Estuaries Lecture Notes Vocabulary

Estuaries

Introduction

• Estuaries are dynamic environments where freshwater meets saltwater.
• The University of Melbourne's Blue Planet series introduces marine biology with a focus on estuaries.

Modified Estuaries

• Estuaries are subject to change and modification.
• NIWA (www.niwa.co.nz) provides information on modified estuaries.

Management of Modified Estuaries

• Management is crucial for heavily urbanized waterways.
• The World Harbour Project brings together international research institutions to address the challenges these estuaries face.
• The project's website is https://sims.org.au/research/flagship-projects/world-harbour-project

Indicators of Pollution

• Microbial indicators can be used for surveillance of sewage contamination in harbors worldwide.
• McLellan et al. (2004) published a paper in Nature Water.
• DOI: https://doi.org/10.1038/s44221-024-00315-5

Study Cities and Pollution Levels

• Human Bacteroides levels (HF183 marker) are measured in impacted sites across 18 harbors.

• Figure 1 shows the locations of the study cities.

• Three impacted sites were sampled at each of four sampling timepoints in each city; each site collection consists of triplicate samples that were analyzed separately and averaged.

• Some cities like Baltimore, Milwaukee, and Los Angeles had four to five impacted sites, while Rio de Janeiro and Brest had two.

• All cities had at least one sample above the quantification limit.

• Key locations

  • Latitude 50° N: Milwaukee, San Francisco, Los Angeles, Honolulu, Baltimore, San Diego, Boston.
  • Latitude 50° S: Brest, Vigo, Ravenna, Darwin.
  • Other cities: Qing Dao, Hong Kong, Xiamen, Singapore, Melbourne, Sydney.

• The box plots represents:

  • The line within each box indicates the median.
  • The box indicates the first (lower) and third (upper) quartiles.
  • Vertical lines indicate minimum and maximum values aside from potential outliers (dots).
  • The asterisk indicates the average of impacted sites for each city.
  • Non-detects are shown as a value of 1 (equal to 0 on the log scale) for visualization.

Management of Changing Estuaries

• Estuaries can be sandy or muddy environments.

Citizen Science and Estuary Monitoring

• EstuaryWatch is a citizen science monitoring program.
• Goals include detecting changes in ecosystem health and informing management.

EstuaryWatch Program

• EstuaryWatch collaborates with Corangamite CMA (http://www.estuarywatch.org.au/).

Citizen Scientist Network

• A network of volunteer groups monitors various estuaries.
• Groups are located in Glenelg Hopkins CMA, Corangamite CMA, East Gippsland CMA, and West Gippsland CMA.

Monitoring Activities

• Volunteers monitor water quality and environmental variables.
• Measurements include temperature, salinity, turbidity, depth, and dissolved oxygen.
• They also monitor the condition of the estuary mouth.

Short-Term and Long-Term Management

• Short-term: Detecting anomalies in water quality and informing catchment management authorities.
• Long-term: Providing data for decision support systems, assessing overall health compared to other estuaries, and supplying scientific data for policies and management plans.

Review Questions

1. What are the benefits of citizen scientists in environmental monitoring?
2. What inconsistencies might arise from data collected by citizen scientists across Victoria, and how can these be addressed?

Estuaries Quiz

• Estuaries Quiz on Friday, March 28th.
• Ocean Circulation module with Josephine Brown.
• Coming up in Blue Planet.

Estuaries Module Lectures

• Lecture 5: Physical characteristics and types of estuaries.
• Lecture 6: Biology.
• Lecture 7: Ecology.
• Lecture 8: Management.

Ecological Principles

• Focus on giant kelp (Marcosystis pyrifera) and diatom communities.
• Giant Kelp reference: https://oceana.org/
• Diatom community photo courtesy of Wipeter (CC BY-SA 3.0).

Ecology in Estuaries

• Overview of ecological principles.

Ecology in Estuaries - Topics

• Bioturbation.
• Species interactions.
• Food webs.

Bioturbation

• Bioturbation is the reworking of sediments by animals and plants.

Bioturbation's Impact

• Bioturbation shapes sediment/soil dynamics and biogeochemistry.
• Common vole (Microtus arvalis) example (Wilske et al 2015, Plos One).

Bioturbation Study

• A study in Western Port, Victoria, Australia, characterized the feeding type of the dominant ghost shrimp species, Biffarius arenosus (Bird & Poore 1999).

