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  • Ferrari, Benoit J.D.  (3)
  • Lafont, Michel  (3)
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  • 1
    Online Resource
    Online Resource
    File S2: Raw data 2
    PeerJ ; 2017
    In:  PeerJ Vol. 5 ( 2017-12-06), p. e4122-
    Details
    In: PeerJ, PeerJ, Vol. 5 ( 2017-12-06), p. e4122-
    Abstract: Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. Methods We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. Results We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. Discussion Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.
    Type of Medium: Online Resource
    ISSN: 2167-8359
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.7717/peerj.4122
    DOI: 10.7717/peerj.4122/fig-1
    DOI: 10.7717/peerj.4122/fig-2
    DOI: 10.7717/peerj.4122/table-1
    DOI: 10.7717/peerj.4122/supp-1
    DOI: 10.7717/peerj.4122/supp-2
    DOI: 10.7717/peerj.4122/supp-3
    DOI: 10.7717/peerj.4122/supp-4
    DOI: 10.7717/peerj.4122/supp-5
    DOI: 10.7717/peerj.4122/supp-6
    Language: English
    Publisher: PeerJ
    Publication Date: 2017
    detail.hit.zdb_id: 2703241-3
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  • 2
    Online Resource
    Online Resource
    Assessment of the effects of wastewater treatment plant effluents on receiving streams using oligochaete communities of the porous matrix
    EDP Sciences ; 2019
    In:  Knowledge & Management of Aquatic Ecosystems , No. 420 ( 2019), p. 18-
    Details
    In: Knowledge & Management of Aquatic Ecosystems, EDP Sciences, , No. 420 ( 2019), p. 18-
    Abstract: Les activités humaines peuvent perturber la dynamique naturelle des échanges entre les eaux de surface et les eaux souterraines dans les cours d'eau. De tels échanges contribuent à l'autoépuration du cours d'eau et un excès d'infiltrations peut conduire à la contamination des eaux souterraines. De plus, le milieu poreux (sédiments grossiers superficiels et zone hyporhéique), à travers lequel se produisent les échanges hydrologiques, a la propriété de stocker les polluants. Il est donc essentiel de prendre en compte la dynamique des échanges hydrologiques verticaux et la qualité biologique du milieu poreux dans le cadre des programmes de surveillance de la qualité des cours d'eau. La méthode des traits fonctionnels (TRF), basée sur l'étude des communautés d'oligochètes des sédiments grossiers superficiels et de la zone hyporhéique, a été proposée comme outil permettant d'évaluer simultanément la dynamique des échanges hydrologiques verticaux et les effets des polluants présents dans le milieu poreux. Dans la présente étude, cette méthode a été appliquée lors de deux périodes différentes (mars et septembre 2016) en amont et en aval de sites affectés par les rejets de stations d'épuration des eaux usées (STEP) situées en Suisse. Une meilleure qualité biologique a été observée en amont des STEP lors des deux campagnes. De plus, les résultats ont suggéré que la capacité d'autoépuration du milieu était inférieure au niveau des sites situés en aval des STEP et qu'au niveau de ces sites les eaux souterraines étaient vulnérables aux pollutions des eaux de surface. La méthode TRF s'est avérée appropriée pour détecter les effets globaux de sources ponctuelles de contamination sur des cours d'eau récepteurs. Dans un futur proche, cette méthode bénéficiera des avancées de la recherche en cours sur l'utilisation de codes-barres génétiques pour l'identification des espèces d'oligochètes.
    Type of Medium: Online Resource
    ISSN: 1961-9502
    URL: Article
    DOI: 10.1051/kmae/2019011
    Language: English
    Publisher: EDP Sciences
    Publication Date: 2019
    detail.hit.zdb_id: 2502926-5
    SSG: 21,3
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  • 3
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    Online Resource
    High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes
    Pensoft Publishers ; 2021
    In:  ARPHA Conference Abstracts Vol. 4 ( 2021-03-04)
    Details
    In: ARPHA Conference Abstracts, Pensoft Publishers, Vol. 4 ( 2021-03-04)
    Abstract: Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.
    Type of Medium: Online Resource
    ISSN: 2603-3925
    URL: Article
    DOI: 10.3897/aca.4.e65394
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2021
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