Sampling Biodiversity in Coastal Communities
Sampling Biodiversity in Coastal Communities
III
RIDGE BOOKS
Sampling Biodiversity in
Coastal Communities
Sampling Biodiversity in
Coastal Communities
Edited by
Ridge Books
an imprint of NUS Press
National University of Singapore
AS3-01-02. 3 Arts Link
Singapore 117569
www.nus.edu.sg/npu
ISBN 978-9971-69-368-8 (Paper)
p. cm.
SLS2006048625
vii
List of Figures
--
Foreword
Part I
IX
Introduction
Section 1
Section 2
Section 3
Sampling Protocols
Section
Section
Section
Section
4
5
6
7
13
17
22
25
Target Groups
Section
Section
Section
Section
Section
Section
Section
8
9
10
11
12
13
14
Macroalgae
Seagrasses
Echinodermata
Polychaeta
Cnidaria
Mollusca
Decapoda
33
37
42
47
52
56
59
Target Groups
Section
Section
Section
Section
15
16
17
18
Porifera
Amphipoda
Isopoda
Meiobenthos
69
73
76
80
Optional Protocols
Section 19
Section 20
Section 21
for Ecologists
Guide to Identification and Surveying of
Nearshore Fishes
Sampling and Monitoring Rhodolith Beds
85
90
93
Section
Section
Section
Section
Section
vi
25
26
27
28
29
Glossary of TelIDs
Bibliography
Online References
Connibutors
Index
108
117
130
138
144
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
5.1
5.2
5.3
6.1
7.1
7.2
7.3
7.4
7.5
8.1
9.1
Fig. 9.2
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---.
Fig.
Fig.
Fig.
Fig.
10.1
11.1
11.2
12.1
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
Fig.
13.1
13.2
13.3
14.1
14.2
14.3
14.4
14.5
14.6
14.7
15.1
16.1
17.1
17.2
18.1
20.1
23.1
Seagrasses
Representative Echinoderms
Phyllodocidae, Syllidae, Polynoidae, & Terebellidae
Polychaete Dissection
A Medusa of a Hydrozoan, a Sea Anemone &
Hydroid Colonies
Parts of the Bivalve Shell
Parts of the Gastropod Shell
Parts of the Polyplacophoran Shell
General Body Plan of Dendrobranchiata
General Body Plan of Caridea
General Body Plan of Stenopodidea
General Body Plan of Brachyura
General Body Plan of Anomura
General Body Plan of Palinura
General Body Plan of Thalassinidea
The Sponge Body Plan
General Amphipod Body Plan
Cirolanid Isopod
Arcturid Isopod
Representative Species of Meiofaunal Phyla
Kelp Bass
NaGISA Field Data Sheet
18
19
20
23
26
27
27
28
29
34
38
39
44
48
49
53
57
58
58
60
61
62
63
64
65
65
70
74
77
77
81
91
103
VB
R.K.
ix
Part I
In trod Detion
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done, but most often because their study will reveal fundamental aspects
of the benthic ecosystem. The guides have been written with the intent of
data sheets, included to ease even the newest researcher's transition into the
field.
P.R.
-iodiversity and global strategies for ensuring its stability have been
global call to establish national species inventories and data co]]ection has
one of three selected target habitats and outlines of the protocols needed
et al. 2002). In 2002, when the Census of Marine Life (CoML) was looking
for its first suite of projects, the ideas laid out during IBOY were adopted
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----
within local areas and between regions and will for the first time elucidate
geographic patterns of biodiversity along latitudinal and longitudinal
directions at scales ranging between a few meters and thousands of kilometers.
The data collection will be ongoing and will serve as a living archive of
global coastal marine biodiversity information from which students,
researchers and stakeholders can receive continuously updated information
on local , regional and global biodiversity and its change over time. The hope
is that NaGISA will grow from a network of individually funded scientific
endeavors to a governmentally supported network, for which national budgets
contribute to the study and understanding of national resources.
Y.
SHIRAYAMA
& PR.
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-..
-
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from all sources including , inter alia , terrestrial, marine and other
aquatic systems and the ecological complexes of which they are pari ;
These include, among others, food and medical resources, drinkable water,
clean air and fertile soils. Biodiversity also contributes to the productivity
--
to estimate variability at each scale and to identify the scale(s) at which most
of the variability occurs. Because different ecological processes generate
variability at different scales, identifying the relevant scales of variability
in patterns of biodiversity or in BEF focu ses attention on the potentially
important causal processes . This provides important clues for directing
subsequent experimental research.
L. B ENEDETII-CECCHl, UNIVERSITY OF PISA, ITALY
10
II l.lUd
--
-INTRODU CTION
Shorelines are areas of transition between the ocean and land. Rocky areas
dominate much of the world's nearshore. The communities that live in these
areas are known for their high biodiversity, as the rocks provide the hard
substrate necessary for the attachment of sessile organisms, particularly
macroalgae. These nearshore macroalgal communities are very productive.
An example of this productivity is the primary production in the giant kelp
(Macrocystis pyrifera) forests in California, which ranges between 250 to
1500 g C/m 2/yr (Mann 1982). Macroalgal communities are important habitat
for many invertebrates, fishes and marine mammals. These organisms use
macroalgae for food and shelter. Many macroalgal habitats are known to
be nursery grounds for recreational, commercial and subsistence invertebrates
and fishes. The nearshore can be said to have two major areas: intertidal
and subtidal. The intertidal zone is alternately exposed to air and water while
the subtidal zone is continuously submerged.
The intertidal area ranges from the splash zone to mean low water level.
The spatial extent of this area varies depending on its slope and tidal
exchange. Due to variations of slope (steeper slopes have less aerial intertidal
space) and tidal exchange (which can range from a few centimeters to as
large as 10m) the spatial extent of the inteltidal zone can vary greatly.
The intertidal area can be divided into four zones: splash, high, mid
and low.
The splash zone is the area that is reached by the ocean's salt spray. Only
the highest tides and storm waves contact this zone. Most of this zone is
bare rock but there are some common organisms found here, including a
few species of periwinkles, limpets, and barnacles. Some species of lichens
and one green alga (Prasiola spp.) also are common in this zone.
in this zone is the barnacle, which cements itself to the substrate and closes
its test during low tides to avoid desiccation. The algal community is not
diverse in this zone and usually consists of ephemeral species such as the
green algae in the Order Ulvales and brown algae of the Order Fucales.
These leafy or thickly branched algae provide protection from desiccation
to resident invertebrates by keeping the animals damp and shaded.
The mid-tide zone is generally more diverse than the higher zones because
it is covered and uncovered by the tides on a shorter, more regular cycle.
Organisms living here have adapted well to this change in emersion. Common
animals in this zone can include many species of anemones and mollusks
(including chitons, limpets, mussels, and gastropods). During low tide,
anemones can conserve water by closing up and covering themselves with
small rocks and shell debris. Molluscs can protect themselves by using their
powetful foot to secure themselves close to the substrate so as to protect
their soft parts or can move to moist areas such as cracks or under macroalgae.
Other molluscs have an operculum so that they can use to close their shells
to avoid water loss. The most common macroalgae in the mid-tide zone are
the Fucales or rockweeds, although others, particularly many red algae, exist
depending on the region.
The low-tide zone is the most diverse of the intertidal zones. It is usually
submerged and only exposed to air during unusually low tides. Because of
the longer submersion period, organisms in this zone are not as adapted to
intertidal living. Common animals found here can include seastars , urchins,
crabs, gastropods, anemones, small crustaceans, and small fishes. Often
these animals will migrate to the subtidal area during particularly low tides.
The subtidal area extends from below the low intertidal into and including
the depths that supp0I1 large macroalgae given the proper substrate (often
as deep as 20m or more). Because the subtidal zone is continuously
submerged, many subhabitats exist along both vertical (through the water
column) and horizontal (along the substrate) depth gradients.
A vertical depth gradient can be understood by invisioning a cross-section
of the subtidal area from the surface to the substrate. On the surface of a
kelp forest, many birds and marine mammals are associated with the canopy
forming blades of the large kelps. These animals forage in the midwater and
at the bottom. Commonly associated with the mid water are phytoplankton,
zooplankton and fish. Many fish utilize the structure afforded by the canopy
and mid water kelps for protection and food. Connected with the kelp structure
floating on the SUliace and in the midwater, many encrusting and mobile
organisms use the blades and stipes for substrate and food . Encrusting
bryozoans, mobile gastropods and limpets, and isopods are often abundant
on mature kelp. The fauna associated with kelp holdfasts is incredibly
diverse. Upward of 351 species from 213 families and 15 phyla were found
in eighty Ecklonia radiata holdfasts in New Zealand (Anderson et al. in
press). The most common groups were the mobile arthropods, annelids,
mollusks and echinoderms. Similar species-rich communities have been
rep0I1ed from holdfasts of Laminaria hyperborea, Durvillaea antarctica,
14
Section 4
and Macrocystis pyrifera. Similar to kelp hold fasts, upright coralline algae
and other turfing algae that are attached to the substrate can contain high
biodiversity (Deam 1987).
.~
nearshore communities.
Temperature is another controlling factor for the subtidal, and particularly
the intertidal zones. In the intertidal zone, desiccation caused by heat and
freezing associated with cold snaps can be detrimental to both algal and
invertebrate populations while they are exposed to air. Over large geographic
areas in the subtidal, temperature will control species distribution. For
example, the giant kelp Macrocystis is not found in subpolar areas while
the bull kelp Nereocystis is not found in warm temperate areas. Similar
species distributions along temperature gradients can be found in invertebrates
and fish.
Other important factors include sedimentation, nutrients, contaminants and
salinity. Of these, sedimentation can be particularly important because it has
many cascading effects. Increased sedimentation can reduce light quality
and quantity available for macroalgae, and it can also cause scouring and
burial, which can be detrimental to the early settlement of many invertebrates
and algae.
SUMMARY
Nearshore rocky shores create habitat and provide food, shelter and nursery
grounds for numerous species, promote increased biodiversity, and enhance
overall organism abundance, primarily because of the structural elements
of macroalgae associated with them (Anderson 1994). Loss of these
macrolagal areas could have profound impacts on regional patterns of
biodiversity and ecosystem functioning, and ultimately on human social and
economic interests through associated reductions in ecologically and
commercially important species.
B.
16
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time lines vs. exploring the undocumented) and how closely related your
area is to other NaGISA sites are also factors that should be considered
a site before committing to it as you will want to assess the practical issues
of getting in and out of the water, determine high, mid and low tide levels
and see how far out 1m, 5m, 10m and the optional 15m and 20m depth
contours lie.
Once the decision of where to sample has been made, carefully read through
the availability of all the necessary equipment for the field and sorting stages
and consult a tide schedule for the specific location. NaGISA Rocky Shore
sampling is done both intertidally and subtidally and so is best done during
63~m and 500~m mesh bags and underwater housing for the camera).
* Optional
MATERIALS NEEDED:
~
---
i;ee
I. Measure and record the surface water temperature and salinity at the
site and the light intensity and temperature of each underwater depth
(-1m. -Sm, -10m, -15m, -20m).
2. Choose a starting point at one of the pre-selected heights/depths
(see Fig. 5.1). Lay out the tape measure for 30m from this point along
the same tidal height/underwater depth contour.
3. Find the location of the first replicate along this line (the first of your
five previously chosen random numbers) . Record the GPS of this
point.
