1,721,276 research outputs found
Unraveling the diversity of eukaryotic microplankton in a large and deep perialpine lake using a high throughput sequencing approach
Full text linkThe structure of microbial communities, microalgae, heterotrophic protozoa and fungi contributes to characterize food webs and productivity and, from an anthropogenic point of view, the qualitative characteristics of water bodies. Traditionally, in freshwater environments many investigations have been directed to the study of pelagic microalgae (“phytoplankton”) and periphyton (i.e., photosynthetic and mixotrophic protists) through the use of light microscopy (LM). While the number of studies on bacterioplankton communities have shown a substantial increase after the advent of high-throughput sequencing (HTS) approaches, the study of the composition, structure, and spatio-temporal patterns of microbial eukaryotes in freshwater environments was much less widespread. Moreover, the understanding of the correspondence between the relative phytoplankton abundances estimated by HTS and LM is still incomplete. Taking into account these limitations, this study examined the biodiversity and seasonality of the community of eukaryotic microplankton in the epilimnetic layer of a large and deep perialpine lake (Lake Garda) using HTS. The analyses were carried out at monthly frequency during 2014 and 2015. The results highlighted the existence of a rich and well diversified community and the presence of numerous phytoplankton taxa that were never identified by LM in previous investigations. Furthermore, the relative abundances of phytoplankton estimated by HTS and LM showed a significant relationship at different taxonomic ranks. In the 2 years of investigation, the temporal development of the whole micro-eukaryotic community showed a clear non-random and comparable distribution pattern, with the main taxonomic groups coherently distributed in the individual seasons. In perspective, the results obtained in this study highlight the importance of HTS approaches in assessing biodiversity and the relative importance of the main protist groups along environmental gradients, including those caused by anthropogenic impacts (e.g., eutrophication and climate change
The composition of apple and pear bark microbiota suggest microbial migrations from soil
No full textThe migration of soil microbial communities possibly define the bark microbiota. The bark microbiota is affected by the bark age and plant specie
Unravelling the composition of apple and pear bark microbiota through a metabarcoding approach
No full textCharacterization of the apple and pear bark microbiota
No full textBark is considered an important overwintering site for pathogenic, beneficial and saprophytic microorganisms and can act as a reservoir of potential plant pathogens and biocontrol agents. However, the majority of the studies regarding plant-associated microbial communities are focused on the phylloplane, fruits and the rhizosphere, while bark is poorly investigated. The aim of this study was to assess the composition of fungal and bacterial communities of pear and apple barks. Results showed that the amount of cultivable colony forming units (CFUs) and the composition of fungal and bacterial communities differed according to bark age and plant species
Temporal variability of bacterioplankton is habitat driven
No full textTemporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high throughput sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, non-metric multidimensional scaling, and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to melt-water inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats
Multifaceted aspects of synchrony between freshwater prokaryotes and protists
No full textCommunity composition of freshwater prokaryotes and protists varies through time. Few studies contemporarily investigate temporal variation of these freshwater communities for more than one year. We compared the temporal patterns of prokaryotes and protists in three distinct habitats for four years (2014-2017) in Lake Tovel, a cold-water lake. This lake showed a marked temperature increase in 2017 linked to altered precipitation patterns. We investigated if microbial communities reflected this change across habitats and if changes occurred at the same time and to the same extent. Furthermore, we tested the concept of hydrological year emphasising the ecological effect of water renewal on communities for its explanatory power of community changes. Microbe diversity was assessed by Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA-gene and 18S rRNA-gene, and we applied co-inertia analysis and asymmetric eigenvector maps modelling to infer synchrony and temporal patterns of prokaryotes and protists. When considering community composition, microbes were invariably in synchrony across habitats and indicated a temporal gradient linked to decreasing precipitation; however when looking at temporal patterns, the extent of synchrony was reduced. Small-scale patterns were similar across habitats and microbes and linked to seasonally varying environmental variables, while large-scale patterns were different and partially linked to an ecosystem change as indicated by increasing water transparency and temperature and decreasing dissolved oxygen. Our advanced statistical approach outlined the multifaceted aspect of synchrony when linked to community composition and temporal patterns
Do inferences about freshwater phytoplankton communities change when based on microscopy or high‐throughput sequencing data?
No full text1. Microscopy and high-throughput sequencing (HTS) detect and quantify algae differently. Little is known if microscopy-based abundance or biomass better compare to HTS data and how methodological differences affect ecological inferences about the phytoplankton communities studied.
2. We investigated methodological (abundancemicroscopy versus abundanceHTS, biomassmicroscopy versus abundanceHTS), habitat (littoral, pelagic, deep hypolimnion), and year differences (2014 versus 2017) for phytoplankton communities of Lake Tovel (Italy) using ANOVA. Specifically, we tested the hypothesis that depending on comparing abundancemicroscopy or biomassmicroscopy, respectively, to abundanceHTS different effects would be indicated; we called this the metric effect. Furthermore using samples from 2014 to 2017, we investigated environment-community relationships by a redundancy analysis (RDA) based on abundancemicroscopy, biomassmicroscopy, and abundanceHTS, and compared the results.
3. Approximately nine times more operational taxonomic units (OTUs) were reported with HTS (n2014 = 819, n2017 = 891) than algal taxa with microscopy (n2014 = 90, n2017 = 109) in 2014 and 2017. While microscopically assessed algal taxa were evenly distributed among phyla, the vast majority of OTUs were attributed to Chrysophyta (2014 = 54%, 2017 = 62%) and Bacillariophyta (2014 = 19%, 2017 = 17%). A metric effect for method differences was generally observed comparing abundancemicroscopy to abundanceHTS with Chlorophyta, Cryptophyta, and Dinophyta showing higher % abundance with microscopy while richness and Chrysophyta showed higher values with HTS. Almost no metric effects were found in 2014, but they were common across phyla in 2017. Bacillariophyta and Eustigmatophyta showed the same habitat differences when comparing biomassmicroscopy to abundanceHTS.
Dinophyta showed habitat differences only with microscopy, while Chyrsophyta showed habitat differences only with HTS; these results were probably related to technical bias and strengths of HTS, respectively.
4. Habitat differences of phyla were reasonably related to their ecological niche and linked to factors such as temperature and feeding preferences; furthermore, phyla often showed a significant 2014-versus-2017 year effect. The year 2014 was very wet while 2017 had a dry winter, and we attributed the patterns found to allochthonous nutrient input by rain and decreased turbulence. RDAs based on phytoplankton communities assessed with microscopy and HTS, respectively, equally indicated the importance of hydrology, nutrients, and temperature for phytoplankton communities and discriminated the littoral from the deep hypolimnion. However, variance explained was higher with HTS, and the pelagic was similar to the deep hypolimnion with microscopy but to the littoral with HTS.
5. Despite the different strengths of microscopy and HTS for biodiversity assessment, both datasets outlined similar large-scale patterns linked to strong environmental control of phytoplankton communities as they related to habitat and year differences. According to our hypothesis, metric effects were common; however, no general rule was found if either abundancemicroscopy or biomassmicroscopy, respectively, should be compared to abundanceHTS. Notwithstanding metric effects, HTS-based data provided similar and more detailed information than microscopy, supporting the promise of HTS becoming the tool of the future for biodiversity research
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