18S-V9 DNA metabarcoding detects the effect of water-quality impairment on stream biofilm eukaryotic assemblages

Minerovic, Alison; Potapova, Marina; Sales, Christopher M.; Price, Jacob R.; Enache, Mihaela

doi:10.1016/j.ecolind.2020.106225

Cited by 26 publications

(15 citation statements)

References 83 publications

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“…Microscopy, HPLC pigments and molecular analysis with either chloroplast 16S rRNA or 18S rRNA each provide useful ways to identify the factors driving differences in the taxonomic composition of microbial communities among sites, sampling times or experimental treatments. It is unusual to apply all five methods in a single study, but previous studies have used pairs of methods to differentiate communities: fluorescence (pigments) and microscopy ( Lévesque et al, 2020 ); 18S rRNA/18S rRNA genes and microscopy ( Gao et al, 2018 ; Rimet et al, 2018 ; Minerovic et al, 2020 ); and chloroplast 16S rRNA and microscopy ( Eiler et al, 2013 ; Bennke et al, 2018 ). In the present study, 18S rRNA and chloroplast 16S rRNA offered better resolution for the separation of the samples among lakes and sample period than microscopy, as observed elsewhere ( Yan et al, 2007 ).…”

Section: Discussionmentioning

confidence: 99%

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

2021

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Salinization of freshwater is increasingly observed in regions where chloride de-icing salts are applied to the roads in winter, but little is known about the effects on microbial communities. In this study, we analyzed the planktonic microbiomes of four lakes that differed in degree of urbanization, eutrophication and salinization, from an oligotrophic reference lake with no surrounding roads, to a eutrophic, salinized lake receiving runoff from a highway. We tested the hypothesis that an influence of road salts would be superimposed on the effects of season and trophic status. We evaluated the microbial community structure by 16S rRNA sequencing for Bacteria, and by four methods for eukaryotes: 16S rRNA chloroplast analysis, 18S rRNA sequencing, photosynthetic pigment analysis and microscopy. Consistent with our hypothesis, chloride and total nitrogen concentrations were among the most important statistical factors explaining the differences in taxonomic composition. These factors were positively correlated with the abundance of cryptophytes, haptophytes, and cyanobacteria. Ice-cover was also a major structuring factor, with clear differences between the winter communities and those of the open-water period. Nitrifying and methane oxidizing bacteria were more abundant in winter, suggesting the importance of anaerobic sediment processes and release of reduced compounds into the ice-covered water columns. The four methods for eukaryotic analysis provided complementary information. The 18S rRNA observations were strongly influenced by the presence of ribosome-rich ciliates, but revealed a much higher degree of taxonomic richness and greater separation of lakes, seasonal changes and potential salinity effects than the other methods.

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Section: Discussionmentioning

confidence: 99%

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

2021

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“…To describe the composition in the diet at the taxonomic level (not for the taxonomic‐free analyses), we joined matched ESVs to the same taxa using a match criteria threshold of >90% base similarity to reference sequences (Dunn et al, 2018; Hatzenbuhler et al, 2017; Leempoel et al, 2020), making a single molecular unit (da Silva et al, 2020). We then labeled them as operational taxonomic units “OTUs” in the study for convenience as this term is more commonly used in the metabarcoding literature (Minerovic et al, 2020). For example, multiple ESVs were identified to the Echinochloa genus, and the reads would be combined to create one unique OTU for this genus.…”

Section: Methodsmentioning

confidence: 99%

Diet DNA reveals novel African Forest elephant ecology on the grasslands of the Congo Basin