4. Place the I x I m quadrat at the replicate mark along the tape measure.
S. Facing the water, place the 50 x SOcm quadrat at the lower left comer
of the I x I m quadrat and the 25 x 2Scm quadrat in the bottom right
comer of the SO x SOcm quadrat (see Fig. 5.2).
6. Photograph the quadrats. Use the full frame and avoid shadows (label
your photos to ensure that they can be identified later).
7. Assess the percent coverage of the different species of macroalgae
in your I x I m quadrat, count the stipes of the larger kelps and count
all the macrofauna that is larger than 2cm. Record this information
on a field datasheet.
8. Take voucher specimens of all the species ; pl ace them in correctly
labeled plastic (or SOO/-lm mesh underwater) bags. The label should
30m
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Coming in from the field you will have a digital camera full of photos, a
handful of datasheets and coolers filled with sample bags. The photos must
be downloaded onto your computer and labeled with their corresponding
location , height/depth, replicate number and quadrat size. A CD library of
the photos will enhance your reference collection, assist in identification and
provide immediate viable comparisons for you and fULUre researchers. The
field data sheets (see section 23) must be combined and entered into the
NaGISA excel data sheet (obtainable from your regional coordinator) , which
can be uploaded to the NaGISA website with preliminary data entered (and
updated later). The sample bags must be carefully sieved and sOlted into
distinguishable groups as soon as possible.
record% coverage
and counts lake
remove all
2Sx2Scm
Quadrat
(Ph olograph.
rt!lllovc
a ll organi sms)
ench replicate
Rul es to work by: Throwaway nothing; record everything; label everything; always take a re ference photo
20
Section
priority. Regional keys are usually not enough to name specimens because
there is no guarantee that they cover all available taxa. Furthennore, there
is a lack of continuous update in the ta xonomy of many groups. The best
alternative is to use your voucher specimens to establish a reference collection
either 'in hou se' or with the assistance of a museum or herbarium . This step
should not be over looked , as reference to properly curated material is
essentia l for all studies.
Museums or herbariums often publish procedures for preservation and
long-tenn storage of the specimens in their institution; these are often related
to the features of taxonomic groups (Green and Lambert 1994; Rose and
de Torres 2002; Rose et al. 2002; Metsger and Byers 2003). In the following
sections Part III and IV we outline specific details for handling targets
groups that have been prioritized for identification within the NaGISA
project.
P.R . RIGB Y &
T.
INTRODU CTION
In the coastal soft bottom areas, seagrass beds are an ecologically important
habitat. The beds occur from the intertidal zone down to the subtidal. Their
communities are highly productive, with a high degree of complexity and
biological diversity. Sea grasses are submerged marine flowering plants that,
unlike seaweeds, have stems , leaves, and rhizomes and produce flowers,
fruits and seeds for their propagation. They provide three-dimensional systems
with a network of underground structure (rhizomes) stabilizing the substrate
condition in coastal areas. With these conditions, the beds can form several
types of microhabitats for associated organisms. Hemminga and Duarte
(2000) noted that animals associated with seagrass systems belong to three
broad categories: infaunal species living within the sediments; epifaunal
species living on the plants and the sediment surface; and epibenthic large
mobile animals moving freely under and over the leaf canopy. Unlike coral
reefs, salt marshes and mangroves, seagrass beds exist in nearly all coastal
areas of the world, from tropical region up to the Arctic. Worldwide there
are about 60 species of seagrasses (Short et al. 2001). They have a wide
range of plant size with scale from a few centimeters (for example, genus
Halophila) to a few meters (for example, genera Posidonia, Phyllospadix
and Enhalus) (Fig. 6.1). Also, there are different morphologies among the
different seagrass species. The different species and species number of
seagrasses are, therefore, a major factor controlling the characteristics of
seagrass communities and their productivity and diversity.
22
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SUMMARY
Seagrasses are submerged marine flowering plants that, unlike seaweeds,
have stems, leaves, and rhizomes and produce flowers, fruits and seeds for
their propagation. They form highly productive and diverse communities on
the soft bottom of all coastal areas of the world. There are about 60 seagrass
specie s known worldwide. Temperate seagrass species often form
monospecific seagrass beds, whereas in the tropical regions mixed species
beds are more common. Obviously, seagrass beds play important ecological
roles as nursery grounds and habitats for various commercial marine resources.
Moreover, the beds are significant for the effective conservation of endangered
species, such as the sea cow, in tropical regions.
C. ARYUTHAKA, KASETSART UNIVERSITY, THAILAND
24
S
.
--
to make sure that the site chosen for sampling is not an anomaly in the
general character of the regions seagrass habitat i.e. the choice of where to
and the seagrass habitat found in the area. Specifically care should be taken
to assess whether the region hosts; (a) intertidal and/or subtidal seagrass,
(b) permanent fixed beds or small transitional beds and (c) mixed stands
or homogeneous beds.
Once the decision of where to sample has been made, the protocols
carefully and all the necessary equipment for the field and sorting stages
samples from the center of the stand (and optionally from the edges). Mixed
be recorded. In general , the seagrass bed should extend beyond the transects,
however as some areas naturally have very small individual beds this will
gauge*, (for underwater sampling add SCUBA gear, 63I-Lm mesh bags and
* Optional
MATERIALS NEEDED:
Mid bed
A 30m transect shown going through the middle of the seagrass bed, with
PRE SAMPLING:
SAMPLING:
I. Measure and record the water temperature and salinity at the surface
and at transect depth, measure and record the light intensity at the
surface and at 1m intervals until reaching the lowest depth obtainable
within the bed.
2. Choose a starting point for the main transect line so that it runs
through the middle of the sea grass bed (Fig. 7.1). Record the height/
underwater depth. Use a tape measure to mark off 30m from this
point along the same depth contour.
3. Go to the first previously chosen random number along this line.
Record the GPS of this point.
4. Place the 50 x 50cm quadrat at this point along the transect line.
5. Photograph the quadrat, taking care to use the full frame of the
picture and getting no shadows in the picture (ensure that quadrat
photos can later be labeled with their replicate number).
6. Count and identify all the macrofauna larger than 2cm taking voucher
specimens as necessary. Be sure to put the vouchers in correctly
labeled plastic (or 500J.!m mesh underwater) bags. The label should
indicate that these are voucher specimens from the 50 x 50cm quadrat
followed by the date, name of the site, tidal height and replicate
number. Put the bags in a cooler.
7. Count the number of seagrass shoots within the 50 x 50cm quadrat.
Record this information on the appropriate data sheet.
8. Place the 15cm core cylinder to the right hand side of the 50 x 50cm
quadrat and place the 2cm core cylinder to the right of that larger
core (see Fig. 7.2).
9. Push/twist the 2cm cylinder into the substrate to a depth of lOcm
(Fig. 7.3). Place the cap on the 2cm corer and remove from the
26
50cm
--
@e)om
.... Tr:r
--
....
--
.. ~
macrofauna (>2cm) and take voucher specimens, count the number of shoots
in at least 11,. of the quadrat. Remove a l5cm diameter by 10cm depth core
substrate smoothly. Either cap the opposite end and place the whole
core in a labeled plastic bag (or 63flm mesh underwater) or empty
the contents into the labeled bag, rinsing the sides of the core with
spray from a squeeze bottle. The label should indicate that it is the
2cm core sample followed by the date, name of the site, tidal height
and replicate number. Make sure to get a full lOcm core - detritus
and/or air bubbles in the sediment can prevent the full IOcm from
being collected. If this happens repeat the core in a yet undisturbed
place as close to the first one as possible. Keep the material damp
and cool by placing the bag in a cooler or the mesh in a tub of
seawater until it can be sieved and sorted.
10. Push/twist the 15cm cylinder into the substrate to a depth of lOcm
(Fig. 7.3). Dig out fr om around the outside of the cylinder. Push
the bottom cover under the cylinder and lift everything up together,
empty the material into a labeled plastic (or 500llm mesh underwater)
bag. The labe l should indicate that it is the 15cm core sample
---:=:;
-
::=:;
--
Both the 2cm sub core and the 15cm main core are pushed/twisted into the
from the substrate and wedge is used to help remove the main core.
Covering the main core with a mesh bag prevents the loss of epifauna and
*over the
-1m
seagrass bed
-1m
* Optional
Fig. 7.4 Sampling Horizontally Distributed Seagrass Beds
Small single species stands should be sampled from the center of the stand
(and optionally from the edges) and care should be taken not to sample
between stands, but mixed stands or horizontally distributed beds are best
sampled with multiple transects at 1m depth intervals.
followed with the date, name of the site, tidal height and replicate
number. Remember to rinse down the sides of the cylinder with
spray from a squeeze bottle. Keep the material damp and cool by
placing the bag in a cooler or the mesh in a tub of seawater until
it can be sorted.
II. Move on to the next random number along the transect line until
all replicates are completed.
12. If the stand spreads over more than one depth contour then supporting
transects placed at 1m depth intervals should be added as necessary,
see Fig. 7.4.
28
In the field
SOISOcruQuadrat
(Photogr:lpll,
measure cOunt
,hoou record
m&:I'OA\unn
take voucher
specimenS)
Nested
sieves
NaGISA Excel data
sheets with info on
= Isite
location, vouchers
and and fmdings from
each replicate
Rules
lO
work by: Throwaway nothing; record everything; lab e l everything; always tak e a reference photo
priority. Regional keys are usually not enough to name specimens because
there is no guarantee that they cover all available taxa. Furthermore, there
long-term storage of the specimens in their institution; these are often related
T.
30
III l.lud
----
----
CHARACTERISTICS OF MACROALGAE
I) Macroalgae are eukaryotic multicellular algae
3) Brown, red and green algae differ in their pigment composition, storage components,
---,-
--
INTRODUCTION
Taxonomic classification is continuously changing and information about
the phylogeny of algae depends on the sources used. Traditionally, algae
were placed in the kingdom Protista and consisted of Rhodophyceae (red
algae), Ulvophyceae (green algae; formally called Chlorophycea) and
Phaeophyceae (brown algae). More recently (see www.algaebase.org) , they
have been placed in the kingdoms Plantae (Chlorophyta: green algae;
Rhodophyta: red algae) and Chromista (Ochrophyta: brown algae). They are
unilocular zo idangia
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and other macroalgae with holdfasts (different from the roots of vascular
plants). Some of them have gas bladders or pockets of air for buoyancy
allowing them to stay relatively erect in the water column. The thalli (fronds,
stipes and holdfasts) of brown macroalgae, such as Laminariales (kelps)
often exceed several meters in length. Cool-temperate regions often harbor
kelp communities that build multi-layered habitats for many associated
smaller macroalgae and animals refened to as kelp forests. In contrast,
tropical communities are usually comprised of small macroalgae that
usually occur in multi-species clusters on reef flats. These so-called turf
algae produce much less biomass but can be as high in species diversity
as temperate kelp forests.
Macroalgae principally propagate by means of zooids (such as zoospores
and gametes), which can be either flagellated as they are in brown and green
algae or non-flagellated such as the tetras pores and carpospores of red algae.
