Publications (Centre for Forest Biology)

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An assessment of Pinus contorta seed production in British Columbia: Geographic variation and dynamically-downscaled climate correlates from the Canadian Regional Climate Model
(Agricultural and Forest Meteorology, 2017-04) Lew, Alicia; von Aderkas, Patrick; Berland, Anne; Curry, Charles L.; Lacourse, Terri; Tencer, Bárbara; Weaver, Andrew
The ecological and economic importance of lodgepole pine (Pinus contorta Douglas ex Louden) in British Columbia (BC) has heightened interest in the adaptability and effective management of the species,especially as climate changes. The relationship between climate and the seed production of natural populations is a key management issue that has yet to be assessed. The purpose of this study is to determine if variation in P. contorta seed yield is related to the climate of BC.Regional differences in the seed production of lodgepole pine were examined using 1924 archived seedlot collections across 18 different natural stand seed planning zones (SPZs) in BC. The relationship between climate variation and the seed production of P. contorta was then evaluated using dynamically-downscaled output from the Canadian Regional Climate Model (CRCM). Seed production is relatively consistent across SPZs spanning a wide range of climate regimes, with the exception of Nass Skeena Transition (NST) where seed yield is an order of magnitude higher than else where. Significant temporal correlations between overall trends in seed production and both temperature and precipitation were found using the CRCM output. However, only three of the 18 SPZs showed a significant overall trend in mean annual seed yield based on cone collections made between 1963 and2013, suggesting that the reproductive capacity of natural populations is well adapted to decadal-scale climate change. Tolerance to significant variation in climate likely plays an important role in explaining the ability of this species to thrive well outside its natural range.
Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling
(BioMed Central, 2008-04-09) Ehlting, Jürgen; Chowrira, Sunita G; Mattheus, Nathalie; Aeschliman, Dana S; Arimura, Gen-Ichiro; Bohlmann, Jörg
Background: Plants are exposed to attack from a large variety of herbivores. Feeding insects can induce substantial changes of the host plant transcriptome. Arabidopsis thaliana has been established as a relevant system for the discovery of genes associated with response to herbivory, including genes for specialized (i.e. secondary) metabolism as well as genes involved in plant-insect defence signalling. Results: Using a 70-mer oligonulceotide microarray covering 26,090 gene-specific elements, we monitored changes of the Arabidopsis leaf transcriptome in response to feeding by diamond back moth (DBM; Plutella xylostella) larvae. Analysis of samples from a time course of one hour to 24 hours following onset of DBM feeding revealed almost three thousand (2,881) array elements (including 2,671 genes with AGI annotations) that were differentially expressed (>2-fold; p[t-test] < 0.05) of which 1,686 also changed more than twofold in expression between at least two time points of the time course with p(ANOVA) < 0.05. While the majority of these transcripts were up-regulated within 8 h upon onset of insect feeding relative to untreated controls, cluster analysis identified several distinct temporal patterns of transcriptome changes. Many of the DBM-induced genes fall into ontology groups annotated as stress response, secondary metabolism and signalling. Among DBM-induced genes associated with plant signal molecules or phytohormones, genes associated with octadecanoid signalling were clearly overrepresented. We identified a substantial number of differentially expressed genes associated with signal transduction in response to DBM feeding, and we compared there expression profiles with those of previously reported transcriptome responses induced by other insect herbivores, specifically Pieris rapae, Frankliniella occidentalis, Bemisia tabaci,Myzus persicae, and Brevicoryne brassicae. Conclusion: Arabidopsis responds to feeding DBM larvae with a drastic reprogramming of the transcriptome, which has considerable overlap with the response induced by other insect herbivores. Based on a meta-analysis of microarray data we identified groups of transcription factors that are either affected by multiple forms of biotic or abiotic stress including DBM feeding or, alternatively, were responsive to DBM herbivory but not to most other forms of stress.
