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Biology Online Module Handbook

BL3308 Methods in Aquatic Biology

(BL3308 online module handbook version 145)

cover image
The study of aquatic environments and organisms requires a wide variety of tools. This module introduces many of the tools used to study freshwater and marine environments and the organisms that inhabit these diverse habitats. Research methods covered include conductivity-temperature-pressure sensors, expendable bathythermographs, remote observational platforms (satellites, drones, ocean gliders, etc), passive and active acoustics, animal borne sensors, and methods for population abundance assessment and behavioural observations. This module involves a residential field trip to a field station in the Scottish Highlands.*

Credits: 20*

Semester: 1†

Module Organiser
Dr Iain Matthews†
imm7@st-andrews.ac.uk†
01334 463004†
Pre-requisite Modules:
Before taking this module you must pass BL2300*
Anti-requisite Modules:
*
Post-requisite Modules:
*
Additional Module Information:
Please check MMS regularly for additional module information


BL3308View content for BL3308 (2023/4) in the Module Management System (MMS)
BL3308Download this handbook as a pdf (may take up to ~30 seconds if updating)
BL3308View BL3308 (2023/4) in the University of St Andrews Module Catalogue
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
† School of Biology Symbiosis Database (module organisers only)
‡ University of St Andrews MMS (St Andrews users only)

Biology Teaching Office:
Level 2, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST

Email: bioteach@st-andrews.ac.uk      Phone: +44 (0)1334 46 3602 or 3566

BL3308: Timetable †

Legend (not all modules have every event type):
lecture
tutorial
workshop
practical
other

Semester 1: Week 1

DATE & TIMEVENUESTAFFEVENT
Monday
11-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L1: Introduction
2023-4_BL3308_L1
Welcome to BL3308. This lecture will introduce the module and provide an overview of the themes to be covered, including details of the assessment.
Tuesday
12-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L2: Lotic systems I: The abiotic environment in rivers and streams
2023-4_BL3308_L2
Lotic systems (flowing freshwater habitats including rivers and streams are unique and globally rare habitats accounting for less than 0.001% of the hydrosphere. This lecture will introduce lotic systems focusing on identifying their defining characteristics and discussing some of their key abiotic factors, in particular looking at the overwhelming importance of flow.
Wednesday
13-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Andrew Blight
-		Lecture L3: Dynamics of aquatic systems: drag and stress
2023-4_BL3308_L3
This lecture will examine the challenges faced by organisms living in an aqueous and flowing environment. It will explore viscosity, velocity gradients, the principle of continuity, life in flow and the forces of drag.

Semester 1: Week 2

DATE & TIMEVENUESTAFFEVENT
Monday
18-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L4: Lotic systems II: Adaptation in rivers and streams
2023-4_BL3308_L4
Following on from the discussion of the abiotic factors, we will look firstly at the movement of carbon in lotic systems and discuss the river continuum concept as a framework for testing hypotheses about the distribution of functional groupings of freshwater macroinvertebrates along the length of rivers and streams. We will also look at adaptations to the challenges of life in flow.
Tuesday
19-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L5: Lentic Systems I: The abiotic environment in lakes and ponds
2023-4_BL3308_L5
Wednesday
20-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L6: Lentic Systems II: Adaptation in lakes and ponds
2023-4_BL3308_L6

Semester 1: Week 3

DATE & TIMEVENUESTAFFEVENT
Monday
25-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L7: Freshwater indicator species and pollution monitoring
2023-4_BL3308_L7
Tuesday
26-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Prof David M. Paterson
-		Lecture L8: The landscape of marine research in Scotland
2023-4_BL3308_L8
Wednesday
27-09-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Andrew Blight
-		Lecture L9: Seafloor mapping I
2023-4_BL3308_L9
These lectures will examine some of the techniques used in current research to explore and map the shallow continental shelf seas. They will explore how sonar and sampling techniques are used to characterise biological habitats and ecosystems. We will examine case studies where these techniques are used to monitor sustainable use and/or restoration of these habitats.