Macroalgae have varied life histories, which often include the alternation
of generations. Sometimes, alternate life history stages have very different
morphologies referred to as heteromorphic and which are presumably an
adaptation to seasonal changes in the environment. Macroalgae are found
from the intertidal zone to depths of over 100m with the highest species
diversity and abundance occurring in the upper subtidal zone. The maximum
depth at which algae can grow is limited by their need for light. The depth
of the light compensation point differs depending on the species, but generally
is in the range of 0.5 to several percent of water sUiface light intensity.
GENERAL MORPHOLOGY
The organization of macroalgal thalli is relatively simple. The thalli of
brown and most red macro algae are composed of a colorless medullary layer
and a richly pigmented cortical layer.
Green algae are often simply organized and undifferentiated in their
organization. In addition to the typical multicellular macroscopic forms,
green algae can also exist as unicellular macroscopic forms. These consist
of a single large cell with numerous nuclei and are call coenocytes or are
referred to having coenocytic organization.
34
---'
::!
Section 8
MACROALGAE
~
~
When collecting macroalgal specimens, the entire thallus (fronds, stems and
holdfasts) must be collected, as identifying macroalgae based on fragmented
specimens can be difficult. In many taxa, the anatomy of the reproductive
structures is an essential character for identification, and so it is possible
that for taxonomic purposes specimens may have to be collected outside
of the N aGISA quadrats or even at a different time of the year so as to collect
plants of different life history stages.
Collected specimens should be observed when fresh and special note
taken of the following features : colour; length, width and thickness of the
thallus; branching pattern; shape of erect thallus (is it terete, flat or foliose);
shape of holdfast (is it cupped or knotted); presence/absence of gas bladders
(are they hollow or solid); tissue anatomy (are the surface and inner layers
differentiated); reproductive structures when present; presence/absence of
special non-reproductive structures such as hairs, glands, ascocysts); presence/
absence of meristematic cells/regions.
Not all the macroalgae from the 50 x 50cm quadrats need to be preserved
but ample examples and vouchers of each species should be preserved.
Pressing macroalgae is the most common method for preservation and
pressed specimens are suitable for later morphological and anatomical
analysis .
Pressing: Place fresh wet specimens on herbarium mounting paper and
using as little water as possible spread the thallus out, displaying the
characteristic branching pattern . Cover with gauze or wax paper and press
between absorbent sheets of paper. Bind specimens together in a herbarium
press dry in a well-ventilated area. NaGISA protocols require that voucher
specimens be pressed (see glossary of methods for greater detail) but the
following methods can complement this technique:
Silica gel: Place the algae in an airtight container covered with silica crystals.
Specimens treated like this are suitable for DNA extractions although less
so for morphological observations as they will shrink and change shape.
Formalin: Place specimens in a jar with 4% neutralized formalin in seawater
(see glossary of methods). Specimens treated like this are suitable for later
anatomical observations, but the thallus will lose its colour; DNA extractions
from formaldehyde-preserved specimens have not been very successful.
Formalin is toxic, and this method requires a relatively large storage space.
36
CHARACTERISTICS OF SEAGRASSES
1)
2)
3)
4)
INTRODUCTION
GENERAL MORPHOLOGY
aboveground
~~:::Q=~==<-I----- rhizome
belowground {
38
Section 9 SEAGRASSES
cross vein
.b"",,"",
male flower
I female flower
1
-{ rhizome/-~
elowground
._... "-_.
~ ~
node
if you are worried that you do not have a complete specimen gently wedge
a trowel or shovel deep underneath a desired specimen. Back in the lab
debris can be washed off the specimens over a coarse sieve 500llm and a
pair of forceps is useful to aid in removing bits of shell, gravel and epiphytic
organisms. Fresh specimens are best kept moist in plastic bags or bottles.
If specimens cannot be examined immediately, they may be stored for a few
days in the vegetable compartment of a refrigerator. For longer maintenance,
specimens have to be preserved in 4% neutralized formalin in seawater
(see glossary of methods), and although seagrass can be preserved wet
long-term preservation is best gained by drying specimens in a plant press
(see glossary of methods). Well-dried specimens should be labeled with
sampling information, such as species name, collector name, sampling place
and date of collection and wrapped with a plastic sheet or put in a paper
holder to protect them from dirt.
DIVERSITY
Seagrasses belong to the subclass Monocotyledoneae within the class
Angiospermae . These marine plants are divided into five families:
Posidoniac eae, Zosteraceae, Ruppiaceae, Cymodoc eaceae and
H ydrocharitaceae. The first two families are predominantly temperate, while
the last two are primarily found in the tropics. The family Ruppiaceae is
found both in temperate and in tropical regions and mostly in low saline
water. There are 13 genera found within the five seagrass families: one
Posidoniaceae (Posidonia); three Zosteraceae (Zostera , Helerozoslera &
Phyllospadix); one Ruppiaceae (Ruppia) ; five Cymodoceaceae (Cymodocea,
HaLoduLe , Syringodium, ThaLa ssodendron & Amphibolis) and three
Hydrocharitaceae (Enhalus, Thalassia & HaLophila). A description of each
genus follows:
Genus Posidonia: Five species (four found in Australia and one in the
Mediterranean region). Strap-like leaf blades, leaves bearing a ligule at
junction of sheath and blade, leaf sheath persists as bundle of fibers,
monoecious; spike inflorescence with various numbers of hermaphroditic
flowers.
Genus Enhalus: one species (Enhalus acoroides from the east coast of
40
-....
- ::
Section
SEAGRASSES
C.
CHARACTERISTICS OF ECHINODERMATA
1)
2)
3)
4)
Pentameric symmetry
Water vascular system
Stereom endoskeleton
Bilaterally symmetric larvae possessing rudiment structure and undergoing
metamorphosis
5) Mutable collagenous tissue
INTRODUCTION
The Echinodermata (echino = "spiny"; derm = "skin") is an entirely marine
phylum of deuterostome macroinvet1ebrates with great morphological
diversity. The echinoderms include forms such as the flower-like sea lilies
and feather stars (Crinoidea), sea stars (Asteroidea) and brittle stars
(Ophiuroidea), hard-bodied, spiny sea urchins (Echinoidea), and the soft
bodied and somewhat wormlike sea cucumbers (Holothuroidea). Most extant
taxa show radial symmetry based on five rays (pentamery), though some
fOlms have supernumerary rays. All echinoderms have a water vascular
system made up of a central water ring that gives rise to five radial vessels
that connect to the tube feet (podia). Tube feet are important external
manifestations of this unique echinoderm character, figuring strongly in
locomotion, feeding, respiration, and as sense organs. Rows of tube feet are
arranged in rays that define regions and systems of plates called ambulacra.
The water vascular system is connected to the sUlface of the animal via a
stone canal leading to an external , sieve-like madreporite perforated by
hydropores, although there sometimes is a secondary loss of this connection.
Most echinoderms have a well-developed internal skeleton of elements
composed of polycrystalline calcium carbonate with a protein matrix called
stereom. All the spines, plates, and other hard parts are made of stereom.
It is important to note that this is not true shell. Even when arranged as a
42
Section 10
.-;
--.
ECHINODERMATA
echinodenn's body. In asteroids, they are usually made of two jaws set low
on the body, either directly upon the plate surface, or on a small ossicle.
GENERAL MORPHOLOGY
The best way to approach the morphology of this phylum is to survey
the representative groups and appreciate the important ways in which
they differ. This helps to detennine which resources to use for further
identification.
Tube feet. External, sometimes suckered extensions of the water vascular
system, usually found in rows along the body or arm to fonn an ambulacrum
Spine. Spikes of stereom that articulate with the body wall
Arm. An extension of the body wall accompanied by an ambulacrum
Disk. The central body at which the anns meet in brittle stars and sea stars
(starfish)
Feeding tentacles; anterior extensions of the water vascular system used for
feeding by sea cucumbers
Madreporite. Special, perforated plate on the top of sea stars, underside of
brittle stars, and in the apical region of sea urchins that covers the external
opening of the water vascular system
ASTEROID (Starfish)
Mouth. Usually centralized. on the underside of sea stars. brittle stars. and
sea urchins. but on the top of the central cup-like body of feather stars. and
at one end of the elongated body of sea cucumbers
Anus. Absent in brittle stars and many sea stars. at the top of the body in
sea urchins. and at the opposite end of the body from the mouth in sea
cucumbers
Petaloid. The flowerlike arrangements of specialized tube feet in irregular
urchins such as sand doll ars and heart urchins
The techniques used for identification are as diverse as the echinoderm
groups. Characteristics used to key out the various taxa are highlighted
below for each of the five main groups.
Crinoidea. Sea lilies are stalked fonns and are generally rare in shallow
water. Feather stars are common in tropical coral reefs. and vary in arm
number and arm branching patterns. The number and form of cirri at the
base of the cuP. and the spination and form of pinnules along the arms are
also used in many keys .
Asteroidea. The presence or absence of suckers on the tube feet. types and
distributions of pedicellariae. and the morphology and number of plate
series along the anns are important features. Many keys also use the ratio
of major radius (center of the disk to the arm tip. "R") to minor radius (center
of the disk to the inter-arm margin. "r") as a diagnostic character.
Ophiuroidea. Keys rely on plate patterns on the central disk. arm plating
and spination. and the arrangement of small papillae and teeth on the jaw
ossicles on the underside of the disk. Color. when it is preserved or recorded
in photographs. can also be helpful.
Holothuroidea. Presence or absence of tube feet along the body. number and
morphology of feeding tentacles. and most importantly. the shapes and
44
,---------------------
Section 10
ECHINODERMATA
distribution of tiny ossicles in the body wall are used in sea cucumber
taxonomy.
Echinoidea. Spination, color, plate architecture and overall shape of the test,
number and types of pedicellariae, presence or absence of the jaw apparatus
(Aristotle's lantern), arrangement of ambulacra, and placement of the anus
within or outside the apical region are only some of the main features of
sea urchins used in identification.
=----!!
Few echinoderms are dangerous, but some echinoids are best handled
carefully, or with gloves. Some forms have poison glands at the spine tips
but the danger from these can be greatly exaggerated. To preserve tube feet
and the body form of soft-bodied taxa like sea cucumbers it is best to relax
the specimens before fi xing them, the use of magnesium chloride, magnesium
sulfate, ethanol or cool water treatment (see glossary of methods) are all
acceptable. Once the echinoderm has become sufficiently unresponsive it
can then be injected with and placed in the fi xative of your choice (see list
below) with little or no change in the orientation of soft parts. Most
echinoderms, excepting the sea cucumbers, lend themselves well to drying
for long-term storage and manipulation for identification. The stereom lends
rigidity, and helps the specimen to keep its form even after desiccation.
However, the specimen should be fi xed in 70% or stronger solutions of
ethanol for several days before drying in a well-ventilated area out of direct
sunlight. Dried sea urchins, sea stars, and brittle stars can be readily identified
with most keys. Wet-preserved material is necessary for the soft-bodied sea
cucumbers. As desiccated specimens can disartic ulate over time, sea lilies,
feather stars, brittle stars, and many of the more delicate sea stars are best
preserved as wet material in >70% ethanol or 4% neutrilized formalin in
seawater.
To preserve soft tissue morphology and the overall body form of sea
cucumbers the specimens must be wet fi xed. This can be done with 4%
neutrali zed formalin-seawater followed by transfer to 75% ethanol for
long-term storage or for material that will be used for molecular studies,
in 95% ethanol. For larger specimens, injection by syringe of the selected
fixative/preservative is recommended. This is especially true for material to
be preserved in ethanol rather than formalin because ethanol must be brought
into contact with the internal organs as soon as possible.
