Browsing by Subject "PLANT"

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  • Randall, Ricardo S.; Miyashima, Shunsuke; Blomster, Tiina; Zhang, Jing; Elo, Annakaisa; Karlberg, Anna; Immanen, Juha; Nieminen, Kaisa; Lee, Ji-Young; Kakimoto, Tatsuo; Blajecka, Karolina; Melnyk, Charles W.; Alcasabas, Annette; Forzani, Celine; Matsumoto-Kitano, Miho; Mähönen, Ari Pekka; Bhalerao, Rishikesh; Dewitte, Walter; Helariutta, Yrjö; Murray, James A. H. (2015)
    Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.
  • Nováková, Eliška; Zablatzká, Lenka; Brus, Jan; Nesrstová, Viktorie; Hanáček, Pavel; Kalendar, Ruslan; Cvrčková, Fatima; Majeský, Ľuboš; Smýkal, Petr (2019)
    Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
  • Kale, Liga; Nakurte, Ilva; Jalakas, Pirko; Kunga-Jegere, Laura; Brosche, Mikael; Rostoks, Nils (2019)
    Arabidopsis thaliana cyclic nucleotide-gated ion channel gene 4 (AtCNGC4) loss-of-function mutant dnd2 exhibits elevated accumulation of salicylic acid (SA), dwarfed morphology, reduced hypersensitive response (HR), altered disease resistance and spontaneous lesions on plant leaves. An orthologous barley mutant, nec1, has been reported to over-accumulate indole-3-acetic acid (IAA) and to exhibit changes in stomatal regulation in response to exogenous auxin. Here we show that the Arabidopsis dnd2 over-accumulates both IAA and abscisic acid (ABA) and displays related phenotypic and physiological changes, such as, reduced stomatal size, higher stomatal density and stomatal index. dnd2 showed increased salt tolerance in root growth assay and significantly reduced stomatal conductance, while maintaining near wt reaction in stomatal conductance upon external application of ABA, and probably consequently increased drought stress tolerance. Introduction of both sid2-1 and fmo1 into dnd2 background resulting in removal of SA did not alter stomatal conductance. Hence, the closed stomata of dnd2 is probably a result of increased ABA levels and not increased SA levels. The triple dnd2sid2abi1-1 mutant exhibited intermediate stomatal conductance compared to dnd2 and abil-1 (ABA insensitive, open stomata), while the response to external ABA was as in abi1-1 suggesting that reduced stomatal conductance in dnd2 is not due to impaired ABA signaling. In conclusion, Arabidopsis dnd2 mutant exhibited ABA overaccumulation and stomatal phenotypes, which may contribute to the observed improvement in drought stress resistance. Thus, Arabidopsis dnd2 mutant may serve as a model for studying crosstalk between biotic and abiotic stress and hormonal response in plants.
  • Dong, Tingfa; Duan, Baoli; Korpelainen, Helena; Niinemets, Ulo; Li, Chunyang (2019)
    Following asymmetric pruning of leaves and/or roots, the functional balance of distribution of carbon, but not of nitrogen, in Cunninghamia lanceolata is more readily achieved for the roots and leaves on the same side of the pruning compared with those on the opposite side. Abstract The functional balance between leaves and roots is believed to be mediated by the specific location of shoots and roots, i.e. differences in transport distances and degrees of organ connectivity. However, it remains unknown whether the adaptive responses of trees to biomass removal depend on the relative orientation of leaf and root pruning. Here, we applied five pruning treatments to saplings of Cunninghamia lanceolata (Chinese fir) under field and glasshouse conditions, namely no pruning (control), half of lateral branches pruned, half of lateral roots pruned, half of the branches and roots pruned on the same side of the plant, and half of the branches and roots pruned on opposite sides of the plant. The effects of pruning on the growth, carbon storage and allocation, and physiology of leaves and fine roots on the same and opposite sides of the plant were investigated. Compared with the effect of root-pruning on leaves, fine roots were more limited by carbon availability and their physiological activity was more strongly reduced by shoot pruning, especially when branches on the same side of the plant were removed. Pruning of branches and roots on the opposite side of the plant resulted in the lowest carbon assimilation rates and growth among all treatments. The results of a stable-isotope labeling indicated that less C was distributed to fine roots from the leaves on the opposite side of the plant compared to those on the same side, but N allocation from roots to leaves depended less on the relative root and leaf orientation. The results collectively indicate that the functional responses of C. lanceolata to pruning are not only determined by the source-sink balance model but are also related to interactions between leaves and fine roots. We argue that the connectivity among lateral branches and roots depends on their relative orientation, which is therefore critical for the functional balance between leaves and fine roots.
