SwissBOL is building a reference genetic catalogue for animals, plants, cryptogams, fungi, lichens and microorganisms living in Switzerland. In order to achieve our goal, SwissBOL contributes to the realization of different projects. All data generated in collaboration with SwissBOL will be disseminated via the GBIF.ch, BOLD and GenBank systems.

Our Vision

The protection of species around the world and theconservation of biological diversity in Switzerland.

Our Mission

Increase knowledge of genetic diversity in Switzerland and participate in better monitoring the global state of biodiversity.

Platforms and Data bases

Objectives

  1. Create a reference genetic encyclopedia for all species present in Switzerland
  2. Certify superior quality of genetic data by ensuring unambiguous links between the different dimensions related to DNA sequences — occurrences; specimens in collection; stored genetic material
  3. Promote collaboration and exchange of professional experiences among specialists involved in the national genetic inventory of biodiversity
  4. Provide data owners with resources and tools to facilitate the centralization of genetic data and related information
  5. Support the development of applications in the fields of conservation, monitoring, forensic sciences, food safety, international trade regulations

Standards

  1. The Swiss genetic inventory of biodiversity is generated from organisms taxonomically identified beforehand
  2. Collected (legally) specimens are deposited in a museum collection
  3. Information about specimen collection and species identification should at a minimum meet the requirements of iBOL (International Barcode Of Life) and for Swiss specimens follow the recommendations of Info Species for the group concerned
  4. Genetic materials are stored in good conditions of DNA preservation

Through the linking of these four dimensions, SwissBOL guarantees Swiss quality to its data and participates in the international effort to catalog genetic diversity.

Recommendations

History

  • 2018 — The merger between SwissBOL and GBIF.ch is initiated with regard to data centralization and management and coordination activities.
  • 2016 — SwissBOL is partnering with GBIF.ch for the development of the concepts for genetic data and the establishment of the reference database for Switzerland.
  • 2015 — The SwissBOL Association is created from the network of partners developed with the support of the Federal Office for the Environment (FOEN).
  • 2012 — The FOEN funds the Swiss biodiversity inventory initiative for 4 years.
  • 2011 — First national networking meeting is held at the University of Geneva, organized by Jan Pawlowski.
  • 2010 — Launch of the International Barcode of Life project (iBOL) and development of different initiatives at the country-level and / or for specific taxonomic groups.
  • 2003 — The concept of DNA barcoding is published and begins the collaboration of a few dozen countries to create a reference library of DNA barcodes.

Projects

In order to reach our goal of obtaining DNA sequence data for all species living in Switzerland, SwissBOL is currently contributing to the following projects. All data generated in collaboration with SwissBOL will be made publicly available on the BOLD Systems website, GenBank, and eventually on the Swiss node of GBIF.org.

Progress

  • Species: 1365
  • Specimens: 4427
  • Sequences: 4260

Associated projects

  • CodeMyBug
  • CodeMyPlant
  • DNAqua-Net

Butterflies

Switzerland is home to about 226 species of diurnal Lepidoptera (Rhopalocera and Zygaenidae). These species are the subject of various national inventories and monitoring in relation to the monitoring of biodiversity evolution. Excellent bioindicators, they are particularly useful for assessing the quality of ecosystems and the impact of global changes on their biodiversity. The identification of many species in the group, which necessarily involves examination of the genitals, is difficult and may in some cases be impossible on the basis of a single specimen. In addition, the taxonomic position of some species of Zygenes is uncertain. This project, for the realization of which the MBD (Monitoring of Biodiversity in Switzerland) and Info fauna - CSCF collaborate aims at documenting the genetic diversity of this group of emblematic insects.

The results obtained are based on a total of 223 species and 1057 specimens. The 867 validated CoI sequences have been registered on BOLD SYSTEMS.

Progress

butterflies

Publications

  • Litman J, Chittaro Y, Birrer S, Praz C, Wermeille E, Fluri M, Stalling T, Schmid S, Wyler S, Gonseth Y (submitted) A DNA barcode reference library for Swiss butterflies and forester moths as a tool for species identification, systematics and conservation. Plos One.

