An open-source machine-learning approach for obtaining high-quality quantitative wood anatomy data from E. grandis and P. radiata xylem

Quantitative wood anatomy is a subfield in dendrochronology that requires effective open-source image analysis tools. In this research, the bioimage analysis software QuPath (v0.4.4) is introduced as a candidate for accurately quantifying the cellular properties of the xylem in an automated manner. Additionally, the potential of QuPath to detect the transition of early- to latewood tracheids over the growing season was evaluated to assess a potential application in dendroecological studies. Various algorithms in QuPath were optimized to quantify different xylem cell types in Eucalyptus grandis and the transition of early- to latewood tracheids in Pinus radiata. These algorithms were coded into cell detection scripts for automatic quantification of stem microsections and compared to a manually curated method to assess the accuracy of the cell detections. The automatic cell detection approach, using QuPath, has been validated to be reproducible with an acceptable error when assessing fibers, vessels, early- and latewood tracheids. However, further optimization for parenchyma is still required. This proposed method developed in QuPath provides a scalable and accurate approach for quantifying anatomical features in stem microsections. With minor amendments to the detection and classification algorithms, this strategy is likely to be viable in other plant species.

Characterization of hemicellulose in Cunninghamia lanceolata stem during xylogenesis

In this study, hemicellulose was isolated from the apical, middle and basal segments of C. lanceolata stem to investigate the dynamic change of its structure during xylogenesis. Results showed that the C. lanceolata hemicellulose is mainly consisted of O-acetylgalactoglucomannan (GGM) which backbone is alternately linked by β-d-mannopyranosyl (Manp) and β-d-glucopyranosyl (Glcp) via (1 → 4)-glycosidic bond, while the side chains are α-d-galactopyranosyl (Galp) and acetyl. In addition, 4-O-methylglucuronoarabinoxylan (GAX) is another dominant structure of C. lanceolata hemicellulose which contains a linear backbone of (1 → 4)-β-d-xylopyranosyl (Xylp) and side chains of 4-O-Me-α-d-glucuronic acid (MeGlcpA) and α-L-arabinofuranose (Araf). The thickness of the cell wall, the ratio of GGM/GAX and the molecular weight of hemicellulose were increased as the extension of growth time. The degree of glycosyl substitutions of xylan and mannan was decreased from 10.34 % (apical) to 8.38 % (basal) and from 15.63 % (apical) to 10.49 % (basal), respectively. However, the total degree of acetylation was enhanced from 0.28 (apical) to 0.37 (basal). Transcriptome analysis showed that genes (CSLA9, IRX9H1, IRX10L, IRX15L, GMGT1, TBL19, TBL25, GUX2, GUX3, GXM1, F8H1 and F8H2) related to hemicellulose biosynthesis are mainly expressed in mature part. This study is of great significance for genetic breeding and high-value utilization of C. lanceolata.

Chronic in situ tissue cooling does not reduce lignification at the Swiss treeline but enhances the risk of 'blue' frost rings

In their 2013 paper, Lenz et al. illustrated how trees growing at the low-temperature limit respond to a chronic in situ warming or cooling by 3 K, by employing Peltier-thermostated branch collars that tracked ambient temperatures. The micro-coring-based analysis of seasonal tree ring formation included double-staining microtome cross sections for lignification, but these data had not been included in the publication. In this short communication, we complement these data, collected in 2009 at the Swiss treeline, and we show that a 3 K cooling that corresponds to a 500-600 m higher elevation, had no influence on lignification. However, when a frost event occurred during the early part of ring formation, the 3 K cooling produced a blue (non-lignified) layer of cells, followed by normally lignified cells for the rest of the season. Hence, the event did not affect the cambium, but interrupted cell wall maturation in cells that were in a critical developmental stage. We conclude, that chronic cooling does not affect lignification at treeline, but it increases the risk of frost damage in premature xylem tissue.

