Global Change Microbiology
Luciana Santoferrara, Hofstra University. Institutional profile – Laboratory website
Location: New York
Abstract
The dramatic impacts of human activities on Earth have catapulted the development of new disciplines across the sciences, humanities, and more. Studying the basis, challenges and responses to the global changes our planet and the human society face has become urgent. In the Global Change Microbiology CURE, students develop semester-long research projects focused on microbial communities and their relationship with a local environmental problem. Students: 1) develop research questions and conduct both field and wet lab work to estimate environmental, cell count and DNA-based diversity metrics; 2) receive training in bioinformatics, data analysis and result presentation; and 3) discuss literature on the interplay between microbes and environmental issues (e.g., global warming, ocean acidification, deoxygenation of coastal waters), the impacts of global changes on microbe-host interactions (e.g., coral bleaching, spreading of infectious diseases) and microbial applications (e.g., bioremediation, waste management). We examine key players in the whole spectrum of microorganisms (from viruses to microscopic animals), with emphasis on often overlooked protists that influence biogeochemical cycles, ecological functioning and host wellbeing.
Student Goals
- To apply scientific reasoning and inquiry skills in field and laboratory settings.
- To develop analytical skills in bioinformatics and statistical tests.
- To increase proficiency in oral and written science communication.
Research Goals
- To record environmental parameters and estimate the abundance of prokaryotic and microeukaryotic cells in a human-impacted, seasonally-hypoxic coastal area.
- To determine the diversity and taxonomic composition of microbial communities before, during and after seasonal hypoxia.
Context
This CURE is implemented as an advanced laboratory course for a maximum of 20 students. The course includes two components: 1) Lab meetings, occurring once a week for 3 h. Activities are described in the CURE Design section. 2) Discussion meetings, occurring twice a week for 85 minutes. These meetings consist of student-led discussion of literature on various global changes and their links to microbiology (e.g., permafrost thawing and methanogens; climate change and spreading of human and other animal diseases; ocean acidification and coral breaching). Each student alternates to conduct a 15-20 min presentation of the paper, followed by class discussion and/or a group activity of the presenter's creation (e.g., design of experiments to answer a given question, simulations of outreach/educational programs, design of microbe-based solutions for global changes).
Prerequisites for this course include the first-year Introductory Biology sequence and a mid-level Laboratory Skills course that covers introductory data analysis, literature review and scientific writing. General Microbiology is a preferred prerequisite, but not required. This course fulfills one of the two upper-level lab courses requirement for Biology majors.
Target Audience: advanced Biology and Urban Ecology BS and BA Majors; the course is also open to Biology and Urban Ecology MS and MA students.
CURE Duration: one term (15 weeks).
Target Audience: Major, Upper Division
CURE Duration:A full term
CURE Design
This CURE focuses on an environmental problem in an estuarine area located 30 minutes from campus and thus familiar to most students. While this course focuses specifically on seasonal hypoxia in Long Island Sound, it can be adapted to other coastal environmental issues. The laboratory portion of the course includes five main components: 1) Field work from a local dock. Students are trained on and use diverse water samplers, measure environmental variables (Secchi depth, water temperature, salinity, pH, dissolved oxygen, concentration of N nutrients and greenhouse gases, etc.), fix samples for cell enumeration, and conduct in situ filtrations for DNA and chlorophyll-a samples. 2) Elaboration of a research proposal. Based on the samples collected and previous data from the same location, students in pairs elaborate a research proposal, including an introduction, research question and hypotheses, and planned experiments/data analyses. Different groups choose to focus on either prokaryotes or eukaryotes, and explore different questions such as relationship to a certain environmental factor. Each proposal receives a double-blinded peer review and feedback from the instructor, all of which is used to revise and resubmit proposals. 3) Lab work. each group processes a subset of the collected samples, including steps for DNA extraction, DNA quantification and PCR amplification of the 16S and 18 rRNA genes for high-throughput DNA sequencing. Each group also observes samples in the microscope to learn basic identification and quantification of key microeukaryotes. If time and resources allow, students can pick individual cells for single-cell PCR and DNA sequencing and/or quantify prokaryote cells by flow cytometry. Students are evaluated for achieved lab milestones and two lab reports. 4) Data analysis. Students analyze environmental, cell count and DNA sequencing data obtained from their work, in combination with previous data from the same location. Students are trained and use diverse software (Excel, RStudio) and a webserver (QIIME2 in Galaxy). Students collect their analyses into two assignments, and receive feedback from the instructor. 5) Data presentation. Each group prepares an oral presentation of their research and are specifically requested to connect results to their research proposal, lab steps, data analyses and preliminary conclusions. After the presentations, the groups reassemble into two teams based on topic affinity and create a more comprehensive "story" that they present in a poster. Hofstra students present their poster at a University-wide event at the end of the semester (Undergraduate Research Day), where faculty, students and the public learn about the projects.
Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Constructing explanations (for science) and designing solutions (for engineering), Planning and carrying out investigations, Using mathematics and computational thinking
Nature of Research: Basic Research, Field Research, Informatics/Computational Research, Wet Lab/Bench Research
Tasks that Align Student and Research Goals
Student Goals ↓
- To make field observations and measurement of seawater environmental variables.
- To collect water samples using a Van Dorn bottle and plankton nets.
- To filter water for chlorophyll-a analyses.
- To extract chlorophyll-a and quantify its concentration by fluorometry.
- To classify and quantify microbial cells by inverted microscopy and/or flow cytometry.
- To record field and experimental metadata, and results from multiple techniques.
- To make field observations and measurement of seawater environmental variables.
- To filter water for DNA analyses.
