On the need to consider wood formation processes in global vegetation models and a suggested approach

Dynamic global vegetation models are key tools for interpreting and forecasting the responses of terrestrial ecosystems to climatic variation and other drivers. They estimate plant growth as the outcome of the supply of carbon through photosynthesis. However, growth is itself under direct control, and not simply controlled by the amount of available carbon. Therefore predictions by current photosynthesis driven models of large increases in future vegetation biomass due to increasing concentrations of atmospheric CO2 may be significant over-estimations. We describe how current understanding of wood formation can be used to reformulate global vegetation models, with potentially major implications for their behaviour

State-of-the-art capabilities in LPJ-GUESS

LPJ-GUESS is an advanced DGVM including detailed forest demography and management, croplands, wetlands, specialised arctic processes, emissions of nonCO2 GHGs and a highly flexible land-use change scheme which tracks transitions between different land-uses. It is the vegetation component of the EC-Earth CMIP6 ESM, the RCA-GUESS regional ESM, and also has a European mode operating at tree species level

Datasets and scripts used for the publication "Direct response of tree growth to soil water and its implications for terrestrial carbon cycle modelling"

This Dataset contains all data files and scripts necessary to replicate the analysis in the linked publication. The project was conducted as part of the Dissertation by the first author. Field data has been collected in Switzerland. A README file contains a description of all files and how they are generated or used in the analysis. Field data generation was funded by the Swiss National science foundation (projects INTEGRAL-121859, LOTFOR-150205, and CLIMWOOD-160077): TRW data have been included in Peters et al. 2017. The soil moisture was originally used in Peters et al. 2019 and the xylogenesis data in Cuny et al 2019. ABSTRACT of the publication: Wood growth constitutes the main process for long-term atmospheric C sequestration in vegetation. However, our understanding of the process of wood growth and its response to environmental drivers is limited. Current Dynamic Global Vegetation Models (DGVMs) are mainly photosynthesis-driven and thus do not explicitly include a direct environmental effect on tree growth. However, physiological evidence suggests that, to realistically model vegetation carbon allocation under increased climatic stressors, it is crucial to treat growth responses independently from photosynthesis. A plausible growth response suitable for global simulations in DGVMs has been lacking. Here, we present the first soil water-growth response function and parameter range for Larch and Spruce in a dry temperate forest, tested and parameterised at a site in a valley in the Swiss Alps. We present a new data-driven approach based on a combination of tree ring width records, growing season length and simulated sub-daily soil hydrology to parameterise ring width increment simulations. We found that a simple linear function, with an intercept at zero moisture stress, could explain up to 62.3% and 59.4% of observed tree ring widths for Larch and Spruce respectively and, importantly, the slope was much steeper than literature values for the effect of soil moisture on photosynthesis or stomatal conductance. For example, we found tree stem growth stops at a soil moisture potential of -0.47 MPa for Larch and -0.66 MPa for Spruce, whereas photosynthesis in trees stops at -1.2 MPa or later, depending on species and measurement method. These results are strong evidence that the response functions of source and sink processes are indeed very different in trees, and need to be considered separately to correctly assess vegetation responses to environmental change. Our results provide a parameterisation for the explicit representation of growth responses to soil water in vegetation models. Peters, R. L., Klesse, S., Fonti, P., & Frank, D. C. (2017). Contribution of climate vs. Larch budmoth outbreaks in regulating biomass accumulation in high-elevation forests. Forest Ecology and Management, 401, 147–158. https://doi.org/10.1016/j.foreco.2017.06.032 Peters, R. L., Speich, M., Pappas, C., Kahmen, A., Arx, G. von, Pannatier, E. G., Steppe, K., Treydte, K., Stritih, A., & Fonti, P. (2019). Contrasting stomatal sensitivity to temperature and soil drought in mature alpine conifers. Plant, Cell & Environment, 42(5), 1674–1689. https://doi.org/10.1111/pce.13500 Peters, R. L., Speich, M., Pappas, C., Kahmen, A., Arx, G. von, Pannatier, E. G., Steppe, K., Treydte, K., Stritih, A., & Fonti, P. (2019). Contrasting stomatal sensitivity to temperature and soil drought in mature alpine conifers. Plant, Cell & Environment, 42(5), 1674–1689. https://doi.org/10.1111/pce.1350