Characterization of hemicellulose during xylogenesis in rare tree species Castanopsis hystrix

Hemicellulose is an important component of the plant cell wall which vary in structure and composition between plant species. The research of hemicellulose structures is primarily focused on fast-growing plants during xylogenesis, with slow-growing and rare trees receiving the least attention. Here, hemicellulose structure of the rare species Castanopsis hystrix during xylogenesis was analyzed. Acetyl methyl glucuronide xylan was the most common type of hemicellulose in C. hystrix, with a unique tetrasaccharide structure at the reducing end. Hemicellulose type, structure, molecular weight, thermal stability, biosynthesis and acetyl substitution content and pattern remained stable during the xylogenesis in C. hystrix, which could be attributed to its slow growth. The stable polymer type, low side chain modification and high acetyl substitution of hemicellulose throughout the stems are among the reasons for the hardness and corrosion resistance properties of C. hystrix wood. Genetic modification can be used to improve these properties.

Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis

Our Induced Somatic Sector Analysis and protein-protein interaction experiments demonstrate that Eucalyptus grandis IAA13 regulates xylem fibre and vessel development, potentially via EgrIAA13 modules involving ARF2, ARF5, ARF6 and ARF19. Auxin is a crucial phytohormone regulating multiple aspects of plant growth and differentiation, including regulation of vascular cambium activity, xylogenesis and its responsiveness towards gravitropic stress. Although the regulation of these biological processes greatly depends on auxin and regulators of the auxin signalling pathway, many of their specific functions remain unclear. Therefore, the present study aims to functionally characterise Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13), a member of the auxin signalling pathway. In Eucalyptus and Populus, EgrIAA13 and its orthologs are preferentially expressed in the xylogenic tissues and downregulated in tension wood. Therefore, to further investigate EgrIAA13 and its function during xylogenesis, we conducted subcellular localisation and Induced Somatic Sector Analysis experiments using overexpression and RNAi knockdown constructs of EgrIAA13 to create transgenic tissue sectors on growing stems of Eucalyptus and Populus. Since Aux/IAAs interact with Auxin Responsive Factors (ARFs), in silico predictions of IAA13-ARF interactions were explored and experimentally validated via yeast-2-hybrid experiments. Our results demonstrate that EgrIAA13 localises to the nucleus and that downregulation of EgrIAA13 impedes Eucalyptus xylem fibre and vessel development. We also observed that EgrIAA13 interacts with Eucalyptus ARF2, ARF5, ARF6 and ARF19A. Based on these results, we conclude that EgrIAA13 is a regulator of Eucalyptus xylogenesis and postulate that the observed phenotypes are likely to result from alterations in the auxin-responsive transcriptome via IAA13-ARF modules such as EgrIAA13-EgrARF5. Our results provide the first insights into the regulatory role of EgrIAA13 during xylogenesis.

Inter and intra-annual links between climate, tree growth and NDVI: improving the resolution of drought proxies in conifer forests

The inter- and intra-annual variability in radial growth reflects responses to climatic variability and water shortage, especially in areas subjected to seasonal drought. However, it is unknown how this variability is related to forest productivity, which can be assessed by measuring changes in canopy greenness and cover through remote sensing products as the Normalized Difference Vegetation Index (NDVI). We combine xylogenesis with measurements of inter-annual changes in seasonal wood production (earlywood width, adjusted latewood width) and NDVI to improve the understanding of climate and drought impacts on growth and forest productivity in a Pinus teocote stand located in northern Mexico. Cambial dynamics accelerated in March and a high production of radially enlarging and thickening tracheids were observed from April to October and from June to October, respectively. Tracheid maturation was very active in October when latewood production peaked. Wet conditions in winter-spring and summer-autumn enhanced earlywood and latewood production, respectively. Earlywood and latewood were constrained by long (4-10 months) and short (2-3 months) droughts, respectively. The earlywood production depended on April soil moisture, which agrees with the peak of radially enlarging tracheid production found during that month. Aligning drought proxies at inter- and intra-annual scales by using growth and productivity measures improves our understanding of conifer forest responses to water shortage.