Certain of the major groups require specialized techniques to view
morphological structures for identification. For pedicellariae of asteroids
and especially echinoids, the pedicell aria can be removed with fin e forceps
and placed in a drop of bleacb (5% sodium bypochlorite in a small dish
or microscope slide). Once the soft tissues are dissolved, the type and
morphology of the jaw and stem ossicles can be observed. Similarly, small
pieces of the body wall of holothuroids can be dissolved to reveal the
ossicles. Monitoring of the tissue digestion process is recommended because
the spatial orientation of the ossicles can also be informative. In echinoids,
notably the irregular fonns (sand dollars, heart urchins) , the plate architecture
of dried specimens can be revealed by brushing a solution of equal parts
of 95% ethanol and glycerin onto the test once the test is lightly cleaned
with a stiff toothbrush. As the ethanol evaporates, the glycerin darkens the
plate sutures. For sand dollars, it is useful to polish the test with a graded
series of sand papers before application of the solution.
46
~
~
~
~
--
~
~
--
.-
:;;.,j
CHARACTERISTICS OF POLYCHAETA
1)
2)
3)
4)
5)
Bilateral symmetry
Segmented worms
Usually have a pair of non-segmented parapodia on each segment
Usually chitinous chaetae arising from parapodia
Abundant in most marine environments, with a few species found in fresh water and
terrestrial environments
INTRODUCTION
Polychaeta is a group of segmented worms belonging to the phylum Annelida.
Commonly known as seaworms or bristle worms they include a vast array
of different groups; fire worms (Amphinomidae), scale worms (for example,
Polynoidae, SigaJionidae), tu beworms (for example, Sabellidae, Serpulidae)
etc. Like other members of the Annelida (such as Clitellata, including
oligochaetes and hirudineans), the body of polychaetes consists of a
longitudinal series of more or less similar body segments. A large number
of polychaetes are easily distinguished from clitellates by having various
well-developed appendages on their heads and other body parts; although
some polychaetes have simple body plans lacking any appendages. Poychaetes
intertidal to abyssal depths, from soft to hard su bstrates and from tropical
to boreal regions .
position and the shape of following appendages arising from the head region
are important taxonomic characteristics: antenna (e), palps (tentacular crown
and operculum, or buccal tentacles in some families), and eyes on prostomium,
nuchal organs (caruncle in some families) from the posterior edge of
prostomium, elongated cirri (usually called tentacular cirri) arising from
cephalised segments. The definition of cephalised segments, however, is
largely artificial, and differently defined between families.
In most polychaetes, the anterior part of the gut (pharynx or proboscis)
is eversible and used for food capture or burrowing. This proboscis may have
fleshy or chitinous papillae, and/or jaws. The trunk is the segmented region
of the body between head and pygidium , usually consisting of a large
number of almost uniform body segments. Body segments can sometimes
be clearly divided into 2 or more body parts (e.g., thorax and abdomen) with
different morphology (Fig. 11.1 D). Even among the uniform body segments,
the shape of parapodia and chaetae can change gradually or abruptly. Each
parapodium is divided into notopodium and neuropodium, and may have
dorsal cirri, ventral cirri, branchiae (gills) and other appendages (Fig. 11.1 C).
Chaetae are chitinous bristles; usually protruding from a pocket in the body
pulps
probosc is
proslomium
M'---~~"-7 dorsa l cini
dorwi cimlS
C
head
notopodium
-~r--'---,.,---?! tentacular
cirri
venlral ci rm s
trunk
pygidium
palps
(tentacles)
t===~~~
48
'---
Section I
..-.
~
POLYCHAETA
.--Ill
...-.
.......
.--;;
~
~
~
==;;
---
amount of glycerol on a glass slide (you can use a cover slip to keep the
proboscis open as you work). After examination, the removed proboscis
should be preserved along with the body (i.e. in the same vial).
The morphological features of parapodia should be examined carefully
from both the anterior and posterior ends. Parapodia should be removed
from the body using a scalpel or a small steel razor blade on a handle. To
observe the difference of parapodial and chaetal features in different body
regions, at least three pat'apodia from the anterior, middle and posterior part
of the body should be examined. To determine the parapodia to be examined
and to avoid damaged parapodia, the specimen should be carefully observed
under a stereomicroscope. Pat'apodia should be cut along the anterior and
posterior margin (Fig. 11.2C), and removed gently to avoid damage on
parapodia and aciculae (if they are present). Removed pat'apodia should be
transferred to a glass slide with glycerol, and examined under a compound
microscope.
DIVERSITY
The classification of Polychaetes is continually changing. Traditionally,
they have been classified into two groups: Errantia and Sedentaria, usually
given the rank of subclass or order. This is cUlTently considered to be an
artificial grouping. Dales (1962) proposed a new classification, based on
the structure of buccal organs and nephridia, dividing polychaetes into
14 groups (orders). Fauchald (1977) listed 17 orders largely similar to those
of Dales, and Pettibone (1982) recognized 25 orders including orders for
five 'archiannelidan' families and new orders for Myzostomidae and
Poeobiidae. Based on cladistic analysis using morphological characters
Rouse and Fauchald (1997) proposed a new classification and that is the
classification used here (Note the lack of taxonomic terms - subclass, order
etc. as they are still being discussed):
Polycheatea are divided in to Scolecida and Palpata.
50
Section 11
POLY CHAETA
CHARACTERISTICS OF CNIDARIA
I)
2)
3)
4)
Cnidae
Radial or biradial sy mmetry
Single body opening
Diploblastic structure
INTRODUCTION
Members of the primarily marine phylum Cnidaria are diverse in morphology
and life cycles. One of the two basic cnidarian body forms is a medusa
(plural medusae), a deep or shallow circular dome with a central mouth
beneath the dome, and tentacles fringing the edge of the dome. Typically
living free in the sea (pelagic), its common name is jelly or jellyfish. The
other cnidarian body form is a polyp, a cylinder with a mouth in the center
of the disc at one end , and few to many tentacles surrounding the mouth.
In a polyp that is part of a colony, the end opposite the mouth is attached
to other members of the colony or to tissue connecting members of the
colony; an example of colonial polyps are soft corals. In a polyp not part
of a colony, the end opposite the mouth may be flat and attached to firm
substrata, or rounded or pointed and bun'owed into soft sediments; an
example of a solitary polyp is a sea anemone.
Cnidarians are considered morphologically simple because oftheir radial
symmetry (biradial in polyps such as sea anemones and corals), single body
52
--
Section 12
C NlDARIA
..-.Ii
..-.i
----
-~
.....
......
opening, and body made of two tissue layers (thus they are diploblastic; most
animals, including humans, are triploblastic, having three tissue layers). Yet
cnidarians secrete the most complex intracellular structures known - cnidae,
for which the phylum is named. All cnidarians possess the type of cnida
(singular of cnidae) called nematocysts, microscopic stinging capsules with
which cnidarians defend themselves and gather food. Nematocysts are a
diagnostic feature of Cnidaria: if they are absent, the animal is not a cnidarian.
However, their presence is not proof an organism is a cnidaria: nematocysts
may be found in some predators of cnidarians. The cnidarian life cycle can
also be complex: many species alternate between polyp and medusa forms ,
the polyps forming medusae through an asexual process, and the medusae
forming eggs and sperm that ultimately develop into polyps. In species
having only a medusa or only a polyp, that stage reproduces sexually, and
may reproduce asexually as well. If asexually generated individu als remain
attached to one another, the resulting group is considered a colony; if they
separate physically, whether they remain beside one another or disperse,
they are collectively termed a clone (i.e. each individual is not a clone but
a clone-mate).
Medusae may be in the water over hard bottom shores or among seagrass
blades, but most cnidarians in these habitats are polyps. Attached to stones
or seagrass blades are commonly hydroids (class Hydrozoa) (some solitary,
but most colonial) and sea anemones (class Anthozoa, order Actiniaria).
Tube anemones (class Anthozoa, order Ceriantharia) may be burrowed into
the sediment in which seagrass is rooted. Rare cnidarians on seagrass blades
or algal thalli are stauromedusae (class Staurozoa) and medusae that crawl
usin g their tentacles (class Hydrozoa, order Limnomedusae) .
GENERAL MORPHOLOGY
Fig. 12.1 A. A
hydrozoan (from
B. A sea anemo
acontia (nemato
threads emitted
disturbed) (From
C. Hydroid colo
close-up of part
upper left, show
tentacles expand
tentacles retracte
cup surroundin g
cups, and two re
structures (from
----
-:=3
--
DIVERSITY
Phylum Cnidaria is divided into five classes (two having been identified only
rather recently), four with members that alternate between medusa and
polyp stages. In these four classes, collectively termed Medusozoa, the
duration of polyp and medusa stages may be unequal and the polyp and
medusa stages may not be equally conspicuous; in some cases, one or the
other stage is absent. The fifth class, Anthozoa, has only polyps.
Scyphozoa . "True" jellyfishes. Medusae larger and more conspicuous than
polyps .
Cubozoa. "Box jellies." Medusae larger and more conspicuous than polyps;
some members can injure or even kill humans.
Staurozoa. Medusa shaped like an eight-pointed star attaches to a firm
substratum; no polyp stage.
Hydrozoa. Medusae typically small, delicate, and short-lived. Polyps of
many species colonial, form a skeleton, and have specialized types of polyps
(i.e. some only feed, some only reproduce, some only protect the colony).
Polyps with a chitinous skeleton are tellned hydroids, those with a calcareous
skeleton are termed hydrocorals. The Portuguese Man-o' -War, which is not
a medusa but a pelagic colony mostly of specialized polyps, belongs to order
Siphonophora. Members of order Chondrophora, also pelagic colonies,
include the By-the-Wind Sailor.
54
Section 12
CNlDARIA
OF KANSAS , USA
Section 13
MOLLUSCA
they have spicules or scales on the body surface. Most species are small
and live in deep water.
!!
~
~
.:=;
anterio r margin
1~ ~ lunule
upper margin
posterior laleralleelh
cardinal teeth
I
umbo
adductor scar
ligament
anterior margin
posterior marg in
pallial sinus
posterior margin
adductor scar
~ pallialJine
low margin
sculpture
suture'~illJrt;spiral
columella
shoulder
aperture
siphonal canal
~~-+
~ insertion plate
central area
lateral area
G::s'.--=::;~jttdorsal area
girdle
c.:J
anterior valve
sutural laminae
median val ve
anal valve
dorsal view
P.
MILOSLAV ICH,
58
"-~----
CHARACTERISTICS OF DECAPODA
1)
2)
3)
4)
5)
Cephalothorax
First tluee thorax appendages function as mouthparts
Five pairs of walking appendages
Sometimes with chela (pincers)
Stalked compound eyes
INTRODUCTION
The decapod crustaceans are among the most familiar crustaceans and
include shrimps, lobsters, crayfishes, and crab-like species. Their well
developed carapace, usually well calcified, is used as protection for the
cephalothorax (head and body), including the branchial chamber where
branchiae have developed as the major respiratory organs. Their name
(Decapoda) means "ten legs", refening to the five pairs of functional
pereopods they use for walking or as defensive or feeding appendages (in
some cases some of these legs end in a strong or weak pincer named
"chela"). There are about 18,000 living species of decapods (Brusca and
Brusca 2003) and they occur in all aquatic environments (fresh , brackish
and marine waters) at all depths, and a few spend most of their lives on
land. Many are pel agic (free-living in the water column), but many others
development stages are free living, pelagic larvae that pass through several
stages before moulting to a small juvenile that will settle in its final
environment. Some species have an abbreviated early development.
