As both aqueous ecosystems become more and more under threat, there is an increasing need to understand the changes. To monitor these changes, technology is an important, and often used, methodology. This weeklong series of lectures, exercises, and student presentations will highlight the use of methods that consist of both collecting sea water and a variety of organisms to the use of in-situ methods such as optics and acoustics. A survey of collecting platforms that use traditional methods from ships as well as newer methods that utilize a variety of autonomous vehicles will be covered. A pragmatic expectation of the instructor is that students will learn about both traditional and contemporary technologies as well as their advantages and limitations.
Dr. Jules S. Jaffe
Scripps Institution of Oceanography, University of California San Diego, United States
The overall objective of the one week of lectures, homework assignments, and a project, is to inform students (prospective researchers) about the variety of methods that can be used to study underwater ecology. Topics will be covered in a more descriptive way; however, we will not shy away from using simple mathematical formulations to describe a variety of physical phenomena such as attenuation. The course will consist of lectures, reading assignments, and a final project, from small student teams, that will be presented on the last day.
Approximate syllabus:
Day 1: Intro to aqueous ecosystems:
A survey of the various habitats such as coastal, sun-lit, middle ocean (mesopelagic), the deep sea and benthic ecosystems. A survey of the variety of organisms that range from viruses to blue whales. Combining those two lists, what lies where and what are the technological methods we can use to study it? As proposed to me by a prominent ocean biologist when I joined the field: What are the organisms that are there? How much of them are there? What are they doing? More interestingly, from the point of view of ecology is the transfer of mass and energy through the ecosystem. What are the inputs? What are the transformations? What are the outputs in terms of chemistry, biology, and even physics?
For starters, I will be going through the more traditional methods such as Salinity, Ph, etc. I will not cover elemental analysis such as Redfield ratios and the details of the biochemical transformations.
Day 2: A survey of optical methods for imaging and photosynthetic energy flow:
As the energy input for “almost” the entire ocean is sunlight, we will first study the physical properties of underwater light, the traditional methods to measure photons and the use of more advanced techniques to measure photosynthetic activity. This will include both the inherent and apparent properties of underwater light propagation. Next, considering both natural and human use of lights, the field of underwater optical imaging will be addressed. This will include considerations of range and contrast, that span the characterization from the smallest organisms (we can’t yet “see” viruses) to the largest.
Day 3: Considerations in using underwater sound: both producing it (active) and listening (passive):
The basic physics of sound propagation, both attenuation and scattering will be covered. This will also include the “sonar equation” that is basically a statement of conservation of energy in sonic systems. Traditional acoustic methods measure the sonic reflection from animals from artificially produced sound as well as reflections from a variety of flora and fauna to characterize marine environments. An engaging application has always been to listen to cetaceans to estimate habitat and abundance.
Day 4: l will cover 2 main topics this day (somewhat unrelated): 1) Deployment Methods and 2) e-DNA:
Traditional methods such as deploying instruments from boats and well as divers will be described. Topics will also include Remote Oceanographic Vehicles (ROVs). A survey of autonomous underwater vehicles will be described. This includes a family of AUVs such as the REMUS or Bluefin vehicles. There is also a variety of wind powered vehicles such as the Sail drone.
information is an emerging area with great promise that takes advantage of the most modern technologies for sequencing. I view this more as an emerging, rather than established area as there are many questions about the method that entail the lifetime of suspended material, the transport of material from other places, and perhaps a variety of in situ transformations that may occur. Nevertheless, the method has received a great deal of attention with several optimistic views.
Day 5: Student presentations:
Day 5 will be dedicated to the results of the student projects to choose an aqueous ecosystem, propose a set of quantitative measures, and present the benefits in terms of additional knowledge gained. It is anticipated that teams of students will present ½ hour talks that highlight the problem, the anticipated increase in knowledge, and how that affects our understanding of the overall ecosystem for that case.
The course will consist of a series of lectures, assignments of reading materials, practical assignments to aid in depth understanding and utilization of the concepts, and a presentation to the group of a participant chosen ecosystem and a formulation of how to study it using present and envisioned technologies. The final project will be chosen by the start of day 2 and will consist of students identifying the ecosystem of their choice, elaborating on the ecological questions that need to be answered, and a proposed suite of technological approaches specifically tailored to answer those questions. As currently envisioned, small teams of students will work together to identify and propose an approach with anticipated results enumerated.
To Be Determined (TBD)