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Barrenechea Angeles I, Nguyen NL, Greco M, Tan KS, Pawlowski J. Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity. PLoS One 2024; 19:e0298440. [PMID: 38422100 PMCID: PMC10903905 DOI: 10.1371/journal.pone.0298440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.
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Affiliation(s)
- Inès Barrenechea Angeles
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Ngoc-Loi Nguyen
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain
| | - Koh Siang Tan
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- ID-Gene Ecodiagnostics Ltd., Plan-les-Ouates, Switzerland
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Fedosov A, Puillandre N, Fischell F, Patmanidis S, Miralles A, Vences M. DNA Barcode-Based Species Diagnosis with MolD. Methods Mol Biol 2024; 2744:297-311. [PMID: 38683327 DOI: 10.1007/978-1-0716-3581-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.
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Affiliation(s)
- Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Frank Fischell
- Institute of Zoology, University of Cologne, Köln, Germany
| | - Stefanos Patmanidis
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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Agatha S, Weißenbacher B, Kirschner M, Ganser MH. Trichite features contribute to the revision of the genus Strombidium (Alveolata, Ciliophora, Spirotricha). J Eukaryot Microbiol 2024; 71:e13001. [PMID: 37746746 PMCID: PMC10952788 DOI: 10.1111/jeu.13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
Strombidium is a species-rich genus of oligotrichid ciliates mainly inhabiting the marine pelagial. In molecular phylogenies, the genus emerged as non-monophyletic, and cladistic analyses suggest that it is largely characterized by plesiomorphies. A reliable split of the genus and the establishment of new genera necessitate, however, support by novel morphological and/or ultrastructural features. In the present study, the arrangement and ultrastructure of trichites are proposed as taxonomically relevant characters. Strombidium biarmatum Agatha et al., 2005 differs in the trichite pattern from the type species Strombidium sulcatum and most congeners. Aside from the trichites inserting anteriorly to the girdle kinety and generating the typical funnel-shaped complex in the posterior cell portion, the species displays additional trichites between the adoral membranelles even visible in live cells. Here, this exceptional trichite arrangement is detailed based on transmission electron microscopic investigations. In molecular phylogenies, S. biarmatum forms a monophylum with two congeners sharing its trichite arrangement. Therefore, the strombidiid genus Heteropilum nov. gen. is established with S. biarmatum as type species to also include H. paracapitatum (Song et al., 2015) nov. comb. and H. basimorphum (Martin & Montagnes, 1993) nov. comb. Further differences discovered in the trichite ultrastructure support the organelles' taxonomic significance.
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Affiliation(s)
- Sabine Agatha
- Department of Environment and BiodiversityParis Lodron University of SalzburgSalzburgAustria
| | - Birgit Weißenbacher
- Department of Environment and BiodiversityParis Lodron University of SalzburgSalzburgAustria
| | | | - Maximilian H. Ganser
- Department of Environment and BiodiversityParis Lodron University of SalzburgSalzburgAustria
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Santoferrara LF, Qureshi A, Sher A, Blanco-Bercial L. The photic-aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean. J Eukaryot Microbiol 2023; 70:e12976. [PMID: 37029732 DOI: 10.1111/jeu.12976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023]
Abstract
The bulk of knowledge on marine ciliates is from shallow and/or sunlit waters. We studied ciliate diversity and distribution across epi- and mesopelagic oceanic waters, using DNA metabarcoding and phylogeny-based metrics. We analyzed sequences of the 18S rRNA gene (V4 region) from 369 samples collected at 12 depths (0-1000 m) at the Bermuda Atlantic Time-series Study site of the Sargasso Sea (North Atlantic) monthly for 3 years. The comprehensive depth and temporal resolutions analyzed led to three main findings. First, there was a gradual but significant decrease in alpha-diversity (based on Faith's phylogenetic diversity index) from surface to 1000-m waters. Second, multivariate analyses of beta-diversity (based on UniFrac distances) indicate that ciliate assemblages change significantly from photic to aphotic waters, with a switch from Oligotrichea to Oligohymenophorea prevalence. Third, phylogenetic placement of sequence variants and clade-level correlations (EPA-ng and GAPPA algorithms) show Oligotrichea, Litostomatea, Prostomatea, and Phyllopharyngea as anti-correlated with depth, while Oligohymenophorea (especially Apostomatia) have a direct relationship with depth. Two enigmatic environmental clades include either prevalent variants widely distributed in aphotic layers (the Oligohymenophorea OLIGO5) or subclades differentially distributed in photic versus aphotic waters (the Discotrichidae NASSO1). These results settle contradictory relationships between ciliate alpha-diversity and depth reported before, suggest functional changes in ciliate assemblages from photic to aphotic waters (with the prevalence of algivory and mixotrophy vs. omnivory and parasitism, respectively), and indicate that contemporary taxon distributions in the vertical profile have been strongly influenced by evolutionary processes. Integration of DNA sequences with organismal data (microscopy, functional experiments) and development of databases that link these sources of information remain as major tasks to better understand ciliate diversity, ecological roles, and evolution in the ocean.
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Affiliation(s)
| | - Aleena Qureshi
- Department of Biology, Hofstra University, Hempstead, New York, USA
| | - Amina Sher
- Department of Biology, Hofstra University, Hempstead, New York, USA
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Ganser MH, Bartel H, Weißenbacher B, Andosch A, Lütz-Meindl U, Radacher P, Agatha S. A light and electron microscopical study on the resting cyst of the tintinnid Schmidingerella (Alveolata, Ciliophora) including a phylogeny-aware comparison. Eur J Protistol 2022; 86:125922. [PMID: 36155308 DOI: 10.1016/j.ejop.2022.125922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 01/26/2023]
Abstract
Resting cysts protect ciliates against adverse environmental conditions. The morphology and ultrastructure of resting cysts has been described in very few Oligotrichea, a group of mainly marine planktonic ciliates. The present study provides the first ultrastructural data for loricate choreotrichids, applying light and electron microscopy on the cysts of the tintinnid Schmidingerella meunieri (Kofoid and Campbell, 1929) Agatha and Strüder-Kypke, 2012. The morphology of live cysts and the wall ultrastructure of cryofixed cysts were morphometrically analysed. The resting cyst is roughly flask-shaped, broadening to a slightly concave, laterally protruding anterior plate. An emergence pore closed by a skull cap-shaped papula is directed to the bottom of the lorica on the opposite side of the cyst. The cyst wall consists of an ectocyst, mesocyst, and endocyst differing in thickness, structure, and nitrogen concentration as revealed by conventional transmission electron microscopy, electron energy loss spectroscopy, and electron spectroscopic imaging. The cysts of S. meunieri belong to the kinetosome-resorbing type, which also occurs in the majority of hypotrich ciliates. Two main features (flask-shape and presence of an emergence pore) are shared with the closely related aloricate choreotrichids and oligotrichids, distinguishing the Oligotrichea from the hypotrich and the more distantly related euplotid ciliates.
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Affiliation(s)
- Maximilian H Ganser
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
| | - Heidi Bartel
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Birgit Weißenbacher
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Ancuela Andosch
- Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Ursula Lütz-Meindl
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria; Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Peter Radacher
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Sabine Agatha
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
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