Ghost Shrimp Information

• Ghost shrimp (Biffarius arenosus) information from the Taxonomic Toolkit for marine life of Port Phillip Bay, Museum Victoria.
• Taylor, J. & Poore, G.C.B., 2011.
• Up to 4.5 cm in size.

Ghost Shrimp Example

• Neotrypaea californiensis is another example of a ghost shrimp.

Videos of Benthos in Action

• Videos available showing benthos activity.
• "The Sound of the Seafloor" was shown at the "Beneath the Waves Film Festival" in Portland, Maine, at the 2016 Benthic Ecology Meeting.
• Link: https://you.stonybrook.edu/voll/videos-benthos-in-action/

Lugworm Example

• Arenicola marina (lugworm) in Germany, 10,000-fold speed.
• Volkenborn et al.
• Link: https://you.stonybrook.edu/voll/videos-benthos-in-action/

Lugworm Illustration

• Illustration of a lugworm.

Conceptual Diagram of Lugworm Activity

• Diagram showing the open and closed regions in a mudflat due to lugworm activity.
• Volkenborn et al. 2007.

Bioturbation Field Experiment Setup

• Images (a, b, c, d) depicting the experimental setup.
• Volkenborn et al. 2007.

Bioturbation Field Experiment Details

• Exclusion: Lugworms excluded (netted).
• Control: Disturbed without net.
• Ambient: Undisturbed.
• Low intertidal (3-4 h emersion period) and mid intertidal (6-7 h emersion period) zones.
• Experiment conducted over 20 meters and 500 meters.
• Volkenborn et al. 2007.

Bioturbation and Sediment Permeability

• Experiment by Volkenborn et al. 2007.
• Excl = lugworm excluded; Lugw = lugworm present (‘normal’).
• Sediment permeability in subtidal sediments.

Oxygen Levels in Exclusion and Lugworm Areas

• A) Exclusion area: Oxygen levels with varying hydraulic head (0-50).
• B) Lugworm area: Oxygen levels with varying hydraulic head (0-40).

Conceptual Diagram Revisited

• Mudflat with open and closed regions due to bioturbation.
• Bioturbated sand vs. permeable sand.
• Volkenborn et al. 2007.

Impact of Lugworms

• Presence of Arenicola marina:
  • Increases sediment permeability.
  • Increases oxygen levels.
  • Reduces anoxia.
  • Changes sediment/soil dynamics and biogeochemistry.
  • Important for maintaining ecosystem health.

Ecology in Estuaries - Topics Revisited

• Bioturbation.
• Species interactions.
• Food webs.

Species Interactions Intro

• Why do types of species interactions occur in estuaries?

Soft Sediments and Fauna

• Macrofauna (> 500 {\mu}m): polychaete worms, crabs, amphipods, molluscs.
• Meiofauna (62 - 500 {\mu}m): nematodes, copepods.
• Microfauna & microflora (< 62 {\mu}m): bacteria, diatoms (Inglis 1995).

Soft Sediments - Locations

• Mahurangi Harbour, Auckland, New Zealand (Lohrer and Hancock 2004).
• Swan Bay, Port Phillip Bay, Victoria.

Annelid Worm Study Locations

• Study locations: Lymner, Tamar, Plymouth, St. John's, Empacombe.
• Davey and George 1986.

Annelid Worm Species - Interactions

• Nereis diversicolor and Nephtys hombergi.
• Nereis larvae and juveniles are prey for Nephtys, crabs, birds, and shrimp.
• Davey and George 1986.

Annelid Worm Species - Size Distribution

• Size-frequency histograms of Nereis diversicolor larvae from St. John's and Empacombe.
• Setigers = number of segments = indicator of size of the animal.

Predation Impact on Annelid Worms

• Smaller size frequency distribution suggests higher predation rates at the experimental site.
• Setigers = number of segments = indicator of size of the animal.
• Davey and George 1986.

Foraging Eagle Rays

• Myliobatis tenuicaudatus (Hines et al. 1997).

Eagle Rays and Prey

• Macomona lilliana is a prey species.
• Ecological questions:
  1. What is the relationship between foraging activity and prey density?
  2. How does this feeding activity and feeding pits affect benthic invertebrate community structure?