Semester 1: Week 4

DATE & TIMEVENUESTAFFEVENT
Monday
02-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Andrew Blight
-		Lecture L10: Seafloor mapping II
2023-4_BL3308_L10
These lectures will examine some of the techniques used in current research to explore and map the shallow continental shelf seas. They will explore how sonar and sampling techniques are used to characterise biological habitats and ecosystems. We will examine case studies where these techniques are used to monitor sustainable use and/or restoration of these habitats.
Tuesday
03-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Andrew Blight
-		Lecture L11: Coastal sediments I
2023-4_BL3308_L11
These lectures will examine some of the novel techniques used in current research to explore and characterise the properties of coastal sediment ecosystems. We will explore the key features of estuarine and other soft sediment habitats and how research has broadened our understanding of these critical ecosystems and the services they provide.
Wednesday
04-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Andrew Blight
-		Lecture L12: Coastal sediments II
2023-4_BL3308_L12
These lectures will examine some of the novel techniques used in current research to explore and characterise the properties of coastal sediment ecosystems. We will explore the key features of estuarine and other soft sediment habitats and how research has broadened our understanding of these critical ecosystems and the services they provide.

Semester 1: Week 5

DATE & TIMEVENUESTAFFEVENT
Tuesday
10-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr James Cant
-		Lecture L13: Coral reef survey techniques
2023-4_BL3308_L13
Wednesday
11-10-2023
10:00 to 11:00		Online
Panpoto
-		Lecture L14: Connectivity on coral reefs
2023-4_BL3308_L14
Prof. Mike Kingsford (JCU)

Semester 1: Week 7

DATE & TIMEVENUESTAFFEVENT
Monday
23-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Debbie Russell
-		Lecture L15: Observation platforms
2023-4_BL3308_L15
Tuesday
24-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Prof Sascha Hooker
-		Lecture L16: Tagging I
2023-4_BL3308_L16
Wednesday
25-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Prof Sascha Hooker
-		Lecture L17: Tagging II
2023-4_BL3308_L17

Semester 1: Week 8

DATE & TIMEVENUESTAFFEVENT
Monday
30-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Lars Boehme
-		Lecture L18: Remote sensing - Animal-borne instruments
2023-4_BL3308_L18
Tuesday
31-10-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Lars Boehme
-		Lecture L19: Remote sensing - Polar Marine Research
2023-4_BL3308_L19
Wednesday
01-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Lars Boehme
-		Lecture L20: Remote sensing - Climate Change and its prediction
2023-4_BL3308_L20

Semester 1: Week 9

DATE & TIMEVENUESTAFFEVENT
Monday
06-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		cnr4
-		Lecture L21: Active acoustics I - Measuring voltage to estimate biomass: an introduction to active acoustics
2023-4_BL3308_L21
Born out of SONAR technology, scientific echosounding has been used since the 1940s to make detections of aquatic mid-trophic level organisms such as zooplankton, fish, squid and jellyfish. Echosounders project sound into the water-column and record backscattered soundwaves produced by organisms. This lecture will introduce the theory of underwater sound scattering and review modern-day instrumentation, data collection and data processing methods.
Friday
10-11-2023
09:00 to 23:59		Offsite
FSC Millport		Dr Andrew Blight
-		Other O1: Residential field course
2023-4_BL3308_O1
Marine field trip to FSC Millport
Saturday
11-11-2023
00:00 to 23:59		Offsite
FSC Millport		Dr Andrew Blight
-		Other O2: Residential field course
2023-4_BL3308_O2
Marine field trip to FSC Millport
Sunday
12-11-2023
00:00 to 17:00		Offsite
FSC Millport		Dr Andrew Blight
-		Other O3: Residential field course
2023-4_BL3308_O3
Marine field trip to FSC Millport

Semester 1: Week 10

DATE & TIMEVENUESTAFFEVENT
Tuesday
14-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Prof Dave Ferrier
-		Lecture L22: Aquaria in research
2023-4_BL3308_L22
Wednesday
15-11-2023
10:00 to 11:00		Scottish Oceans Institute
SOI Building		Prof Dave Ferrier
-		Lecture L23: Tour of SOI aquaria
2023-4_BL3308_L23
Wednesday
15-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		cnr4
-		Lecture L24: Active acoustics II - From isolated targets to basin-scale scattering layers: counting fish using sound
2023-4_BL3308_L24
Echosounders can detect a myriad of biological structures in the water-column, from fine-scale highly dynamic formations such as swarms and schools, to large mixed-species assemblages known as scattering layers that can span entire ocean basins. Echosounder detections, along with net and trawl samples, can be used to estimate species abundance and biomass and study species distribution patterns and behaviour. This lecture provides a detailed description of how echosounder observations from fish can be used to estimate biomass.
Friday
17-11-2023
09:00 to 23:59		Offsite
Loch Lomond		Dr Iain Matthews
-		Other O4: Residential field course
2023-4_BL3308_O4
Freshwater field trip to Loch Lomond
Saturday
18-11-2023
00:00 to 23:59		Offsite
Loch Lomond		Dr Iain Matthews
-		Other O5: Residential field course
2023-4_BL3308_O5
Freshwater field trip to Loch Lomond
Sunday
19-11-2023
00:00 to 17:00		Offsite
Loch Lomond		Dr Iain Matthews
-		Other O6: Residential field course
2023-4_BL3308_O6
Freshwater field trip to Loch Lomond

