1. Framing cutting-edge integrative deep-sea biodiversity monitoring via environmental DNA and optoacoustic augmented infrastructuresSergio Stefanni, Luca Mirimin, David Stanković, Damianos Chatzievangelou, Lucia Bongiorni, Simone Marini, Maria Vittoria Modica, Elisabetta Manea, Federico Bonofiglio, Joaquin del Rio Fernandez, Neven Cukrov, Ana Gavrilović, Fabio C. De Leo, Jacopo Aguzzi, 2022, pregledni znanstveni članek Povzetek: Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources.
Objavljeno v DiRROS: 05.08.2024; Ogledov: 111; Prenosov: 134
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2. Zoantharians (Hexacorallia: Zoantharia) associated with cold-water corals in the Azores Region: new species and associations in the deep seaMarina Carreiro-Silva, Oscar Ocaňa, David Stanković, ĺris Sampaio, Filipe M. Porteiro, Marie-Claire Fabri, Sergio Stefanni, 2017, izvirni znanstveni članek Povzetek: Zoantharians are a group of cnidarians that are often found in association with marine invertebrates, including corals, in shallow and deep-sea environments. However, little is known about deep-sea zoantharian taxonomy, specificity and nature of their associations with their coral hosts. In this study, analyses of molecular data (mtDNA COI, 16S, and 12S rDNA) coupled with ecological and morphological characteristics were used to examine zoantharian specimens associated with cold-water corals (CWC) at depths between 110 and 800 m from seamounts and island slopes in the Azores region. The zoantharians examined were found living in association with stylasterids, antipatharians and octocorals. From the collected specimens, four new species were identified: (1) Epizoanthus martinsae sp. n. associated with the antipatharian Leiopathes sp.; (2) Parazoanthus aliceae sp. n. associated with the stylasterid Errina dabneyi (Pourtalès, 1871); (3) Zibrowius alberti sp. n. associated with octocorals of the family Primnoidae [Paracalyptrophora josephinae (Lindström, 1877)] and the family Plexauridae (Dentomuricea aff. meteor Grasshoff, 1977); (4) Hurlizoanthus hirondelleae sp. n. associated with the primnoid octocoral Candidella imbricata (Johnson, 1862). In addition, based on newly collected material, morphological and molecular data and phylogenic reconstruction, the zoantharian Isozoanthus primnoidus Carreiro-Silva, Braga-Henriques, Sampaio, de Matos, Porteiro & Ocaña, 2011, associated with the primnoid octocoral Callogorgia verticillata (Pallas, 1766), was reclassified as Zibrowius primnoidus comb. nov. The zoantharians, Z. primnoidus comb. nov., Z. alberti sp. n., and H. hirondelleae sp. n. associated with octocorals showed evidence of a parasitic relationship, where the zoantharian progressively eliminates gorgonian tissue and uses the gorgonian axis for structure and support, and coral sclerites for protection. In contrast, the zoantharian P. aliceae sp. n. associated with the stylasterid E. dabneyi and the zoantharian E. martinsae sp. n. associated with the antipatharian Leiopathes sp., appear to use the coral host only as support with no visible damage to the host. The monophyly of octocoral-associated zoantharians suggests that substrate specificity is tightly linked to the evolution of zoantharians.
Ključne besede: antipatharians, octocorals, Azores, gorgonians, molecular taxonomy, phylogeny, stylasterids
Objavljeno v DiRROS: 24.07.2024; Ogledov: 132; Prenosov: 104
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3. Multi-marker metabarcoding approach to study mesozooplankton at basin scaleSergio Stefanni, David Stanković, Diego Borme, Alessandra De Olazabal, Tea Juretić, Alberto Pallavicini, Valentina Tirelli, 2018, izvirni znanstveni članek Povzetek: Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.