Eagle Ray Study Site

• Study site location: Wiroa Island, near Auckland International Airport.
• Hines et al. 1997.

Eagle Ray Pits and Prey Density

• Correlation between total number of ray pits per 707 m^2 and neighborhood density; R^2 = 0.74.
• Hines et al. 1997.

Eagle Rays as a Physical Disturbance

• Hines et al. 1997, Thrush et al. 1997.
• How do these pits recover?
  • Size of the pit.
  • Particle size.
  • Organic carbon.
  • Infauna species abundance.

Pit Recovery and Species

• Thrush et al. 1997.
• Annelid worm (polychaete) dominated vs. bivalve dominated.
• Median number of tides since the start of the experiment.

Pit Recovery - Species and Time

• Thrush et al. 1997: Boccardia syrtis.
• Bivalves return to disturbed areas within 2 days.
• Annelid worms take up to 12 days.
• Boccardia syris did not recover within the time of the experiment.

Species Interactions - Summary

• Competition between species (e.g., two annelid worm species).
• Predator-prey interactions (e.g., eagle rays and bivalves).
  1. Close relationship between prey density and predator activity at high prey densities.
  2. The effect of physical disturbance created by feeding activity on community structure.

Food Webs

• Another example of species interactions.

Food Webs in Different Estuarine Environments

• Salt marsh (temperate regions).
• Mangrove forest (tropical regions).
• Key components: Primary producers, consumers, predators, detritus.

Manukau Harbour Sandflat Food Web

• Thrush et al. 1994, Castro & Huber 2008.
• Key components: Primary producers, consumers, predators.

Field Experiment - Predator Exclusion

• Exclude shorebirds.

• Exclude birds and rays.

• Control plots.

  • Thrush 2014.

Food Web Interactions – After 6 Months

• Number of individuals mean per 3 cores compared between:
  • Reference.
  • No birds.
  • No birds & rays.

Food Web Interactions – After 14 Months

• Number of individuals mean per 3 cores compared between:
  • Reference.
  • No birds.
  • No birds & rays.

Port Phillip Bay Food Web

• Morris and Keough 2003.
• Key components: Primary producers, consumers, predators, nutrients.

Nutrient Addition Experiment

• Field experiment that added nutrients.

Food Web Interactions

• Independent of predator exclusion.
• Impact of nutrient addition on Capitella sp. abundance.

Food Web Interactions - Locations

• Manukau Harbour, New Zealand:
  • Strong predation pressure.
  • Seasonal effects.
  • Evidence of adult-juvenile interactions.
• Port Phillip Bay, Australia:
  • Weak predation pressure.
  • Strong nutrient effects.
  • Strength of these effects depend on location and background nutrient levels.

Review Questions - Ecology

1. What factors determine interactions between species? Use examples of biological and physical factors.
2. Explain what can occur when predators are excluded from soft-bottom invertebrate communities?
3. Provide a definition of bioturbation and describe an example of a bioturbator. Describe the organism’s activities or processes, plus explain how these activities help maintain a healthy ecosystem.

Lecture 5,6,7,8 Topics

• Lecture 5: Physical characteristics and types of estuaries.
• Lecture 6: Biological environments in estuaries.
• Lecture 7: Ecology of estuaries.
• Lecture 8: Management of estuaries.

Biological Environments in Estuaries - Topics

• Adaptations.
• Distributions driven by physical factors.
• Distributions driven by biological factors.

Estuaries: Sheltered Environments

• Estuaries are relatively sheltered, low-energy environments.

Salinity Fluctuations

• Not just the level of salinity but also its fluctuations.

Estuarine Biota

• Size of blue area = number of species (Castro & Huber 2008).

Adaptations to Salinity

• Adaptations to low and variable salinity conditions:
  • Morphology (e.g., oysters).
  • Behavior (e.g., worms).
  • Ability to osmoregulate (e.g., fish).

Osmosis

• Osmosis is the movement of water from high to low concentrations across a membrane.

Osmoregulation in Fish

• Marine fish: body fluids less concentrated than seawater =
  Rightarrow water loss by osmosis.
• Freshwater fish: body fluids more concentrated than seawater =
  Rightarrow water gain by osmosis (Castro & Huber 2008, Figure 4.14).

