| 1. |
- Abarenkov, Kessy, et al.
(author)
-
The curse of the uncultured fungus
- 2022
-
In: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
-
Journal article (peer-reviewed)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.
|
|
| 2. |
- Abarenkov, Kessy, et al.
(author)
-
The curse of the uncultured fungus
- 2022
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
-
Journal article (peer-reviewed)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.
|
|
| 3. |
- Eriksson, Martin, 1970, et al.
(author)
-
Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations
- 2020
-
In: Ecotoxicology. - : Springer Science and Business Media LLC. - 0963-9292 .- 1573-3017. ; 29:7, s. 1083-1094
-
Journal article (peer-reviewed)abstract
- The antibacterial agent Triclosan (TCS) is a ubiquitous environmental contaminant due to its widespread use. Sensitivity to TCS varies substantially among eu- and pro-karyotic species and its risk for the marine environment remains to be better elucidated. In particular, the effects that TCS causes on marine microbial communities are largely unknown. In this study we therefore used 16S amplicon rDNA sequencing to investigate TCS effects on the bacterial composition in marine periphyton communities that developed under long-term exposure to different TCS concentrations. Exposure to TCS resulted in clear changes in bacterial composition already at concentrations of 1 to 3.16 nM. We conclude that TCS affects the structure of the bacterial part of periphyton communities at concentrations that actually occur in the marine environment. Sensitive taxa, whose abundance decreased significantly with increasing TCS concentrations, include the Rhodobiaceae and Rhodobacteraceae families of Alphaproteobacteria, and unidentified members of the Candidate division Parcubacteria. Tolerant taxa, whose abundance increased significantly with higher TCS concentrations, include the families Erythrobacteraceae (Alphaproteobacteria), Flavobacteriaceae (Bacteroidetes), Bdellovibrionaceae (Deltaproteobacteria), several families of Gammaproteobacteria, and members of the Candidate phylum Gracilibacteria. Our results demonstrate the variability of TCS sensitivity among bacteria, and that TCS can change marine bacterial composition at concentrations that have been detected in the marine environment.
|
|
| 4. |
- Gómez-Martínez, Daniela, et al.
(author)
-
Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican
- 2023
-
In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 875
-
Journal article (peer-reviewed)abstract
- Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC50 of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.
|
|
| 5. |
- Guasch, H., et al.
(author)
-
Interactions between microplastics and benthic biofilms in fluvial ecosystems: Knowledge gaps and future trends
- 2022
-
In: Freshwater Science. - : University of Chicago Press. - 2161-9549 .- 2161-9565. ; 41:3
-
Journal article (peer-reviewed)abstract
- Plastics, especially microplastics (<5 mm in length), are anthropogenic polymer particles that have been detected in almost all environments. Microplastics are extremely persistent pollutants and act as long-lasting reactive surfaces for additives, organic matter, and toxic substances. Biofilms are microbial assemblages that act as a sink for particulate matter, including microplastics. They are ubiquitous in freshwater ecosystems and provide key services that promote biodiversity and help sustain ecosystem function. Here, we provide a conceptual framework to describe the transient storage of microplastics in fluvial biofilm and develop hypotheses to help explain how microplastics and biofilms interact in fluvial ecosystems. We identify lines of future research that need to be addressed to better manage microplastics and biofilms, including how the sorption and desorption of environmental contaminants in microplastics affect biofilms and how microbial exchange between microplastics and the biofilm matrix affects biofilm characteristics like antibiotic resistance, speciation, biodiversity, species composition, and function. We also address the uptake mechanisms of microplastics by consumers and their propagation through the food web.
