ENVSCI 702 : Applied Estuarine Ecology


2020 Semester Two (1205) (15 POINTS)

Course Prescription

Emphasises multi-disciplinary science that integrates across different empirical and theoretical approaches to better understand the functioning of soft-sediment ecosystems. Covers fundamental ecological principles of soft-sediment systems through to the impacts associated with human activities. Includes practical exercises in experimental field ecology which will introduce students to key research methods. No formal prerequisite but knowledge of Stage III marine ecology/science, or equivalent, will be assumed.

Course Overview



This paper emphasises multi-disciplinary science to better understand the functioning of soft-sediment ecosystems. The course will cover fundamental ecological principles of soft-sediment systems through to the impacts associated with human activities. Student participation in practical exercises in experimental field ecology will be at the core of the learning process. This course is designed to help you learn about seafloor ecology. It is an ideal primer for further research in marine science and will help you develop the scientific skills needed for many technical and environmental management roles. In the course we try to help you transition from knowledge consumer to knowledge producer by helping you develop ideas, work in teams, present information and question our relationships to our coastal ecosystems.

Contributors:  Simon Thrush (Auckland), Conrad Pilditch (Waikato), Candida Savage (Otago), Joanne Ellis (Waikato)
Covid-19 Response
We have run this course in a blended delivery mode for the past five years with students from Auckland, Waikato & Otago engaging online with set reading before an intensive one-week course hosted by the University of Auckland at the Leigh Marine Laboratory. During this week we deliver seminars based on the set topics, design and undertake a field experiment and students present some of their assignments.
Unfortunately, we find ourselves in a great deal of uncertainty with respect to the Covid-19 situation. The University of Auckland made the decision to close Leigh Marine Laboratory for teaching, a decision that will not be changed in time for our field course.  This decision is consistent across all NZ universities as they committed to an online delivery mode for at least A Semester.
We discussed at length the viability of this course without the field trip and instead of cancelling, decided to commit to running it in an online mode only. Obviously, it will not be the same experience but we have tried very hard to stay true to the philosophy of the course and devise new approaches to delivering and assessing the content. It has also meant some adjustment to the learning outcomes and delivery modes but we believe it will still be an interesting and informative learning experience.
We recognise that online learning presents numerous challenges for everyone and especially for a course that was built around an in person interactive field trip. We do not pretend for a moment that this will be a seamless operation but please remember we are committed to being flexible, responsive to your needs, and willing to evolve in real time. To ensure this happens we need your help, please communicate, telling us where problems may exist (for example, tutorials scheduled at inconvenient times, assessment due dates) and collectively we can reach a solution.
We have kept the “block” course element (virtually) in so much that seminar tutorials, student presentations and introductions to key assignments will all be held during the week of Jul 6-10 when we would have been at Leigh. We have decided to this because staff and students should already have this time blocked out and it should not clash with the start of B semester.
Below is a revised introduction and outline to the course.   At this time, it is important to check through the proposed timetable and let us know if there are any anticipated problems. Depending on the Covid-19 alert level it might be possible to run a one day field trip from Auckland (UoA), Tauranga (UoW) and Dunedin (OU) for those that can make it to provide some context.  Please note, if this field trip goes ahead it, attendance is NOT compulsory and non-attendance will not affect your ability to complete the course.