Ključne besede: zooplankton, genetics, biodiversity
Objavljeno v DiRROS: 24.07.2024; Ogledov: 151; Prenosov: 106
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4. ITS2 metabarcoding analysis complements lichen mycobiome diversity dataElisa Banchi, David Stanković, Fernando Fernández-Mendoza, Fabrizia Gionechetti, Alberto Pallavicini, Lucia Muggia, 2018, izvirni znanstveni članek Povzetek: Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.
Ključne besede: ascomycetes, basidiomycetes, endophytes, fungal isolates, ion torrent, ITS1
Objavljeno v DiRROS: 24.07.2024; Ogledov: 109; Prenosov: 108
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5. DNA metabarcoding uncovers fungal diversity of mixed airborne samples in ItalyElisa Banchi, Claudio Gennaro Ametrano, David Stanković, Pierluigi Verardo, Olga Moretti, Francesca Gabrielli, Stefania Lazzarin, Maria Francesca Borney, Francesca Tassan, Mauro Tretiach, Alberto Pallavicini, Lucia Muggia, 2018, izvirni znanstveni članek Povzetek: Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments. The microscopic method used to analyze aerobiological samples and the inconspicuous fungal characters do not allow a in depth taxonomical identification. Here, we present a first assessment of fungal diversity from airborne samples using a DNA metabarcoding analysis. The nuclear ITS2 region was selected as barcode to catch fungal diversity in mixed airborne samples gathered during two weeks in four sites of North-Eastern and Central Italy. We assessed the taxonomic composition and diversity within and among the sampled sites and compared the molecular data with those obtained by traditional microscopy. The molecular analyses provide a tenfold more comprehensive determination of the taxa than the traditional morphological inspections. Our results prove that the metabarcoding analysis is a promising approach to increases quality and sensitivity of the aerobiological monitoring. The laboratory and bioinformatic workflow implemented here is now suitable for routine, high-throughput, regional analyses of airborne fungi.
Ključne besede: fungi, fungal spores, taxonomy, sequence databases
Objavljeno v DiRROS: 24.07.2024; Ogledov: 283; Prenosov: 111
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6. Genetic characterisation of European mudminnow (Umbra krameri) populations from the Sava River systemSaša Marić, David Stanković, Radek Šanda, Marko Ćaleta, Srećko Čolić, Goran Šukalo, Aleš Snoj, 2019, izvirni znanstveni članek Povzetek: Two new populations of the European mudminnow (Umbra krameri Walbaum, 1792) were discovered in the Sava River system, one in its middle part (Bosnia and Herzegovina) and the other in a tributary to the Kupa River (Croatia). The Croatian population is the most upstream mudminnow discovery in the Sava River system known to date. The genetic structure of the newly recorded mudminnow populations was examined using mitochondrial DNA and microsatellite loci. By adding these new populations to the analysis of the population genetic structure of mudminnow from the Sava River system, previously unresolved relationships between the populations from the upper and the lower Sava were clarified: the middle Sava populations were shown to be well outside the hybridisation zone with the Danubian clade, meaning the upstream boundary of this zone is confined to the lower Sava. The results also suggest that mudminnow populations in the Sava River system are less isolated than previously believed. Namely, intermediate gene-flow was detected when comparing the uppermost Sava population with the lower Sava populations. Taking these results into account, appropriate guidelines are proposed to preserve mudminnow populations from the Sava River system.
Objavljeno v DiRROS: 23.07.2024; Ogledov: 121; Prenosov: 69
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7. PLANiTS : a curated sequence reference dataset for plant ITS DNA metabarcodingElisa Banchi, Claudio Gennaro Ametrano, Samuele Greco, David Stanković, Lucia Muggia, Alberto Pallavicini, 2020, izvirni znanstveni članek Povzetek: DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering.
