Marine Ecological Field Methods E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Fachliteratur
• Sprache: Englisch

Seitenzahl: 395

Veröffentlichungsjahr: 2017

Beschreibung

A comprehensive, clear, and detailed guide to procedures for conducting marine ecological field studies Marine Ecological Field Methods is a comprehensive resource that offers the most relevant sampling methodologies for quantitative and qualitative studies of mesopelagic, demersal, littoral, and soft-bottom organisms, as well as relevant physical parameters. The authors describe how various sampling gears work, how to operate them, their limitations, guides on sorting and measuring collected organisms, and how to deal with subsamples of large catches. The text also explains how to use acoustic equipment for monitoring aggregations of organisms, for example fish shoals, as well as the use of sensors for registering environmental variables such as salinity, temperature, oxygen, and light. The text contains cutting-edge research techniques that are in their final stages of development for use in research surveys. Marine Ecological Field Methods is designed to help with the entire procedure for conducting a field study, including the generation of hypotheses, planning field collection of data, conducting field work, data exploration and statistical analysis with the use of R, and presentation of results in a final report. This essential resource: * Covers a wide range of techniques and methods for the marine environment * Includes tried and trusted methodologies and techniques from a team of noted experts in the field * Contains information on sampling equipment ranging from those that are useful in the littoral zone to shallow nearshore areas, including bottles, secchi discs, and gillnets, and finally large trawls, benthic sleds, ROV and advanced technologies for remote sensing in the open ocean. * Explores the step-by-step procedures for conducting a field study, from formulating hypotheses to the process of registering and reporting results Written for students and professionals in the field, this vital resource describes marine ecological sampling equipment, methods and analysis, ranging from physical parameters to fish, microalgae, zooplankton, benthos and macroalgae.

Leseprobe

Table of Contents

Cover

Title Page

List of Contributors

Foreword

Acknowledgements

1 The Marine Environment

1.1 Marine Habitats

1.2 The Coastal and Fjord Biotopes

1.3 Physical Characteristics of the Pelagic System

1.4 Temperate Marine Communities – Environment and Organisms

References

2 Planning Marine Field Studies

2.1 Survey and Sampling Design

2.2 Littoral Survey Design

2.3 Benthos Survey Design

2.4 Oceanic Survey Design

2.5 Ecological Process Studies

References

Further Reading

3 Sampling Gears and Equipment

3.1 Sampling Organisms

3.2 Sampling the Physical Environment

3.3 Suitability of Equipment in Given Habitat Types

References

4 Sorting Specimens and Preserving Materials

4.1 Sampling Diary

4.2 Sorting and Preserving Littoral Collections

4.3 Sorting Zooplankton

4.4 Sieving and Sorting Benthic Samples

4.5 Fish and Nekton

4.6 Data Records

4.7 Samples for Storage

References

5 Data Analysis

5.1 Scripts

5.2 Setting the Working Directory

5.3 Importing Data

5.4 Working with Data

5.5 Data Exploration and Statistical Testing

References

Index

End User License Agreement

List of Tables

Chapter 01

Table 1.1 Plankton size classes.

Chapter 03

Table 3.1 Dimensions of different plankton nets. Length of forward cylindrical part (h1) and conical after part (h2). See Figure 3.13 for schematic showing cylindrical and conical sections.

Table 3.2 Overview of sampling gears and equipment and the habitats in which they are used.

Chapter 04

Table 4.1 General description of maturity stages of fish (Mjanger

et al

. 2016).

Table 4.2 Condition of gall bladder and hind guts used to differentiate between empty and regurgitated stomachs of fish.

Chapter 05

Table 5.1 Typical structure of a multivariate data set prepared for ordination analysis. Note that the first column lacks a header name. This column represents row names, which are the different sites investigated. The numbers in each column represent percent cover of a given species within a given site.

Table 5.2 A key for how to choose which method of ordination to use.

Table 5.3 An example of applying the Bray‐Curtis dissimilarity index to a hypothetical case with samples from one square quadrat plot at each station. According to Equation 5.1, D

jk

 = 140/(165 + 145) = 0.45.

Table 5.4 The values of Table 5.3 after a fourth root transformation. This homogenizes values to give a more accurate picture of differences between the stations. Recalculation of D

jk

changes it to 0.20.

Table 5.5 A Bray‐Curtis dissimilarity matrix showing the calculated pairwise dissimilarities between samples taken at four sites (four subsamples at each site), where two of the sites are sheltered from waves (s) and the other two are exposed (e).

Table 5.6 Part of the example data set showing sites as row names (first column), where the first and second numbers represent site and subsample number, respectively. The letter at the end on each row name represents site type, where “e” means wave exposed and “s” is sheltered site. The rest of the data are the species abundance matrix.

List of Illustrations

Chapter 01

Figure 1.1 Topographic chart of the North Sea.

Figure 1.2 Part of the coastline of Western Norway, showing the complex bathymetry characteristic of fjords and many other coastal systems.

