Botany and Mycology

Algae are a large and diverse assembly of photosynthetic eukaryotes that are divided into three major groups (green, brown and red algae) as well as diatoms, cyanobacteria and Dinoflagellates. They range from unicellular (e.g. Chlorella) to multicellular algae (e.g. seaweeds). Informatics developments, global biodiversity data standards and the capacity to record, link and retrieve digital specimen data have led to exciting new possibilities in collection management as well in facilitating digital access to specimen data (name, geographic origin, collector(s), collection date, ecology) and to associated biological data (images, DNA sequences, chemical composition). The algae collection in G is not well-documented and it is an ‘invisible collection.’ Algae Reveal plans to change this by reorganising the collection by major group, updating scientific names and digitally processing specimens (databasing / imaging). The focus will be on types and historical specimens, and those of scientific interest or that are nationally relevant. The digitised algae will be in the Swiss Virtual Natural History Collection, contributing to efforts to mobilize Swiss natural history collections. Algae Reveal will also provide algal names, databasing and scanning protocols and best practices in curating algae collections. The SwissCollNet funding is an unprecedented opportunity to curate this unique collection and make it physically and digitally accessible for biodiversity research.

Diatoms form a group of microscopic, unicellular algae found ubiquitously in aquatic habitats. Beside playing a key role in the planktonic food chain and global carbon cycle, they constitute highly sensitive bioindicators to monitor physical or chemical changes in water bodies. The Herbarium of ETH Zurich owns the biggest historical diatom collection of Switzerland by Dr Friedrich Meister (1860-1954), which served as basis for the first indigenous diatom flora, but also contains important foreign samples. We herewith propose to (i) inventory all the artefacts (about 2,000 raw probes, 12,000 microscope slides, 2,000 glass diapositives and several thousand reprints), (ii) bookmark 3,000 digitised notes and transcribe the most relevant information they entail (i.a. geographic origin and taxonomic content of the probes), (iii) scan all glass diapositives, and (iv) secure the connections between all the objects in a customised database. By making Meister’s legacy easily accessible, we will facilitate research aimed at evaluating the biotic integrity of streams and rivers in the face of pollution, climate change and the invasion of non-indigenous species in our country, support international taxonomic and systematic work necessitating Meister’s type material, lay the foundation for the (digital) management of Swiss diatom collections, and finally raise public awareness on the value of diatoms in various fields of biology.

More than 1,000 type specimens of bryophytes are hidden in the collection of the United Herbaria Zurich Z+ZT. Type specimens are preserved specimens that have been used to describe new species or subspecies. These type specimens are the physical evidence for the occurrence of organisms on our planet. They are therefore the most important specimens in our collections.

In this project, these hidden type specimens of bryophytes will be awakened from their slumber. In a first step, they will be professionally curated in order to protect them permanently from damage and loss. Then they will be photographed and the information on the labels is recorded in a database. Finally, all the information gathered will be made available online through several channels.

The aim of this project is to permanently conserve the type specimens of bryophytes in the collection of the United Herbaria Zurich Z+ZT and to make them visible to researchers and interested parties through digitisation. By making previously inaccessible data publicly available, this project contributes to enhancing bryological research in the fields of species knowledge and biodiversity.

The main objective of this project is the digitization of three herbaria of the Bündner Naturmuseum and selected herbarium collections from the Grisons maintained by the United Herbaria of Zürich. These collections consist of about 5000 and 10’000 herbarium specimens. They were collected at the end of the 19th century, or more recently until the beginning of the 21st century. The main collection areas are Chur, Davos, Arosa, Schanfigg, Bergell and the Upper Engadin.

The Bündner Naturmuseum owns 34 herbarium collections in total, of which one so far has been digitized in collaboration with the United Herbaria of Zürich. The long-term goal, however, is to digitize all herbaria. In order to ensure efficient digitization and optimal long-term conservation, the plant specimens are mounted on acid-free paper sheets. The digitization will be carried out at the United Herbaria of Zürich with their infrastructure.

The United Herbaria of Zürich comprise some 2.8 Mio vascular plant specimens, of which an estimate of some 80’000 to 100’000 have been collected in the Grisons, some 30’000 are already digitized and online accessible.