Semester 1: Week 11

DATE & TIMEVENUESTAFFEVENT
Monday
20-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Julie Oswald
-		Lecture L25: Passive acoustics I - Eavesdropping on the oceans
2023-4_BL3308_L25
In this lecture we will talk about methods used to monitor sounds in the oceans and what we can learn using these methods. We will discuss passive acoustic methods such as towed hydrophone arrays, seafloor-mounted recorders and animal borne tags.
Monday
20-11-2023
14:00 to 17:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Other O7: Student seminar talks
2023-4_BL3308_O7
Tuesday
21-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Julie Oswald
-		Lecture L26: Passive acoustics II - Analysing passive acoustic data
2023-4_BL3308_L26
In this lecture we will talk about ways to analyse passive acoustic data to address different types of environmental and biological questions.
Wednesday
22-11-2023
10:00 to 11:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Lecture L27: Salmon management and conservation in Scotland
2023-4_BL3308_L27
Dr Nora Hanson (Marine Scotland)
Thursday
23-11-2023
14:00 to 17:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Other O8: Student seminar talks
2023-4_BL3308_O8
Friday
24-11-2023
14:00 to 17:00		Bute Building
Lecture Theatre D		Dr Iain Matthews
-		Other O9: Student seminar talks
2023-4_BL3308_O9
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
† School of Biology Symbiosis Database (module organisers only)
‡ University of St Andrews MMS (St Andrews users only)

BL3308: Reading List

BL3308Click for BL3308 reading list

BL3308: Assessment

Written Exam = 50%, Coursework = 50%*

BL3308View coursework assessment details for BL3308 (2023/4) in MMS

The following related information applies to all Biology modules:

School of Biology Marking Criteria: See JH booklet info (st-andrews.ac.uk) 
Late submission of continuous assessment work:

 All late submissions of coursework that do not require electronic submission should be made via the Biology Teaching Office, Level 2, BMS Building, North Haugh.
Exam details: See School of Biology UG Handbook JH booklet info (st-andrews.ac.uk)  : All Biology exams will be conducted online for 2022-23.
Exam timetable: See Timetables - Exams - University of St Andrews (st-andrews.ac.uk) 
Expected attendance: See JH booklet info (st-andrews.ac.uk)  for detailed attendance requirements.
Good Academic Practice & Avoiding Academic Misconduct: See JH booklet info (st-andrews.ac.uk)
University Student Handbook: University Student Handbook
School and University regulations in the School and University Undergraduate Handbook relating to absence reporting, penalties and rules for late submission of work, extensions for coursework, return of coursework, S-coding, good academic practice and Academic Alerts.: JH booklet info (st-andrews.ac.uk)
University Student Handbook
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
† School of Biology Symbiosis Database (module organisers only)
‡ University of St Andrews MMS (St Andrews users only)

Who to ask †

(Information in this section applies to all Biology Modules)

Before contacting staff, students should check the content of the Biology Undergraduate Handbook, the module handbook and specific task instructions.

Questions about Contact
General teaching matters Biology Teaching Office ( bioteach@st-andrews.ac.uk )
Rescheduled or cancelled events Check your University email
Lecture or practical content The lecturer who presented the material
Completing assessed practical assignments The lecturer who set the assignment
Completing assessments Module Organiser (Dr Iain Matthews imm7@st-andrews.ac.uk)
Marking on continuous assessment The Demonstrator or Module Organiser (Dr Iain Matthews imm7@st-andrews.ac.uk)
Marking on exams Module Organiser (Dr Iain Matthews imm7@st-andrews.ac.uk)
Rearranging practical days
Module Organiser (Dr Iain Matthews imm7@st-andrews.ac.uk)
Absence and/or extensions Module Organiser (Dr Iain Matthews imm7@st-andrews.ac.uk)

and the Biology Teaching Office ( bioteach@st-andrews.ac.uk )

Difficulties with academic progress which impact more than one module:

Year Coordinator

See School of Biology UG Handbook for list:
JH booklet info (st-andrews.ac.uk)

Overall performance, progress or future directions:

Advisor of Studies

Disability:

Disability Coordinator ( biodisabilities@st-andrews.ac.uk )