Figure 1.3 The three “universal zones” recognized by Lewis (1961), showing the zones in a gradient from extreme shelter (right) to strong wave‐exposure (left). The area between the dotted lines is the intertidal area between extreme high and low water level (EHWL, ELWL). The littoral zone is composed of the splash zone (littoral fringe) and the eulittoral zone, where the limits are set by zone‐forming organisms. The littoral zone is defined as the area inhabited by organisms influenced by the tidal cycle and is separated from the sublittoral zone. The width of the littoral zone is strongly extended towards the wave‐exposed side due to higher waves and a much wider splash zone. In addition, the limits are shifted upwards on the wave‐exposed side due to the more‐or‐less constant wave action.

Figure 1.4 An early map illustrating the Norwegian Coastal Water (yellow and green) between the Norwegian coastline and the oceanic North Atlantic Water (blue) (Hjort and Gran, 1899).

Figure 1.5 A transect from the head of a fjord (right) to an oceanic location (left) showing (a) the three main water masses: local brackish water, Norwegian Coastal Water (NCW), and North Atlantic Water (NAW). A summer situation is indicated in (b). The arrows indicate the gradients in salinity, temperature, and density stratification; broken lines indicate isoclines for the three variables. Fresher water contains higher concentrations of CDOM with terrestrial origin causing isolumes, like the euphotic depth, to shoal toward locations more affected by freshwater. Depth of euphotic zone and Mesopelagic isolume is indicated in (c).

Figure 1.6 Difference in vertical distributions of (a) salinity, (b) temperature, (c) density, (d) phytoplankton, and (e) nutrients at a coastal (grey) and an oceanic location (black) in an idealized steady state summer situation.

Figure 1.7 Effects of coastal winds on circulation patterns of coastal areas and fjords. Northerly and southerly winds cause (a) upwelling and (b) downwelling with opposite circulation patterns in the intermediate layer (the water layer between the brackish water and the sill depth) of a fjord.

Figure 1.8 Measurements of downwelling irradiance with a spectroradiometer in the Norwegian Sea. Note that most of the light that remains at large depth narrows to around 480 nm.

Figure 1.9 The intertidal community at a locality with high degree of wave exposure. The shore is dominated by barnacles and small, turf‐forming algae.

Figure 1.10 The intertidal community at a sheltered locality with low degree of wave exposure. The shore is dominated by large brown algae.

Figure 1.11 A typical sublittoral habitat illustrating trophic relations and links to the physical environment.

Figure 1.12 Classification of fish communities by depth using the Norwegian Sea shelf slope summer situation as an example. .

Figure 1.13 The helmet jelly

Periphylla periphylla

.

Figure 1.14 The alien ctenophore

Mnemiopsis leidyi

was first observed in the North Sea in 2005. .

Figure 1.15 (a) A typical pelagic fish is the sprat (

Sprattus sprattus

). (b) Pictured are some specimens of the local Lustrafjord population caught in the Fjøsne Bay, September 2016.

Figure 1.16 Typical mesopelagic organisms from fjord areas. Pictured are specimens caught in Masfjord. (a) Left;

Maurolicus muelleri

and right;

Benthosema glaciale

. (b) Top;

Pasiphaea

spp., middle;

Meganyctiphanes norvegica

, and bottom;

Sergestes

spp.

Chapter 02

Figure 2.1 Still images from a video equipped ROV of two typical invertebrate inhabitants of a west‐Norwegian fjord. (a) The squat lobster

Munida sarsi

in a soft bottom habitat. (b) The sea star

Hippasteria phrygiana

on the rocky substrate of an undersea mountain.

Figure 2.2 Northeast Atlantic mackerel (

Scomber scombrus

) swimming inside a pelagic trawl.

Figure 2.3 Map showing the ten strata used for estimation of mackerel biomass during the International Ecosystem Summer Survey in the Nordic Seas (IESSNS).

Figure 2.4 Side view of the Multpelt 832 as deployed from a vessel. The Multpelt 832 is rigged with 350 m of warp, 80 m of sweeps, buoys, a kite, and 400 kg chain weights on each lower wing.

Figure 2.5 Standard rigging of the GOV trawl for use in the IBTS North Sea surveys. Modified from the IBTS survey manual (ICES, 2015a).

Figure 2.6 MIK‐M trawl for use in the North Sea IBTS first quarter surveys. The depth sensor (orange sensor) is visible on the metal ring. Small nets at side of MIK net are used to collect fish eggs. The flow meter is hanging in the center of the net (only the cord is visible).

Figure 2.7 Example of a CTD rosette with 11 water collection canisters.

Figure 2.8 Example of Type I and II diel vertical migration. Type I diel vertical migration describes the movement of organisms from a bright surface environment to darker, deeper depths during daytime, while type II diel vertical migration describes the movement of organisms from a darker to a brighter environment during daytime.