Degradome and Secretome of Pollination Drops of Ephedra
(Botanical Review, 2015-03) von Aderkas, Patrick; Prior, Natalie; Gagnon, Susannah; Little, Stefan; Cross, Tyra; Hardie, Darryl; Borchers, Christoph; Thornburg, Robert; Hou, Chen; Lunny, Alexandra
Although secreted proteins (a secretome) are known to occur in gymnosperm pollination drops, this study shows evidence for the presence of a protein degradome for the first time. A protein degradome is composed of protein and peptide fragments, a product of protein breakdown, whereas a secretome is composed of whole, secreted, and often biologically active extracellular proteins. Harvested Ephedra pollination drops from seven species were pooled either by collection date or, in the case of less abundant sample volumes, by species. Samples were processed by one of two methods: 1. gel electophoresis or by 2. liquid-liquid extraction, followed by chromatographic separation. Processed samples were trypsin-digested and analyzed with a Thermo Scientific LTQ Orbitrap Velos. On average, two-thirds of the detected and characterized proteins found in Ephedra spp. pollination drops were intracellular proteins, such as ubiquitin. The remaining third represent proteins known to be secreted, often involved in apoplastic processes such as defense and carbohydrate-modification, typical of known conifer pollination drop proteins. Characterized proteins detected in our comparative study of Ephedra spp drops ranged from 6 in E. monosperma to 20 in E. foeminea. We propose that the intracellular proteins detected are present as the result of nucellar tissue degeneration during pollination drop formation; previous proteomic investigations of pollination drops were in taxa that lack nucellar degeneration during drop formation Discovery of a degradome in pollination drops is novel and significant in that its presence has biological implications for pollination biology. We predict that degradomes in pollination drops are not restricted to Ephedra, but should also occur in species with nucellar tissue breakdown that coincides with pollination drop formation, such as in cycads and Ginkgo and some Pinaceae. Analysis of several collection dates of E. monosperma shows a large number of proteins that change over the course of the pollination drop secretion period, which suggests that variation in pollination drop contents over time may be important in the pollination biology of Ephdera.
Diatom responses to long-term climate and sea-level rise at low-elevation lake in coastal British Columbia, Canada
(Ecosphere, 2019) Neil, Karen; Lacourse, Terri
Diatom assemblages from Lake Stowell, a low‐elevation lake in coastal British Columbia, were used to assess limnological responses associated with changes in relative sea level (RSL) and climate over the past 14,500 yr. Marine diatom taxa dominated the early record and disappeared abruptly by 14,000 cal yr BP in response to glacio‐isostatic uplift and an ensuing decrease in RSL. A brackish‐freshwater phase from 14,200 to 13,400 cal yr BP was marked by increases in several diatom taxa with tolerance for low‐to‐moderate salinity, after which assemblages became strictly freshwater. Biostratigraphic changes in both diatom and chironomid assemblages from Lake Stowell occurred more or less simultaneously throughout the record in response to long‐term changes in climate forcings, such as temperature. Increases in cold‐adapted diatom (Staurosirella pinnata, Staurosira construens, Staurosirella dubia ) and chironomid (Sergentia ) taxa between 12,900 and 11,700 cal yr BP coincided with Younger Dryas cooling, suggesting a direct link with summer temperature. Shifts in aquatic biota also reflected indirect mechanisms through which climate affected the Lake Stowell ecosystem, for example, by altering thermal stratification, disturbance regimes, and nutrient concentrations. For instance, high summer insolation and warm summer temperatures from 11,700 to 8500 cal yr BP were associated with greater abundances of Stephanodiscus hantzschii and especially Aulacoseira subarctica . A concurrent opening of the forest canopy triggered by warming would have exposed the lake to strong winds and enhanced mixing, favoring these more heavily silicified taxa as an indirect consequence of climatic changes. Diatom assemblages appear to have been impacted by the deposition of Mount Mazama tephra at 7600 cal yr BP; a notable increase in Aulacoseira tenella suggests a response to increased silica availability in association with tephra deposition.
