Changes in genomic signatures of anthropogenic stress on revived diatoms from natural archives
This is a suggestion for a Degree Project for Bachelor's and Master's levels at the Department of Marine Sciences. Degree projects at the Department of Marine Sciences are done independently and must be written and assessed individually.
Subject: Marine Biology
Level: Master's degree project in Plant Ecology and Evolution
Available earliest: 2022
Principal Investigator: Anushree Sanyal
Where: Department of Environmental Science and Sustainability Studies, Södertörns högskola
Project description
Human activities have raised temperatures, CO2 levels, nutrients in the oceans creating hypoxic zones which has affected the biodiversity in oceans across the world.
In this project we will be investigating how to predict the impact of anthropogenic stressors and climate change on the diversity of marine life over long timescales. This knowledge will eventually allow us to understand how species adapt to changing environmental conditions due to climate change and human activities.
In this project you will examine the response of algae; which are the primary producers and at the base of food web in the ocean to changing environmental conditions of temperature, light and salinity.
You will acquire skills in:
• Algae culture
• Light microscopy
• Working with a new model system Chaetoceros muelleri for long-term evolutionary studies
• Analyze gene expression data in algae
• Analyzing genomic data to identify single nucleotide polymorphisms
• DNA and RNA extraction methods
Project background
We show for the first time the revival, viability and germination rate of resting spores of the diatom Chaetoceros deposited in sub-seafloor sediments from three ages (recent: 0-80 years; ancient: ~1250 (Medieval Climate Anomaly) and ~6600 (Holocene Thermal Maximum) calendar year before present). Our findings showed that ~6600 calendar year before present (cal. yr BP) old Chaetoceros resting spores are still viable and the physiological response pertaining to reproduction in recent and ancient resting spores vary.
The time taken to germinate is three hours to 2-3 days in both recent and ancient spores but the germination rate (%) of the spores decreased with increasing age. The germination rate of the recent spores was ~41 % while that of the ancient spores were ~31 % and ~12 % for the ~1250 and ~6600 cal. year BP old resting spores. Based on the morphology of the resting spores as well as the germinated vegetative cells we were able to identify the species as Chaetoceros muelleri var. subsalsum (Lemmerman) J.R. Johansen and Rushforth. Sanger sequences of nuclear and chloroplast markers identified the species as Chaetoceros muelleri.
The knowledge gained for examining the genomic signatures of Chaetoceros muelleri populations over time and the response of the species to environmental change will eventually allow us to predict the response and adaptation of this and other species to climate change. In this project you will develop an approach for waking up and culturing ancient resting spores and use genomics, transcriptomics and single-cell genomics approaches and analyses to reveal the response of marine species to climate change and human actions.
Project goals
1. Revival of algal resting spores and culturing of algae.
2. Analyzing gene expression data subjected to different environmental conditions.
3. Analyzing genomic data to identify single nucleotide polymorphisms.
4. Learn DNA and RNA extraction
5. Measuring of the absorbance of chlorophyll a with a spectrophotometer to determine the differences in growth rate between different strains subjected to high and low light, temperature and salinity conditions.
Contact
Maria Asplund
Email: maria.asplund@gu.se
Anushree Sanyal
Department of Environmental Science and Sustainability Studies,
Södertörns högskola
E-mail: anushree.sanyal@sh.se