Figure 2.9 Schematic showing the various types of equipment used to sample the water column. (1) An upward facing EK60 38 kHz transducer located on the bottom of the fjord at 390 m depth sent sound waves toward the surface. This was connected to (2) a laptop on land, where (3) echograms could be followed in real‐time. Data from (4) the hull‐mounted echosounder was used to visualize acoustic targets/scattering layers at different depths. (5) A pelagic trawl combined with a MultiSampler was used to verify the species composition of the acoustic signals/targets (a, b, and d). (6) A plankton sampler collected depth‐stratified plankton samples (c). (7) A CTDO recorded hydrographic data throughout the water column. (8) A light sensor measured radiation every 15 minutes. Large predatory fish (d) were also caught with rod and reel.

Figure 2.10 Movement of fish species in the water column over a 24‐hour period; species in each layer were predominantly, from top to bottom, larvae, juvenile and adult pearlside (

Maurolicus muelleri

). (a) Larvae, juveniles and adult pearlside are distributed at progressively deeper depths during daytime and aggregate in the upper water layer between dusk and dawn (type I migration). (b) Juvenile pearlside display nocturnal descents from the surface to approximately 50 m depth after dusk, while the deeper located adult fish (150–200 m) stay at depth throughout the diel period, with only a small proportion performing reverse diel migrations to 120 m. (c) Juvenile fish migrating to the surface stop their migration at different depths and descend again.

Figure 2.11 Migration of pearlside under different levels of light. (a) (upper panel) The arrival to and (lower panel) departure from the surface at civil twilight end and civil twilight start, respectively. Lines indicate the timing of the end and start of civil twilight, while symbols indicate when pearlside arrived or departed from the surface layer in a particular month. (b) Relationship between surface irradiation and SL depth over two days. The July 10 (blue triangles) was a clear day with high surface irradiation, while July 13 (circles) was overcast and had much lower irradiation recordings. Pearlside were distributed at deeper depths on July 10 compared to July 13.

Figure 2.12 Diving channel and submersible cage setup. The channel was 500 cm in length and consisted of black knotless netting (20 mm mesh size). The channel was stabilized by eight rings which had a diameter ranging from 70 cm in the top (1) to 55 cm on the bottom (2). Directly above the lower end of the channel, a round net cage was attached, which consisted of black knotless netting. The cage was stabilized by two rings (90 cm in diameter (3)), which were 80 cm apart from each other, that is, the approximate cage height was 80 cm. At the top of the cage mouth was 75 cm of excess netting, which could be closed by a mouth rope (4) that was drawn through the net meshes. The cage was attached to the diving channel by putting the excess net over the lowest ring of the channel and tightening the cage mouth using the mouth rope (4) to a diameter of 30 cm. At the bottom of the cage, a cage retrieval rope (5) with a 3 kg weight (6) was attached (90 cm of rope between cage bottom and weight). Additionally, a 1.5 kg weight (7) was fixed 1 m from the 3 kg weight to buffer potential wave action after cage submersion. The cage could be retrieved to the surface by pulling on an extension (8) of the mouth rope that closed the cage mouth. After detachment of the cage from the channel, a small trawl float (9) was attached to the mouth rope to keep the cage upright after submersion. When the cage was lowered to the bottom, the retrieval rope was held at the surface using a large trawl float. This figure is reprinted with permission from Ferter

et al

. (2015a).

Figure 2.13 The occurrence of external barotrauma signs in angled cod from 0 to 90 m for each 10 m depth interval. As several individuals had more than one barotrauma sign, the sum of occurrence adds up to >100%. This figure is reprinted with permission from Ferter

et al

. (2015a).

Figure 2.14 The probability of (a) swimbladder rupture and (b) gas bubble formation in the venous blood system (venous gas embolism) in angled cod with increasing capture depth. Points represent individual fish presence (1) and absence (0) data (many points overlap). The continuous lines show the model predictions and the dotted lines the range of the 95% confidence intervals. This figure is reprinted with permission from Ferter

et al

. (2015a).

Chapter 03

Figure 3.1 A schematic figure showing macroalgal zones in an intertidal, demonstrating the principles for measuring vertical levels and zones in relation to Chart Datum (0‐level or LAT).

Figure 3.2 An example of a steel quadrat and grid overlay used for sampling.

Figure 3.3 Use of sample quadrats in the field. The sample frames are positioned by attaching the underlying frame to two permanently fixed bolts in the rock.

Figure 3.4 A remotely operated vehicle (ROV).

Figure 3.5 Illustration of a pelagic trawl and its components. For some pelagic trawls, lift is created along the headrope by a kite or additional cable connected to the vessel.

Figure 3.6 Illustration of a bottom trawl and its components. Mud clouds created by the otter boards (trawl doors), lower bridles, and footrope serve to herd fish into the opening of the trawl.

Figure 3.7 Beam Trawl.

Figure 3.8 (a) DeepVision system placed between the trawl and codend of a pelagic trawl. (b) Example of a 100 cm Atlantic cod (

Gadus morhua

) taken by the DeepVision system. Precise time and position are indicated in the white overlay text.

Figure 3.9 Vertical position, length, and density of fish in the water column as measured by DeepVision system, overlaid on an acoustic echogram. Trawl path is indicated by the thin gray line, while location of fish is by colored circles with diameter scaled to indicate the number of fish passing per second. Seabed is indicated by the sloping red band. Images above the figure are the specific fish indicated on the depth profile.