Autophagy-an underestimated coordinator of construction and destruction during plant root ontogeny

MAIN CONCLUSION

Autophagy is a key but undervalued process in root ontogeny, ensuring both the proper development of root tissues as well as the senescence of the entire organ. Autophagy is a process which occurs during plant adaptation to changing environmental conditions as well as during plant ontogeny. Autophagy is also engaged in plant root development, however, the limitations of belowground studies make it challenging to understand the entirety of the developmental processes. We summarize and discuss the current data pertaining to autophagy in the roots of higher plants during their formation and degradation, from the beginning of root tissue differentiation and maturation; all the way to the aging of the entire organ. During root growth, autophagy participates in the processes of central vacuole formation in cortical tissue development, as well as vascular tissue differentiation and root senescence. At present, several key issues are still not entirely understood and remain to be addressed in future studies. The major challenge lies in the portrayal of the mechanisms of autophagy on subcellular events in belowground plant organs during the programmed control of cellular degradation pathways in roots. Given the wide range of technical areas of inquiry where root-related research can be applied, including cutting-edge cell biological methods to track, sort and screen cells from different root tissues and zones of growth, the identification of several lines of evidence pertaining to autophagy during root developmental processes is the most urgent challenge. Consequently, a substantial effort must be made to ensure whether the analyzed process is autophagy-dependent or not.

Characterization of hemicellulose in Cassava (Manihot esculenta Crantz) stem during xylogenesis

Cassava is one of the three major potato crops due to the high starch content in its tubers. Unlike most current studies on the utilization of cassava tubers, our research is mainly focused on the stem of cassava plant. Through nuclear magnetic resonance (NMR), fourier transform infrared spectrometer (FTIR) and other methods, we found that cassava stalk hemicellulose consists of β-1,4 glycosidic bond-linked xylan backbone with a tetrasaccharide reducing end and decorated with methylated glucuronic acid, acetyl groups and a high degree of arabinose substitutions. Hemicellulose content gradually increased from the upper to the lower parts of the stem. The apical part of cassava stalk contained more branched and heterogeneous glycans than the middle and basal parts, and the molecular weight of hemicellulose increased from top to bottom. Our findings will be helpful in understanding of structural variations of cassava hemicellulose during xylogenesis, as well as in better utilization of cassava plant waste in industry.

Hevea brasiliensis coniferaldehyde-5-hydroxylase (HbCAld5H) regulates xylogenesis, structure and lignin chemistry of xylem cell wall in Nicotiana tabacum

KEY MESSAGE

The HbCAld5H1 gene cloned from Hevea brasiliensis regulates the cambial activity, xylem differentiation, syringyl-guaiacyl ratio, secondary wall structure, lignification pattern and xylan distribution in xylem fibres of transgenic tobacco plants. Molecular characterization of lignin biosynthesis gene coniferaldehyde-5-hydroxylase (CAld5H) from Hevea brasiliensis and its functional validation was performed. Both sense and antisense constructs of HbCAld5H1 gene were introduced into tobacco through Agrobacterium-mediated genetic transformation for over expression and down-regulation of this key enzyme to understand its role affecting structural and cell wall chemistry. The anatomical studies of transgenic tobacco plants revealed the increase of cambial activity leading to xylogenesis in sense lines and considerable reduction in antisense lines. The ultra-structural studies showed that the thickness of secondary wall (S2 layer) of fibre had been decreased with non-homogenous lignin distribution in antisense lines, while sense lines showed an increase in S2 layer thickness. Maule color reaction revealed that syringyl lignin distribution in the xylem elements was increased in sense and decreased in antisense lines. The immunoelectron microscopy revealed a reduction in LM 10 and LM 11 labelling in the secondary wall of antisense tobacco lines. Biochemical studies showed a radical increase in syringyl lignin in sense lines without any significant change in total lignin content, while S/G ratio decreased considerably in antisense lines. Our results suggest that CAld5H gene plays an important role in xylogenesis stages such as cambial cell division, secondary wall thickness, xylan and syringyl lignin distribution in tobacco. Therefore, CAld5H gene could be considered as a promising target for lignin modification essential for timber quality improvement in rubber.