Scientists associated

  • Yannick Chittaro
  • Stefan Birrer
  • Jessica Litman
  • Christophe Praz

Institutions involved

  • info fauna CSCF
  • Hintermann & Weber AG
  • Muséum d’Histoire Naturelle de Neuchâtel
  • Université de Neuchâtel

Click beetles (Coleoptera Elateridae)

Elateridae family has more than 150 species in Switzerland. Two genera, Ampedus (23 species) and Brachygonus (4 species), are phylogenetically very close. These two genera include several cryptic species whose presence in Switzerland must be confirmed. In addition, some of these species are of particular importance because of their status as patrimonial species. A taxonomic revision of these two genera was performed using morphological and molecular data. Additional analyses identify their phylogenetic relationships and attempt to date the origin, evaluate the duration and describe speciation patterns in Switzerland and Central Europe.

The results obtained are based on a total of 30 species and 129 specimens. The CoI and ITS2 sequences validated for this study (111 and 101) were registered on BOLD SYSTEMS. Progress

Publications

  • Vuataz L, Sanchez A, Wyler S, Blanc M, Chittaro Y (submitted) Diversity and relationships of click beetles (Coleoptera, Elateridae) in Switzerland and Europe: the case of the tribe Ampedini Gistel, 1848. Invertebrate Systematics.

Scientists associated

  • Laurent Vuataz
  • Yannick Chittaro
  • Mickaël Blanc

Institutions involved

  • Musée de Zoologie de Lausanne
  • info fauna CSCF
  • Muséum d’Histoire Naturelle de la ville de Genève

Endemic beetles (Coleoptera)

The Coleoptera order represents nearly 40% of the native animal species of Switzerland and contains about 60% of the endemic arthropods of the country. This project aiming at identifying the DNA barcodes of endemic beetles in Switzerland is therefore an important contribution to the endemic fauna genebank of Switzerland and an original contribution of Switzerland to global genomic data banks.

The first results obtained are based on a total of 98 species and 187 specimens. The validated CoI and ITS2 sequences (162 and 103) were registered on BOLD SYSTEMS. This project continues with a second batch of data based on 98 new specimens. Progress

Publications

  • Germann C, Wyler S, Bernasconi MV (2017) DNA barcoding of selected alpine beetles with focus on Curculionoidea (Coleoptera). Revue Suisse de Zoologie 124(1): 15-38.

Scientists associated

  • Marco Bernasconi
  • Christoph Germann

Institutions involved

  • Natur-Museum Luzern

Eumenes (Hymenoptera: Vespidae: Eumeninae)

Eight of the twelve European species of solitary wasps of the genus Eumenes Latreille 1802 (Hymenoptera: Vespidae: Eumeninae) are found in Switzerland. They are distinguished mainly by hair and color characteristics. These two families of characters, however, are very variable under the probable action of humidity and temperature. The objective of this project is to use genetic data to assess the diversity of Eumenes species and to determine their phylogenetic relationships. The expected results will refine our knowledge of the distribution of species of this genus in Switzerland and thus contribute to the assessment of their Red List status.

The first results obtained are based on a total of 10 species and 41 specimens. The CoI sequences obtained for all the specimens were registered on BOLD SYSTEMS. Progress

Publications

  • Neumeyer R, Praz C (2015) DNA barcoding of the potter wasp genus Eumenes Latreille, 1802 (Hymenoptera: Vespidae: Eumeninae) in Switzerland. Bulletin de la Société Entomologique Suisse 88 : 307–320.

Scientists associated

  • Rainer Neumeyer
  • Christophe Praz

Institutions involved

  • Université de Neuchâtel

Plecoptera

DNA barcodes are a fundamental tool for monitoring the biodiversity of aquatic environments in Switzerland. It is particularly useful for the identification of specimens hitherto impossible to determine (the early larval stages, for example), the identification and description of the larvae of species of which only adults are known and the demonstration of systematic problems (eg identification of cryptic species). There are about 500 species of EPT (ephemera, plecoptera and trichoptera) in Switzerland, including 112 Plecoptera.

The results obtained are based on a total of 90 species and 440 specimens. The 270 CoI sequences obtained for this study are being validated before being registered on BOLD SYSTEMS. Progress

Publications

  • Gattolliat J-L, Vinçon G, Wyler S, Pawlowski J, Sartori M (2016) Toward a comprehensive COI DNA barcode library for Swiss Stoneflies (Insecta: Plecoptera) with special emphasis on the genus Leuctra. Zoosymposia 11 : 135-155.