Figure 3.10 Schematic view of the MultiSampler. Insets illustrate the circled area and show the MultiSampler in (a) open position, no catch retained; (b) first codend activated; and (c) first codend closed, trawl being flushed prior to activating second codend.

Figure 3.11 Deployment of a beach seine.

Figure 3.12 Retrieval of a plankton ring net.

Figure 3.13 (a) Schematic of a WP‐2 cylindrical‐conical net (mesh size 200 µm, mouth opening 0.25 m

2

).

Figure 3.14 MOCNESS in operation. The net is towed obliquely behind the ship at a 45° angle. In this schematic, the eight nets at the bottom have all collected samples at various depths and are now closed; the top net is sampling the shallowest depths on its way back to the surface. The codends at the ends of the nets hold the samples after the nets have filtered plankton from the water.

Figure 3.15 Deployment of the MOCNESS. The first net (net 0) is kept open while lowering to maximum fishing depth. When the maximum sampling depth is reached, net 0 is triggered to close, and net 1 will open for the ascent.

Figure 3.16 Examples of (a) a 0.125 m

2

, 5 nets MultiNet.

Figure 3.17 (a) RP sledge; (b) Schander sledge; (c) Sneli sledge.

Figure 3.18 An Agassiz trawl on deck.

Figure 3.19 (a) Triangular dredge, (b) Blue‐mussel dredge.

Figure 3.20 Sampling of the sediments using a grab.

Figure 3.21 A multicorer on deck.

Figure 3.22 Various water samples. (a) The original Nansen sampler with housing for thermometers. (b) The Van Dorn sampler with messenger weight. (c) The newer generation Niskin bottle, shown with lids open, with housing for thermometers on the backside. (d) Ruttner sampler in open position.

Figure 3.23 An example of a Multi Water Sampler System, with attached CTD.

Figure 3.24 Schematic showing gillnets and entangling nets. (a) Gillnets can be set at the bottom or midwater, where weights and floats keep the net open, upright, and at the correct depth; buoys at the surface are then used to find the nets for retrieval. Drift nets are set at the surface. (b) Entangling nets operate by capturing fish as they attempt to swim through the net. (c) Schematic showing the weights along the groundrope and floats along the headline, which keep the net fully open when set.

Figure 3.25 An example of a lobster and crab pot. The open holes illustrate escape openings for undersized lobster.

Figure 3.26 An example of a cod fyke net. The leading net is to the left and the net bag with funnels is to the right.

Figure 3.27 Schematic illustration of how an echo sounder works. (a) sound is directed downwards from a transducer located on the hull of a vessel, some of which is reflected back to the transducer by organisms, such as fish schools in the water column or located near the water bottom, as well as the seabed.

Figure 3.28 Echogram from Nordkapp of predominantly single targets at relatively low density, where every horizontal mark is an individual fish. The individual marks within the bottom 150 m are Atlantic cod. The small schools near the surface are capelin and are made up of many individuals.

Figure 3.29 Example echogram of herring in Ofotfjord. The green to red colored targets from 50 to 150 m depth are herring and the faint (blue) single targets at deeper depths are blue whiting. The echogram shows five nautical miles (9.3 km), where individual miles are marked with vertical lines. After safely removing the bottom echo (red line), the echo integral for mile no. 4 is 53 016 (including the blue whiting) and 53 000 without the blue whiting.

Figure 3.30 A Kongsberg Seaglider on deck, ready to be launched into the Norwegian Sea.

Figure 3.31 Main principle of ocean color remote sensing by a satellite. Some part of visible light is scattered by the atmosphere and some is reflected at the sea surface. These signals can be corrected for, thereby allowing the “water‐leaving radiance” to be the signal containing information about water constituents.

Figure 3.32 A false‐color picture of the global annual mean of chlorophyll

a

(mg m

3

) based on satellite remote sensing from Aqua‐Modis (NASA), Ocean Color web, http://daac.gsfc.nasa.gov./MODIS/

Figure 3.33 Chlorophyll

a

concentration (mg m

3

) in the North Sea and Skagerrak based on satellite remote sensing measurements from European MERIS (ESA), representing May 8 2008.

Figure 3.34 (a) A CTD rosette with mounted water samplers and a Lowered Acoustic Doppler Current Profiler (LADCP) mounted on top. (b) One LADCP is mounted to face downwards, while (c) the other points upwards.

Figure 3.35 Visualization of currents using VMDas. (a) Graph showing magnitude (red) and direction (green) of current as a function of depth. (b) Graph shows data quality as a function of depth. (c) Plot of ship track showing the current velocity vectors along the ship track at three separate depth bins. (d) Same as plot in bottom left, after setting bottom track as the reference velocity; minor deviations in track and current velocities may be apparent because the reference velocities have been subtracted from the profile before output.

Figure 3.36 (a) A boat mounted ADCP transducer surface with four transducers. The direction of two of the beams are along‐ship and two are across‐ship. (b) Simple description of the Doppler effect.

