Biology subjects

Davidson, T. A.

Publications and source records attributed to Davidson, T. A..

3 recordsLinked to original sources

bioRxiv2023

Dynamics of associated microbiomes during algal bloom development: to see and to be seeing

Our understanding of the interactions between bacteria and phytoplankton in the freshwater phycosphere, including the development of algal blooms, is very limited. To identify the taxa and compositional variation within microbial communities, we performed 16S rRNA amplicon sequencing research on samples collected weekly through summer from mesocosms that differed in temperature and mixing regimes. We investigated, for the first time, the abundance diversity of microalgae, including Chlorophyta, Cryptophyta, and Cyanobacteria species, using visualization-based FlowCAM analysis and classification of microbial communities to species level by nanopore next-generation sequencing. We found that nanopore metagenomics, in parallel with complementary imaging flow cytometry, can depict the fine temporal dynamics of microbiomes associated with visually identified Microcystis morphospecies, Chlorophyta, and Cryptophyta during algal bloom development. Our results showed that the temporal characteristics of microbiomes combined with a visual approach may be a key tool to predict the metacommunity structure and dynamics of algal blooms in response to anthropogenic effects and climate change.

microbiology↗

bioRxiv2023

From colonial clusters to colonial "sheaths": analysis of Microcystis morphospecies in mesocosm by imaging flow cytometry

The alarming increase in the frequency of blooms of Microcystis in freshwater lakes and reservoirs occurs worldwide, with major implications for their ecosystem functioning and water quality. We applied FlowCAM-based imaging flow cytometry together with PCR and sequencing to get a comprehensive picture of the seasonal development of Microcystis community in a long-term running lake mesocosm experiment. The IFC analysis with manual taxonomic classification confirmed early findings with a machine learning algorithm that some Microcystis morphospecies completely disappeared and re-appeared along the mesocosm experiment timeline. This observation supports the hypothesis of the main transition pathways of colonial Microcystis. For the first time, colonial mucilaginous envelopes or sheaths were reported as separate entities, and not as a part of Microcystis colonies. The colonial sheaths may contain a few single Microcystis cells and reach significant numbers (thousands) during a cyanobacterial bloom. We also found that non-identifiable colonial small clusters of Microcystis cells are an important stage in the complex mosaic of a Microcystis bloom and are associated with the development of colonial forms. Our findings were validated by the principal component analysis coupled with the constructed associative matrices. We hypothesize that colonial sheaths may be crucial at Microcystis spp. dispersal and represent one of the stages of colonies development.

ecology↗

bioRxiv2023

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy natures services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

ecology↗