Towards optimizing wood development in bioenergy trees

To secure a sustainable energy source for the future, we need to develop an alternative to fossil fuels. Cellulose-based biofuel production has great potential for development into a sustainable and renewable energy source. The thick secondary walls of xylem cells provide a natural source of cellulose. As a result of the extensive production of wood through cambial activity, massive amounts of xylem cells can be harvested from trees. How can we obtain a maximal cellulose biomass yield from these trees? Thus far, tree breeding has been very challenging because of the long generation time. Currently, new breeding possibilities are emerging through the development of high-throughput technologies in molecular genetics. What potential does our current knowledge on the regulation of cambial activity provide for the domestication of optimal bioenergy trees? We examine the hormonal and molecular regulation of wood development with the aim of identifying the key regulatory aspects. We describe traits, including stem morphology and xylem cell dimensions, that could be modified to enhance wood production. Finally, we discuss the potential of novel marker-assisted tree breeding technologies.     

Bioenergy production and forest landscape change in the southeastern United States

Production of woody biomass for bioenergy, whether wood pellets or liquid biofuels, has the potential to cause substantial landscape change and concomitant effects on forest ecosystems, but the landscape effects of alternative production scenarios have not been fully assessed. We simulated landscape change from 2010 to 2050 under five scenarios of woody biomass production for wood pellets and liquid biofuels in North Carolina, in the southeastern United States, a region that is a substantial producer of wood biomass for bioenergy and contains high biodiversity. Modeled scenarios varied biomass feedstocks, incorporating harvest of ‘conventional’ forests, which include naturally regenerating as well as planted forests that exist on the landscape even without bioenergy production, as well as purpose‐grown woody crops grown on marginal lands. Results reveal trade‐offs among scenarios in terms of overall forest area and the characteristics of the remaining forest in 2050. Meeting demand for biomass from conventional forests resulted in more total forest land compared with a baseline, business‐as‐usual scenario. However, the remaining forest was composed of more intensively managed forest and less of the bottomland hardwood and longleaf pine habitats that support biodiversity. Converting marginal forest to purpose‐grown crops reduced forest area, but the remaining forest contained more of the critical habitats for biodiversity. Conversion of marginal agricultural lands to purpose‐grown crops resulted in smaller differences from the baseline scenario in terms of forest area and the characteristics of remaining forest habitats. Each scenario affected the dominant type of land‐use change in some regions, especially in the coastal plain that harbors high levels of biodiversity. Our results demonstrate the complex landscape effects of alternative bioenergy scenarios, highlight that the regions most likely to be affected by bioenergy production are also critical for biodiversity, and point to the challenges associated with evaluating bioenergy sustainability.     

Projected gains and losses of wildlife habitat from bioenergy‐induced landscape change

Domestic and foreign renewable energy targets and financial incentives have increased demand for woody biomass and bioenergy in the southeastern United States. This demand is expected to be met through purpose‐grown agricultural bioenergy crops, short‐rotation tree plantations, thinning and harvest of planted and natural forests, and forest harvest residues. With results from a forest economics model, spatially explicit state‐and‐transition simulation models, and species–habitat models, we projected change in habitat amount for 16 wildlife species caused by meeting a renewable fuel target and expected demand for wood pellets in North Carolina, USA. We projected changes over 40 years under a baseline ‘business‐as‐usual’ scenario without bioenergy production and five scenarios with unique feedstock portfolios. Bioenergy demand had potential to influence trends in habitat availability for some species in our study area. We found variation in impacts among species, and no scenario was the ‘best’ or ‘worst’ across all species. Our models projected that shrub‐associated species would gain habitat under some scenarios because of increases in the amount of regenerating forests on the landscape, while species restricted to mature forests would lose habitat. Some forest species could also lose habitat from the conversion of forests on marginal soils to purpose‐grown feedstocks. The conversion of agricultural lands on marginal soils to purpose‐grown feedstocks increased habitat losses for one species with strong associations with pasture, which is being lost to urbanization in our study region. Our results indicate that landscape‐scale impacts on wildlife habitat will vary among species and depend upon the bioenergy feedstock portfolio. Therefore, decisions about bioenergy and wildlife will likely involve trade‐offs among wildlife species, and the choice of focal species is likely to affect the results of landscape‐scale assessments. We offer general principals to consider when crafting lists of focal species for bioenergy impact assessments at the landscape scale.     