Figure 3.37 Two types of ADCPs typically attached to deployed subsurface moorings. (a) An Aanderaa SeaGuardII DCP Black.

Figure 3.38 Illustration of current measurement solutions and mounted ADCPs attached to floating and subsurface buoys and a platform on the seabed.

Chapter 04

Figure 4.1 Procedures for processing zooplankton samples. See text in Box 4.1.

Figure 4.2 (a) A simple vacuum pump filtering system used for processing small zooplankton samples for total biomass estimation. (c) Removing a filtered sample from the vacuum pump. (b and d) Examples of how to label zooplankton samples after filtration.

Figure 4.3 Using seawater to sieve a sample through two different size‐fraction sieves stacked on top of each other, where the largest mesh size is placed on top.

Figure 4.4 Sampling with a MultiSampler. (a) Preparing to set a pelagic trawl fitted with a MultiSampler and 3 codends. (b) The MultiSampler trawl hauled on deck. (c) A typical mesopelagic catch in Masfjord, western Norway. (d) A night catch from three codends; the catch in T1 from the deepest mesopelagic layer, in T2 between two mesopelagic layers, and in T3 from the shallowest mesopelagic layer.

Figure 4.5 A typical catch from a bottom trawl from 490 m depth in Masfjord, western Norway. (a) The trawl after being hauled onboard. (b) The trawl catch on deck, prior to sorting into baskets of single species. (c) Weighing the baskets of individual species in the wet lab and recording the data. (d) A roundnose grenadier (

Coryphaenoides rupestris

) on a measuring board. Grenadier tails are fragile and easily break off in the trail, therefore the standard length measurement is from the tip of the snout to the posterior edge of the dorsal fin.

Figure 4.6 A typical catch from a bottom trawl from 90–150 m depth in the North Sea. (a) The catch is hauled on deck and placed into a large container before entering the fish lab. (b) The catch is placed into baskets (still unsorted at this stage) to be weighed; (c) the catch is sorted and measured; (d) a basket containing only saithe (

Pollachius virens

). (e) A hake (

Merluccius merlucciu

s) on an electronic measuring board.

Figure 4.7 How to subsample and measure the catch of a mesopelagic community.

Figure 4.8 Sorting the mesopelagic catch in Masfjord. (a) A typical catch from a 5–10 min haul. (b) The most often caught species: pearlside (

Maurolicus muelleri

), lanternfish (

Benthosema glaciale

),

Sergestes

spp.,

Pasiphaea

spp., krill (

Meganyctiphanes norvegica

), and the helmet jellyfish (

Periphylla periphylla

). (c) Sorting a subsample. Counting of (d) pearlside and (e)

Sergestes

spp. by placing in piles of 10 individuals. (f) Measuring individuals and recording standard length (SL).

Figure 4.9 How to measure the length of various fish species at the Institute of Marine Research, Norway.

Figure 4.10 Large saithe (

Pollachius virens

) are found in the pelagic as well as just above the seabed in deep west Norwegian fjords. (a) A 5 kg saithe caught by hand‐line at 90 m depth, immediately below the shallowest mesopelagic sound scattering layer. (b) The individual with its belly opened and the stomach removed. (c) The stomach of the fish was packed with pearlside

(Maurolicus muelleri

).

Figure 4.11 An example of a station form used during the field course in Masfjord, Norway. The top part of the form contains station information, while catch information is recorded at the bottom.

Figure 4.12 (a) Example of label information when freezing a sample. (b) Frozen samples should be flat packed and the label must be visible through the plastic bag.

Figure 4.13 An example of a length measurement form used during the field course in Masfjord, Norway. Measurement units can be in either mm or cm. One form is used for each species. Data should also include the number and total weight of the measured fish.

Figure 4.14 An example of a form to use for individual biological data for large fish that feed on mesopelagic organisms during the field course in Masfjord, Norway.

Chapter 05

Figure 5.1 Example of how to obtain the path to a directory (first red line) and set a new working directory (second red line). Note that on MacOS or Linux, a forward slash instead of double or single backslash must be used. A forward slash will also work with Windows versions of R. A forward slash is recommended for producing platform independent syntax. Thus, a more general syntax for the second red line is:

setwd(“C:/Documents and Settings/Administrator/My Documents/rwork”)

.

Figure 5.2 A PCA analysis plot from the data shown in Table 5.1. PCA plots are interpreted as follows: sites that are close together in the diagram have a similar species composition; sites 4 and 5 are quite similar. The origin (0,0) is species averages. Points near the origin are either average or poorly explained. Species increase in the direction of the arrow and decrease in the opposite direction. Distance from the origin reflects the magnitude of change. Variables near each other are similar. Angles between arrows approximate their correlations: 90° = 0 correlation, <90° = positive correlation, >90° = negative correlation, and 0° implies correlation = 1.

Figure 5.3 A dendrogram showing a hierarchical clustering of sampling sites 11e–24e (samples from wave exposed sites) and 31 s–44 s (samples from sheltered sites) based on a Bray‐Curtis dissimilarity matrix. Connections made at values close to 0 indicate sample sites have a high degree of similarity (“low degree of dissimilarity”).