Scientists associated

  • Michel Sartori
  • Jean-Luc Gatolliat

Institutions involved

  • Musée de Zoologie de Lausanne

Ants (Hymenoptera, Formicidae)

In 2012, ants were collected in twelve localities south of the Swiss Alps. The objective of this project is to obtain genetic data for about half of the ant species present in Switzerland and to answer the taxonomic and systematic questions that remain open for at least six genera of this group.

The first results obtained are based on a total of 81 species and 146 specimens. The 115 CoI sequences obtained for this study are in course of validation before being registered on BOLD SYSTEMS. Progress

Scientists associated

  • Anya Rossi-Pedruzzi
  • Isa Forini

Institutions involved

  • Museo Cantonale di Storia Naturale

Long-legged flies (Diptera, Dolichopodidae)

Dolichopodidae (Diptera, Dolichopodidae) have almost 6,000 species worldwide, of which 227 are found in Switzerland. The members of this family are useful bioindicators, especially for wetlands. The objective of this project is to obtain the DNA barcode of the 145 species in the Lugano Natural History Museum collection, which represents about two-thirds of the Swiss fauna of this family of Diptera.

This study is based on a total of 158 species and 446 specimens. Only 134 sequences could be obtained at the moment. Progress Scientists associated

  • Lucia Pollini
  • Marco Bernasconi

Institutions involved

  • Museo Cantonale di Storia Naturale

Dung fauna

The objective of this project is to develop a cost-effective kit using next generation sequencing based on DNA barcodes for the identification of all species of cow dung in Switzerland. Such a kit should be able to analyze a sample of hundreds of insects as a single sample and better assess the environmental effects of veterinary products than methods arbitrarily based on a single species.

It is a project based on NGS sequencing technologies. Two new sequences for public databases (2 species, 2 specimens) were registered on BOLD SYSTEMS. Progress Publications

  • Blanckenhorn W, Rohner P, Bernasconi MV, Haugstetter J, Buser A (2016). Is qualitative and quantitative metabarcoding of dung fauna diversity feasible? Environmental Toxicology and Chemistry 35(8): 1970-1977 (PubMed).

Scientists associated

  • Wolf Blanckenhorn
  • Andreas Buser

Institutions involved

  • Université de Zurich
  • Ecogenics GmbH

Spiders (Araneae)

Spiders colonize most terrestrial ecosystems, whether natural or more artificial. With nearly 900 species, spiders represent a significant part of Swiss biodiversity. Predatory, they contribute to the regulation of insect populations in the ecosystems that shelter them and can also serve as indicators of the quality of the different habitats. This project involves the sampling of two spider communities, one on the north side and one on the southern side of the Alps. The analyses carried out on the collected material should make it possible to highlight infraspecific divergences, the Alps representing effective migratory barriers.

At the moment, data have been obtained for 130 species and 192 specimens. With a sequencing failure rate of around 27%, 140 CoI sequences were obtained. This study targets 300 species and 500 specimens. Progress Scientists associated

  • Christian Kropf
  • Wolfgang Nentwig

Institutions involved

  • Naturhistorisches Museum Bern

Gastropoda

Switzerland is home to 284 species of molluscs. This high diversity is attributed to the different climates, to the varied topography and diversity of Switzerland’s vegetation, as well as to its climatic history. It is estimated that between 33% and 41% of Swiss molluscs species are endangered, particularly wetlands, natural springs and lean and dry grasslands, three habitat types that have declined significantly over the past century. During the last twenty years, 20 species have been added to the list of terrestrial gastropods in Switzerland, which indicates new discoveries are still possible. The sequences of the official DNA barcode will facilitate the discovery of these new species and clarify the taxonomy of difficult species complexes.

This study is based on 94 species and 97 specimens. A success rate for amplification and sequencing of about 50% was observed and only about 50 species were sequenced. Progress Scientists associated

  • Bertrand Fournier
  • Edward Mitchell

Institutions involved

  • Université de Neuchâtel

Soil nematodes (Nematoda)

A detailed analysis of community diversity and genetic diversity of nematode populations will provide a solid basis for promoting the use of this group as a biological indicator of soil health. The objective of this project is to establish a repository for a single site and to compare this repository with the results of DNA CoI barcode sequencing, samples from different soil types in Switzerland.