All digitized data will be made accessible online via the Swiss Virtual Natural History Collection (SVNHC) and, in part, the online platform of the United Herbaria of Zürich or Info Flora. This way, all digitized specimen information is online accessible for interested people and creates a large potential for future research and cooperation.

Herbaria are valuable tools for botanical, ecological and historical research and are unique testimonies of the flora of past centuries. For example, today, researchers use herbaria to illustrate and understand variations in biodiversity and the impact of climate change on biodiversity. The JURASSICA Museum has a large collection of herbaria illustrating the biodiversity of Swiss flora, and more specifically that of Jura. Currently, our interest focuses on three herbaria that were assembled locally during the 19th century by renowned botanists: Jules Thurmann, Jean-Amédée Watt and Francois Joseph Bonanomi. Despite a partial inventory of plant specimens, the exploitation of these herbaria is at its very beginning yet and requires more analysis and conservation efforts. In this project, we will select and work on the maintenance of the plates, the revision of the taxonomy and the establishment of a complete inventory of plant specimens that are present in the three herbaria. We will digitize these samples with high resolution and hope to upload more than 9,000 new specimens to online databases. Our goal is to ensure the physical and digital preservation of these precious herbaria, and to guarantee their visibility and accessibility to the scientific communities and to the public.

The Conservatory and Botanic Garden of Geneva and the Nature Museum of Sion hold important herbarium collections that are critical for our understanding of plant diversity, both regionally and internationally. Despite their relevance to knowledge of plant biodiversity, parts of these collections have been long unavailable for on-site consultation, and their digitization to make them accessible online has been impeded or slow. In the next couple of years, our institutions are joining efforts to curate, digitalize and make available online more than 30,000 specimens. Approximately 20,000 of these, stored in Geneva, are of plants of the sunflower family (Asteraceae) and are associated with the herbarium of the renowned Geneva botanist Georges Reuter. Approximately 12,000 of the specimens, stored in the Nature Museum of Sion, come from several important regional collections gathered in the highly biodiverse canton of Wallis. Through a close partnership between our institutions, including particularly exchanges of herbarium management practices and short-term internships for the technical staff, we aim to provide public access to a scientifically and historically critical set collections that until now have been largely inaccessible to the scientific community.

The Schaffhausen region is botanically very rich and very special in its composition. The first comprehensive compilation of the plant species was made by J.G. Laffon around 1850. With the completion of G. Kummer's Schaffhausen Flora about a hundred years later, Schaffhausen was one of the best floristically studied areas in Switzerland. To this day, however, the herbaria have not been processed and are thus only accessible to the public, research or nature conservation to a limited extent. With the SwissCollNet project, the two herbaria of Laffon and Kummer will be completely digitised from the end of 2022. This involves around 7000 herbarium specimens. The identification of each plant per sheet will first be checked. Subsequently, the available information on the collector, place of discovery and date are entered into the database and a photograph of the herbarium leaf is created. In the next step, the coordinates of the respective site are determined. After completion of the two-year project, the data will be publicly accessible. On the one hand, the data will be transmitted to national and international internet platforms and data centres. On the other hand, the herbarium specimens will go online as part of the virtual museum collection. In this way, the data can be used, e.g. for nature conservation work. In addition, these unique collections allow scientific evaluations of the changes in the flora of Schaffhausen over the last 150 years. In addition, the rich flora of Schaffhausen will once again receive increased attention, as public events are planned throughout the duration of the project.

The Gentianaceae family (ca. 1,800 species and 100 genera) occurs on all continents and in a wide range of habitats. In Switzerland, most taxa occupy fragile or threatened vegetation types. Within the United Herbaria of the University of Zurich (Z) and ETH Zurich (ZT), the Gentianaceae family comprises ca. 25,000 vouchers, of which half (52%) are indigenous. Thanks to a recent and complete inventory of our holdings, we know that 58 genera are represented in our herbaria and that the majority of the specimens (51%) are assigned to the emblematic genus Gentiana. We also estimate that more than 40% of the 727 inventoried species need to be corrected due to determination errors or obsolete nomenclature. This outdated classification notably prevents the integration of an important donation from 2020. We therefore propose to revise the integrity of the Gentianaceae family and simultaneously digitise (i.e. image, transcribe and georeference) all the specimens.

