| 1. |
- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 2. |
- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 3. |
- Bonet, Berta, et al.
(författare)
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Antioxidant enzyme activities as biomarkers of Zn pollution in fluvial biofilms
- 2012
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Ingår i: Ecotoxicology and Environmental Safety. - : Elsevier BV. - 0147-6513 .- 1090-2414. ; 80, s. 172-178
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Tidskriftsartikel (refereegranskat)abstract
- The potential of the antioxidant enzyme catalase (CAT) and ascorbate peroxidase (APX) as molecular biomarkers of Zn toxicity in freshwater biofilms has been explored in this study jointly with other classical functional and structural endpoints (photosynthetic parameters, algal group composition and bioaccumulation). Biofilms were colonized in an indoor microcosm system for 5 weeks and then exposed to Zn for 5 weeks. To evaluate Zn effects, biofilms were sampled 5 and 3 days before exposure, just before exposure (time 0), and after 6h, 1, 3, 7, 21 and 35 days of metal exposure. Most endpoints measured were affected by Zn exposure (320μgZnL -1) during both periods of exposure. APX was the only functional parameter responding after a few hours of Zn exposure, highlighting its use as an early toxicity biomarker. Structural changes began after 3 days of exposure, starting with a decrease in algal biomass and an increase in the OD 430:665 ratio. Structural changes in biofilm communities were observed after 1 week, leading to a shift from diatoms to cyanobacteria and green algae-dominated communities. CAT activity was thereafter enhanced (after three weeks of exposure) and attributed not only to a direct effect of Zn bioaccumulation but also to an indirect effect of the community composition changes driven by chronic metal exposure. It can be concluded that biofilm antioxidant enzyme activities may provide evidence of early stress caused by metal exposure and also provide information about the mechanism of community adaptation. This information can be of great interest to improve current tools used for risk assessment. © 2012 Elsevier Inc.
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| 4. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Chl-a fluorescence parameters as biomarkers of metal toxicity in fluvial biofilms: An experimental study
- 2011
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Ingår i: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 673, s. 119-136
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Tidskriftsartikel (refereegranskat)abstract
- A study was carried out to evaluate the sensitivity of different chlorophyll-a (chl-a) fluorescence parameters measured in freshwater biofilms as metal pollution biomarkers of short- and long-term metal exposures at environmentally realistic concentrations. A microcosm experiment was performed using indoor channels. Mature biofilms were exposed from hours to weeks to three different treatments: No-Metal, Zn (400 μg l-1); and Zn plus Cd (400 μg l-1 and 20 μg l-1, respectively). Metal concentration was based on a real case study: the Riou-Mort River (France). Biofilms exposed to Zn bioaccumulated similar Zn contents per dry weight to those exposed to the mixture (Zn plus Cd) causing a similar inhibition of the effective quantum yield, during the first hours of exposure. A reduction of the algal biomass, a shift in the community composition (a high reduction of diatoms), a reduction of the maximal quantum yield (ΦM) and a strong reduction of non-photochemical quenching (NPQ) were observed from day 14 until the end of the experiment (35 days). The results indicate that the effects of the metal mixture present in the Riou-Mort on biofilms could be attributed to Zn toxicity. The use of a set of chl-a fluorescence measurements, including photochemical and NPQ parameters, are recommended as a reliable biomarker tool box to evaluate both short- and long-term effects of metals on biofilms containing oxygenic photoautotrophs, suggesting its use in field applications. © 2011 Springer Science+Business Media B.V.
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| 5. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Comparison of different DNA extraction methods for marine periphyton and its implications for ecotoxico-metagenomics
- 2015
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Ingår i: Poster Presentation at the SETAC Europe 25th Annual Meeting, Barcelona, Spain.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This is a time with unprecedented capacity of DNA sequencing technologies for metagenomic analysis (identifying new genes and species living in environmental samples) in natural communities. However, sequencing efforts on non-model organisms or communities, such as marine periphyton communities, are still scarce in ecotoxicology. Also, uncertainties in basic aspects, such as choice of appropriate DNA extraction method, are still not resolved. This study aims to compare the effects of different DNA extraction methods for marine periphyton in terms of DNA yield, purity and integrity, as well as eukaryotic and prokaryotic diversity. Cost-effectiveness among the methods was also assessed. Four different methods (the Plant DNAzol reagent (Invitrogen), the Fast DNA Spin kit for soil (MP Biomedicals), the PowerPlant and the PowerBiofilm DNA Isolation Kits (MoBio Laboratories)) commonly used for DNA extraction of eukaryotic and prokaryotic microorganisms from marine periphyton were compared. Results showed that the commercial method Plant DNAzol reagent and the Fast DNA Spin kit for soil appear to be the best to extract high quantities of DNA (> 50 ng/μL). DNA fragments obtained with these methods cover a wide range of sizes, from 250 to 15000 bp. With the PowerPlant and the PowerBiofilm DNA Isolation Kits, lower amounts of DNA were obtained (< 23 ng/μL), but the purity of these extractions, in terms of protein and polysaccharide contamination, was higher. Extractions from these latter kits also produced DNA size distributions with larger sizes, between 3000 and 15000 bp. Obtained DNA products were used for amplicon sequencing of the 18S rRNA and 16S rRNA genes, targeting eukaryotes and prokaryotes, respectively. Such DNA amplicon sequencing will be a powerful tool to compare community composition and biodiversity across samples, and to select DNA extraction method for further metagenomics of periphyton communities exposed to toxicants.