For the 300 specimens planned for this study, at this stage, 20 species were identified based on 190 SSU rDNA sequences. The 710 sequences obtained for the SSU rDNA and CoI markers that remain to be analyzed will probably provide more complete data for this group Progress Publications

  • Kiewnick S, Frey J (2014) Swiss NEMA-BOL: Barcoding of Swiss Soil Nematodes – A Proof of Concept. Julius- Kühn- Archiv. 447:532.
  • Kiewnick S, Büchler U, Roth I, Frey J (2015) SWISSBOL: Barcoding of Swiss Soil Nematodes. Tagung d. DPG Arbeitskreises Nematologie

Scientists associated Institutions impliquées

  • Juerg Frey
  • Sebastian Kiewnick

Institutions involved

  • Agroscope Changins-Wädenswil

Earthworms (Annelida, Oligochaeta)

The identification of earthworm species is traditionally based on particular morphological characters, such as the characteristics of the reproductive system of adults. Juveniles and cocoons are thus often impossible to determine. In addition, recent research has shown that several species may be present in a single morphotype. However, it is likely that these “cryptic species” play different roles in ecosystems. DNA sequencing is a promising approach to overcome the limitations of classical taxonomy and is therefore an essential tool for studies of worm diversity and more generally soil ecology. The main objectives of this research are: a) to improve knowledge on worm diversity in Switzerland at different spatial scales (ecosystems, phytocenoses) and functional levels (community, species); b) to validate the taxonomic identifications already made on the Swiss plateau, in the alluvial zones and in urban environments by comparing with the DNA sequences, in particular the CoI barcode; and c) validate the reference catalog initiated and document the occurrence of earthworm species in the different soil types.

At the moment data have been obtained for 6 species and 60 specimens, with CoI sequences obtained for all specimens. This study targets the 10 species and 100 specimens. Progress Scientists associated

  • Claire Le Bayon
  • Enrique Lara

Institutions involved

  • Université de Neuchâtel

Aquatic oligochaetes

Aquatic oligochaetes are an abundant and diverse group of six families with more than 100 species commonly found in European waters. Species in this group are highly sensitive to pollution and are widely used as bioindicators of sediment and water quality in rivers and lakes. Recent studies report 58 species (69 taxa) of oligochaetes in the Geneva area; This number is however provisional and we know very little about their diversity in the other regions of Switzerland. The objective of this study is to obtain DNA sequences for the CoI marker for aquatic oligochaetes in Switzerland. Our database will help improve existing oligochaete indices and allow the development of new genetic tests using oligochaetes for the biomonitoring of freshwater ecosystems. DNA barcoding will also detect new cryptic species and highlight taxonomic groups requiring revision.

This project is based on two components: i) acquisition of DNA sequences for the official barcode for about 30 species and 300 specimens; ii) development of protocols for the use of NGS technologies in biomonitoring studies based on oligochaete communities. At this point, a total of 818 new sequences (733 CoI and 85 ITS2) have been published in GenBank. Progress Publications

  • Vivien R, Holzmann M, Werner I, Pawlowski J, Lafont M, Ferrari B (2017) Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database. PeerJ 5:e4122 (PubMed).
  • Vivien R, Ferrari B, Pawlowski J (2016) DNA barcoding of formalin fixed oligochaetes for biomonitoring. BMC Research Notes 9:342 (PubMed).
  • Vivien R, Lejzerowicz F, Pawlowski J (2016) Next-generation sequencing of aquatic oligochaetes: comparison of experimental communities. PLoS ONE 11(2):e0148644 (PubMed).
  • Vivien R, Ferrari B (2016) Les oligochètes indicateurs de la qualité des sédiments. Centre Ecotox News, 3-5. Centre Suisse d’Ecotoxicologie Appliquée Eawag-EPFL.
  • Vivien R, Lafont M, Ferrari B (2015) Utilisation des communautés d’oligochètes pour l’évaluation de la qualité biologique et du fonctionnement des cours d’eau : un bilan à partir de données genevoises (Suisse). Archives des sciences 68, 105-113.
  • Vivien R, Lafont M (2015) Faunistic note on the aquatic oligochaetes of the Geneva area and of Switzerland. Revue Suisse de Zoologie 122(2).
  • Vivien R, Wyler S, Lafont M, Pawlowski J (2015) Molecular barcoding of aquatic oligochaetes: implications for biomonitoring. PloS ONE 10(4): e0125485 (PubMed).

