Mycorrhizal fungi of the Americas and human impacts: uncovering hidden diversity
We are investigating the impact of human activities on arbuscular mycorrhizal fungal (AMF) diversity. Using sequencing amplicon data collected across the Americas (Alaska, Kansas, and Brazil) this study will (1) determine if human-induced land use changes significantly diminish the diversity of AMF and (2) evaluating the importance of the determination of AMF, either using our tree placement pipeline or BLASTing. For (2), our goal is to understand biases in these different approaches in (a) recovering AMF, particularly proportion in each AMF family or undescribed and (b) for inferences of human land use impact of AMF diversity. |
Alexis Aellen is a Master's student in Ecology and Evolution at ETH Zürich. He is particularly interested in understanding plant dependencies to AMF and how these microorganisms can be used to minimize human negative impacts on ecosystems and help improve agriculture.
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Soil Sample Storage and DNA Degradation
Many experimental results may depend on how samples are stored and transported. While working in the tropics and with field sites that are relatively isolated, this is a big issue. There is some work looking at DNA degradation over time, but over rather short periods of time and mostly at different temperatures. This methods study will examine impacts of different storage methods of field soil as well as impacts of thaw time on extracted DNA. We will store soil using 4 methods: room temperature, cooler, liquid N2, and RNAlater. We will look at thaw times over 2 months (60 days). Finally, we will be measuring DNA through qPCR for bacteria and fungal communities as well as sequencing communities and comparing community structure. This project is in partnership with Luke Bainard, a research scientist at the Swift Current Research and Development Centre with Agriculture and Agri-Food Canada.
Many experimental results may depend on how samples are stored and transported. While working in the tropics and with field sites that are relatively isolated, this is a big issue. There is some work looking at DNA degradation over time, but over rather short periods of time and mostly at different temperatures. This methods study will examine impacts of different storage methods of field soil as well as impacts of thaw time on extracted DNA. We will store soil using 4 methods: room temperature, cooler, liquid N2, and RNAlater. We will look at thaw times over 2 months (60 days). Finally, we will be measuring DNA through qPCR for bacteria and fungal communities as well as sequencing communities and comparing community structure. This project is in partnership with Luke Bainard, a research scientist at the Swift Current Research and Development Centre with Agriculture and Agri-Food Canada.