Meyer

Honig²,

Hadly

2022

Environmental DNA

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Elephants are essential ecological engineers, creating and maintaining landscape structure and ecosystem function. The recently distinguished and critically endangered forest elephant is currently classified as a selective, non‐destructive frugivorous browser that maintains forest diversity, while the savanna elephant is a mixed feeder, often pushing over trees while maintaining grasslands. The presence and diets of forest elephants on grasslands and the potential maintenance of these systems remain largely unexplored. In the ecotone between the Guinea‐Congolian forest and Sudanian‐Guinean savanna ecosystems in Garamba National Park, DRC, we investigated forest elephant diet selection as a function of sex, age, and habitat using diet DNA (dDNA) metabarcoding of non‐invasively collected dung. GPS collar data were used to determine annual habitat use. Dietary niche partitioning was assessed among megaherbivores in the grasslands. Fecal samples represented the diet of individuals within each habitat, providing valuable insight into the plant biodiversity. Ecological patterns of diet were also revealed using a taxonomically free exact sequence variance approach, highlighting useability in a poorly characterized region. In the early wet season, these typically frugivorous forest elephants were consuming mostly grasses in both the woodland and grassland habitats and showing no sexual dimorphism in diet selection when in the same habitats. However, males were greater risk‐takers, entering the human‐altered landscape to forage on fruit. The forest elephants play a distinctive role within this tropical grassland when compared to other megaherbivores and utilize the unique ecosystem throughout the year. This elephant population is exhibiting behavioral plasticity and shifting their gardening efforts to a novel resource in the grasslands as opposed to their standard role in the forests, which is key to understanding their impact as ecosystem drivers within this landscape. This shift in behavior may result in this recovering elephant population playing a functional role in the restoration and maintenance of these grasslands.

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“…Owing to rapid community succession, periphyton tends to adapt to these external stressors by altering its community structure (Larned, 2010). Therefore, periphyton is commonly used as an ecological model for monitoring and evaluating the effects exerted by anthropogenic and natural factors in aquatic ecosystems (Minerovic et al, 2020; Peng et al, 2020; Vis et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, periphyton is commonly used as an ecological model for monitoring and evaluating the effects exerted by anthropogenic and natural factors in aquatic ecosystems (Minerovic et al, 2020;Peng et al, 2020;Vis et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Distribution and photosynthetic potential of epilithic periphyton along an altitudinal gradient in Jue River (Qinling Mountain, China)

Hao

Sun

et al. 2022

Freshwater Biology

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1. Periphyton in aquatic ecosystems play a crucial ecological role in element cycling and are susceptible to natural disturbances and anthropogenic activities.To understand the responses of periphytic communities to water quality factors and altitude gradients, DNA metabarcoding was employed to investigate the distribution characteristics of epilithic periphyton (comprising prokaryotes and eukaryotes).2. Epilithic periphyton and water were sampled at 26 sampling sites with an altitude ranging from 445 to 1,565 m in the Jue River and its three tributaries in Qinling Mountain, China. The altitudinal patterns of water quality variables were initially investigated, followed by redundancy analysis and distance-based linear models to explore the responses of community structure to altitudes and water quality. Meanwhile, the relationship between these variables and fluorescence parameters to reflect the photosynthesis of epilithic periphyton along an altitudinal gradient was examined.3. The results indicated that with decreasing elevation, water quality variables including total dissolved solids (TDS), water temperature, conductivity, salinity, and concentrations of NO − 3 -N, total nitrogen, and NO − 2 -N increased. This pattern was closely associated with the intensification of anthropogenic disturbance downstream. Specifically, higher salinity and water temperature downstream may reduce the prokaryotic biodiversity but promote the diversity and evenness of eukaryotes; higher concentrations of total nitrogen may increase the diversity, richness, and evenness of the whole periphyton community. Furthermore, salinity, nutrients, and TDS were identified as crucial variables shaping periphyton community structure, especially salinity and TDS, which were linked to the growth of chlorophytes.4. The attenuated maximum photochemical efficiency of periphyton at high altitudes indicated that photosystem II was inhibited, while the enhancement of maximum photochemical efficiency at low altitudes may be attributed to the

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18S-V9 DNA metabarcoding detects the effect of water-quality impairment on stream biofilm eukaryotic assemblages

Cited by 26 publications

References 83 publications

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

Diet DNA reveals novel African Forest elephant ecology on the grasslands of the Congo Basin

Distribution and photosynthetic potential of epilithic periphyton along an altitudinal gradient in Jue River (Qinling Mountain, China)

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