The nearshore, rocky and coral reefs environments are among the most
diverse with respect to decapod crustaceans. These environments offer
multiple microhabitats for protection (e.g. rock fissures, protected areas
below rocks, dead and living coral, associated fauna like sponges, ciniped
beds and mollusks, attached algae) and a large food supply. Rocky areas
with strong wave action are usually less di verse than more-protected areas;
small rocks and boulders also favor higher species richness than very large
rocks as they offer a more protected area in term of refuges. Seagrass and
algal beds offer good shelter for many species of decapod, although decapod
species richness may be lower than in bare rocky shores where densities
may be high. Species either live on the plant stems and leaves, or wander
on or close to the bottom, under the plants. Many species of decapod living
among corals, seagrass and algae are mimetic species that have the same
or similar color (or even shape) as the substrate on which they live (i.e. the
coral branch or the algal thallus). Some species of spider crabs also use
algae, sponges or other material to decorate their carapace, making them
hard to detect in their natural environment (Wicksten 1993).
Dendrobranchiata
2
60
Section 14
DECAPODA
pelagic realm ("pelagic shrimps"). They are rarely found in the intertidal
zone but many species come close to the coast during reproductive or
recruitment periods. Many benthic species are of great economic importance
and they are fished all over the world (Holthuis 1980). These decapods
possess dendrobranchiate gills (two branches divided into multiple secondary
branches), their body is fusifOlm, long, usually strong , with a well developed
abdomen, often with a spiny rostrum (extension of the carapace), their first
three pereopods end in a generally small chela (pincer). Contrary to all other
shrimp-like decapods, females of this group do not brood their eggs.
Fertilization of released eggs is external. Many of these animals are quite
large, over 30cm lon g. Although some of the pelagic species might have
a peculiar morphology due to adaptation to their environment (e.g. longer
and slender appendages, spines, additional hairs), all dendrobranchiata shrimp
look similar in shape.
Group 2. Pleocyem a ta Includes all the remaining decapods. Spec ies
included in this group never possess dendrobranchiate gills; they either have
trichobranchiate gills (series of radiating unbranc hed tubular filaments) or
phyllobranchiate gills (platelike or leaflike branches) . The embryos are
brooded by the femal e before they hatch (egg mass kept below the abdomen).
This very large group of decapods includes several kinds of shrimps, the
crabs, crayfish, lobsters, and many less famili ar forms. Seven infraorders
are currently recogni zed within the Pleocyemata but one (Astacidea) is
almost exclusively from fresh water or deep marine habitat. The division
into Natantia (swimming species) and Reptantia (walking species) has been
abandoned as formal ta xa, but is still found in many textbooks and guides.
Caridea
~
l.
2.
3.
4.
5.
6.
1.
2.
3.
4.
5.
6.
Caridea (Fig. 14.2). The caridean shrimps include over 2,500 living
species and are mostly marine, although an important group of species
(e.g. genera Macrohrachium, Atya, Palaemonetes) are found in fresh water
(lakes, rivers) and in estuaries or brackish lagoons. The first 1 or 2 pairs
of legs end in a chela (pincer) and vary considerably in size among species.
The lateral part of the second abdominal segment overlaps both the ftrst and
third pleura. As in the case of the Dendrobranchiata shrimp, caridean shrimps
are either pelagic or benthic. Deep-water species are often bright red,
intertidal and shallow water species are usually brightly colored (particularly
species associated with coral reefs) and estuarine species are generally
whitish or transparent. Some species are important fo r fisheries (e.g. the
Pandalid shrimps) (Hendrich 1995). Many species are small and colorful
and live in sponges, among corals, algae and seagrasses.
Stenopodidea (Fig. 14.3). With less than 30 species, this is a little known
group of curious shrimps, all marine. The first three pairs of pereopods are
chelate, and the third pair is larger than the others. The lateral portion of
the second abdominal segment is not expanded as in carid eans. Usually
colorful, they are mostly tropical and benthic (coral reefs), although a few
species are found in deep water. Shallow water species are often associated
to other animals, like the cleaner shrimps of tropical fishes.
Brachyura (Fig. 14.4). This grou p, also known as the "true crabs", contains
over 10,000 species. The body is protected beneath a well-developed, calcified
carapace. The carapace is flattened dorsoventrally, ei ther smooth or
ornamented with spines (lateral or dorsal), tubercles, or protuberances, and
is oval, round, squ arish , rectangul ar, triangular or polygonal in shape. The
abdo men is symmetrical, flattened and reduced, and flexed beneath the
thorax. Females keep the eggs between the flexed abdomen and the ventral
part of the carapace until larvae are released. The first pair of legs, or
chelipeds, ends in a chela (pincer) sometimes very much enlarged and
adapted for defense, feeding or courtship. In many species cheJipeds are
asymmetrical and often larger in males than in females. Brachyuran crabs
62
Section 14
DECAPODA
Brachyura
..
1.
2.
3.
4.
tropics.
Anomllra (Fig. 14.5). This group includes species with very different external
aspects, like the hermit crabs, porcelain crabs, mole crabs, galatheid crabs,
and king crabs. The latter two groups are only found in deep water while
the others contain a various number of species occurring from the intertidal
and shallow shelf water. Hermit crabs are typically found in empty marine
snails shells in which they retract for protection; indeed, they possess a soft,
short, abdomen flexed beneath the thorax (as in true crabs); porcelain crabs
are usually extremely flattened, very fragile (they tend to loose their legs
when attacked or disturbed) and adapted for hiding in small, narrow crevices
or below algae, shells or sponges. Mole crabs are oval to rectangular in shape
and live in shallow water along sandy beaches, often in the surf zone where
they hide in the sand. In all Anomura, the fifth pair of legs (and sometimes
the fourth) are much reduced and are not used for walking.
Palinllra (Fig. 14.6). Spiny lobsters and slipper lobsters are characterized
in a large tail fan. The chelation of the legs in Palinura varies but in spiny
lobsters all five legs lack terminal claws (except in females). All species are
marine and they are found in a vaJiety of habitats throughout the tropics.
There is a large fishery for lobsters around the world. Although spiny
lobsters are commonly caught near shore, in rocky areas or in algal and
seagrass beds, the other Palinura species live in much deeper water.
Thalassinidea (Fig. 14.7). Mud and ghost shrimps are particularly difficult
to collect as many species make burrows that occasionally reach well over
one meter deep. As their common name indicates, they look like small
shrimp but they are also often confused with small lobsters. Many species
1. Body oval to subreClangular in shape, fron tal margin with teeth or spines.
2. First pair of leg ending in a fl at segment or in an imperfect (subchelate) claw, with
moving finger closing vertically.
3. Legs 1-4 or 2-4 adapted for excavating in sand.
S. Leg 5 reduced in size.
live in muddy substrate, but they are also occasionally found in rocky areas
and among rubble, in deeper water, in muddy-sand or in mud. Their
symmetrical abdomen is generally fl attened dorsoventrall y or subcylindrically,
with a laterally compressed carapace; the first 2 pairs (or sometimes the first
pair only) of legs are chelate, and the first pair is usually much larger than
the second. Mud shrimps are very characteristic of tidal flats, generally
64
Section 14
...
DECAPODA
Palinura
- .....
1. Body extended , abdomen long and robust, cylindrical or dorsoventra lly flattened.
2. Five strong, similarly shaped walking legs, not ending in a pincer (except for a
small pincer on leg 5 in female s) .
3. No conspicuous rostrum.
4. Antenna long, wipe-like and spiny (spiny lobsters) or flattened (slipper lobsters).
Thalassinidea
--
MEXICO
66
AI l.lBd
CHARACTERISTICS OF PORIFERA
I)
2)
3)
4)
5)
Sessile lifestyle
INTRODUCTION
Sponges are motionless, aquatic, benthic organisms with a unique body plan
within the Animal kingdom , A sponge specimen may look like an amorphous
mass, a branching tree, a perfect sphere, or a thin skin , Its body is formed
by aggregations of cells differentiated into two layers of ill-defined tissues
(the pinacoderm and the choanoderm). These flank a middle "matrix-like"
layer (the mesohyl) that contains various ce ll types (reproductive, skeleton
secreting, undifferentiated, or specialized cells, and bacteria), and the skeletal
elements (spicules and/or collagen fibers). These basic three layers line up
around a system of pores , canals , water-pumping chambers (covered by
specialized flagelfated collared-cells), and oscules (excurrent openings),
making the sponge the most efficient water-filtering organism in the sea.
Sponges are present in all aquatic environments. In the ocean they occur
from low to sub-tidal depths, on rocky outcrops and crevices where macroalgal
communities splurge, to the deepest parts of the seas. In the rocky seashore
sponges are usually small, while in seagrass beds sponges can be small thin
crusts overgrowing seagrass blades to stand alone organisms as large as
truck tires.
GENERAL MORPHOLOGY
The sponge body shows distinct features such as: shape, color, oscule
morphology, surface features, and consistency, which may characterize a
~~
~
/'
/'
/'
.... ."
/'
,.
'
Sp
Surface features
projections, papillae, etc.
particular species (Fig. IS . IA) . The surface of the sponge reflects the
morphology of the skeleton under it. Depending on how the sponge skeleton
reaches to the surface a species may produce a different texture effect on
the sponge "skin". Projections shaped like small cones (conulose), spikes,
spatula, or with irregular shapes may characterize members of a species or
even a genus. Smooth surfaces usually reflect the existence of a specialized
skeleton layered tangentially to the sponge surface.
Sponges do not have a mouth or a digestive tract. Ambient water enters
their body through small pores (ostia) and follows tlu'ough incurrent canals
that reach flagellated "water-pumping chambers" (choanocyte chambers).
These chambers open into excurrent canals that converge into a larger cavity
(atrium) that reaches the outside through the oscule (Fig. IS.IB). These
water-filtration systems present various grades of complexity, ranging from
the simplest body with a single central cavity lined by choanocytes (Ascon)
to those with choanocytes restricted to small chambers and with simple
canal systems (Sycon) to those with complex and numerous subdivisions
of the internal canals (Leucon) such as the one represented in Figure 15.1.
Sponges possess an internal skeleton, which provides support for growth.
The skeleton is composed of one or more of the following elements: spicules
70
Section 15 PORIFERA
shapes. Large spicules (the megascleres) usually form the main skeletal
rays), and other special features (spines, rounded ends etc.). Small spicules
(the microscleres) usually fill in the main skeleton, or are located in particular
should be removed from the substrate where they grow using a knife, or
another cutting tool, and preferably wearing diving gloves to avoid contact
needs to be taken, leaving the major functional body parts (oscula, peduncle,
outer surface) intact to allow the recovery of the sampled specimen. The
sample should contain a portion of the external and the intemal body parts
solution. Never place a calcareous sponge into a formalin solution since the
for skeletal studies then it can be directly placed into 80 to 90% alcohol.
For DNA studies a small sponge piece (2 g) can be placed in >90% Ethanol
or chopped into less than I mm pieces and placed into a 1.5 cc tube filled
with Silica Gel (electrophoretic grade) for later DNA extraction and analyses.