Figure 5.4 A MDS plot showing distances between sampling sites 11e–24e (samples from wave exposed sites) and 31 s–44 s (samples from sheltered sites) on a two‐dimensional plane. The elliptical borders show cluster overlays from the separate cluster analysis with dissimilarity less than 0.6. For 34 s and 44 s the ellipse has collapsed since there are only two data points in this cluster.

Figure 5.5 Environmental data from CTD station 0683. The panels show profiles of temperature, oxygen, salinity, and light (PAR) over depth (m). The CTD records pressure (dbar) which is then used as the depth. Note that the depth is not on the same scale for the PAR curve because the light measuring unit cannot measure PAR values

<

10

−12

.

Figure 5.6 The density of zooplankton (measured in dry weight per cubic meter) at different depths and time of day, day and night. This figure was made using the code in

(2) Create a simple plot of the data

. Open and solid circles represent day and night samples respectively.

Figure 5.7 The density of zooplankton (measured in dry weight per cubic meter) at different depths and time of day, day and night. The lines show mean density at each depth, while symbols are the density of zooplankton in each sample.

Figure 5.8 CPUE (kg per hour) for all fish species caught by hook‐and‐line.

Figure 5.9 Median depth (thick black line) and depth range of echo‐layers depending on time of day. The left panel shows the median depth (thick line), the upper and lower quartiles (upper and lower borders of the box), and the minimum and maximum values (upper and lower whiskers). Note that the surface of the water (0 m) is at the bottom of the y‐axis. The right panel shows the same information in a slightly different way: 0 m is at the top of the y‐axis, boxplots from day sampling are white and night are shaded grey.

Figure 5.10 Size of

M. muelleri

caught in the upper and lower echo‐layers during the day and night.

Figure 5.11 Total biomass as catch per hour (kg) in each echo‐layer, lower and upper, during day and night. The sample size for each group, left to right, is 3, 2, 3, and 2 hauls for each of the layers.

Figure 5.12 The proportion of total biomass of each species caught during day and night in the upper and lower echo layers. Data have not been standardized to a similar unit of effort before plotting.

Figure 5.13 The proportion (in numbers) of each species caught during day and night in the upper and lower echo layers. Data have not been standardized to a similar unit of effort before plotting.

Figure 5.14 Catch (kg) per hour at three depth ranges by species from pelagic trawling during the day (white bars) or night (shaded bars). Depth ranges were 0–100 m, 100–200 m, and 200–300 m.

Figure 5.15 Catch (numbers) per hour at three depth ranges by species from pelagic trawling during the day (white bars) or night (shaded bars). Depth ranges were 0–100 m, 100–200 m, and 200–300 m.

Figure 5.16 Catch per hour of

B. glaciale

(biomass) from day (white) and night (shaded) for three depth ranges: 0–100 m, 100–200 m, and 200–300 m. Solid black lines represent median values.

Figure 5.17 Length (mm) of

B. glaciale

from day (white) and night (shaded) for three depth ranges: 0–100 m, 100–200 m, and 200–300 m. Solid lines indicate median values.

Figure 5.18 Abundance (g, numbers) of five prey items eaten by saithe and pollack.

Figure 5.19 Catch (kg per hour of trawling) of species captured by bottom trawls.

Figure 5.20 Catch (number of individuals per hour of trawling) of species captured by bottom trawls.

Figure 5.21 Boxplots showing the size range (mm) of all species caught using bottom trawls.

Figure 5.22 A map of the North Atlantic showing bottom trawling locations as red dots.

Figure 5.23 A map of Norway with the location of Masfjord shown as a red dot.

Figure 5.24 Low resolution map of Masfjord created with the

sp

package. The four sampling stations are marked as red numbers.

Figure 5.25 Map of Masfjord created with the

RgoogleMaps

package, which uses maps from Google Maps. The four sampling stations are marked as red numbers.

Guide

Cover

Table of Contents

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Marine Ecological Field Methods

A Guide for Marine Biologists and Fisheries Scientists

Edited by

Anne Gro Vea Salvanes

Department of Biology, University of BergenBergen, Norway

Jennifer Devine

Institute of Marine Research (IMR)Bergen, Norway

Knut Helge Jensen

Department of Biology, University of BergenBergen, Norway

Jon Thomassen Hestetun

Department of Biology, University of BergenBergen, Norway

Kjersti Sjøtun

Department of Biology, University of BergenBergen, Norway

Henrik Glenner

Department of Biology, University of BergenBergen, Norway

This edition first published 2018© 2018 John Wiley & Sons Ltd

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions.

The right of Anne Gro Vea Salvanes, Jennifer Devine, Knut Helge Jensen, Jon Thomassen Hestetun, Kjersti Sjøtun and Henrik Glenner to be identified as the authors of the editorial material in this work has been asserted in accordance with law.