Salmon and Osmoregulation

• Salmon and freshwater eels migrate between rivers and sea, therefore they are good at osmoregulation.
• Friedman et al 2019, Ecosphere, on Chinook salmon in central California, USA (Oncorhynchus tshawytscha).

Plant Adaptations - Mangroves

• Mangroves (Avicennia marina).

Plant Adaptations - Salt Glands

• Mangroves have salt glands.

Plant Adaptations - Spartina

• Spartina anglica.
• CABI, 2021. Spartina anglica. In: Invasive Species Compendium.

Behavioural Adaptations

• Mobile species:
  • Change longitudinal position within estuary.
  • Change position between the water and sediment.
• Sessile or sedentary species:
  • Hide in burrows.
  • Close shell.

Behavioural Adaptations Examples

• Arenicola marina (lugworm).
• Neotrypaea californiensis (ghost shrimp).

Chironomids

• Chironomids life cycle: egg mass, larva, pupa, adult.
• Kranzfelder et al 2015, Journal of Visualized Experiments.

Nereid Annelid Worms and Salinity

• Nereid annelid worms distribution in relation to salinity.
• Davila-Jimenez et al 2019.

Biological Environments in Estuaries - Topics Revisited

• Adaptations.
• Distributions driven by physical factors.
• Distributions driven by biological factors.

Salinity and Location

• Relationship between salinity and location in estuaries.
• Davila-Jimenez et al 2019.

Salinity and Species Distribution

• Relationship between salinity, number of species, and density of organisms.
• Davila-Jimenez et al 2019.

Salinity and Species Examples

• Examples of species: Hypereteone heteropoda, Ceratonereis longicirrata, Leitoscoloplos sp.
• Davila-Jimenez et al 2019.

Grain Size and CO2

• Ingels et al 2018.
  1. Temperature
  2. CO_2 concentration
  3. Sediment type (sandy or muddy sediments).

Grain Size and CO2 Effects

• Ingels et al 2018.
  1. Temperature – no effect.
  2. Sediment type - What is the effect?

Sediment Type and CO2

• Ingels et al 2018.
• Mud samples only.
• CO_2 concentration - What is the effect?

Sediment Analysis

• Relative number of individuals in relation to sediment type (sand vs. mud).
• Ingels et al 2018.

Sediment Type vs. Temperature and CO2

• Sediment type (grain size) had a greater influence over community composition.
• Possible explanations for these effects.

Biological Environments in Estuaries - Topics Revisited Once More

• Adaptations.
• Distributions driven by physical factors.
• Distributions driven by biological factors.

Species Distribution by Predation

• Sanchez et al. 2006.
• Study of twelve ponds covering a range of salinities.

Chironomid Larvae and Predation

• Quantities of small and large larvae; Sanchez et al. 2006.

Shorebirds and Chironomid Larvae

• Percentage of feeding shorebirds at high tide vs. Chironomid larvae abundance.
• Sanchez et al. 2006.

Class activity

1. Read Chapman and Wang 2001, pages 9 – 10. “Types and distribution of estuarine benthos”.
2. In your own words, describe why are there relatively few truly estuarine species?

Estuarine Species Numbers

• Why are there relatively few truly estuarine species?
• Comparison of Freshwater Species, Estuarine Species, and Marine Species Number vs. Salinity (g/L).
• Chapman and Wang 2001.

Review Questions - Biology

1. Describe the biology and ecology of the estuarine species.
2. Explain the physical and/or biological factors influencing the distribution of the species in the estuary.
3. Explain how it copes with the variable estuarine conditions.
4. Explain in the context of morphological and behavioural adaptations.

Marine Biology Textbook

• Peter Castro, Michael E Huber (2013) 12th Edition
• Recommended textbook.

Physical Characteristics - Topics

• What is an estuary?
• Physical characteristics – salinity.
• Physical characteristics – oxygen.

What is an Estuary?

• A body of water partially surrounded by land, where freshwater from a river mixes with ocean water (Garrison 2007).
• A place where freshwater and saltwater meet; the transition zone between these two aquatic systems (Nybakken 1997).

Importance of Estuaries

• Globally, 22 of 32 largest cities are on estuaries.
  • Why? Sheltered environment, drinking water, food, waterway for transport, recreational activities, high biodiversity.

Estuaries in Australia

• In Australia, 65% of the population lives on estuaries.