The first question to answer is what type of skeletal elements the sponge
A rapid acid test (see glossary of methods) will allow you to identify
asci dian (round spined spicules) , or a soft coral (long spined spicules). If
The next step is to classify the sponge skeleton. For this it is necessary to
make thin sections of preserved material (Dr. Klaus Riietzler, per.comm , see
glossary of methods for an explanation of the technique using both wet and
dry specimens). Other methods are used for histological studies. Sections
DIVERSITY
Sponges inhabit all aquatic habitats, and have been an important faunal
component of marine systems since the early Cambrian era (560 mya).
Approximately, 10,000 species have been described; however, their diversity
is believed to reach at least 15,000 species. Extant sponges are cUlTently
classified into three major classes: Hexactinellida, Demospongiae, and
Calcarea.
72
(ph%
courtesy of M. Shimomura)
CHARACTERISTICS OF AMPHIPODA
1)
2)
3)
4)
5)
INTRODUCTION
Amphipods are very common small crustaceans living mainly in marine and
freshwater environments, although some live their entire lives in supralitoral
and terrestrial domains. More than 6000 species are described from the
marine waters, and they are considered to be one of the more important
groups of invertebrate animals in the benthic realm (although almost 200
species live planktonicaUy) .
-..
-....
MORPHOLOGY
These crustaceans are distinguished very easily by the fact th at the first four
pairs of legs are directed forw ard, unlike the last three, which are directed
backward; that is why they are named "amphipods"; amphi-both , pods-legs,
in Latin. Amphipods usually are small lcm in length, although much
larger species exist) and are laterally compressed. The head is followed by
seven pereonal (thoracic), three pleonal, and three urosomal segments. As
in aU crustaceans, one appendage fro m each segment is articulated. On the
pereon are two pairs of gnathopods and five pairs of pereopods. On the pleon
are three pairs of pleopods. On the urosome three pairs of uropods are
always present. The telson is a very small additional piece at the posterior
end of the animal.
telson
uropods
epimeron
DIVERSITY
Amphipods are separated taxonomically into the planktonic amphipods
(Hyperiidea) and benthic amphipods (Gammaridean, Caprellidean, and
Ingolfiellidean).
74
Section 16
AMPHfPODA
,- =
CHARACTERISTICS OF ISOPODA
I) Bod y divided into three regions: head of fu sed segments; pereon of seven segments,
usually free; and abdomen of five segments, sometimes fu sed, plus pleotelson (fu sed
last segment and telson)
2) Head with lwo pairs of antennae, mandible, two pairs of maxilla, and maxillipeds
3) Pereo/! with seven pairs of pereopods (often but not always similar walking legs),
each of only one branch
4 ) Abdomen with fiv e pairs of pleopod s plus one pair of uropods attached to pleotelson
5) Females carrying eggs, embryos and juveniles in a marsupium silling under the
pereon and derived from branches of the pereopods (as in all peracarid cru staceans)
6) Males with pair of sty lets on inner edges of second pleopods
7) Juveniles without last pairs of pereopods (s ix pairs only)
INTRODUCTION
The Isopoda are one of the orders of peracarid crustaceans, that is, those
that brood their young in a marsupium under the body. They are uniquely
defined by the combination of one pair of uropods attached to the pleotelson
and pereopods of only one branch . The order is the most morphologically
diverse of all peracarids, including flattened forms with similar legs,
cylindrical bodies with legs very different from each other, and sexually
dimorphic parasitic forms.
Most of these forms are found in the nearshore rocky environment, some
specialising as bUITowers in sand or mud and others as inhabitants of algae
or seagrasses.
76
--
Section 17 IsoPoDA
A)
/J~~\
maxilliped
coxa
basis
y~is chium
oostegites ___
(j.
merus
carpus
propodus
dactylus
#n
-;;
-.-.
--
pedUncle}
exopod
pereopod
endopod
head
B)
peduncle } antenna 2
flagellum
pereoll,
pereonites
1-7
coxal plates
pleonites 1-5
abdomen
--
=:2
lp'=~d
pleotelson---'
pedUncle }
exopod
uropod
endopod
-.........
--
antenna 2
=3
~
uropod
similar, or which antelior ones are setose or hooked will help define the
family. A compound microscope can be used to differentiate species by
examining setation or mouthparts after they have been dissected from the
body. To dissect an isopod place the specimen in glycerol and dissect parts
off with a needle; then transfer the dissected limbs to glycerol on a microslide
and cover with a coverslip.
DIVERSITY
The order Isopoda is classified into seven suborders not all of which are
found in macroalgal and seagrass communities. Several families are
micropredators or parasites on fishes or decapods and rarely encountered
freeliving in these environments. The suborder Onisicidea, with many families
are the most familiar isopods, slaters and woodlice, but are entirely tenestrial
and have few representatives associated with marine habitats, and then only
high on the shore. The truly marine and freeliving suborders likely to be
found in coastal seagrass and macroalgae are:
78
Section 17
-...
Many papers, websites and books on isopods recognise the now obsolete
traditional isopod suborder "Flabellifera", a catchall grouping of the
families now included in Cymothoida, Limnoriidea and Sphaeromatidea.
The keys to families of Flabellifera in these older works are still useful for
practical purposes.
G.C.B.
ISOPoDA
INTRODUCTION
Meiobenthos is not a taxonomic group but rather a size class of the benthic
community (Mare 1942), which is smaller than 1-O.Smm and larger than
32-63!J.m. ]n NaGlSA, it is defined as those organisms that pass through
the O.Smm mesh sieve and are retained by the 63!J.m mesh sieve. Meiobenthos
consists of Metazoa and Protozoa. The dominant metazoan taxa are
Nematoda and harpacticoid Copepoda. Usually the former accounts for
about 80% of total metazoan meiobenthos, and the latter for about 10%.
Other meiobenthic metazoans include: Kinorhyncha, Gastrotricha, Loricifera,
Tardigrada, Ostracoda, Turbellaria, Nemertenea (Fig. 17.1). Among
protozoans, Foraminifera and Ciliata are the most abundant.
Along with the permanent meiofauna listed, juveniles of macrofauna
(e.g. Polychaeta) are also found in meiobenthic samples, and are considered
temporary meiofauna. Meiobenthos is abundant in both rocky nearshore
habitats and seagrass beds. The number of individuals living per m 2 can
often be as high as 107 .
80
Section 18
MEIOBENTHOS
82
SlOJ010Jd IBUO!ldO
A l.lBd
three to four seconds and the sea level changes produced by tides every six
to 12 hours, (2) medium period, like the seasonal changes in turbidity and
productivity due to the effect of the seasons occurring in six month cycles,
and (3) long period processes like the global circulation of a major CUITent
(such as the Gulf Stream), hurricanes and typhoons or El Nino events that
occur every three to seven years. The shorter the period, the more evident
the changes are to us.
We must also consider the spatial dynamics of the environment that
surrounds our sampling site. The spatial variability of the physical variables
on a shore could determine the structure of a community. Fresh water from
a river might have more impact on intertidal communities if they are located
in a place where the dominant littoral CUlTent transports the freshwater or
the sediments. Exposed shores have different communities (in species
composition and/or community structure) than protected ones.
86
Section 19
Waves: Waves are ondulations of the sea surface. Ocean waves have particular
characteristics (wave-height, wave-length) that are modified when they
reach the shallow coastal environment. The interaction with the sea floor
causes the breaking of the wave and the ocean wave theory cannot be used
in this situation. Normally, the waves we observe are caused by the wind
stress over the sea surface, but other waves, often impressive in size and
energy, are related to storm surges and earthquakes or submarine volcanic
eruptions. The energy of the waves is a determinant factor in shaping the
community structure and thu s highly pertinent to the areas biodiversity.
Different degrees of exposure and energy can be determined by observing
wave patterns (Beer 1996).
Light: Light is of utmost importance to the great maJonty of primary
producers. In rocky shores light is rarely a limiting factor, but it is for
submerged vegetation communities. In water, light is scattered, absorbed
and reflected. Depending on the wavelength, light attenuates rapidly with
depth and after a few meters in coastal waters (5-30 m depending on
suspended sediments and dissolved colored matter), less than 1 % of the
incoming light remains (Jerlov 1976; B ukata 1995). Several instruments can
be used to measure the penetration of light (a photometer or radiometer for
example), but the simplest one is the Secchi disk. Different Secchi disks
give us different transparency values . It is important to always use the same
disk and measure the transparency in the same conditions.
Land inputs: Sediments from land can be a limiting factor for many
communities, as they block the light and clog respiratory or alimentary
mechanisms of marine organisms. Land run offs can also supply important
nutrients to the sea. Suspended sediments can be observed using remote
sensing im agery and its concentration can be estimated by simple laboratory
detenninations. Sediment traps can also be used and together with a carefully
designed sampling plan , they can provide us with estimates of sedimentation
rates. This variable is rarely found in any marine station data set.
Temperature: Temperature governs all metabolic processes. In general,
animals and plants live within a relati vely narrow temperature range. In the
sea, extreme temperatures outside this normal range are rare, but seasonal
variations can determine the presence of certain species over time. Measuring
temperature is easy and several automatic sensors exist that can be deployed
to obtain a continuou s record. However, it is always necessary to calibrate
sensors and take into account manufacturing calibration parameters in order
to have a reliable data series. Daily sea surface temperature maps are
available from the Internet derived from different satellite sensors (see li st
of further resources). Marine data stations routinely measure sea temperature
and buoy data normally provide a depth profile.
Salinity: Salinity was originally defined as the content of salts dissolved
in the water. In general and as in temperature, animals and plants live in
a relatively nanow sal inity range. In the open sea the sal inity is usuall y
around 36 parts per thousand (roughly 36g of salt in one liter of water), but
in coastal waters, freshwater inputs can significantly lower this value.
Nowadays salinity is defined operationally fro m its electrochemical
measurement and it is expressed as practical salinity units (PSU). It can be
measured with a conductivimeter or salinometer. Refractometers are also
used although the results are less precise . Almost all marine data stations
measure salinity.
.FURTHER RESOURCES
Edwards, A.J. 2000. Remote Sensing Hand book for Tropical Coastal
Management. UNESCO Publishing
l erlov, N.G. 1976. Marine Optics. Elsevier Oceanography Series, 14. Elsevier.
Open University. 1989. Ocean Circulation. Oxford: Pergamon Press.
Open University. 1989. Seawater: Its Composition, Properties, and Behavior:
Pergamon Press.
Open University. 1989. The Ocean Basins: Their Structure and Evolution.
Pergamon Press.
88
Section 19
E.
INTRODUCTION
Macroalgae and seagrass beds are dominant structural components in
nearshore subtidal zones, providing habitat for many organisms. Assemblages
of fi shes are conspicuous in these vegetative habitats, using this biogenic
structure for food and shelter. The most conspicuous macroalgae are kelps
that form extensive canopies at the water surface (primarily giant kelp,
Macrocystis pyrifera, and bull kelp, Nereocystis leutkeana) and seagrasses
that occur very close to shore on open coastlines (surfgrass , Phyllospadix
spp.) or in embayments (seagrasses, Zostera marina and other species).
Several other brown macroalgae layer the bottom or fonTI subsurface canopies
I-2m above the sea floor.