|
|
| 6. |
- Motiei, Asa, 1980-
(author)
-
Microbiome Of Ecotoxicity Assays
- 2021
-
Doctoral thesis (other academic/artistic)abstract
- Microorganisms are ubiquitous and present in animal microbiomes, particulates, and colonizable surfaces of test systems. From an ecotoxicological perspective, they are metabolically active biological compartments that respond to test conditions, including test substances. In exposure experiments, microorganisms can both alleviate toxicity via, for example, biotransformation, and reinforce the adverse effects via, for example, disrupted microbiome-host interactions. Acknowledging these interactions is essential for a mechanistic understanding of results in effect studies and developing assays towards more ecologically relevant hazard assessment. Therefore, there is increasing attention toward “microbiome aware ecotoxicology” in recent years, focusing mostly on test organism microbiomes. I studied how microorganisms present in systems designed for acute and chronic toxicity assays with Daphnia magna affect the test outcome. The experimental studies showed that bacteria introduced in the system intentionally (as a part of the experimental design; Papers I, II, and III) or unintentionally (with the microbiome of the test animals; Paper IV) responded to the test substances and mediated the exposure for the target species. In these studies, we employed the emerging contaminants ciprofloxacin (an antibiotic drug; Paper I) and various fossil-based polymers (microplastic; Papers II, III, and IV), representing a microbiome disrupting and a biofilm promoting type of substance respectively. In Paper I, we hypothesized that exposure to antibiotics would primarily target the daphnid microbiome with downstream effects on the host fitness. To test this hypothesis, we chronically exposed daphnids to ciprofloxacin, which resulted in decreased microbiome diversity. However, contrary to our hypothesis, there were significant stimulatory effects on the host fitness and antioxidant production due to the direct pro-oxidative ciprofloxacin effects on the host. Although the microbiome was not directly involved in the growth-related responses to the ciprofloxacin exposure, the microbiome’s alterations suggest that exposure to any antimicrobials, which – unlike ciprofloxacin – do not stimulate antioxidant production, would result in gut dysbiosis with possible adverse effects on the host. Further, we hypothesized that in assays with particulate test materials, such as microplastic, bacterial biofilms increase particle aggregation, affecting exposure levels. This hypothesis was tested using D. magna exposed to a mixture of kaolin clay and polystyrene with and without biofilm (Paper II). We found that biofilm significantly decreased the adverse effects exerted by particulates directly, most likely, by providing nutrition for the daphnids, and indirectly, by inducing particle aggregation. In Paper III, we compared biofilm communities established on the plastic (polyethylene, polypropylene, and polystyrene) vs. non-plastic (cellulose and glass) substrates. The biofilm communities on the plastic were significantly different from those on the non-plastic materials; hence, microplastic contribution to the suspended solids in the exposure can drive the biofilm community composition in the system. Finally, in Paper IV, we found that in a closed system designed to evaluate microplastic effects on D. magna, bacteria originated from the daphnid microbiome colonize particulates and affect their aggregation and animal survival. Together, these findings suggest that chemical exposure (Paper I), the microbiome of the test animal (Paper IV), the composition of the suspended solids (SS) (Papers II and IV), and their surface properties (Paper III) contribute to the diversity and abundance of the biofilm in the test system, which can affect the test outcome. Thus, the microbiome reacts to and interacts with contaminants within a test system, which calls for the appreciation of these interactions when interpreting the results as well as new developments toward standardization of the bacterial component in (eco)toxicity assays with eukaryotic test species.
|
|
| 7. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
-
Journal article (peer-reviewed)abstract
- Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
|
|
| 8. |
- Tlili, Ahmed, et al.
(author)
-
Addendum to Tolerance Patterns in Stream Biofilms Link Complex Chemical Pollution to Ecological Impacts
- 2021
-
In: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 55:1
-
Journal article (peer-reviewed)abstract
- Following publication of our paper, we were made aware that we might not have sufficiently pointed out the potential role that microorganisms released with wastewater effluents could play in the increased tolerance of downstream biofilms toward micropollutants. Indeed, a large survey in 23 wastewaterimpacted streams, including the three sampling sites investigated in our study, showed that downstream bacterialcommunity profiles in the water column were a mixture between the upstream and the effluent.1 Whether these microorganisms go from a planktonic into a benthic biofilm state and play a role in the tolerance to micropollutants remains unclear. Nevertheless, it is plausible that suchmicroorganisms might have developed a tolerance to micropollutants in the wastewater treatment plants (WWTP) before their release into the streams. Mußmann et al.2 have shown that, among all identified nitrifying bacteria in the WWTP effluent, only one taxa preferentially added to the downstream biofilm community whereas the others did not. Similarly, Chonova3 showed that less than 5% and not the most abundant bacterial taxa were found in the biofilms downstream of urban and hospital WWTP. Even if actively colonizing downstream biofilms, monitoring the diversity profile of these microorganisms alone does not answer the question whether they contribute to the community tolerance to micropollutants. Therefore, controlled experiments focusing on both benthic bacterial and algal communities are needed to address this issue.
|
|
| 9. |
- Tlili, A., et al.
(author)
-
Tolerance Patterns in Stream Biofilms Link Complex Chemical Pollution to Ecological Impacts
- 2020
-
In: Environmental Science & Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 54:17, s. 10735-10743
-
Journal article (peer-reviewed)abstract
- Preventing and remedying fresh waters from chemical pollution is a fundamental societal and scientific challenge. With other nonchemical stressors potentially co-occurring, assessing the ecological consequences of reducing chemical loads in the environment is arduous. In this case study, we comparatively assessed the community structure, functions, and tolerance of stream biofilms to micropollutant mixtures extracted from deployed passive samplers at wastewater treatment plant effluents. These biofilms were growing up- and downstream of one upgraded and two nonupgraded wastewater treatment plants before being sampled for analyses. Our results showed a substantial decrease in micropollutant concentrations by 85%, as the result of upgrading the wastewater treatment plant at one of the sampling sites with activated carbon filtration. This decrease was positively correlated with a loss of community tolerance to micropollutants and the recovery of the community structure downstream of the effluent. On the other hand, downstream biofilms at the nonupgraded sites displayed higher tolerance to the extracts than the upstream biofilms. The observed higher tolerance was positively linked to micropollutant levels both in stream water and in biofilm samples, and to shifts in the community structure. Although more investigations of upgraded sites are needed, our findings point toward the suitability of using community tolerance for the retrospective assessment of the risks posed by micropollutants, to assess community recovery, and to relate effects to causes in complex environmental conditions.
|
|
| 10. |
|
|