Types of Estuaries - Geomorphology Based

1. Based on historical geomorphology
   • a) (for you to fill in)
   • b) -
   • c) -
   • d) -

Coastal Plain Estuary Example

• Coastal plain estuary - Sydney Harbour.

Tectonic Estuary Example

• Tectonic estuary - San Francisco Bay.

Semi-Enclosed Bay or Lagoon Examples

• Coorong and mouth of the Murray River in South Australia (www.parks.sa.gov.au).
• Gippsland Lakes, eastern Victoria (www.gippslandports.vic.gov.au).

Fjord Example

• Tracy Arm Fjord near Juneau, Alaska.
• Photograph: Graham Starczewski, MyShot.

Types of Estuaries - Geomorphology Recap

1. Based on historical geomorphology
   • a) Coastal plain estuary
   • b) Tectonic estuary
   • c) Semi-enclosed bay or lagoon
   • d) Fjord
2. Based on processes
   • a) (for you to fill in)
   • b) -

Types of Estuaries - Process Based

• Wave-dominated estuaries.
• Tide-dominated estuaries.

Tide-Dominated Estuaries - Characteristics

• Mudflats.
• High turbidity.
• Meandering channel.
• Salt marsh & mangroves.

Tide-Dominated Estuaries - Features

• Large difference between high and low tide.
• Meandering channel.
• Salt marsh & mangroves.

Wave-Dominated Estuaries - Characteristics

• Barriers.
• Sand dunes (coarse sands).
• Low-energy central basin.

Wave-Dominated Estuaries - Locations

• Barwon River, Andersons Inlet, Wingan Inlet, Tamboon Inlet, Fitzroy River, Darby River.

Wave-Dominated Estuaries - Open or Closed

1. Permanently open OR
2. Intermittently open and closed (IOCE = intermittently open/closed estuaries).
   • IOCE definition: Entrances that can close to tide when tidal currents and river flow are low and can not erode sediment delivered onshore by waves (McSweeney et al 2017).

Estuary Type Recap

• Types of estuaries based on coastal geomorphology and on processes.

Importance of Understanding Estuary Types

• Why important? What decisions does this inform?

Physical Characteristics - Topics Revisited

• What is an estuary?
• Physical characteristics – salinity.
• Physical characteristics – oxygen.

Salinity Stratification

• Density is affected by salinity.
• Halocline = layer in which salinity changes rapidly.

Port Phillip Bay Story

• A story of Port Phillip Bay, Victoria.

Highly Stratified/Salt Wedge Estuary

• Salt wedge formation in a typical estuary, with limited mixing across the saltwater-freshwater interface.

Moderately Stratified/Partially Mixed Estuary

• Salt wedge formation in a typical estuary, with increased mixing across the saltwater-freshwater interface.

Gippsland Lakes, Victoria - Examples

• Lake Wellington, Lake Victoria, Lake King, Lakes Entrance.

Gippsland Lakes, Victoria - Map

Lake Wellington

• Avon River, Latrobe River flow into Lake Wellington.

Lake Wellington Salinity

• Average monthly salinity in Lake Wellington.

Negatively Stratified Estuary

• Negatively stratified (or inverse) estuary e.g., McLennan Strait and Lake Wellington.

Coorong, South Australia

• Qifeng et al 2019 SARDI Research Report.

Coorong Substrates

• Soft, muddy substrates.

Mud Substrate and Overlying Water Salinity

• Salinity in the substrate vs. overlying water.

Physical Characteristics - Topics Final Time

• What is an estuary?
• Physical characteristics – salinity.
• Physical characteristics – oxygen.

Oxygen and the Salt Wedge

• Salt wedge formation in a typical estuary, with limited mixing across the saltwater-freshwater interface.

Oxygen Levels in a River Example

• Maribyrnong River: Dights Falls, Yarra River.
• Roberts et al 2012 (Limnology and Oceanography).

Oxygen Levels at Site C

• Site C bottom water (Roberts et al 2012).

Anoxic Muddy Sediments

• Anoxic intertidal muddy sediments.

Review Questions - Synthesis

• Under what conditions does a salt wedge in an estuary occur?
• When and where do low oxygen levels occur in an estuary?
• Explain the key differences between a wave-dominated estuary and a tide-dominated estuary.
• Describe the sediment type in an estuary that is tide-dominated and compare it to sediments in a wave-dominated estuary.