Course Introduction
In this course we want to make you think about estuarine and coastal soft sediment ecosystems. We plan to run the course as seminars covering seven key topics addressing important elements of how these ecosystems work and how that might influence the ways we manage them. We want to make this course real so we will be spending quite thinking critically about how science is undertaken.
We are focused on estuaries as these ecosystems have been crucial to the development of our species, but dominated by soft-sediment habitats they also provide us with and easy place to ask and test some important questions that relate to the structure and function of the most common seafloor habitat.
Estuaries are complex ecological systems that mark the transition between freshwater and the open coast. They cover a diverse cross-section of habitats supporting a wide range of human activities and values and are an integral part of the cultural identity of New Zealanders. Estuaries are transitional environments, the meeting place of land, freshwater and marine ecosystems. 
New Zealand has an extensive shoreline (about 18 000 km) that includes more than 400 estuaries, collectively covering about 5300 km2.  The transitional nature of estuaries makes them hard to define, but they are generally considered to be tidally influenced water bodies largely enclosed by land in which there is a measurable dilution of seawater due to freshwater inputs from rivers and runoff.  Thus all of our harbours and much of our iconic coastline are, by definition, estuaries.  New Zealand’s estuaries have a wide diversity of coastal geomorphological forms ranging from the fiords of southwestland (e.g., Doubtful Sound), to drowned river valleys (e.g., Hokianga Harbour), to lagoons (e.g., Okarito). Our biggest harbours are Kaipara and Manukau, although much of the Hauraki Gulf can also be defined as an estuary. Areas within estuaries that fall between the high and low tide marks are exposed and inundated during the rise and fall of the tide. These intertidal flats and reefs are particularly important to ecological processes in estuaries and often occupy a large part of the estuary. 
Biodiversity and ecosystem services are intimately linked.  Biodiversity encompasses the variety of life and its interaction with the environment, ranging from genotypes to ecosystems. Dominated by marine organisms, our estuaries are diverse and contain representatives of a wide range of phyla from micro-organisms to whales.  On the intertidal sandflats of the estuaries around Auckland we can easily collect 200 species of organisms big enough to see with the naked eye. By marine standards estuaries are generally considered species poor ecosystems.  Nevertheless, the resident species, the strong physical and chemical gradients found within estuaries and the supply of nutrients from the adjacent catchment make estuaries functionally diverse
Across New Zealand, the range of habitats found on the floor of estuaries is tremendous, from the terrestrial fringing habitats of saltmarsh and mangrove to the deep-water muddy basins at the bottom of the fiords.  There is more to the description of estuary habitats than rock, sand and mud.  Just like terrestrial habitats, estuarine habitats are most informatively defined based on dominant and habitat structuring species.  These habitats can include tube mats, scallop beds, oyster reefs, crab burrowed mudflats, cockle beds, mussel beds, sponge gardens, kelp reefs and turfing algae.  These descriptive habitat designations often give us clues as to dominant ecological.
Many species fundamentally influence ecosystem processes by altering the physical architecture of the sediment. Organisms and their burrows, mounds and tubes, modify flow over the seafloor and provide settlement sites and refugia from predators.  On the sediment surface, predators (e.g., rays, birds, fish, starfish and crabs) digging into the sediment in search of food create pits, adding to the heterogeneity of the seafloor, while microscopic algae bind the sediment surface and the movement of animals crawling over the surface affect sediment erodability.  Below the sediment surface, physical structures such as tubes and burrows and the activities of animals that affect the movement of particles and pore water, influence habitat heterogeneity and many important microbial and geochemical processes.  Microbes in the sediments drive nutrient and carbon cycling, but this is strongly facilitated by the movement, burrowing, hydraulic pumping and feeding of animals living both on (epifaunal) or within (infauna) the sediment.  These processes highlight important links between seabed and water-column ecosystems that affect nutrient recycling, the processing of organic material and carbon storage.
Collectively the activities of estuarine organisms significantly influence the nature and rate of biogeochemical processes that sustain the biosphere. The shallow comparatively warm, sunlit, well mixed waters and extensive soft-sediment habitats of estuaries are often considered to play significant roles in processing contaminants from land and fuelling productivity on the adjacent coast. Fish live within and pass through estuaries, either to spawn in rivers, or to spend their adulthood in the open sea.
Most of our major cities are located beside estuaries and these ecosystems have served us well in terms of transport, trade and the provision of food.  Estuaries also represent some of our most iconic tourist destinations. The wide range of human uses of estuaries, together with the number of people living beside them, means that inevitably not all activities can be supported everywhere. This dilemma is a major environmental challenge for New Zealand and most other countries with coastlines. This enhances the need to understand the ecosystem processes and the threats to them. Estuaries represent important meeting places between the land and sea and consequently are subjected to multiple and cumulative stressors.  Despite the long list of potential stressors and the need for restoration in some locations, our estuarine and coastal ecosystems still exhibit high biodiversity values and are critical to our tourism industry and our sense of national identity.
Rivers, streams, drains and direct runoff from land bring a variety of contaminants to our estuaries and coasts. Modification of coastal and estuarine shorelines through reclamation, dredging and in-water structures (e.g., causeways, bridges, piers, marinas and structures associated with aquaculture) can also affect ecosystem process and as a result service delivery.  While from the sea we bring stressors associated with fishing, mining and invasive species.
Estuaries, like coral reefs, are especially prone to the effects of climate change.  Climate change in an estuarine setting can only be realistically viewed through a multiple stressor lens.  With increased storminess and episodic rainfall we can expect changes in freshwater inputs and sediment runoff in many areas. In the estuary, temperatures and sea level are expected to rise, affecting habitats, species distributions and many of the processes that underpin provisioning ecosystem services.  At the coast, changes in storminess, increased storm surge, changes in wave climate and changes in coastal productivity and coastal ocean currents are likely to affect estuarine ecology. Estuaries are also regions with high variation in water column pH, while this can be due to a number of natural factors it is exasperated by both local anthropogenic stress and global climate change. All of these stressors interact with other future cumulative effects on the ecosystem.  For example,  profound eutrophication effects such as decreasing the oxygen concentration in the floor of the estuary, creating dead zones, while primarily influenced by nutrient loading is also affected by temperature and salinity induced water stratification that may also change with change.  Furthermore, the eutrophication status of estuaries can feed back on climate change through the production of greenhouse gases.
We will further explore these issues in the seminars (below).  We expect you to have read and thought about the papers and we will be assessing you on your contribution to the seminars and discussions.
Seminar Topics (CP=Conrad Pilditch, ST=Simon Thrush, CS=Candida Savage, JE=Joanne Ellis)
1.    Structure & functioning of soft sediment ecosystems
a.    Basic introduction to biogeochemistry, primary production and macrofauna -CP
b.    Trophic interactions -CS
c.    Biodiversity, feedback loops & resilience - ST
2.    Human impacts & management
a.    Stressors, disturbance & recovery from catastrophic events: Sedimentation as a case study - CP
b.    Ecosystem based management - ST
3.    Conducting science in estuaries
a.    Monitoring for change – CS
b.    Experimental field ecology – JE
In the folders on moodle you will find a short introduction to the seminar topics and the assigned reading.  You will be expected to have read the papers thoroughly and come to the scheduled zoom tutorial with questions and prepared to engage in discussion.