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Library of Congress Cataloging‐in‐Publication data applied for

ISBN: 9781119184300

Cover Design: WileyCover Images: Northeast Atlantic mackerel swimming, Courtesy of Leif Nøttestad; Intertidal community at a wave‐exposed site, Courtesy of Kjersti Sjøtun

List of Contributors

Dag L. AksnesDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Lars AsplinInstitute of Marine Research (IMR), Bergen, Norway

Martin DahlInstitute of Marine Research (IMR), Bergen, Norway

Jennifer DevineDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway;Institute of Marine Research (IMR), Bergen, Norway

Arill EngåsInstitute of Marine Research (IMR), Bergen, Norway

Tone FalkenhaugInstitute of Marine Research, Flødevigen, His, Norway

Svein Rune ErgaDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Keno FerterInstitute of Marine Research (IMR), Bergen, Norway

Henrik GlennerDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Jon Thomassen Hestetun Department of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Mette HordnesDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Ragnhild Aakre Jakobsen Hunstadsvingen, Bergen, Norway

Knut Helge JensenDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Frank MidtøyDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Leif NøttestadInstitute of Marine Research (IMR), Bergen, Norway

Egil OnaInstitute of Marine Research (IMR), Bergen, Norway

Michael Pennington Institute of Marine Research (IMR), Bergen, Norway

David John ReesDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Shale RosenInstitute of Marine Research (IMR), Bergen, Norway

Anne Gro Vea Salvanes Department of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Kjersti SjøtunDepartment of Biology, University of Bergen (BIO, UiB), Bergen, Norway

Arved StabyInstitute of Marine Research (IMR), Bergen, Norway

Foreword

Despite covering over 70% of the surface of the planet, the marine environment is less accessible, and thus less well‐known than terrestrial habitats. A variety of technologies allow for marine field studies on environments ranging from the shallow nearshore to depths of thousands of meters, on individuals, populations, communities, and ecosystems. This book describes marine ecological sampling equipment, methods, and analysis, ranging from physical parameters to fish, microalgae, zooplankton, benthos, and macroalgae. It will be useful for graduate students and early‐stage professionals in marine biology and fisheries, even those not directly involved in fieldwork, by giving an overview of marine biological data collection, handling and analysis.

This handbook provides a guide to the use of marine ecological sampling methods used for pure research and for fisheries management purposes. The book covers survey and sampling design, sample and data collection and processing, and data analysis. The research question and characteristics of the organisms and habitat dictate what sampling equipment is required. Information is included on sampling equipment, ranging from those that are useful in shallow nearshore areas, such as bottles, secchi discs, and gillnets or beach seines to those deployed from large research ships for studies offshore, such as remotely operated vehicles (ROVs), fishing trawls, and hydroacoustics, or remote observation using satellites.

The development of this book started at the Department of Biology at the University of Bergen in 2011; when due to lack of suitable literature, students attending a marine field course were provided with short handouts. The handouts became more and more advanced from year to year. In 2014 the publisher Wiley became aware of the initiative and invited us to write a textbook for broader use. The six editors of the book have, over several years, been involved in the writing and development of the book project. As we came across additional themes relevant for the handbook, and that we ourselves felt we did not know well enough, we invited experts from our network at the Institute of Marine Research and the Department of Biology at the University of Bergen to contribute as co‐authors. The editors have produced text, and in addition taken the lead on the structure, contents, and in the editing of the entire manuscript. All editors have worked on the full text. A.G.V. Salvanes has had the main responsibility for coordinating the work, J. Devine has had the final edit on all chapters, J.T. Hestetun was mainly responsible for keeping references organized and for quality evaluation of figures. All artwork was produced by R. Jakobsen. We hope the handbook will help reader to plan and execute fieldwork to answer research questions, and provide basic knowledge of the most common methods for collecting field data for modern marine research. We also hope the handbook will enable readers to explain and evaluate the principles of different sampling approaches, their strengths and weaknesses, and not least how to process, catalog, and interpret collected field samples and experimental data.

The provided R code with this book (http://filer.uib.no/mnfa/mefm/) is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. If the code and data are used for teaching (or other) purposes, we ask those using the material to reference the textbook. The code is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Bergen, January 20, 2017

Anne Gro Vea SalvanesJennifer DevineKnut Helge JensenJon Thomassen HestetunKjersti SjøtunHenrik Glenner

