Adrià Antich

Bjerknes Centre for Climate Research

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Xavier Turón

Centre d'Estudis Avançats de Blanes

Creu Palacín

Institut de Biologia Evolutiva

Jesús Zarcero

Centre d'Estudis Avançats de Blanes

Owen S. Wangensteen

Universitat de Barcelona

Alberto Maceda‐Veiga

Universitat de Barcelona

Inés Castejón‐Silvo

Mediterranean Institute for Advanced Studies

Ina Csenteri

Universidad de Las Palmas de Gran Canaria

Yoana Del‐Pilar‐Ruso

University of Alicante

Miquel A. Arnedo

Universitat de Barcelona

Carlos Barata

Institute of Environmental Assessment and Water Research

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Universitat de Barcelona

Institut de Biologia Evolutiva

Consejo Superior de Investigaciones Científicas

Universidad de Las Palmas de Gran Canaria

Centre d'Estudis Avançats de Blanes

Mediterranean Institute for Advanced Studies

Institute of Environmental Assessment and Water Research

Institut de Recerca de la Biodiversitat de la Universitat de Barcelona

Universitat de les Illes Balears

University of Alicante

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DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets

PeerJ (2022)

Adrià Antich Creu Palacín Xavier Turón Owen S. Wangensteen

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.

Parallelizable manifold

10.7717/peerj.12758

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Citations (8)

From biomarkers to community composition: Negative effects of UV/chlorine-treated reclaimed urban wastewater on freshwater biota

The Science of The Total Environment (2023)

Cesc Múrria Alberto Maceda‐Veiga Carlos Barata Joan Gomà Melissa Faria

The use of urban wastewater reclaimed water has recently increased across the globe to restore stream environmental flows and mitigate the effects of water scarcity. Reclaimed water is disinfected using different treatments, but their effects into the receiving rivers are little studied. Physiological bioassays and biomarkers can detect sub-lethal effects on target species, but do not provide information on changes in community structure. In contrast, official monitoring programs use community structure information but often at coarse taxonomic resolution level that may fail to detect species level impacts. Here, we combined commonly used biomonitoring approaches from organism physiology to community species composition to scan a broad range of effects of disinfection of reclaimed water by UV-light only and both UV/chlorine on the biota. We (1) performed bioassays in one laboratory species (water flea Daphnia magna) and measured biomarkers in two wild species (caddisfly Hydropsyche exocellata and the barbel Luciobarbus graellsii), (2) calculated standard indices of biotic quality (IBQ) for diatoms, benthic macroinvertebrates, and fishes, and (3) analysed community species composition of eukaryotes determined by Cytochrome Oxidase C subunit I (cox1) metabarcoding. Only the UV/chlorine treatment caused significant changes in feeding rates of D. magna and reduced antioxidant defenses, increased anaerobic metabolism and altered the levels of lipid peroxidiation in H. exocellata. However, inputs of reclaimed water were significantly associated with a greater proportion of circulating neutrophils and LG-PAS cells in L. graellsii. Despite IBQ did not discriminate between the two water treatments, metabarcoding data detected community composition changes upon exposure to UV/chlorine reclaimed water. Overall, despite the effects of UV/chlorine-treated water were transient, our study suggests that UV-light treated is less harmful for freshwater biota than UV/chlorine-treated reclaimed water, but those effects depend of the organizational level.

Daphnia magna

Biota

Reclaimed water

10.1016/j.scitotenv.2023.169561

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Biogeographical scenarios modulate seagrass resistance to small‐scale perturbations

Journal of Ecology (2018)

Fernando Tuya Yolanda Fernández‐Torquemada Jesús Zarcero Yoana Del‐Pilar‐Ruso Ina Csenteri

Abstract Seagrasses constitute a key coastal habitat world‐wide, but are exposed to multiple perturbations. Understanding elements affecting seagrass resistance to disturbances is critical for conservation. Distinct biogeographical scenarios are intrinsically linked with varying ecological and evolution backgrounds shaped across millennia. We addressed whether the resistance (change in shoot abundances) and performance (change in leaf morphology and growth) of the seagrass Cymodocea nodosa to a local stressor, light reduction, varied across three regions (Southeast Iberia, the Balearic Sea, and the Canaries) within the temperate northern Atlantic realm. We hypothesized that distinct biogeographical scenarios, in terms of distinct ecological/environmental conditions and genetic diversity of meadows, would affect seagrass resistance and performance, with flow‐on effects on associated epifauna. The same experiments, in terms of shading intensities, timing and duration, were replicated at three seagrass meadows within each region. Results demonstrated inter‐regional variation in the resistance and performance of C. nodosa . Under moderate and high shading, shoot abundance was abruptly decreased, relative to controls, in the Canaries with concurrent, but less accentuated, changes in leaf morphology and no changes in growth. In the other two regions, however, moderate and high shading had a negligible effect on shoot abundance, leaf morphology, and growth. Shading had no overall effect over the total abundance and assemblage structure of epifauna; these faunal attributes, however, varied between regions. Low seagrass resistance at the Canaries is linked with the peripheral distribution of the species there, favouring isolation and decreased genetic diversity. Synthesis . Different biogeographical scenarios shape seagrass resistance to local perturbations. From a conservation perspective, if resistance differs among biogeographical scenarios, universal conservation rules for seagrasses are challenging.

10.1111/1365-2745.13114

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Citations (33)

Metabarcoding reveals high‐resolution biogeographical and metaphylogeographical patterns through marine barriers

Journal of Biogeography (2022)

Adrià Antich Creu Palacín Jesús Zarcero Owen S. Wangensteen Xavier Turón

Abstract Aim It has been predicted that there should be concordance between biogeographical and phylogeographical processes structuring multi‐species regional assemblages. We hypothesise that oceanographic barriers in the marine environment affect concomitantly the distribution and the connectivity of the marine biota, thus producing congruent biogeographical and phylogeographical structures. We also predict that macro‐ and meio‐eukaryotes will be differentially affected by hydrological features. Location The Atlanto‐Mediterranean transition along the E Iberian coast marked by the Almeria‐Oran Front (AOF) and the Ibiza Channel hydrological discontinuities. Taxon Eukaryotes. Methods A new analytical framework based in the metabarcoding of community DNA and a hypervariable marker is presented. This framework allows the simultaneous detection of multispecies biogeographical and phylogeographical structures. Shallow hard‐bottom communities were sampled at 12 sites over the littoral zone and community‐DNA metabarcoding was performed using the cytochrome c oxidase I marker. The resulting dataset was analysed at several levels: beta diversity of Molecular Operational Taxonomic Units (MOTUs) as surrogate for species, and Exact Sequence Variants as surrogate for haplotypes. We also assessed genetic differentiation within MOTUs (metaphylogeography). Analyses were performed for the combined dataset and separately for macro‐ and meio‐eukaryotes. Results Both hydrological discontinuities had a detectable effect, more marked at all levels for the AOF than for the Ibiza Channel. The MOTU dataset provided more clear‐cut patterns than the ESVs. The metaphylogeographical approach provided the highest resolution in terms of differentiating localities and identifying geographical barriers. The separate analyses of macro‐ and meio‐eukaryotes showed a higher differentiation of the latter, both in terms of beta diversity and genetic differentiation. Main Conclusions Metabarcoding coupled with metaphylogeography allowed the characterisation of the heterogeneity in community composition and population genetic structure along the Atlanto‐Mediterranean transition, coherent with known hydrological discontinuities. This methodology unlocks a vast amount of information on the geographical distribution of different components of biodiversity for basic and applied research.

10.1111/jbi.14548

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Citations (14)