Ključne besede: DNA metabarcoding, reference datasets
Objavljeno v DiRROS: 19.07.2024; Ogledov: 137; Prenosov: 89
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8. Molecular systematics of the long-snouted deep water dogfish (Centrophoridae, Deania) with implications for identification, taxonomy, and conservationSergio Stefanni, Diana Catarino, Pedro A. Ribeiro, Mafalda Freitas, Gui Menezes, Francis Neat, David Stanković, 2021, izvirni znanstveni članek Povzetek: According to the most recent taxonomical revision, the deep-sea dogfish genus Deania encompasses four species. Three of them, D. calcea, D. profundorum, and D. hystricosa, occur in the North Atlantic. Whilst D. profundorum can be identified by the presence of a subcaudal keel, the other two species are not easily visually distinguished. Uncertainties over identification raises concerns over stock units and whether management plans are adequate. In this study we compared onboard visual identification of Deania specimens, with morphological inspection of skin denticles under stereo microscope and with independent molecular taxonomical assignment using two molecular markers. Particular emphasis was paid to specimens identified as D. calcea and D. hystricosa in the NE Atlantic where these species potentially occur sympatrically and may be easily confused. In the past the species have been discriminated on the basis of the size of skin denticles (skin roughness), but our study showed that the crown length of skin denticles covaries with size (and sex), irrespective of species, and therefore this is not a reliable morphological character and should not be used to discriminate between the two species. Phylogenetic analyses did not indicate that D. hystricosa to be a distinct lineage from D. calcea. Interestingly, however four individuals (specimens from: UK, Azores Is., Madeira Is. and Seine seamount) formed a well-defined sub-clade nested within the D. calcea clade, possibly a signature of a past vicariance event or a result of coalescent stochasticity.
Ključne besede: deep-sea sharks, fishery by-catch, phylogeny, Atlantic Ocean, deep-sea dogfish, skin denticles
Objavljeno v DiRROS: 19.07.2024; Ogledov: 132; Prenosov: 82
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9. Detection of the endangered stone crayfish Austropotamobius torrentium (Schrank, 1803) and its congeneric A. pallipes in its last italian biotope by eDNA analysisChiara Manfrin, Massimo Zanetti, David Stanković, Umberto Fattori, Victoria Bertucci-Maresca, Piero G. Giulianini, Alberto Pallavicini, 2022, izvirni znanstveni članek Povzetek: The stone crayfish, Austropotamobius torrentium, is a European freshwater crayfish. Although this species is relatively widespread throughout the continent, it is undergoing significant declines throughout its range. However, as the decline rates have not been quantified in detail, this species is classified as data deficient by the IUCN Red List of Threatened Species. The present study describes the development and validation of two species-specific assays based on hydrolysis probe chemistry for the detection of A. torrentium and A. pallipes environmental DNA (eDNA) in water samples collected in the Julian Alps of Italy (Friuli Venezia Giulia). The eDNA-based method was applied to 14 sites within the Danubian Slizza basin, known to be inhabited by A. torrentium, but with insufficient information on their distribution. In addition, one station in the Tagliamento River basin was sampled to test the performance of the A. pallipes probe. The presence of A. torrentium is confirmed at 6 out of 15 sites. At four of these sites, A. torrentium is detected for the first time. In contrast, the presence of A. torrentium was not detected at two sites already known to harbour the species. Finally, the presence of A. pallipes was confirmed in the station belonging to the Tagliamento basin. The methodology described, which allows the distinction between the two species, paves the way for the parallel detection of the stone crayfish and the white-clawed crayfish (A. pallipes) through eDNA analysis.
Objavljeno v DiRROS: 16.07.2024; Ogledov: 138; Prenosov: 85
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10. An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populationsJody Robbemont, Sam van Veldhuijzen, Steven J. R. Allain, Johanna Ambu, Ryan Boyle, David Stanković, 2023, izvirni znanstveni članek Povzetek: Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding.
Ključne besede: citizen science, Ichthyosaura alpestris, invasive species, mtDNA barcoding, skin swabbing
Objavljeno v DiRROS: 12.07.2024; Ogledov: 150; Prenosov: 125
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