  • Aalto, Juha; Scherrer, Daniel; Lenoir, Jonathan; Guisan, Antoine; Luoto, Miska (2018)
    Soil temperature (ST) has a key role in Arctic ecosystem functioning and global environmental change. However, soil thermal conditions do not necessarily follow synoptic temperature variations. This is because local biogeophysical processes can lead to a pronounced soil-atmosphere thermal offset (Delta T) while altering the coupling (beta Tau) between ST and ambient air temperature (AAT). Here, we aim to uncover the spatiotemporal variation in these parameters and identify their main environmental drivers. By deploying a unique network of 322 temperature loggers and surveying biogeophysical processes across an Arctic landscape, we found that the spatial variation in Delta T during the AAT 0 period, Delta T was controlled by soil characteristics, vegetation and solar radiation (Delta T = -0.6 degrees C +/- 1.0 degrees C). Importantly, Delta T was not constant throughout the seasons reflecting the influence of beta Tau on the rate of local soil warming being stronger after (mean beta Tau = 0.8 +/- 0.1) than before (beta Tau = 0.2 +/- 0.2) snowmelt. Our results highlight the need for continuous microclimatic and local environmental monitoring, and suggest a potential for large buffering and non-uniform warming of snow-dominated Arctic ecosystems under projected temperature increase.
  • Dawson, Samantha K.; Berglund, Håkan; Ovaskainen, Otso; Snäll, Tord; Jonsson, Bengt G.; Jönsson, Mari (2020)
    Setting aside small remnant patches of high biodiversity forest within managed forest landscapes is often used as conservation measure to provide a refuge and future source population of forest biodiversity, including wood-inhabiting fungal communities. Yet little is known about the long-term fungal community assembly, how these small, isolated patches change through time and how forest management in the surrounding landscape impacts traits and community functionality housed within. We applied a joint species distribution model to compare how fungal traits and communities changed over two survey periods undertaken similar to 20 years apart in boreal forest set-aside and natural patches. Natural patches in naturally fragmented landscapes were considered reference forests for small, remnant, near-natural forest patches in intensively managed forest landscapes. We found the majority of fungal traits converged over time between set-aside and natural patches, without changes in overall species richness. Red-listed species occurrence was initially lower in set-aside patches, but reached a comparable level of natural patches over time as a result of opposing changes in both patch types. Functional trait changes were larger in set-aside patches, but convergence was also related to opposing changes in natural patches. This is the first study to directly measure and test wood fungal community trait-environment relationships over time in small, high-conservation value forest patches. The long-term functional trait and red-listed species values of set-asides, coupled with their capacity for old-growth recovery, make them valuable focal areas for conservation.