Occurrence of autophagy during pioneer root and stem development in Populus trichocarpa

Autophagy is involved in developmentally programmed cell death and is identified during the early development of phloem, as well as xylem with a dual role, as both an inducer and executioner of cell death. The regulation of primary and secondary development of roots and stems is important for the establishment of root systems and for the overall survival of trees. The molecular and cellular basis of the autophagic processes, which are used at distinct moments during the growth of both organs, is crucial to understand the regulation of their development. To address this, we use Populus trichocarpa seedlings grown in a rhizotron system to examine the autophagy processes involved in root and stem development. To monitor the visual aspects of autophagy, transmission electron microscopy (TEM) and immunolocalization of AuTophaGy-related protein (ATG8) enabled observations of the phenomenon at a structural level. To gain further insight into the autophagy process at the protein and molecular level, we evaluated the expression of ATG gene transcripts and ATG protein levels. Alternations in the expression level of specific ATG genes and localization of ATG8 proteins were observed during the course of root or stem primary and secondary development. Specifically, ATG8 was present in the cells exhibiting autophagy, during the differentiation and early development of xylem and phloem tissues, including both xylary and extraxylary fibers. Ultrastructural observations revealed tonoplast invagination with the formation of autophagic-like bodies. Additionally, the accumulation of autophagosomes was identifiable during the differentiation of xylem in both organs, long before the commencement of cell death. Taken together, these results provide evidence in support of the dual role of autophagy in developmental PCD. A specific role of the controller of cell death, which is a committed step with the release of hydrolytic enzymes from the vacuole and final digestion of protoplast, from which there is no return once initiated, is only attributed to mega-autophagy.

Jasmonate promotes auxin-induced adventitious rooting in dark-grown Arabidopsis thaliana seedlings and stem thin cell layers by a cross-talk with ethylene signalling and a modulation of xylogenesis

BACKGROUND

Adventitious roots (ARs) are often necessary for plant survival, and essential for successful micropropagation. In Arabidopsis thaliana dark-grown seedlings AR-formation occurs from the hypocotyl and is enhanced by application of indole-3-butyric acid (IBA) combined with kinetin (Kin). The same IBA + Kin-treatment induces AR-formation in thin cell layers (TCLs). Auxin is the main inducer of AR-formation and xylogenesis in numerous species and experimental systems. Xylogenesis is competitive to AR-formation in Arabidopsis hypocotyls and TCLs. Jasmonates (JAs) negatively affect AR-formation in de-etiolated Arabidopsis seedlings, but positively affect both AR-formation and xylogenesis in tobacco dark-grown IBA + Kin TCLs. In Arabidopsis the interplay between JAs and auxin in AR-formation vs xylogenesis needs investigation. In de-etiolated Arabidopsis seedlings, the Auxin Response Factors ARF6 and ARF8 positively regulate AR-formation and ARF17 negatively affects the process, but their role in xylogenesis is unknown. The cross-talk between auxin and ethylene (ET) is also important for AR-formation and xylogenesis, occurring through EIN3/EIL1 signalling pathway. EIN3/EIL1 is the direct link for JA and ET-signalling. The research investigated JA role on AR-formation and xylogenesis in Arabidopsis dark-grown seedlings and TCLs, and the relationship with ET and auxin. The JA-donor methyl-jasmonate (MeJA), and/or the ET precursor 1-aminocyclopropane-1-carboxylic acid were applied, and the response of mutants in JA-synthesis and -signalling, and ET-signalling investigated. Endogenous levels of auxin, JA and JA-related compounds, and ARF6, ARF8 and ARF17 expression were monitored.

RESULTS

MeJA, at 0.01 μM, enhances AR-formation, when combined with IBA + Kin, and the response of the early-JA-biosynthesis mutant dde2-2 and the JA-signalling mutant coi1-16 confirmed this result. JA levels early change during TCL-culture, and JA/JA-Ile is immunolocalized in AR-tips and xylogenic cells. The high AR-response of the late JA-biosynthesis mutant opr3 suggests a positive action also of 12-oxophytodienoic acid on AR-formation. The crosstalk between JA and ET-signalling by EIN3/EIL1 is critical for AR-formation, and involves a competitive modulation of xylogenesis. Xylogenesis is enhanced by a MeJA concentration repressing AR-formation, and is positively related to ARF17 expression.

CONCLUSIONS

The JA concentration-dependent role on AR-formation and xylogenesis, and the interaction with ET opens the way to applications in the micropropagation of recalcitrant species.