Course Requirements

No pre-requisites or restrictions

Capabilities Developed in this Course

Capability 1: Disciplinary Knowledge and Practice
Capability 2: Critical Thinking
Capability 3: Solution Seeking
Capability 4: Communication and Engagement
Capability 5: Independence and Integrity
Capability 6: Social and Environmental Responsibilities

Learning Outcomes

By the end of this course, students will be able to:
  1. Engage in informed discussions related to: complexity and functioning of soft sediment ecosystems, how science is conducted in these systems, the science behind management/conservation, and possible solutions to challenges caused by human activities. (Capability 1, 2, 3, 4, 5 and 6)
  2. Evaluate critically relevant scientific literature. (Capability 1, 2, 5 and 6)
  3. Collect and analyse field data using appropriate sampling strategies. (Capability 1, 2, 3, 4 and 5)
  4. Write a scientific report that is integrated with the relevant literature. (Capability 3, 4 and 5)


Assessment Type Percentage Classification
Participation 5% Individual Coursework
Presentation 15% Individual Coursework
Essay 30% Individual Coursework
Field trip report 50% Individual Coursework
Assessment Type Learning Outcome Addressed
1 2 3 4
Field trip report

Key Topics

Seminar Topics (CP=Conrad Pilditch, ST=Simon Thrush, CS=Candida Savage, JE=Joanne Ellis)
1.    Structure & functioning of soft sediment ecosystems
a.    Basic introduction to biogeochemistry, primary production and macrofauna -CP
b.    Trophic interactions -CS
c.    Biodiversity, feedback loops & resilience - ST
2.    Human impacts & management
a.    Stressors, disturbance & recovery from catastrophic events: Sedimentation as a case study - CP
b.    Ecosystem based management - ST
3.    Conducting science in estuaries
a.    Monitoring for change – CS
b.    Experimental field ecology – JE
In the folders on moodle you will find a short introduction to the seminar topics and the assigned reading.  You will be expected to have read the papers thoroughly and come to the scheduled zoom tutorial with questions and prepared to engage in discussion.

Learning Resources

Papers linked to seminars are available via UoW website - Moodle

Special Requirements

NA for 2020
The block course will run from Mon Jul 06 – Fri Jul 10 - inclusive.  We have a provide  summary of key dates followed by a more detailed program for the online block course where we will be running tutorials based on the recorded seminars and assigned reading, answering questions and introducing the field data analysis assignment. Depending on the Covid-19 alert level it might be possible to run a one day field trip from Auckland (UoA), Tauranga (UoW) and Dunedin (OU) for those that can make it early in the week.  Please note, if this field trip goes ahead it, attendance is NOT compulsory and non-attendance will not affect your ability to complete the course.

Workload Expectations

This course is a standard [15] point block course .

For this course, you can expect [0] hours of lectures, a [11] hour tutorial, [15] hours of reading and thinking about the content and [30] hours of work on assignments and/or test preparation.