  • Sivaranjani, Murugesan; Leskinen, Katarzyna; Aravindraja, Chairmandurai; Saavalainen, Päivi; Pandian, Shunmugiah Karutha; Skurnik, Mikael; Ravi, Arumugam Veera (2019)
    Background: Alpha-mangostin (alpha-MG) is a natural xanthone reported to exhibit rapid bactericidal activity against Gram-positive bacteria, and may therefore have potential clinical application in healthcare sectors. This study sought to identify the impact of alpha-MG on Staphylococcus epidermidis RP62A through integrated advanced omic technologies. Methods: S. epidermidis was challenged with sub-MIC (0.875 mu g/ml) of alpha-MG at various time points and the differential expression pattern of genes/proteins were analyzed in the absence and presence of alpha-MG using RNA sequencing and LC-MS/MS experiments. Bioinformatic tools were used to categorize the biological processes, molecular functions and KEGG pathways of differentially expressed genes/proteins. qRT-PCR was employed to validate the results obtained from these analyses. Results: Transcriptomic and proteomic profiling of alpha-MG treated cells indicated that genes/proteins affected by alpha-MG treatment were associated with diverse cellular functions. The greatest reduction in expression was observed in transcription of genes conferring cytoplasmic membrane integrity (yidC2, secA and mscL), cell division (ftsY and divlB), teichoic acid biosynthesis (tagG and dltA), fatty-acid biosynthesis (accB, accC, fabD, fabH, fabl, and fabZ), biofilm formation (icaA) and DNA replication and repair machinery (polA, polC, dnaE, and uvrA). Those with increased expression were involved in oxidative (katA and sodA) and cellular stress response (clpB, clpC, groEL, and asp23). The qRT-PCR analysis substantiated the results obtained from transcriptomic and proteomic profiling studies. Conclusion: Combining transcriptomic and proteomic methods provided comprehensive information about the antibacterial mode of action of alpha-MG. The obtained results suggest that alpha-MG targets S. epidermidis through multifarious mechanisms, and especially prompts that loss of cytoplasmic membrane integrity leads to rapid onset of bactericidal activity.
  • Trebichalsky, Andrej; Kalendar, Ruslan; Schulman, Alan; Stratula, Olga; Galova, Zdenka; Balazova, Zelmira; Chnapek, Milan (2013)
  • Zweifel, Roman; Etzold, Sophia; Sterck, Frank; Gessler, Arthur; Anfodillo, Tommaso; Mencuccini, Maurizio; von Arx, Georg; Lazzarin, Martina; Haeni, Matthias; Feichtinger, Linda; Meusburger, Katrin; Knuesel, Simon; Walthert, Lorenz; Salmon, Yann; Bose, Arun K.; Schoenbeck, Leonie; Hug, Christian; De Girardi, Nicolas; Giuggiola, Arnaud; Schaub, Marcus; Rigling, Andreas (2020)
    Tree responses to altered water availability range from immediate (e.g. stomatal regulation) to delayed (e.g. crown size adjustment). The interplay of the different response times and processes, and their effects on long-term whole-tree performance, however, is hardly understood. Here we investigated legacy effects on structures and functions of mature Scots pine in a dry inner-Alpine Swiss valley after stopping an 11-yr lasting irrigation treatment. Measured ecophysiological time series were analysed and interpreted with a system-analytic tree model. We found that the irrigation stop led to a cascade of downregulations of physiological and morphological processes with different response times. Biophysical processes responded within days, whereas needle and shoot lengths, crown transparency, and radial stem growth reached control levels after up to 4 yr only. Modelling suggested that organ and carbon reserve turnover rates play a key role for a tree's responsiveness to environmental changes. Needle turnover rate was found to be most important to accurately model stem growth dynamics. We conclude that leaf area and its adjustment time to new conditions is the main determinant for radial stem growth of pine trees as the transpiring area needs to be supported by a proportional amount of sapwood, despite the growth-inhibiting environmental conditions.