A comparative study of cambium histology of Ceiba speciosa (A. St.-Hil.) Ravenna (Malvaceae) under urban pollution

Air pollution is considered to be one of the main causes of forest decline. The cambium is responsible for increase in tree girth, and its functioning is determined by environmental pressures. This study compared cambium histology of Ceiba speciosa (A. St.-Hil.) Ravenna (Malvaceae) in polluted and preserved sites in the Atlantic Rainforest domain. Samples were obtained during periods of cambial activity and dormancy and were processed and examined according to standard light microscopy techniques. In addition to differences typically observed in cambium during periods of activity and dormancy, the fusiform initials were shorter in trees of the polluted site. Furthermore, cambial rays were shorter, but larger, in the polluted site. It should be noted that all parameters related to cambial rays showed significant differences between the study sites. This is the first report of the effects of pollution on cambial activity in a South American species. The results suggest a tolerance of C. speciosa to pollution and reveal this species to be an important biomarker for environmental monitoring studies.

Xylogenesis in zinnia (Zinnia elegans) cell cultures: unravelling the regulatory steps in a complex developmental programmed cell death event

MAIN CONCLUSION

Physiological and molecular studies support the view that xylogenesis can largely be determined as a specific form of vacuolar programmed cell death (PCD). The studies in xylogenic zinnia cell culture have led to many breakthroughs in xylogenesis research and provided a background for investigations in other experimental models in vitro and in planta . This review discusses the most essential earlier and recent findings on the regulation of xylem elements differentiation and PCD in zinnia and other xylogenic systems. Xylogenesis (the formation of water conducting vascular tissue) is a paradigm of plant developmental PCD. The xylem vessels are composed of fused tracheary elements (TEs)-dead, hollow cells with patterned lignified secondary cell walls. They result from the differentiation of the procambium and cambium cells and undergo cell death to become functional post-mortem. The TE differentiation proceeds through a well-coordinated sequence of events in which differentiation and the programmed cellular demise are intimately connected. For years a classical experimental model for studies on xylogenesis was the xylogenic zinnia (Zinnia elegans) cell culture derived from leaf mesophyll cells that, upon induction by cytokinin and auxin, transdifferentiate into TEs. This cell system has been proven very efficient for investigations on the regulatory components of xylem differentiation which has led to many discoveries on the mechanisms of xylogenesis. The knowledge gained from this system has potentiated studies in other xylogenic cultures in vitro and in planta. The present review summarises the previous and latest findings on the hormonal and biochemical signalling, metabolic pathways and molecular and gene determinants underlying the regulation of xylem vessels differentiation in zinnia cell culture. Highlighted are breakthroughs achieved through the use of xylogenic systems from other species and newly introduced tools and analytical approaches to study the processes. The mutual dependence between PCD signalling and the differentiation cascade in the program of TE development is discussed.

Rich at different altitudes

BACKGROUND

The dynamics of cambial activity and xylogenesis provide information on how and to what extent wood formation respond to climatic variability. The Lebanon Cedar (Cedrus libani A.Rich) is a montane tree species which is distributed along a wide altitudinal range in the northeastern Mediterranean region, currently considered as a potential forest species for Central Europe with respect to climate change. This study provides first data on intra-annual growth dynamics at cellular level using the microcore technique for a montane Mediterranean tree species at different altitudes within and outside its natural range.

RESULTS

Microcores were collected fortnightly in the growing season of 2013 in order to study temporal dynamics of cambial activity and xylogenesis in stems of C. libani at different altitudes in the Taurus Mountains (1000 - 2000 m a.s.l.) and at a plantation at Bayreuth (330 m a.s.l.; Germany). The dormant cambium consisted of about 5 cells at the Turkish sites and 7 cells at Bayreuth. Cambial activity set in, when daily minimum temperatures exceeded 0 °C and daily means of air and stem temperature exceeded 5 °C. Xylogenesis started between April and May, ended approximately the end of September to the beginning of October and lasted 134 (at tree line) to 174 days (at the lowest Turkish site). Mean ring widths varied from 0.55 to 3.35 mm, with highest values observed at Bayreuth very likely resulting from a steady water supply during growing season. Means of daily cell production rates varied from 0.73 to 0.12. Samples containing traumatic resin ducts occurred only rarely and where not used for analysis.