Effect of light conditions on anatomical and biochemical aspects of somatic and zygotic embryos of hybrid larch (Larix x marschlinsii)
(Annals of Botany, 2015-12) von Aderkas, Patrick; Teyssier, Caroline; Charpentier, Jean-Paul; Gutmann, Markus; Pâques, Luc; Le Metté, Claire; Ader, Kevin; Label, Philippe; Kong, Lisheng; Lelu-Walter, Marie-Anne
Background and Aims: In conifers, mature somatic embryos and zygotic embryos appear to resemble one another physiologically and morphologically. However, phenotypes of cloned conifer embryos can be strongly influenced by a number of in vitro factors and in some instances clonal variation can exceed that found in nature. This study examines whether zygotic embryos that develop within light-opaque cones differ from somatic embryos developing in dark/light conditions in vitro. Embryogenesis in larch is well understood both in situ and in vitro and thus provides a suitable system for addressing this question. Methods: Features of somatic and zygotic embryos of hybrid larch, Larix × marschlinsii, were quantified, including cotyledon numbers, protein concentration and phenol chemistry. Somatic embryos were placed either in light or darkness for the entire maturation period. Embryos at different developmental stages were embedded and sectioned for histological analysis. Key Results: Light, and to a lesser degree abscisic acid (ABA), influenced accumulation of protein and phenolic compounds in somatic and zygotic embryos. Dark-grown mature somatic embryos had more protein (91·77 ± 11·26 µg protein mg–1 f.wt) than either dark-grown zygotic embryos (62·40 ± 5·58) or light-grown somatic embryos (58·15 ± 10·02). Zygotic embryos never accumulated phenolic compounds at any stage, whereas somatic embryos stored phenolic compounds in the embryonal root caps and suspensors. Light induced the production of quercetrin (261·13 ± 9·2 µg g–1 d.wt) in somatic embryos. Mature zygotic embryos that were removed from seeds and placed on medium in light rapidly accumulated phenolics in the embryonal root cap and hypocotyl. Delaying germination with ABA delayed phenolic compound accumulation, restricting it to the embryonal root cap. Conclusions: In larch embryos, light has a negative effect on protein accumulation, but a positive effect on phenol accumulation. Light did not affect morphogenesis, e.g. cotyledon number. Somatic embryos produced different amounts of phenolics, such as quercetrin, depending on light conditions. The greatest difference was seen in the embryonal root cap in all embryo types and conditions.
Effects of Exogenously Applied Gibberellins and Thidiazuron on Phytohormone Profiles of Long-Shoot Buds and Cone Gender Determination in Lodgepole Pine
(Journal of Plant Growth Regulation, 2016-03) Kong, Lisheng; von Aderkas, Patrick; Zaharia, L. Irina
In long-shoot buds of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm), cone-bud initiation and gender differentiation occur in a site-specific manner: female cone buds are normally restricted to the distal portion, whereas male cone buds are located in the proximal portion. Application of a paste containing two plant growth regulators gibberellins A4 + A7 (GA4/7) combined with thidiazuron (TDZ) to long-shoot buds prior to cone-bud gender determination altered endogenous phytohormone profiles and induced female cone-bud formation in the proximal portion of the long-shoot bud, where male cone buds normally occur. Induced cone clusters observed in the following spring were either entirely female or a mixture of both female and male cones. Endogenous phytohormones in the long-shoot bud tissues were quantified by the stable isotope dilution method using high performance liquid chromatography-electrospray ionization tandem mass spectrometry in multiple-reaction monitoring mode. Applied GA4/7 + TDZ led to increased concentrations of endogenous zeatin-type cytokinins, that is, trans-zeatin riboside and dihydrozeatin riboside, whereas concentrations of abscisic acid (ABA) and its catabolite, ABA glucose ester, were decreased, all relative to control, in untreated long-shoot bud tissue. Concentrations of extractable GA4 and GA7 declined in long-shoot bud tissues over 4 weeks following treatment with exogenous GA4/7. This study demonstrates that high levels of endogenous zeatin-type cytokinins, together with reduced levels of ABA, both induced by applied GA4/7 + TDZ, are positively associated with an increased female cone-bud formation in long-shoot buds.
