions using 16S rRNA sequencing and integrated these data with host genomic variation and 22 agronomic traits. The two microbiomes exhibited distinct taxonomic structures, diversity patterns, and predicted metabolic functions. Microbiome genome⍰wide association studies identified extensive host genetic control over microbial abundance, including 49 shared genomic loci that explained nearly half of the heritable variation in both microbiomes. Microbiome⍰wide association studies revealed biologically meaningful associations between specific ASVs and agronomic traits. However, network analysis demonstrated that microbial sub⍰communities, rather than individual taxa, contributed substantially to phenotypic variation. Then, colocalization analysis further identified genetic variants jointly influencing microbial abundance and metabolite traits, highlighting potential host-microbe-trait causal links. Incorporating microbiome data into genomic selection models, we successfully improved prediction accuracy for several traits, especially plant architecture and flowering. Together, this work provides a comprehensive population⍰level framework linking host genetics, microbiome composition, and agronomic traits in tobacco, offering new insights for microbiome⍰informed breeding strategies.

Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5-7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.

Plant vascular systems exhibit a wide developmental spectrum, from rigid woody tissues to soft, fleshy storage tissues. We show that increasing polyamine thermospermine transport into wild‑type rootstocks, together with cytokinin, reprograms xylem identity from woody to fleshy in Arabidopsis. Our findings establish thermospermine as a mobile developmental signal and suggest a strategy for engineering plant vascular architecture.

SUMMARY Together with biosynthesis and transport, inactivation regulates the concentration of indole-3-acetic acid (IAA), a key auxinic compound with a myriad of functions in plant development. Main inactive IAA metabolites are categorised into oxidised forms and ester- or amide-linked conjugates. DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) and DAO2, 2-oxoglutarate and iron-dependent dioxygenases, contribute to IAA oxidative inactivation in collaboration with group II GRETCHEN HAGEN3 (GH3) IAA-amido synthetases, while a group of UDP-glycosyltransferases (UGTs) conjugate IAA to sugars. To study the IAA inactivation routes, we generated combinatorial mutants between all group II GH3 s ( gh3oct ) and DAO1 or DAO2 , as well as between the DAOs and main UGT s. In vivo [ 13 C 6 ]IAA feeding experiments traced the metabolic fate of the exogenously applied IAA, supporting the main IAA inactivation pathway, in which DAO acts downstream of GH3s. They also indicated that UGT-mediated IAA glycosylation is more important than previously assumed for modulating IAA levels and plant development. Our metabolic and transcriptomic data further revealed that gh3oct may still produce some GH3 activity, explaining previous reported phenotypic inconsistencies. Our data additionally suggest that other not yet identified metabolic activities might play a role in IAA overproducing plants, and that the premature downregulation of flowering time integrators like FLOWERING LOCUS C ( FLC ) likely underlies the early flowering of gh3oct and gh3oct dao1 plants.

ABSTRACTNitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L‐glutamine (L‐GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L‐GLN's role as a carbon or ammonium source or of potential L‐GLN‐induced pH changes due to ammonium release, indicating a specific function of L‐GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)‐mediated uptake and GLUTAMINE SYNTHETASE (GS)‐dependent assimilation as essential for L‐GLN‐induced root biomass. In contrast, the N‐sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L‐GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L‐GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L‐GLN conditions. L‐GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone‐dependent regulation. Together, these findings establish L‐GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.

Forest management has the potential to impact the net forest carbon (C) balance, and a better understanding of how tree species influence soil C provides a potential tool to promote higher C uptake and storage in forests. In this study, we utilized two common garden experiments located in northern and central Sweden to compare soil organic C stocks associated with six different boreal tree species ( Betula pendula , Larix sp. , Picea abies , Picea glauca , Pinus contorta and Pinus sylvestris ), approximately 30 years after planting. We measured both above- and below-ground C inputs and C outputs via decomposition and analyzed how these factors influenced soil C stocks. Our results showed that the vertical distribution of SOC differed between the species, and furthermore, many of the SOC input and output processes measured were species-dependent. Despite this, we found no differences in total belowground soil C stock between the species. The aboveground biomass C stocks, in contrast, were highly species-specific, with the rank order of species differing between the two sites. As such, our study indicates that tree species choice may serve as a tool to promote ecosystem C stocks, and in turn enhance the climate change mitigation potential of forests. • Boreal tree species effects on carbon stocks were evaluated. • Above ground biomass C stock was highly species dependent. • Belowground C stocks were not species dependent. • Belowground C stock varied more by site than by tree species.

<title>Abstract</title> Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource spanning the wood transcriptomes of six tree species - three dicots and three conifers - capturing 250 million years of evolutionary divergence. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a foundational resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.