Cloning and characterization of cellulose synthase-like gene, PtrCSLD2 from developing xylem of aspen trees

Genetic improvement of cell wall polymer synthesis in forest trees is one of the major goals of forest biotechnology that could possibly impact their end product utilization. Identification of genes involved in cell wall polymer biogenesis is essential for achieving this goal. Among various candidate cell wall-related genes, cellulose synthase-like D (CSLD) genes are intriguing due to their hitherto unknown functions in cell wall polymer synthesis but strong structural similarity with cellulose synthases (CesAs) involved in cellulose deposition. Little is known about CSLD genes from trees. In the present article PtrCSLD2, a first CSLD gene from an economically important tree, aspen (Populus tremuloides) is reported. PtrCSLD2 cDNA was isolated from an aspen xylem cDNA library and encodes a protein that shares 90% similarity with Arabidopsis AtCSLD3 protein involved in root hair tip growth. It is possible that xylem fibers that also grow by intrusive tip growth may need expression of PtrCSLD2 for controlling the length of xylem fibers, a wood quality trait of great economical importance. PtrCSLD2 protein has a N-terminal cysteine-rich putative zinc-binding domain; eight transmembrane domains; alternating conserved and hypervariable domains; and a processive glycosyltransferases signature, D, D, D, QXXRW; all similar to aspen CesA proteins. However, PtrCSLD2 shares only 43-48% overall identity with the known aspen CesAs suggesting its distinct functional role in cell wall polymer synthesis perhaps other than cellulose biosynthesis. Based on Southern analysis, the aspen CSLD gene family consists of at least three genes and this gene copy estimate is supported by phylogenetic analysis of available CSLDs from plants. Moreover, gene expression studies using RT-PCR and in situ mRNA hybridization showed that PtrCSLD2 is expressed at a low level in all aspen tissues examined with a slightly higher expression level in secondary cell wall-enriched aspen xylem as compared to primary cell wall enriched tissues. Together, these observations suggest that PtrCSLD2 gene may be involved in the synthesis of matrix polysaccharides that are dominant in secondary cell walls of poplar xylem. Future molecular genetic analyses will clarify the functional significance of CSLD genes in the development of woody trees.     

Damaged forests provide an opportunity to mitigate climate change

British Columbia (BC) forests are estimated to have become a net carbon source in recent years due to tree death and decay caused primarily by mountain pine beetle (MPB) and related post‐harvest slash burning practices. BC forest biomass has also become a major source of wood pellets, exported primarily for bioenergy to Europe, although the sustainability and net carbon emissions of forest bioenergy in general are the subject of current debate. We simulated the temporal carbon balance of BC wood pellets against different reference scenarios for forests affected by MPB in the interior BC timber harvesting area using the Carbon Budget Model of the Canadian Forest Sector (CBM‐CFS3). We evaluated the carbon dynamics for different insect‐mortality levels, at the stand‐ and landscape level, taking into account carbon storage in the ecosystem, wood products and fossil fuel displacement. Our results indicate that current harvesting practices, in which slash is burnt and only sawdust used for pellet production, require between 20–25 years for beetle‐impacted pine and 37–39 years for spruce‐dominated systems to reach pre‐harvest carbon levels (i.e. break‐even) at the stand‐level. Using pellets made from logging slash to replace coal creates immediate net carbon benefits to the atmosphere of 17–21 tonnes C ha^?1, shortening these break‐even times by 9–20 years and resulting in an instant carbon break‐even level on stands most severely impacted by the beetle. Harvesting pine dominated sites for timber while using slash for bioenergy was also found to be more carbon beneficial than a protection reference scenario on both stand‐ and landscape level. However, harvesting stands exclusively for bioenergy resulted in a net carbon source unless the system contained a high proportion of dead trees (>85%). Systems with higher proportions of living trees provide a greater climate change mitigation if used for long lived wood products.     

Xylem-specific and tension stress-responsive coexpression of KORRIGAN endoglucanase and three secondary wall-associated cellulose synthase genes in aspen trees

In nature, angiosperm trees develop tension wood on the upper side of their leaning trunks and drooping branches. Development of tension wood is one of the straightening mechanisms by which trees counteract leaning or bending of stem and resume upward growth. Tension wood is characterized by the development of a highly crystalline cellulose-enriched gelatinous layer next to the lumen of the tension wood fibers. Thus experimental induction of tension wood provides a system to understand the process of cellulose biosynthesis in trees. Since KORRIGAN endoglucanases (KOR) appear to play an important role in cellulose biosynthesis in Arabidopsis, we cloned PtrKOR, a full-length KOR cDNA from aspen xylem. Using RT-PCR, in situ hybridization, and tissue-print assays, we show that PtrKOR gene expression is significantly elevated on the upper side of the bent aspen stem in response to tension stress while KOR expression is significantly suppressed on the opposite side experiencing compression stress. Moreover, three previously reported aspen cellulose synthase genes, namely, PtrCesA1, PtrCesA2, and PtrCesA3 that are closely associated with secondary cell wall development in the xylem cells exhibited similar tension stress-responsive behavior. Our results suggest that coexpression of these four proteins is important for the biosynthesis of highly crystalline cellulose typically present in tension wood fibers. Their simultaneous genetic manipulation may lead to industrially relevant improvement of cellulose in transgenic crops and trees.Suchita Bhandari and Takeshi Fujino contributed equally to this research.     