Acknowledgements

The editors acknowledge the Olav Thon Foundation for funding which made the completion of this book possible. Thanks especially to the many students on our marine field courses that over years have inspired us to write this book. We are particularly grateful to the 2016 master students on the Ocean Science Course (BIO325) at the Department of Biology, University of Bergen. They tested out and gave us valuable input to improve the draft version of the book: M.V. Bjordal, A. Delaval, C. Djønne, N.E. Frogg, K.F. Furseth, S. Hjelle, J.S. Høie, I. Nilsen, D. Notvik, H. Seal, M.R. Solås, E. Tessin, and S. Tonheim. G.J. Macaulay, Institute of Marine Research and L.H. Pettersson; Nansen Environmental and Remote Sensing Center are thanked for professional help and production of topographic and remote sensing maps. We thank T. Klevjer, J.H. Vølstad, and K. Korsbrekke, Institute of Marine Research for comments and B.H. Bjørnhaug, Bergen Technology Transfer Office for help with contract issues. Many colleagues and companies are thanked for illustrations; Aanderaa, G. Anderson, Santa Barbara, Fagbokforlaget, Institute of Marine Research, T. Hovland, G. Macaulay, K. Mæstad, R.D.M. Nash, Ø. Paulsen, Scantrol/Deep Vision, H. Saivolainen, H.R. Skjoldal, Son Tec, E. Svendsen, T. Sørlie, G. Sætra, University of Bergen Library. We thank: A. Hobæk, Norwegian Institute for Water Research; C. Todt, Rådgivende Biologer AS; M. Malaquias, University Museum of Bergen; L. and P. Buhl‐Mortensen, Institute of Marine Research, H.T. Rapp and K. Meland, University of Bergen, T. Dahlgren, University of Gothenburg, and U. Båmstedt, Umeå University, for valuable contributions to benthic studies. Our special thanks goes to the crew onboard the research vessels; RV Håkon Mosby, RV G.O. Sars, RV Hans Brattstrøm and RV Dr. Fritjof Nansen; the crew are experts and have deep knowledge on operating advanced as well as the simple gears used to sample marine organisms. We could not have done our research or field courses without their skills and support.

1The Marine Environment

Jon Thomassen Hestetun*, Kjersti Sjøtun*, Dag L. Aksnes, Lars Asplin, Jennifer Devine, Tone Falkenhaug, Henrik Glenner, Knut Helge Jensen and Anne Gro Vea Salvanes

The marine environment covers over 70% of the surface of the Earth, yet represents special challenges when it comes to scientific inquiry. When compared to terrestrial systems, the marine environment is much less easily accessible and, despite great effort, remains less well known. With the rise of the modern natural sciences, tools and methods have been continually developed to explore marine environments, from the littoral zone and nearshore environment to open waters and the shelf and abyssal seafloor. From tried and true collection equipment, often identical to or based on fishing gear, to new innovations in remotely controlled and autonomous vehicles, exploration of the underwater world is heavily dependent on the tools used.

Technological advancement now allows marine field studies to be conducted at all levels: from individuals to populations, to groups of populations, and to entire ecosystems. Habitats from the shallow nearshore to depths of thousands of meters are increasingly accessible; studies of interactions between specific organisms and physical and biological components are possible. The equipment used for sampling is dependent on the research questions asked and the characteristics and depth of the studied organisms and their habitat. Gears range from simple tools that are useful in shallow nearshore areas, such as bottles, secchi discs, and gillnets or beach seines to advanced equipment, such as remotely operated vehicles (ROVs), fishing trawls, and hydroacoustics deployed from large research ships for studies offshore and at greater depths. Even remote observation from space can be performed using satellites.

A characteristic transect from a continental landmass to the deep ocean includes nearshore environments that, depending on local geology, may consist of sandy beaches, cliffs or fjord systems. The continental shelf may stretch out some distance from the continental landmasses, gradually giving way to the continental slope, which descends down to the abyssal plains of the world’s major oceans. As an example, the western coast of Norway contains an elaborate fjord system with numerous deep basins divided by shallower sills, giving way to the Norwegian Channel and then the shallower continental shelf. To the southwest, the North Sea is a shallow sea on top of a continental shelf only, while to the northwest, the Norwegian Sea descends into a deep‐sea basin which also contains the Mid‐Arctic Ridge, separating the Eurasian and North American continental plates. Banks, seamounts and submarine canyons are features that add to the topographical complexity of this general system (Figure 1.1).

Figure 1.1 Topographic chart of the North Sea.

Source: G. Macaulay, Institute of Marine Research, Norway.

Species composition changes with depth and distance from the coast, both for pelagic species and for organisms associated with the seafloor. Organisms are morphologically, physiologically, and behaviorally adapted to their environment through natural selection. Individuals with favorable genetic traits have increased breeding success than those lacking these traits (genetic adaptation). Some species are able to shift between environments and habitats, for instance benthic species with a pelagic egg and larval phase, or species that shift diurnally between different water depths (diel vertical migration, DVM). Diel vertical migration typically occurs between water masses with different properties in terms of light, temperature, oxygen, and salinity, requiring a physiological response from the organism. In general, effects of abiotic and biotic factors influence morphology, physiology, and behavior and thus how animals adapt to their habitat.

Examples of abiotic factors are the optical properties of the water column and include: light and the amount of suspended particles, which are important for visual predation; temperature, which regulates physiology, metabolic processes, and swimming activity; salinity, which affects physiology and osmoregulation; oxygen levels, which regulate respiration and metabolism and can limit reproduction or growth at low levels; and depth, which regulates pressure and affects buoyancy of fish that use swim bladders to obtain neutral buoyancy. Stratification of water masses, which often is seasonally dependent, limits nutrient availability in upper strata (the photic zone, as well as oxygen concentration in the lower strata or in isolated basins. Eutrophication and closeness to urbanized regions will also affect the level of primary production and the depth range where visual feeding is possible.

Biotic factors