CONCLUSIONS

In C. libani, onset and dynamics of cambial activity and xylogenesis are triggered by daily means of stem and air temperatures whereas water availability has a higher influence on growth rates and cessation of wood formation. Within sites, duration of xylogenesis does not significantly differ with respect to age and tree size. C. libani grows well outside its natural range and thus may be a promising species for forestation in Central Europe with respect to climate change. We suggest further studies on if/how traumatic resin ducts influence tree ring width.

In vitro protein profiles in the early and late stages of Douglas-fir xylogenesis

The process of wood formation is of great interest to control and manipulate wood quality for economically important gymnosperms. A Douglas-fir tissue culture system was developed that could be induced to differentiate into tracheary elements (fibers) making it possible to monitor xylogenesis in vitro by a proteomics approach. Two proteomes were analyzed and compared, one from an early and one from a late stage of the fiber differentiation process. After 18 weeks in a differentiation-inducing medium, 80% of the callus cells were elongated while 20% showed advanced spiral thickening indicating full wood fiber differentiation. Based on 2D electrophoresis, MS, and data analyses (data are available via ProteomeXchange with identifier PXD001484.), it was shown that in nondifferentiated callus (representing an early stage of development), proteins related to protein metabolism, cellular energy, and primary cell wall metabolism were abundant. By comparison, in cells actively differentiating wood fibers (representing a late stage of development), proteins involved in cell wall polysaccharide biosynthesis predominated together with housekeeping and stress-associated proteins.

Lignin and lignans in plant defence: insight from expression profiling of cinnamyl alcohol dehydrogenase genes during development and following fungal infection in Populus

Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step in the biosynthesis of monolignol, the main component of lignin. Lignins, deposited in the secondary cell wall, play a role in plant defence against pathogens. We re-analysed the phylogeny of CAD/CAD-like genes using sequences from recently sequenced genomes, and analysed the temporal and spatial expression profiles of CAD/CAD-like genes in Populus trichocarpa healthy and infected plants. Three fungal pathogens (Rhizoctonia solani, Fusarium oxysporum, and Cytospora sp.), varying in lifestyle and pathogenicity, were used for plant infection. Phylogenetic analyses showed that CAD/CAD-like genes were distributed in classes represented by all members from angiosperm lineages including basal angiosperms and Selaginella. The analysed genes showed different expression profiles during development and demonstrated that three genes were involved in primary xylem maturation while five may function in secondary xylem formation. Expression analysis following inoculation with fungal pathogens, showed that five genes were induced in either stem or leaves. These results add further evidence that CAD/CAD-like genes have evolved specialised functions in plant development and defence against various pest and pathogens. Two genes (PoptrCAD11 and PoptrCAD15), which were induced under various stresses, could be treated as universal markers of plant defence using lignification or lignan biosynthesis.

Xylem and phloem phenology in co-occurring conifers exposed to drought

KEY MESSAGE

Variability in xylem and phloem phenology among years and species is caused by contrasting temperatures prevailing at the start of the growing season and species-specific sensitivity to drought.

ABSTRACT

The focus of this study was to determine temporal dynamics of xylem and phloem formation in co-occurring deciduous and evergreen coniferous species in a dry inner Alpine environment (750 m a.s.l., Tyrol, Austria). By repeated micro-sampling of the stem, timing of key phenological dates of xylem and phloem formation was compared among mature Pinus sylvestris, Larix decidua and Picea abies during two consecutive years. Xylem formation in P. sylvestris started in mid and late April 2011 and 2012, respectively, and in both years about 2 week later in P. abies and L. decidua. Phloem formation preceded xylem formation on average by 3 week in P. sylvestris, and c. 5 week in P. abies and L. decidua. Based on modeled cell number increase, tracheid production peaked between early through late May 2011 and late May through mid-June 2012. Phloem formation culminated between late April and mid-May in 2011 and in late May 2012. Production of xylem and phloem cells continued for about 4 and 5-6 months, respectively. High variability in xylem increment among years and species is related to exogenous control by climatic factors and species-specific sensitivity to drought, respectively. On the other hand, production of phloem cells was quite homogenous and showed asymptotic decrease with respect to xylem cells indicating endogenous control. Results indicate that onset and culmination of xylem and phloem formation are controlled by early spring temperature, whereby strikingly advanced production of phloem compared to xylem cells suggests lower temperature requirement for initiation of the former.