Scientists associated

  • Régis Vivien
  • Jan Pawlowski

Institutions involved

  • Université de Genève

Hydrazoa

Only five species of hydrozoans are known from Switzerland. It is possible, however, that they are more numerous and that certain morphotypes actually contain several biological species. This project will collect several individuals from each of these five species and compare the interspecific limits indicated by the genetic data with those predicted by morphology. It should also make it possible to determine whether the genetic diversity of hydrozoans differs between Swiss lakes and whether it increases from upstream to downstream of the hydrographic systems.

This study is based on all 5 species listed in Switzerland and 28 specimens. The 28 validated CoI sequences were registered on BOLD SYSTEMS. Progress

Scientists associated

  • Peter Schuchert

Institutions involved

  • Muséum d’Histoire Naturelle de la ville de Genève

Pipistrelle bats (Chiroptera, Vespertilionidae)

Deux lignées mitochondriales fortement divergentes sont connues au sein des pipistrelles de Kuhl. De telles divergences sont rares parmi les mammifères conspécifiques et pourraient indiquer la présence d’espèces cryptiques. Ces deux lignées coexistent en sympatrie mais il n’est pas clair si elles représentent d’anciens haplotypes qui ont survécu au tri incomplet des lignées « lineage sorting » ou s’ils indiquent la présence d’espèces cryptiques biologiquement indépendantes. L’objectif de ce projet est de tester la présence de deux lignées majeures sympatriques dans les pipistrelles de Kuhl et d’estimer la diversité moléculaire au sein de chaque lignée.

Les résultats obtenus se basent sur un total de 2 sous-espèces de la même espèce et 102 spécimens. Les 102 séquences CoI validées ont été enregistrées auprès de BOLD SYSTEMS. Progress Publications

  • Andriollo T, Naciri Y, Ruedi M (2015) Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl’s Pipistrelles (Chiroptera). PLoS ONE 10(8): e0134881. doi:10.1371/journal.pone.0134881 (PubMed)

Scientists associated

  • Manuel Ruedi
  • Tommy Andriollo

Institutions involved

  • Muséum d’Histoire Naturelle de la ville de Genève

Vascular plants of the canton of Geneva

A DNA reference library of Swiss species of vascular plants will allow the identification of any specimen observed in the vegetative state, ie in the absence of flowers and / or fruits. The objective of this project is to demonstrate on the basis of concrete examples that DNA sequences, and in particular the official DNA barcodes, provide more in-depth knowledge of the flora of a region, notably the canton of Geneva. It also aims to promote the realization of similar projects in other regions.

The results obtained are based on a total of 139 species and 145 specimens. The validated rbcL and matK sequences (142 and 134) were registered on BOLD SYSTEMS. Progress Scientists associated

  • Yamama Naciri

Institutions involved

  • Conservatoire et jardin botaniques de la ville de Genève

Fern allies (Ophioglassaceae, Isoetaceae and Equisetaceae)

Switzerland has 19 species of primitive pteridophytes, nine of which are on the Red List of vascular plants. This project aims at sequencing different genetic markers of several individuals from each of these 19 Jura and Alps species in order to explore the genetic diversity of the group.

The results obtained are based on a total of 13 species (plus two hybrids) and 48 specimens. At this point, rbcL marker DNA sequences were obtained for the total of the specimens, and additional sequences for a nuclear spacer and the trnH-psbA spacer are expected. Progress Scientists associated

  • Jason Grant

Institutions involved

  • Université de Neuchâtel

Lichens

Lichens are a mutualistic and stable association between a fungus (mycobionte) and a population of green algae or cyanobacterial photobionts. Lichens are often used as bioindicators of air contamination and the ecological integrity of forest ecosystems. The Red List of tree and soil colonizing lichens includes 295 (37%) threatened species; the proportion of threatened species that colonize trees (44%, 230 species) is particularly alarming. Traditional sequencing (ie, Sanger sequencing) of crustacean lichens is difficult because of saprophytic, endophytic and parasitic fungi mixed with mycobiont. The objective of this project is to develop and test a protocol for sequencing the DNA barcode of these lichens using 454 sequencing.