Tree genetic engineering and applications to sustainable forestry and biomass production

Forest trees provide raw materials, help to maintain biodiversity and mitigate the effects of climate change. Certain tree species can also be used as feedstocks for bioenergy production. Achieving these goals may require the introduction or modified expression of genes to enhance biomass production in a sustainable and environmentally responsible manner. Tree genetic engineering has advanced to the point at which genes for desirable traits can now be introduced and expressed efficiently; examples include biotic and abiotic stress tolerance, improved wood properties, root formation and phytoremediation. Transgene confinement, including flowering control, may be needed to avoid ecological risks and satisfy regulatory requirements. This and stable expression are key issues that need to be resolved before transgenic trees can be used commercially.     

Forest biotechnology: Innovative methods, emerging opportunities

Summary The productivity of plantation forests is essential to meet the future world demand for wood and wood products in a sustainable fashion and in a manner that preserves natural stands and biodiversity. Plantation forestry has enormously benefited from development and implementation of improved silvicultural and forest management practices during the past century. A second wave of improvements has been brought about by the introduction of new germplasm developed through genetics and breeding efforts for both hardwood and conifer tree species. Coupled with the genetic gains achieved through tree breeding, the emergence of new biotechnological approaches that span the fields of plant developmental biology, genetic transformation, and discovery of genes associated with complex multigenic traits have added a new dimension to forest tree improvement programs. Significant progress has been made during the past five years in the area of plant regeneration via organogenesis and somatic embryogenesis (SE) for economically important tree species. These advances have not only helped the development of efficient gene transfer techniques, but also have opened up avenues for deployment of new high-performance clonally replicated planting stocks in forest plantations. One of the greatest challenges today is the ability to extend this technology to the most elite germplasm, such that it becomes an, economically feasible means for large-scale production and delivery of improved planting stock. Another challenge will be the ability of the forestry research community to capitalize rapidly on current and future genomics-based elucidation of the underlying mechanisms for important but complex phenotypes. Advancements in gene cloning and genomics technology in forest trees have enabled the discovery and introduction of value-added traits for wood quality and resistance to biotic and abiotic stresses into improved genotypes. With these technical advancements, it will be necessary for reliable regulatory infrastructures and processes to be in place worldwide for testing and release of trees improved through biotechnology. Commercialization of planting stocks, as new varieties generated through clonal propagation and advanced breeding programs or as transgenic trees with high-value traits, is expected in the near future, and these trees will enhance the quality and productivity of our plantation forests.     

Learning from methylomes: epigenomic correlates of Populus balsamifera traits based on deep learning models of natural DNA methylation

Epigenomes have remarkable potential for the estimation of plant traits. This study tested the hypothesis that natural variation in DNA methylation can be used to estimate industrially important traits in a genetically diverse population of Populus balsamifera L. (balsam poplar) trees grown at two common garden sites. Statistical learning experiments enabled by deep learning models revealed that plant traits in novel genotypes can be modelled transparently using small numbers of methylated DNA predictors. Using this approach, tissue type, a nonheritable attribute, from which DNA methylomes were derived was assigned, and provenance, a purely heritable trait and an element of population structure, was determined. Significant proportions of phenotypic variance in quantitative wood traits, including total biomass (57.5%), wood density (40.9%), soluble lignin (25.3%) and cell wall carbohydrate (mannose: 44.8%) contents, were also explained from natural variation in DNA methylation. Modelling plant traits using DNA methylation can capture tissue‐specific epigenetic mechanisms underlying plant phenotypes in natural environments. DNA methylation‐based models offer new insight into natural epigenetic influence on plants and can be used as a strategy to validate the identity, provenance or quality of agroforestry products.     