Other Information

Detailed timetable for 6-10 Jul: Interactive Online Block Course
Some notes:
1.    We have released the course content in way to achieve some learning objectives
a.    First look at the seminar outlines and complete the required reading thinking about the questions posed. This is an exercise in learning about a new topic where you need to read scientific papers to acquire knowledge and come up to speed on concepts that maybe unfamiliar to you (i.e. research). Do not worry if you do not understand everything, we do not expect you to and there is no exam in this course! Think about some questions you would like answers to. Also think about selecting an essay topic then delve deeper into the literature.
b.    Go through the recorded seminar on the topic where we link together the important concepts from the readings which will hopefully help in building more understanding. Our objective is to build a knowledge infra-structure with respect to estuary environments that you can continue to add. These seminars will be available a week before the block course. Write down any questions you may have and be prepared for the scheduled interactive discussion.
c.    The interactive discussion is an opportunity to ask any questions and reinforce the key concepts. It is also an opportunity to ask questions related to your chosen essay topic.
2.    Interactive discussions
a.    We have set out a schedule for the interactive discussions below that will get us through everything in a week. We have set the interactive discussions for each afternoon recognising that some of our student colleagues may be based overseas.
b.    We expect students enrolled in the course will participate and contribute to these discussions – it is the primary way in which you will be able to engage with us directly and improve your grasp of the material.
c.    If for some reason attending these discussions is not possible please contact us. We will record all the interactive discussions so students can review what was talked about.
d.    All the interactive discussions will be done via Zoom and we will post details/linkages on how to access these via the course moodle page closer to the time.
3.    Please remember the main goal here is to have some fun, for you to get outside your comfort zone and embrace the opportunity to engage with some researchers who are passionate about what they do. You will get as much out of this course as you are willing to put into it. If you have any questions please do not hesitate to ask – we are here to help!

Digital Resources

Course materials are made available in a learning and collaboration tool called Canvas which also includes reading lists and lecture recordings (where available).

Please remember that the recording of any class on a personal device requires the permission of the instructor.


The content and delivery of content in this course are protected by copyright. Material belonging to others may have been used in this course and copied by and solely for the educational purposes of the University under license.

You may copy the course content for the purposes of private study or research, but you may not upload onto any third party site, make a further copy or sell, alter or further reproduce or distribute any part of the course content to another person.

Academic Integrity

The University of Auckland will not tolerate cheating, or assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student's own work, reflecting their learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the internet. A student's assessed work may be reviewed against online source material using computerised detection mechanisms.

Inclusive Learning

All students are asked to discuss any impairment related requirements privately, face to face and/or in written form with the course coordinator, lecturer or tutor.

Student Disability Services also provides support for students with a wide range of impairments, both visible and invisible, to succeed and excel at the University. For more information and contact details, please visit the Student Disability Services’ website at http://disability.auckland.ac.nz

Special Circumstances

If your ability to complete assessed coursework is affected by illness or other personal circumstances outside of your control, contact a member of teaching staff as soon as possible before the assessment is due.

If your personal circumstances significantly affect your performance, or preparation, for an exam or eligible written test, refer to the University’s aegrotat or compassionate consideration page: https://www.auckland.ac.nz/en/students/academic-information/exams-and-final-results/during-exams/aegrotat-and-compassionate-consideration.html.

This should be done as soon as possible and no later than seven days after the affected test or exam date.

Student Feedback

During the course Class Representatives in each class can take feedback to the staff responsible for the course and staff-student consultative committees.

At the end of the course students will be invited to give feedback on the course and teaching through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback.

Your feedback helps to improve the course and its delivery for all students.

Student Charter and Responsibilities

The Student Charter assumes and acknowledges that students are active participants in the learning process and that they have responsibilities to the institution and the international community of scholars. The University expects that students will act at all times in a way that demonstrates respect for the rights of other students and staff so that the learning environment is both safe and productive. For further information visit Student Charter (https://www.auckland.ac.nz/en/students/forms-policies-and-guidelines/student-policies-and-guidelines/student-charter.html).


Elements of this outline may be subject to change. The latest information about the course will be available for enrolled students in Canvas.

In this course you may be asked to submit your coursework assessments digitally. The University reserves the right to conduct scheduled tests and examinations for this course online or through the use of computers or other electronic devices. Where tests or examinations are conducted online remote invigilation arrangements may be used. The final decision on the completion mode for a test or examination, and remote invigilation arrangements where applicable, will be advised to students at least 10 days prior to the scheduled date of the assessment, or in the case of an examination when the examination timetable is published.

Published on 13/07/2020 04:47 p.m.