The results obtained are based on a total of 100 species and 100 specimens, for which 99 standard barcode marker sequences were obtained. Progress Publications

  • Mark K, Scheidegger C (2015) Barcoding the Swiss Lichens and Associated Fungi. Barcode Bulletin, 6(3), 21-22.

Scientists associated

  • Christoph Scheidegger

Institutions involved

  • WSL

Basidiomycetes

Several alpine macromycetes are on the Swiss Red List, mainly because of their very limited areas of occupancy and occurrence. As global warming progresses, it is likely that species from lower regions will establish in the alpine zone. The planned molecular studies will help to understand if these new species will replace or coexist with the native species of the alpine zone. In addition, a comprehensive taxonomic base is essential for the national fungi database (Swissfungi), the main source of information for conservation issues at the federal level. Finally, it is planned to explore issues related to morphological variation and altitudinal distribution of some species.

The results obtained are based on a total of 70 species and 122 specimens. All specimens were sequenced for the ITS marker and 27 for LSU. Progress

Scientists associated

  • Beatrice Senn-Irlet
  • Carolina Cornejo

Institutions involved

  • WSL

Wheat fungus

Farm workers are among those most at risk of developing acute or chronic respiratory problems. Despite this fact, the etiology of these diseases is poorly understood, even in important sectors of agriculture. It is therefore imperative that the microbial community present in such environments is characterized on a large scale and that its effects on human health are analyzed. The objectives of this project are to determine the composition of the wheat fungus community to assess the impact of exposure to these fungi on the health of grain workers, and to characterize the etiology of respiratory problems.

The results obtained are based on a total of 13 species unambiguously identified using the DNA sequences obtained for five molecular markers. Progress

Publications

  • Wild P, Dorribo V, Pralong J, Reboux G, Oppliger A, Danuser B, Krief P, Niculita-Hirzel H (2014) Respiratory effects of an exposure to wheat dust among grain workers and farmers: a longitudinal study. EPICOH, Chicago (USA).
  • Niculita-Hirzel H, Wild P, Dorribo V, Pralong J, Reboux G, Danuser B, Krief P (2015) Types de poussières de blé et effets respiratoires. 27ème Journées Franco-Suisse de Santé au travail, Strasbourg (France).
  • Barrera C, Wild P, Dorribo V, Savova-Bianchi D, Laboissière A, Pralong J, Danuser B, Krief P, Millon L, Reboux G, Niculita-Hirzel H (2018) Exposure to field vs. storage wheat dust: different consequences on respiratory symptoms and immune response among grain workers. International Archives of Occupational and Environmental Health, 91:745–757 (PubMed).

Scientists associated

  • Hélène Niculita-Hirzel

Institutions involved

  • IST

Invasive Oomycetes (Oomycota, Saprolegniaceae)

An epidemic and a significant mortality have recently affected the fish fauna of Doubs in French-speaking Switzerland. Analysis of the samples taken from the lesions of infected fish showed the presence of an invasive Oomycete species of the genus Saprolegnia. The catastrophic effects that the spread of this epidemic might have, require a large-scale monitoring of Swiss rivers. The ability to distinguish foreign Saprolegnia species from native phylogenetically related species is essential. The goal of this project is to develop a protocol for the detection of Saprolegnia species using the DNA barcode sequences, to make recommendations for monitoring Saprolegnia and to define effective quarantine measures to prevent the spread of these invasive Saprolegnia species to nearby rivers.

For the thirty specimens identified, representing 2 species, DNA sequences were obtained. Progress Publications

  • Steciow MM, Lara E, Paul C, Pillonel A, Belbahri L (2014) Multiple barcode assessment within the Saprolegnia-Achlya clade (Saprolegniales, Oomycota, Straminipila) brings order in a neglected group of pathogens. IMA Fungus volume 5(2): 439–448.
  • Alenezi FN, Weitz HJ, Belbahri L, Nidhal J, Luptakova L, Jaspars M, Woodward S (2015) Draft genome sequence of Aneurinibacillus migulanus NCTC 7096. Genome Announcements 3(2):e00234-15. doi:10.1128/genomeA.00234-15 (PubMed).
  • Alenezi FN, Weitz HJ, Belbahri L, Ben Rebah H, Luptakova L, Jaspars M, Woodward S (2015) Draft genome sequence of Aneurinibacillus migulanus strain Nagano. Genome Announcements 3(2):e00232-15. doi:10.1128/genomeA.00232-15.