Effects of stem-injected gibberellins and 6-benzylaminopurine on phytohormone profiles and cone yield in two lodgepole pine genotypes
(Trees, 2018) Kong, Lisheng; von Aderkas, Patrick; Zaharia, Irina
Effects of exogenously applied gibberellins (GAs) and 6-benzylaminopurine (BA) on profiles of phytohormones and some of their metabolites relative to controls in long-shoot buds of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) were analyzed during cone bud initiation and differentiation. Differential responses in phytohormones and in cone yield were observed in ramets of the two tested genotypes (478 and 276) to stem-injected mixtures of GA4 and GA7 (GA4/7) and /or BA. Injected GA4/7 affected bud concentrations of GA4 and GA7. Injected PGRs, with the exception of BA injection, decreased concentrations of abscisic acid (ABA) and ABA glucose-ester at week 5 and/or week 7. Internal concentrations of trans-zeatin riboside (t-ZR) increased in response to all treatments at week 3 in genotype 276. In genotype 478, t-ZR only increased with treatments of BA or GA4/7 plus BA. Dihydrozeatin riboside concentrations increased in response to GA4/7 plus BA treatment at week 7 in genotype 276. Concentrations of isopentenyl adenosine declined with treatments of GA4/7 and GA4/7 plus BA in genotype 276 at week 5. In genotype 478, a similar decrease was caused by GA4/7 plus BA treatment. For both genotypes, the highest ratio of zeatin-type cytokinins to isopentenyl-type cytokinins occurred at weeks 5 and 7 after injection with GA4/7 plus BA. Stem-injection of GA4/7, especially in combination with BA, increased female cone yields significantly in genotype 276, but not in genotype 478.
Evolution of a Secondary Metabolic Pathway from Primary Metabolism: Shikimate and quinate biosynthesis in plants
(the Plant Journal, 2018-06) Carrington, Yuriko; Guo, Jia; Le, Cuong H.; Fillo, Alexander; Kwon, Junsu; Tran, Lan T.; Ehlting, Jurgen
The shikimate pathway synthesizes aromatic amino acids essential for protein biosynthesis. Shikimate dehydrogenase (SDH) is a central enzyme of this primary metabolic pathway, producing shikimate. The structurally similar quinate is a secondary metabolite synthesized by quinate dehydrogenase (QDH). SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a deﬁning gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorﬁi) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, represented here by Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in P. taeda maintained speciﬁcity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displayed a signature of positive selection at the node deﬁning the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-speciﬁc angiosperm SDH was sufﬁcient to gain some QDH function. Thus, very few mutations were necessary to facilitate the evolution of QDH genes.
Evolutionary classification of ammonium, nitrate, and peptide transporters in land plants
(BMC Evolutionary Biology, 2014-01-20) Von Wittgenstein, Neil JJB; Le, Cuong H; Hawkins, Barbara J.; Ehlting, Jürgen
Background: Nitrogen uptake, reallocation within the plant, and between subcellular compartments involves ammonium, nitrate and peptide transporters. Ammonium transporters are separated into two distinct families (AMT1 and AMT2), each comprised of five members on average in angiosperms. Nitrate transporters also form two discrete families (NRT1 and NRT2), with angiosperms having four NRT2s, on average. NRT1s share an evolutionary history with peptide transporters (PTRs). The NRT1/PTR family in land plants usually has more than 50 members and contains also members with distinct activities, such as glucosinolate and abscisic acid transport. Results: Phylogenetic reconstructions of each family across 20 land plant species with available genome sequences were supplemented with subcellular localization and transmembrane topology predictions. This revealed that both AMT families diverged prior to the separation of bryophytes and vascular plants forming two distinct clans, designated as supergroups, each. Ten supergroups were identified for the NRT1/PTR family. It is apparent that nitrate and peptide transport within the NRT1/PTR family is polyphyletic, that is, nitrate and/or peptide transport likely evolved multiple times within land plants. The NRT2 family separated into two distinct clans early in vascular plant evolution. Subsequent duplications occurring prior to the eudicot/monocot separation led to the existence of two AMT1, six AMT2, 31 NRT1/PTR, and two NRT2 clans, designated as groups. Conclusion: Phylogenetic separation of groups suggests functional divergence within the angiosperms for each family. Distinct groups within the NRT1/PTR family appear to separate peptide and nitrate transport activities as well as other activities contained within the family, for example nitrite transport. Conversely, distinct activities, such as abscisic acid and glucosinolate transport, appear to have recently evolved from nitrate transporters.
An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana
(BioMed Central, 2008-04-23) Ehlting, Jürgen; Sauveplane, Vincent; Olry, Alexandre; Ginglinger, Jean-François; Provart, Nicholas J; Werck-Reichhart, Danièle
Background: Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s) is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism. Results: We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here. Conclusion: The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.