The fishes that reside in such habitats often vary in their density and
diversity depending on the area, abundance, and structural features of
vegetation. These fishes come in man y different shapes, sizes, and with
distinctive coloration that make their identification underwater possible.
90
Section
20
two main groups, fishes are generally organized and recognized according
to family, for example: rockfishes (Scorpae nidae), basses (Serranidae) , and
surfperches (Embiotocidae), and within a family class ified by genus and
species. For underwater ide ntification, many nearshore fishes can be
distinguished by their shape, color, and pattem of coloration. Several excellent
guides to the identification of fi shes have been published (see Further
Resources), and the use of keys for identifi cation (for example, Miller and
Lea 1972, Eschmeyer et at. 1983 , Lamb and Edgell 1986, Love 1996) can
be helpful if a fi sh can be examined closely or if preserved specimens are
available. Familiarize yourself with the guides to the near shore fishes in
your location.
T.w.
92
CHARACTERISTICS OF RHODOLITHS
I) Free living, non-geniculate coralline red algae
INTRODUCTION
Rhodoliths are free-living forms of non-geniculate coralline red algae
(Corallinaceae, Rhodophyta) that form extensive beds worldwide over broad
latitudinal and depth ranges (Foster 2001). Synonymous with the maerl beds
common in the northeastem Atlantic, rhodolith beds are hard benthic
substrates, albeit mobile, made up of branching crustose coralline thalli.
Collectively they create a fragile biogenic matrix over carbonate sediment
deposits thought to be the result of long-term accumulation of dead thalli
(Minoura and Nakamori 1982; Steller and Foster 1995). To persist these
algal beds require light, nutrients and movement from water motion (waves
and currents) or bioturbation, which maintains them in an unattached and
unburied state (Bosence 1976). A wide morphological variation of individuals
exists and appears to be a response to variation in physical factors (Bosence
1976; Steller and Foster 1995). This variation in morphology and incorporation
of whole rhodoliths and carbonates into the fossil record has led to their
use as paleoindicators of environmental conditions (Foster et at. 1997).
Despite their global representation in both living beds and fossil deposits,
presently no world monograph exists for the taxonomy of rhodolith-forming
species. However, the few existing accounts have both modern species
descriptions and represent major geographic areas.
Rhodolith beds support a rich community of flora and fauna found
to be higher in species diversity than soft-sediment benthos alone (Steller
et at. 2003). Organisms within a bed can associate with the surface of algal
thalli (epi-fauna/f1ora), within the branches (crypto-faunalflora) or in the
underlying sediments (in-faunalflora) (Steller el at. 2003). Factors influencing
diversity patterns include increased architectural complexity and grain size,
reduced sedimention (Grall and Glemarec 1997), seasonal variation
(Ballesteros 1988) and reduced predation.
Unconsolidated rhodolith deposits have long been harvested for human
use as soil amendment in European waters (Blunden et al. 1977). However,
SAMPLING METHODS
Localing and mapping a site: Subtidal rhodolith beds are commonly asso
ciated with both extensive areas of carbonate sediments (Steller and Foster
1995) and onshore deposits of fossilized rhodoliths (Foster et al. 1997).
Locating rhodolith beds may be expedited by seeking local knowledge from
fi shermen , information from herbarium collections, and aerial observations.
Locating a site can be enhanced using a benthic grab for exploration and
SCUBA surveys for Subtidal exploration. verification and mapping. In all
cases, have a buoy and a GPS to mark the location and enhance rel ocation .
Remote mapping of rhodolith distribution at a site can be efficiently
determined using sonar and mapping done using side scan sonar appears
promising (Tsuji. 1993).
DEVELOPING AN OPTIMAL SAMPLING PROTOCOL: Planing is required to
develop an optimal quantitative sampling protocol that minimizes the impact
of sampling and combines methods to max imize sample design while
maintaining unbiased sampling. The first priOlity is determining the population
or community feature( s) to be described and then determining the number
of samples needed to reasonably estimate a mean and variance. Described
here is a combined method for an initial sampling of a variety of rhodolith
bed features using depth stratified sampling at multiple sites within one bed
to characterize population and species distributions within a bed . This
example is for a typical bed that spans a depth gradient and - 1km of
coastline. The design allows for unbiased characterization of the following
features within the bed: rhodolith taxonomic distribution and make up,
rhod olith size frequency distribution and community composition. A
description of how sample units are distributed in space will be followed
by speci fics for each feature .
SAMPLING EQUIPMENT NEEDED
30-m waterproof transect tapes
- Underwater slate with pencil that holds data sheets on underwater
paper
Quadrats for estimating density of mobile organisms (lm 2 collapsible)
and rhodoliths (0.16m2)
Random Point Quadrat (RPQ) bar for estimating percent cover of
sess ile organisms (lm pvc bar with a 1.5m rope with 10 knots tied
at random distances)
Pre-Iabled collecting zip-Ioc bags
GPS - for site relocation
- PVC stakes + sledge hammer for marking sites in soft-sediment
94
Section 21
96
Seclion
21
S100~
aJuaJ:aJaH
IA l.lBd
~----------------==~~.
The following are given as general guidelines, they are listed here to give
you a sense of the priority the NaGISA project puts on different parts of
the protocols.
SP = Scientific Personnel running a Core NaGISA Site
PRIORITY OF QUADRATES
Rocky Shore Set
1. Temperature (surfacelbottom), latitude and longitude:
2. 1 x 1m - photograph and counts: Mandatory
3. SO x SOcm - collecting: Mandatory for SP, preferable
4. 25 x 2Scm - collecting: Mandatory for SP, preferable
S. Optional
Light, Salinity, pH
Include a 6th replicate for DNA analyses (preserve
Plankton Pulls (see ,online protocols)
Fish Transects (Section 20)
Mandatory
for NP
for NP
in 98% ethanol)
Seagrass Set
1. Temperature (surfacelbottom), latitude and longitude: Mandatory
2. SO x SOcm (picture): Mandatory
PRIORITY OF ANALYSIS
Locality and physical information: Mandatory
Species (presence) list: Mandatory
Quantified data of selected taxa: Macroalgae/Seagrass (including dry
and wet weights), mollusks, decapods, echinoderms, and corals:
Mandatory
Quantified data of other macrofauna: Mandatory for SP, preferable for
NP
Species list of meiofauna: Mandatory for SP, preferable for NP
Quantified data of meiofauna: Mandatory for SP, preferable for NP
Optional: Species list of plankton, fish and/or meiofauna from the
15cm core
102
NaGISA..,~
ID nu mber
1.;1(,111(['\
l..oc. llon
Collccliond.ne
" "'""'-'-_
Ti mc ofealleeliou -"
!!rm,,"''''''-~_ _
-{hh.mm)
CJ' II CClOt.!!l
rfA lC n f h 3h; [".
T"OlP<''''\U''''
Lis: hl 'Surf~c c
- 11
:-1 8
: 19
High
Mod
Low
OOI>m ~
(~' n; l (
unel "
i n ~p! ('
S.llinLly
",, ~c roaI8;1C
;.;:a~ r .. ~~
Rc.Q)OC"IC numl>er
8 u r r~" ----5..L
bonc m ----1.l....
:. 14 _
-15-----...: , 16
--20
~:~~:C~[!~:~:~:O::::i~)nlnc I:o~oUr'~:~'I~'~dO:aIS
rcm ~ rtlber )
I % Co ve rage o r
I'D.orln dl ...ldu alj.
If stored in good (dry) conditions, they can last several centuries. Although
they are less suitable for anatomical studies than liquid-preserved specimens,
the color and gross morphology are retained for much longer. DNA can be
extracted from voucher specimens even after many years, if the specimens
were not treated with formalin, and were quickly dried and stored properly.
Place fresh, wet specimens on herbarium mounting paper and using as little
water as possible spread the thallus out, displaying the characteristic branching
pattern. Cover with gauze, blotter paper, non-stick wax paper or cloth, and
press between absorbent matelial sheets; paper, newspapers or paper towels.
Bind the sheets together in a herbarium press or simply stack one on top
of another, bind with twine and weigh down with weights. Dry in a well
ventilated area at ambient room temperature. During the first week, due to
the high water content of the specimens, the sheets of absorbent material
have to be changed daily. The specimens should be dried for several weeks.
Circulating air (fans, or simply allowing air to flow below, above and around
the stack) will help dry the specimens faster. Well-dried specimens should
be labeled with sampling information; species name, collector name, sampling
place and date of collection. Wrap with a plastic sheet or put in a paper
holder to protect from dirt.
FROZEN PRESERVATION: Place the specimen in a plastic bag, if possible
laying it out flat. Specimens treated like this are suitable for DNA extractions,
morphological observations and will not lose colour but consume considerable
space and energy, and risk damage by mechanical failure of freezers or by
power interruptions.
104
Section 24
GLOSSARY OF METHODS
material is
to be used for DNA analysis, it should be put directly in > 80% ethanol.
Pressed specimens and those preserved in Silica Gel (see preservation
techniques) can also be used to save DNA for extraction and analyses. As
water escaping from the sample will dilute the concentration of ethanol it
is prudent to replace the ethanol within 24/48 hours.
Small pieces (2g) chopped into less than lmm
of fresh dry algae, seagrass or sponge can be placed in an airtight container
covered with silica crystals (electrophoretic grade) . Specimens treated like
this are suitable for DNA extractions although less so for morphological
observations as they will shrink and change shape.
SILICA GEL PRESERVATION:
containing sufficient seawater for the animal to expand fully, useful for
cnidarians
106
Section 24
GLOSSARY OF METHODS
Abdomen. In crustaceans this is the posterior part of the body (the second
region of the two part body plan of decapods and the third region of the
thee part body plan of amphipods) consisting of six segments, sometimes
including a tail fan. In shrimps and lobsters the abdomen is well extended,
thick and strong. In crab-like species, the abdomen is flattened, reduced in
size and fold under the body.
Ambulacrum. The region that runs along the oral surface of an echinoderm's
ray containing the tube feet.
Annuli. Segments of the flagellum or antennae (often erroneously called
articles or segments).
Antenna(e) (1 & 2). Appendages found on the head. In shrimps and lobsters
they are long, wipe-like, sometimes spiny; in crabs these are shorter,
sometimes inconspicuous but in all crustaceans, they are the first (antennule)
and second (antenna) appendages and are comprised of a peduncle and
flagellum of various length; and may have antennal scales and annuli . In
polychaetes, antenna refers to the sensory appendages arising from the
anterior end or dorsal surface of the prostomium.
Appendage(s). A 'limb-like' extension from the main body, including legs,
rays, antennae and antennules.
Appendix masculina. A stylet-like copulatory structure on the inner margin
of the endopod of a male crustaceans' second pleopod.
Area. A distinct geographic region. The NaGISA plan outlines that 3 areas
should be chosen so that they combine to represent the maximum biodiversity
found along the shoreline within each project specified 20 box (20 latitude
x 20 longitude). Each area is to have at least 3 sites.
108
Continental shelf. Sea floor extending between the low water line and
(usually) about 150-200 m depth, where most fishing activities occur.
Core/Corer. A cylindrical tube (corer) of defined radius (I5cm or 2cm) that
is wedged into the soft sediment to a defined depth (IOcm) and removed
with the sediment intact (core), the sediments is then sifted and sorted for
specimens.