A spatial assessment of potential biomass for bioenergy in Australia in 2010, and possible expansion by 2030 and 2050

This paper provides spatial estimates of potentially available biomass for bioenergy in Australia in 2010, 2030 and 2050 (under clearly stated assumptions) for the following biomass sources: crop stubble, native grasses, pulpwood and residues (created either during forest harvesting or wood processing) from plantations and native forests, bagasse, organic municipal solid waste and new short‐rotation tree crops. For each biomass type, we estimated annual potential availability at the finest scale possible with readily accessible data, and then aggregated to make estimates for each of 60 Statistical Divisions (administrative areas) across Australia. The potentially available lignocellulosic biomass is estimated at approximately 80 Mt per year, with the major contributors of crop stubble (27.7 Mt per year), grasses (19.7 Mt per year) and forest plantations (10.9 Mt per year). Over the next 20–40 years, total potentially available biomass could increase to 100–115 Mt per year, with new plantings of short‐rotation trees being the major source of the increase (14.7 Mt per year by 2030 and 29.3 Mt per year by 2050). We exclude oilseeds, algae and ‘regrowth’, that is woody vegetation naturally regenerating on previously cleared land, which may be important in several regions of Australia (Australian Forestry 77 , 2014, 1; Global Change Biology Bioenergy 7 , 2015, 497). We briefly discuss some of the challenges to providing a reliable and sustainable supply of the large amounts of biomass required to build a bioenergy industry of significant scale. More detailed regional analyses, including of the costs of delivered biomass, logistics and economics of harvest, transport and storage, competing markets for biomass and a full assessment of the sustainability of production are needed to underpin investment in specific conversion facilities (e.g. Opportunities for forest bioenergy: An assessment of the environmental and economic opportunities and constraints associated with bioenergy production from biomass resources in two prospective regions of Australia, 2011a).     

Forest bioenergy climate impact can be improved by allocating forest residue removal

Bioenergy from forest residues can be used to avoid fossil carbon emissions, but removing biomass from forests reduces carbon stock sizes and carbon input to litter and soil. The magnitude and longevity of these carbon stock changes determine how effective measures to utilize bioenergy from forest residues are to reduce greenhouse gas (GHG) emissions from the energy sector and to mitigate climate change. In this study, we estimate the variability of GHG emissions and consequent climate impacts resulting from producing bioenergy from stumps, branches and residual biomass of forest thinning operations in Finland, and the contribution of the variability in key factors, i.e. forest residue diameter, tree species, geographical location of the forest biomass removal site and harvesting method, to the emissions and their climate impact. The GHG emissions and the consequent climate impacts estimated as changes in radiative forcing were comparable to fossil fuels when bioenergy production from forest residues was initiated. The emissions and climate impacts decreased over time because forest residues were predicted to decompose releasing CO₂ even if left in the forest. Both were mainly affected by forest residue diameter and climatic conditions of the forest residue collection site. Tree species and the harvest method of thinning wood (whole tree or stem‐only) had a smaller effect on the magnitude of emissions. The largest reduction in the energy production climate impacts after 20 years, up to 62%, was achieved when coal was replaced by the branches collected from Southern Finland, whereas the smallest reduction 7% was gained by using stumps from Northern Finland instead of natural gas. After 100 years the corresponding values were 77% and 21%. The choice of forest residue biomass collected affects significantly the emissions and climate impacts of forest bioenergy.     

Will genomics guide a greener forest biotech?

Forest biotechnology has been increasingly associated with wood production using plantation forestry, and has stressed applications that use pedigreed material and transgenic trees. Reasons for this emphasis include limitations of available technologies to conform to underlying genetic features of undomesticated forest tree populations. More recently, genomic technologies have rapidly begun to expand the scope of forest biotechnology. Genomic technologies are well suited to describe and make use of the abundant genetic variation present in undomesticated forest tree populations. Genomics thus enables new research and applications for conservation and management of natural forests, and is a primary technological driver for new research addressing the use of forests trees for carbon sequestration, biofuels feedstocks, and other 'green' applications.     

Association genetics in Corymbia citriodora subsp. variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield

Wood is an important biological resource which contributes to nutrient and hydrology cycles through ecosystems, and provides structural support at the plant level. Thousands of genes are involved in wood development, yet their effects on phenotype are not well understood. We have exploited the low genomic linkage disequilibrium (LD) and abundant phenotypic variation of forest trees to explore allelic diversity underlying wood traits in an association study. Candidate gene allelic diversity was modelled against quantitative variation to identify SNPs influencing wood properties, growth and disease resistance across three populations of Corymbia citriodora subsp. variegata, a forest tree of eastern Australia. Nine single nucleotide polymorphism (SNP) associations from six genes were identified in a discovery population (833 individuals). Associations were subsequently tested in two smaller populations (130-160 individuals), 'validating' our findings in three cases for actin 7 (ACT7) and COP1 interacting protein 7 (CIP7). The results imply a functional role for these genes in mediating wood chemical composition and growth, respectively. A flip in the effect of ACT7 on pulp yield between populations suggests gene by environment interactions are at play. Existing evidence of gene function lends strength to the observed associations, and in the case of CIP7 supports a role in cortical photosynthesis.