Our project aims at providing open access to the botanical collections of the Museums of Natural History in St.Gallen and Winterthur. For St.Gallen the main focus lies on the collection “Flora von St.Gallen und Appenzell”. The digitising of about 25’000 herbarium specimens includes capturing information on taxonomy, collector, collection date, habitat, locality of the finding place including georeferencing in the Swiss system of coordinates. At the same time, we also plan to scan the images of 45'000 specimens and link these digitally to the original label information. For scanning the specimens a suitable scanner will be purchased. Towards the end of the project all data including images will be uploaded to the SVNHC for public access. In addition to the digitization and imaging of the specimens a goal of this project is the transfer of knowledge and experience on herbarium digitization from the Natural History Museum of St.Gallen to Winterthur.

The study of brambles (Rubus L.) has been neglected for decades in Europe and Switzerland. Yet, a recent increase of interest for this complex taxonomic group fostered a high dynamic of interactions between Rubus specialists. In this sense, the MJBC play a central role, as they host an important collection of 9500 Rubus specimens, 4500 of which come from Philippe-Jacques Müller (1832-1889), a famous botanist of the 19th century who described many species. However, this collection, which has an international importance and a high scientific value, is not databased nor digitized and is poorly accessible to researchers, which makes it a perfect candidate project within the SwissCollNet initiative. Our project consists in a detailed research on this collection for making it accessible to scientists and to the public. To achieve this, the collection requires special reconditioning, taxonomic revision, digitization, databasing, as well as identification of type specimens. The taxonomic revision will be performed by Rubus specialists and the taxonomic expertise gained by our staff from the transfer of knowledge will enable a long-term monitoring of the collection. This project will have an important scientific impact and significantly contribute to the availability of natural history collections held in Switzerland.

Herbarium specimens are well suited for digital imagery, since many important features can be captured in one picture. The process of taking good quality images of large collections can be immensely accelerated by using a rapid digitalization process by conveyor belt that can photograph up to 4,000 specimens per day. For this technique, the specimens require a certain quality (mounted on herbarium sheets, good condition and correctly labelled). The herbaria of the Botanical Garden of the University of Bern (BOGA) and the Naturama Aargau (NAAG), count a total of 90,000 herbarium specimens that are ready for rapid digitalization. These specimens will be sent to a professional company (Picturae) that runs a conveyor belt. At the end of this project, all 90,000 specimens will be barcoded, photographed and the label information will be transcribed, electronically recorded and ready for publication at the Info Flora national plant database and the Swiss Virtual Natural History Collection. This way, we immensely improve the visibility and accessibility of our collections and unlock information that is currently only accessible by visiting the collections on site or on request by asking for data or loans. Both collections represent unique Swiss cultural and scientific heritages and their digitalization is a valuable contribution to the protection and conditioning of these Swiss cultural possessions of national importance.

The herbaria of Zurich and Geneva house important mycological collections (fungaria) that include specimens from all fungal groups and geographic regions of the world. Plant-pathogenic micro-fungi, namely rust- smut and mildew fungi, are particularly well represented in both fungaria and count approx. 150,000 specimens.

Our project aims at developing the collections of the named fungal groups at all curatorial levels. The specimens will first be accessioned and conditioned for imaging and then be databased and photographed. Accessioning includes tagging of the specimens with an accession number and updating their nomenclature. Upon accessioning and eventual conditioning, the specimens will be databased and imaged at two different depths according to their scientific importance: In all specimens, we will take photographs of the

labels to capture the complete original collection data; type specimens will be “deep-digitized” in addition which means that macro- and microphotographs of the specimens’ distinctive morphological characters are taken after suitable preparation.

In the course of the project, the fungarium in Zurich will treat its complete rust, smut- and mildew fungi collections while Geneve will restrict its work to rust and smut fungi. On the whole, the present project is considered as a first and major step towards the ultimate goal, a full digital inventory of plant-pathogenic fungi in Switzerland.

The state of digitisation of natural history collections in Switzerland is still unsatisfactory. The Swiss Academy of Sciences recently found that around 80% of natural history collections in Switzerland are still waiting to be digitised. This is regrettable in view of global environmental changes and the current biodiversity crisis, because natural history collections could provide important data resources for research into the impact of human activities on the environment.