Development and interrogation of approaches to modelling xylogenesis with a view towards their suitability for inclusion in Dynamic Global Vegetation Models

This thesis aims to contribute to increased understanding and predictability of vegetation responses to changes in the environment. This is achieved via the development and interrogation of wood formation process formulations suitable for resolving hitherto missing growth processes in Dynamic Global Vegetation Models (DGVMs). Current understanding of environmental controls on plant carbon dynamics is encapsulated in DGVMs. These models are today largely ‘source-driven’, meaning that they assume growth to be the direct outcome of photosynthesis. Contrary to plant physiological evidence, they neglect that growth itself may be under stronger environmental controls than photosynthesis. If not considered in models, this may have large implications for projections of vegetation carbon dynamics and, ultimately, climate change. Testing the impact of including a growth sink in DGVMs has to date been hampered by the fact that we have limited understanding of sink processes and therefore lack an explicit sink representation for DGVMs. This thesis is a solution to this issue by providing a mechanistic approach, RINGSlite.1.0, to represent vegetation sink processes for trees in DGVMs, and so enables the source-driven paradigm to be challenged. To provide this mechanistic approach I first investigate the validity of the sink hypothesis using a data-driven method wherein I derive a soil-moisture growth (sink) response curve on the basis of tree ring observations and soil moisture simulations. Comparison of this new sink response curve against source response curves from observations and those currently in use in DGVMs confirms the sink limitation hypothesis under water stress for trees. This highlights the need for separate representation of the source and sink processes in DGVMs. I then review past and contemporary wood formation models and identify five critical features for a wood formation model required for global application. I use these features to modify an existing model and create RINGSlite.1.0, which I compare with other wood formation models in a Bayesian model-intercomparison framework. More testing is still required against additional observations at environmentally diverse sites to verify the usefulness of RINGSlite.1.0 globally. Nevertheless, the comparison reveals that RINGSlite.1.0 is the most validated by data at the non-water limited test site. The implications for resolving sink processes in DGVMs through wood formation are numerous. Firstly, it provides a more realistic sink response to the environment. Secondly, it allows for additional data sources to be used in model benchmarking, calibration and initialisation. Finally, through simulating wood formation responses to local environments, additional features such as ring width and density can serve as emergent functional traits and provide a mechanistic link to modelling ecological and hydrological processes in DGVMs

Wood structure explained by complex spatial source-sink interactions.

Wood is a remarkable material with great cultural, economic, and biogeochemical importance. However, our understanding of its formation is poor. Key properties that have not been explained include the anatomy of growth rings (with consistent transitions from low-density earlywood to high density latewood), strong temperature-dependence of latewood density (used for historical temperature reconstructions), the regulation of cell size, and overall growth-temperature relationships in conifer and ring-porous tree species. We have developed a theoretical framework based on observations on Pinus sylvestris L. in northern Sweden. The observed anatomical properties emerge from our framework as a consequence of interactions in time and space between the production of new cells, the dynamics of developmental zone widths, and the distribution of carbohydrates across the developing wood. Here we find that the diffusion of carbohydrates is critical to determining final ring anatomy, potentially overturning current understanding of how wood formation responds to environmental variability and transforming our interpretation of tree rings as proxies of past climates

3. Engagement through Training

Direct training requires substantial time and effort, but is one of the most effective ways to make people aware of the importance of Research Data Management (RDM) best practices. The following case studies are each aimed to engage researchers with research data through different training methods: Bring Your Own Data (B.Y.O.D.) workshop at the University of Cambridge; Methods Class Outreach at the University of Minnesota; PhD course at UiT The Arctic University of Norway; Open courses at UiT..