Depth contour (Transect). An imaginary line connecting the ground of the
same height/depth. A transect following the depth contour follows the
undulations of the shoreline and thus is very rarely a 'straight' line.
Endopod. Inner ramus (branch) of a limb, paired with the exopod, in
crustaceans.
Es. An index of biodiversity. Usually followed by two numbers as in
Es (50) = 25, the number in brackets refers to the number of randomly
selected specimens from the area in question and the second number refers
to the number of unique species expected to be found amongst those
specimens.
Exopod. Outer ramus (branch) of a limb paired with the endopod, in
crustaceans.
Flagellum. Distal part of a crustaceans antenna 1 or 2, generally made of
many annuli.
Gamete. Sexual reproductive cell.
Gametophyte. A haploid generation that forms male and/or female gametes
in algae.
Gland cell. A specialized vegetative cell in red algae, involved in secretion
or storage.
Gnathopod. First or second pereopod in amphipods, differing in function
and appearance to the following pereopods, usually chelate or subchelate.
Habitus. General appearance, body build and constitution of an organism.
Head. Anterior section of the body. In crustaceans it is the first of two or
three regions of body, incorporating segments bearing pairs of antennae and
mouthparts.
Hinge. In bivalves, the interlocking, often toothed, structure in the dorsal
region of the valves.
Hydropore(s). Minute pores, usually contained within the madreporite,
that lead to a canal that connects internally to the water ring of the water
vascular system of echinoderms. Hydropores are believed to replenish water
lost through the tube feet.
Incisor process. Distal biting part of a crustaceans mandible, typically
found with teeth.
110
Section 25
GLOSSARY OF T ERMS
112
Section 25
GLOSSARY OF TERMS
and ambulacrum.
Section 25
GLOSSARY OF TERMS
116
118
Section 26
BlBLIOGRAPHY
Section 26
BlBUOGRAPHY
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Hurlbert, S.H. (1984) Pseudoreplication and the design of ecological field
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Imbach, M.e. (1967) Gammaridean Amphipoda from the South China
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Section 26
-
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BIBLIOGRAPHY
Cnidaria
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members of subclass Hexacorallia of class Anthozoa.
Fautin, D. G. (2006) Hexacorallians of the World
hllp ://geoporla I.kgs. ku .edu/Hexacora l/anemone2
Crustacea
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University of Troms
Myers, A., D. McGrath, R. King (2006) Keys to the North East Atlantic
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--
--=--
--......
--~
Section 27
---
http://toweb.org/notes/note_ id==3004
-=-
hup://lol web.org/accessory /
---
--.
--......
ht Ip://www.vi ms.edu/-.ieff/isopod.hlm
Echinodermata
Taxonomic resource for the scientific community in which the genera
and higher taxa of echinoid s can be simply and rapidly identified.
Andrew, B. S. (2004) Echinoid directory illustrated key to families and
genera
http ://www.nhm.ac .uk/research-curation/projects/ech inoid-directo ry/
index.hlml
Guide to Echinodermata. Life history, Systematics and Morphology.
--.
..=...
PDF brochure).
Heritage (2007)
Flora
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Australia (a book in PDF form).
Barrier Reef region, Great Barrier Reef Marine Park Authority Special
Publication Series, 3
htLp ://wwlV.gbnnpa. gOY.aLl/corp.,sile/info_serv ices/ pub lications/misc_pub/
misc_O 11/mp_OI J _ful1.pdf
Illustrated guide and key to Queensland area Seagrasses (a PDF
handout).
Appendix III
hup ://wlVw.qccqld.org.au/scagrass/monilOring/
seagrasses.
132
Section 27
ONLINE REFERENCES
==0
ht lp://www.algaebase.org/
.-
......
General Taxonomy
Taxonomic information on plants, animals, fungi and microbes of North
the Environment
hllp://faunai talia.it/imlex.htm
~
. . -.
(BIODIDAC)
-=
--=
......=
......
....=
Meiobenthos
The webpage of the International Association of Meiobenthologists,
http://www.meiofauna.org/
htlp://web. pml.ac.uk/nematode/
research .
hLlp://www.gaslrotrich.a.unimore.itj
Mollusca
Key s and information on Venezuelan Mollusks (Echinoderms and
Crustaceans are also mentioned). In Spanish
Bordas H. and G. Griffon (2004) Le conchiglie dei litorali veneziani
http://www.liceofoscalini.it/didattic/conchiglie/
134
Section 27
O NLINE R EFERENCES
=-
Searchable Molluskan Key, information and links. In Japanese and
English
---
hltp://data .acnarsci.org/wasp/
--
. -.
Images of seashells from the Alboran Sea and North West Africa,
Shells
ilttp://www.alboransilells .comj
---
Physical Oceanography
--.
--
-.
--.
""'
Satellite maps.
SeaWiFS, MODIS
Polychaeta
Online identification key to Polychetes. In French
researchers.
http://www.an ne lida.ne t/
Online bibliography containing 17500 references from the last 300 years
on polychaete annelids.
projec t.
higher taxa.
index.htm!
136
Section 27
ONLlN E REFERENCES
Porifera
Guide to Poriferans (Sponges). Life history, Systematics and Morphology.
Collins , A. G. , B. Waggoner (2006) Introduction to Porifera Electronic
publication
hllp://www.ucmp.berkeley.edu/porifera/porifera .html
----.
A guide to classification and identification of Sponge Porifera.
Hooper, J. N. A. et al. (2000) 'SPONGUIDE' Guide to sponge collection
and identification (Ver. Aug. 2000)
hltp://www. qmuseum .qld .gov. au/organisati on/sections/
Sess ileMarineJ Ilvertebrates/index . a.~r
Key to Porifera focusing on the class Demospongiae taken from
Museum of Nature
138
Section 28
--.
=
CONTRIBUTORS
leader for the NaGISA European Seas region. Web Site: http://www.
disc at. uni pi.it/BioIMar/people/LBC!LBC. htm Contribution: Sampling
design
Juan M. Diaz is a malacologist and marine ecologist. He is the author of
more than 60 contributions in scientific journals, most of them dealing
with Caribbean molluscs (taxonomy and biogeography), coral reefs and
seagrass beds . He has also written several books that describe the distribution
and features of marine environments in Colombia and an ex hau stive field
guide of molluscs of the Colombian Caribbean. He was the leader of the
Marine Biodiversity Program at The Instituto de Investigaciones Marinas
y Costeras -INVEMAR- in Santa Marta, Colombia, for 18 years. At present,
he is Associate Researcher of the Humboldt Institute in Bogota and
scientific advisor of The Nature Conservancy for conservation planning of
the Tropical Eastern Pacific region . His tele phone number is 57-1-6278858,
and his e-mail address is [email protected]. Contribution: Mollusca
identification guide
Maria Cristina Diaz specializes in the taxonomy of intertid al and tropical
sponges but has a special interest in biodiversity and community structure
of the Caribbean. She has been fascinated with sea life since her very first
dive and has been working on sponges since focusing on the coral reef of
Los Rogues National Park for her undergraduate research project. When
not being followed by film crews (as she was for the Shape of li fe project
http://www.pbs.org/kcetls hapeoflife/) or getting species named after her
(Halicnemia diazae Desgueyroux-Faundez & Van Soest, 1997), she can be
reached at [email protected] or [email protected] or found at
the Mu seo Marino de Margarita in Venezuela at the Smithsonian Institute,
National Mu seum of Natural History. Contribution : Sponge identification
guide
Daphne G. Fautin is a student of sea anemones, specializing in their natural
history (reproduction and symbiosis) and evolution (their relationship to
scleractini an corals) . She is a Professor in the Department of Ecology and
Evolutionary Bi ology at the University of Kansas, USA , and a Curator in
the University of Kansas Natural History Museum and Biodiversity Research
Center. Her office is in Haworth Hall, University of Kansas, 1200 Sunnyside
Avenue, Lawrence, Kansas 66045-7534 USA. Her telephone number is
1-785-864-3062, and her e-mail [email protected]
of her stude nts, and other related information is on her we bs i te,
www.nhm.ku. e du/~inverts. The website has a link to her taxonomic and
biogeographic database of "Hexacorallians of the World" (reef-forming
corals, black corals, tube anemones, sea anemones, etc.): http://
geoportal.kgs .ku .ed u/Hex acora l/an emone2. Contribution: Cnidarian
identification guide
Michael S. Foster is a Professor Emeritus at Moss Landing Marine
Laboratories. He obtained his PhD in biology ( 1972) from the University
of California, Santa Barbara and is a Fellow of the Califomia Academy
of Sciences and a Fulbright Scholar. His research interests center on the
ecology of subtidal and intertidal reefs, particularly algal populations and
assemblages in kelp forests, rhodolith beds and rocky shores, and have
resulted in 70 peer-reviewed professional papers, 4 books and numerous
reports. He is also interested in an thropogenic impacts to these habitats, and
Section 28
--
CONTRlBUTORS
.-
......
,----~
--"
Section 28
CONTRIBUTORS
ecology and the ecology of the Gulf of California. She has been working
in the Gulf of California for the past 17 years and is particularly interested
in the role that macroalgae playas a substrate and food resource in subtidal
communities and how algal dynamics int1uence community dynamics and
the growth and establishment of carbonate reefs - past, present and future.
Contribution: Sampling and monitoring rhodolith beds
Ambulacrum 43
76-77
75
44-45,58,60,86,90-91,95
Article 77
Ascocyst 35
Chela 59,61-64,71,75
Choanocyte 70, 72
Coenocyte 34
Columella 58
Concentric 46
Core/Corer 8, 25-29, 38
Beak 40-41
96
Body whorl 58
Endopod 77
Exopod 77-78
Calyx 46
Cancellate 58
Carpospore 34
Carposporophyte 36
Cephalothorax 59
Chaetae 47-51
144
Flagellum 74, 77
Gamete 34, 51
Gametophyte 35
Gnathopod 73-74
Head 47-4.9,56-57,59,73-77
Hinge 57-58
Hydropore 42
Lip 51, 58
Section 29
Madreporite 42--44
Mandible 51,76-78
Marsupium 74, 76
Maxilliped 74-77
Medusa 52-54
Meristem 35-36
Metamorphosis 42--43
Nematocyst 53-54
Neuropodia/Neuropodium 48
Notopodia!Notopodium 48
Oscule(a) 69-71
Parapodia/Parapodium 47-50
Pedicellariae 43--45
40,71,74 , 77
Pentamery 42
Pereonite 74, 77
76-78
Peristomium 48 , 51
Pleopod(s) 73-76, 78
Pleotelson 76-78
Plication 3, 9, 45
Proboscis 48-50
Prostomium 47--48 , 51
Protoconch 58
Pygidium 48--49
Quadrat 8, 18-20, 27
Quadrat set 27
INDEX
Radial canal 44
Ray 71
Reticulate 71
Rhodophyceae 33, 93
Rudiment 42--43
Seta 76-77
97
Slate 91-92, 94
Spiral 58
Spire 58
Sporophyte 35-36
76, 81
Stone canal 42
Subchelate 64
Tetraspore 34
Thallus 35-36, 60
94-95
Ulvophyceae 33
Umbilicus 58
Umbo 57
Varix 58
Water ring 42
Whorl 58
Zoospore 33-34
CENSUS F'.
OF MARINE LIFE
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This pub lication was supported
by the Nippon Fou ndation