Four nature museums in north-eastern Switzerland, Naturmuseum Thurgau, Naturmuseum Winterthur, Naturmuseum St. Gallen and Museum zu Allerheiligen Schaffhausen, would like to contribute to this by jointly processing their lichen collections and digitally recording the collection data. A total of around 4,000 lichen specimens from the period from 1850 to the turn of the millennium will be processed.

Lichens are particularly important as bioindicators for the detection of environmental changes: due to their physiology, they react very sensitively to air pollution, for example, and their longevity results in cumulative effects of environmental stressors. Furthermore, it has recently been shown that lichens can also serve as indicators of climatic changes. By processing their lichen collections, the four museums are making them accessible for scientific work on such and other topics.

Bulk collections of preserved plants and fungi keep their 3-dimensional structure in contrast to pressed 2-dimensional herbarium specimens. Due to their uneven dimensions, bulk objects are usually stored separately and have become neglected over time. Therefore, most bulk collections are nowadays inaccessible via analogue or digital means although they are of outstanding scientific and cultural value. In addition, many of them are linked to individual herbarium specimens. In this joint project, we will digitalize the historical bulk (± 5150 objects) and linked herbarium specimens (10000 sheets) of four Swiss natural history institutions: the Botanical Museum of the Univ. of Zurich, the United Herbaria of the Univ. of Zurich and the ETH Zurich, the Herbarium of the Botanical Garden of the Univ. of Bern and the Nature Museum of Winterthur. To preserve these unique collections and to make them accessible to professional and amateur public at a national and international scale, our project has four main objectives: restauration, reviewing, digitalization and cross-referencing to herbarium sheets. All data will be connected to the Swiss Virtual Natural History Collection. This opens up a large potential for future research projects and collaborations. All collections represent important Swiss cultural and scientific heritage, and their digitalization is a valuable contribution to the protection and conditioning of these Swiss cultural possessions of national importance.

Herbarium collecting started in the 16th century in Italy, but Basel soon became an important centre. Caspar Bauhin (1560-1624), Basel's first Professor of Botany, had learned how to permanently preserve plants while traveling extensively. Thus he started globally one of the oldest traditions of plant collecting that survives to today. He compiled a global index of all known plants based on his herbarium (his "Pinax" of 1623), which strongly influenced Linnaeus, who started modern plant nomenclature in 1753. Bauhins herbarium, one of the oldest surviving globally, is thus of singular historic and scientific value, as it provides direct evidence on four centuries of floristic change, systematics, plant evolution, and history of science. However, it remains incompletely digitised, impeding its use in research. Similarly, four other historic and scientifically important herbaria are also broadly relevant but remain inaccessible digitally. In this project, we aim to create digital specimens for our five most important historic herbaria (C Bauhin 1560-1624; J Hagenbach, 1595-1640; JR Stähelin (1724-1800); W Lachenal (1736-1800); JL Buxtorf 1736-1804), integrate these in our specimen management software, so they meet the standards to be incorporated in the Swiss Virtual Natural History Collection as soon as it is operational, and present them online. Moreover, we add or replace damaged single-specimen folders to minimize (future) damage from handling them.

Switzerland has an estimated 2’000 species of lichens and many of the Types of these largely broad-ranging species were based on Swiss material. Therefore, the aim of this project is to demonstrate the local, national, and international value of overlooked Swiss lichen collections, and make available this material that is currently inaccessible to researchers by implementing a collaborative project on the lichen collections in Neuchâtel (estimated 10’000 specimens), Lausanne (about 11’300), and Geneva. This project requires special reconditioning, digitization, databasing, taxonomic revision, as well as a search for Types. The platform hallerNetbased in Bern will provide the technical infrastructure for the project.

Notably, these lichen collections have the complete main sets of material collected by Swiss naturalist Schleicher. His collections were used by others to describe many new species yet have never been systematically studied. Schleicher in the Alps and his contemporaneous correspondent Chaillet in the Jura in Neuchâtel sent material to notable mycologists such as Acharius in Uppsala (a student of Linnaeus, whose material was later sold to Helsinki), de Candolle in Geneva, Persoon in Paris, and Fries in Lund. These important collections abroad are being studied within the framework of a Swiss National Science Foundation Sinergia grant, while the corresponding Swiss material will be studied in this SwissCollNet project.