Fossil chironomid assemblages and inferred summer temperatures for the past 14,000 years from a low-elevation lake in Pacific Canada
(Journal of Paleolimnology, 2018-04) Lemmen, J.; Lacourse, Terri
Fossil midge remains in a sediment core from Lake Stowell, a low-elevation lake in coastal British Columbia, Canada, were used to assess temporal changes in chironomid communities and to produce quantitative estimates of mean July air temperature (MJAT) for the past 14,000 years based on two different transfer functions. Chironomid assemblages are diverse throughout much of the record, with most taxa present at low relative abundances. The basal portion of the sediment record is characterized by low head capsule concentrations, taxonomic diversity and organic matter content, all of which increase towards the early Holocene. Inferred temperatures suggest a cool late-glacial interval with a minimum MJAT of 12.5 °C, ~2 °C cooler than the inferred modern temperature. Summer temperatures gradually increased from this minimum until a brief cooling of as much as ~3 °C relative to modern that coincides with the Younger Dryas chronozone. An interval of warmer summers with MJAT of ~16 to 18 °C (2–3 °C warmer than modern) is inferred between ~10,500 and 8000 cal year BP. This early Holocene warm period was followed by generally cooler inferred temperatures in the middle and late Holocene. The midge-inferred temperature record from Lake Stowell is generally consistent with other temperature reconstructions from the region based on chironomid remains and other climate proxies. This research underscores the potential of low-elevation, mid-latitude sites for chironomid-based temperature reconstructions. In order to maximize the availability of modern analogues for robust temperature reconstructions from similar sites, calibration datasets should be expanded to include more sites from the warm end of the temperature gradient.
Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi
(BioMed Central, 2011-08-24) Hintz, William E.; Pinchback, Michael; De la Bastide, Paul; Burgess, Steven; Jacobi, Volker; Hamelin, Richard; Breuil, Colette; Bernier, Louis
Background: The highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to understand the mechanisms of virulence of this introduced pathogen and its evolving population structure, with a view to identifying potential strategies for the control of Dutch elm disease. As part of a larger study to examine the genomes of economically important Ophiostoma spp. and the genetic basis of virulence, we have constructed an expressed sequence tag (EST) library using total RNA extracted from the yeast-like growth phase of O. novo-ulmi (isolate H327). Results: A total of 4,386 readable EST sequences were annotated by determining their closest matches to known or theoretical sequences in public databases by BLASTX analysis. Searches matched 2,093 sequences to entries found in Genbank, including 1,761 matches with known proteins and 332 matches with unknown (hypothetical/ predicted) proteins. Known proteins included a collection of 880 unique transcripts which were categorized to obtain a functional profile of the transcriptome and to evaluate physiological function. These assignments yielded 20 primary functional categories (FunCat), the largest including Metabolism (FunCat 01, 20.28% of total), Subcellular localization (70, 10.23%), Protein synthesis (12, 10.14%), Transcription (11, 8.27%), Biogenesis of cellular components (42, 8.15%), Cellular transport, facilitation and routes (20, 6.08%), Classification unresolved (98, 5.80%), Cell rescue, defence and virulence (32, 5.31%) and the unclassified category, or known sequences of unknown metabolic function (99, 7.5%). A list of specific transcripts of interest was compiled to initiate an evaluation of their impact upon strain virulence in subsequent studies. Conclusions: This is the first large-scale study of the O. novo-ulmi transcriptome. The expression profile obtained from the yeast-like growth phase of this species will facilitate a multigenic approach to gene expression studies to assess their role in the determination of pathogenicity for this species. The identification and evaluation of gene targets in such studies will be a prerequisite to the development of biological control strategies for this pathogen.
The Functional Characterization of the SLC Gene in Populus trichocarpa, and its Potential Role in Lignin Biosynthesis
(2016-04-27) Irwin, Tyler; Tran, Lan; Ehlting, Jürgen
Wood is an extraordinary, sustainable feedstock for construction, pulp and paper, and potentially for bioenergy production. Wood is largely composed of secondary cell walls containing carbohydrates (such as cellulose) and lignin. The latter provides mechanical stability, but negatively impacts pulp and bioethanol generation. To better understand the genetic architecture of wood biogenesis, genome wide genetic association studies have been performed previously, linking genetic variation within a population of poplar trees with wood trait variations. Among other genes, it was suggested that a putative solute carrier gene, named SLC, in Populus trichocarpa was genetically associated with secondary cell wall biogenesis and lignin biosynthesis. SLC belongs to a large family of transporters involved in nitrate, peptide, and secondary metabolite transport, but its actual physiological function is unknown. The connection and possible role of SLC in secondary cell wall biogenesis will be examined in my Honours research by using reverse genetic approaches: Poplar trees and isolated roots will be used to characterize transgenic plants overexpressing or down-regulating SLC. The mutants will be analyzed through chemical analysis using HPLC to test for changes in secondary metabolites in the mutants compared to wild-type. Furthermore, a nutrient experiment will be performed by growing mutant whole plants under different nitrogen fertilization regimes. This will test the hypothesis that differences in nutrient uptake efficiencies may indirectly explain the observed association of SLC with wood chemistry traits. In summary, the purpose of this project is to gain insight into the biological role of SLC using a functional genomics approach.
