B_Introduction
B_1. Earth Metabolome Initiative
The Earth Metabolome Initiative (EMI) was founded in 2022 by Pierre-Marie Allard (UNIFR) and Emmanual Defossez (UNINE). It is a collective open science project aiming to better understand the metabolomic on our planet.
The goal of the Earth Metabolome Initiatve is similar in scale to the Earth Biogenome Project. Yet instead of gene diversity, it takes an interest in chemical diversity (chemiodiversity). Its goal is simple, yet ambitious: Document the entirety of the chemiodiversity of all known living organisms, from the humblest of bacteria to the gigantic redwood. All the while anthropogenic biodiversity loss is speeding up.
Similarly to the Human Genome Project, which was an ambitious project aswell, the means necessary to achieve the goal of the EMI are massive and wouldn't have been reachable without the collaboration of many teams from around the world. Yet the benefits Humanity sowed from it were enormous (development in bioarcheology, evolution, forensic sciences, animal husbandry, ...). Like the Human Genome project, the EMI should benefit Humanity as a whole, by helping better understand the chemical fundations of the biosphere, help develop biosinspired drugs, providing molecular arguments in favor of the protection of biodiversity.
It roots for the creation of a new web of knowledge, linking metabolomics, biology, chemistry, and other open datasets together. To reach this goal, the EMI team will have to develop informatical, organisational, and scientific tools tailor made for its needs. This is where the Digital Botanical Gardens Initiative (DBGI) comes into place (The EMI Consortium., 2022).
B_2. Digital Botanical Gardens Initiative
The Digital Botanical Gardens Initiative (DBGI) is designed as a pilot of the EMI. It has a central role to play in it as its goals are to design, automate, and optimize the workflow leading to metabolomic analysis. Said workflow has to be scalable to be appliable to the EMI.
Its main goal is the collection, management, and sharing of digital informations and physical dryed plant samples acquired in living botanical collections. To do so, it focuses on large scale characterisation of the chemiodiverstiy of plants through mass spectrometric approaches. Not to forget the creation of a knowledge graphe by recouping the informations from many databases (such as Botalista, Open tree of life (Rutz et al. 2022), LOTUS (Rutz et al. 2019), ...) to organise, structure and connect them all.
As the methods of the DBGI will be applied to the EMI, its methods and workflow need to be scalable to match the scale of such an ambitious project. And ultimately, be applicable in wild, hard to reach ecosystems. This should help visualise and search the functioning of ecosystems, orient research and conservation efforts.
Using botanical gardens as a stepping stone to reach your goal of having a methodology usable in wild, uncotrolled environment makes sense. Indeed, as botanical gardens are semi-controlled environment it is a sensible middle point to use them to test new methodology.. The DBGI restricts itself to botanical gardens for they are species rich, easily accessible, somewhat controlled environment.
As of now, only the Jardin Botanique de l'Université de Fribourg (JBUF) and the Jardin Botanique de Neuchâtel (JBN) are part of the initiative. The causes being practical, founding teams have their offices located in Fribourg and Neuchâtel respectively, and ther unique characteristics, the JBUF organised a part of its collection according to the APG IV (UNIFR about JBUF), and the JBN has a plants collection of ethnomedicinal value (The DBGI Consortium, 2022).
B_3. Definition of "tree"
Defining what a tree is might seem childish at first glance. However, this simple question is all the more relevant as many definitions exist (Lund, 2015), but none seem to be universally agreed upon in botany (Hallé, 2008).
Phylogeny leaves us somewhat clueless to what a tree is, as tree-like growth forms appeared indepentently many time through Life's long history. Indeed, lycopods, ferns, sphenopsids, gymnosperms and a few families of angiosperms, such as palms, Dracaena, Fagaceae, Malvaceae, ... (John, Peter, 2007) all came up with their own version of what we would today call a tree. The first modern tree, Archaeopteris appeared during the Devonian (Meyer-Berthaud et all,. 1999) period forming large forests. It lived through the Carboniferous aswell, where it formed massive forests along Equisetaceae of the family Lepidondendron (Fairon-Demaret, 1986), (Barry, 1978). Still observable to this day, the tree ferns (Cyatheales) are also a fascinanting exemple of non-spermatophytes arborescent growth forms.
The JBUF has been using sigils provided in the "Zander. Handwörterbuch der Pflanzennamen", a horticultural dictionnary, as a taxonomic basis to classify their plants. In horticulture, a tree is often described as a plant producing a lignified trunk and reaching a minimum of 4 meters in height in its adult stage. As it is somewhat arbitrary, and wouldn't be applicable to many plants one would call a tree, this definition doesn't seem relevant in the context of the DBGI.
A more scientific way of describing what a tree is would be to use the life forms of the Raunkier system, which are the Phanerophytes, the Epiphytes, the Chamaephytes, the Hemicryptophytes, the Cryptophytes, the Therophytes, the Aerophytes, the Geophytes, the Helophytes, the Hydrophytes, in order to separate the different forms of plants. In our case, all the trees would fall into the category of the phanerophytes. However, this category doesn't allow to differentiate between bush, shrubs, and trees. This, in itself is a big enough problem. The Raunkier system is based on the location of the plant's growth-point during seasons providing adverse conditions, such as cold, and dry seasons. Thus excluding plants living in environment presenting only good seasons, i.e. tropical plants. As the DBGI, and by extension the EMI, is a project of international scope, the Raunkier system doesn't seem to provide a relevant definition. Furthermore, it defines the lignification of the trunk as a necessary criteria for being a tree and the presence of a single trunk. Excluding many arborescent growth forms people would consider trees such as the banana tree, thuja, or the papaya tree in the process.
In this regard, the definition suggested by Francis Hallé seems more suited to the international ideal of the EMI as it doesn't go against the personal intuition of what a tree is, independently of time and space. It originally reads as follow:
Un arbre est une plante habituellement pérenne possédant un ou plusieurs tronc à croissance verticale. Son anatomie rend le tronc autoportant et lui permet d'élever au-dessus des plantes voisines, concurrentes pour la lumière, une cime, ou couronne qui selon les espèces peut avoir trois constitutions différentes:
- De grandes feuilles si l'arbre n'a pas de branches;
- Des branches qui assurent la photosynthèse si les feuilles sont trop petite pour assurer cette fonction ou absentes;
- Des branches feuillées dans le cas général.
- Enfin, l’arbre est un «grand» végétal. Sa hauteur, le diamètre de son tronc, sa longévité sont évalués au regard des dimensions et de la durée de vie de l’être humain.
Which could be roughly translated as :
A tree is a generally perennial plant possessing one or more trunk growing vertically. Its anatomy makes the trunk self-supporting, allowing to rise above its neighbours, competitors for light, a summit, or crown, which, can have three different constitutions depending on the species:
- Large leaves if the tree doesn't have any branches; - Branches ensuring photosynthesis if the leaves are to small to ensure this function, or absent; - Leafed branches in most cases.Finally, a tree is a "large" plant. Its height, the diameter of its trunk, its lifespan are evaluated taking human beings as a reference.
In short, a tree is a rather large plant, when compared to human standards, which grows a self-supporting trunk.
B_4. iNaturalist
All pictures taken while sampling are periodically uploaded on the iNaturalist website on the DBGI profile. This allows to confirm the belonging of a sampled individual to a certain species by external experts.
This tool is crucial for the DBGI, and mostly for the EMI, due to their scale. The quantity of organisms to sample is large. Therefore, specialists working on all branches of the tree of life are needed to reach the EMI's goal. Using iNaturalist allows to save up ressources by having a preexisting channel of access to them.
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