Scientists associated

  • Lassaâd Belbahri

Institutions involved

  • Université de Neuchâtel

Quadrulella (Hyalospheniidae, Arcellinida)

The genus Quadrulella belongs to the group of Testaceae amoebae Arcellinida, a group of protists useful as bioindicators of environmental health. Some members of this genus seem to be a species complex: while all European samples are attributed to the Q. symmetrica species, we find a great genetic diversity among European specimens and clear differences between the size and shape of the species. This genus is one of the rare arcellinids to harbor self-secreted plates, which appear to be a valid taxonomic trait, making it a good model for studying cryptic diversity in protists. Our goal is to characterize the genetic diversity hidden in Q. symmetrica and to link this diversity to different ecological niches.

The 27 CoI sequences were obtained for 27 individuals representing 5 species, increasing the number of species listed in Switzerland from one to three. Progress

Scientists associated

  • Anush Kosakyan
  • Enrique Lara

Institutions involved

  • Université de Neuchâtel

Nebela (Hyalospheniidae, Arcellinida)

Protists are increasingly recognized for their fundamental role in the functioning of almost all ecosystems on a global scale. Despite their importance, they remain largely unknown and much of their diversity is not yet documented. Arcellinida amoebae are often used as a model group for monitoring past and present environmental conditions. Changes in the composition of their communities are well correlated with different pollutants. Recent studies in our laboratory have demonstrated a great diversity within a morphospecies, Nebela collaris, comprising up to nine genetic species. Nebela collaris s.I. is known to occupy not only sphagnum peatlands, but also other environments such as acid forest litter. Our goal is to sequence the DNA barcode CoI of most of the group’s diversity in Switzerland. To achieve this goal, we will study a wider range of habitats.

The 29 sequences obtained for the 29 individuals representing 8 species at the origin of the project were registered on Genbank. Genbank counts today 78 Nebela sp sequences related to this project. Progress

Publications

  • Singer D, Kosakyan A, Seppey, CVW, Pillonel A, Fernandez LD, Fontaneto D, Mitchell EAD, Lara E (2018) Environmental filtering and phylogenetic clustering correlate with the distribution patterns of cryptic protist species. Ecology, 99(4), 2018, pp. 904–914.
  • Singer D, Kosakyan A, Pillonel A, Mitchell EAD, Lara E (2015) Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog. European Journal of Protistology 51, 79-85.
  • Kosakyan A, Gomaa F, Mitchell EAD, Heger TJ, Lara E (2013) Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae). European Journal of Protistology 49, 222-237.
  • Kosakyan A, Heger TJ, Leander BS, et al. (2012) COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze. Protist 163, 415-434.

Scientists associated

  • David Singer
  • Enrique Lara
  • Edward Mitchell

Institutions involved

  • Université de Neuchâtel

Diatoms

Diatoms are widely used as bioindicators of water quality in Switzerland and other European countries. The Swiss Diatom Index is based on the ecological properties of the selected diatom species. Traditionally, these species are identified under the microscope using morphological characteristics distinct from diatom frustules. However, this approach is time consuming and requires good taxonomic expertise, which is not always available. In our project, we propose to overcome these limitations by developing a molecular method that will make it possible to identify diatom species more quickly and reliably. We will use high throughput sequencing to increase the number of processed samples and reduce the costs of routine application of the Swiss Diatom Index for biological monitoring of water bodies.

It is a project based on NGS sequencing technologies from environmental DNA. A total of 194 sequences have already been registered on Genbank. Progress

Publications

  • Apothéloz‐Perret‐Gentil L, Cordonier A, Straub F, Iseli J, Esling P, Pawlowski J (2017) Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring. Mol Ecol Resour, 17: 1231-1242. doi:10.1111/1755-0998.12668 (PubMed).
  • Visco JA, Apothéloz-Perret-Gentil L, Cordonier A, Esling P, Pillet L, Pawlowski J (2015) Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data. Environmental Science & Technology 49 (13), 7597-7605 DOI: 10.1021/es506158m.

Scientists associated

  • Laure Apothéloz-Perret-Gentil
  • Jan Pawlowski

Institutions involved

  • Université de Genève