Fungal colonizers and seed loss in lodgepole pine orchards of British Columbia
(Botany, 2018) de la Bastide, Paul Y.; LeBlanc, Jonathon; Kong, Lisheng; Finston, Terrie; May, Emily M.; Reich, Richard; Hintz, William E.; von Aderkas, Patrick
Lodgepole pine is an important lumber species in Canada and seed orchards are expected to meet the increased demand for seed. However, seed production has been consistently low in the Okanagan region orchards of British Columbia. To determine whether the fungal microbiome contributes to seed loss, histological and molecular approaches were used. Seed production was studied at seven Okanagan orchards, all outside the natural range of lodgepole pine, and at one near Prince George, within its natural range. Seed losses were highest in the Okanagan, compared with Prince George. The role of fungal colonizers in consuming seed during the last stages of maturation is described. Fungal hyphae were frequently observed at all locations in developing seed, particularly once storage substances accumulated. Fungi identified from host tissues using molecular and morphological techniques included Alternaria, Cladosporium, Fusarium, Penicillium, and Sydowia. The opportunistic foliar pathogen Sydowia polyspora, which is known to have a variable biotrophic status, was detected at most orchards within different host tissues (seeds, needles and conelets), in association with pollen and in the air column. Reduced seed viability observed in Okanagan orchards is most likely due to a combination of factors, including the composition of the fungal microbiome.
Fungal community composition as affected by litter chemistry and weather during four years of litter decomposition in rainshadow coastal Douglas-fir forests
(Journal of Fungi, 2022) Shay, Philip-Edouard; Winder, Richard S.; Constabel, C. Peter; Trofymow, J. A. (Tony)
Climate and litter chemistry are major factors influencing litter decay, a process mediated by microbes, such as fungi, nitrogen-fixing bacteria and ammonia-oxidizing bacteria. Increasing atmospheric CO2 concentrations can decrease nitrogen (N) and increase condensed tannin (CT) content in foliar litter, reducing litter quality and slowing decomposition. We hypothesized that reduced litter quality inhibits microbes and is the mechanism causing decomposition to slow. Litterbags of Douglas-fir needles and poplar leaves with a range of N (0.61–1.57%) and CT (2.1–29.1%) treatment and natural acid unhydrolyzable residue (35.3–41.5%) concentrations were placed along climatic gradients in mature Douglas-fir stands of coastal British Columbia rainshadow forests. The structure (diversity, richness and evenness) and composition of microbial communities were analyzed using DGGE profiles of 18S, NifH-universal and AmoA PCR amplicons in foliar litter after 7, 12, 24 and 43 months of decay. High CT and low N concentrations in leaf litter were associated with changes in microbial community composition, especially fungi. Contrary to our hypothesis, high CT and low N treatments did not inhibit microbial colonization or diversity. The joint effects of air temperature and soil moisture on microbial community composition at our sites were more important than the effects of initial litter chemistry.
Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis
(BioMed Central, 2008-11-20) Xue, Tongtong; Wang, Dong; Zhang, Shizhong; Ehlting, Juergen; Ni, Fei; Jakab, Stephen; Zheng, Chengchao; Zhong, Yuan
Background: The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes. A genome-wide overview of the PP2C gene family in plants is not yet available. Results: A comprehensive computational analysis identified 80 and 78 PP2C genes in Arabidopsis thaliana (AtPP2Cs) and Oryza sativa (OsPP2Cs), respectively, which denotes the PP2C gene family as one of the largest families identified in plants. Phylogenic analysis divided PP2Cs in Arabidopsis and rice into 13 and 11 subfamilies, respectively, which are supported by the analyses of gene structures and protein motifs. Comparative analysis between the PP2C genes in Arabidopsis and rice identified common and lineagespecific subfamilies and potential 'gene birth-and-death' events. Gene duplication analysis reveals that whole genome and chromosomal segment duplications mainly contributed to the expansion of both OsPP2Cs and AtPP2Cs, but tandem or local duplication occurred less frequently in Arabidopsis than rice. Some protein motifs are widespread among the PP2C proteins, whereas some other motifs are specific to only one or two subfamilies. Expression pattern analysis suggests that 1) most PP2C genes play functional roles in multiple tissues in both species, 2) the induced expression of most genes in subfamily A by diverse stimuli indicates their primary role in stress tolerance, especially ABA response, and 3) the expression pattern of subfamily D members suggests that they may constitute positive regulators in ABAmediated signaling pathways. The analyses of putative upstream regulatory elements by two approaches further support the functions of subfamily A in ABA signaling, and provide insights into the shared and different transcriptional regulation machineries in dicots and monocots. Conclusion: This comparative genome-wide overview of the PP2C family in Arabidopsis and rice provides insights into the functions and regulatory mechanisms, as well as the evolution and divergence of the PP2C genes in dicots and monocots. Bioinformatics analyses suggest that plant PP2C proteins from different subfamilies participate in distinct signaling pathways. Our results have established a solid foundation for future studies on the functional divergence in different PP2C subfamilies.
Host-Parasite Interactions from the Inside: Plant Reproductive Ontogeny Drives Specialization in Parasitic Insects
(PLoS One, 2015-10) Boivin, Thomas; Gidoin, Cindy; von Aderkas, Patrick; Safrana, Jonathan; Candau, Jean- Noël; Chalon, Alain; Sondo, Marion; El Maâtaoui, Mohamed
Host plant interactions are likely key drivers of evolutionary processes involved in the diversification of phytophagous insects. Granivory has received substantial attention for its crucial role in shaping the interaction between plants and their seed parasites, but fine-scale mechanisms explaining the role of host plant reproductive biology on specialization of seed parasites remain poorly described. In a comparative approach using plant histological techniques, we tested the hypotheses that different seed parasite species synchronize their life cycles to specific stages in seed development, and that the stage they target depends on major differences in seed development programs. In a pinaceous system, seed storage products are initiated before ovule fertilization and the wasps target the ovule’s nucellus during megagametogenesis, a stage at which larvae may benefit from the by-products derived from both secreting cells and dying nucellar cells. In a cupressaceous system, oviposition activity peaks later, during embryogenesis, and the wasps target the ovule’s megagametophyte where larvae may benefit from cell disintegration during embryogenesis. Our cytohistological approach shows for the first time how, despite divergent oviposition targets, different parasite species share a common strategy that consists of first competing for nutrients with developing plant structures, and then consuming these developed structures to complete their development. Our results support the prediction that seed developmental program is an axis for specialization in seed parasites, and that it could be an important parameter in models of their ecological and taxonomic divergence. This study provides the basis for further investigating the possibility of the link between plant ontogeny and pre-dispersal seed parasitism.
Insights from the pollination drop proteome and the ovule transcriptome of Cephalotaxus at the time of pollination drop production
(Annals of Botany, 2016-05) Pirone-Davies, Cary; Prior, Natalie; von Aderkas, Patrick; Smith, Derek; Hardie, Darryl; Friedman, William E.; Matthews, Sarah
Background and Aims: Many gymnosperms produce an ovular secretion, the pollination drop, during reproduction. The drops serve as a landing site for pollen, but also contain a suite of ions and organic compounds, including proteins, that suggests diverse roles for the drop during pollination. Proteins in the drops of species of Chamaecyparis, Juniperus, Taxus, Pseudotsuga, Ephedra and Welwitschia are thought to function in the conversion of sugars, defence against pathogens, and pollen growth and development. To better understand gymnosperm pollination biology, the pollination drop proteomes of pollination drops from two species of Cephalotaxus have been characterized and an ovular transcriptome for C. sinensis has been assembled. Methods: Mass spectrometry was used to identify proteins in the pollination drops of Cephalotaxus sinensis and C. koreana. RNA-sequencing (RNA-Seq) was employed to assemble a transcriptome and identify transcripts present in the ovules of C. sinensis at the time of pollination drop production. Key Results: About 30 proteins were detected in the pollination drops of both species. Many of these have been detected in the drops of other gymnosperms and probably function in defence, polysaccharide metabolism and pollen tube growth. Other proteins appear to be unique to Cephalotaxus, and their putative functions include starch and callose degradation, among others. Together, the proteins appear either to have been secreted into the drop or to occur there due to breakdown of ovular cells during drop production. Ovular transcripts represent a wide range of gene ontology categories, and some may be involved in drop formation, ovule development and pollen–ovule interactions. Conclusions: The proteome of Cephalotaxus pollination drops shares a number of components with those of other conifers and gnetophytes, including proteins for defence such as chitinases and for carbohydrate modification such as β-galactosidase. Proteins likely to be of intracellular origin, however, form a larger component of drops from Cephalotaxus than expected from studies of other conifers. This is consistent with the observation of nucellar breakdown during drop formation in Cephalotaxus. The transcriptome data provide a framework for understanding multiple metabolic processes that occur within the ovule and the pollination drop just before fertilization. They reveal the deep conservation of WUSCHEL expression in ovules and raise questions about whether any of the S-locus transcripts in Cephalotaxus ovules might be involved in pollen–ovule recognition.