  • Maria del Mar Delgadoa,1,2, Tomas Roslinb,2, Gleb Tikhonovc, Evgeniy Meyked, Coong Loc, Eliezer Gurariee, Marina Abadonovaf, Ozodbek Abduraimovg, Olga Adrianovah, Tatiana Akimovai, Muzhigit Akkievj, Aleksandr Ananink,l, Elena Andreevam, Natalia Andriychukn, Maxim Antipino, Konstantin Arzamascevp, Svetlana Babinaq, Miroslav Babushkinr, Oleg Bakins, Anna Barabancovat, Inna Basilskajau, Nina Belovav, Natalia Belyaevaw, Tatjana Bespalovax, Evgeniya Bisikalovay, Anatoly Bobretsovz, Vladimir Bobrovaa, Vadim Bobrovskyibb, Elena Bochkarevacc,dd, Gennady Bogdanovee, Vladimir Bolshakovff, Svetlana Bondarchukgg, Evgeniya Bukharovak,3, Alena Butuninax, Yuri Buyvolovhh, Anna Buyvolovaii, Yuri Bykovjj, Elena Chakhirevas, Olga Chashchinakk, Nadezhda Cherenkovall, Sergej Chistjakovmm, Svetlana Chuhontsevai, Evgeniy A. Davydovcc,nn, Viktor Demchenkooo, Elena Diadichevaoo, Aleksandr Dobrolyubovpp, Ludmila Dostoyevskayaqq, Svetlana Drovninall, Zoya Drozdovajj, Akynaly Dubanaevrr, Yuriy Dubrovsky...; Kurhinen, Juri (2020)
    For species to stay temporally tuned to their environment, they use cues such as the accumulation of degree-days. The relationships between the timing of a phenological event in a population and its environmental cue can be described by a population-level reaction norm. Variation in reaction norms along environmental gradients may either intensify the envi- ronmental effects on timing (cogradient variation) or attenu- ate the effects (countergradient variation). To resolve spatial and seasonal variation in species’ response, we use a unique dataset of 91 taxa and 178 phenological events observed across a network of 472 monitoring sites, spread across the nations of the former Soviet Union. We show that compared to local rates of advancement of phenological events with the advancement of temperature-related cues (i.e., variation within site over years), spatial variation in reaction norms
  • Hagner, Marleena; Mikola, Juha; Saloniemi, Irma; Saikkonen, Kari; Helander, Marjo (2019)
  • Bergstrom, L. Gunnar W.; Bergquist, Sara; Stenhagen, Gunnar; Gahmberg, Carl G.; Maia, Artur Campos D.; Nordenstam, Bertil (2018)
    Beauty bush' and twin flower' are common names attributed to two well-recognizable species belonging to the genus Linnaea (16 spp.) - L. amabilis and L. borealis - long admired by botanists and gardeners for their perfumed paired bell-shaped flowers. In the present study, we investigated their floral scent compositions through gas chromatography - mass spectrometry (GC-MS) analysis of dynamic headspace samples. Because the flowers of L. borealis in wild populations are fragrant both during the day and in the evening, circadian variation of scent emission was also assessed for this species. In total, 26 chemical compounds comprise the floral scent bouquets of L. amabilis and L. borealis, identified as monoterpenes (14), benzenoids and phenylpropanoids (5), aliphatics (3), sesquiterpenes (3) and irregular terpenes (1). Whereas monoterpenes, notably (-)-- and -pinene, dominated the scent of L. amabilis (over 82% relative abundance), benzene derivates: 1,4 dimethoxybenzene, anisaldehyde, 2-phenylethanol, benzaldehyde and nicotinaldehyde were exclusive to analysed headspace samples of L. borealis, accounting for 52% to 100% of their relative compositions, in three Swedish populations. A southwestern Finnish population was characterized by the four first mentioned benzenoid compounds and large amounts of (-)-- and -pinenes plus two aliphatic substances. The scent compounds identified for both species are ubiquitous and may serve as generalist attractants/stimulants for a broad assortment of anthophilous insects. The basic work on the flower scent of L. amabilis and L. borealis should inspire studies of their pollination biology, primarily the behaviour-guiding roles of the characteristic emitted volatiles.