- To extract DNA, conduct PCR amplification and gel electrophoresis, and to quantify and pool amplicons in preparation for Illumina high-throughput sequencing.
- To record field and experimental metadata, and results from multiple techniques.
- To recognize and manipulate diverse types of data (environmental, cell counts) in large datasets.
- To design and conduct statistical tests that compare environmental and cell count data under diverse conditions (e.g., different years, or different stages of hypoxia).
- To design and conduct statistical tests that correlate environmental and cell count data.
- To prepare informative and compelling visualizations in RStudio.
- To recognize and manipulate diverse types of DNA sequencing data in large datasets.
- To design and conduct statistical tests that compare DNA sequencing data under diverse conditions (e.g., different years, or different stages of hypoxia).
- To design and conduct statistical tests that correlate environmental and DNA sequencing data.
- To learn and conduct basic bioinformatic analyses of diversity and taxonomic composition of microbial communities.
- To prepare informative and compelling visualizations in RStudio and QIIME2/Galaxy.
- To elaborate a research proposal in collaboration with a peer.
- To provide an informative and constructive written peer review.
- To incorporate peer and instructor feedback in written assignments.
- To link a research proposal, results and preliminary conclusions in an oral presentation.
- To effectively communicate research results to peers, faculty and the general public in a final poster.
- To elaborate a research proposal in collaboration with a peer.
-To provide an informative and constructive written peer review.
- To incorporate peer and instructor feedback in written assignments.
- To link a research proposal, results and preliminary conclusions in an oral presentation.
- To effectively communicate research results to peers, faculty and the general public in a final poster.
Instructional Materials
Sample Syllabus (Acrobat (PDF) 73kB Feb15 25)
Literature (Excel 2007 (.xlsx) 19kB Feb15 25)
Final Poster Template (PowerPoint 2007 (.pptx) 39kB Feb15 25)
Assessment
1) Student learning isassessed by formative presentations of published work, a research proposal for the semester, and a final poster presentation at a University-wide event. Evidence of student outcomes includes proficiency in the science process and skills in troubleshooting, teamwork and communication. 2) Impact is assessed by anonymous Google Form surveys at the beginning, mid-term and end of the semester for the instructor to assess research experience, perceived accomplishments and interest in environmental topics before and after taking this course. The mid-semester survey also enabled formative assessment to confirm what each student was learning, given that this course did not include any exams. 3) Course and teaching effectiveness are assessed by the institution's anonymous Course Teaching Evaluation at the end of the semester.
Instructional Staffing
Dr. Luciana Santoferrara, Department of Biology, Hofstra University
Roles: The instructor prepares materials, maintains equipment and oversees field and lab work. The instructor provides instructions, guidance and feedback for individual and group assignments.
![[creative commons]](/images/creativecommons_16.png)
Motivation
Luciana Santoferrara, Hofstra University
Research experiences are crucial in the education and professional development of undergraduate STEM students (Auchincloss et al., 2014; Lopatto, 2009). The emerging field of Global Change Microbiology (Boetius, 2019) offers unique chances for training students in marketable skills (molecular biology, bioinformatics) and development of critical thinking on causes, consequences and strategies for mitigation and adaptation to global environmental changes. The Global Change Microbiology CURE offers transformative experiences, while raising awareness on new career horizons in the environmental workforce that our society urgently needs to face critical challenges in climate and ecosystem services.
Advice for Implementation
While the typical cap for upper-level lab courses at Hofstra is 20 students, the first iteration of this course had 12 students enrolled. This ended being the perfect size for this course, enabling for a scaffolded process where students worked and were assessed individually, in pairs, in groups of 3 or in two final teams of 6 students each. The CURE component of the class not only enabled for all the experiences mentioned above, but also for reinforcement of concepts from previous courses (e.g., to apply the central dogma of molecular biology into experimental design, as students have to differentiate detecting a gene vs. measuring its expression). The discussion part of the class can be optional at other institutions, but it helped reinforcing the scientific method, exemplifying wet lab and computational analyses, providing background on research topics, etc.
Iteration
There are two designated field dates to have some weather-related flexibility. Duplicate samples are collected to have a backup. For lab work, there is flexibility fir iteration, given students are learning many new techniques and may need to troubleshoot. For written assignments (proposal) and the final poster, there are at least two rounds of feedback and improvements.
Using CURE Data
All data produced by students is deposited in a Google Drive folder managed by the instructor. Students also have access to data previously collected by the instructor's team. In the first iteration of the course, most students have only contributed marginally to the datasets and analyses; some students are or have become lab team members and will be co-authors in eventual publications. For broader use by the scientific community, this project incorporates FAIR Guiding Principles for Scientific Data Management and Stewardship (Wilkinson et al., 2016).
Resources
General references
Auchincloss LC, Laursen SL, Branchaw JL, Eagan K, Graham M, Hanauer DI, Lawrie G, McLinn CM, Pelaez N, Rowland S, Towns M, Trautmann NM, Varma-Nelson P, Weston TJ, Dolan EL (2014) Assessment of Course-Based Undergraduate Research Experiences: A Meeting Report. CBE—Life Sciences Education 13:29-40
Boetius A (2019) Global Change Microbiology — big questions about small life for our future. Nature Reviews Microbiology 17:331–332
Lopatto D (2009). Science in Solution: The Impact of Undergraduate Research on Student Learning. Research Corporation for Science Advancement.
Wilkinson M, Dumontier M, Aalbersberg I et al. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3:160018
Course-specific references
Provided in a separate Literature file
Acknowledgments
The development of this CURE was supported by the Department of Biology at Hofstra University and the USA National Science Foundation (DBI 2334522).
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