Realistic and Robust Reproducible Research for Biostatistics

The complexity of analysis pipelines in biomedical sciences poses a severe challenge for the transparency and reproducibility of results. Researchers are increasingly incorporating software development technologies and methods into their analyses, but this is a quickly evolving landscape and teams may lack the capabilities to set up their own complex IT infrastructure to aid reproducibility. Basing a reproducible research strategy on readily available solutions with zero or low set-up costs whilst maintaining technological flexibility to incorporate domain-specific software tools is therefore of key importance. We outline a practical approach for robust reproducibility of analysis results. In our examples, we rely exclusively on established open-source tools and free services. Special emphasis is put on the integration of these tools with best practices from software development and free online services for the biostatistics domain

Wood Formation Modeling - A Research Review and Future Perspectives.

Wood formation has received considerable attention across various research fields as a key process to model. Historical and contemporary models of wood formation from various disciplines have encapsulated hypotheses such as the influence of external (e.g., climatic) or internal (e.g., hormonal) factors on the successive stages of wood cell differentiation. This review covers 17 wood formation models from three different disciplines, the earliest from 1968 and the latest from 2020. The described processes, as well as their external and internal drivers and their level of complexity, are discussed. This work is the first systematic cataloging, characterization, and process-focused review of wood formation models. Remaining open questions concerning wood formation processes are identified, and relate to: (1) the extent of hormonal influence on the final tree ring structure; (2) the mechanism underlying the transition from earlywood to latewood in extratropical regions; and (3) the extent to which carbon plays a role as "active" driver or "passive" substrate for growth. We conclude by arguing that wood formation models remain to be fully exploited, with the potential to contribute to studies concerning individual tree carbon sequestration-storage dynamics and regional to global carbon sequestration dynamics in terrestrial vegetation models

Divergent responses of photosynthesis and wood growth to climatic drivers

Our understanding of the terrestrial carbon cycle is strongly focussed on C fixation in the leaf, the process of photosynthesis, while the process whereby trees actually sequester C in durable form, i.e., tissue growth, has received much less attention and is neglected in global vegetation models 1,2. Significant uncertainty exists in estimating the response of terrestrial C sequester to climatic change if photosynthesis and growth respond differently to environmental drivers 3. Here we analysed the long-term (1984-2010) annual aboveground growth biomass response (AABIper_area) across North America to temperature and precipitation by combining tree-ring observations and satellite-based tree stem-density variations. We discover a contrasting spatio-temporal pattern of climatic responses between photosynthesis and AABIper_area, resulting in a weak correlation of their inter-annual variations. Moreover, AABIper_area is significantly more strongly limited by climatic variability than is predicted by dynamic global vegetation models (DGVMs), with significant consequences for the predicted response to terrestrial C uptake projections. Our findings question current understanding of controls on terrestrial carbon cycling with major implications for future atmospheric CO 2 concentrations

Inter-annual and inter-species tree growth explained by phenology of xylogenesis.

Wood formation determines major long-term carbon (C) accumulation in trees and therefore provides a crucial ecosystem service in mitigating climate change. Nevertheless, we lack understanding of how species with contrasting wood anatomical types differ with respect to phenology and environmental controls on wood formation. In this study, we investigated the seasonality and rates of radial growth and their relationships with climatic factors, and the seasonal variations of stem nonstructural carbohydrates (NSC) in three species with contrasting wood anatomical types (red oak: ring-porous; red maple: diffuse-porous; white pine: coniferous) in a temperate mixed forest during 2017-2019. We found that the high ring width variability observed in both red oak and red maple was caused more by changes in growth duration than growth rate. Seasonal radial growth patterns did not vary following transient environmental factors for all three species. Both angiosperm species showed higher concentrations and lower inter-annual fluctuations of NSC than the coniferous species. Inter-annual variability of ring width varied by species with contrasting wood anatomical types. Due to the high dependence of annual ring width on growth duration, our study highlights the critical importance of xylem formation phenology for understanding and modelling the dynamics of wood formation