  • Saari, Susanna; Sundell, Janne; Huitu, Otso; Helander, Marjo; Ketoja, Elise; Ylonen, Hannu; Saikkonen, Kari (2010)
  • Jerney, Jacqueline; Suikkanen, Sanna; Lindehoff, Elin; Kremp, Anke (2019)
    Abstract Environmental conditions regulate the germination of phytoplankton resting stages. While some factors lead to synchronous germination, others stimulate germination of only a small fraction of the resting stages. This suggests that habitat filters may act on the germination level and thus affect selection of blooming strains. Benthic ?seed banks? of the toxic dinoflagellate Alexandrium ostenfeldii from the Baltic Sea are genetically and phenotypically diverse, indicating a high potential for adaptation by selection on standing genetic variation. Here, we experimentally tested the role of climate-related salinity and temperature as selection filters during germination and subsequent establishment of A. ostenfeldii strains. A representative resting cyst population was isolated from sediment samples, and germination and reciprocal transplantation experiments were carried out, including four treatments: Average present day germination conditions and three potential future conditions: high temperature, low salinity, and high temperature in combination with low salinity. We found that the final germination success of A. ostenfeldii resting cysts was unaffected by temperature and salinity in the range tested. A high germination success of more than 80% in all treatments indicates that strains are not selected by temperature and salinity during germination, but selection becomes more important shortly after germination, in the vegetative stage of the life cycle. Moreover, strains were not adapted to germination conditions. Instead, highly plastic responses occurred after transplantation and significantly higher growth rates were observed at higher temperature. High variability of strain-specific responses has probably masked the overall effect of the treatments, highlighting the importance of testing the effect of environmental factors on many strains. It is likely that A. ostenfeldii populations can persist in the future, because suitable strains, which are able to germinate and grow well at potential future climate conditions, are part of the highly diverse cyst population. OPEN RESEARCH BADGES This article has been awarded Open Data badge. All materials and data are publicly accessible via the Open Science Framework at Learn more about the Open Practices badges from the Center for Open Science:
  • Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E.; Garibaldi, Lucas A.; Irisarri, J. Gonzalo N.; Saloniemi, Irma; Saikkonen, Kari (2016)
    Polyploidy and symbiotic Epichloe fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southern-most end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local adaptations to past or prevailing selection forces such as vertebrate grazing.
  • Reichel, Philipp; Munz, Sebastian; Hartung, Jens; Prager, Achim; Kotiranta, Stiina; Burgel, Lisa; Schober, Torsten; Graeff-Honninger, Simone (2021)
    Cannabis is one of the oldest cultivated plants, but plant breeding and cultivation are restricted by country specific regulations. Plant growth, morphology and metabolism can be manipulated by changing light quality and intensity. Three morphologically different strains were grown under three different light spectra with three real light repetitions. Light dispersion was included into the statistical evaluation. The light spectra considered had an influence on the morphology of the plant, especially the height. Here, the shade avoidance induced by the lower R:FR ratio under the ceramic metal halide lamp (CHD) was of particular interest. The sugar leaves seemed to be of elementary importance in the last growth phase for yield composition. Furthermore, the last four weeks of flowering were crucial to influence the yield composition of Cannabis sativa L. through light spectra. The dry flower yield was significantly higher under both LED treatments compared to the conventional CHD light source. Our results indicate that the plant morphology can be artificially manipulated by the choice of light treatment to create shorter plants with more lateral branches which seem to be beneficial for yield development. Furthermore, the choice of cultivar has to be taken into account when interpreting results of light studies, as Cannabis sativa L. subspecies and thus bred strains highly differ in their phenotypic characteristics.
  • Elbers, Jean P.; Rogers, Mark F.; Perelman, Polina L.; Proskuryakova, Anastasia A.; Serdyukova, Natalia A.; Johnson, Warren E.; Horin, Petr; Corander, Jukka; Murphy, David; Burger, Pamela A. (2019)
    Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing.