Late Pleistocene vegetation and sedimentary charcoal at Kilgii Gwaay archaeological site in coastal British Columbia, Canada, with possible proxy evidence for human presence by 13,000 cal bp
(Vegetation History and Archaeobotany, 2020) Mathewes, Rolf W.; Lacourse, Terri; Helmer, E. F.; Howarth, C. R.; Fedje, Daryl
Kilgii Gwaay is an early Holocene archaeological wet site located in the intertidal zone of Ellen Island in the southern Haida Gwaii archipelago of coastal British Columbia, Canada. The Kilgii site includes one of the oldest shell middens in western North America and provides evidence of early maritime adaptations by humans. Radiocarbon-dated cultural deposits that surround a small palaeopond (Kilgii Pond) include hearth features, abundant lithic, bone and wood artifacts, and a diverse fossil fauna and flora. The known occupation dates between 10,800 and 10,500 cal bp, when relative sea level was 1–3 m lower than today. The site was submerged and capped by marine deposits by 10,500 cal bp as relative sea level rose. We conducted multi-proxy palaeoenvironmental analyses (magnetic susceptibility, pollen, charcoal, macrofossils) on Kilgii Pond sediments from a core taken beneath the coarse intertidal deposits. Pollen analysis indicates establishment of herb–shrub tundra by 14,500 cal bp, followed by pine-dominated communities after 13,800 cal bp and spruce forest with abundant ferns from about 13,250 cal bp. Macroscopic charcoal in the core is most abundant during the period of confirmed human occupation; however, significant peaks in charcoal abundance are present well below the known occupation horizon. Since lightning and natural forest fires are infrequent in this wet hypermaritime setting, we consider that the charcoal peaks from Kilgii Pond may serve as a proxy for human presence, potentially as early as 13,000 cal bp, approximately 2,200 years earlier than indicated by the AMS-dated cultural deposits and artifacts.
Latitudinal limits to the predicted increase of the peatland carbon sink with warming
(Nature Climate Change, 2018) Gallego-Sala, Angela V.; Charman, Dan J.; Brewer, Simon; Page, Susan E.; Prentice, I. Colin; Friedlingstein, Pierre; Moreton, Steve; Lacourse, Terri; et. al.
The carbon sink potential of peatlands depends on the balance of carbon uptake by plants and microbial decomposition. The rates of both these processes will increase with warming but it remains unclear which will dominate the global peatland response. Here we examine the global relationship between peatland carbon accumulation rates during the last millennium and planetary-scale climate space. A positive relationship is found between carbon accumulation and cumulative photosynthetically active radiation during the growing season for mid- to high-latitude peatlands in both hemispheres. However, this relationship reverses at lower latitudes, suggesting that carbon accumulation is lower under the warmest climate regimes. Projections under Representative Concentration Pathway (RCP)2.6 and RCP8.5 scenarios indicate that the present-day global sink will increase slightly until around ad 2100 but decline thereafter. Peatlands will remain a carbon sink in the future, but their response to warming switches from a negative to a positive climate feedback (decreased carbon sink with warming) at the end of the twenty-first century.

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