For advice and support on any issue e.g. academic, financial, international, personal or health matters, or if you are unsure of who to go to for help:

Advice & Support Centre

Address: 79 North Street, St Andrews

Email: theasc@st-andrews.ac.uk

Web: https://www.standrews.ac.uk/ask-a-question/

Tel: 01334 462020
University assistance with urgent matters out of office hours:

Tel: 01334 476161

Web: https://www.st-andrews.ac.uk/students/advice/counselling/incrisis/

Biology Teaching Office:

We are happy to hear from you about teaching matters. The School of Biology Teaching Office is open Monday to Friday 09.00 - 13.00 and 14.00 - 17.00. School of Biology staff will respond to your emails during these hours. Our team will provide a response to you within three working days.

Biology Teaching Office (Level 2), University of St Andrews, Biomolecular Sciences Building, North Haugh, St Andrews, Fife KY16 9ST

Email: bioteach@st-andrews.ac.uk

Tel: 01334 46 3602 or 3566

BL3308: Contributing Staff †

Dr Iain Matthews
(Module Organiser)

Senior Teaching Fellow & Pro-Dean for the Faculty of ScienceIMM7@st-andrews.ac.uk
Dr Andrew BlightLecturerAJB34@st-andrews.ac.uk
Dr Lars BoehmeReaderLB284@st-andrews.ac.uk
Dr James CantResearch Fellowjic2@st-andrews.ac.uk
Prof Dave FerrierReader in Biology and Deputy Director of the Scottish Oceans Institutedekf@st-andrews.ac.uk
Prof Sascha HookerProfessorsh43@st-andrews.ac.uk
Dr Iain Matthews
(Module Organiser)		Senior Teaching Fellow & Pro-Dean for the Faculty of ScienceIMM7@st-andrews.ac.uk
Dr Julie OswaldSenior Lecturerjno@st-andrews.ac.uk
Prof David M. PatersonExecutive Director of MASTS:
The Marine Alliance for Science and Technology for Scotland 		dp1@st-andrews.ac.uk
Dr Debbie RussellPrincipal Research Fellowdr60@st-andrews.ac.uk
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
† School of Biology Symbiosis Database (module organisers only)
‡ University of St Andrews MMS (St Andrews users only)

BL3308: Learning Outcomes †

No details are currently available for Learning Outcomes †

Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
† School of Biology Symbiosis Database (module organisers only)
‡ University of St Andrews MMS (St Andrews users only)

BL3308: Acquired Skills †

Practical Skills

  • Collecting animals and plants
  • Field sampling methods (Botanics)
  • Field sampling methods (Invertebrates)
  • Field sampling methods (Vertebrates)
  • Fieldwork safety awareness
  • Sampling of sensitive sites / organisms
  • Labelling specimens and managing collections
  • Measuring structures using microscopes
  • Species identification (Botany)
  • Species identification (Invertebrates)
  • Using dichotomous keys
  • Sustainability related practical skills

Transferable Skills

  • Group discussion - leading
  • Group discussion - participating
  • Short individual presentation on given topic (up to 15 min)
  • Handout (for presentation or poster)
  • Long essay (>2000 words)
  • Critically evaluating sources/information
  • Finding information on the web
  • Finding literature
  • Referencing
  • Sourcing figures/tables
  • Ethical considerations
  • Generating questions
  • Role play
  • Biodiversity analysis
  • Data analysis
  • Data analysis (depending on project)
  • Descriptive statistics
  • Produce graphs/figures
  • Significant figures
  • Use Excel
  • Use R or R Studio
  • Lab or field notebook
  • Critiquing experimental design
  • Designing experiments
  • Sustainability Related Skills
  • Generate class dataset
  • Managing a team
  • Organising group work
  • Working in large groups
  • Working in pairs/small groups
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
† School of Biology Symbiosis Database (module organisers only)
‡ University of St Andrews MMS (St Andrews users only)

Policies †

(Information in this section applies to all Biology Modules)

  • The procedures and regulations followed by the School of Biology are outlined in the University Handbook and in the School of Biology UG handbook  JH booklet info (st-andrews.ac.uk) 
  • All coursework associated with the module must be completed and submitted by its due date.
  • Specific School regulations relating to absence reporting, penalties and rules for late submission of work, extensions for coursework, return of coursework, S-coding, Good Academic Practice and Academic Alert are stated in the School of Biology UG hand book JH booklet info (st-andrews.ac.uk)  and students are required to carefully read these regulations.
  • Students are also referred to the University Handbook, available at: http://www.st-andrews.ac.uk/studenthandbook/