  • Sattar, Muhammad Naeem; Iqbal, Zafar; Al-Khayri, Jameel M.; Jain, Shri Mohan (2021)
    Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses.
  • Kerchev, Pavel; Waszczak, Cezary; Lewandowska, Aleksandra; Willems, Patrick; Shapiguzov, Alexey; Li, Zhen; Alseekh, Saleh; Muhlenbock, Per; Hoeberichts, Frank A.; Huang, Jingjing; Van der Kelen, Katrien; Kangasjärvi, Jaakko; Fernie, Alisdair R.; De Smet, Riet; Van de Peer, Yves; Messens, Joris; Van Breusegem, Frank (2016)
    The genes coding for the core metabolic enzymes of the photorespiratory pathway that allows plants with C3-type photosynthesis to survive in an oxygen-rich atmosphere, have been largely discovered in genetic screens aimed to isolate mutants that are unviable under ambient air. As an exception, glycolate oxidase (GOX) mutants with a photorespiratory phenotype have not been described yet in C3 species. Using Arabidopsis (Arabidopsis thaliana) mutants lacking the peroxisomal CATALASE2 (cat2-2) that display stunted growth and cell death lesions under ambient air, we isolated a second-site loss-of-function mutation in GLYCOLATE OXIDASE1 (GOX1) that attenuated the photorespiratory phenotype of cat2-2. Interestingly, knocking out the nearly identical GOX2 in the cat2-2 background did not affect the photorespiratory phenotype, indicating that GOX1 and GOX2 play distinct metabolic roles. We further investigated their individual functions in single gox1-1 and gox2-1 mutants and revealed that their phenotypes can be modulated by environmental conditions that increase the metabolic flux through the photorespiratory pathway. High light negatively affected the photosynthetic performance and growth of both gox1-1 and gox2-1 mutants, but the negative consequences of severe photorespiration were more pronounced in the absence of GOX1, which was accompanied with lesser ability to process glycolate. Taken together, our results point toward divergent functions of the two photorespiratory GOX isoforms in Arabidopsis and contribute to a better understanding of the photorespiratory pathway.
  • Abrego, Nerea; Norberg, Anna; Ovaskainen, Otso (2017)
    1. The identification of traits that influence the responses of the species to environmental variation provides a mechanistic perspective on the assembly processes of ecological communities. While much research linking functional ecology with assembly processes has been conducted with animals and plants, the development of predictive or even conceptual frameworks for fungal functional community ecology remains poorly explored. Particularly, little is known about the contribution of traits to the occurrences of fungal species under different environmental conditions. 2. Wood-inhabiting fungi are known to strongly respond to habitat disturbance, and thus provide an interesting case study for investigating to what extent variation in occurrence patterns of fungi can be related to traits. We apply a trait-based joint species distribution model to a data set consisting of fruit-body occurrence data on 321 wood-inhabiting fungal species collected in 22 460 dead wood units from managed and natural forest sites. 3. Our results show that environmental filtering plays a big role on shaping wood-inhabiting fungal communities, as different environments held different communities in terms of species and trait compositions. Most importantly, forest management selected against species with large and long-lived fruit-bodies as well as late decayers, and promoted the occurrences of species with small fruit-bodies and early decayers. A strong phylogenetic signal in the data suggested the existence of also some other functionally important traits than the ones we considered. 4. We found that those species groups that were more prevalent in natural conditions had more associations to other species than species groups that were tolerant to or benefitted from forest management. Therefore, the changes that forest management causes on wood-inhabiting fungal communities influence ecosystem functioning through simplification of interactive associations among the fungal species. 5. Synthesis. Our results show that functional traits are linked to the responses of wood-inhabiting fungi to variation in their environment, and thus environmental changes alter ecosystem functions via promoting or reducing species with different fruit-body types. However, further research is needed to identify other functional traits and to provide conclusive evidence for the adaptive nature of the links from traits to occurrence patterns found here.