The Natural History Museum of Fribourg and the Botanical Garden of the University of Bern preciously preserve herbarium collections of naturalists who have explored and surveyed the flora not only of Switzerland but almost all over the world and over the last two centuries. The dried plants and the information they have meticulously collected represent a wealthy source of information of primary importance allowing researchers to reconstruct the ancient flora and its evolution on a given territory. Faced with the generalized and dramatic erosion of biodiversity that we are currently experiencing, data from such herbaria have become essential in the development of conservation activities and action plans such as for endangered species.

However, all these data are only useful if researchers and nature conservationists can easily access them thanks to the digitization of these collections. With this in mind, the Natural History Museum of Fribourg and the Botanical Garden of Bern have decided to join forces to accelerate the digitization of their herbarium collections. A close collaboration will allow both institutions to save a considerable amount of time and avoid many pitfalls in the demanding work of digitizing these collections. This partnership will be marked by the joint training of two young botanists who will have the mission of highlighting the botanical heritage collections of the cantons of Fribourg and Bern and their treasures that are just waiting to be discovered.

Many of the first descriptions of plants were based on material stemming from adventurous collection expeditions and remarkable personalities, such as the famous Sarasin cousins (Fritz & Paul, 1850s-1940s) from Basel, who profoundly impacted cultural and natural history and conservation. Sadly, their botanical collections, many from southeast Asia, were neglected compared to their famous zoological and ethnographic collections, even though they are critically important for taxonomy. For instance, Hermann Christ (1833-1933) described many new fern species from these collections. Yet, historic neglect and lack of digitalization renders them inaccessible to present-day science.

In this project, we unlock the botanical treasure trove of the Sarasin cousins by conditioning, taxonomic updating, and digitizing thousands of Sarasin specimens in the Herbaria Basel and the United Herbaria Zurich. By expanding our digitization efforts to additional fern specimens in our herbaria, we will make 60'000 digital specimens publicly available for science and society.

Wet collections of plants and fungi are comparatively rare, since these organisms are mostly preserved as dried herbarium specimens or bulk collections. Preserving plants and fungi in ethanol-based fluids has the great advantage, that 3-dimensional structures (e.g. of flowers) can be preserved and the tissue remains intact for anatomical analyses. To our knowledge, the Botanical Museum of the University of Zurich and the Herbarium of the Botanical Garden of the University of Bern contain the two largest historical wet collections in Switzerland with a total of ± 2250 specimens that were collected in its majority more than a century ago. Both collections contain unique specimens – including type specimens – and are mainly stored in hand-made jars with finely arranged plants and fungi for display. Unfortunately, both collections are in urgent need of conditioning and harmful substances such as formaldehyde were detected in the fluids. To preserve these unique collections and make them accessible, our project has four main goals: detoxification, restauration, reviewing, and digitalization. All data will be connected to the Swiss Virtual Natural History Collection. This opens up a large potential for future research projects and collaborations. Both collections represent unique Swiss cultural and scientific heritages and their digitalization is a valuable contribution to the protection and conditioning of these Swiss cultural possessions of national importance.

Biodiversity repositories such as seed and DNA banks are fundamental pillars to study and conserve our natural capital. Seeds as living organisms open the possibility for research, not only on the seeds themselves, but also on the development, ecology and biology of the plant they growth into. DNA collections in turn are of strategic importance for genetic research, particularly for inferring the phylogenetic relationships among lineages and assessing the genetic diversity within wild species or cultivated crops. Despite the importance of these genetic resources, the databasing of the information associated to these samples is not yet properly achieved. The data of the national seed bank and CJBG DNA bank is indeed scattered into different files not accessible to the public. Our aim is to digitise these existing pieces of information using the database system Botalista (https://botalista.community/about). This project will facilitate the management of these biobanks and the development of common curation practices across the different sites and institutions. It will also secure the link between the sample object and the rich biodiversity information related to it (e.g. herbarium specimens, species biology and distribution, germination tests, genetic data) and will allow data transfer towards dedicated biodiversity portals including Info Flora, GBIF and the Swiss Virtual Natural History Collection (SVNHC), once it is operational.