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| 6. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
- 2017
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 364:14
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterization of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the Fast DNATM SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77 - 130 μg g wet wt-1). Lower amounts of DNA were obtained (
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| 7. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Copper affects composition and functioning of microbial communities in marine biofilms at environmentally relevant concentrations
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Copper (Cu) pollution in coastal areas is a worldwide threat for aquatic communities. This study aims to demonstrate the usefulness of the DNA metabarcoding analysis in order to describe the ecotoxicological effect of Cu at environmental concentrations on marine periphyton. Additionally, the study investigates if Cu-induced changes in community structure co-occurs with changes in community functioning (i.e. photosynthesis and community tolerance to Cu). Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and photosynthetic activity. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the high biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 0.01 µM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (0.06 µM), which is still in the range of the Cu concentrations observed in the area (0.08 µM). The current environmental quality standard for Cu of 0.07 µM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of photosynthetic activity. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including taxa within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic taxa, and therefore to identify particularly sensitive, non-cultivable taxa.
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| 8. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Light History Influences the Response of Fluvial Biofilms to Zn Exposure
- 2012
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Ingår i: Journal of Phycology. - : Wiley. - 0022-3646 .- 1529-8817. ; 48, s. 1411-1423
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Tidskriftsartikel (refereegranskat)abstract
- Fluvial biofilms are subject to multistress situations in natural ecosystems, such as the co-occurrence of light intensity changes and metal toxicity. However, studies simultaneously addressing both factors are rare. This study evaluated in microcosm conditions the relationship between short-term light intensity changes and Zn toxicity on fluvial biofilms with long-term photoacclimation to different light conditions. Biofilms that had long-term photoacclimation to 25 μmol photons · m-2 · s-1 (low light [LL] biofilms), 100 μmol photons · m-2 · s-1 (medium light [ML] biofilms), and 500 μmol photons · m-2 · s-1 (high light [HL] biofilms) were characterized by different structural (Chlorophyll-a [Chl-a], total biomass-AFDW, EPS, algal groups, and diatom taxonomy) and physiological attributes (ETR-I curves and photosynthetic pigments). HL biofilms showed higher light saturation intensity and a higher production of xanthophylls than LL biofilms. In contrast, LL biofilms had many structural differences; a higher proportion of diatoms and lower AFDW and EPS contents than ML and HL biofilms. A clear effect of light intensity changes on Zn toxicity was also demonstrated. Zn toxicity was enhanced when a sudden increase in light intensity also occurred, mainly with LL biofilms, causing higher inhibition of both the Φ′PSII and the ΦPSII. A decoupling of NPQ from de-epoxidation reaction (DR) processes was also observed, indicating substantial damage to photoprotective mechanisms functioning in biofilms (i.e., xanthophyll cycle of diatoms) due to Zn toxicity. This study highlights the need to take into account environmental stress (e.g., light intensity changes) to better assess the environmental risks of chemicals (e.g., metals). © Phycological Society of America.
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| 9. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Linking pesticide pollution with periphyton quality in agricultural streams: a fatty-acids approach
- 2018
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Ingår i: SETAC Europe 28th Annual Meeting 13−17 May 2018 | Rome, Italy. Abstract Book.. - 2309-8031.
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Konferensbidrag (refereegranskat)abstract
- Although the environmental risks associated with pesticide pollution in agricultural streams are quite well documented, little is know about its potential effects on periphyton quality. Periphyton provides many of the essential polyunsaturated fatty acids (PUFA) that are needed for organisms at higher trophic levels in river food webs. This study aims to assess the effects of pesticide mixtures on periphyton quality in situ. Three streams (Höje å, Skivarpsån and M42) located in the agriculturally dominated region of Skåne (SE Sweden) were sampled in September and October 2016. The effects of pesticide pollution were assessed by passive field sampling coupled with laboratory ecotoxicity tests, by mixture toxicity modelling to predict which chemical stressors were potentially driving the toxicity, and by examining the fatty acid profiles, pigment content and algal diversity of periphyton communities. Results from water chemical analyses clearly showed higher levels of nutrients and pesticide pollution in Skivarpsån and M42 than in Höje å. Ecotoxicity tests using the passive sampler extracts demonstrated that the pesticide mixtures ocurring at Skivarpsån and M42 were toxic for periphyton communities from Höje å, causing an inhibition of the photosynthetic activity up to 63% and 53%, respectively. Cluster and principal component analyses based on pigments content, algal diversity and fatty acid profiles, clearly separated the periphyton from the three river sites studied. Algal biomass from periphyton of pesticide polluted streams (Skivarpsån and M42) was higher than in Höje å. The nutritive quality of the periphyton differed among streams, and fatty acids considered high-quality such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were also more abundant in pesticide polluted streams (Skivarpsån and M42). Overal, even though results from the lab show that the mixture of pesticides pollution in the studied streams might be toxic for periphyton (i.e. inhibiting the photosynthetic activity), being herbicides the driving chemical stressors. Results from the field, indicate that when the levels of pesticide pollution are low and co-occur with high levels of nutrients pollution, nutrients migh mask pesticides effects on periphyton quantity and quality because compensatory effects from nutrients
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| 10. |
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